diff --git a/Utilities/ITK/Utilities/nifti/CMakeLists.txt b/Utilities/ITK/Utilities/nifti/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c45f77239d2a054bfca1b4ab6baa1783437a0d0a
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/CMakeLists.txt
@@ -0,0 +1,30 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(NIFTI)
+# Configure Dart testing support.
+INCLUDE(${CMAKE_ROOT}/Modules/Dart.cmake)
+
+SUBDIRS(znzlib niftilib)
+ADD_DEFINITIONS(-DHAVE_ZLIB)
+
+
+### USE AS PART OF ITK
+IF("${ITK_VERSION_MAJOR}" GREATER 0.0)
+# MESSAGE(STATUS "---------------------ITK ZLIB ${ITK_ZLIB_LIBRARIES}")
+ SET(PACKAGE_PREFIX "ITK")
+ SET(LIB_INSTALL_DIR "/lib/InsightToolkit")
+ SET(INCLUDE_INSTALL_DIR "/include/InsightToolkit")
+ SET(NIFTI_ZLIB_LIBRARIES ${ITK_ZLIB_LIBRARIES})
+ELSE("${ITK_VERSION_MAJOR}" GREATER 0.0)
+### USE AS STAND ALONE PACKAGE
+ FIND_PACKAGE(ZLIB)
+# MESSAGE(STATUS "---------------------SYSTEM ZLIB ${ZLIB_LIBRARY}")
+ SET(NIFTI_ZLIB_LIBRARIES ${ZLIB_LIBRARIES})
+ SET(PACKAGE_PREFIX "")
+ SET(LIB_INSTALL_DIR "/lib")
+ SET(INCLUDE_INSTALL_DIR "/include")
+
+ #Needs an if clause and more work before testing can take place.
+ SUBDIRS(Testing utils fsliolib examples)
+ ENABLE_TESTING()
+ENDIF("${ITK_VERSION_MAJOR}" GREATER 0.0)
diff --git a/Utilities/ITK/Utilities/nifti/DartConfig.cmake b/Utilities/ITK/Utilities/nifti/DartConfig.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..44974d184f9416b5dfa6c463e310c4eed7d7de07
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/DartConfig.cmake
@@ -0,0 +1,16 @@
+# Dashboard is opened for submissions for a 24 hour period starting at
+# the specified NIGHLY_START_TIME. Time is specified in 24 hour format.
+SET (NIGHTLY_START_TIME "1:00:00 EDT")
+
+# Dart server to submit results (used by client)
+
+# Project Home Page
+SET (PROJECT_URL "http://sourceforge.net/projects/niftilib")
+
+# Dart server to submit results (used by client)
+SET (DROP_METHOD "xmlrpc")
+SET (DROP_SITE "delta.psychiatry.uiowa.edu:8081")
+SET (DROP_LOCATION "NIFTI")
+
+SET (CVS_WEB_URL "http://cvs.sourceforge.net/viewcvs.py/niftilib/")
+SET (CVS_WEB_CVSROOT "Clibs")
diff --git a/Utilities/ITK/Utilities/nifti/Makefile b/Utilities/ITK/Utilities/nifti/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..88e4c758999a176aa60f1b4df81ec48067339f4d
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/Makefile
@@ -0,0 +1,221 @@
+
+SHELL = csh
+
+## Projects
+NIFTI = niftilib
+ZNZ = znzlib
+FSLIO = fsliolib
+EXAMPLES = examples
+UTILS = utils
+UTILS_PROGS = nifti_stats nifti_tool nifti1_test
+THIS_DIR = `basename ${PWD}`
+
+## Note the TARFILE_NAME embeds the release version number
+TARFILE_NAME = nifticlib-0.2
+
+
+## Compiler defines
+cc = gcc
+CC = gcc
+AR = ar
+RANLIB = ranlib
+DEPENDFLAGS = -MM
+GNU_ANSI_FLAGS = -Wall -ansi -pedantic
+ANSI_FLAGS = ${GNU_ANSI_FLAGS}
+CFLAGS = $(ANSI_FLAGS)
+
+## Command defines
+## gmake does not work on MacOSX or some versions of linux MAKE = gmake
+RM = rm
+MV = mv
+CP = cp
+TAR = /usr/freeware/bin/tar
+
+
+## Installation
+INSTALL_BIN_DIR = bin
+INSTALL_LIB_DIR = lib
+INSTALL_INC_DIR = include
+
+
+## Zlib defines
+ZLIB_INC = -I/usr/include
+ZLIB_PATH = -L/usr/lib
+ZLIB_LIBS = $(ZLIB_PATH) -lm -lz
+
+
+
+## Platform specific redefines
+
+## SGI 32bit
+ifeq ($(ARCH),SGI)
+ZLIB_INC = -I/usr/freeware/include
+ZLIB_PATH = -L/usr/freeware/lib32
+endif
+
+
+## RedHat Fedora Linux
+## ZLIB_INC = -I/usr/include
+## ZLIB_PATH = -L/usr/lib
+
+
+
+
+
+#################################################################
+
+## ZNZ defines
+ZNZ_INC = -I../$(ZNZ)
+ZNZ_PATH = -L../$(ZNZ)
+ZNZ_LIBS = $(ZNZ_PATH) -lznz
+USEZLIB = -DHAVE_ZLIB
+
+## NIFTI defines
+NIFTI_INC = -I../$(NIFTI)
+NIFTI_PATH = -L../$(NIFTI)
+NIFTI_LIBS = $(NIFTI_PATH) -lniftiio
+
+## FSLIO defines
+FSLIO_INC = -I../$(FSLIO)
+FSLIO_PATH = -L../$(FSLIO)
+FSLIO_LIBS = $(FSLIO_PATH) -lfslio
+
+
+
+## Rules
+
+.SUFFIXES: .c .o
+
+.c.o:
+ $(CC) -c $(CFLAGS) $(INCFLAGS) $<
+
+## Targets
+
+all: znz nifti fslio install
+
+install: znz_install nifti_install fslio_install utils_install
+
+clean: znz_clean nifti_clean fslio_clean examples_clean utils_clean
+
+clean_all: clean install_clean doc_clean
+
+
+znz:
+ (cd $(ZNZ); $(MAKE) depend; $(MAKE) lib;)
+ @echo " ----------- $(ZNZ) build completed."
+ @echo ""
+
+nifti: znz
+ (cd $(NIFTI); $(MAKE) depend; $(MAKE) lib;)
+ @echo " ----------- $(NIFTI) build completed."
+ @echo ""
+
+fslio: nifti
+ (cd $(FSLIO); $(MAKE) depend; $(MAKE) lib;)
+ @echo " ---------- $(FSLIO) build completed."
+ @echo ""
+
+example:nifti
+ (cd $(EXAMPLES); $(MAKE) all;)
+ @echo Example programs built.
+ @echo ""
+
+
+utils: nifti
+ (cd $(UTILS); $(MAKE) all;)
+ @echo Utility programs built.
+ @echo ""
+
+doc:
+ (cd docs; doxygen Doxy_nifti.txt;)
+ @echo "doxygen doc rebuilt, run netscape docs/html/index.html to view."
+ @echo ""
+
+$(INSTALL_BIN_DIR):
+ mkdir -p $@
+
+$(INSTALL_INC_DIR):
+ mkdir -p $@
+
+$(INSTALL_LIB_DIR):
+ mkdir -p $@
+
+znz_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
+ ($(CP) $(ZNZ)/*.a $(INSTALL_LIB_DIR); $(CP) $(ZNZ)/*.h $(INSTALL_INC_DIR);)
+ $(RANLIB) $(INSTALL_LIB_DIR)/*.a
+ @echo " $(ZNZ) installed."
+ @echo ""
+
+nifti_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
+ ($(CP) $(NIFTI)/*.a $(INSTALL_LIB_DIR); $(CP) $(NIFTI)/*.h $(INSTALL_INC_DIR);)
+ $(RANLIB) $(INSTALL_LIB_DIR)/*.a
+ @echo " $(NIFTI) installed."
+ @echo ""
+
+fslio_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
+ ($(CP) $(FSLIO)/*.a $(INSTALL_LIB_DIR); $(CP) $(FSLIO)/*.h $(INSTALL_INC_DIR);)
+ $(RANLIB) $(INSTALL_LIB_DIR)/*.a
+ @echo " $(FSLIO) installed."
+ @echo ""
+
+utils_install: utils $(INSTALL_BIN_DIR)
+ (cd $(UTILS); $(CP) $(UTILS_PROGS) ../$(INSTALL_BIN_DIR);)
+ @echo " $(UTILS) installed."
+ @echo ""
+
+install_clean:
+ ($(RM) -f $(INSTALL_INC_DIR)/* $(INSTALL_LIB_DIR)/* $(INSTALL_BIN_DIR)/*;)
+
+znz_clean:
+ (cd $(ZNZ); $(RM) -f *.o *.a core; $(RM) -f depend.mk;)
+
+nifti_clean:
+ (cd $(NIFTI); $(RM) -f *.o *.a core; $(RM) -f depend.mk;)
+
+fslio_clean:
+ (cd $(FSLIO); $(RM) -f *.o *.a core; $(RM) -f depend.mk;)
+
+examples_clean:
+ (cd $(EXAMPLES); $(MAKE) clean;)
+
+utils_clean:
+ (cd $(UTILS); $(MAKE) clean;)
+
+doc_clean:
+ ($(RM) -fr docs/html;)
+
+tar:
+ (cd .. ; ln -s $(THIS_DIR) ${TARFILE_NAME} ; \
+ $(TAR) --exclude=CVS -cf ${TARFILE_NAME}.tar ${TARFILE_NAME}/*; \
+ rm -f ${TARFILE_NAME});
+ @echo ''
+ @echo 'tar file ../${TARFILE_NAME}.tar has been created.'
+ @echo ''
+
+
+help:
+ @echo ""
+ @echo "all: build and install znz, nifti1 and fslio"
+ @echo " libraries, and the utils programs"
+ @echo "install: install znz, nifti1, and fslio libraries"
+ @echo "doc: build the doxygen docs for this project."
+ @echo " (Need doxygen installed, see"
+ @echo " http://www.stack.nl/~dimitri/doxygen/index.html"
+ @echo "tar: make a tar file of all nifti_io code, put in .."
+ @echo ""
+ @echo "clean: remove .o .a etc. files from source directories,"
+ @echo " and remove examples and utils programs"
+ @echo "clean_all: make clean and delete all installed files in bin,"
+ @echo " include and lib, and remove any autogenerated"
+ @echo " docs (docs/html)"
+ @echo ""
+ @echo "znz: build the znz library"
+ @echo "znz_install: install the znz library"
+ @echo "nifti: build the nifti1 library"
+ @echo "nifti_install: install the nifti1 library"
+ @echo "fslio: build the fslio library"
+ @echo "fslio_install: install the fslio library"
+ @echo "example: make the example program(s)"
+ @echo "utils: make the utils programs"
+ @echo "utils_install: install the utils programs"
+ @echo ""
diff --git a/Utilities/ITK/Utilities/nifti/README b/Utilities/ITK/Utilities/nifti/README
new file mode 100644
index 0000000000000000000000000000000000000000..53d9feea55fb1c36e0ed62dcea6c4c358a2259d8
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/README
@@ -0,0 +1,63 @@
+
+Nifti-1 C libraries
+-------------------
+
+Version 0.2 beta release August 12, 2005
+Version 0.1 beta release March 11, 2005
+
+niftilib code is released into the public domain.
+
+
+Library directories
+-------------------
+znzlib -- low level library for handling read/write of compressed files.
+
+niftilib -- core i/o routines for reading and writing nifti-1 format files.
+ Primarily routines to read/write and manipulate the header field
+ information, including orientation matrices. Volume-wise,
+ timecourse-wise, access to image data.
+
+fsliolib -- i/o routines for reading and writing nifti-1 format files, higher
+ level than niftilib, includes routines for reading the data blob by
+ volume, timecourse, etc., and, addresses image orientation issues.
+ *** work in progress, subject to significant revision.....
+
+utils -- directory containing library utility programs (nifti_tool)
+
+
+
+
+Destination directories
+-----------------------
+bin -- destination directory for installed programs
+include -- destination directory for library header files
+lib -- destination directory for compiled libraries
+docs -- destination directory Doxygen html (created via "make doc")
+
+
+
+Example directories
+-------------------
+examples -- directory containing sample code using nifti reference library
+real_easy -- code snippets to read nifti-1 files, not using nifti ref. lib.
+
+
+Instructions to build
+---------------------
+
+command -- "make all"
+
+ results will be left in the directories: bin/ include/ lib/
+
+command -- "make help"
+
+ will show more build options
+
+
+For more information
+--------------------
+
+See the niftilib webpage at http://niftilib.sourceforge.net/
+See the NIFTI webpage at http://nifti.nimh.nih.gov/
+
+
diff --git a/Utilities/ITK/Utilities/nifti/Testing/CMakeLists.txt b/Utilities/ITK/Utilities/nifti/Testing/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7284c483debbb8f8271e6239a360b4063deed7c8
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/Testing/CMakeLists.txt
@@ -0,0 +1,9 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(TESTING)
+
+
+SUBDIRS(niftilib)
+
+
+
diff --git a/Utilities/ITK/Utilities/nifti/Testing/niftilib/CMakeLists.txt b/Utilities/ITK/Utilities/nifti/Testing/niftilib/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..500b9510038be56f4d9473ab26fa6a9c0e879bce
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/Testing/niftilib/CMakeLists.txt
@@ -0,0 +1,11 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(NIFTILIB_TESTS)
+
+INCLUDE_DIRECTORIES(${NIFTILIB_SOURCE_DIR} ${ZNZLIB_SOURCE_DIR})
+
+ADD_EXECUTABLE(first_test nifti_test.c)
+TARGET_LINK_LIBRARIES(first_test niftiio )
+
+ADD_TEST(first_test first_test )
+
diff --git a/Utilities/ITK/Utilities/nifti/Testing/niftilib/nifti_test.c b/Utilities/ITK/Utilities/nifti/Testing/niftilib/nifti_test.c
new file mode 100644
index 0000000000000000000000000000000000000000..eb6e4dab99f3cab1bf232b9e99cf53cdec9ba2e9
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/Testing/niftilib/nifti_test.c
@@ -0,0 +1,260 @@
+#include <nifti1_io.h>
+
+enum NIFTITEST_BOOL {
+ NIFTITEST_TRUE=1,
+ NIFTITEST_FALSE=0
+};
+
+void PrintTest(const int line,const char * message,const int FailureOccured, const enum NIFTITEST_BOOL isFatal,int *ErrorAccum)
+{
+ if(FailureOccured==NIFTITEST_TRUE) /* This line can be commented out for a more verbose output */
+ {
+ char const * const PREFIX= (FailureOccured)?"==========ERROR":"..........SUCCESS";
+ char const * const ISFATALPREFIX= (isFatal && FailureOccured)?" FATAL":"";
+ printf("%s%s (LINE %d): %s\n",PREFIX,ISFATALPREFIX,line,message);
+ fflush(stdout);
+ *ErrorAccum+=FailureOccured;
+ if(isFatal==NIFTITEST_TRUE && FailureOccured==NIFTITEST_TRUE)
+ {
+ printf("\n\nTOTAL ERRORS=%d\n",*ErrorAccum);
+ exit( *ErrorAccum);
+ }
+ }
+ return;
+}
+
+nifti_image * generate_reference_image( const char * write_image_filename , int * const Errors)
+{
+ nifti_1_header reference_header;
+ memset(&reference_header,0,sizeof(reference_header));
+ reference_header.sizeof_hdr=sizeof(reference_header);
+ reference_header.regular='r';
+ reference_header.extents=16384;
+
+ reference_header.dim[0]=5;
+ reference_header.dim[1]=23;
+ reference_header.dim[2]=17;
+ reference_header.dim[3]=11;
+ reference_header.dim[4]=7;
+ reference_header.dim[5]=3;
+ reference_header.dim[6]=1; //This MUST be 1 anything else is invalid due to code that usees huristics to fix other possible problems;
+ reference_header.dim[7]=1; //This MUST be 1 anything else is invalid due to code that usees huristics to fix other possible problems;
+ reference_header.intent_p1=10101010.101F;
+ reference_header.intent_p2=987654321.0F;
+ reference_header.intent_p3=-1234.0F;
+ reference_header.intent_code=NIFTI_INTENT_ESTIMATE;
+ reference_header.datatype=DT_INT32;
+ reference_header.pixdim[0]=-1.0F; /* this is really qfac */
+ reference_header.pixdim[1]=0.25F;
+ reference_header.pixdim[2]=0.5F;
+ reference_header.pixdim[3]=1.0F;
+ reference_header.pixdim[4]=2.0F;
+ reference_header.pixdim[5]=4.0F;
+ reference_header.pixdim[6]=-2.0e10F;
+ reference_header.pixdim[7]=-2.0e10F;
+ reference_header.vox_offset=0;
+ reference_header.scl_slope=0.25;
+ reference_header.scl_inter=128;
+ reference_header.qform_code=NIFTI_XFORM_SCANNER_ANAT;
+ reference_header.quatern_b=-0.5F;
+ reference_header.quatern_c= 0.5F;
+ reference_header.quatern_d=-0.5F;
+ reference_header.qoffset_x=reference_header.dim[1]/2.0F;
+ reference_header.qoffset_y=reference_header.dim[2]/2.0F;
+ reference_header.qoffset_z=reference_header.dim[3]/2.0F;
+ reference_header.sform_code=NIFTI_XFORM_SCANNER_ANAT;
+ reference_header.srow_x[0]=0.5;
+ reference_header.srow_x[1]=0.0;
+ reference_header.srow_x[2]=0.0;
+ reference_header.srow_x[3]=0.0;
+ reference_header.srow_y[0]=0.0;
+ reference_header.srow_y[1]=1.0;
+ reference_header.srow_y[2]=0.0;
+ reference_header.srow_y[3]=0.0;
+ reference_header.srow_z[0]=0.0;
+ reference_header.srow_z[1]=0.0;
+ reference_header.srow_z[2]=2.0;
+ reference_header.srow_z[3]=0.0;
+ reference_header.magic[0]='n';
+ reference_header.magic[1]='+';
+ reference_header.magic[2]='1';
+ reference_header.magic[3]='\0';
+ /* String is purposfully too long */
+ strncpy(reference_header.intent_name,"PHANTOM_DATA to be used for regression testing the nifti reader/writer",16);
+ strncpy(reference_header.descrip,"This is a very long dialog here to use up more than 80 characters of space to test to see if the code is robust enough to deal appropriatly with very long and obnoxious lines.",80);
+
+ {
+ int nbyper;
+ int swapsize;
+ nifti_datatype_sizes(reference_header.datatype ,&nbyper,&swapsize);
+ reference_header.bitpix=nbyper*8;
+ }
+
+ nifti_image * reference_image=nifti_convert_nhdr2nim(reference_header,write_image_filename);
+ {
+ const unsigned int NumVoxels=reference_image->nx*reference_image->ny*reference_image->nz*reference_image->nt*reference_image->nu;
+ reference_image->data=(signed int *)calloc(NumVoxels,sizeof(signed int)) ; /*!< pointer to data: nbyper*nvox bytes */
+ PrintTest(__LINE__,"Checking memory allocation",reference_image->data ==0 ,NIFTITEST_TRUE,Errors);
+ {
+ signed int i=0;
+ for(; i < NumVoxels ; i++)
+ {
+ ((signed int *)(reference_image->data))[i]=i;
+ }
+ }
+ }
+ PrintTest(__LINE__,"Setting filenames",nifti_set_filenames( reference_image,write_image_filename, 0, 0 ) != 0, NIFTITEST_TRUE,Errors);
+ PrintTest(__LINE__,"Setting type from names",nifti_set_type_from_names( reference_image ) != 0, NIFTITEST_TRUE,Errors);
+/* PrintTest(__LINE__,"Checking type and names",nifti_type_and_names_match( reference_image , 1 ) != 1, NIFTITEST_TRUE,Errors); */
+ PrintTest(__LINE__,"Check reference_image data is non null",(reference_image->data==0),NIFTITEST_TRUE,Errors);
+ return reference_image;
+}
+
+
+void compare_reference_image_values(nifti_image const * const reference_image, nifti_image const * const reloaded_image, int * const Errors)
+{
+ PrintTest(__LINE__,"Checking nifti_type",(reference_image->nifti_type!=reloaded_image->nifti_type),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking fname",(strcmp(reference_image->fname,reloaded_image->fname)),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking iname",(strcmp(reference_image->iname,reloaded_image->iname)),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking ndim",(reference_image->ndim!=reloaded_image->ndim),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking nx",(reference_image->nx!=reloaded_image->nx),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking ny",(reference_image->ny!=reloaded_image->ny),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking nz",(reference_image->nz!=reloaded_image->nz),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking nt",(reference_image->nt!=reloaded_image->nt),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking nu",(reference_image->nu!=reloaded_image->nu),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking dx",(reference_image->dx!=reloaded_image->dx),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking dy",(reference_image->dy!=reloaded_image->dy),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking dz",(reference_image->dz!=reloaded_image->dz),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking dt",(reference_image->dt!=reloaded_image->dt),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking du",(reference_image->du!=reloaded_image->du),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking datatype",(reference_image->datatype!=reloaded_image->datatype),NIFTITEST_FALSE,Errors);
+ {
+ const unsigned int NumVoxels=reference_image->nx*reference_image->ny*reference_image->nz*reference_image->nt*reference_image->nu;
+ PrintTest(__LINE__,"Check loaded data is non null",(reloaded_image->data==0),NIFTITEST_TRUE,Errors);
+ PrintTest(__LINE__,"Check reference_image data is non null",(reference_image->data==0),NIFTITEST_TRUE,Errors);
+ {
+ unsigned int CurrVoxel=0;
+ for(; CurrVoxel < NumVoxels ; CurrVoxel++)
+ {
+ /*printf("%d ",CurrVoxel); fflush(stdout);*/
+ if( ((int *)(reference_image->data))[CurrVoxel] != ((int *)(reloaded_image->data))[CurrVoxel])
+ {
+ PrintTest(__LINE__,"Incorrect Pixel Value Found",0,NIFTITEST_FALSE,Errors);
+ }
+ }
+ }
+ }
+ PrintTest(__LINE__,"Checking xyz_units",(reference_image->xyz_units!=reloaded_image->xyz_units),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking time_units",(reference_image->time_units!=reloaded_image->time_units),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking intent_code",(reference_image->intent_code!=reloaded_image->intent_code),NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking intent_name",(strncmp(reference_image->intent_name,reloaded_image->intent_name,16) )!=0,NIFTITEST_FALSE,Errors);
+ PrintTest(__LINE__,"Checking description",(strncmp(reference_image->descrip,reloaded_image->descrip,80))!=0,NIFTITEST_FALSE,Errors);
+ return ;
+}
+
+int main (int argc, char *argv[])
+{
+ char TEMP_STR[256];
+ int Errors=0;
+ {
+ PrintTest(__LINE__,"NOT REALLY AN ERROR, JUST TESTING THE ERROR TEST REPORTING MECHANISM",1,NIFTITEST_FALSE,&Errors);
+ PrintTest(__LINE__,"NOT REALLY AN ERROR, JUST TESTING THE ERROR COUNTING MECHANISM",Errors==1,NIFTITEST_FALSE,&Errors);
+ Errors=0;
+ }
+ {
+ const char write_image_filename[6][64]={
+ "ATestReferenceImageForReadingAndWriting.nii",
+ "ATestReferenceImageForReadingAndWriting.hdr",
+ "ATestReferenceImageForReadingAndWriting.img",
+ "ATestReferenceImageForReadingAndWriting.nii.gz",
+ "ATestReferenceImageForReadingAndWriting.hdr.gz",
+ "ATestReferenceImageForReadingAndWriting.img.gz"
+ };
+ printf("======= Testing All Nifti Valid Names ======\n");
+ fflush(stdout);
+ unsigned int filenameindex;
+ for(filenameindex=0;filenameindex<6; filenameindex++)
+ {
+ printf("======= Testing with filename: %s ======\n",write_image_filename[filenameindex]);
+ fflush(stdout);
+ nifti_image * reference_image = generate_reference_image(write_image_filename[filenameindex],&Errors);
+ PrintTest(__LINE__,"Create reference image",reference_image==0,NIFTITEST_TRUE,&Errors);
+ nifti_image_write ( reference_image ) ;
+ {
+ nifti_image * reloaded_image = nifti_image_read(reference_image->fname,1);
+ PrintTest(__LINE__,"Reload of image ",reloaded_image==0,NIFTITEST_TRUE,&Errors);
+ nifti_image_infodump(reloaded_image);
+ compare_reference_image_values(reference_image,reloaded_image,&Errors);
+ nifti_image_free(reloaded_image);
+ }
+ nifti_image_free(reference_image);
+ }
+ }
+ {
+ enum { NUM_FILE_NAMES=8 };
+ const char * FILE_NAMES[NUM_FILE_NAMES]={
+ "myimage",
+ "myimage.tif",
+ "myimage.tif.gz",
+ "myimage.nii",
+ "myimage.img.gz",
+ ".nii",
+ ".myhiddenimage",
+ ".myhiddenimage.nii"
+ };
+ const char * KNOWN_FILE_BASENAMES[NUM_FILE_NAMES]={
+ "myimage",
+ "myimage.tif",
+ "myimage.tif.gz",
+ "myimage",
+ "myimage",
+ "",
+ ".myhiddenimage",
+ ".myhiddenimage"
+ };
+ const int KNOWN_nifti_validfilename[NUM_FILE_NAMES]={
+ 1,
+ 1,
+ 1,
+ 1,
+ 1,
+ 0,
+ 1,
+ 1
+ };
+ const int KNOWN_nifti_is_complete_filename[NUM_FILE_NAMES]={
+ 0,
+ 0,
+ 0,
+ 1,
+ 1,
+ 0,
+ 0,
+ 1
+ };
+ unsigned int fni;
+ for(fni=0;fni<NUM_FILE_NAMES;fni++)
+ {
+ printf("\nTesting \"%s\" filename\n",FILE_NAMES[fni]);
+ {
+ int KnownValid=nifti_validfilename(FILE_NAMES[fni]);
+ snprintf(TEMP_STR,256,"nifti_validfilename(\"%s\")=%d",FILE_NAMES[fni],KnownValid);
+ PrintTest(__LINE__,TEMP_STR,KnownValid != KNOWN_nifti_validfilename[fni],NIFTITEST_FALSE,&Errors);
+ }
+ {
+ int KnownValid=nifti_is_complete_filename(FILE_NAMES[fni]);
+ snprintf(TEMP_STR,256,"nifti_is_complete_filename(\"%s\")=%d",FILE_NAMES[fni],KnownValid);
+ PrintTest(__LINE__,TEMP_STR,KnownValid != KNOWN_nifti_is_complete_filename[fni],NIFTITEST_FALSE,&Errors);
+ }
+
+ {
+ char * basename=nifti_makebasename(FILE_NAMES[fni]);
+ snprintf(TEMP_STR,256,"nifti_makebasename(\"%s\")=\"%s\"",FILE_NAMES[fni],basename);
+ PrintTest(__LINE__,TEMP_STR,strcmp(basename,KNOWN_FILE_BASENAMES[fni]) != 0,NIFTITEST_FALSE,&Errors);
+ free(basename);
+ }
+ }
+ }
+ printf("\n\nTOTAL ERRORS=%d\n",Errors);
+ return Errors;
+}
diff --git a/Utilities/ITK/Utilities/nifti/docs/Doxy_nifti.txt b/Utilities/ITK/Utilities/nifti/docs/Doxy_nifti.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2011c627ee7bb9fbcab45642c06437436555e5b2
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/docs/Doxy_nifti.txt
@@ -0,0 +1,123 @@
+# Doxyfile 1.2.4
+
+# This file describes the settings to be used by doxygen for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# General configuration options
+#---------------------------------------------------------------------------
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+# by quotes) that should identify the project.
+
+PROJECT_NAME = nifti1_io
+
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY =
+
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = ../fsliolib ../niftilib ../znzlib
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+FILE_PATTERNS = *.c *.h
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE = testprog.c nifti1_test.c mjtest.c
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+
+EXCLUDE_PATTERNS =
+
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = NO
+
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimised for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation. Warning: This feature
+# is still experimental and very incomplete.
+
+GENERATE_XML = NO
+
diff --git a/Utilities/ITK/Utilities/nifti/docs/Doxyfile.ORIG b/Utilities/ITK/Utilities/nifti/docs/Doxyfile.ORIG
new file mode 100644
index 0000000000000000000000000000000000000000..aa3ba73ffdfde1e866319613f94f44cdc43ba9ae
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/docs/Doxyfile.ORIG
@@ -0,0 +1,746 @@
+# Doxyfile 1.2.4
+
+# This file describes the settings to be used by doxygen for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# General configuration options
+#---------------------------------------------------------------------------
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+# by quotes) that should identify the project.
+
+PROJECT_NAME =
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY =
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Dutch, French, Italian, Czech, Swedish, German, Finnish, Japanese,
+# Korean, Hungarian, Norwegian, Spanish, Romanian, Russian, Croatian,
+# Polish, Portuguese and Slovene.
+
+OUTPUT_LANGUAGE = English
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these class will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF = YES
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. It is allowed to use relative paths in the argument list.
+
+STRIP_FROM_PATH =
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a class diagram (in Html and LaTeX) for classes with base or
+# super classes. Setting the tag to NO turns the diagrams off.
+
+CLASS_DIAGRAMS = YES
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower case letters. If set to YES upper case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# users are adviced to set this option to NO.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like the Qt-style comments (thus requiring an
+# explict @brief command for a brief description.
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# reimplements.
+
+INHERIT_DOCS = YES
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE = 8
+
+# The ENABLE_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS =
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = YES
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text.
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT =
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+FILE_PATTERNS =
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE =
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+
+EXCLUDE_PATTERNS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output.
+
+INPUT_FILTER =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse.
+
+FILTER_SOURCE_FILES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet
+
+HTML_STYLESHEET =
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS = YES
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX = NO
+
+# This tag can be used to set the number of enum values (range [1..20])
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE = 4
+
+# If the GENERATE_TREEVIEW tag is set to YES, a side pannel will be
+# generated containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript and frames is required (for instance Netscape 4.0+
+# or Internet explorer 4.0+).
+
+GENERATE_TREEVIEW = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 250
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = YES
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, a4wide, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = NO
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = NO
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimised for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = YES
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using a WORD or other.
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assigments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = YES
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation. Warning: This feature
+# is still experimental and very incomplete.
+
+GENERATE_XML = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_PREDEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_PREDEF_ONLY tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED =
+
+#---------------------------------------------------------------------------
+# Configuration::addtions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tagfiles.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = NO
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, INCLUDE_GRAPH, and HAVE_DOT tags are set to
+# YES then doxygen will generate a graph for each documented file showing
+# the direct and indirect include dependencies of the file with other
+# documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, INCLUDED_BY_GRAPH, and HAVE_DOT tags are set to
+# YES then doxygen will generate a graph for each documented header file showing
+# the documented files that directly or indirectly include this file
+
+INCLUDED_BY_GRAPH = YES
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found on the path.
+
+DOT_PATH =
+
+# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than
+# this value, doxygen will try to truncate the graph, so that it fits within
+# the specified constraint. Beware that most browsers cannot cope with very
+# large images.
+
+MAX_DOT_GRAPH_WIDTH = 1024
+
+# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than
+# this value, doxygen will try to truncate the graph, so that it fits within
+# the specified constraint. Beware that most browsers cannot cope with very
+# large images.
+
+MAX_DOT_GRAPH_HEIGHT = 1024
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+#---------------------------------------------------------------------------
+# Configuration::addtions related to the search engine
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE = NO
+
+# The CGI_NAME tag should be the name of the CGI script that
+# starts the search engine (doxysearch) with the correct parameters.
+# A script with this name will be generated by doxygen.
+
+CGI_NAME = search.cgi
+
+# The CGI_URL tag should be the absolute URL to the directory where the
+# cgi binaries are located. See the documentation of your http daemon for
+# details.
+
+CGI_URL =
+
+# The DOC_URL tag should be the absolute URL to the directory where the
+# documentation is located. If left blank the absolute path to the
+# documentation, with file:// prepended to it, will be used.
+
+DOC_URL =
+
+# The DOC_ABSPATH tag should be the absolute path to the directory where the
+# documentation is located. If left blank the directory on the local machine
+# will be used.
+
+DOC_ABSPATH =
+
+# The BIN_ABSPATH tag must point to the directory where the doxysearch binary
+# is installed.
+
+BIN_ABSPATH = /usr/local/bin/
+
+# The EXT_DOC_PATHS tag can be used to specify one or more paths to
+# documentation generated for other projects. This allows doxysearch to search
+# the documentation for these projects as well.
+
+EXT_DOC_PATHS =
diff --git a/Utilities/ITK/Utilities/nifti/examples/CMakeLists.txt b/Utilities/ITK/Utilities/nifti/examples/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33721ec5100c804377a1995b2b99f5541ba1df6b
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/examples/CMakeLists.txt
@@ -0,0 +1,10 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(FSLEXAMPLES)
+
+INCLUDE_DIRECTORIES(${NIFTILIB_SOURCE_DIR} ${ZNZLIB_SOURCE_DIR} ${FSLIOLIB_SOURCE_DIR} )
+
+ADD_EXECUTABLE( ${PACKAGE_PREFIX}fsl_api_driver fsl_api_driver.c )
+TARGET_LINK_LIBRARIES( fsl_api_driver ${PACKAGE_PREFIX}fslio)
+
+INSTALL_TARGETS(/bin ${PACKAGE_PREFIX}fsl_api_driver)
diff --git a/Utilities/ITK/Utilities/nifti/examples/Makefile b/Utilities/ITK/Utilities/nifti/examples/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..2451479c7e752f33eed504e86384eb0e9d837a46
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/examples/Makefile
@@ -0,0 +1,38 @@
+CC = gcc
+CFLAGS = -ansi -pedantic
+
+FSLIO_INCS = -I../include
+NIFTI_INCS = -I../include
+ZNZ_INCS = -I/usr/include
+
+FSLIO_LIBS = -L../lib -lfslio
+NIFTI_LIBS = -L../lib -lniftiio
+ZNZ_LIBS = -L/usr/lib -L../lib -lznz -lm -lz
+
+
+
+## SGI 32bit
+ifeq ($(ARCH),SGI)
+ZNZ_INCS = -I/usr/freeware/include
+ZNZ_LIBS = -L/usr/freeware/lib32 -L../lib -lznz -lm -lz
+endif
+
+
+## Redhat Fedora Linux
+##ZNZ_INCS = -I/usr/include
+##ZNZ_LIBS = -L/usr/lib -L../lib -lznz -lm -lz
+
+
+
+
+all: fsl_api_driver
+
+clean:
+ rm -f fsl_api_driver
+
+fsl_api_driver: fsl_api_driver.c ../lib/libfslio.a
+ $(CC) $(CFLAGS) -o fsl_api_driver fsl_api_driver.c $(FSLIO_INCS) $(NIFTI_INCS) $(ZNZ_INCS) $(FSLIO_LIBS) $(NIFTI_LIBS) $(ZNZ_LIBS)
+
+help:
+ @echo "all: make the fsl_api_driver program"
+ @echo "clean: rm the fsl_api_driver program"
diff --git a/Utilities/ITK/Utilities/nifti/examples/fsl_api_driver.c b/Utilities/ITK/Utilities/nifti/examples/fsl_api_driver.c
new file mode 100644
index 0000000000000000000000000000000000000000..88a0e6aef40957c687a1a65f8318f31f9be059de
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/examples/fsl_api_driver.c
@@ -0,0 +1,142 @@
+/*******************************************************************
+ *
+ * fsl_api_driver.c
+ *
+ * Test fslio API
+ *
+ * Usage: fsl_api_driver <command> <dataset(s)> [params]
+ *
+ *
+ * print <dataset>
+ * print dataset header fields
+ * peek <dataset> X Y Z T
+ * print value at voxel location X Y Z T (0-based index)
+ * timecourse <dataset> X Y Z
+ * print timecourse at voxel location X Y Z (0-based index)
+ *
+ * Kate Fissell, University of Pittsburgh
+ * 12/04
+ *******************************************************************/
+
+
+#include <stdio.h>
+#include <strings.h>
+
+#include <nifti1.h>
+#include <fslio.h>
+
+void pusage(char *cmd);
+
+int main(int argc, char * argv[])
+{
+
+FSLIO *fslio;
+void *buffer;
+char *f1name;
+double ***vol;
+int x,y,z,t;
+
+
+/*** process commandline parameters */
+if (argc < 2) {
+ pusage(argv[0]);
+ exit(1);
+}
+
+
+/************************* PRINT ***************************/
+if (!strncmp(argv[1],"print",5)) {
+ if (argc != 3) {
+ fprintf(stderr, "\nError, print command takes one parameter: print <dataset>\n");
+ exit(1);
+ }
+
+ f1name = argv[2];
+ /** open nifti dataset */
+ fslio = FslInit();
+ buffer = FslReadAllVolumes(fslio,f1name);
+ if (buffer == NULL) {
+ fprintf(stderr, "\nError opening and reading %s.\n",f1name);
+ exit(1);
+ }
+
+ nifti_image_infodump(fslio->niftiptr);
+
+ exit(0);
+}
+
+
+
+/************************* PEEK ***************************/
+if (!strncmp(argv[1],"peek",4)) {
+ if (argc != 7) {
+ fprintf(stderr, "\nError, peek command takes five parameters: peek <dataset> X Y Z T\n");
+ exit(1);
+ }
+
+ /**** get inputs */
+ f1name = argv[2];
+ x = atoi(argv[3]);
+ y = atoi(argv[4]);
+ z = atoi(argv[5]);
+ t = atoi(argv[6]);
+
+ /** open nifti dataset header */
+ fslio = FslReadHeader(f1name);
+ if (fslio == NULL) {
+ fprintf(stderr, "\nError, could not read header info for %s.\n",f1name);
+ exit(1);
+ }
+
+ /**** check inputs */
+ if ( (x<0) || (x>=fslio->niftiptr->nx) ) {
+ fprintf(stderr, "\nError: x index (%d) out of range [0..%d]\n",x,fslio->niftiptr->nx-1);
+ exit(1);
+ }
+ if ( (y<0) || (y>=fslio->niftiptr->ny) ) {
+ fprintf(stderr, "\nError: y index (%d) out of range [0..%d]\n",y,fslio->niftiptr->ny-1);
+ exit(1);
+ }
+ if ( (z<0) || (z>=fslio->niftiptr->nz) ) {
+ fprintf(stderr, "\nError: z index (%d) out of range [0..%d]\n",z,fslio->niftiptr->nz-1);
+ exit(1);
+ }
+ if ( (t<0) || (t>=fslio->niftiptr->nt) ) {
+ fprintf(stderr, "\nError: t index (%d) out of range [0..%d]\n",t,fslio->niftiptr->nt-1);
+ exit(1);
+ }
+
+ /*** get volume data as scaled doubles */
+
+ vol = FslGetVolumeAsScaledDouble(fslio,t);
+ if (vol == NULL) {
+ fprintf(stderr, "\nError accessing %s\n",f1name);
+ exit(1);
+ }
+ else {
+ fprintf(stderr, "\nLocation %d %d %d %d: %.4f\n",x,y,z,t,vol[z][y][x]);
+ exit(0);
+ }
+
+}
+
+
+
+fprintf(stderr, "\nError, unrecognized command %s\n",argv[1]);
+pusage(argv[0]);
+
+
+exit(1);
+}
+
+
+void pusage(char *cmd) {
+ fprintf(stderr, "\n%s is a small driver program to test out the fslio API.\n",cmd);
+ fprintf(stderr, "\nUsage: %s <command> <dataset(s)> <parameters>",cmd);
+ fprintf(stderr, "\n\n\tCommands:");
+ fprintf(stderr, "\n\tprint <dataset>\t\t\tprint dataset header");
+ fprintf(stderr, "\n\tpeek <dataset> X Y Z T\t\tprint dataset value at location (0-based) (x,y,z,t).");
+
+ fprintf(stderr, "\n");
+return;
+}
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/CMakeLists.txt b/Utilities/ITK/Utilities/nifti/fsliolib/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63fa445d29df74f04bc93bac5160623f74559a65
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/CMakeLists.txt
@@ -0,0 +1,12 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(FSLIOLIB)
+
+INCLUDE_DIRECTORIES(${NIFTILIB_SOURCE_DIR} ${ZNZLIB_SOURCE_DIR})
+SET(FSLIOLIB_SRC fslio.c)
+
+ADD_LIBRARY(${PACKAGE_PREFIX}fslio ${FSLIOLIB_SRC} )
+TARGET_LINK_LIBRARIES( ${PACKAGE_PREFIX}fslio ${PACKAGE_PREFIX}niftiio)
+
+INSTALL_TARGETS(/lib ${PACKAGE_PREFIX}fslio)
+INSTALL_FILES(/include "(\\.h)$")
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/Makefile b/Utilities/ITK/Utilities/nifti/fsliolib/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..32901de88a23f9f6946b1221855306ae4603aad9
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/Makefile
@@ -0,0 +1,29 @@
+include ../Makefile
+
+
+PROJNAME = fslio
+
+INCFLAGS = $(ZLIB_INC) $(ZNZ_INC) $(NIFTI_INC)
+LIBS = $(ZLIB_LIBS) $(ZNZ_LIBS) $(NIFTI_LIBS) $(FSL_LIBS)
+
+SRCS=fslio.c
+OBJS=fslio.o
+
+SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv
+
+
+
+depend:
+ $(RM) -f depend.mk
+ $(MAKE) depend.mk
+
+depend.mk:
+ $(CC) $(DEPENDFLAGS) $(INCFLAGS) $(SRCS) >> depend.mk
+
+lib: libfslio.a
+
+libfslio.a: ${OBJS}
+ ${AR} -r libfslio.a ${OBJS}
+
+
+include depend.mk
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/dbh.h b/Utilities/ITK/Utilities/nifti/fsliolib/dbh.h
new file mode 100644
index 0000000000000000000000000000000000000000..eff0a50a67abc645098ecb828aa904dd021a5d3e
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/dbh.h
@@ -0,0 +1,102 @@
+#ifndef _DBH_H_
+#define _DBH_H_
+
+/*
+ *
+ * (c) Copyright, 1986-1994
+ * Biomedical Imaging Resource
+ * Mayo Foundation
+ *
+ * dbh.h
+ *
+ *
+ * database sub-definitions
+ */
+
+struct header_key /* header_key */
+ { /* off + size*/
+ int sizeof_hdr; /* 0 + 4 */
+ char data_type[10]; /* 4 + 10 */
+ char db_name[18]; /* 14 + 18 */
+ int extents; /* 32 + 4 */
+ short int session_error; /* 36 + 2 */
+ char regular; /* 38 + 1 */
+ char hkey_un0; /* 39 + 1 */
+ }; /* total=40 */
+
+struct image_dimension /* image_dimension */
+ { /* off + size*/
+ short int dim[8]; /* 0 + 16 */
+ char vox_units[4]; /* 16 + 4 */
+ char cal_units[8]; /* 20 + 4 */
+ short int unused1; /* 24 + 2 */
+ short int datatype; /* 30 + 2 */
+ short int bitpix; /* 32 + 2 */
+ short int dim_un0; /* 34 + 2 */
+ float pixdim[8]; /* 36 + 32 */
+ /*
+ pixdim[] specifies the voxel dimensions:
+ pixdim[1] - voxel width
+ pixdim[2] - voxel height
+ pixdim[3] - interslice distance
+ ..etc
+ */
+ float vox_offset; /* 68 + 4 */
+ float funused1; /* 72 + 4 */
+ float funused2; /* 76 + 4 */
+ float funused3; /* 80 + 4 */
+ float cal_max; /* 84 + 4 */
+ float cal_min; /* 88 + 4 */
+ int compressed; /* 92 + 4 */
+ int verified; /* 96 + 4 */
+ int glmax, glmin; /* 100 + 8 */
+ }; /* total=108 */
+
+struct data_history /* data_history */
+ { /* off + size*/
+ char descrip[80]; /* 0 + 80 */
+ char aux_file[24]; /* 80 + 24 */
+ char orient; /* 104 + 1 */
+ char originator[10]; /* 105 + 10 */
+ char generated[10]; /* 115 + 10 */
+ char scannum[10]; /* 125 + 10 */
+ char patient_id[10]; /* 135 + 10 */
+ char exp_date[10]; /* 145 + 10 */
+ char exp_time[10]; /* 155 + 10 */
+ char hist_un0[3]; /* 165 + 3 */
+ int views; /* 168 + 4 */
+ int vols_added; /* 172 + 4 */
+ int start_field; /* 176 + 4 */
+ int field_skip; /* 180 + 4 */
+ int omax,omin; /* 184 + 8 */
+ int smax,smin; /* 192 + 8 */
+ }; /* total=200 */
+
+struct dsr /* dsr */
+ { /* off + size*/
+ struct header_key hk; /* 0 + 40 */
+ struct image_dimension dime; /* 40 + 108 */
+ struct data_history hist; /* 148 + 200 */
+ }; /* total=348 */
+
+/* Acceptable values for hdr.dime.datatype */
+
+#define DT_NONE 0
+#define DT_UNKNOWN 0
+#define DT_BINARY 1
+#define DT_UNSIGNED_CHAR 2
+#define DT_SIGNED_SHORT 4
+#define DT_SIGNED_INT 8
+#define DT_FLOAT 16
+#define DT_COMPLEX 32
+#define DT_DOUBLE 64
+#define DT_RGB 128
+#define DT_ALL 255
+
+typedef struct
+ {
+ float real;
+ float imag;
+ } COMPLEX;
+
+#endif
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/fslio.c b/Utilities/ITK/Utilities/nifti/fsliolib/fslio.c
new file mode 100644
index 0000000000000000000000000000000000000000..5b21d88e1b61e6d27db7acc4d0904c821b2e91fd
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/fslio.c
@@ -0,0 +1,2413 @@
+/*
+ fslio.c (Input and output routines for images in FSL)
+
+ Mark Jenkinson
+ FMRIB Image Analysis Group
+*/
+
+
+
+/*
+
+ Part of FSL - FMRIB's Software Library
+ http://www.fmrib.ox.ac.uk/fsl
+ fsl@fmrib.ox.ac.uk
+
+ Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+ Imaging of the Brain), Department of Clinical Neurology, Oxford
+ University, Oxford, UK
+
+*/
+
+/** \file fslio.c
+ \brief Main collection of FSL i/o routines, written by Mark Jenkinson, FMRIB
+
+ - updates by Rick Reynolds, SSCC, NIMH
+ */
+
+#include "fslio.h"
+#include "assert.h"
+
+static int FslIgnoreMFQ=0;
+static int FslOverrideOutputType=-1;
+
+#define FSLIOERR(x) { fprintf(stderr,"Error:: %s\n",(x)); fflush(stderr); exit(EXIT_FAILURE); }
+
+
+/************************************************************
+ * FslFileTypeString
+ ************************************************************/
+/*! \fn char* FslFileTypeString(int filetype)
+ \brief Return a string describing the format of the dataset
+ \param filetype FSL data format code. Legal values are as defined
+ by FSL_TYPE.
+ \return A string with the data format name, e.g. "ANALYZE-7.5"
+ \sa FSL_TYPE
+*/
+char* FslFileTypeString(int filetype)
+{
+ if (filetype==FSL_TYPE_ANALYZE) return "ANALYZE-7.5";
+ if (filetype==FSL_TYPE_NIFTI) return "NIFTI-1+";
+ if (filetype==FSL_TYPE_NIFTI_PAIR) return "NIFTI-1";
+ if (filetype==FSL_TYPE_ANALYZE_GZ) return "ANALYZE-7.5";
+ if (filetype==FSL_TYPE_NIFTI_GZ) return "NIFTI-1+";
+ if (filetype==FSL_TYPE_NIFTI_PAIR_GZ) return "NIFTI-1";
+ return "UNKNOWN";
+}
+
+
+int FslIsValidFileType(int filetype)
+{
+ if ( (filetype!=FSL_TYPE_ANALYZE) && (filetype!=FSL_TYPE_ANALYZE_GZ) &&
+ (filetype!=FSL_TYPE_NIFTI) && (filetype!=FSL_TYPE_NIFTI_GZ) &&
+ (filetype!=FSL_TYPE_NIFTI_PAIR) && (filetype!=FSL_TYPE_NIFTI_PAIR_GZ) &&
+ (filetype!=FSL_TYPE_MINC) && (filetype!=FSL_TYPE_MINC_GZ) ) {
+ fprintf(stderr,"Error: unrecognised file type: %d\n",filetype);
+ return 0;
+ }
+ return 1;
+}
+
+
+int FslBaseFileType(int filetype)
+{
+ /* returns -1 to indicate error - unrecognised filetype */
+ if ( (filetype==FSL_TYPE_ANALYZE_GZ) || (filetype==FSL_TYPE_ANALYZE) )
+ return FSL_TYPE_ANALYZE;
+ if ( (filetype==FSL_TYPE_NIFTI_GZ) || (filetype==FSL_TYPE_NIFTI) )
+ return FSL_TYPE_NIFTI;
+ if ( (filetype==FSL_TYPE_NIFTI_PAIR_GZ) || (filetype==FSL_TYPE_NIFTI_PAIR) )
+ return FSL_TYPE_NIFTI_PAIR;
+ if ( (filetype==FSL_TYPE_MINC_GZ) || (filetype==FSL_TYPE_MINC) )
+ return FSL_TYPE_MINC;
+ fprintf(stderr,"Error: unrecognised file type (%d)\n",filetype);
+ return -1;
+}
+
+
+int FslGetFileType2(const FSLIO *fslio, int quiet)
+{
+ FSLIO *mutablefslio;
+ if (fslio==NULL) FSLIOERR("FslGetFileType: Null pointer passed for FSLIO");
+ if ( (fslio->file_mode==FSL_TYPE_MINC) || (fslio->file_mode==FSL_TYPE_MINC_GZ) ) {
+ return fslio->file_mode;
+ }
+ if ( !FslIsValidFileType(fslio->file_mode) ) return -1;
+
+ if (fslio->niftiptr!=NULL) { /* check that it is nifti_type and filetype are consistent */
+ if (fslio->niftiptr->nifti_type != FslBaseFileType(fslio->file_mode)) {
+ if (!quiet) {
+ fprintf(stderr,"Warning: nifti structure and fsl structure disagree on file type\n");
+ fprintf(stderr,"nifti = %d and fslio = %d\n",fslio->niftiptr->nifti_type,fslio->file_mode);
+ }
+ mutablefslio = (FSLIO *) fslio; /* dodgy and will generate warnings */
+ mutablefslio->niftiptr->nifti_type = FslBaseFileType(fslio->file_mode);
+ return fslio->file_mode;
+ }
+ }
+ return fslio->file_mode;
+}
+
+int FslGetFileType(const FSLIO *fslio)
+{
+ return FslGetFileType2(fslio,0);
+}
+
+
+
+void FslSetFileType(FSLIO *fslio, int filetype)
+{
+ if (fslio==NULL) FSLIOERR("FslSetFileType: Null pointer passed for FSLIO");
+ if ( (filetype==FSL_TYPE_MINC) || (filetype==FSL_TYPE_MINC_GZ) ) {
+ fslio->file_mode = filetype;
+ return;
+ }
+ if (! FslIsValidFileType(filetype)) { return; }
+ fslio->file_mode = filetype; /* indicates general nifti - details in niftiptr */
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->nifti_type = FslBaseFileType(filetype);
+ nifti_set_iname_offset(fslio->niftiptr);
+ }
+}
+
+
+
+int FslIsSingleFileType(int filetype)
+{
+ if ( (filetype==FSL_TYPE_NIFTI) || (filetype==FSL_TYPE_NIFTI_GZ) ||
+ (filetype==FSL_TYPE_MINC) || (filetype==FSL_TYPE_MINC_GZ) )
+ return 1;
+ return 0;
+}
+
+
+int FslIsCompressedFileType(int filetype)
+{
+ if ( filetype >=100 ) return 1;
+ return 0;
+}
+
+
+int FslGetWriteMode(const FSLIO *fslio)
+{
+ if (fslio==NULL) FSLIOERR("FslGetWriteMode: Null pointer passed for FSLIO");
+ return fslio->write_mode;
+}
+
+
+void FslSetWriteMode(FSLIO *fslio, int mode)
+{
+ if (fslio==NULL) FSLIOERR("FslSetWriteMode: Null pointer passed for FSLIO");
+ fslio->write_mode = mode;
+}
+
+
+int FslGetEnvOutputType(void)
+{
+ /* return type is one of FSL_TYPE_* or -1 to indicate error */
+ char *otype;
+ if (FslOverrideOutputType>=0) return FslOverrideOutputType;
+ otype = getenv("FSLOUTPUTTYPE");
+ if (otype == NULL) {
+ fprintf(stderr,"ERROR:: Environment variable FSLOUTPUTTYPE is not set!\n");
+ fprintf(stderr,"Please make sure that the appropriate configuration file is sourced by your shell (e.g. by putting it in .profile).\n");
+ fprintf(stderr,"e.g. bash or sh users add the line \". ${FSLDIR}/etc/fslconf/fsl.sh\"\n");
+ fprintf(stderr,"e.g. tcsh or csh users add the line \"source ${FSLDIR}/etc/fslconf/fsl.csh\"\n");
+ exit(EXIT_FAILURE);
+ }
+ if (strcmp(otype,"ANALYZE")==0) { return FSL_TYPE_ANALYZE; }
+ if (strcmp(otype,"ANALYZE_GZ")==0) { return FSL_TYPE_ANALYZE_GZ; }
+ if (strcmp(otype,"NIFTI")==0) { return FSL_TYPE_NIFTI; }
+ if (strcmp(otype,"NIFTI_GZ")==0) { return FSL_TYPE_NIFTI_GZ; }
+ if (strcmp(otype,"NIFTI_PAIR")==0) { return FSL_TYPE_NIFTI_PAIR; }
+ if (strcmp(otype,"NIFTI_PAIR_GZ")==0) { return FSL_TYPE_NIFTI_PAIR_GZ; }
+ if (strcmp(otype,"MINC")==0) { return FSL_TYPE_MINC; }
+ if (strcmp(otype,"MINC_GZ")==0) { return FSL_TYPE_MINC_GZ; }
+ fprintf(stderr,"ERROR:: Unrecognised value (%s) of environment variable FSLOUTPUT\n",otype);
+ fprintf(stderr,"Legal values are: ANALYZE, NIFTI, NIFTI_PAIR, MINC, ANALYZE_GZ, NIFTI_GZ, NIFTI_PAIR_GZ, MINC_GZ\n");
+ exit(EXIT_FAILURE);
+ return -1;
+}
+
+
+int FslFileType(const char* fname)
+{
+ /* return type is FSL_TYPE_* or -1 to indicate undetermined */
+ /* use name as first priority but if that is ambiguous then resolve using environment */
+ int flen;
+ int retval=-1;
+ if (fname==NULL) return retval;
+ flen = strlen(fname);
+ if (flen<5) return retval; /* smallest name + extension is a.nii */
+ if (strcmp(fname + flen - 4,".nii")==0) retval=FSL_TYPE_NIFTI;
+ if (strcmp(fname + flen - 7,".nii.gz")==0) retval=FSL_TYPE_NIFTI_GZ;
+ if (strcmp(fname + flen - 4,".mnc")==0) retval=FSL_TYPE_MINC;
+ if (strcmp(fname + flen - 7,".mnc.gz")==0) retval=FSL_TYPE_MINC;
+ if (strcmp(fname + flen - 4,".hdr")==0) retval=FSL_TYPE_NIFTI_PAIR;
+ if (strcmp(fname + flen - 4,".img")==0) retval=FSL_TYPE_NIFTI_PAIR;
+ if (strcmp(fname + flen - 7,".hdr.gz")==0) retval=FSL_TYPE_NIFTI_PAIR_GZ;
+ if (strcmp(fname + flen - 7,".img.gz")==0) retval=FSL_TYPE_NIFTI_PAIR_GZ;
+ if ( (retval==FSL_TYPE_NIFTI_PAIR) || (retval==FSL_TYPE_NIFTI_PAIR_GZ) ) {
+ /* If it was hdr or img, check if Analyze was requested by environment */
+ if ( (FslGetEnvOutputType() == FSL_TYPE_ANALYZE) && (retval == FSL_TYPE_NIFTI_PAIR) )
+ retval=FSL_TYPE_ANALYZE;
+ if ( (FslGetEnvOutputType() == FSL_TYPE_ANALYZE_GZ) && (retval == FSL_TYPE_NIFTI_PAIR_GZ) )
+ retval=FSL_TYPE_ANALYZE_GZ;
+ }
+ return retval;
+}
+
+
+/************************************************************
+ * FslGetReadFileType
+ ************************************************************/
+/*! \fn int FslGetReadFileType(const FSLIO *fslio)
+ \brief return the best estimate of the true file type
+
+ This function is used to return the best estimate of the true file type once
+ a simple open has occurred - for now it is used after a nifti open call is made
+
+ \param fslio data structure
+ \return FSL_TYPE filetype code
+ \sa FSL_TYPE
+*/
+int FslGetReadFileType(const FSLIO *fslio)
+{
+ int filetype=FSL_TYPE_ANALYZE; /* unused default */
+ if (fslio==NULL) FSLIOERR("FslReadGetFileType: Null pointer passed for FSLIO");
+ /* Don't use fslio->file_mode as it hasn't been set yet */
+ if (fslio->niftiptr!=NULL) {
+ /* use the nifti_type and hdr or img name to determine the actual type */
+ if (fslio->niftiptr->nifti_type == FSL_TYPE_ANALYZE) {
+ if (FslIsCompressedFileType(FslFileType(fslio->niftiptr->iname))) {
+ filetype = FSL_TYPE_ANALYZE_GZ;
+ } else {
+ filetype = FSL_TYPE_ANALYZE;
+ }
+ }
+ if (fslio->niftiptr->nifti_type == FSL_TYPE_NIFTI_PAIR) {
+ if (FslIsCompressedFileType(FslFileType(fslio->niftiptr->iname))) {
+ filetype = FSL_TYPE_NIFTI_PAIR_GZ;
+ } else {
+ filetype = FSL_TYPE_NIFTI_PAIR;
+ }
+ }
+ if (fslio->niftiptr->nifti_type == FSL_TYPE_NIFTI) {
+ if (FslIsCompressedFileType(FslFileType(fslio->niftiptr->fname))) {
+ filetype = FSL_TYPE_NIFTI_GZ;
+ } else {
+ filetype = FSL_TYPE_NIFTI;
+ }
+ }
+
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ filetype = FSL_TYPE_MINC;
+ }
+ return filetype;
+}
+
+
+int FslFileExists(const char *filename)
+{
+ /* return 1 if file(s) exists, otherwise return 0 */
+ char *hdrname = nifti_findhdrname(filename);
+ char *imgname = NULL;
+ if (hdrname!=NULL){
+ imgname = nifti_findimgname(filename,
+ FslBaseFileType(FslFileType(hdrname)));
+ free(hdrname);
+ if (imgname != NULL) { free(imgname); return 1; }
+ }
+ return 0;
+}
+
+char *FslMakeBaseName(const char *fname)
+{
+ char *basename;
+ int blen;
+ basename = nifti_makebasename(fname);
+ blen = strlen(basename);
+#ifdef HAVE_ZLIB
+ if (strcmp(basename + blen-7,".mnc.gz") == 0)
+ { basename[blen-7]='\0'; return basename; }
+#endif
+ if (strcmp(basename + blen-4,".mnc") == 0)
+ { basename[blen-4]='\0'; return basename; }
+ return basename;
+}
+
+
+void FslGetHdrImgNames(const char* filename, const FSLIO* fslio,
+ char** hdrname, char** imgname)
+{
+ char *basename;
+ int filetype;
+ basename = FslMakeBaseName(filename);
+ *hdrname = (char *)calloc(sizeof(char),strlen(basename)+8);
+ *imgname = (char *)calloc(sizeof(char),strlen(basename)+8);
+ strcpy(*hdrname,basename);
+ strcpy(*imgname,basename);
+ filetype = FslGetFileType(fslio);
+ if (filetype==FSL_TYPE_NIFTI_GZ) {
+ strcat(*hdrname,".nii.gz");
+ strcat(*imgname,".nii.gz");
+ free(basename);
+ return;
+ }
+ if (filetype==FSL_TYPE_NIFTI) {
+ strcat(*hdrname,".nii");
+ strcat(*imgname,".nii");
+ free(basename);
+ return;
+ }
+ if (filetype==FSL_TYPE_MINC_GZ) {
+ strcat(*hdrname,".mnc.gz");
+ strcat(*imgname,".mnc.gz");
+ free(basename);
+ return;
+ }
+ if (filetype==FSL_TYPE_MINC) {
+ strcat(*hdrname,".mnc");
+ strcat(*imgname,".mnc");
+ free(basename);
+ return;
+ }
+ if ( (filetype==FSL_TYPE_NIFTI_PAIR_GZ) || (filetype==FSL_TYPE_ANALYZE_GZ) ) {
+ strcat(*hdrname,".hdr.gz");
+ strcat(*imgname,".img.gz");
+ free(basename);
+ return;
+ }
+ if ( (filetype==FSL_TYPE_NIFTI_PAIR) || (filetype==FSL_TYPE_ANALYZE) ) {
+ strcat(*hdrname,".hdr");
+ strcat(*imgname,".img");
+ free(basename);
+ return;
+ }
+
+ fprintf(stderr,"Error: Unrecognised filetype (%d)\n",FslGetFileType(fslio));
+ free(basename);
+ /* Failure */
+ *hdrname = NULL;
+ *imgname = NULL;
+}
+
+
+
+/***************************************************************
+ * FslInit()
+ ***************************************************************/
+/*! \fn FSLIO *FslInit()
+ \brief allocate space for the FSLIO struct and set some sensible defaults
+ \return A pointer to an initialized FSLIO data structure
+ */
+FSLIO *FslInit(void)
+{
+ FSLIO *fslio;
+ fslio = (FSLIO *) calloc(1,sizeof(FSLIO));
+ FslSetInit(fslio);
+ return fslio;
+}
+
+void FslSetInit(FSLIO* fslio)
+{
+ /* set some sensible defaults */
+ fslio->niftiptr = NULL;
+ fslio->mincptr = NULL;
+ FslSetFileType(fslio,FslGetEnvOutputType());
+ FslSetWriteMode(fslio,0);
+ fslio->written_hdr = 0;
+}
+
+
+
+void FslInit4Write(FSLIO* fslio, const char* filename, int ft)
+{
+ /* ft determines filetype if ft>=0*/
+ int imgtype;
+
+ FslSetWriteMode(fslio,1);
+
+ /* Determine file type from image name (first priority) or environment (default) */
+ imgtype = FslFileType(filename);
+ if (imgtype<0) imgtype = FslGetEnvOutputType();
+
+ if (ft >= 0) imgtype = ft;
+
+ if (!FslIsValidFileType(imgtype)) {
+ fprintf(stderr,"Error: Failed to determine file type for writing in FslOpen()\n");
+ exit(EXIT_FAILURE);
+ }
+
+ if ( (FslBaseFileType(imgtype)!=FSL_TYPE_MINC) ) {
+ FslInitHeader(fslio, NIFTI_TYPE_FLOAT32,
+ 1, 1, 1, 3, 0.0, 0.0, 0.0, 0.0, 4, "mm");
+
+ FslSetFileType(fslio,imgtype); /* this is after InitHeader as niftiptr set there */
+
+ /* determine the header and image filename */
+ FslGetHdrImgNames(filename,fslio,&(fslio->niftiptr->fname),&(fslio->niftiptr->iname));
+ if ( (fslio->niftiptr->fname == NULL) || (fslio->niftiptr->iname == NULL) ) {
+ fprintf(stderr,"Error: cannot find filenames for %s\n",filename);
+ }
+
+ } else if (FslBaseFileType(imgtype)==FSL_TYPE_MINC) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ return;
+ } else {
+ fprintf(stderr,"Error:: unrecognised image type requested\n");
+ return;
+ }
+
+ return;
+}
+
+
+
+void FslInitHeader(FSLIO *fslio, short t,
+ size_t x, size_t y, size_t z, size_t v,
+ float vx, float vy, float vz, float tr,
+ size_t dim,
+ const char* units)
+{
+ /* NB: This function does not set the file type or write mode*/
+
+ if (fslio==NULL) FSLIOERR("FslInitHeader: Null pointer passed for FSLIO");
+
+ fslio->niftiptr = nifti_simple_init_nim();
+ /* make nifti type consistent with fslio */
+ fslio->niftiptr->nifti_type = FslBaseFileType(fslio->file_mode);
+
+ fslio->mincptr = NULL;
+
+ FslSetDataType(fslio,t);
+ FslSetDim(fslio,x,y,z,v);
+ FslSetVoxDim(fslio,vx,vy,vz,tr);
+ FslSetTimeUnits(fslio,"s");
+ FslSetDimensionality(fslio,dim);
+}
+
+
+void FslCloneHeader(FSLIO *dest, const FSLIO *src)
+{
+ /* only clone the information that is stored in the disk version of the header */
+ /* - therefore _not_ the filenames, output type, write mode, etc */
+
+ char *fname=NULL, *iname=NULL;
+ void *data=NULL;
+ int filetype, writemode;
+ int preserve_nifti_values = 0;
+ if (dest==NULL) FSLIOERR("FslCloneHeader: Null pointer passed for FSLIO");
+ if (src==NULL) FSLIOERR("FslCloneHeader: Null pointer passed for FSLIO");
+
+ if (src->niftiptr!=NULL) {
+ /* preserve the filenames, output type and write mode */
+ if (dest->niftiptr != NULL) {
+ fname = dest->niftiptr->fname;
+ iname = dest->niftiptr->iname;
+ data = dest->niftiptr->data;
+ preserve_nifti_values = 1;
+ }
+ filetype = FslGetFileType2(dest,1);
+ writemode = FslGetWriteMode(dest);
+
+ /* copy _all_ info across */
+ dest->niftiptr = nifti_copy_nim_info(src->niftiptr);
+
+ /* restore old values */
+ if (preserve_nifti_values) {
+ dest->niftiptr->data = data;
+ } else {
+ /* destroy the values that the nifti copy creates */
+ free(dest->niftiptr->fname);
+ free(dest->niftiptr->iname);
+ nifti_free_extensions(dest->niftiptr);
+
+ dest->niftiptr->fname = NULL;
+ dest->niftiptr->iname = NULL;
+ dest->niftiptr->data = NULL; /* should already be NULL */
+ }
+ FslSetFileType(dest,filetype);
+ FslSetWriteMode(dest,writemode);
+ }
+
+ if (src->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+
+}
+
+
+int fsl_fileexists(const char* fname)
+{
+ znzFile fp;
+ fp = znzopen( fname , "rb" , 1 ) ;
+ if( !znz_isnull(fp) ) { znzclose(fp); return 1; }
+ return 0;
+}
+
+
+int FslCheckForMultipleFileNames(const char* filename)
+{
+ char *basename, *tmpname;
+ int singlecount=0, hdrcount=0, imgcount=0, ambiguous=0;
+ basename = nifti_makebasename(filename);
+ tmpname = (char *)calloc(strlen(basename) + 10,sizeof(char));
+
+ strcpy(tmpname,basename);
+ strcat(tmpname,".nii");
+ if (fsl_fileexists(tmpname)) { singlecount++; }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".nii.gz");
+ if (fsl_fileexists(tmpname)) { singlecount++; }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".mnc");
+ if (fsl_fileexists(tmpname)) { singlecount++; }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".mnc.gz");
+ if (fsl_fileexists(tmpname)) { singlecount++; }
+
+ strcpy(tmpname,basename);
+ strcat(tmpname,".img");
+ if (fsl_fileexists(tmpname)) { imgcount++; }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".img.gz");
+ if (fsl_fileexists(tmpname)) { imgcount++; }
+
+ strcpy(tmpname,basename);
+ strcat(tmpname,".hdr");
+ if (fsl_fileexists(tmpname)) { hdrcount++; }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".hdr.gz");
+ if (fsl_fileexists(tmpname)) { hdrcount++; }
+
+ ambiguous = 1;
+ if ( (hdrcount==1) && (imgcount==1) && (singlecount==0) ) { ambiguous=0; }
+ if ( (hdrcount==0) && (imgcount==0) && (singlecount==1) ) { ambiguous=0; }
+
+ /* treat no image found as not ambiguous - want opening errors instead */
+ if ( (hdrcount==0) && (imgcount==0) && (singlecount==0) ) { ambiguous=0; }
+
+ free(tmpname);
+ free(basename);
+ return ambiguous;
+}
+
+
+
+int check_for_multiple_filenames(const char* filename)
+{
+ char *basename, *tmpname;
+ char *otype;
+ if (FslCheckForMultipleFileNames(filename))
+ { /* take action */
+ basename = nifti_makebasename(filename);
+ tmpname = (char *)calloc(strlen(basename) + 10,sizeof(char));
+ fprintf(stderr,"\n\n\nWARNING!!!! Multiple image files detected:\n");
+ /* list the offending files */
+ strcpy(tmpname,basename);
+ strcat(tmpname,".nii");
+ if (fsl_fileexists(tmpname)) { fprintf(stderr,"%s ",tmpname); }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".nii.gz");
+ if (fsl_fileexists(tmpname)) { fprintf(stderr,"%s ",tmpname); }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".mnc");
+ if (fsl_fileexists(tmpname)) { fprintf(stderr,"%s ",tmpname); }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".mnc.gz");
+ if (fsl_fileexists(tmpname)) { fprintf(stderr,"%s ",tmpname); }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".img");
+ if (fsl_fileexists(tmpname)) { fprintf(stderr,"%s ",tmpname); }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".img.gz");
+ if (fsl_fileexists(tmpname)) { fprintf(stderr,"%s ",tmpname); }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".hdr");
+ if (fsl_fileexists(tmpname)) { fprintf(stderr,"%s ",tmpname); }
+ strcpy(tmpname,basename);
+ strcat(tmpname,".hdr.gz");
+ if (fsl_fileexists(tmpname)) { fprintf(stderr,"%s ",tmpname); }
+ fprintf(stderr,"\n\n");
+
+ if (!FslIgnoreMFQ) {
+ otype = getenv("FSLMULTIFILEQUIT");
+ if (otype!=NULL) {
+ fprintf(stderr,"STOPPING PROGRAM\n");
+ exit(EXIT_FAILURE);
+ }
+ }
+ return 1;
+ }
+ return 0;
+}
+
+
+
+/***************************************************************
+ * FslOpen
+ ***************************************************************/
+/*! \fn FSLIO *FslOpen(const char *filename, const char *opts)
+ \brief Opens a file for either reading or writing.
+
+ The format of the output dataset is determined automatically by
+ passing filetype -1 to FslXOpen.
+ \sa FslXOpen
+ */
+FSLIO *FslOpen(const char *filename, const char *opts)
+{
+ /* Note: -1 for filetype indicates that FslXOpen should determine filetype for itself */
+ return FslXOpen(filename,opts,-1);
+}
+
+
+/***************************************************************
+ * FslXOpen
+ ***************************************************************/
+/*! \fn FSLIO *FslXOpen(const char *filename, const char *opts, int filetype)
+ \brief Opens a file for either reading or writing
+
+ Files to be read are automatically read whether
+ compressed or not. Also, reading uses the file extension
+ and will fail if that file does not exist.
+ For a more robust read, pass the basename in as then all types
+ will be tried.
+ \param filename Name (or basename) of the file to open
+ \param opts Flags for fopen() of dataset, eg "r", "wb", etc.
+ \param filetype specifies the type of file to be written. Legal
+ values are as defined by FSL_TYPE. If filetype is less than
+ zero, then it is ignored and the type is determined by the
+ filename extension or, failing that, the environment default.
+ \return pointer to FSLIO dataset datastructure
+ \sa FSLIO
+ \sa FSL_TYPE
+ */
+FSLIO *FslXOpen(const char *filename, const char *opts, int filetype)
+{
+
+ FSLIO *fslio;
+ char bopts[1024];
+ size_t i, bi;
+ int imgtype;
+
+ fslio = FslInit();
+
+ bi=0;
+ for(i=0;i<strlen(opts);i++) {
+ if (opts[i]=='w') { FslSetWriteMode(fslio,1); }
+ if (opts[i]!='b' && opts[i]!='t') { bopts[bi++]=opts[i]; }
+ }
+ /* add in 'b' (at the end) for windows compatibility */
+ bopts[bi++]='b';
+ bopts[bi]='\0';
+
+
+ if (FslGetWriteMode(fslio)==1) {
+
+ /** ====================== Open file for writing ====================== **/
+
+ FslInit4Write(fslio,filename,filetype);
+ imgtype = FslGetFileType(fslio);
+ fslio->written_hdr = 0;
+
+ /* open the image file - not the header */
+ fslio->fileptr = znzopen(fslio->niftiptr->iname,bopts,FslIsCompressedFileType(imgtype));
+ if (znz_isnull(fslio->fileptr)) {
+ fprintf(stderr,"Error: failed to open file %s\n",fslio->niftiptr->iname);
+ return NULL;
+ }
+
+ if (!FslIsSingleFileType(imgtype)) {
+ /* set up pointer at end of iname_offset for dual file formats (not singles) */
+ FslSeekVolume(fslio,0);
+ }
+ return fslio;
+
+ }
+
+
+
+ /** ======================== Open file for reading ====================== **/
+
+ check_for_multiple_filenames(filename);
+
+ /* see if the extension indicates a minc file */
+ imgtype = FslFileType(filename);
+ if ((imgtype>=0) && (FslBaseFileType(imgtype)==FSL_TYPE_MINC)) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ return NULL;
+ }
+
+ /* otherwise open nifti file: read header and open img file (may be same file) */
+ fslio->fileptr = nifti_image_open(filename,bopts,&(fslio->niftiptr));
+ if (znz_isnull(fslio->fileptr)) {
+ fprintf(stderr,"Error: failed to open file %s\n",filename);
+ return NULL;
+ }
+
+ /* set the file type given what has been read - it uses nifti_type and filenames */
+ imgtype = FslGetReadFileType(fslio);
+ FslSetFileType(fslio,imgtype);
+ FslSetWriteMode(fslio,0);
+
+ if (FslBaseFileType(FslGetFileType(fslio))==FSL_TYPE_ANALYZE) {
+ /* For the ANALYZE case in FSL, must cheat and grab the originator field! */
+ /* Note that the header file is always separate here and closed by now */
+ struct dsr ahdr;
+ short orig[5];
+ FslReadRawHeader(&ahdr,fslio->niftiptr->fname);
+ if (fslio->niftiptr->byteorder != nifti_short_order()) {
+ AvwSwapHeader(&ahdr);
+ }
+ /* Read the origin and set the sform up (if origin is non-zero) */
+ /* Note that signed pixdims are passed in to set the LR orientation */
+ memcpy(orig,&(ahdr.hist.originator),10);
+ FslSetAnalyzeSform(fslio, orig, fslio->niftiptr->pixdim[1],
+ fslio->niftiptr->pixdim[2], fslio->niftiptr->pixdim[3]);
+ }
+
+ /* from now on force all vox dims to be positive - LR info is in sform */
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->dx = fabs(fslio->niftiptr->dx);
+ fslio->niftiptr->dy = fabs(fslio->niftiptr->dy);
+ fslio->niftiptr->dz = fabs(fslio->niftiptr->dz);
+ fslio->niftiptr->pixdim[1] = fabs(fslio->niftiptr->pixdim[1]);
+ fslio->niftiptr->pixdim[2] = fabs(fslio->niftiptr->pixdim[2]);
+ fslio->niftiptr->pixdim[3] = fabs(fslio->niftiptr->pixdim[3]);
+ }
+ /* set up pointer at end of iname_offset , ready for reading */
+ FslSeekVolume(fslio,0);
+
+ return fslio;
+
+}
+
+
+
+/***************************************************************
+ * FslReadAllVolumes
+ ***************************************************************/
+/*! \fn void* FslReadAllVolumes(FSLIO* fslio, char* filename)
+ \brief Read the header and all data into the FSLIO structure
+
+ There is no need for FslOpen or FslClose calls when FslReadAllVolumes()
+ is called.
+ <br>This routine allocates the buffer to hold the entire dataset.
+ <br>The data block returned will contain the data in whatever
+ datatype it is stored as on disk (therefore it is a void *).
+ <br>The data buffer will be byteswapped to native-endian.
+ <br>The data buffer will not be scaled.
+ <br>The best call to make before this is FslInit() or a calloc() for
+ fslio. (??? why calloc if this allocates the buffer ???)
+
+ \param fslio pointer to an open dataset
+ \param filename Name of the dataset to read.
+ \return A pointer to the data block buffer (allocated by this function).
+ <br> Return Null on error ??? is this true ???
+ <ul>
+ <li>Note this pointer is also in the FSLIO structure as
+ fslio->niftiptr->data.</li>
+ <li>Note a void pointer is returned, as the datablock is of
+ variable datatype.</li>
+ </ul>
+
+ */
+void* FslReadAllVolumes(FSLIO* fslio, char* filename)
+{
+
+ int imgtype;
+ if (fslio==NULL) FSLIOERR("FslReadAllVolumes: Null pointer passed for FSLIO");
+
+ /* see if the extension indicates a minc file */
+ imgtype = FslFileType(filename);
+ if ((imgtype>=0) && (FslBaseFileType(imgtype)==FSL_TYPE_MINC)) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ return NULL;
+ }
+
+ /** otherwise it is a nifti file - so read it! **/
+ fslio->mincptr = NULL;
+ /* make sure an FslOpen hasn't locked the file */
+ if (!znz_isnull(fslio->fileptr)) FslClose(fslio);
+
+ fslio->niftiptr = nifti_image_read(filename,1);
+ FslSetFileType(fslio,fslio->niftiptr->nifti_type);
+ FslSetWriteMode(fslio,0);
+ return fslio->niftiptr->data;
+}
+
+
+
+/***************************************************************
+ * FslReadVolumes
+ ***************************************************************/
+/*! \fn size_t FslReadVolumes(FSLIO *fslio, void *buffer, size_t nvols)
+ \brief Read the first nvols Volumes from a 4D dataset
+
+ \param fslio pointer to open dataset
+ \param buffer buffer to read data into, allocated by ???
+ \param nvols number of volumes to read
+ \return Number of volumes read.
+ */
+size_t FslReadVolumes(FSLIO *fslio, void *buffer, size_t nvols)
+{
+ int volbytes;
+ size_t retval=0;
+ if (fslio==NULL) FSLIOERR("FslReadVolumes: Null pointer passed for FSLIO");
+ if (znz_isnull(fslio->fileptr)) FSLIOERR("FslReadVolumes: Null file pointer");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->data = buffer;
+ volbytes = FslGetVolSize(fslio) * fslio->niftiptr->nbyper;
+ retval = nifti_read_buffer(fslio->fileptr,fslio->niftiptr->data,nvols*volbytes,fslio->niftiptr);
+ retval /= volbytes;
+ }
+
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return retval;
+}
+
+
+
+/***************************************************************
+ * FslWriteAllVolumes
+ ***************************************************************/
+/*! \fn void FslWriteAllVolumes(FSLIO *fslio, const void *buffer)
+ \brief Writes all data from buffer (using size info from fslio) to file.
+
+ Dimension and datatype of buffer are as is specified in nifti_image structure
+ fslio->niftiptr.
+ Note: If file format is Analyze (not nifti) and in Neurological order then
+ SWAP DATA into Radiological order.
+
+ \param fslio pointer to open dataset
+ \param buffer pointer to data array. Size and datatype of this buffer
+ */
+void FslWriteAllVolumes(FSLIO *fslio, const void *buffer)
+{
+ short x,y,z,t;
+
+ if (fslio==NULL) FSLIOERR("FslWriteAllVolumes: Null pointer passed for FSLIO");
+
+ FslGetDim(fslio,&x,&y,&z,&t);
+ FslWriteHeader(fslio);
+ FslWriteVolumes(fslio,buffer,t);
+ return;
+}
+
+
+
+/***************************************************************
+ * FslWriteVolumes
+ ***************************************************************/
+/*! \fn size_t FslWriteVolumes(FSLIO *fslio, const void *buffer, size_t nvols)
+ \brief Write the first nvols volumes in buffer to disk.
+
+ Dimension and datatype of buffer are as is specified in nifti_image structure
+ fslio->niftiptr.
+ Note: If file format is Analyze (not nifti) and in Neurological order then
+ SWAP DATA into Radiological order.
+
+
+ \param fslio pointer to open dataset
+ \param buffer pointer to data array. Size and datatype of this buffer
+ \param nvols number of volumes to write
+ \return ??? looks like return of retval is missing ??? 0 on error.
+ */
+size_t FslWriteVolumes(FSLIO *fslio, const void *buffer, size_t nvols)
+{
+ /* The dimensions and datatype must be set before calling this function */
+ int retval;
+ if (fslio==NULL) FSLIOERR("FslWriteVolumes: Null pointer passed for FSLIO");
+ if ( (!fslio->written_hdr) && (FslIsSingleFileType(FslGetFileType(fslio))) &&
+ (FslIsCompressedFileType(FslGetFileType(fslio))) )
+ { FSLIOERR("FslWriteVolumes: header must be written before data for single compressed file types"); }
+
+ if (fslio->niftiptr!=NULL) {
+ long int nbytes, bpv;
+ bpv = fslio->niftiptr->nbyper; /* bytes per voxel */
+ nbytes = nvols * FslGetVolSize(fslio) * bpv;
+
+ if ( (FslBaseFileType(FslGetFileType(fslio))==FSL_TYPE_ANALYZE)
+ && (FslGetLeftRightOrder(fslio)==FSL_NEUROLOGICAL) ) {
+ /* If it is Analyze and Neurological order then SWAP DATA into Radiological order */
+ /* This is nasty - but what else can be done?!? */
+ char *tmpbuf, *inbuf;
+ long int x, b, n, nrows;
+ short nx, ny, nz, nv;
+ inbuf = (char *) buffer;
+ tmpbuf = (char *)calloc(nbytes,1);
+ FslGetDim(fslio,&nx,&ny,&nz,&nv);
+ nrows = nbytes / (nx * bpv);
+ for (n=0; n<nrows; n++) {
+ for (x=0; x<nx; x++) {
+ for (b=0; b<bpv; b++) {
+ tmpbuf[b + bpv * (n*nx + nx - 1 - x)] = inbuf[b + bpv * (n*nx + x)];
+ }
+ }
+ }
+ retval = nifti_write_buffer(fslio->fileptr, tmpbuf, nbytes);
+ free(tmpbuf);
+ } else {
+ retval = nifti_write_buffer(fslio->fileptr, buffer, nbytes);
+ }
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return 0; /* failure */
+}
+
+
+/***************************************************************
+ * FslWriteHeader
+ ***************************************************************/
+/*! \fn void FslWriteHeader(FSLIO *fslio)
+ \brief Writes nifti/anz header and opens img file ready for writing
+
+ \param fslio pointer to open dataset
+ */
+void FslWriteHeader(FSLIO *fslio)
+{
+ /* writes header and opens img file ready for writing */
+ if (fslio==NULL) FSLIOERR("FslWriteHeader: Null pointer passed for FSLIO");
+
+ if (fslio->niftiptr!=NULL) {
+ fslio->written_hdr = 1;
+ if (znz_isnull(fslio->fileptr)) FSLIOERR("FslWriteHeader: no file opened!");
+
+ strcpy(fslio->niftiptr->descrip,"FSL3.2beta");
+ if (FslIsSingleFileType(FslGetFileType(fslio))) {
+ /* write header info but don't close the file */
+ nifti_image_write_hdr_img2(fslio->niftiptr,2,"wb",fslio->fileptr,NULL);
+ /* set up pointer at end of iname_offset for single files only */
+ FslSeekVolume(fslio,0);
+ } else {
+ /* open a new hdr file, write it and close it */
+ nifti_image_write_hdr_img(fslio->niftiptr,0,"wb");
+ }
+ }
+
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return;
+}
+
+
+/***************************************************************
+ * FslReadSliceSeries
+ ***************************************************************/
+/*! \fn size_t FslReadSliceSeries(FSLIO *fslio, void *buffer, short slice, size_t nvols)
+ \brief Read one slice from each of the first nvols volumes in the dataset, ie get an xyt buffer.
+
+ Dimension and datatype of buffer are as is specified in nifti_image structure
+ fslio->niftiptr.
+ Note: filepointer in file data array is restored to its initial position.
+
+ \param fslio pointer to open dataset
+ \param buffer buffer large enough to hold 1 slice from each volume
+ \param slice slice number (0 based) to read [0 z-1]
+ \param nvols number of volumes to read a slice from
+ \return Number of volumes from which a slice was successfully read. 0 on error.
+ */
+size_t FslReadSliceSeries(FSLIO *fslio, void *buffer, short slice, size_t nvols)
+{
+ size_t slbytes,volbytes;
+ size_t n, orig_offset;
+ short x,y,z,v,type;
+
+ if (fslio==NULL) FSLIOERR("FslReadSliceSeries: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+
+ FslGetDim(fslio,&x,&y,&z,&v);
+
+ if ((slice<0) || (slice>=z)) FSLIOERR("FslReadSliceSeries: slice outside valid range");
+
+ slbytes = x * y * (FslGetDataType(fslio, &type) / 8);
+ volbytes = slbytes * z;
+
+ orig_offset = znztell(fslio->fileptr);
+ znzseek(fslio->fileptr, slbytes*slice, SEEK_CUR);
+
+ for (n=0; n<nvols; n++) {
+ if (n>0) znzseek(fslio->fileptr, volbytes - slbytes, SEEK_CUR);
+ if (znzread((char *)buffer+n*slbytes, 1, slbytes, fslio->fileptr) != slbytes)
+ FSLIOERR("FslReadSliceSeries: failed to read values");
+ if (fslio->niftiptr->byteorder != nifti_short_order())
+ nifti_swap_Nbytes(slbytes / fslio->niftiptr->swapsize,
+ fslio->niftiptr->swapsize, (char *)buffer+n*slbytes);
+ }
+
+
+ /* restore file pointer to original position */
+ znzseek(fslio->fileptr,orig_offset,SEEK_SET);
+ return n;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return 0;
+}
+
+
+/***************************************************************
+ * FslReadRowSeries
+ ***************************************************************/
+/*! \fn size_t FslReadRowSeries(FSLIO *fslio, void *buffer, short row, short slice, size_t nvols)
+ \brief Read one row from one slice for first nvols volumes in dataset; ie get an xt buffer.
+
+ Dimension and datatype of buffer are as is specified in nifti_image structure
+ fslio->niftiptr.
+ Note: filepointer in file data array is restored to its initial position.
+
+ \param fslio pointer to open dataset
+ \param buffer buffer to hold one row from each volume.
+ \param row row number (0 based) to read [0 y-1]
+ \param slice slice number (0 based) to read
+ \param nvols number of volumes to read a row from
+ \return Number of volumes from which a row was successfully read. 0 on error.
+ */
+size_t FslReadRowSeries(FSLIO *fslio, void *buffer, short row, short slice, size_t nvols)
+{
+ size_t rowbytes,slbytes,volbytes;
+ size_t n, orig_offset;
+ short x,y,z,v,type;
+
+ if (fslio==NULL) FSLIOERR("FslReadRowSeries: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+
+ FslGetDim(fslio,&x,&y,&z,&v);
+
+ if ((slice<0) || (slice>=z)) FSLIOERR("FslReadRowSeries: slice outside valid range");
+ if ((row<0) || (row>=y)) FSLIOERR("FslReadRowSeries: row outside valid range");
+
+ rowbytes = x * (FslGetDataType(fslio, &type)) / 8;
+ slbytes = rowbytes * y;
+ volbytes = slbytes * z;
+
+ orig_offset = znztell(fslio->fileptr);
+ znzseek(fslio->fileptr, rowbytes*row + slbytes*slice, SEEK_CUR);
+
+ for (n=0; n<nvols; n++){
+ if (n>0) znzseek(fslio->fileptr, volbytes - rowbytes, SEEK_CUR);
+ if (znzread((char *)buffer+n*rowbytes, 1, rowbytes, fslio->fileptr) != rowbytes)
+ FSLIOERR("FslReadRowSeries: failed to read values");
+ if (fslio->niftiptr->byteorder != nifti_short_order())
+ nifti_swap_Nbytes(rowbytes / fslio->niftiptr->swapsize,
+ fslio->niftiptr->swapsize, (char *)buffer+n*rowbytes);
+ }
+
+ /* restore file pointer to original position */
+ znzseek(fslio->fileptr,orig_offset,SEEK_SET);
+ return n;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return 0;
+}
+
+
+/***************************************************************
+ * FslReadTimeSeries
+ ***************************************************************/
+/*! \fn size_t FslReadTimeSeries(FSLIO *fslio, void *buffer, short xVox, short yVox, short zVox, size_t nvols)
+ \brief Read one voxel (xyz location) from first nvols volumes in dataset; ie get a t dim buffer.
+
+ Dimension and datatype of buffer are as is specified in nifti_image structure
+ fslio->niftiptr.
+ Note: filepointer in file data array is restored to its initial position.
+
+ \param fslio pointer to open dataset
+ \param buffer buffer to hold one timeseries vector
+ \param xVox x voxel [0 x-1]
+ \param yVox y voxel [0 y-1]
+ \param zVox z voxel [0 z-1]
+ \param nvols number of volumes to read a voxel from
+ \return Number of volumes from which a voxel was successfully read. 0 on error.
+ */
+size_t FslReadTimeSeries(FSLIO *fslio, void *buffer, short xVox, short yVox, short zVox,
+ size_t nvols)
+{
+ size_t volbytes, offset, orig_offset;
+ size_t n;
+ short xdim,ydim,zdim,v,wordsize;
+
+ if (fslio==NULL) FSLIOERR("FslReadTimeSeries: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+
+ FslGetDim(fslio,&xdim,&ydim,&zdim,&v);
+
+ if ((xVox<0) || (xVox >=xdim)) FSLIOERR("FslReadTimeSeries: voxel outside valid range");
+ if ((yVox<0) || (yVox >=ydim)) FSLIOERR("FslReadTimeSeries: voxel outside valid range");
+ if ((zVox<0) || (zVox >=zdim)) FSLIOERR("FslReadTimeSeries: voxel outside valid range");
+
+ wordsize = fslio->niftiptr->nbyper;
+ volbytes = xdim * ydim * zdim * wordsize;
+
+ orig_offset = znztell(fslio->fileptr);
+ offset = ((ydim * zVox + yVox) * xdim + xVox) * wordsize;
+ znzseek(fslio->fileptr,offset,SEEK_CUR);
+
+ for (n=0; n<nvols; n++) {
+ if (n>0) znzseek(fslio->fileptr, volbytes - wordsize, SEEK_CUR);
+ if (znzread((char *)buffer+(n*wordsize), 1, wordsize,fslio->fileptr) != wordsize)
+ FSLIOERR("FslReadTimeSeries: failed to read values");
+ if (fslio->niftiptr->byteorder != nifti_short_order())
+ nifti_swap_Nbytes(1,fslio->niftiptr->swapsize,
+ (char *)buffer+(n*wordsize));
+ }
+
+ /* restore file pointer to original position */
+ znzseek(fslio->fileptr,orig_offset,SEEK_SET);
+ return n;
+
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return 0;
+}
+
+
+size_t FslReadCplxVolumes(FSLIO *fslio, void *buffer, size_t nvols, char mode)
+{
+ if (fslio==NULL) FSLIOERR("FslReadCplxVolumes: Null pointer passed for FSLIO");
+ fprintf(stderr,"Warning:: FslReadCplxVolumes is not yet supported\n");
+ return 0;
+}
+
+size_t FslWriteCplxVolumes(FSLIO *fslio, void *buffer, size_t nvols, char mode)
+{
+ if (fslio==NULL) FSLIOERR("FslWriteCplxVolumes: Null pointer passed for FSLIO");
+ fprintf(stderr,"Warning:: FslWriteCplxVolumes is not yet supported\n");
+ return 0;
+}
+
+int FslSeekVolume(FSLIO *fslio, size_t vols)
+{
+ int offset;
+ if (fslio==NULL) FSLIOERR("FslSeekVolume: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ offset = fslio->niftiptr->iname_offset +
+ vols * FslGetVolSize(fslio) * fslio->niftiptr->nbyper;
+ if (znz_isnull(fslio->fileptr)) FSLIOERR("FslSeekVolume: Null file pointer");
+ return znzseek(fslio->fileptr,offset,SEEK_SET);
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return 0;
+}
+
+
+size_t FslGetVolSize(FSLIO *fslio)
+{
+ /* returns number of voxels per 3D volume */
+ if (fslio==NULL) FSLIOERR("FslGetVolSize: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ return (fslio->niftiptr->nx * fslio->niftiptr->ny * fslio->niftiptr->nz);
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return 0;
+}
+
+
+void FslSetDim(FSLIO *fslio, short x, short y, short z, short v)
+{
+ int ndim;
+ if (fslio==NULL) FSLIOERR("FslSetDim: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+
+ ndim=4;
+ if (v<=1) {ndim--; if (z<=1) {ndim--; if (y<=1) {ndim--; if (x<=1) {ndim--;}}}}
+
+ fslio->niftiptr->ndim = ndim;
+
+ if (x>=1) fslio->niftiptr->nx = x; else fslio->niftiptr->nx=1;
+ if (y>=1) fslio->niftiptr->ny = y; else fslio->niftiptr->ny=1;
+ if (z>=1) fslio->niftiptr->nz = z; else fslio->niftiptr->nz=1;
+ if (v>=1) fslio->niftiptr->nt = v; else fslio->niftiptr->nt=1;
+ fslio->niftiptr->nu = 1;
+ fslio->niftiptr->nv = 1;
+ fslio->niftiptr->nw = 1;
+
+ /* deal with stupid redundancies */
+ fslio->niftiptr->dim[0] = fslio->niftiptr->ndim ;
+ fslio->niftiptr->dim[1] = fslio->niftiptr->nx;
+ fslio->niftiptr->dim[2] = fslio->niftiptr->ny;
+ fslio->niftiptr->dim[3] = fslio->niftiptr->nz;
+ fslio->niftiptr->dim[4] = fslio->niftiptr->nt;
+ fslio->niftiptr->dim[5] = fslio->niftiptr->nu;
+ fslio->niftiptr->dim[6] = fslio->niftiptr->nv;
+ fslio->niftiptr->dim[7] = fslio->niftiptr->nw;
+
+ fslio->niftiptr->nvox = fslio->niftiptr->nx * fslio->niftiptr->ny * fslio->niftiptr->nz
+ * fslio->niftiptr->nt * fslio->niftiptr->nu * fslio->niftiptr->nv * fslio->niftiptr->nw ;
+
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslGetDim(FSLIO *fslio, short *x, short *y, short *z, short *v)
+{
+ if (fslio==NULL) FSLIOERR("FslGetDim: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ *x = fslio->niftiptr->nx;
+ *y = fslio->niftiptr->ny;
+ *z = fslio->niftiptr->nz;
+ *v = fslio->niftiptr->nt;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslSetDimensionality(FSLIO *fslio, size_t dim)
+{
+ if (fslio==NULL) FSLIOERR("FslSetDimensionality: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->ndim = dim;
+ fslio->niftiptr->dim[0] = dim;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslGetDimensionality(FSLIO *fslio, size_t *dim)
+{
+ if (fslio==NULL) FSLIOERR("FslGetDimensionality: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ *dim = fslio->niftiptr->ndim;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslSetVoxDim(FSLIO *fslio, float x, float y, float z, float tr)
+{
+ if (fslio==NULL) FSLIOERR("FslSetVoxDim: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->dx = fabs(x);
+ fslio->niftiptr->dy = fabs(y);
+ fslio->niftiptr->dz = fabs(z);
+ fslio->niftiptr->dt = fabs(tr);
+ fslio->niftiptr->pixdim[1] = fabs(x);
+ fslio->niftiptr->pixdim[2] = fabs(y);
+ fslio->niftiptr->pixdim[3] = fabs(z);
+ fslio->niftiptr->pixdim[4] = fabs(tr);
+ /* set the units to mm and seconds */
+ fslio->niftiptr->xyz_units = NIFTI_UNITS_MM;
+ fslio->niftiptr->time_units = NIFTI_UNITS_SEC;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslGetVoxDim(FSLIO *fslio, float *x, float *y, float *z, float *tr)
+{
+ if (fslio==NULL) FSLIOERR("FslGetVoxDim: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ *x = fabs(fslio->niftiptr->dx);
+ *y = fabs(fslio->niftiptr->dy);
+ *z = fabs(fslio->niftiptr->dz);
+ *tr = fabs(fslio->niftiptr->dt);
+ /* now check the units and convert to mm and sec */
+ if (fslio->niftiptr->xyz_units == NIFTI_UNITS_METER)
+ { *x *= 1000.0; *y *= 1000.0; *z *= 1000.0; }
+ if (fslio->niftiptr->xyz_units == NIFTI_UNITS_MICRON)
+ { *x /= 1000.0; *y /= 1000.0; *z /= 1000.0; }
+ if (fslio->niftiptr->xyz_units == NIFTI_UNITS_MSEC)
+ { *tr /= 1000.0; }
+ if (fslio->niftiptr->xyz_units == NIFTI_UNITS_USEC)
+ { *tr /= 1000000.0; }
+ /* if it is Hz or other frequency then leave it */
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslGetCalMinMax(FSLIO *fslio, float *min, float *max)
+{
+ if (fslio==NULL) FSLIOERR("FslGetCalMinMax: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ *min = fslio->niftiptr->cal_min;
+ *max = fslio->niftiptr->cal_max;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslSetCalMinMax(FSLIO *fslio, float min, float max)
+{
+ if (fslio==NULL) FSLIOERR("FslSetCalMinMax: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->cal_min = min;
+ fslio->niftiptr->cal_max = max;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslGetAuxFile(FSLIO *fslio,char *aux_file)
+{
+ if (fslio==NULL) FSLIOERR("FslGetAuxFile: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ strncpy(aux_file,fslio->niftiptr->aux_file, 24);
+ aux_file[23] = '\0';
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslSetAuxFile(FSLIO *fslio,const char *aux_file)
+{
+ if (fslio==NULL) FSLIOERR("FslSetAuxFile: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ strncpy(fslio->niftiptr->aux_file, aux_file, 24);
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslSetVoxUnits(FSLIO *fslio, const char *units)
+{
+ int unitcode=0;
+ if (fslio==NULL) FSLIOERR("FslSetVoxUnits: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ if (strcmp(units,nifti_units_string(NIFTI_UNITS_METER))==0) {
+ unitcode = NIFTI_UNITS_METER;
+ } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_MM))==0) {
+ unitcode = NIFTI_UNITS_MM;
+ } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_MICRON))==0) {
+ unitcode = NIFTI_UNITS_MICRON;
+ }
+ fslio->niftiptr->xyz_units = unitcode;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslGetVoxUnits(FSLIO *fslio, char *units)
+{
+ if (fslio==NULL) FSLIOERR("FslGetVoxUnits: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ strcpy(units,nifti_units_string(fslio->niftiptr->xyz_units));
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+void FslSetTimeUnits(FSLIO *fslio, const char *units)
+{
+ int unitcode=0;
+ if (fslio==NULL) FSLIOERR("FslSetTimeUnits: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ if (strcmp(units,nifti_units_string(NIFTI_UNITS_HZ))==0) {
+ unitcode = NIFTI_UNITS_HZ;
+ } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_PPM))==0) {
+ unitcode = NIFTI_UNITS_PPM;
+ } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_RADS))==0) {
+ unitcode = NIFTI_UNITS_RADS;
+ } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_SEC))==0) {
+ unitcode = NIFTI_UNITS_SEC;
+ } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_MSEC))==0) {
+ fprintf(stderr,"Warning::Setting time units to msec is not fully recommended in fslio\n");
+ unitcode = NIFTI_UNITS_MSEC;
+ } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_USEC))==0) {
+ fprintf(stderr,"Warning::Setting time units to msec is not fully recommended in fslio\n");
+ unitcode = NIFTI_UNITS_USEC;
+ }
+ fslio->niftiptr->time_units = unitcode;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslGetTimeUnits(FSLIO *fslio, char *units)
+{
+ if (fslio==NULL) FSLIOERR("FslGetTimeUnits: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ strcpy(units,nifti_units_string(fslio->niftiptr->time_units));
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslSetDataType(FSLIO *fslio, short t)
+{
+ int nbytepix=0, ss=0;
+ if (fslio==NULL) FSLIOERR("FslSetDataType: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->datatype = t;
+ nifti_datatype_sizes(t,&nbytepix,&ss);
+ fslio->niftiptr->nbyper = nbytepix;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+size_t FslGetDataType(FSLIO *fslio, short *t)
+{
+ /* returns bits per pixel */
+ int nbytepix=32, ss=0;
+ if (fslio==NULL) FSLIOERR("FslGetDataType: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ *t = fslio->niftiptr->datatype;
+ nifti_datatype_sizes(*t,&nbytepix,&ss);
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return (size_t) 8 * nbytepix;
+}
+
+
+void FslGetMMCoord(mat44 stdmat, float voxx, float voxy, float voxz,
+ float *mmx, float *mmy, float *mmz)
+{
+ *mmx = stdmat.m[0][0] * voxx + stdmat.m[0][1] * voxy + stdmat.m[0][2] * voxz
+ + stdmat.m[0][3];
+ *mmy = stdmat.m[1][0] * voxx + stdmat.m[1][1] * voxy + stdmat.m[1][2] * voxz
+ + stdmat.m[1][3];
+ *mmz = stdmat.m[2][0] * voxx + stdmat.m[2][1] * voxy + stdmat.m[2][2] * voxz
+ + stdmat.m[2][3];
+}
+
+
+void FslGetVoxCoord(mat44 stdmat, float mmx, float mmy, float mmz,
+ float *voxx, float *voxy, float *voxz)
+{
+ mat44 mm2vox;
+
+ mm2vox = nifti_mat44_inverse(stdmat);
+ *voxx = mm2vox.m[0][0] * mmx + mm2vox.m[0][1] * mmy + mm2vox.m[0][2] * mmz
+ + mm2vox.m[0][3];
+ *voxy = mm2vox.m[1][0] * mmx + mm2vox.m[1][1] * mmy + mm2vox.m[1][2] * mmz
+ + mm2vox.m[1][3];
+ *voxz = mm2vox.m[2][0] * mmx + mm2vox.m[2][1] * mmy + mm2vox.m[2][2] * mmz
+ + mm2vox.m[2][3];
+}
+
+
+void FslSetStdXform(FSLIO *fslio, short sform_code, mat44 stdmat)
+{
+ /* NB: stdmat must point to a 4x4 array */
+ if (fslio==NULL) FSLIOERR("FslSetStdXform: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->sform_code = sform_code;
+ fslio->niftiptr->sto_xyz.m[0][0] = stdmat.m[0][0];
+ fslio->niftiptr->sto_xyz.m[0][1] = stdmat.m[0][1];
+ fslio->niftiptr->sto_xyz.m[0][2] = stdmat.m[0][2];
+ fslio->niftiptr->sto_xyz.m[0][3] = stdmat.m[0][3];
+ fslio->niftiptr->sto_xyz.m[1][0] = stdmat.m[1][0];
+ fslio->niftiptr->sto_xyz.m[1][1] = stdmat.m[1][1];
+ fslio->niftiptr->sto_xyz.m[1][2] = stdmat.m[1][2];
+ fslio->niftiptr->sto_xyz.m[1][3] = stdmat.m[1][3];
+ fslio->niftiptr->sto_xyz.m[2][0] = stdmat.m[2][0];
+ fslio->niftiptr->sto_xyz.m[2][1] = stdmat.m[2][1];
+ fslio->niftiptr->sto_xyz.m[2][2] = stdmat.m[2][2];
+ fslio->niftiptr->sto_xyz.m[2][3] = stdmat.m[2][3];
+ fslio->niftiptr->sto_xyz.m[3][0] = 0;
+ fslio->niftiptr->sto_xyz.m[3][1] = 0;
+ fslio->niftiptr->sto_xyz.m[3][2] = 0;
+ fslio->niftiptr->sto_xyz.m[3][3] = 1;
+ fslio->niftiptr->sto_ijk = nifti_mat44_inverse(fslio->niftiptr->sto_xyz);
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+short FslGetStdXform(FSLIO *fslio, mat44 *stdmat)
+{
+ /* returns sform code (NB: stdmat must point to a 4x4 array) */
+ float dx,dy,dz,tr;
+ if (fslio==NULL) FSLIOERR("FslGetStdXform: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ stdmat->m[0][0] = fslio->niftiptr->sto_xyz.m[0][0];
+ stdmat->m[0][1] = fslio->niftiptr->sto_xyz.m[0][1];
+ stdmat->m[0][2] = fslio->niftiptr->sto_xyz.m[0][2];
+ stdmat->m[0][3] = fslio->niftiptr->sto_xyz.m[0][3];
+ stdmat->m[1][0] = fslio->niftiptr->sto_xyz.m[1][0];
+ stdmat->m[1][1] = fslio->niftiptr->sto_xyz.m[1][1];
+ stdmat->m[1][2] = fslio->niftiptr->sto_xyz.m[1][2];
+ stdmat->m[1][3] = fslio->niftiptr->sto_xyz.m[1][3];
+ stdmat->m[2][0] = fslio->niftiptr->sto_xyz.m[2][0];
+ stdmat->m[2][1] = fslio->niftiptr->sto_xyz.m[2][1];
+ stdmat->m[2][2] = fslio->niftiptr->sto_xyz.m[2][2];
+ stdmat->m[2][3] = fslio->niftiptr->sto_xyz.m[2][3];
+ stdmat->m[3][0] = 0.0;
+ stdmat->m[3][1] = 0.0;
+ stdmat->m[3][2] = 0.0;
+ stdmat->m[3][3] = 1.0;
+
+ /* the code below gives a default but it really should never be used */
+ if (fslio->niftiptr->sform_code == NIFTI_XFORM_UNKNOWN) {
+ FslGetVoxDim(fslio,&dx,&dy,&dz,&tr);
+ stdmat->m[0][0] = -dx; /* default Radiological convention */
+ stdmat->m[0][1] = 0;
+ stdmat->m[0][2] = 0;
+ stdmat->m[0][3] = 0;
+ stdmat->m[1][0] = 0;
+ stdmat->m[1][1] = dy;
+ stdmat->m[1][2] = 0;
+ stdmat->m[1][3] = 0;
+ stdmat->m[2][0] = 0;
+ stdmat->m[2][1] = 0;
+ stdmat->m[2][2] = dz;
+ stdmat->m[2][3] = 0;
+ stdmat->m[3][0] = 0.0;
+ stdmat->m[3][1] = 0.0;
+ stdmat->m[3][2] = 0.0;
+ stdmat->m[3][3] = 1.0;
+ }
+ return fslio->niftiptr->sform_code;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return NIFTI_XFORM_UNKNOWN;
+}
+
+
+void FslSetRigidXform(FSLIO *fslio, short qform_code, mat44 rigidmat)
+{
+ /* NB: rigidmat must point to an allocated mat44 */
+ float dx, dy, dz;
+ if (fslio==NULL) FSLIOERR("FslSetRigidXform: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->qform_code = qform_code;
+ fslio->niftiptr->qto_xyz.m[0][0] = rigidmat.m[0][0];
+ fslio->niftiptr->qto_xyz.m[0][1] = rigidmat.m[0][1];
+ fslio->niftiptr->qto_xyz.m[0][2] = rigidmat.m[0][2];
+ fslio->niftiptr->qto_xyz.m[0][3] = rigidmat.m[0][3];
+ fslio->niftiptr->qto_xyz.m[1][0] = rigidmat.m[1][0];
+ fslio->niftiptr->qto_xyz.m[1][1] = rigidmat.m[1][1];
+ fslio->niftiptr->qto_xyz.m[1][2] = rigidmat.m[1][2];
+ fslio->niftiptr->qto_xyz.m[1][3] = rigidmat.m[1][3];
+ fslio->niftiptr->qto_xyz.m[2][0] = rigidmat.m[2][0];
+ fslio->niftiptr->qto_xyz.m[2][1] = rigidmat.m[2][1];
+ fslio->niftiptr->qto_xyz.m[2][2] = rigidmat.m[2][2];
+ fslio->niftiptr->qto_xyz.m[2][3] = rigidmat.m[2][3];
+ fslio->niftiptr->qto_xyz.m[3][0] = 0;
+ fslio->niftiptr->qto_xyz.m[3][1] = 0;
+ fslio->niftiptr->qto_xyz.m[3][2] = 0;
+ fslio->niftiptr->qto_xyz.m[3][3] = 1;
+ nifti_mat44_to_quatern(
+ fslio->niftiptr->qto_xyz,&(fslio->niftiptr->quatern_b),
+ &(fslio->niftiptr->quatern_c),&(fslio->niftiptr->quatern_d),
+ &(fslio->niftiptr->qoffset_x),&(fslio->niftiptr->qoffset_y),
+ &(fslio->niftiptr->qoffset_z),&dx,&dy,&dz,&(fslio->niftiptr->qfac));
+ fslio->niftiptr->qto_ijk = nifti_mat44_inverse(fslio->niftiptr->qto_xyz);
+
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+short FslGetRigidXform(FSLIO *fslio, mat44 *rigidmat)
+{
+ /* returns qform code (NB: rigidmat must point to an allocated mat44) */
+ float dx,dy,dz,tr;
+ if (fslio==NULL) FSLIOERR("FslGetRigidXform: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ rigidmat->m[0][0] = fslio->niftiptr->qto_xyz.m[0][0];
+ rigidmat->m[0][1] = fslio->niftiptr->qto_xyz.m[0][1];
+ rigidmat->m[0][2] = fslio->niftiptr->qto_xyz.m[0][2];
+ rigidmat->m[0][3] = fslio->niftiptr->qto_xyz.m[0][3];
+ rigidmat->m[1][0] = fslio->niftiptr->qto_xyz.m[1][0];
+ rigidmat->m[1][1] = fslio->niftiptr->qto_xyz.m[1][1];
+ rigidmat->m[1][2] = fslio->niftiptr->qto_xyz.m[1][2];
+ rigidmat->m[1][3] = fslio->niftiptr->qto_xyz.m[1][3];
+ rigidmat->m[2][0] = fslio->niftiptr->qto_xyz.m[2][0];
+ rigidmat->m[2][1] = fslio->niftiptr->qto_xyz.m[2][1];
+ rigidmat->m[2][2] = fslio->niftiptr->qto_xyz.m[2][2];
+ rigidmat->m[2][3] = fslio->niftiptr->qto_xyz.m[2][3];
+ rigidmat->m[3][0] = 0.0;
+ rigidmat->m[3][1] = 0.0;
+ rigidmat->m[3][2] = 0.0;
+ rigidmat->m[3][3] = 1.0;
+
+ /* the code gives a default but it should never really be used */
+ if (fslio->niftiptr->sform_code == NIFTI_XFORM_UNKNOWN) {
+ FslGetVoxDim(fslio,&dx,&dy,&dz,&tr);
+ rigidmat->m[0][0] = dx;
+ rigidmat->m[0][1] = 0;
+ rigidmat->m[0][2] = 0;
+ rigidmat->m[0][3] = 0;
+ rigidmat->m[1][0] = 0;
+ rigidmat->m[1][1] = dy;
+ rigidmat->m[1][2] = 0;
+ rigidmat->m[1][3] = 0;
+ rigidmat->m[2][0] = 0;
+ rigidmat->m[2][1] = 0;
+ rigidmat->m[2][2] = dz;
+ rigidmat->m[3][0] = 0.0;
+ rigidmat->m[3][1] = 0.0;
+ rigidmat->m[3][2] = 0.0;
+ rigidmat->m[3][3] = 1.0;
+ }
+ return fslio->niftiptr->qform_code;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return NIFTI_XFORM_UNKNOWN;
+}
+
+
+void FslSetIntent(FSLIO *fslio, short intent_code, float p1, float p2, float p3)
+{
+ if (fslio==NULL) FSLIOERR("FslSetIntent: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->intent_code = intent_code;
+ fslio->niftiptr->intent_p1 = p1;
+ fslio->niftiptr->intent_p2 = p2;
+ fslio->niftiptr->intent_p3 = p3;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+short FslGetIntent(FSLIO *fslio, short *intent_code, float *p1, float *p2,
+ float *p3)
+{
+ /* also returns intent code */
+ if (fslio==NULL) FSLIOERR("FslGetIntent: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ *intent_code = fslio->niftiptr->intent_code;
+ *p1 = fslio->niftiptr->intent_p1;
+ *p2 = fslio->niftiptr->intent_p2;
+ *p3 = fslio->niftiptr->intent_p3;
+ return fslio->niftiptr->intent_code;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return NIFTI_INTENT_NONE;
+}
+
+
+
+
+void FslSetIntensityScaling(FSLIO *fslio, float slope, float intercept)
+{
+ if (fslio==NULL) FSLIOERR("FslSetIntensityScaling: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ fslio->niftiptr->scl_slope = slope;
+ fslio->niftiptr->scl_inter = intercept;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+int FslGetIntensityScaling(FSLIO *fslio, float *slope, float *intercept)
+{
+ /* returns 1 if scaling required or 0 otherwise */
+ if (fslio==NULL) FSLIOERR("FslGetIntensityScaling: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ *slope = fslio->niftiptr->scl_slope;
+ *intercept = fslio->niftiptr->scl_inter;
+ if (fabs(*slope)<1e-30) {
+ *slope = 1.0;
+ *intercept = 0.0;
+ return 0;
+ }
+ if ( (fabs(*slope - 1.0)>1e-30) || (fabs(*intercept)>1e-30) ) {
+ return 1;
+ } else {
+ return 0;
+ }
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return 0;
+
+}
+
+
+mat33 mat44_to_mat33(mat44 x)
+{
+ mat33 y;
+ int i,j;
+ for (i=0; i<3; i++) {
+ for (j=0; j<3; j++) {
+ y.m[i][j] = x.m[i][j];
+ }
+ }
+ return y;
+}
+
+
+int FslGetLeftRightOrder(FSLIO *fslio)
+{
+ /* Determines if the image is stored in neurological or radiological convention */
+ int order=FSL_RADIOLOGICAL, sform_code, qform_code;
+ float det=-1.0;
+ mat44 sform44, qform44;
+ mat33 sform33, qform33;
+ if (fslio==NULL) FSLIOERR("FslGetLeftRightOrder: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ sform_code = FslGetStdXform(fslio,&sform44);
+ qform_code = FslGetRigidXform(fslio,&qform44);
+ if (sform_code!=NIFTI_XFORM_UNKNOWN) {
+ sform33 = mat44_to_mat33(sform44);
+ det = nifti_mat33_determ(sform33);
+ } else if (qform_code!=NIFTI_XFORM_UNKNOWN) {
+ qform33 = mat44_to_mat33(qform44);
+ det = nifti_mat33_determ(qform33);
+ }
+
+ if (det<0.0) order=FSL_RADIOLOGICAL;
+ else order=FSL_NEUROLOGICAL;
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+ return order;
+}
+
+
+
+void FslSetAnalyzeSform(FSLIO *fslio, const short *orig,
+ float dx, float dy, float dz)
+{
+ /* Creates an sform matrix for an Analyze file */
+ /* THIS ALWAYS CREATES A RADIOLOGICAL ORDERED SFORM */
+ /* NB: the origin passed in here is in Analyze convention - starting at 1, not 0 */
+ float x, y, z;
+ if (fslio==NULL) FSLIOERR("FslSetAnalyzeSform: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ if (FslBaseFileType(FslGetFileType(fslio))==FSL_TYPE_ANALYZE) {
+ /* default case */
+ fslio->niftiptr->sform_code = NIFTI_XFORM_UNKNOWN;
+ }
+ /* ignore all zero origins - really all serious coord stuff should
+ be done via the FslSetStdCoord call */
+ if ((orig[0]!=0) || (orig[1]!=0) || (orig[2]!=0))
+ {
+ short origx=0, origy=0, origz=0;
+ if ((orig[0]!=0) || (orig[1]!=0) || (orig[2]!=0)) {
+ /* convert to nifti conventions (start at 0 not 1) */
+ origx = orig[0] - 1;
+ origy = orig[1] - 1;
+ origz = orig[2] - 1;
+ }
+ if ( dx * dy * dz > 0 ) {
+ /* change neurological convention to radiological if necessary */
+ dx = -dx;
+ }
+ if ( (FslBaseFileType(FslGetFileType(fslio))==FSL_TYPE_ANALYZE)
+ || (fslio->niftiptr->sform_code == NIFTI_XFORM_UNKNOWN) ) {
+ /* make a default transform with the requested origin at xyz=000 */
+ fslio->niftiptr->sform_code = NIFTI_XFORM_ALIGNED_ANAT;
+ fslio->niftiptr->sto_xyz.m[0][0] = dx;
+ fslio->niftiptr->sto_xyz.m[0][1] = 0;
+ fslio->niftiptr->sto_xyz.m[0][2] = 0;
+ fslio->niftiptr->sto_xyz.m[0][3] = -(origx)*(dx);
+ fslio->niftiptr->sto_xyz.m[1][0] = 0;
+ fslio->niftiptr->sto_xyz.m[1][1] = dy;
+ fslio->niftiptr->sto_xyz.m[1][2] = 0;
+ fslio->niftiptr->sto_xyz.m[1][3] = -(origy)*(dy);
+ fslio->niftiptr->sto_xyz.m[2][0] = 0;
+ fslio->niftiptr->sto_xyz.m[2][1] = 0;
+ fslio->niftiptr->sto_xyz.m[2][2] = dz;
+ fslio->niftiptr->sto_xyz.m[2][3] = -(origz)*(dz);
+ fslio->niftiptr->sto_xyz.m[3][0] = 0;
+ fslio->niftiptr->sto_xyz.m[3][1] = 0;
+ fslio->niftiptr->sto_xyz.m[3][2] = 0;
+ fslio->niftiptr->sto_xyz.m[3][3] = 1;
+ fslio->niftiptr->sto_ijk =
+ nifti_mat44_inverse(fslio->niftiptr->sto_xyz);
+ } else {
+ /* update the existing origin */
+ /* find out what the existing xyz of the requested origin is */
+ x = fslio->niftiptr->sto_xyz.m[0][0] * origx
+ + fslio->niftiptr->sto_xyz.m[0][1] * origy
+ + fslio->niftiptr->sto_xyz.m[0][2] * origz
+ + fslio->niftiptr->sto_xyz.m[0][3];
+ y = fslio->niftiptr->sto_xyz.m[1][0] * origx
+ + fslio->niftiptr->sto_xyz.m[1][1] * origy
+ + fslio->niftiptr->sto_xyz.m[1][2] * origz
+ + fslio->niftiptr->sto_xyz.m[1][3];
+ z = fslio->niftiptr->sto_xyz.m[2][0] * origx
+ + fslio->niftiptr->sto_xyz.m[2][1] * origy
+ + fslio->niftiptr->sto_xyz.m[2][2] * origz
+ + fslio->niftiptr->sto_xyz.m[2][3];
+ /* subtract off whatever is currently the xyz of the origin */
+ fslio->niftiptr->sto_xyz.m[0][3] -= x;
+ fslio->niftiptr->sto_xyz.m[1][3] -= y;
+ fslio->niftiptr->sto_xyz.m[2][3] -= z;
+ fslio->niftiptr->sto_ijk =
+ nifti_mat44_inverse(fslio->niftiptr->sto_xyz);
+ }
+
+ }
+
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+void FslGetAnalyzeOrigin(FSLIO *fslio, short orig[5])
+{
+ /* NB: orig returned here is in Analyze convention - starting at 1, not 0 */
+ if (fslio==NULL) FSLIOERR("FslGetAnalyzeOrigin: Null pointer passed for FSLIO");
+ if (fslio->niftiptr!=NULL) {
+ /* Use sform or qform to determine the origin - default is zero */
+ orig[0]=0;
+ orig[1]=0;
+ orig[2]=0;
+ orig[3]=0;
+ orig[4]=0;
+
+ if (fslio->niftiptr->qform_code != NIFTI_XFORM_UNKNOWN) {
+ orig[0]=(short) fslio->niftiptr->qto_ijk.m[0][3] + 1;
+ orig[1]=(short) fslio->niftiptr->qto_ijk.m[1][3] + 1;
+ orig[2]=(short) fslio->niftiptr->qto_ijk.m[2][3] + 1;
+ }
+
+ if (fslio->niftiptr->sform_code != NIFTI_XFORM_UNKNOWN) {
+ orig[0]=(short) fslio->niftiptr->sto_ijk.m[0][3] + 1;
+ orig[1]=(short) fslio->niftiptr->sto_ijk.m[1][3] + 1;
+ orig[2]=(short) fslio->niftiptr->sto_ijk.m[2][3] + 1;
+ }
+ }
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+}
+
+
+
+/***************************************************************
+ * FslClose
+ ***************************************************************/
+/*! \fn int FslClose(FSLIO *fslio)
+ \brief Write header and image data if this dataset was open for
+ writing. Close the dataset header and data files.
+
+
+ \param fslio pointer to FSLIO data structure
+ \return -1 on error, 0 OK ???.
+ */
+int FslClose(FSLIO *fslio)
+{
+ int retval=0, filetype;
+ struct dsr *hdr;
+ znzFile hptr=NULL;
+
+ if (fslio==NULL) return 0;
+
+ /* close the (data) file */
+ if (!znz_isnull(fslio->fileptr)) retval=znzclose(fslio->fileptr);
+
+ /** ----- if writing the image, need to worry about the header bit ----- **/
+
+ if ( (fslio->niftiptr!=NULL) && (FslGetWriteMode(fslio)==1)
+ && (fslio->written_hdr==0) ) {
+
+ /* ensure that the type is set correctly */
+ fslio->niftiptr->nifti_type = FslBaseFileType(FslGetFileType(fslio));
+
+ /* must write the header now */
+ filetype = FslGetFileType(fslio);
+ strcpy(fslio->niftiptr->descrip,"FSL3.2beta");
+ if (!FslIsSingleFileType(filetype)) {
+ /* for file pairs - open new header file and write it */
+ nifti_image_write_hdr_img(fslio->niftiptr,0,"wb");
+ } else {
+ /* for single files it is more complicated */
+ if (!FslIsCompressedFileType(filetype)) {
+ /* noncompressed -> reopen this file in r+ mode and write the header part again */
+ nifti_image_write_hdr_img(fslio->niftiptr,0,"r+b");
+ } else {
+ /* compressed mode -> not possible! */
+ fprintf(stderr,"Error:: header must be written before writing any other data.\n");
+ return -1;
+ }
+ }
+ }
+
+ /* --- nasty hack to write the origin in Analyze files --- */
+
+ if ( (FslGetWriteMode(fslio)==1) && (fslio->niftiptr!=NULL) &&
+ (FslBaseFileType(FslGetFileType(fslio))==FSL_TYPE_ANALYZE) ) {
+
+ /* read in the old header, change the origin and write it out again */
+ hdr = (struct dsr *) calloc(1,sizeof(struct dsr));
+ FslReadRawHeader(hdr,fslio->niftiptr->fname);
+ if (fslio->niftiptr->byteorder != nifti_short_order()) {AvwSwapHeader(hdr);}
+
+ /* calculate origin from sform (if set) */
+ {
+ short blah[5];
+ FslGetAnalyzeOrigin(fslio,blah);
+ memcpy(hdr->hist.originator,blah,5*sizeof(short));
+
+ /* Write out in radiological order if origin is non-zero */
+ /* set negative pixdim if needed to keep LR orientation consistent */
+ if ( (blah[0]!=0) || (blah[1]!=0) || (blah[2]!=0) ) {
+ if (hdr->dime.pixdim[1] * hdr->dime.pixdim[2] * hdr->dime.pixdim[3] > 0) {
+ hdr->dime.pixdim[1] = - hdr->dime.pixdim[1];
+ }
+ }
+ }
+
+ /* swap back byte order and write out */
+ if (fslio->niftiptr->byteorder != nifti_short_order()) {AvwSwapHeader(hdr);}
+ hptr = znzopen(fslio->niftiptr->fname,"wb",FslIsCompressedFileType(FslGetFileType(fslio)));
+ if (znz_isnull(hptr)) {
+ fprintf(stderr,"Error:: Could not write origin data to header file %s.\n",
+ fslio->niftiptr->fname);
+ return -1;
+ };
+
+ znzwrite(hdr,1,sizeof(struct dsr),hptr);
+ znzclose(hptr);
+ free(hdr);
+ }
+
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ return -1;
+ }
+
+ return retval;
+}
+
+
+void AvwSwapHeader(struct dsr *avw)
+{
+ char *ptr;
+
+ ptr = (char *) &(avw->hk);
+ nifti_swap_4bytes(1,ptr); /* sizeof_hdr */
+ ptr += 32;
+ nifti_swap_4bytes(1,ptr); /* extents */
+ ptr += 4;
+ nifti_swap_2bytes(1,ptr); /* session_error */
+
+ ptr = (char *) &(avw->dime);
+ nifti_swap_2bytes(8,ptr); /* dims */
+ ptr += 28;
+ nifti_swap_2bytes(4,ptr); /* unused1, datatype, bitpix, dim_un0 */
+ ptr += 8;
+ nifti_swap_4bytes(18,ptr); /* pixdim, vox_offset, ... */
+ /* cal_min, compressed, ... glmin */
+
+ ptr = (char *) &(avw->hist);
+ ptr += 105;
+ nifti_swap_2bytes(5,ptr); /* originator (used to store origin) */
+ ptr += 63;
+ nifti_swap_4bytes(8,ptr); /* views, ... smin */
+}
+
+
+int FslReadRawHeader(void *buffer, const char* filename)
+{
+ znzFile fp;
+ int retval;
+ fp = znzopen(filename,"rb",1);
+ if (znz_isnull(fp)) {
+ fprintf(stderr,"Could not open header %s\n",filename);
+ return 0;
+ }
+ retval = znzread(buffer,1,348,fp);
+ znzclose(fp);
+ if (retval != 348) {
+ fprintf(stderr,"Could not read header %s\n",filename);
+ return retval;
+ }
+ return retval;
+}
+
+void FslSetOverrideOutputType(int type)
+{
+ if ( (type==-1) || (FslIsValidFileType(type)) ) {
+ FslOverrideOutputType=type;
+ } else {
+ fprintf(stderr,"Invalid file type (%d) requested - ignoring this\n",type);
+ }
+}
+
+int FslGetOverrideOutputType(void)
+{
+ return FslOverrideOutputType;
+}
+
+void FslSetIgnoreMFQ(int flag)
+{
+ assert((flag==0) || (flag==1));
+ FslIgnoreMFQ=flag;
+}
+
+
+int FslGetIgnoreMFQ(void)
+{
+ return FslIgnoreMFQ;
+}
+
+/***************************************************************
+ * FslReadHeader
+ ***************************************************************/
+/*! \fn FSLIO * FslReadHeader(char *fname)
+ \brief Reads nifti/anz header, no data is read
+
+ \param fname filename specification (could be .img,.hdr,.nii, or no ext
+ \return FSLIO data structure with the nifti_image structure fields filled
+ as per fname header.
+ NULL on error
+ */
+FSLIO * FslReadHeader(char *fname)
+{
+ char *hdrname, *imgname;
+ FSLIO *fslio;
+
+
+ fslio = FslInit();
+
+ /** get header file name */
+ FslGetHdrImgNames(fname, fslio, &hdrname, &imgname);
+
+ /** read header information */
+ fslio->niftiptr = nifti_image_read(hdrname, 0);
+
+ if (fslio->niftiptr == NULL) {
+ FSLIOERR("FslReadHeader: error reading header information");
+ return(NULL);
+ }
+
+ fslio->file_mode = FslGetReadFileType(fslio);
+
+ return(fslio);
+}
+
+
+/***************************************************************
+ * FslGetVolumeAsScaledDouble
+ ***************************************************************/
+/*! \fn double *** FslGetVolumeAsScaledDouble(FSLIO *fslio, int vol)
+ \brief Return volume #vol (0-based) as a 3D array of scaled doubles.
+
+ Volume Array is indexed as [0..zdim-1][0..ydim-1][0..xdim-1].
+ <br>The array will be byteswapped to native-endian.
+ <br>Array values are scaled as per fslio header slope and intercept fields.
+
+ \param fslio pointer to open dataset
+ \param vol volume number to read (legal range [0..tdim-1])
+ \return Pointer to 3D double array, NULL on error
+ */
+double ***FslGetVolumeAsScaledDouble(FSLIO *fslio, int vol)
+{
+ double ***newbuf;
+ void *diskbuf;
+ int xx,yy,zz;
+ int ret;
+ float inter, slope;
+ int dims_to_get[8];
+ int i;
+
+ if (fslio==NULL) FSLIOERR("FslGetVolumeAsScaledDouble: Null pointer passed for FSLIO");
+
+ if ((fslio->niftiptr->dim[0] < 3) || (fslio->niftiptr->dim[0] > 4))
+ FSLIOERR("FslGetVolumeAsScaledDouble: Incorrect dataset dimension, 3D-4D needed");
+
+ /***** nifti dataset */
+ if (fslio->niftiptr!=NULL) {
+ xx = (fslio->niftiptr->nx == 0 ? 1 : (long)fslio->niftiptr->nx);
+ yy = (fslio->niftiptr->ny == 0 ? 1 : (long)fslio->niftiptr->ny);
+ zz = (fslio->niftiptr->nz == 0 ? 1 : (long)fslio->niftiptr->nz);
+
+ if (fslio->niftiptr->scl_slope == 0) {
+ slope = 1.0;
+ inter = 0.0;
+ }
+ else {
+ slope = fslio->niftiptr->scl_slope;
+ inter = fslio->niftiptr->scl_inter;
+ }
+
+
+ /** allocate new 3D buffer */
+ newbuf = d3matrix(zz-1,yy-1,xx-1);
+
+
+ /** read in the data in disk format */
+ dims_to_get[0] = 0;
+ for (i=1; i<8; i++)
+ dims_to_get[i] = -1;
+ dims_to_get[4] = vol;
+
+
+ diskbuf = NULL;
+ ret = nifti_read_collapsed_image(fslio->niftiptr, dims_to_get, &diskbuf );
+ if (ret <= 0) {
+ fprintf(stderr,"ERROR:: read of disk buffer for volume %d from %s failed.\n",vol,fslio->niftiptr->iname);
+ return(NULL);
+ }
+
+
+ /** cvt disk buffer to scaled double buffer */
+ ret = convertBufferToScaledDouble(newbuf[0][0], diskbuf, (long)(xx*yy*zz), slope, inter, fslio->niftiptr->datatype);
+
+ if (ret == 0)
+ return(newbuf);
+ else
+ return(NULL);
+
+ } /* nifti data */
+
+
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+
+ return(NULL);
+}
+
+
+
+
+/***************************************************************
+ * FslGetBufferAsScaledDouble
+ ***************************************************************/
+/*! \fn double **** FslGetBufferAsScaledDouble(FSLIO *fslio)
+ \brief Return the fslio data buffer of a 1-4D dataset as a 4D array of
+ scaled doubles.
+
+ Array is indexed as buf[0..tdim-1][0..zdim-1][0..ydim-1][0..xdim-1].
+ <br>The array will be byteswapped to native-endian.
+ <br>Array values are scaled as per fslio header slope and intercept fields.
+
+ \param fslio pointer to open dataset
+ \return Pointer to 4D double array, NULL on error
+ */
+double ****FslGetBufferAsScaledDouble(FSLIO *fslio)
+{
+ double ****newbuf;
+ int xx,yy,zz,tt;
+ int ret;
+ float inter, slope;
+
+ if (fslio==NULL) FSLIOERR("FslGetBufferAsScaledDouble: Null pointer passed for FSLIO");
+
+ if ((fslio->niftiptr->dim[0] <= 0) || (fslio->niftiptr->dim[0] > 4))
+ FSLIOERR("FslGetBufferAsScaledDouble: Incorrect dataset dimension, 1-4D needed");
+
+ /***** nifti dataset */
+ if (fslio->niftiptr!=NULL) {
+ xx = (fslio->niftiptr->nx == 0 ? 1 : (long)fslio->niftiptr->nx);
+ yy = (fslio->niftiptr->ny == 0 ? 1 : (long)fslio->niftiptr->ny);
+ zz = (fslio->niftiptr->nz == 0 ? 1 : (long)fslio->niftiptr->nz);
+ tt = (fslio->niftiptr->nt == 0 ? 1 : (long)fslio->niftiptr->nt);
+
+ if (fslio->niftiptr->scl_slope == 0) {
+ slope = 1.0;
+ inter = 0.0;
+ }
+ else {
+ slope = fslio->niftiptr->scl_slope;
+ inter = fslio->niftiptr->scl_inter;
+ }
+
+
+ /** allocate new 4D buffer */
+ newbuf = d4matrix(tt-1,zz-1,yy-1,xx-1);
+
+ /** cvt it */
+ ret = convertBufferToScaledDouble(newbuf[0][0][0], fslio->niftiptr->data, (long)(xx*yy*zz*tt), slope, inter, fslio->niftiptr->datatype);
+
+ if (ret == 0)
+ return(newbuf);
+ else
+ return(NULL);
+
+ } /* nifti data */
+
+
+ if (fslio->mincptr!=NULL) {
+ fprintf(stderr,"Warning:: Minc is not yet supported\n");
+ }
+
+ return(NULL);
+}
+
+/***************************************************************
+ * convertBufferToScaledDouble
+ ***************************************************************/
+/*! \fn int convertBufferToScaledDouble(double *outbuf, void *inbuf, long len, float slope, float inter, int nifti_datatype )
+ \brief allocate a 4D buffer, use 1 contiguous buffer for the data
+
+ Array is indexed as buf[0..th-1][0..zh-1][0..yh-1][0..xh-1].
+ <br>To access all elements as a vector, use buf[0][0][0][i] where
+ i can range from 0 to th*zh*yh*xh - 1.
+
+ \param outbuf pointer to array of doubles of size len
+ \param inbuf void pointer to an array of len items of datatype nifti_datatype
+ \param len number of elements in outbuf and inbuf
+ \param slope slope term of scaling to be applied
+ \param inter intercept term of scaling to be applied: out = (in*slope)+inter
+ \param nifti_datatype NIFTI datatype code for the datatype of the elements in inbuf
+ \return error code: 0=OK -1=error
+ */
+int convertBufferToScaledDouble(double *outbuf, void *inbuf, long len, float slope, float inter, int nifti_datatype )
+{
+
+ long i;
+
+
+ /** fill the buffer */
+ for (i=0; i<len; i++)
+ switch(nifti_datatype) {
+ case NIFTI_TYPE_UINT8:
+ outbuf[i] = (double) ( *((THIS_UINT8 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_INT8:
+ outbuf[i] = (double) ( *((THIS_INT8 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_UINT16:
+ outbuf[i] = (double) ( *((THIS_UINT16 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_INT16:
+ outbuf[i] = (double) ( *((THIS_INT16 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_UINT64:
+ outbuf[i] = (double) ( *((THIS_UINT64 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_INT64:
+ outbuf[i] = (double) ( *((THIS_INT64 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_UINT32:
+ outbuf[i] = (double) ( *((THIS_UINT32 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_INT32:
+ outbuf[i] = (double) ( *((THIS_INT32 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_FLOAT32:
+ outbuf[i] = (double) ( *((THIS_FLOAT32 *)(inbuf)+i) * slope + inter);
+ break;
+ case NIFTI_TYPE_FLOAT64:
+ outbuf[i] = (double) ( *((THIS_FLOAT64 *)(inbuf)+i) * slope + inter);
+ break;
+
+ case NIFTI_TYPE_FLOAT128:
+ case NIFTI_TYPE_COMPLEX128:
+ case NIFTI_TYPE_COMPLEX256:
+ case NIFTI_TYPE_COMPLEX64:
+ default:
+ fprintf(stderr, "\nWarning, cannot support %s yet.\n",nifti_datatype_string(nifti_datatype));
+ return(-1);
+ }
+
+return(0);
+}
+
+/***************************************************************
+ * d3matrix
+ ***************************************************************/
+/*! \fn double ****d3matrix(int zh, int yh, int xh)
+ \brief allocate a 3D buffer, use 1 contiguous buffer for the data
+
+ Array is indexed as buf[0..zh][0..yh][0..xh].
+ <br>To access all elements as a vector, use buf[0][0][i] where
+ i can range from 0 to zh*yh*xh - 1.
+ Adaptation of Numerical Recipes in C nrutil.c allocation routines.
+
+ \param zh slowest changing dimension
+ \param yh 2nd fastest changing dimension
+ \param xh fastest changing dimension
+ \return Pointer to 3D double array
+ */
+double ***d3matrix(int zh, int yh, int xh)
+{
+
+ int j;
+ int nslice = zh+1;
+ int nrow = yh+1;
+ int ncol = xh+1;
+ double ***t;
+
+
+ /** allocate pointers to slices */
+ t=(double ***) malloc((size_t)((nslice)*sizeof(double**)));
+ if (!t) FSLIOERR("d3matrix: allocation failure");
+
+ /** allocate pointers for ydim */
+ t[0]=(double **) malloc((size_t)((nslice*nrow)*sizeof(double*)));
+ if (!t[0]) FSLIOERR("d3matrix: allocation failure");
+
+
+ /** allocate the data blob */
+ t[0][0]=(double *) malloc((size_t)((nslice*nrow*ncol)*sizeof(double)));
+ if (!t[0][0]) FSLIOERR("d3matrix: allocation failure");
+
+
+ /** point everything to the data blob */
+ for(j=1;j<nrow*nslice;j++) t[0][j]=t[0][j-1]+ncol;
+ for(j=1;j<nslice;j++) t[j]=t[j-1]+nrow;
+
+ return t;
+}
+
+
+/***************************************************************
+ * d4matrix
+ ***************************************************************/
+/*! \fn double ****d4matrix(int th, int zh, int yh, int xh)
+ \brief allocate a 4D buffer, use 1 contiguous buffer for the data
+
+ Array is indexed as buf[0..th][0..zh][0..yh][0..xh].
+ <br>To access all elements as a vector, use buf[0][0][0][i] where
+ i can range from 0 to th*zh*yh*xh - 1.
+ Adaptation of Numerical Recipes in C nrutil.c allocation routines.
+
+ \param th slowest changing dimension
+ \param zh 2nd slowest changing dimension
+ \param yh 2nd fastest changing dimension
+ \param xh fastest changing dimension
+ \return Pointer to 4D double array
+ */
+double ****d4matrix(int th, int zh, int yh, int xh)
+{
+
+ int j;
+ int nvol = th+1;
+ int nslice = zh+1;
+ int nrow = yh+1;
+ int ncol = xh+1;
+ double ****t;
+
+
+ /** allocate pointers to vols */
+ t=(double ****) malloc((size_t)((nvol)*sizeof(double***)));
+ if (!t) FSLIOERR("d4matrix: allocation failure");
+
+ /** allocate pointers to slices */
+ t[0]=(double ***) malloc((size_t)((nvol*nslice)*sizeof(double**)));
+ if (!t[0]) FSLIOERR("d4matrix: allocation failure");
+
+ /** allocate pointers for ydim */
+ t[0][0]=(double **) malloc((size_t)((nvol*nslice*nrow)*sizeof(double*)));
+ if (!t[0][0]) FSLIOERR("d4matrix: allocation failure");
+
+
+ /** allocate the data blob */
+ t[0][0][0]=(double *) malloc((size_t)((nvol*nslice*nrow*ncol)*sizeof(double)));
+ if (!t[0][0][0]) FSLIOERR("d4matrix: allocation failure");
+
+
+ /** point everything to the data blob */
+ for(j=1;j<nrow*nslice*nvol;j++) t[0][0][j]=t[0][0][j-1]+ncol;
+ for(j=1;j<nslice*nvol;j++) t[0][j]=t[0][j-1]+nrow;
+ for(j=1;j<nvol;j++) t[j]=t[j-1]+nslice;
+
+ return t;
+}
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/fslio.h b/Utilities/ITK/Utilities/nifti/fsliolib/fslio.h
new file mode 100644
index 0000000000000000000000000000000000000000..a9f2c3d1a306fd55a405336bd71cfa5eb2eef3e4
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/fslio.h
@@ -0,0 +1,274 @@
+/** \file fslio.h
+ \brief Data structures for using the fslio API. Written by Mark Jenkinson, FMRIB.
+ */
+
+/*
+ fslio.h (Input and output routines for images in FSL)
+
+ Mark Jenkinson
+ FMRIB Image Analysis Group
+
+*/
+
+
+/*
+ Part of FSL - FMRIB's Software Library
+ http://www.fmrib.ox.ac.uk/fsl
+ fsl@fmrib.ox.ac.uk
+
+ Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+ Imaging of the Brain), Department of Clinical Neurology, Oxford
+ University, Oxford, UK
+*/
+
+#if !defined(__FSLIO_H)
+#define __FSLIO_H
+
+#include <stdio.h>
+#include <nifti1_io.h>
+#include <znzlib.h>
+#include "dbh.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+ /*
+ Note that this library is similar to avwio but has changed in many ways.
+ It is almost fully backwards compatible, but not quite, as it cannot write
+ .nii.gz files using the old style functions.
+
+ Recommended ways of reading and writing images are:
+
+ Reading
+ -------
+ Use the FslOpen(), FslReadVolumes() and FslClose() functions. e.g.
+ FSLIO *fslio;
+ void *buffer;
+ int nvols;
+ fslio = FslOpen("/some/path/name_of_file","rb");
+ ... can now access header info via the FslGet calls ...
+ ... allocate room for buffer ...
+ FslReadVolumes(fslio,buffer,nvols);
+ ... do something ...
+ FslClose(fslio);
+
+
+ Writing
+ -------
+ This is more complicated due to the nature of gzipped writing, which must be
+ done in the correct order, and for single files (*.nii.gz) this means that
+ the header information must be written before any image data.
+
+ (1)
+ The best method to use is almost backwards compatible, but requires
+ an FslWriteHeader() call:
+
+ FSLIO* fslio;
+ fslio = FslOpen("/some/path/name_of_file","wb");
+ ... set the appropriate header information using FslSet calls ...
+ FslWriteHeader(fslio);
+
+ ... now can write one or more volumes at a time using
+ FslWriteVolumes(fslio,buffer,nvols) ...
+
+ FslClose(fslio);
+
+ This version is useful if your image data needs to be written from different blocks
+ of memory.
+
+ (2)
+ Another method is available, but which is discouraged, is:
+ FSLIO* fslio;
+ fslio = FslOpen("/some/path/name_of_file","wb");
+
+ ... set some appropriate header information using FslSet calls ...
+ ... now can write one or more volumes at a time using
+ FslWriteVolumes(fslio,buffer,nvols) ...
+ ... set more appropriate header information using FslSet calls ...
+
+ FslClose(fslio);
+
+ WARNING: this cannot write .nii.gz files as the header information cannot be
+ written by FslClose() after the image data is written, which is how the previous
+ versions have worked.
+
+
+ */
+
+/*! \defgroup FSL_TYPE
+ \brief FSL data format type codes
+ @{
+ */
+#define FSL_TYPE_ANALYZE 0
+#define FSL_TYPE_NIFTI 1
+#define FSL_TYPE_NIFTI_PAIR 2
+#define FSL_TYPE_MINC 4
+#define FSL_TYPE_ANALYZE_GZ 100
+#define FSL_TYPE_NIFTI_GZ 101
+#define FSL_TYPE_NIFTI_PAIR_GZ 102
+#define FSL_TYPE_MINC_GZ 104
+/* @} */
+
+#define FSL_RADIOLOGICAL -1
+#define FSL_NEUROLOGICAL 1
+
+
+/*! \struct FSLIO
+ \brief High level data structure for open datasets in the fslio API.
+ \sa nifti_image
+ \sa minc_image
+ */
+typedef struct
+{
+ znzFile fileptr;
+ nifti_image *niftiptr;
+#ifdef USE_MINC
+ minc_image *mincptr;
+#else
+ void *mincptr;
+#endif
+ int file_mode;
+ int write_mode;
+ int written_hdr;
+} FSLIO;
+
+
+ /* basic file i/o commands */
+
+FSLIO *FslOpen(const char *filename, const char *opts);
+FSLIO *FslXOpen(const char *filename, const char *opts, int filetype);
+int FslSeekVolume(FSLIO *fslio, size_t vols);
+int FslClose(FSLIO *fslio);
+
+ /* basic read and write commands */
+
+void* FslReadAllVolumes(FSLIO* fslio, char* filename);
+void FslWriteAllVolumes(FSLIO *fslio, const void *buffer);
+
+size_t FslReadVolumes(FSLIO *fslio, void *buffer, size_t nvols);
+size_t FslWriteVolumes(FSLIO *fslio, const void *buffer, size_t nvols);
+
+void FslWriteHeader(FSLIO *fslio);
+
+ /* support functions for file names and types */
+
+int FslFileExists(const char *filename);
+char *FslMakeBaseName(const char *fname);
+int FslCheckForMultipleFileNames(const char* filename);
+int FslGetEnvOutputType(void);
+
+void FslSetIgnoreMFQ(int flag);
+int FslGetIgnoreMFQ(void);
+void FslSetOverrideOutputType(int type);
+int FslGetOverrideOutputType(void);
+
+
+int FslGetFileType(const FSLIO *fslio);
+void FslSetFileType(FSLIO *fslio, int filetype);
+int FslIsSingleFileType(int filetype);
+int FslIsCompressedFileType(int filetype);
+int FslBaseFileType(int filetype);
+char* FslFileTypeString(int filetype);
+
+int FslGetWriteMode(const FSLIO *fslio);
+void FslSetWriteMode(FSLIO *fslio, int mode);
+
+void AvwSwapHeader(struct dsr *avw);
+int FslReadRawHeader(void *buffer, const char* filename);
+
+
+ /* simple creation and clone/copy operations */
+
+FSLIO *FslInit(void);
+void FslInitHeader(FSLIO *fslio, short t,
+ size_t x, size_t y, size_t z, size_t v,
+ float vx, float vy, float vz, float tr,
+ size_t dim,
+ const char* units);
+void FslSetInit(FSLIO* fslio);
+void FslCloneHeader(FSLIO *dest, const FSLIO *src);
+
+
+ /* get and set routines for properties */
+
+size_t FslGetVolSize(FSLIO *fslio);
+
+void FslSetDim(FSLIO *fslio, short x, short y, short z, short v);
+void FslGetDim(FSLIO *fslio, short *x, short *y, short *z, short *v);
+void FslSetDimensionality(FSLIO *fslio, size_t dim);
+void FslGetDimensionality(FSLIO *fslio, size_t *dim);
+void FslSetVoxDim(FSLIO *fslio, float x, float y, float z, float tr);
+void FslGetVoxDim(FSLIO *fslio, float *x, float *y, float *z, float *tr);
+void FslGetCalMinMax(FSLIO *fslio, float *min, float *max);
+void FslSetCalMinMax(FSLIO *fslio, float min, float max);
+void FslGetAuxFile(FSLIO *fslio,char *aux_file);
+void FslSetAuxFile(FSLIO *fslio,const char *aux_file);
+void FslSetTimeUnits(FSLIO *fslio, const char *units);
+void FslGetTimeUnits(FSLIO *fslio, char *units);
+void FslSetDataType(FSLIO *fslio, short t);
+size_t FslGetDataType(FSLIO *fslio, short *t);
+int FslGetIntensityScaling(FSLIO *fslio, float *slope, float *intercept);
+void FslSetIntent(FSLIO *fslio, short intent_code, float p1, float p2, float p3);
+short FslGetIntent(FSLIO *fslio, short *intent_code, float *p1, float *p2,
+ float *p3);
+
+
+short FslGetStdXform(FSLIO *fslio, mat44 *stdmat);
+void FslSetStdXform(FSLIO *fslio, short sform_code, mat44 stdmat);
+void FslGetMMCoord(mat44 stdmat, float voxx, float voxy, float voxz,
+ float *mmx, float *mmy, float *mmz);
+
+void FslGetVoxCoord(mat44 stdmat, float mmx, float mmy, float mmz,
+ float *voxx, float *voxy, float *voxz);
+short FslGetRigidXform(FSLIO *fslio, mat44 *rigidmat);
+void FslSetRigidXform(FSLIO *fslio, short qform_code, mat44 rigidmat);
+int FslGetLeftRightOrder(FSLIO *fslio);
+
+ /* these two functions are deprecated with the nifti/analyze support */
+ /* please do all spatial coordinate origins via the Std and Rigid Xforms */
+void FslSetAnalyzeSform(FSLIO *fslio, const short *orig,
+ float dx, float dy, float dz);
+void FslGetAnalyzeOrigin(FSLIO *fslio, short orig[5]);
+
+ /* other read and write commands */
+
+size_t FslReadSliceSeries(FSLIO *fslio, void *buffer,short slice, size_t nvols);
+size_t FslReadRowSeries(FSLIO *fslio, void *buffer, short row, short slice, size_t nvols);
+size_t FslReadTimeSeries(FSLIO *fslio, void *buffer, short xVox, short yVox, short zVox, size_t nvols);
+
+ /* miscellaneous helper stuff */
+
+mat33 mat44_to_mat33(mat44 x);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+
+
+/* added by KF pending discussion w/ Mark */
+typedef unsigned char THIS_UINT8;
+typedef char THIS_INT8;
+typedef unsigned short THIS_UINT16;
+typedef short THIS_INT16;
+typedef unsigned int THIS_UINT32;
+typedef int THIS_INT32;
+typedef unsigned long THIS_UINT64;
+typedef long THIS_INT64;
+typedef float THIS_FLOAT32;
+typedef double THIS_FLOAT64;
+
+FSLIO * FslReadHeader(char *fname);
+double ****FslGetBufferAsScaledDouble(FSLIO *fslio);
+double ***FslGetVolumeAsScaledDouble(FSLIO *fslio, int vol);
+int convertBufferToScaledDouble(double *outbuf, void *inbuf, long len, float slope, float inter, int nifti_datatype ) ;
+double ****d4matrix(int th, int zh, int yh, int xh);
+double ***d3matrix(int zh, int yh, int xh);
+
+
+
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/fslio.tcl b/Utilities/ITK/Utilities/nifti/fsliolib/fslio.tcl
new file mode 100644
index 0000000000000000000000000000000000000000..84589d295211dd01e7b3cdc6c7a189f584ae195c
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/fslio.tcl
@@ -0,0 +1,83 @@
+#{{{ copyright and setup
+
+# FEAT TCL FSLIO wrappers
+#
+# Stephen Smith, FMRIB Image Analysis Group
+#
+#
+#
+# Part of FSL - FMRIB's Software Library
+# http://www.fmrib.ox.ac.uk/fsl
+# fsl@fmrib.ox.ac.uk
+#
+# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+# Imaging of the Brain), Department of Clinical Neurology, Oxford
+# University, Oxford, UK
+#
+#
+
+#}}}
+
+proc imcp { args } {
+ global FSLDIR
+
+ regsub -all "\{" $args "" cleanedargs
+ regsub -all "\}" $cleanedargs "" cleanedargs
+
+ return [ exec sh -c "${FSLDIR}/bin/imcp $args" ]
+}
+
+proc imglob { args } {
+ global FSLDIR
+
+ regsub -all "\{" $args "" cleanedargs
+ regsub -all "\}" $cleanedargs "" cleanedargs
+
+ return [ exec sh -c "${FSLDIR}/bin/imglob $args" ]
+}
+
+proc imln { args } {
+ global FSLDIR
+
+ regsub -all "\{" $args "" cleanedargs
+ regsub -all "\}" $cleanedargs "" cleanedargs
+
+ return [ exec sh -c "${FSLDIR}/bin/imln $args" ]
+}
+
+proc immv { args } {
+ global FSLDIR
+
+ regsub -all "\{" $args "" cleanedargs
+ regsub -all "\}" $cleanedargs "" cleanedargs
+
+ return [ exec sh -c "${FSLDIR}/bin/immv $args" ]
+}
+
+proc imrm { args } {
+ global FSLDIR
+
+ regsub -all "\{" $args "" cleanedargs
+ regsub -all "\}" $cleanedargs "" cleanedargs
+
+ return [ exec sh -c "${FSLDIR}/bin/imrm $args" ]
+}
+
+proc imtest { args } {
+ global FSLDIR
+
+ regsub -all "\{" $args "" cleanedargs
+ regsub -all "\}" $cleanedargs "" cleanedargs
+
+ return [ exec sh -c "${FSLDIR}/bin/imtest $args" ]
+}
+
+proc remove_ext { args } {
+ global FSLDIR
+
+ regsub -all "\{" $args "" cleanedargs
+ regsub -all "\}" $cleanedargs "" cleanedargs
+
+ return [ exec sh -c "${FSLDIR}/bin/remove_ext $cleanedargs" ]
+}
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/imcp b/Utilities/ITK/Utilities/nifti/fsliolib/imcp
new file mode 100644
index 0000000000000000000000000000000000000000..c108ef4e850eb6b4aadb2bd1a34b428e52415b98
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/imcp
@@ -0,0 +1,65 @@
+#!/bin/sh
+
+# imcp - copy image files
+#
+# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+# Part of FSL - FMRIB's Software Library
+# http://www.fmrib.ox.ac.uk/fsl
+# fsl@fmrib.ox.ac.uk
+#
+#
+# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+# Imaging of the Brain), Department of Clinical Neurology, Oxford
+# University, Oxford, UK
+#
+#
+
+if [ $# -lt 1 ] ; then
+ echo "Usage: $0 <file1> <file2>"
+ echo "Usage: $0 <file1> <file2> ... <fileN> <directory>"
+ echo " Copies images from file1 to file2 (including all extensions)"
+ echo " NB: filenames can be basenames or include an extension"
+ exit 1;
+fi
+
+if [ $# -eq 2 -a ! -d $2 ] ; then
+ f1=`${FSLDIR}/bin/remove_ext $1`;
+ f2=`${FSLDIR}/bin/remove_ext $2`;
+ # do the copies
+ if [ -f ${f1}.hdr ] ; then /bin/cp ${f1}.hdr ${f2}.hdr ; fi
+ if [ -f ${f1}.hdr.gz ] ; then /bin/cp ${f1}.hdr.gz ${f2}.hdr.gz ; fi
+ if [ -f ${f1}.img ] ; then /bin/cp ${f1}.img ${f2}.img ; fi
+ if [ -f ${f1}.img.gz ] ; then /bin/cp ${f1}.img.gz ${f2}.img.gz ; fi
+ if [ -f ${f1}.nii ] ; then /bin/cp ${f1}.nii ${f2}.nii ; fi
+ if [ -f ${f1}.nii.gz ] ; then /bin/cp ${f1}.nii.gz ${f2}.nii.gz ; fi
+ if [ -f ${f1}.mnc ] ; then /bin/cp ${f1}.mnc ${f2}.mnc ; fi
+ if [ -f ${f1}.mnc.gz ] ; then /bin/cp ${f1}.mnc.gz ${f2}.mnc.gz ; fi
+fi
+
+if [ $# -gt 2 -o -d $2 ] ; then
+ for nm in $@ ; do
+ dir=$nm;
+ done
+ if [ ! -d $dir ] ; then
+ echo "When using multiple arguments, last name must be a directory"
+ exit 1;
+ fi
+ # remove directory from list of files
+ flist="echo $@ | sed s/$dir \*\$//";
+ for fn in $flist ; do
+ f1=`${FSLDIR}/bin/remove_ext $fn`;
+ # do the copies
+ if [ -f ${f1}.hdr ] ; then /bin/cp ${f1}.hdr ${dir} ; fi
+ if [ -f ${f1}.hdr.gz ] ; then /bin/cp ${f1}.hdr.gz ${dir} ; fi
+ if [ -f ${f1}.img ] ; then /bin/cp ${f1}.img ${dir} ; fi
+ if [ -f ${f1}.img.gz ] ; then /bin/cp ${f1}.img.gz ${dir} ; fi
+ if [ -f ${f1}.nii ] ; then /bin/cp ${f1}.nii ${dir} ; fi
+ if [ -f ${f1}.nii.gz ] ; then /bin/cp ${f1}.nii.gz ${dir} ; fi
+ if [ -f ${f1}.mnc ] ; then /bin/cp ${f1}.mnc ${dir} ; fi
+ if [ -f ${f1}.mnc.gz ] ; then /bin/cp ${f1}.mnc.gz ${dir} ; fi
+ done
+fi
+
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/imglob b/Utilities/ITK/Utilities/nifti/fsliolib/imglob
new file mode 100644
index 0000000000000000000000000000000000000000..12345b1b93255109354ef2adc8507da1a9478a90
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/imglob
@@ -0,0 +1,59 @@
+#!/bin/sh
+
+# imglob - expand list of image filenames
+#
+# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+# Part of FSL - FMRIB's Software Library
+# http://www.fmrib.ox.ac.uk/fsl
+# fsl@fmrib.ox.ac.uk
+#
+#
+# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+# Imaging of the Brain), Department of Clinical Neurology, Oxford
+# University, Oxford, UK
+#
+#
+
+if [ $# -lt 1 ] ; then
+ echo "Usage: $0 [-oneperimage] <list of names>"
+ exit 0;
+fi
+
+oneperimg=0;
+if [ X"$1"X = "X-oneperimageX" ] ; then
+ oneperimg=1;
+ shift;
+fi
+
+# process each argument, removing any possible extension and
+# then expanding for valid extensions
+
+lst="";
+for aa in $@ ; do
+ # repeat remove_ext a few times to expand out all wildmasking
+ a=`${FSLDIR}/bin/remove_ext ${aa}`;
+ # at this point variable 'a' may have been expanded into a list
+ for b in $a ; do
+ if [ $oneperimg = 1 ] ; then
+ fn=`echo ${b}.hdr ${b}.hdr.gz ${b}.nii ${b}.nii.gz ${b}.mnc ${b}.mnc.gz`;
+ else
+ fn=`echo ${b}.hdr ${b}.hdr.gz ${b}.nii ${b}.nii.gz ${b}.mnc ${b}.mnc.gz ${b}.img ${b}.img.gz`;
+ fi
+ lst="$lst $fn";
+ done
+done
+
+# remove any instances of unmatched wildmasks (still with * in them)
+lst2="";
+for fn in $lst ; do
+ if [ -f $fn ] ; then
+ lst2="$lst2 $fn";
+ fi
+done
+
+# make list unique
+lst=`echo $lst2 | tr ' ' '\n' | sort -u`;
+echo $lst
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/imln b/Utilities/ITK/Utilities/nifti/fsliolib/imln
new file mode 100644
index 0000000000000000000000000000000000000000..a6601a825a0f5d6006d119417b2e920f00a8ba99
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/imln
@@ -0,0 +1,37 @@
+#!/bin/sh
+
+# imln - make symbolic link(s) to image file(s)
+#
+# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+# Part of FSL - FMRIB's Software Library
+# http://www.fmrib.ox.ac.uk/fsl
+# fsl@fmrib.ox.ac.uk
+#
+#
+# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+# Imaging of the Brain), Department of Clinical Neurology, Oxford
+# University, Oxford, UK
+#
+#
+
+if [ $# -lt 2 ] ; then
+ echo "Usage: $0 <file1> <file2>"
+ echo " Makes a link (called file2) to file1"
+ echo " NB: filenames can be basenames or include an extension"
+ exit 1;
+fi
+
+f1=`${FSLDIR}/bin/remove_ext $1`;
+f2=`${FSLDIR}/bin/remove_ext $2`;
+
+if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi
+if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi
+if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi
+if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi
+if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi
+if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi
+if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi
+if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/immv b/Utilities/ITK/Utilities/nifti/fsliolib/immv
new file mode 100644
index 0000000000000000000000000000000000000000..68c61c3f7192f8df15acb2c5b25d71b41f590110
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/immv
@@ -0,0 +1,64 @@
+#!/bin/sh
+
+# immv - rename/move image files
+#
+# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+# Part of FSL - FMRIB's Software Library
+# http://www.fmrib.ox.ac.uk/fsl
+# fsl@fmrib.ox.ac.uk
+#
+#
+# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+# Imaging of the Brain), Department of Clinical Neurology, Oxford
+# University, Oxford, UK
+#
+#
+
+if [ $# -lt 1 ] ; then
+ echo "Usage: $0 <file1> <file2>"
+ echo " Moves images from file1 to file2 (including all extensions)"
+ echo " NB: filenames can be basenames or include an extension"
+ exit 1;
+fi
+
+if [ $# -eq 2 -a ! -d $2 ] ; then
+ f1=`${FSLDIR}/bin/remove_ext $1`;
+ f2=`${FSLDIR}/bin/remove_ext $2`;
+ # do the moves
+ if [ -f ${f1}.hdr ] ; then /bin/mv ${f1}.hdr ${f2}.hdr ; fi
+ if [ -f ${f1}.hdr.gz ] ; then /bin/mv ${f1}.hdr.gz ${f2}.hdr.gz ; fi
+ if [ -f ${f1}.img ] ; then /bin/mv ${f1}.img ${f2}.img ; fi
+ if [ -f ${f1}.img.gz ] ; then /bin/mv ${f1}.img.gz ${f2}.img.gz ; fi
+ if [ -f ${f1}.nii ] ; then /bin/mv ${f1}.nii ${f2}.nii ; fi
+ if [ -f ${f1}.nii.gz ] ; then /bin/mv ${f1}.nii.gz ${f2}.nii.gz ; fi
+ if [ -f ${f1}.mnc ] ; then /bin/mv ${f1}.mnc ${f2}.mnc ; fi
+ if [ -f ${f1}.mnc.gz ] ; then /bin/mv ${f1}.mnc.gz ${f2}.mnc.gz ; fi
+fi
+
+if [ $# -gt 2 -o -d $2 ] ; then
+ for nm in $@ ; do
+ dir=$nm;
+ done
+ if [ ! -d $dir ] ; then
+ echo "When using multiple arguments, last name must be a directory"
+ exit 1;
+ fi
+ # remove directory from list of files
+ flist="echo $@ | sed s/$dir \*\$//";
+ for fn in $flist ; do
+ f1=`${FSLDIR}/bin/remove_ext $fn`;
+ # do the copies
+ if [ -f ${f1}.hdr ] ; then /bin/mv ${f1}.hdr ${dir} ; fi
+ if [ -f ${f1}.hdr.gz ] ; then /bin/mv ${f1}.hdr.gz ${dir} ; fi
+ if [ -f ${f1}.img ] ; then /bin/mv ${f1}.img ${dir} ; fi
+ if [ -f ${f1}.img.gz ] ; then /bin/mv ${f1}.img.gz ${dir} ; fi
+ if [ -f ${f1}.nii ] ; then /bin/mv ${f1}.nii ${dir} ; fi
+ if [ -f ${f1}.nii.gz ] ; then /bin/mv ${f1}.nii.gz ${dir} ; fi
+ if [ -f ${f1}.mnc ] ; then /bin/mv ${f1}.mnc ${dir} ; fi
+ if [ -f ${f1}.mnc.gz ] ; then /bin/mv ${f1}.mnc.gz ${dir} ; fi
+ done
+fi
+
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/imrm b/Utilities/ITK/Utilities/nifti/fsliolib/imrm
new file mode 100644
index 0000000000000000000000000000000000000000..ab16dbbf5893802d1e9142a3ee50afbc627708e6
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/imrm
@@ -0,0 +1,29 @@
+#!/bin/sh
+
+# imrm - remove image files
+#
+# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+# Part of FSL - FMRIB's Software Library
+# http://www.fmrib.ox.ac.uk/fsl
+# fsl@fmrib.ox.ac.uk
+#
+# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+# Imaging of the Brain), Department of Clinical Neurology, Oxford
+# University, Oxford, UK
+#
+#
+
+if [ $# -lt 1 ] ; then
+ echo "Usage: $0 <list of image names to remove>"
+ echo "NB: filenames can be basenames or not"
+ exit 1;
+fi
+
+for f in $@ ; do
+ fn=`${FSLDIR}/bin/remove_ext $f`;
+ # do the rm silently
+ /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz
+done
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/imtest b/Utilities/ITK/Utilities/nifti/fsliolib/imtest
new file mode 100644
index 0000000000000000000000000000000000000000..37b9a2f05317c2e9c45ef68feefaf552811fa35a
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/imtest
@@ -0,0 +1,53 @@
+#!/bin/sh
+
+# imtest - test to see if a valid image file exists with this name (root)
+#
+# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+#
+# Part of FSL - FMRIB's Software Library
+# http://www.fmrib.ox.ac.uk/fsl
+# fsl@fmrib.ox.ac.uk
+#
+# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+# Imaging of the Brain), Department of Clinical Neurology, Oxford
+# University, Oxford, UK
+#
+#
+
+# return 0 if no image exists or 1 if the image exists
+
+if [ $# -lt 1 ] ; then
+ echo "0";
+ exit;
+fi
+
+filename=`${FSLDIR}/bin/remove_ext $1`;
+
+if [ -r ${filename}.nii -o -r ${filename}.nii.gz ] ; then
+ echo "1";
+ exit;
+fi
+
+if [ -r ${filename}.mnc -o -r ${filename}.mnc.gz ] ; then
+ echo "1";
+ exit;
+fi
+
+if [ ! -r ${filename}.hdr -a ! -r ${filename}.hdr.gz ] ; then
+ # return 0 here as no header exists and no single image means no image!
+ echo "0";
+ exit;
+fi
+
+if [ ! -r ${filename}.img -a ! -r ${filename}.img.gz ] ; then
+ # return 0 here as no img file exists and no single image means no image!
+ echo "0";
+ exit;
+fi
+
+# only gets to here if there was a hdr and an img file
+
+echo "1";
+exit;
+
diff --git a/Utilities/ITK/Utilities/nifti/fsliolib/remove_ext b/Utilities/ITK/Utilities/nifti/fsliolib/remove_ext
new file mode 100644
index 0000000000000000000000000000000000000000..67f2d1734d9b6602bad5d415bd8c6d1435c902e2
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/fsliolib/remove_ext
@@ -0,0 +1,86 @@
+#!/bin/sh
+
+# remove_ext - remove extension from image filename
+#
+# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#
+# Copyright (C) 1999-2004 University of Oxford
+#
+# Part of FSL - FMRIB's Software Library
+# http://www.fmrib.ox.ac.uk/fsl
+# fsl@fmrib.ox.ac.uk
+#
+# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+# Imaging of the Brain), Department of Clinical Neurology, Oxford
+# University, Oxford, UK
+#
+#
+# LICENCE
+#
+# FMRIB Software Library, Release 3.2beta (c) 2004, The University of
+# Oxford (the "Software")
+#
+# The Software remains the property of the University of Oxford ("the
+# University").
+#
+# The Software is distributed "AS IS" under this Licence solely for
+# non-commercial use in the hope that it will be useful, but in order
+# that the University as a charitable foundation protects its assets for
+# the benefit of its educational and research purposes, the University
+# makes clear that no condition is made or to be implied, nor is any
+# warranty given or to be implied, as to the accuracy of the Software,
+# or that it will be suitable for any particular purpose or for use
+# under any specific conditions. Furthermore, the University disclaims
+# all responsibility for the use which is made of the Software. It
+# further disclaims any liability for the outcomes arising from using
+# the Software.
+#
+# The Licensee agrees to indemnify the University and hold the
+# University harmless from and against any and all claims, damages and
+# liabilities asserted by third parties (including claims for
+# negligence) which arise directly or indirectly from the use of the
+# Software or the sale of any products based on the Software.
+#
+# No part of the Software may be reproduced, modified, transmitted or
+# transferred in any form or by any means, electronic or mechanical,
+# without the express permission of the University. The permission of
+# the University is not required if the said reproduction, modification,
+# transmission or transference is done without financial return, the
+# conditions of this Licence are imposed upon the receiver of the
+# product, and all original and amended source code is included in any
+# transmitted product. You may be held legally responsible for any
+# copyright infringement that is caused or encouraged by your failure to
+# abide by these terms and conditions.
+#
+# You are not permitted under this Licence to use this Software
+# commercially. Use for which any financial return is received shall be
+# defined as commercial use, and includes (1) integration of all or part
+# of the source code or the Software into a product for sale or license
+# by or on behalf of Licensee to third parties or (2) use of the
+# Software or any derivative of it for research with the final aim of
+# developing software products for sale or license to a third party or
+# (3) use of the Software or any derivative of it for research with the
+# final aim of developing non-software products for sale or license to a
+# third party, or (4) use of the Software to provide any service to an
+# external organisation for which payment is received. If you are
+# interested in using the Software commercially, please contact Isis
+# Innovation Limited ("Isis"), the technology transfer company of the
+# University, to negotiate a licence. Contact details are:
+# innovation@isis.ox.ac.uk quoting reference DE/1112.
+
+
+if [ $# -lt 1 ] ; then
+ exit 0
+fi
+
+lst="";
+for fn in $@ ; do
+ # for the ones at the end of the line
+ f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`;
+ # for the ones in the middle of the line
+ f=`echo "$f" | sed 's/\.hdr\.gz[ ]/ /g' | sed 's/\.img\.gz[ ]/ /g' | sed 's/\.hdr[ ]/ /g' | sed 's/\.img[ ]/ /g' | sed 's/\.nii\.gz[ ]/ /g' | sed 's/\.nii[ ]/ /g' | sed 's/\.mnc\.gz[ ]/ /g' | sed 's/\.mnc[ ]/ /g' |sed 's/\.[ ]/ /g'`;
+ lst="$lst $f";
+done
+echo $lst;
+
+
diff --git a/Utilities/ITK/Utilities/nifti/niftilib/CMakeLists.txt b/Utilities/ITK/Utilities/nifti/niftilib/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a7e34866494c2870c7b5e40e9bacb0a63a0247d
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/niftilib/CMakeLists.txt
@@ -0,0 +1,16 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(NIFTILIB)
+
+INCLUDE_DIRECTORIES(${ZNZLIB_SOURCE_DIR})
+SET(NIFTILIB_SRC nifti1_io.c)
+
+ADD_LIBRARY(${PACKAGE_PREFIX}niftiio ${NIFTILIB_SRC} )
+TARGET_LINK_LIBRARIES( ${PACKAGE_PREFIX}niftiio ${PACKAGE_PREFIX}znz)
+
+IF(UNIX)
+TARGET_LINK_LIBRARIES(${PACKAGE_PREFIX}niftiio -lm)
+ENDIF(UNIX)
+
+INSTALL_TARGETS(${LIB_INSTALL_DIR} ${PACKAGE_PREFIX}niftiio)
+INSTALL_FILES(${INCLUDE_INSTALL_DIR} "(\\.h)$")
diff --git a/Utilities/ITK/Utilities/nifti/niftilib/Makefile b/Utilities/ITK/Utilities/nifti/niftilib/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..c463b88580f723530ea66c75feeaec66f8fd5725
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/niftilib/Makefile
@@ -0,0 +1,31 @@
+include ../Makefile
+
+PROJNAME = niftiio
+
+
+INCFLAGS = $(ZLIB_INC) $(ZNZ_INC)
+LIBS = $(ZLIB_LIBS) $(ZNZ_LIBS) $(NIFTI_LIBS)
+
+SRCS=nifti1_io.c
+OBJS=nifti1_io.o
+MOBJS=mjtest.o
+
+SCRIPTS =
+
+depend:
+ $(RM) -f depend.mk
+ $(MAKE) depend.mk
+
+depend.mk:
+ $(CC) $(DEPENDFLAGS) $(INCFLAGS) $(SRCS) >> depend.mk
+
+lib: libniftiio.a
+
+nifti1_io.o: nifti1_io.c nifti1_io.h
+ $(CC) -c $(CFLAGS) $(USEZLIB) $(INCFLAGS) $<
+
+libniftiio.a: $(OBJS)
+ $(AR) -r libniftiio.a $(OBJS)
+ $(RANLIB) $@
+
+include depend.mk
diff --git a/Utilities/ITK/Utilities/nifti/niftilib/nifti1.h b/Utilities/ITK/Utilities/nifti/niftilib/nifti1.h
new file mode 100644
index 0000000000000000000000000000000000000000..abe8892674f7e232f0df1d5e036ca2969c43b9d6
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/niftilib/nifti1.h
@@ -0,0 +1,1441 @@
+/** \file nifti1.h
+ \brief Official definition of the nifti1 header. Written by Bob Cox, SSCC, NIMH.
+ */
+
+#ifndef _NIFTI_HEADER_
+#define _NIFTI_HEADER_
+
+/*****************************************************************************
+ ** This file defines the "NIFTI-1" header format. **
+ ** It is derived from 2 meetings at the NIH (31 Mar 2003 and **
+ ** 02 Sep 2003) of the Data Format Working Group (DFWG), **
+ ** chartered by the NIfTI (Neuroimaging Informatics Technology **
+ ** Initiative) at the National Institutes of Health (NIH). **
+ **--------------------------------------------------------------**
+ ** Neither the National Institutes of Health (NIH), the DFWG, **
+ ** nor any of the members or employees of these institutions **
+ ** imply any warranty of usefulness of this material for any **
+ ** purpose, and do not assume any liability for damages, **
+ ** incidental or otherwise, caused by any use of this document. **
+ ** If these conditions are not acceptable, do not use this! **
+ **--------------------------------------------------------------**
+ ** Author: Robert W Cox (NIMH, Bethesda) **
+ ** Advisors: John Ashburner (FIL, London), **
+ ** Stephen Smith (FMRIB, Oxford), **
+ ** Mark Jenkinson (FMRIB, Oxford) **
+******************************************************************************/
+
+/*---------------------------------------------------------------------------*/
+/* Note that the ANALYZE 7.5 file header (dbh.h) is
+ (c) Copyright 1986-1995
+ Biomedical Imaging Resource
+ Mayo Foundation
+ Incorporation of components of dbh.h are by permission of the
+ Mayo Foundation.
+
+ Changes from the ANALYZE 7.5 file header in this file are released to the
+ public domain, including the functional comments and any amusing asides.
+-----------------------------------------------------------------------------*/
+
+/*---------------------------------------------------------------------------*/
+/*! INTRODUCTION TO NIFTI-1:
+ ------------------------
+ The twin (and somewhat conflicting) goals of this modified ANALYZE 7.5
+ format are:
+ (a) To add information to the header that will be useful for functional
+ neuroimaging data analysis and display. These additions include:
+ - More basic data types.
+ - Two affine transformations to specify voxel coordinates.
+ - "Intent" codes and parameters to describe the meaning of the data.
+ - Affine scaling of the stored data values to their "true" values.
+ - Optional storage of the header and image data in one file (.nii).
+ (b) To maintain compatibility with non-NIFTI-aware ANALYZE 7.5 compatible
+ software (i.e., such a program should be able to do something useful
+ with a NIFTI-1 dataset -- at least, with one stored in a traditional
+ .img/.hdr file pair).
+
+ Most of the unused fields in the ANALYZE 7.5 header have been taken,
+ and some of the lesser-used fields have been co-opted for other purposes.
+ Notably, most of the data_history substructure has been co-opted for
+ other purposes, since the ANALYZE 7.5 format describes this substructure
+ as "not required".
+
+ NIFTI-1 FLAG (MAGIC STRINGS):
+ ----------------------------
+ To flag such a struct as being conformant to the NIFTI-1 spec, the last 4
+ bytes of the header must be either the C String "ni1" or "n+1";
+ in hexadecimal, the 4 bytes
+ 6E 69 31 00 or 6E 2B 31 00
+ (in any future version of this format, the '1' will be upgraded to '2',
+ etc.). Normally, such a "magic number" or flag goes at the start of the
+ file, but trying to avoid clobbering widely-used ANALYZE 7.5 fields led to
+ putting this marker last. However, recall that "the last shall be first"
+ (Matthew 20:16).
+
+ If a NIFTI-aware program reads a header file that is NOT marked with a
+ NIFTI magic string, then it should treat the header as an ANALYZE 7.5
+ structure.
+
+ NIFTI-1 FILE STORAGE:
+ --------------------
+ "ni1" means that the image data is stored in the ".img" file corresponding
+ to the header file (starting at file offset 0).
+
+ "n+1" means that the image data is stored in the same file as the header
+ information. We recommend that the combined header+data filename suffix
+ be ".nii". When the dataset is stored in one file, the first byte of image
+ data is stored at byte location (int)vox_offset in this combined file.
+ The minimum allowed value of vox_offset is 352; for compatibility with
+ some software, vox_offset should be an integral multiple of 16.
+
+ GRACE UNDER FIRE:
+ ----------------
+ Most NIFTI-aware programs will only be able to handle a subset of the full
+ range of datasets possible with this format. All NIFTI-aware programs
+ should take care to check if an input dataset conforms to the program's
+ needs and expectations (e.g., check datatype, intent_code, etc.). If the
+ input dataset can't be handled by the program, the program should fail
+ gracefully (e.g., print a useful warning; not crash).
+
+ SAMPLE CODES:
+ ------------
+ The associated files nifti1_io.h and nifti1_io.c provide a sample
+ implementation in C of a set of functions to read, write, and manipulate
+ NIFTI-1 files. The file nifti1_test.c is a sample program that uses
+ the nifti1_io.c functions.
+-----------------------------------------------------------------------------*/
+
+/*---------------------------------------------------------------------------*/
+/* HEADER STRUCT DECLARATION:
+ -------------------------
+ In the comments below for each field, only NIFTI-1 specific requirements
+ or changes from the ANALYZE 7.5 format are described. For convenience,
+ the 348 byte header is described as a single struct, rather than as the
+ ANALYZE 7.5 group of 3 substructs.
+
+ Further comments about the interpretation of various elements of this
+ header are after the data type definition itself. Fields that are
+ marked as ++UNUSED++ have no particular interpretation in this standard.
+ (Also see the UNUSED FIELDS comment section, far below.)
+
+ The presumption below is that the various C types have particular sizes:
+ sizeof(int) = sizeof(float) = 4 ; sizeof(short) = 2
+-----------------------------------------------------------------------------*/
+
+/*=================*/
+#ifdef __cplusplus
+extern "C" {
+#endif
+/*=================*/
+
+/*! \struct nifti_1_header
+ \brief Data structure defining the fields in the nifti1 header.
+ This binary header should be found at the beginning of a valid
+ NIFTI-1 header file.
+ */
+ /*************************/ /************************/
+struct nifti_1_header { /* NIFTI-1 usage */ /* ANALYZE 7.5 field(s) */
+ /*************************/ /************************/
+
+ /*--- was header_key substruct ---*/
+ int sizeof_hdr; /*!< MUST be 348 */ /* int sizeof_hdr; */
+ char data_type[10]; /*!< ++UNUSED++ */ /* char data_type[10]; */
+ char db_name[18]; /*!< ++UNUSED++ */ /* char db_name[18]; */
+ int extents; /*!< ++UNUSED++ */ /* int extents; */
+ short session_error; /*!< ++UNUSED++ */ /* short session_error; */
+ char regular; /*!< ++UNUSED++ */ /* char regular; */
+ char dim_info; /*!< MRI slice ordering. */ /* char hkey_un0; */
+
+ /*--- was image_dimension substruct ---*/
+ short dim[8]; /*!< Data array dimensions.*/ /* short dim[8]; */
+ float intent_p1 ; /*!< 1st intent parameter. */ /* short unused8; */
+ /* short unused9; */
+ float intent_p2 ; /*!< 2nd intent parameter. */ /* short unused10; */
+ /* short unused11; */
+ float intent_p3 ; /*!< 3rd intent parameter. */ /* short unused12; */
+ /* short unused13; */
+ short intent_code ; /*!< NIFTI_INTENT_* code. */ /* short unused14; */
+ short datatype; /*!< Defines data type! */ /* short datatype; */
+ short bitpix; /*!< Number bits/voxel. */ /* short bitpix; */
+ short slice_start; /*!< First slice index. */ /* short dim_un0; */
+ float pixdim[8]; /*!< Grid spacings. */ /* float pixdim[8]; */
+ float vox_offset; /*!< Offset into .nii file */ /* float vox_offset; */
+ float scl_slope ; /*!< Data scaling: slope. */ /* float funused1; */
+ float scl_inter ; /*!< Data scaling: offset. */ /* float funused2; */
+ short slice_end; /*!< Last slice index. */ /* float funused3; */
+ char slice_code ; /*!< Slice timing order. */
+ char xyzt_units ; /*!< Units of pixdim[1..4] */
+ float cal_max; /*!< Max display intensity */ /* float cal_max; */
+ float cal_min; /*!< Min display intensity */ /* float cal_min; */
+ float slice_duration;/*!< Time for 1 slice. */ /* float compressed; */
+ float toffset; /*!< Time axis shift. */ /* float verified; */
+ int glmax; /*!< ++UNUSED++ */ /* int glmax; */
+ int glmin; /*!< ++UNUSED++ */ /* int glmin; */
+
+ /*--- was data_history substruct ---*/
+ char descrip[80]; /*!< any text you like. */ /* char descrip[80]; */
+ char aux_file[24]; /*!< auxiliary filename. */ /* char aux_file[24]; */
+
+ short qform_code ; /*!< NIFTI_XFORM_* code. */ /*-- all ANALYZE 7.5 ---*/
+ short sform_code ; /*!< NIFTI_XFORM_* code. */ /* fields below here */
+ /* are replaced */
+ float quatern_b ; /*!< Quaternion b param. */
+ float quatern_c ; /*!< Quaternion c param. */
+ float quatern_d ; /*!< Quaternion d param. */
+ float qoffset_x ; /*!< Quaternion x shift. */
+ float qoffset_y ; /*!< Quaternion y shift. */
+ float qoffset_z ; /*!< Quaternion z shift. */
+
+ float srow_x[4] ; /*!< 1st row affine transform. */
+ float srow_y[4] ; /*!< 2nd row affine transform. */
+ float srow_z[4] ; /*!< 3rd row affine transform. */
+
+ char intent_name[16];/*!< 'name' or meaning of data. */
+
+ char magic[4] ; /*!< MUST be "ni1\0" or "n+1\0". */
+
+} ; /**** 348 bytes total ****/
+
+typedef struct nifti_1_header nifti_1_header ;
+
+/*---------------------------------------------------------------------------*/
+/* HEADER EXTENSIONS:
+ -----------------
+ After the end of the 348 byte header (e.g., after the magic field),
+ the next 4 bytes are a char array field named "extension". By default,
+ all 4 bytes of this array should be set to zero. In a .nii file, these
+ 4 bytes will always be present, since the earliest start point for
+ the image data is byte #352. In a separate .hdr file, these bytes may
+ or may not be present. If not present (i.e., if the length of the .hdr
+ file is 348 bytes), then a NIfTI-1 compliant program should use the
+ default value of extension={0,0,0,0}. The first byte (extension[0])
+ is the only value of this array that is specified at present. The other
+ 3 bytes are reserved for future use.
+
+ If extension[0] is nonzero, it indicates that extended header information
+ is present in the bytes following the extension array. In a .nii file,
+ this extended header data is before the image data (and vox_offset
+ must be set correctly to allow for this). In a .hdr file, this extended
+ data follows extension and proceeds (potentially) to the end of the file.
+
+ The format of extended header data is weakly specified. Each extension
+ must be an integer multiple of 16 bytes long. The first 8 bytes of each
+ extension comprise 2 integers:
+ int esize , ecode ;
+ These values may need to be byte-swapped, as indicated by dim[0] for
+ the rest of the header.
+ * esize is the number of bytes that form the extended header data
+ + esize must be a positive integral multiple of 16
+ + this length includes the 8 bytes of esize and ecode themselves
+ * ecode is a non-negative integer that indicates the format of the
+ extended header data that follows
+ + different ecode values are assigned to different developer groups
+ + at present, the "registered" values for code are
+ = 0 = unknown private format (not recommended!)
+ = 2 = DICOM format (i.e., attribute tags and values)
+ = 4 = AFNI group (i.e., ASCII XML-ish elements)
+ In the interests of interoperability (a primary rationale for NIfTI),
+ groups developing software that uses this extension mechanism are
+ encouraged to document and publicize the format of their extensions.
+ To this end, the NIfTI DFWG will assign even numbered codes upon request
+ to groups submitting at least rudimentary documentation for the format
+ of their extension; at present, the contact is mailto:rwcox@nih.gov.
+ The assigned codes and documentation will be posted on the NIfTI
+ website. All odd values of ecode (and 0) will remain unassigned;
+ at least, until the even ones are used up, when we get to 2,147,483,646.
+
+ Note that the other contents of the extended header data section are
+ totally unspecified by the NIfTI-1 standard. In particular, if binary
+ data is stored in such a section, its byte order is not necessarily
+ the same as that given by examining dim[0]; it is incumbent on the
+ programs dealing with such data to determine the byte order of binary
+ extended header data.
+
+ Multiple extended header sections are allowed, each starting with an
+ esize,ecode value pair. The first esize value, as described above,
+ is at bytes #352-355 in the .hdr or .nii file (files start at byte #0).
+ If this value is positive, then the second (esize2) will be found
+ starting at byte #352+esize1 , the third (esize3) at byte #352+esize1+esize2,
+ et cetera. Of course, in a .nii file, the value of vox_offset must
+ be compatible with these extensions. If a malformed file indicates
+ that an extended header data section would run past vox_offset, then
+ the entire extended header section should be ignored. In a .hdr file,
+ if an extended header data section would run past the end-of-file,
+ that extended header data should also be ignored.
+
+ With the above scheme, a program can successively examine the esize
+ and ecode values, and skip over each extended header section if the
+ program doesn't know how to interpret the data within. Of course, any
+ program can simply ignore all extended header sections simply by jumping
+ straight to the image data using vox_offset.
+-----------------------------------------------------------------------------*/
+
+/*! \struct nifti1_extender
+ \brief This structure represents a 4-byte string that should follow the
+ binary nifti_1_header data in a NIFTI-1 header file. If the char
+ values are {1,0,0,0}, the file is expected to contain extensions,
+ values of {0,0,0,0} imply the file does not contain extensions.
+ Other sequences of values are not currently defined.
+ */
+struct nifti1_extender { char extension[4] ; } ;
+typedef struct nifti1_extender nifti1_extender ;
+
+/*! \struct nifti1_extension
+ \brief Data structure defining the fields of a header extension.
+ */
+struct nifti1_extension {
+ int esize ; /*!< size of extension, in bytes (must be multiple of 16) */
+ int ecode ; /*!< extension code, one of the NIFTI_ECODE_ values */
+ char * edata ; /*!< raw data, with no byte swapping */
+} ;
+typedef struct nifti1_extension nifti1_extension ;
+
+/*---------------------------------------------------------------------------*/
+/* DATA DIMENSIONALITY (as in ANALYZE 7.5):
+ ---------------------------------------
+ dim[0] = number of dimensions;
+ - if dim[0] is outside range 1..7, then the header information
+ needs to be byte swapped appropriately
+ - ANALYZE supports dim[0] up to 7, but NIFTI-1 reserves
+ dimensions 1,2,3 for space (x,y,z), 4 for time (t), and
+ 5,6,7 for anything else needed.
+
+ dim[i] = length of dimension #i, for i=1..dim[0] (must be positive)
+ - also see the discussion of intent_code, far below
+
+ pixdim[i] = voxel width along dimension #i, i=1..dim[0] (positive)
+ - cf. ORIENTATION section below for use of pixdim[0]
+ - the units of pixdim can be specified with the xyzt_units
+ field (also described far below).
+
+ Number of bits per voxel value is in bitpix, which MUST correspond with
+ the datatype field. The total number of bytes in the image data is
+ dim[1] * ... * dim[dim[0]] * bitpix / 8
+
+ In NIFTI-1 files, dimensions 1,2,3 are for space, dimension 4 is for time,
+ and dimension 5 is for storing multiple values at each spatiotemporal
+ voxel. Some examples:
+ - A typical whole-brain FMRI experiment's time series:
+ - dim[0] = 4
+ - dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM
+ - dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC
+ - dim[3] = 20 pixdim[3] = 5.0
+ - dim[4] = 120 pixdim[4] = 2.0
+ - A typical T1-weighted anatomical volume:
+ - dim[0] = 3
+ - dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM
+ - dim[2] = 256 pixdim[2] = 1.0
+ - dim[3] = 128 pixdim[3] = 1.1
+ - A single slice EPI time series:
+ - dim[0] = 4
+ - dim[1] = 64 pixdim[1] = 3.75 xyzt_units = NIFTI_UNITS_MM
+ - dim[2] = 64 pixdim[2] = 3.75 | NIFTI_UNITS_SEC
+ - dim[3] = 1 pixdim[3] = 5.0
+ - dim[4] = 1200 pixdim[4] = 0.2
+ - A 3-vector stored at each point in a 3D volume:
+ - dim[0] = 5
+ - dim[1] = 256 pixdim[1] = 1.0 xyzt_units = NIFTI_UNITS_MM
+ - dim[2] = 256 pixdim[2] = 1.0
+ - dim[3] = 128 pixdim[3] = 1.1
+ - dim[4] = 1 pixdim[4] = 0.0
+ - dim[5] = 3 intent_code = NIFTI_INTENT_VECTOR
+ - A single time series with a 3x3 matrix at each point:
+ - dim[0] = 5
+ - dim[1] = 1 xyzt_units = NIFTI_UNITS_SEC
+ - dim[2] = 1
+ - dim[3] = 1
+ - dim[4] = 1200 pixdim[4] = 0.2
+ - dim[5] = 9 intent_code = NIFTI_INTENT_GENMATRIX
+ - intent_p1 = intent_p2 = 3.0 (indicates matrix dimensions)
+-----------------------------------------------------------------------------*/
+
+/*---------------------------------------------------------------------------*/
+/* DATA STORAGE:
+ ------------
+ If the magic field is "n+1", then the voxel data is stored in the
+ same file as the header. In this case, the voxel data starts at offset
+ (int)vox_offset into the header file. Thus, vox_offset=352.0 means that
+ the data starts immediately after the NIFTI-1 header. If vox_offset is
+ greater than 352, the NIFTI-1 format does not say much about the
+ contents of the dataset file between the end of the header and the
+ start of the data.
+
+ FILES:
+ -----
+ If the magic field is "ni1", then the voxel data is stored in the
+ associated ".img" file, starting at offset 0 (i.e., vox_offset is not
+ used in this case, and should be set to 0.0).
+
+ When storing NIFTI-1 datasets in pairs of files, it is customary to name
+ the files in the pattern "name.hdr" and "name.img", as in ANALYZE 7.5.
+ When storing in a single file ("n+1"), the file name should be in
+ the form "name.nii" (the ".nft" and ".nif" suffixes are already taken;
+ cf. http://www.icdatamaster.com/n.html ).
+
+ BYTE ORDERING:
+ -------------
+ The byte order of the data arrays is presumed to be the same as the byte
+ order of the header (which is determined by examining dim[0]).
+
+ Floating point types are presumed to be stored in IEEE-754 format.
+-----------------------------------------------------------------------------*/
+
+/*---------------------------------------------------------------------------*/
+/* DETAILS ABOUT vox_offset:
+ ------------------------
+ In a .nii file, the vox_offset field value is interpreted as the start
+ location of the image data bytes in that file. In a .hdr/.img file pair,
+ the vox_offset field value is the start location of the image data
+ bytes in the .img file.
+ * If vox_offset is less than 352 in a .nii file, it is equivalent
+ to 352 (i.e., image data never starts before byte #352 in a .nii file).
+ * The default value for vox_offset in a .nii file is 352.
+ * In a .hdr file, the default value for vox_offset is 0.
+ * vox_offset should be an integer multiple of 16; otherwise, some
+ programs may not work properly (e.g., SPM). This is to allow
+ memory-mapped input to be properly byte-aligned.
+ Note that since vox_offset is an IEEE-754 32 bit float (for compatibility
+ with the ANALYZE-7.5 format), it effectively has a 24 bit mantissa. All
+ integers from 0 to 2^24 can be represented exactly in this format, but not
+ all larger integers are exactly storable as IEEE-754 32 bit floats. However,
+ unless you plan to have vox_offset be potentially larger than 16 MB, this
+ should not be an issue. (Actually, any integral multiple of 16 up to 2^27
+ can be represented exactly in this format, which allows for up to 128 MB
+ of random information before the image data. If that isn't enough, then
+ perhaps this format isn't right for you.)
+
+ In a .img file (i.e., image data stored separately from the NIfTI-1
+ header), data bytes between #0 and #vox_offset-1 (inclusive) are completely
+ undefined and unregulated by the NIfTI-1 standard. One potential use of
+ having vox_offset > 0 in the .hdr/.img file pair storage method is to make
+ the .img file be a copy of (or link to) a pre-existing image file in some
+ other format, such as DICOM; then vox_offset would be set to the offset of
+ the image data in this file. (It may not be possible to follow the
+ "multiple-of-16 rule" with an arbitrary external file; using the NIfTI-1
+ format in such a case may lead to a file that is incompatible with software
+ that relies on vox_offset being a multiple of 16.)
+
+ In a .nii file, data bytes between #348 and #vox_offset-1 (inclusive) may
+ be used to store user-defined extra information; similarly, in a .hdr file,
+ any data bytes after byte #347 are available for user-defined extra
+ information. The (very weak) regulation of this extra header data is
+ described elsewhere.
+-----------------------------------------------------------------------------*/
+
+/*---------------------------------------------------------------------------*/
+/* DATA SCALING:
+ ------------
+ If the scl_slope field is nonzero, then each voxel value in the dataset
+ should be scaled as
+ y = scl_slope * x + scl_inter
+ where x = voxel value stored
+ y = "true" voxel value
+ Normally, we would expect this scaling to be used to store "true" floating
+ values in a smaller integer datatype, but that is not required. That is,
+ it is legal to use scaling even if the datatype is a float type (crazy,
+ perhaps, but legal).
+ - However, the scaling is to be ignored if datatype is DT_RGB24.
+ - If datatype is a complex type, then the scaling is to be
+ applied to both the real and imaginary parts.
+
+ The cal_min and cal_max fields (if nonzero) are used for mapping (possibly
+ scaled) dataset values to display colors:
+ - Minimum display intensity (black) corresponds to dataset value cal_min.
+ - Maximum display intensity (white) corresponds to dataset value cal_max.
+ - Dataset values below cal_min should display as black also, and values
+ above cal_max as white.
+ - Colors "black" and "white", of course, may refer to any scalar display
+ scheme (e.g., a color lookup table specified via aux_file).
+ - cal_min and cal_max only make sense when applied to scalar-valued
+ datasets (i.e., dim[0] < 5 or dim[5] = 1).
+-----------------------------------------------------------------------------*/
+
+/*---------------------------------------------------------------------------*/
+/* TYPE OF DATA (acceptable values for datatype field):
+ ---------------------------------------------------
+ Values of datatype smaller than 256 are ANALYZE 7.5 compatible.
+ Larger values are NIFTI-1 additions. These are all multiples of 256, so
+ that no bits below position 8 are set in datatype. But there is no need
+ to use only powers-of-2, as the original ANALYZE 7.5 datatype codes do.
+
+ The additional codes are intended to include a complete list of basic
+ scalar types, including signed and unsigned integers from 8 to 64 bits,
+ floats from 32 to 128 bits, and complex (float pairs) from 64 to 256 bits.
+
+ Note that most programs will support only a few of these datatypes!
+ A NIFTI-1 program should fail gracefully (e.g., print a warning message)
+ when it encounters a dataset with a type it doesn't like.
+-----------------------------------------------------------------------------*/
+
+#undef DT_UNKNOWN /* defined in dirent.h on some Unix systems */
+
+/*! \defgroup NIFTI1_DATATYPES
+ \brief nifti1 datatype codes
+ @{
+ */
+ /*--- the original ANALYZE 7.5 type codes ---*/
+#define DT_NONE 0
+#define DT_UNKNOWN 0 /* what it says, dude */
+#define DT_BINARY 1 /* binary (1 bit/voxel) */
+#define DT_UNSIGNED_CHAR 2 /* unsigned char (8 bits/voxel) */
+#define DT_SIGNED_SHORT 4 /* signed short (16 bits/voxel) */
+#define DT_SIGNED_INT 8 /* signed int (32 bits/voxel) */
+#define DT_FLOAT 16 /* float (32 bits/voxel) */
+#define DT_COMPLEX 32 /* complex (64 bits/voxel) */
+#define DT_DOUBLE 64 /* double (64 bits/voxel) */
+#define DT_RGB 128 /* RGB triple (24 bits/voxel) */
+#define DT_ALL 255 /* not very useful (?) */
+
+ /*----- another set of names for the same ---*/
+#define DT_UINT8 2
+#define DT_INT16 4
+#define DT_INT32 8
+#define DT_FLOAT32 16
+#define DT_COMPLEX64 32
+#define DT_FLOAT64 64
+#define DT_RGB24 128
+
+ /*------------------- new codes for NIFTI ---*/
+#define DT_INT8 256 /* signed char (8 bits) */
+#define DT_UINT16 512 /* unsigned short (16 bits) */
+#define DT_UINT32 768 /* unsigned int (32 bits) */
+#define DT_INT64 1024 /* long long (64 bits) */
+#define DT_UINT64 1280 /* unsigned long long (64 bits) */
+#define DT_FLOAT128 1536 /* long double (128 bits) */
+#define DT_COMPLEX128 1792 /* double pair (128 bits) */
+#define DT_COMPLEX256 2048 /* long double pair (256 bits) */
+/* @} */
+
+
+ /*------- aliases for all the above codes ---*/
+
+/*! \defgroup NIFTI1_DATATYPE_ALIASES
+ \brief aliases for the nifti1 datatype codes
+ @{
+ */
+ /*! unsigned char. */
+#define NIFTI_TYPE_UINT8 2
+ /*! signed short. */
+#define NIFTI_TYPE_INT16 4
+ /*! signed int. */
+#define NIFTI_TYPE_INT32 8
+ /*! 32 bit float. */
+#define NIFTI_TYPE_FLOAT32 16
+ /*! 64 bit complex = 2 32 bit floats. */
+#define NIFTI_TYPE_COMPLEX64 32
+ /*! 64 bit float = double. */
+#define NIFTI_TYPE_FLOAT64 64
+ /*! 3 8 bit bytes. */
+#define NIFTI_TYPE_RGB24 128
+ /*! signed char. */
+#define NIFTI_TYPE_INT8 256
+ /*! unsigned short. */
+#define NIFTI_TYPE_UINT16 512
+ /*! unsigned int. */
+#define NIFTI_TYPE_UINT32 768
+ /*! signed long long. */
+#define NIFTI_TYPE_INT64 1024
+ /*! unsigned long long. */
+#define NIFTI_TYPE_UINT64 1280
+ /*! 128 bit float = long double. */
+#define NIFTI_TYPE_FLOAT128 1536
+ /*! 128 bit complex = 2 64 bit floats. */
+#define NIFTI_TYPE_COMPLEX128 1792
+ /*! 256 bit complex = 2 128 bit floats */
+#define NIFTI_TYPE_COMPLEX256 2048
+/* @} */
+
+ /*-------- sample typedefs for complicated types ---*/
+#if 0
+typedef struct { float r,i; } complex_float ;
+typedef struct { double r,i; } complex_double ;
+typedef struct { long double r,i; } complex_longdouble ;
+typedef struct { unsigned char r,g,b; } rgb_byte ;
+#endif
+
+/*---------------------------------------------------------------------------*/
+/* INTERPRETATION OF VOXEL DATA:
+ ----------------------------
+ The intent_code field can be used to indicate that the voxel data has
+ some particular meaning. In particular, a large number of codes is
+ given to indicate that the the voxel data should be interpreted as
+ being drawn from a given probability distribution.
+
+ VECTOR-VALUED DATASETS:
+ ----------------------
+ The 5th dimension of the dataset, if present (i.e., dim[0]=5 and
+ dim[5] > 1), contains multiple values (e.g., a vector) to be stored
+ at each spatiotemporal location. For example, the header values
+ - dim[0] = 5
+ - dim[1] = 64
+ - dim[2] = 64
+ - dim[3] = 20
+ - dim[4] = 1 (indicates no time axis)
+ - dim[5] = 3
+ - datatype = DT_FLOAT
+ - intent_code = NIFTI_INTENT_VECTOR
+ mean that this dataset should be interpreted as a 3D volume (64x64x20),
+ with a 3-vector of floats defined at each point in the 3D grid.
+
+ A program reading a dataset with a 5th dimension may want to reformat
+ the image data to store each voxels' set of values together in a struct
+ or array. This programming detail, however, is beyond the scope of the
+ NIFTI-1 file specification! Uses of dimensions 6 and 7 are also not
+ specified here.
+
+ STATISTICAL PARAMETRIC DATASETS (i.e., SPMs):
+ --------------------------------------------
+ Values of intent_code from NIFTI_FIRST_STATCODE to NIFTI_LAST_STATCODE
+ (inclusive) indicate that the numbers in the dataset should be interpreted
+ as being drawn from a given distribution. Most such distributions have
+ auxiliary parameters (e.g., NIFTI_INTENT_TTEST has 1 DOF parameter).
+
+ If the dataset DOES NOT have a 5th dimension, then the auxiliary parameters
+ are the same for each voxel, and are given in header fields intent_p1,
+ intent_p2, and intent_p3.
+
+ If the dataset DOES have a 5th dimension, then the auxiliary parameters
+ are different for each voxel. For example, the header values
+ - dim[0] = 5
+ - dim[1] = 128
+ - dim[2] = 128
+ - dim[3] = 1 (indicates a single slice)
+ - dim[4] = 1 (indicates no time axis)
+ - dim[5] = 2
+ - datatype = DT_FLOAT
+ - intent_code = NIFTI_INTENT_TTEST
+ mean that this is a 2D dataset (128x128) of t-statistics, with the
+ t-statistic being in the first "plane" of data and the degrees-of-freedom
+ parameter being in the second "plane" of data.
+
+ If the dataset 5th dimension is used to store the voxel-wise statistical
+ parameters, then dim[5] must be 1 plus the number of parameters required
+ by that distribution (e.g., intent_code=NIFTI_INTENT_TTEST implies dim[5]
+ must be 2, as in the example just above).
+
+ Note: intent_code values 2..10 are compatible with AFNI 1.5x (which is
+ why there is no code with value=1, which is obsolescent in AFNI).
+
+ OTHER INTENTIONS:
+ ----------------
+ The purpose of the intent_* fields is to help interpret the values
+ stored in the dataset. Some non-statistical values for intent_code
+ and conventions are provided for storing other complex data types.
+
+ The intent_name field provides space for a 15 character (plus 0 byte)
+ 'name' string for the type of data stored. Examples:
+ - intent_code = NIFTI_INTENT_ESTIMATE; intent_name = "T1";
+ could be used to signify that the voxel values are estimates of the
+ NMR parameter T1.
+ - intent_code = NIFTI_INTENT_TTEST; intent_name = "House";
+ could be used to signify that the voxel values are t-statistics
+ for the significance of 'activation' response to a House stimulus.
+ - intent_code = NIFTI_INTENT_DISPVECT; intent_name = "ToMNI152";
+ could be used to signify that the voxel values are a displacement
+ vector that transforms each voxel (x,y,z) location to the
+ corresponding location in the MNI152 standard brain.
+ - intent_code = NIFTI_INTENT_SYMMATRIX; intent_name = "DTI";
+ could be used to signify that the voxel values comprise a diffusion
+ tensor image.
+
+ If no data name is implied or needed, intent_name[0] should be set to 0.
+-----------------------------------------------------------------------------*/
+
+ /*! default: no intention is indicated in the header. */
+
+#define NIFTI_INTENT_NONE 0
+
+ /*-------- These codes are for probability distributions ---------------*/
+ /* Most distributions have a number of parameters,
+ below denoted by p1, p2, and p3, and stored in
+ - intent_p1, intent_p2, intent_p3 if dataset doesn't have 5th dimension
+ - image data array if dataset does have 5th dimension
+
+ Functions to compute with many of the distributions below can be found
+ in the CDF library from U Texas.
+
+ Formulas for and discussions of these distributions can be found in the
+ following books:
+
+ [U] Univariate Discrete Distributions,
+ NL Johnson, S Kotz, AW Kemp.
+
+ [C1] Continuous Univariate Distributions, vol. 1,
+ NL Johnson, S Kotz, N Balakrishnan.
+
+ [C2] Continuous Univariate Distributions, vol. 2,
+ NL Johnson, S Kotz, N Balakrishnan. */
+ /*----------------------------------------------------------------------*/
+
+ /*! [C2, chap 32] Correlation coefficient R (1 param):
+ p1 = degrees of freedom
+ R/sqrt(1-R*R) is t-distributed with p1 DOF. */
+
+/*! \defgroup NIFTI1_INTENT_CODES
+ \brief nifti1 intent codes, to describe intended meaning of dataset contents
+ @{
+ */
+#define NIFTI_INTENT_CORREL 2
+
+ /*! [C2, chap 28] Student t statistic (1 param): p1 = DOF. */
+
+#define NIFTI_INTENT_TTEST 3
+
+ /*! [C2, chap 27] Fisher F statistic (2 params):
+ p1 = numerator DOF, p2 = denominator DOF. */
+
+#define NIFTI_INTENT_FTEST 4
+
+ /*! [C1, chap 13] Standard normal (0 params): Density = N(0,1). */
+
+#define NIFTI_INTENT_ZSCORE 5
+
+ /*! [C1, chap 18] Chi-squared (1 param): p1 = DOF.
+ Density(x) proportional to exp(-x/2) * x^(p1/2-1). */
+
+#define NIFTI_INTENT_CHISQ 6
+
+ /*! [C2, chap 25] Beta distribution (2 params): p1=a, p2=b.
+ Density(x) proportional to x^(a-1) * (1-x)^(b-1). */
+
+#define NIFTI_INTENT_BETA 7
+
+ /*! [U, chap 3] Binomial distribution (2 params):
+ p1 = number of trials, p2 = probability per trial.
+ Prob(x) = (p1 choose x) * p2^x * (1-p2)^(p1-x), for x=0,1,...,p1. */
+
+#define NIFTI_INTENT_BINOM 8
+
+ /*! [C1, chap 17] Gamma distribution (2 params):
+ p1 = shape, p2 = scale.
+ Density(x) proportional to x^(p1-1) * exp(-p2*x). */
+
+#define NIFTI_INTENT_GAMMA 9
+
+ /*! [U, chap 4] Poisson distribution (1 param): p1 = mean.
+ Prob(x) = exp(-p1) * p1^x / x! , for x=0,1,2,.... */
+
+#define NIFTI_INTENT_POISSON 10
+
+ /*! [C1, chap 13] Normal distribution (2 params):
+ p1 = mean, p2 = standard deviation. */
+
+#define NIFTI_INTENT_NORMAL 11
+
+ /*! [C2, chap 30] Noncentral F statistic (3 params):
+ p1 = numerator DOF, p2 = denominator DOF,
+ p3 = numerator noncentrality parameter. */
+
+#define NIFTI_INTENT_FTEST_NONC 12
+
+ /*! [C2, chap 29] Noncentral chi-squared statistic (2 params):
+ p1 = DOF, p2 = noncentrality parameter. */
+
+#define NIFTI_INTENT_CHISQ_NONC 13
+
+ /*! [C2, chap 23] Logistic distribution (2 params):
+ p1 = location, p2 = scale.
+ Density(x) proportional to sech^2((x-p1)/(2*p2)). */
+
+#define NIFTI_INTENT_LOGISTIC 14
+
+ /*! [C2, chap 24] Laplace distribution (2 params):
+ p1 = location, p2 = scale.
+ Density(x) proportional to exp(-abs(x-p1)/p2). */
+
+#define NIFTI_INTENT_LAPLACE 15
+
+ /*! [C2, chap 26] Uniform distribution: p1 = lower end, p2 = upper end. */
+
+#define NIFTI_INTENT_UNIFORM 16
+
+ /*! [C2, chap 31] Noncentral t statistic (2 params):
+ p1 = DOF, p2 = noncentrality parameter. */
+
+#define NIFTI_INTENT_TTEST_NONC 17
+
+ /*! [C1, chap 21] Weibull distribution (3 params):
+ p1 = location, p2 = scale, p3 = power.
+ Density(x) proportional to
+ ((x-p1)/p2)^(p3-1) * exp(-((x-p1)/p2)^p3) for x > p1. */
+
+#define NIFTI_INTENT_WEIBULL 18
+
+ /*! [C1, chap 18] Chi distribution (1 param): p1 = DOF.
+ Density(x) proportional to x^(p1-1) * exp(-x^2/2) for x > 0.
+ p1 = 1 = 'half normal' distribution
+ p1 = 2 = Rayleigh distribution
+ p1 = 3 = Maxwell-Boltzmann distribution. */
+
+#define NIFTI_INTENT_CHI 19
+
+ /*! [C1, chap 15] Inverse Gaussian (2 params):
+ p1 = mu, p2 = lambda
+ Density(x) proportional to
+ exp(-p2*(x-p1)^2/(2*p1^2*x)) / x^3 for x > 0. */
+
+#define NIFTI_INTENT_INVGAUSS 20
+
+ /*! [C2, chap 22] Extreme value type I (2 params):
+ p1 = location, p2 = scale
+ cdf(x) = exp(-exp(-(x-p1)/p2)). */
+
+#define NIFTI_INTENT_EXTVAL 21
+
+ /*! Data is a 'p-value' (no params). */
+
+#define NIFTI_INTENT_PVAL 22
+
+ /*! Data is ln(p-value) (no params).
+ To be safe, a program should compute p = exp(-abs(this_value)).
+ The nifti_stats.c library returns this_value
+ as positive, so that this_value = -log(p). */
+
+
+#define NIFTI_INTENT_LOGPVAL 23
+
+ /*! Data is log10(p-value) (no params).
+ To be safe, a program should compute p = pow(10.,-abs(this_value)).
+ The nifti_stats.c library returns this_value
+ as positive, so that this_value = -log10(p). */
+
+#define NIFTI_INTENT_LOG10PVAL 24
+
+ /*! Smallest intent_code that indicates a statistic. */
+
+#define NIFTI_FIRST_STATCODE 2
+
+ /*! Largest intent_code that indicates a statistic. */
+
+#define NIFTI_LAST_STATCODE 24
+
+ /*---------- these values for intent_code aren't for statistics ----------*/
+
+ /*! To signify that the value at each voxel is an estimate
+ of some parameter, set intent_code = NIFTI_INTENT_ESTIMATE.
+ The name of the parameter may be stored in intent_name. */
+
+#define NIFTI_INTENT_ESTIMATE 1001
+
+ /*! To signify that the value at each voxel is an index into
+ some set of labels, set intent_code = NIFTI_INTENT_LABEL.
+ The filename with the labels may stored in aux_file. */
+
+#define NIFTI_INTENT_LABEL 1002
+
+ /*! To signify that the value at each voxel is an index into the
+ NeuroNames labels set, set intent_code = NIFTI_INTENT_NEURONAME. */
+
+#define NIFTI_INTENT_NEURONAME 1003
+
+ /*! To store an M x N matrix at each voxel:
+ - dataset must have a 5th dimension (dim[0]=5 and dim[5]>1)
+ - intent_code must be NIFTI_INTENT_GENMATRIX
+ - dim[5] must be M*N
+ - intent_p1 must be M (in float format)
+ - intent_p2 must be N (ditto)
+ - the matrix values A[i][[j] are stored in row-order:
+ - A[0][0] A[0][1] ... A[0][N-1]
+ - A[1][0] A[1][1] ... A[1][N-1]
+ - etc., until
+ - A[M-1][0] A[M-1][1] ... A[M-1][N-1] */
+
+#define NIFTI_INTENT_GENMATRIX 1004
+
+ /*! To store an NxN symmetric matrix at each voxel:
+ - dataset must have a 5th dimension
+ - intent_code must be NIFTI_INTENT_SYMMATRIX
+ - dim[5] must be N*(N+1)/2
+ - intent_p1 must be N (in float format)
+ - the matrix values A[i][[j] are stored in row-order:
+ - A[0][0]
+ - A[1][0] A[1][1]
+ - A[2][0] A[2][1] A[2][2]
+ - etc.: row-by-row */
+
+#define NIFTI_INTENT_SYMMATRIX 1005
+
+ /*! To signify that the vector value at each voxel is to be taken
+ as a displacement field or vector:
+ - dataset must have a 5th dimension
+ - intent_code must be NIFTI_INTENT_DISPVECT
+ - dim[5] must be the dimensionality of the displacment
+ vector (e.g., 3 for spatial displacement, 2 for in-plane) */
+
+#define NIFTI_INTENT_DISPVECT 1006 /* specifically for displacements */
+#define NIFTI_INTENT_VECTOR 1007 /* for any other type of vector */
+
+ /*! To signify that the vector value at each voxel is really a
+ spatial coordinate (e.g., the vertices or nodes of a surface mesh):
+ - dataset must have a 5th dimension
+ - intent_code must be NIFTI_INTENT_POINTSET
+ - dim[0] = 5
+ - dim[1] = number of points
+ - dim[2] = dim[3] = dim[4] = 1
+ - dim[5] must be the dimensionality of space (e.g., 3 => 3D space).
+ - intent_name may describe the object these points come from
+ (e.g., "pial", "gray/white" , "EEG", "MEG"). */
+
+#define NIFTI_INTENT_POINTSET 1008
+
+ /*! To signify that the vector value at each voxel is really a triple
+ of indexes (e.g., forming a triangle) from a pointset dataset:
+ - dataset must have a 5th dimension
+ - intent_code must be NIFTI_INTENT_TRIANGLE
+ - dim[0] = 5
+ - dim[1] = number of triangles
+ - dim[2] = dim[3] = dim[4] = 1
+ - dim[5] = 3
+ - datatype should be an integer type (preferably DT_INT32)
+ - the data values are indexes (0,1,...) into a pointset dataset. */
+
+#define NIFTI_INTENT_TRIANGLE 1009
+
+ /*! To signify that the vector value at each voxel is a quaternion:
+ - dataset must have a 5th dimension
+ - intent_code must be NIFTI_INTENT_QUATERNION
+ - dim[0] = 5
+ - dim[5] = 4
+ - datatype should be a floating point type */
+
+#define NIFTI_INTENT_QUATERNION 1010
+
+ /*! Dimensionless value - no params - although, as in _ESTIMATE
+ the name of the parameter may be stored in intent_name. */
+
+#define NIFTI_INTENT_DIMLESS 1011
+/* @} */
+
+/*---------------------------------------------------------------------------*/
+/* 3D IMAGE (VOLUME) ORIENTATION AND LOCATION IN SPACE:
+ ---------------------------------------------------
+ There are 3 different methods by which continuous coordinates can
+ attached to voxels. The discussion below emphasizes 3D volumes, and
+ the continuous coordinates are referred to as (x,y,z). The voxel
+ index coordinates (i.e., the array indexes) are referred to as (i,j,k),
+ with valid ranges:
+ i = 0 .. dim[1]-1
+ j = 0 .. dim[2]-1 (if dim[0] >= 2)
+ k = 0 .. dim[3]-1 (if dim[0] >= 3)
+ The (x,y,z) coordinates refer to the CENTER of a voxel. In methods
+ 2 and 3, the (x,y,z) axes refer to a subject-based coordinate system,
+ with
+ +x = Right +y = Anterior +z = Superior.
+ This is a right-handed coordinate system. However, the exact direction
+ these axes point with respect to the subject depends on qform_code
+ (Method 2) and sform_code (Method 3).
+
+ N.B.: The i index varies most rapidly, j index next, k index slowest.
+ Thus, voxel (i,j,k) is stored starting at location
+ (i + j*dim[1] + k*dim[1]*dim[2]) * (bitpix/8)
+ into the dataset array.
+
+ N.B.: The ANALYZE 7.5 coordinate system is
+ +x = Left +y = Anterior +z = Superior
+ which is a left-handed coordinate system. This backwardness is
+ too difficult to tolerate, so this NIFTI-1 standard specifies the
+ coordinate order which is most common in functional neuroimaging.
+
+ N.B.: The 3 methods below all give the locations of the voxel centers
+ in the (x,y,z) coordinate system. In many cases, programs will wish
+ to display image data on some other grid. In such a case, the program
+ will need to convert its desired (x,y,z) values into (i,j,k) values
+ in order to extract (or interpolate) the image data. This operation
+ would be done with the inverse transformation to those described below.
+
+ N.B.: Method 2 uses a factor 'qfac' which is either -1 or 1; qfac is
+ stored in the otherwise unused pixdim[0]. If pixdim[0]=0.0 (which
+ should not occur), we take qfac=1. Of course, pixdim[0] is only used
+ when reading a NIFTI-1 header, not when reading an ANALYZE 7.5 header.
+
+ N.B.: The units of (x,y,z) can be specified using the xyzt_units field.
+
+ METHOD 1 (the "old" way, used only when qform_code = 0):
+ -------------------------------------------------------
+ The coordinate mapping from (i,j,k) to (x,y,z) is the ANALYZE
+ 7.5 way. This is a simple scaling relationship:
+
+ x = pixdim[1] * i
+ y = pixdim[2] * j
+ z = pixdim[3] * k
+
+ No particular spatial orientation is attached to these (x,y,z)
+ coordinates. (NIFTI-1 does not have the ANALYZE 7.5 orient field,
+ which is not general and is often not set properly.) This method
+ is not recommended, and is present mainly for compatibility with
+ ANALYZE 7.5 files.
+
+ METHOD 2 (used when qform_code > 0, which should be the "normal" case):
+ ---------------------------------------------------------------------
+ The (x,y,z) coordinates are given by the pixdim[] scales, a rotation
+ matrix, and a shift. This method is intended to represent
+ "scanner-anatomical" coordinates, which are often embedded in the
+ image header (e.g., DICOM fields (0020,0032), (0020,0037), (0028,0030),
+ and (0018,0050)), and represent the nominal orientation and location of
+ the data. This method can also be used to represent "aligned"
+ coordinates, which would typically result from some post-acquisition
+ alignment of the volume to a standard orientation (e.g., the same
+ subject on another day, or a rigid rotation to true anatomical
+ orientation from the tilted position of the subject in the scanner).
+ The formula for (x,y,z) in terms of header parameters and (i,j,k) is:
+
+ [ x ] [ R11 R12 R13 ] [ pixdim[1] * i ] [ qoffset_x ]
+ [ y ] = [ R21 R22 R23 ] [ pixdim[2] * j ] + [ qoffset_y ]
+ [ z ] [ R31 R32 R33 ] [ qfac * pixdim[3] * k ] [ qoffset_z ]
+
+ The qoffset_* shifts are in the NIFTI-1 header. Note that the center
+ of the (i,j,k)=(0,0,0) voxel (first value in the dataset array) is
+ just (x,y,z)=(qoffset_x,qoffset_y,qoffset_z).
+
+ The rotation matrix R is calculated from the quatern_* parameters.
+ This calculation is described below.
+
+ The scaling factor qfac is either 1 or -1. The rotation matrix R
+ defined by the quaternion parameters is "proper" (has determinant 1).
+ This may not fit the needs of the data; for example, if the image
+ grid is
+ i increases from Left-to-Right
+ j increases from Anterior-to-Posterior
+ k increases from Inferior-to-Superior
+ Then (i,j,k) is a left-handed triple. In this example, if qfac=1,
+ the R matrix would have to be
+
+ [ 1 0 0 ]
+ [ 0 -1 0 ] which is "improper" (determinant = -1).
+ [ 0 0 1 ]
+
+ If we set qfac=-1, then the R matrix would be
+
+ [ 1 0 0 ]
+ [ 0 -1 0 ] which is proper.
+ [ 0 0 -1 ]
+
+ This R matrix is represented by quaternion [a,b,c,d] = [0,1,0,0]
+ (which encodes a 180 degree rotation about the x-axis).
+
+ METHOD 3 (used when sform_code > 0):
+ -----------------------------------
+ The (x,y,z) coordinates are given by a general affine transformation
+ of the (i,j,k) indexes:
+
+ x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
+ y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
+ z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
+
+ The srow_* vectors are in the NIFTI_1 header. Note that no use is
+ made of pixdim[] in this method.
+
+ WHY 3 METHODS?
+ --------------
+ Method 1 is provided only for backwards compatibility. The intention
+ is that Method 2 (qform_code > 0) represents the nominal voxel locations
+ as reported by the scanner, or as rotated to some fiducial orientation and
+ location. Method 3, if present (sform_code > 0), is to be used to give
+ the location of the voxels in some standard space. The sform_code
+ indicates which standard space is present. Both methods 2 and 3 can be
+ present, and be useful in different contexts (method 2 for displaying the
+ data on its original grid; method 3 for displaying it on a standard grid).
+
+ In this scheme, a dataset would originally be set up so that the
+ Method 2 coordinates represent what the scanner reported. Later,
+ a registration to some standard space can be computed and inserted
+ in the header. Image display software can use either transform,
+ depending on its purposes and needs.
+
+ In Method 2, the origin of coordinates would generally be whatever
+ the scanner origin is; for example, in MRI, (0,0,0) is the center
+ of the gradient coil.
+
+ In Method 3, the origin of coordinates would depend on the value
+ of sform_code; for example, for the Talairach coordinate system,
+ (0,0,0) corresponds to the Anterior Commissure.
+
+ QUATERNION REPRESENTATION OF ROTATION MATRIX (METHOD 2)
+ -------------------------------------------------------
+ The orientation of the (x,y,z) axes relative to the (i,j,k) axes
+ in 3D space is specified using a unit quaternion [a,b,c,d], where
+ a*a+b*b+c*c+d*d=1. The (b,c,d) values are all that is needed, since
+ we require that a = sqrt(1.0-(b*b+c*c+d*d)) be nonnegative. The (b,c,d)
+ values are stored in the (quatern_b,quatern_c,quatern_d) fields.
+
+ The quaternion representation is chosen for its compactness in
+ representing rotations. The (proper) 3x3 rotation matrix that
+ corresponds to [a,b,c,d] is
+
+ [ a*a+b*b-c*c-d*d 2*b*c-2*a*d 2*b*d+2*a*c ]
+ R = [ 2*b*c+2*a*d a*a+c*c-b*b-d*d 2*c*d-2*a*b ]
+ [ 2*b*d-2*a*c 2*c*d+2*a*b a*a+d*d-c*c-b*b ]
+
+ [ R11 R12 R13 ]
+ = [ R21 R22 R23 ]
+ [ R31 R32 R33 ]
+
+ If (p,q,r) is a unit 3-vector, then rotation of angle h about that
+ direction is represented by the quaternion
+
+ [a,b,c,d] = [cos(h/2), p*sin(h/2), q*sin(h/2), r*sin(h/2)].
+
+ Requiring a >= 0 is equivalent to requiring -Pi <= h <= Pi. (Note that
+ [-a,-b,-c,-d] represents the same rotation as [a,b,c,d]; there are 2
+ quaternions that can be used to represent a given rotation matrix R.)
+ To rotate a 3-vector (x,y,z) using quaternions, we compute the
+ quaternion product
+
+ [0,x',y',z'] = [a,b,c,d] * [0,x,y,z] * [a,-b,-c,-d]
+
+ which is equivalent to the matrix-vector multiply
+
+ [ x' ] [ x ]
+ [ y' ] = R [ y ] (equivalence depends on a*a+b*b+c*c+d*d=1)
+ [ z' ] [ z ]
+
+ Multiplication of 2 quaternions is defined by the following:
+
+ [a,b,c,d] = a*1 + b*I + c*J + d*K
+ where
+ I*I = J*J = K*K = -1 (I,J,K are square roots of -1)
+ I*J = K J*K = I K*I = J
+ J*I = -K K*J = -I I*K = -J (not commutative!)
+ For example
+ [a,b,0,0] * [0,0,0,1] = [0,0,-b,a]
+ since this expands to
+ (a+b*I)*(K) = (a*K+b*I*K) = (a*K-b*J).
+
+ The above formula shows how to go from quaternion (b,c,d) to
+ rotation matrix and direction cosines. Conversely, given R,
+ we can compute the fields for the NIFTI-1 header by
+
+ a = 0.5 * sqrt(1+R11+R22+R33) (not stored)
+ b = 0.25 * (R32-R23) / a => quatern_b
+ c = 0.25 * (R13-R31) / a => quatern_c
+ d = 0.25 * (R21-R12) / a => quatern_d
+
+ If a=0 (a 180 degree rotation), alternative formulas are needed.
+ See the nifti1_io.c function mat44_to_quatern() for an implementation
+ of the various cases in converting R to [a,b,c,d].
+
+ Note that R-transpose (= R-inverse) would lead to the quaternion
+ [a,-b,-c,-d].
+
+ The choice to specify the qoffset_x (etc.) values in the final
+ coordinate system is partly to make it easy to convert DICOM images to
+ this format. The DICOM attribute "Image Position (Patient)" (0020,0032)
+ stores the (Xd,Yd,Zd) coordinates of the center of the first voxel.
+ Here, (Xd,Yd,Zd) refer to DICOM coordinates, and Xd=-x, Yd=-y, Zd=z,
+ where (x,y,z) refers to the NIFTI coordinate system discussed above.
+ (i.e., DICOM +Xd is Left, +Yd is Posterior, +Zd is Superior,
+ whereas +x is Right, +y is Anterior , +z is Superior. )
+ Thus, if the (0020,0032) DICOM attribute is extracted into (px,py,pz), then
+ qoffset_x = -px qoffset_y = -py qoffset_z = pz
+ is a reasonable setting when qform_code=NIFTI_XFORM_SCANNER_ANAT.
+
+ That is, DICOM's coordinate system is 180 degrees rotated about the z-axis
+ from the neuroscience/NIFTI coordinate system. To transform between DICOM
+ and NIFTI, you just have to negate the x- and y-coordinates.
+
+ The DICOM attribute (0020,0037) "Image Orientation (Patient)" gives the
+ orientation of the x- and y-axes of the image data in terms of 2 3-vectors.
+ The first vector is a unit vector along the x-axis, and the second is
+ along the y-axis. If the (0020,0037) attribute is extracted into the
+ value (xa,xb,xc,ya,yb,yc), then the first two columns of the R matrix
+ would be
+ [ -xa -ya ]
+ [ -xb -yb ]
+ [ xc yc ]
+ The negations are because DICOM's x- and y-axes are reversed relative
+ to NIFTI's. The third column of the R matrix gives the direction of
+ displacement (relative to the subject) along the slice-wise direction.
+ This orientation is not encoded in the DICOM standard in a simple way;
+ DICOM is mostly concerned with 2D images. The third column of R will be
+ either the cross-product of the first 2 columns or its negative. It is
+ possible to infer the sign of the 3rd column by examining the coordinates
+ in DICOM attribute (0020,0032) "Image Position (Patient)" for successive
+ slices. However, this method occasionally fails for reasons that I
+ (RW Cox) do not understand.
+-----------------------------------------------------------------------------*/
+
+ /* [qs]form_code value: */ /* x,y,z coordinate system refers to: */
+ /*-----------------------*/ /*---------------------------------------*/
+
+/*! \defgroup NIFTI1_XFORM_CODES
+ \brief nifti1 xform codes to describe the "standard" coordinate system
+ @{
+ */
+ /*! Arbitrary coordinates (Method 1). */
+
+#define NIFTI_XFORM_UNKNOWN 0
+
+ /*! Scanner-based anatomical coordinates */
+
+#define NIFTI_XFORM_SCANNER_ANAT 1
+
+ /*! Coordinates aligned to another file's,
+ or to anatomical "truth". */
+
+#define NIFTI_XFORM_ALIGNED_ANAT 2
+
+ /*! Coordinates aligned to Talairach-
+ Tournoux Atlas; (0,0,0)=AC, etc. */
+
+#define NIFTI_XFORM_TALAIRACH 3
+
+ /*! MNI 152 normalized coordinates. */
+
+#define NIFTI_XFORM_MNI_152 4
+/* @} */
+
+/*---------------------------------------------------------------------------*/
+/* UNITS OF SPATIAL AND TEMPORAL DIMENSIONS:
+ ----------------------------------------
+ The codes below can be used in xyzt_units to indicate the units of pixdim.
+ As noted earlier, dimensions 1,2,3 are for x,y,z; dimension 4 is for
+ time (t).
+ - If dim[4]=1 or dim[0] < 4, there is no time axis.
+ - A single time series (no space) would be specified with
+ - dim[0] = 4 (for scalar data) or dim[0] = 5 (for vector data)
+ - dim[1] = dim[2] = dim[3] = 1
+ - dim[4] = number of time points
+ - pixdim[4] = time step
+ - xyzt_units indicates units of pixdim[4]
+ - dim[5] = number of values stored at each time point
+
+ Bits 0..2 of xyzt_units specify the units of pixdim[1..3]
+ (e.g., spatial units are values 1..7).
+ Bits 3..5 of xyzt_units specify the units of pixdim[4]
+ (e.g., temporal units are multiples of 8).
+
+ This compression of 2 distinct concepts into 1 byte is due to the
+ limited space available in the 348 byte ANALYZE 7.5 header. The
+ macros XYZT_TO_SPACE and XYZT_TO_TIME can be used to mask off the
+ undesired bits from the xyzt_units fields, leaving "pure" space
+ and time codes. Inversely, the macro SPACE_TIME_TO_XYZT can be
+ used to assemble a space code (0,1,2,...,7) with a time code
+ (0,8,16,32,...,56) into the combined value for xyzt_units.
+
+ Note that codes are provided to indicate the "time" axis units are
+ actually frequency in Hertz (_HZ), in part-per-million (_PPM)
+ or in radians-per-second (_RADS).
+
+ The toffset field can be used to indicate a nonzero start point for
+ the time axis. That is, time point #m is at t=toffset+m*pixdim[4]
+ for m=0..dim[4]-1.
+-----------------------------------------------------------------------------*/
+
+/*! \defgroup NIFTI1_UNITS
+ \brief nifti1 units codes to describe the unit of measurement for
+ each dimension of the dataset
+ @{
+ */
+ /*! NIFTI code for unspecified units. */
+#define NIFTI_UNITS_UNKNOWN 0
+
+ /** Space codes are multiples of 1. **/
+ /*! NIFTI code for meters. */
+#define NIFTI_UNITS_METER 1
+ /*! NIFTI code for millimeters. */
+#define NIFTI_UNITS_MM 2
+ /*! NIFTI code for micrometers. */
+#define NIFTI_UNITS_MICRON 3
+
+ /** Time codes are multiples of 8. **/
+ /*! NIFTI code for seconds. */
+#define NIFTI_UNITS_SEC 8
+ /*! NIFTI code for milliseconds. */
+#define NIFTI_UNITS_MSEC 16
+ /*! NIFTI code for microseconds. */
+#define NIFTI_UNITS_USEC 24
+
+ /*** These units are for spectral data: ***/
+ /*! NIFTI code for Hertz. */
+#define NIFTI_UNITS_HZ 32
+ /*! NIFTI code for ppm. */
+#define NIFTI_UNITS_PPM 40
+ /*! NIFTI code for radians per second. */
+#define NIFTI_UNITS_RADS 48
+/* @} */
+
+#undef XYZT_TO_SPACE
+#undef XYZT_TO_TIME
+#define XYZT_TO_SPACE(xyzt) ( (xyzt) & 0x07 )
+#define XYZT_TO_TIME(xyzt) ( (xyzt) & 0x38 )
+
+#undef SPACE_TIME_TO_XYZT
+#define SPACE_TIME_TO_XYZT(ss,tt) ( (((char)(ss)) & 0x07) \
+ | (((char)(tt)) & 0x38) )
+
+/*---------------------------------------------------------------------------*/
+/* MRI-SPECIFIC SPATIAL AND TEMPORAL INFORMATION:
+ ---------------------------------------------
+ A few fields are provided to store some extra information
+ that is sometimes important when storing the image data
+ from an FMRI time series experiment. (After processing such
+ data into statistical images, these fields are not likely
+ to be useful.)
+
+ { freq_dim } = These fields encode which spatial dimension (1,2, or 3)
+ { phase_dim } = corresponds to which acquisition dimension for MRI data.
+ { slice_dim } =
+ Examples:
+ Rectangular scan multi-slice EPI:
+ freq_dim = 1 phase_dim = 2 slice_dim = 3 (or some permutation)
+ Spiral scan multi-slice EPI:
+ freq_dim = phase_dim = 0 slice_dim = 3
+ since the concepts of frequency- and phase-encoding directions
+ don't apply to spiral scan
+
+ slice_duration = If this is positive, AND if slice_dim is nonzero,
+ indicates the amount of time used to acquire 1 slice.
+ slice_duration*dim[slice_dim] can be less than pixdim[4]
+ with a clustered acquisition method, for example.
+
+ slice_code = If this is nonzero, AND if slice_dim is nonzero, AND
+ if slice_duration is positive, indicates the timing
+ pattern of the slice acquisition. The following codes
+ are defined:
+ NIFTI_SLICE_SEQ_INC == sequential increasing
+ NIFTI_SLICE_SEQ_DEC == sequential decreasing
+ NIFTI_SLICE_ALT_INC == alternating increasing
+ NIFTI_SLICE_ALT_DEC == alternating decreasing
+ NIFTI_SLICE_ALT_INC2 == alternating increasing #2
+ NIFTI_SLICE_ALT_DEC2 == alternating decreasing #2
+ { slice_start } = Indicates the start and end of the slice acquisition
+ { slice_end } = pattern, when slice_code is nonzero. These values
+ are present to allow for the possible addition of
+ "padded" slices at either end of the volume, which
+ don't fit into the slice timing pattern. If there
+ are no padding slices, then slice_start=0 and
+ slice_end=dim[slice_dim]-1 are the correct values.
+ For these values to be meaningful, slice_start must
+ be non-negative and slice_end must be greater than
+ slice_start. Otherwise, they should be ignored.
+
+ The following table indicates the slice timing pattern, relative to
+ time=0 for the first slice acquired, for some sample cases. Here,
+ dim[slice_dim]=7 (there are 7 slices, labeled 0..6), slice_duration=0.1,
+ and slice_start=1, slice_end=5 (1 padded slice on each end).
+
+ slice
+ index SEQ_INC SEQ_DEC ALT_INC ALT_DEC ALT_INC2 ALT_DEC2
+ 6 : n/a n/a n/a n/a n/a n/a n/a = not applicable
+ 5 : 0.4 0.0 0.2 0.0 0.4 0.2 (slice time offset
+ 4 : 0.3 0.1 0.4 0.3 0.1 0.0 doesn't apply to
+ 3 : 0.2 0.2 0.1 0.1 0.3 0.3 slices outside
+ 2 : 0.1 0.3 0.3 0.4 0.0 0.1 the range
+ 1 : 0.0 0.4 0.0 0.2 0.2 0.4 slice_start ..
+ 0 : n/a n/a n/a n/a n/a n/a slice_end)
+
+ The SEQ slice_codes are sequential ordering (uncommon but not unknown),
+ either increasing in slice number or decreasing (INC or DEC), as
+ illustrated above.
+
+ The ALT slice codes are alternating ordering. The 'standard' way for
+ these to operate (without the '2' on the end) is for the slice timing
+ to start at the edge of the slice_start .. slice_end group (at slice_start
+ for INC and at slice_end for DEC). For the 'ALT_*2' slice_codes, the
+ slice timing instead starts at the first slice in from the edge (at
+ slice_start+1 for INC2 and at slice_end-1 for DEC2). This latter
+ acquisition scheme is found on some Siemens scanners.
+
+ The fields freq_dim, phase_dim, slice_dim are all squished into the single
+ byte field dim_info (2 bits each, since the values for each field are
+ limited to the range 0..3). This unpleasantness is due to lack of space
+ in the 348 byte allowance.
+
+ The macros DIM_INFO_TO_FREQ_DIM, DIM_INFO_TO_PHASE_DIM, and
+ DIM_INFO_TO_SLICE_DIM can be used to extract these values from the
+ dim_info byte.
+
+ The macro FPS_INTO_DIM_INFO can be used to put these 3 values
+ into the dim_info byte.
+-----------------------------------------------------------------------------*/
+
+#undef DIM_INFO_TO_FREQ_DIM
+#undef DIM_INFO_TO_PHASE_DIM
+#undef DIM_INFO_TO_SLICE_DIM
+
+#define DIM_INFO_TO_FREQ_DIM(di) ( ((di) ) & 0x03 )
+#define DIM_INFO_TO_PHASE_DIM(di) ( ((di) >> 2) & 0x03 )
+#define DIM_INFO_TO_SLICE_DIM(di) ( ((di) >> 4) & 0x03 )
+
+#undef FPS_INTO_DIM_INFO
+#define FPS_INTO_DIM_INFO(fd,pd,sd) ( ( ( ((char)(fd)) & 0x03) ) | \
+ ( ( ((char)(pd)) & 0x03) << 2 ) | \
+ ( ( ((char)(sd)) & 0x03) << 4 ) )
+
+/*! \defgroup NIFTI1_SLICE_ORDER
+ \brief nifti1 slice order codes, describing the acquisition order
+ of the slices
+ @{
+ */
+#define NIFTI_SLICE_UNKNOWN 0
+#define NIFTI_SLICE_SEQ_INC 1
+#define NIFTI_SLICE_SEQ_DEC 2
+#define NIFTI_SLICE_ALT_INC 3
+#define NIFTI_SLICE_ALT_DEC 4
+#define NIFTI_SLICE_ALT_INC2 5 /* 05 May 2005: RWCox */
+#define NIFTI_SLICE_ALT_DEC2 6 /* 05 May 2005: RWCox */
+/* @} */
+
+/*---------------------------------------------------------------------------*/
+/* UNUSED FIELDS:
+ -------------
+ Some of the ANALYZE 7.5 fields marked as ++UNUSED++ may need to be set
+ to particular values for compatibility with other programs. The issue
+ of interoperability of ANALYZE 7.5 files is a murky one -- not all
+ programs require exactly the same set of fields. (Unobscuring this
+ murkiness is a principal motivation behind NIFTI-1.)
+
+ Some of the fields that may need to be set for other (non-NIFTI aware)
+ software to be happy are:
+
+ extents dbh.h says this should be 16384
+ regular dbh.h says this should be the character 'r'
+ glmin, } dbh.h says these values should be the min and max voxel
+ glmax } values for the entire dataset
+
+ It is best to initialize ALL fields in the NIFTI-1 header to 0
+ (e.g., with calloc()), then fill in what is needed.
+-----------------------------------------------------------------------------*/
+
+/*---------------------------------------------------------------------------*/
+/* MISCELLANEOUS C MACROS
+-----------------------------------------------------------------------------*/
+
+/*.................*/
+/*! Given a nifti_1_header struct, check if it has a good magic number.
+ Returns NIFTI version number (1..9) if magic is good, 0 if it is not. */
+
+#define NIFTI_VERSION(h) \
+ ( ( (h).magic[0]=='n' && (h).magic[3]=='\0' && \
+ ( (h).magic[1]=='i' || (h).magic[1]=='+' ) && \
+ ( (h).magic[2]>='1' && (h).magic[2]<='9' ) ) \
+ ? (h).magic[2]-'0' : 0 )
+
+/*.................*/
+/*! Check if a nifti_1_header struct says if the data is stored in the
+ same file or in a separate file. Returns 1 if the data is in the same
+ file as the header, 0 if it is not. */
+
+#define NIFTI_ONEFILE(h) ( (h).magic[1] == '+' )
+
+/*.................*/
+/*! Check if a nifti_1_header struct needs to be byte swapped.
+ Returns 1 if it needs to be swapped, 0 if it does not. */
+
+#define NIFTI_NEEDS_SWAP(h) ( (h).dim[0] < 0 || (h).dim[0] > 7 )
+
+/*.................*/
+/*! Check if a nifti_1_header struct contains a 5th (vector) dimension.
+ Returns size of 5th dimension if > 1, returns 0 otherwise. */
+
+#define NIFTI_5TH_DIM(h) ( ((h).dim[0]>4 && (h).dim[5]>1) ? (h).dim[5] : 0 )
+
+/*****************************************************************************/
+
+/*=================*/
+#ifdef __cplusplus
+}
+#endif
+/*=================*/
+
+#endif /* _NIFTI_HEADER_ */
diff --git a/Utilities/ITK/Utilities/nifti/niftilib/nifti1_io.c b/Utilities/ITK/Utilities/nifti/niftilib/nifti1_io.c
new file mode 100644
index 0000000000000000000000000000000000000000..4831386c6244fcce0555a7f850443901f1c0ab7c
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/niftilib/nifti1_io.c
@@ -0,0 +1,6375 @@
+#define _NIFTI1_IO_C_
+
+#include "nifti1_io.h" /* typedefs, prototypes, macros, etc. */
+
+/*****===================================================================*****/
+/***** Sample functions to deal with NIFTI-1 and ANALYZE files *****/
+/*****...................................................................*****/
+/***** This code is released to the public domain. *****/
+/*****...................................................................*****/
+/***** Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH *****/
+/***** Date: August 2003 *****/
+/*****...................................................................*****/
+/***** Neither the National Institutes of Health (NIH), nor any of its *****/
+/***** employees imply any warranty of usefulness of this software for *****/
+/***** any purpose, and do not assume any liability for damages, *****/
+/***** incidental or otherwise, caused by any use of this document. *****/
+/*****===================================================================*****/
+
+/** \file nifti1_io.c
+ \brief main collection of nifti1 i/o routines
+ - written by Bob Cox, SSCC NIMH
+ - revised by Mark Jenkinson, FMRIB
+ - revised by Rick Reynolds, SSCC, NIMH
+ - revised by Kate Fissell, University of Pittsburgh
+
+ The library history can be viewed via "nifti_tool -nifti_hist".
+ <br>The library version can be viewed via "nifti_tool -nifti_ver".
+ */
+
+/*! global history and version strings, for printing */
+static char * gni_history[] =
+{
+ "----------------------------------------------------------------------\n"
+ "history (of nifti library changes):\n"
+ "\n",
+ "0.0 August, 2003 [rwcox]\n"
+ " (Robert W Cox of the National Institutes of Health, SSCC/DIRP/NIMH)\n"
+ " - initial version\n"
+ "\n",
+ "0.1 July/August, 2004 [Mark Jenkinson]\n"
+ " (FMRIB Centre, University of Oxford, UK)\n"
+ " - Mainly adding low-level IO and changing things to allow gzipped\n"
+ " files to be read and written\n"
+ " - Full backwards compatability should have been maintained\n"
+ "\n",
+ "0.2 16 Nov 2004 [rickr]\n"
+ " (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n"
+ " - included Mark's changes in the AFNI distribution (including znzlib/)\n"
+ " (HAVE_ZLIB is commented out for the standard distribution)\n"
+ " - modified nifti_validfilename() and nifti_makebasename()\n"
+ " - added nifti_find_file_extension()\n"
+ "\n",
+ "0.3 3 Dec 2004 [rickr]\n"
+ " - note: header extensions are not yet checked for\n"
+ " - added formatted history as global string, for printing\n"
+ " - added nifti_disp_lib_hist(), to display the nifti library history\n"
+ " - added nifti_disp_lib_version(), to display the nifti library history\n",
+ " - re-wrote nifti_findhdrname()\n"
+ " o used nifti_find_file_extension()\n"
+ " o changed order of file tests (default is .nii, depends on input)\n"
+ " o free hdrname on failure\n"
+ " - made similar changes to nifti_findimgname()\n"
+ " - check for NULL return from nifti_findhdrname() calls\n",
+ " - removed most of ERREX() macros\n"
+ " - modified nifti_image_read()\n"
+ " o added debug info and error checking (on gni_debug > 0, only)\n"
+ " o fail if workingname is NULL\n"
+ " o check for failure to open header file\n"
+ " o free workingname on failure\n"
+ " o check for failure of nifti_image_load()\n"
+ " o check for failure of nifti_convert_nhdr2nim()\n",
+ " - changed nifti_image_load() to int, and check nifti_read_buffer return\n"
+ " - changed nifti_read_buffer() to fail on short read, and to count float\n"
+ " fixes (to print on debug)\n"
+ " - changed nifti_image_infodump to print to stderr\n"
+ " - updated function header comments, or moved comments above header\n"
+ " - removed const keyword\n"
+ " - added LNI_FERR() macro for error reporting on input files\n"
+ "\n",
+ "0.4 10 Dec 2004 [rickr] - added header extensions\n"
+ " - in nifti1_io.h:\n"
+ " o added num_ext and ext_list to the definition of nifti_image\n"
+ " o made many functions static (more to follow)\n"
+ " o added LNI_MAX_NIA_EXT_LEN, for max nifti_type 3 extension length\n",
+ " - added __DATE__ to version output in nifti_disp_lib_version()\n"
+ " - added nifti_disp_matrix_orient() to print orientation information\n"
+ " - added '.nia' as a valid file extension in nifti_find_file_extension()\n"
+ " - added much more debug output\n"
+ " - in nifti_image_read(), in the case of an ASCII header, check for\n"
+ " extensions after the end of the header\n",
+ " - added nifti_read_extensions() function\n"
+ " - added nifti_read_next_extension() function\n"
+ " - added nifti_add_exten_to_list() function\n"
+ " - added nifti_check_extension() function\n"
+ " - added nifti_write_extensions() function\n"
+ " - added nifti_extension_size() function\n"
+ " - in nifti_set_iname_offest():\n"
+ " o adjust offset by the extension size and the extender size\n",
+ " o fixed the 'ceiling modulo 16' computation\n"
+ " - in nifti_image_write_hdr_img2(): \n"
+ " o added extension writing\n"
+ " o check for NULL return from nifti_findimgname()\n"
+ " - include number of extensions in nifti_image_to_ascii() output\n"
+ " - in nifti_image_from_ascii():\n"
+ " o return bytes_read as a parameter, computed from the final spos\n"
+ " o extract num_ext from ASCII header\n"
+ "\n",
+ "0.5 14 Dec 2004 [rickr] - added sub-brick reading functions\n"
+ " - added nifti_brick_list type to nifti1_io.h, along with new prototypes\n"
+ " - added main nifti_image_read_bricks() function, with description\n"
+ " - added nifti_image_load_bricks() - library function (requires nim)\n"
+ " - added valid_nifti_brick_list() - library function\n"
+ " - added free_NBL() - library function\n",
+ " - added update_nifti_image_for_brick_list() for dimension update\n"
+ " - added nifti_load_NBL_bricks(), nifti_alloc_NBL_mem(),\n"
+ " nifti_copynsort() and force_positive() (static functions)\n"
+ " - in nifti_image_read(), check for failed load only if read_data is set\n"
+ " - broke most of nifti_image_load() into nifti_image_load_prep()\n"
+ "\n",
+ "0.6 15 Dec 2004 [rickr] - added sub-brick writing functionality\n"
+ " - in nifti1_io.h, removed znzlib directory from include - all nifti\n"
+ " library files are now under the nifti directory\n"
+ " - nifti_read_extensions(): print no offset warning for nifti_type 3\n"
+ " - nifti_write_all_data():\n"
+ " o pass nifti_brick_list * NBL, for optional writing\n"
+ " o if NBL, write each sub-brick, sequentially\n",
+ " - nifti_set_iname_offset(): case 1 must have sizeof() cast to int\n"
+ " - pass NBL to nifti_image_write_hdr_img2(), and allow NBL or data\n"
+ " - added nifti_image_write_bricks() wrapper for ...write_hdr_img2()\n"
+ " - included compression abilities\n"
+ "\n",
+ "0.7 16 Dec 2004 [rickr] - minor changes to extension reading\n"
+ "\n",
+ "0.8 21 Dec 2004 [rickr] - restrict extension reading, and minor changes\n"
+ " - in nifti_image_read(), compute bytes for extensions (see remaining)\n"
+ " - in nifti_read_extensions(), pass 'remain' as space for extensions,\n"
+ " pass it to nifti_read_next_ext(), and update for each one read \n"
+ " - in nifti_check_extension(), require (size <= remain)\n",
+ " - in update_nifti_image_brick_list(), update nvox\n"
+ " - in nifti_image_load_bricks(), make explicit check for nbricks <= 0\n"
+ " - in int_force_positive(), check for (!list)\n"
+ " - in swap_nifti_header(), swap sizeof_hdr, and reorder to struct order\n"
+ " - change get_filesize functions to signed ( < 0 is no file or error )\n",
+ " - in nifti_validfilename(), lose redundant (len < 0) check\n"
+ " - make print_hex_vals() static\n"
+ " - in disp_nifti_1_header, restrict string field widths\n"
+ "\n",
+ "0.9 23 Dec 2004 [rickr] - minor changes\n"
+ " - broke ASCII header reading out of nifti_image_read(), into new\n"
+ " functions has_ascii_header() and read_ascii_image()\n",
+ " - check image_read failure and znzseek failure\n"
+ " - altered some debug output\n"
+ " - nifti_write_all_data() now returns an int\n"
+ "\n",
+ "0.10 29 Dec 2004 [rickr]\n"
+ " - renamed nifti_valid_extension() to nifti_check_extension()\n"
+ " - added functions nifti_makehdrname() and nifti_makeimgname()\n"
+ " - added function valid_nifti_extensions()\n"
+ " - in nifti_write_extensions(), check for validity before writing\n",
+ " - rewrote nifti_image_write_hdr_img2():\n"
+ " o set write_data and leave_open flags from write_opts\n"
+ " o add debug print statements\n"
+ " o use nifti_write_ascii_image() for the ascii case\n"
+ " o rewrote the logic of all cases to be easier to follow\n",
+ " - broke out code as nifti_write_ascii_image() function\n"
+ " - added debug to top-level write functions, and free the znzFile\n"
+ " - removed unused internal function nifti_image_open()\n"
+ "\n",
+ "0.11 30 Dec 2004 [rickr] - small mods\n"
+ " - moved static function prototypes from header to C file\n"
+ " - free extensions in nifti_image_free()\n"
+ "\n",
+ "1.0 07 Jan 2005 [rickr] - INITIAL RELEASE VERSION\n"
+ " - added function nifti_set_filenames()\n"
+ " - added function nifti_read_header()\n"
+ " - added static function nhdr_looks_good()\n"
+ " - added static function need_nhdr_swap()\n"
+ " - exported nifti_add_exten_to_list symbol\n",
+ " - fixed #bytes written in nifti_write_extensions()\n"
+ " - only modify offset if it is too small (nifti_set_iname_offset)\n"
+ " - added nifti_type 3 to nifti_makehdrname and nifti_makeimgname\n"
+ " - added function nifti_set_filenames()\n"
+ "\n",
+ "1.1 07 Jan 2005 [rickr]\n"
+ " - in nifti_read_header(), swap if needed\n"
+ "\n",
+ "1.2 07 Feb 2005 [kate fissell c/o rickr] \n"
+ " - nifti1.h: added doxygen comments for main struct and #define groups\n"
+ " - nifti1_io.h: added doxygen comments for file and nifti_image struct\n"
+ " - nifti1_io.h: added doxygen comments for file and some functions\n"
+ " - nifti1_io.c: changed nifti_copy_nim_info to use memcpy\n"
+ "\n",
+ "1.3 09 Feb 2005 [rickr]\n"
+ " - nifti1.h: added doxygen comments for extension structs\n"
+ " - nifti1_io.h: put most #defines in #ifdef _NIFTI1_IO_C_ block\n"
+ " - added a doxygen-style description to every exported function\n"
+ " - added doxygen-style comments within some functions\n"
+ " - re-exported many znzFile functions that I had made static\n"
+ " - re-added nifti_image_open (sorry, Mark)\n"
+ " - every exported function now has 'nifti' in the name (19 functions)\n",
+ " - made sure every alloc() has a failure test\n"
+ " - added nifti_copy_extensions function, for use in nifti_copy_nim_info\n"
+ " - nifti_is_gzfile: added initial strlen test\n"
+ " - nifti_set_filenames: added set_byte_order parameter option\n"
+ " (it seems appropriate to set the BO when new files are associated)\n"
+ " - disp_nifti_1_header: prints to stdout (a.o.t. stderr), with fflush\n"
+ "\n",
+ "1.4 23 Feb 2005 [rickr] - sourceforge merge\n"
+ " - merged into the nifti_io CVS directory structure at sourceforge.net\n"
+ " - merged in 4 changes by Mark, and re-added his const keywords\n"
+ " - cast some pointers to (void *) for -pedantic compile option\n"
+ " - added nifti_free_extensions()\n"
+ "\n",
+ "1.5 02 Mar 2005 [rickr] - started nifti global options\n"
+ " - gni_debug is now g_opts.debug\n"
+ " - added validity check parameter to nifti_read_header\n"
+ " - need_nhdr_swap no longer does test swaps on the stack\n"
+ "\n",
+ "1.6 05 April 2005 [rickr] - validation and collapsed_image_read\n"
+ " - added nifti_read_collapsed_image(), an interface for reading partial\n"
+ " datasets, specifying a subset of array indices\n"
+ " - for read_collapsed_image, added static functions: rci_read_data(),\n"
+ " rci_alloc_mem(), and make_pivot_list()\n",
+ " - added nifti_nim_is_valid() to check for consistency (more to do)\n"
+ " - added nifti_nim_has_valid_dims() to do many dimensions tests\n"
+ "\n",
+ "1.7 08 April 2005 [rickr]\n"
+ " - added nifti_update_dims_from_array() - to update dimensions\n"
+ " - modified nifti_makehdrname() and nifti_makeimgname():\n"
+ " if prefix has a valid extension, use it (else make one up)\n"
+ " - added nifti_get_intlist - for making an array of ints\n"
+ " - fixed init of NBL->bsize in nifti_alloc_NBL_mem() {thanks, Bob}\n"
+ "\n",
+ "1.8 14 April 2005 [rickr]\n"
+ " - added nifti_set_type_from_names(), for nifti_set_filenames()\n"
+ " (only updates type if number of files does not match it)\n"
+ " - added is_valid_nifti_type(), just to be sure\n"
+ " - updated description of nifti_read_collapsed_image() for *data change\n"
+ " (if *data is already set, assume memory exists for results)\n"
+ " - modified rci_alloc_mem() to allocate only if *data is NULL\n"
+ "\n",
+ "1.9 19 April 2005 [rickr]\n"
+ " - added extension codes NIFTI_ECODE_COMMENT and NIFTI_ECODE_XCEDE\n"
+ " - added nifti_type codes NIFTI_MAX_ECODE and NIFTI_MAX_FTYPE\n"
+ " - added nifti_add_extension() {exported}\n"
+ " - added nifti_fill_extension() as a static function\n"
+ " - added nifti_is_valid_ecode() {exported}\n",
+ " - nifti_type values are now NIFTI_FTYPE_* file codes\n"
+ " - in nifti_read_extensions(), decrement 'remain' by extender size, 4\n"
+ " - in nifti_set_iname_offset(), case 1, update if offset differs\n"
+ " - only output '-d writing nifti file' if debug > 1\n"
+ "\n",
+ "1.10 10 May 2005 [rickr]\n"
+ " - files are read using ZLIB only if they end in '.gz'\n"
+ "\n",
+ "1.11 12 August 2005 [kate fissell]\n"
+ " - Kate's 0.2 release packaging, for sourceforge\n"
+ "\n",
+ "1.12 17 August 2005 [rickr] - comment (doxygen) updates\n"
+ " - updated comments for most functions (2 updates from Cinly Ooi)\n"
+ " - added nifti_type_and_names_match()\n"
+ "\n",
+ "1.12a 24 August 2005 [rickr] - remove all tabs from Clibs/*/*.[ch]\n",
+ "1.12b 25 August 2005 [rickr] - changes by Hans Johnson\n",
+ "1.13 25 August 2005 [rickr]\n",
+ " - finished changes by Hans for Insight\n"
+ " - added const in all appropraite parameter locations (30-40)\n"
+ " (any pointer referencing data that will not change)\n"
+ " - shortened all string constants below 509 character limit\n"
+ "1.14 28 October 2005 [HJohnson]\n",
+ " - use nifti_set_filenames() in nifti_convert_nhdr2nim()\n"
+ "1.15 02 November 2005 [rickr]\n",
+ " - added skip_blank_ext to nifti_global_options\n"
+ " - added nifti_set_skip_blank_ext(), to set option\n"
+ " - if skip_blank_ext and no extensions, do not read/write extender\n"
+ "1.16 18 November 2005 [rickr]\n",
+ " - removed any test or access of dim[i], i>dim[0]\n"
+ " - do not set pixdim for collapsed dims to 1.0, leave them as they are\n"
+ " - added magic and dim[i] tests in nifti_hdr_looks_good()\n"
+ " - added 2 size_t casts\n"
+ "1.17 22 November 2005 [rickr]\n",
+ " - in hdr->nim, for i > dim[0], pass 0 or 1, else set to 1\n"
+ "----------------------------------------------------------------------\n"
+};
+static char gni_version[] = "nifti library version 1.17 (Nov 22, 2005)";
+
+/*! global nifti options structure */
+static nifti_global_options g_opts = { 1, 0 };
+
+/*---------------------------------------------------------------------------*/
+/* prototypes for internal functions - not part of exported library */
+
+/* extension routines */
+static int nifti_read_extensions( nifti_image *nim, znzFile fp, int remain );
+static int nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim, int remain, znzFile fp );
+static int nifti_check_extension(nifti_image *nim, int size,int code, int rem);
+static void update_nifti_image_for_brick_list(nifti_image * nim , int nbricks);
+static int nifti_add_exten_to_list(nifti1_extension * new_ext,
+ nifti1_extension ** list, int new_length);
+static int nifti_fill_extension(nifti1_extension * ext, const char * data,
+ int len, int ecode);
+
+/* NBL routines */
+static int nifti_load_NBL_bricks(nifti_image * nim , int * slist, int * sindex, nifti_brick_list * NBL, znzFile fp );
+static int nifti_alloc_NBL_mem( nifti_image * nim, int nbricks,
+ nifti_brick_list * nbl);
+static int nifti_copynsort(int nbricks, const int *blist, int **slist,
+ int **sindex);
+
+/* for nifti_read_collapsed_image: */
+static int rci_read_data(nifti_image *nim, int *pivots, int *prods, int nprods,
+ const int dims[], char *data, znzFile fp, int base_offset);
+static int rci_alloc_mem(void ** data, int prods[8], int nprods, int nbyper );
+static int make_pivot_list(nifti_image * nim, const int dims[], int pivots[],
+ int prods[], int * nprods );
+
+/* misc */
+static int need_nhdr_swap (short dim0, int hdrsize);
+static int print_hex_vals (const char * data, int nbytes, FILE * fp);
+static int unescape_string (char *str); /* string utility functions */
+static char *escapize_string (const char *str);
+
+/* internal I/O routines */
+static znzFile nifti_image_load_prep( nifti_image *nim );
+static int has_ascii_header(znzFile fp);
+/*---------------------------------------------------------------------------*/
+
+
+/* for calling from some main program */
+
+/*----------------------------------------------------------------------*/
+/*! display the nifti library module history (via stdout)
+*//*--------------------------------------------------------------------*/
+void nifti_disp_lib_hist( void )
+{
+ int c, len = sizeof(gni_history)/sizeof(char *);
+ for( c = 0; c < len; c++ )
+ fputs(gni_history[c], stdout);
+}
+
+/*----------------------------------------------------------------------*/
+/*! display the nifti library version (via stdout)
+*//*--------------------------------------------------------------------*/
+void nifti_disp_lib_version( void )
+{
+ printf("%s, compiled %s\n", gni_version, __DATE__);
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! nifti_image_read_bricks - read nifti data as array of bricks
+ *
+ * 13 Dec 2004 [rickr]
+ *
+ * \param hname - filename of dataset to read (must be valid)
+ * \param nbricks - number of sub-bricks to read
+ * (if blist is valid, nbricks must be > 0)
+ * \param blist - list of sub-bricks to read
+ * (can be NULL; if NULL, read complete dataset)
+ * \param NBL - pointer to empty nifti_brick_list struct
+ * (must be a valid pointer)
+ *
+ * \return
+ * <br> nim - same as nifti_image_read, but nim->data will be NULL
+ * <br> NBL - filled with data
+ *
+ * By default, this function will read the nifti dataset and break the data
+ * into a list of nt*nu*nv*nw sub-bricks, each having size nx*ny*nz elements.
+ * That is to say, instead of reading the entire dataset as a single array,
+ * break it up into sub-bricks, each of size nx*ny*nz elements.
+ *
+ * If 'blist' is valid, it is taken to be a list of sub-bricks, of length
+ * 'nbricks'. The data will still be separated into sub-bricks of size
+ * nx*ny*nz elements, but now 'nbricks' sub-bricks will be returned, of the
+ * caller's choosing via 'blist'.
+ *
+ * E.g. consider a dataset with 12 sub-bricks (numbered 0..11), and the
+ * following code:
+ *
+ * <pre>
+ * { nifti_brick_list NB_orig, NB_select;
+ * nifti_image * nim_orig, * nim_select;
+ * int blist[5] = { 7, 0, 5, 5, 9 };
+ *
+ * nim_orig = nifti_image_read_bricks("myfile.nii", 0, NULL, &NB_orig);
+ * nim_select = nifti_image_read_bricks("myfile.nii", 5, blist, &NB_select);
+ * }
+ * </pre>
+ *
+ * Here, nim_orig gets the entire dataset, where NB_orig.nbricks = 11. But
+ * nim_select has NB_select.nbricks = 5.
+ *
+ * Note that the first case is not quite the same as just calling the
+ * nifti_image_read function, as here the data is separated into sub-bricks.
+ *
+ * Note that valid blist elements are in [0..nt*nu*nv*nw-1],
+ * or written [ 0 .. (dim[4]*dim[5]*dim[6]*dim[7] - 1) ].
+ *
+ * Note that, as is the case with all of the reading functions, the
+ * data will be allocated, read in, and properly byte-swapped, if
+ * necessary.
+ *
+ * \sa nifti_image_load_bricks, nifti_free_NBL, valid_nifti_brick_list,
+ nifti_image_read
+*//*----------------------------------------------------------------------*/
+nifti_image *nifti_image_read_bricks(const char * hname, int nbricks,
+ const int * blist, nifti_brick_list * NBL)
+{
+ nifti_image * nim;
+
+ if( !hname || !NBL ){
+ fprintf(stderr,"** nifti_image_read_bricks: bad params (%p,%p)\n",
+ hname, (void *)NBL);
+ return NULL;
+ }
+
+ if( blist && nbricks <= 0 ){
+ fprintf(stderr,"** nifti_image_read_bricks: bad nbricks, %d\n", nbricks);
+ return NULL;
+ }
+
+ nim = nifti_image_read(hname, 0); /* read header, but not data */
+
+ if( !nim ) return NULL; /* errors were already printed */
+
+ /* if we fail, free image and return */
+ if( nifti_image_load_bricks(nim, nbricks, blist, NBL) <= 0 ){
+ nifti_image_free(nim);
+ return NULL;
+ }
+
+ if( blist ) update_nifti_image_for_brick_list(nim, nbricks);
+
+ return nim;
+}
+
+
+/*----------------------------------------------------------------------
+ * update_nifti_image_for_brick_list - update nifti_image
+ *
+ * When loading a specific brick list, the distinction between
+ * nt, nu, nv and nw is lost. So put everything in t, and set
+ * dim[0] = 4.
+ *----------------------------------------------------------------------*/
+static void update_nifti_image_for_brick_list( nifti_image * nim , int nbricks )
+{
+ int ndim;
+
+ if( g_opts.debug > 2 ){
+ fprintf(stderr,"+d updating image dimensions for %d bricks in list\n",
+ nbricks);
+ fprintf(stderr," ndim = %d\n",nim->ndim);
+ fprintf(stderr," nx,ny,nz,nt,nu,nv,nw: (%d,%d,%d,%d,%d,%d,%d)\n",
+ nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw);
+ }
+
+ nim->nt = nbricks;
+ nim->nu = nim->nv = nim->nw = 1;
+ nim->dim[4] = nbricks;
+ nim->dim[5] = nim->dim[6] = nim->dim[7] = 1;
+
+ /* compute nvox */
+ /* do not rely on dimensions above dim[0] 16 Nov 2005 [rickr] */
+ for( nim->nvox = 1, ndim = 1; ndim <= nim->dim[0]; ndim++ )
+ nim->nvox *= nim->dim[ndim];
+
+ /* update the dimensions to 4 or lower */
+ for( ndim = 4; (ndim > 1) && (nim->dim[ndim] <= 1); ndim-- )
+ ;
+
+ if( g_opts.debug > 2 ){
+ fprintf(stderr,"+d ndim = %d -> %d\n",nim->ndim, ndim);
+ fprintf(stderr," --> (%d,%d,%d,%d,%d,%d,%d)\n",
+ nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw);
+ }
+
+ nim->dim[0] = nim->ndim = ndim;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! nifti_update_dims_from_array - update nx, ny, ... from nim->dim[]
+
+ Fix all the dimension information, based on a new nim->dim[].
+
+ Note: we assume that dim[0] will not increase.
+
+ Check for updates to pixdim[], dx,..., nx,..., nvox, ndim, dim[0].
+*//*--------------------------------------------------------------------*/
+int nifti_update_dims_from_array( nifti_image * nim )
+{
+ int c, ndim;
+
+ if( !nim ){
+ fprintf(stderr,"** update_dims: missing nim\n");
+ return 1;
+ }
+
+ if( g_opts.debug > 2 ){
+ fprintf(stderr,"+d updating image dimensions given nim->dim:");
+ for( c = 0; c < 8; c++ ) fprintf(stderr," %d", nim->dim[c]);
+ fputc('\n',stderr);
+ }
+
+ /* verify dim[0] first */
+ if(nim->dim[0] < 1 || nim->dim[0] > 7){
+ fprintf(stderr,"** invalid dim[0], dim[] = ");
+ for( c = 0; c < 8; c++ ) fprintf(stderr," %d", nim->dim[c]);
+ fputc('\n',stderr);
+ return 1;
+ }
+
+ /* set nx, ny ..., dx, dy, ..., one by one */
+
+ /* less than 1, set to 1, else copy */
+ if(nim->dim[1] < 1) nim->nx = nim->dim[1] = 1;
+ else nim->nx = nim->dim[1];
+ nim->dx = nim->pixdim[1];
+
+ /* if undefined, or less than 1, set to 1 */
+ if(nim->dim[0] < 2 || (nim->dim[0] >= 2 && nim->dim[2] < 1))
+ nim->ny = nim->dim[2] = 1;
+ else
+ nim->ny = nim->dim[2];
+ /* copy delta values, in any case */
+ nim->dy = nim->pixdim[2];
+
+ if(nim->dim[0] < 3 || (nim->dim[0] >= 3 && nim->dim[3] < 1))
+ nim->nz = nim->dim[3] = 1;
+ else /* just copy vals from arrays */
+ nim->nz = nim->dim[3];
+ nim->dz = nim->pixdim[3];
+
+ if(nim->dim[0] < 4 || (nim->dim[0] >= 4 && nim->dim[4] < 1))
+ nim->nt = nim->dim[4] = 1;
+ else /* just copy vals from arrays */
+ nim->nt = nim->dim[4];
+ nim->dt = nim->pixdim[4];
+
+ if(nim->dim[0] < 5 || (nim->dim[0] >= 5 && nim->dim[5] < 1))
+ nim->nu = nim->dim[5] = 1;
+ else /* just copy vals from arrays */
+ nim->nu = nim->dim[5];
+ nim->du = nim->pixdim[5];
+
+ if(nim->dim[0] < 6 || (nim->dim[0] >= 6 && nim->dim[6] < 1))
+ nim->nv = nim->dim[6] = 1;
+ else /* just copy vals from arrays */
+ nim->nv = nim->dim[6];
+ nim->dv = nim->pixdim[6];
+
+ if(nim->dim[0] < 7 || (nim->dim[0] >= 7 && nim->dim[7] < 1))
+ nim->nw = nim->dim[7] = 1;
+ else /* just copy vals from arrays */
+ nim->nw = nim->dim[7];
+ nim->dw = nim->pixdim[7];
+
+ for( c = 1, nim->nvox = 1; c <= nim->dim[0]; c++ )
+ nim->nvox *= nim->dim[c];
+
+ /* compute ndim, assuming it can be no larger than the old one */
+ for( ndim = nim->dim[0]; (ndim > 1) && (nim->dim[ndim] <= 1); ndim-- )
+ ;
+
+ if( g_opts.debug > 2 ){
+ fprintf(stderr,"+d ndim = %d -> %d\n",nim->ndim, ndim);
+ fprintf(stderr," --> (%d,%d,%d,%d,%d,%d,%d)\n",
+ nim->nx, nim->ny, nim->nz, nim->nt, nim->nu, nim->nv, nim->nw);
+ }
+
+ nim->dim[0] = nim->ndim = ndim;
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! Load the image data from disk into an already-prepared image struct.
+ *
+ * \param nim - initialized nifti_image, without data
+ * \param nbricks - the length of blist (must be 0 if blist is NULL)
+ * \param blist - an array of xyz volume indices to read (can be NULL)
+ * \param NBL - pointer to struct where resulting data will be stored
+ *
+ * If blist is NULL, read all sub-bricks.
+ *
+ * \return the number of loaded bricks (NBL->nbricks),
+ * 0 on failure, < 0 on error
+ *
+ * NOTE: it is likely that another function will copy the data pointers
+ * out of NBL, in which case the only pointer the calling function
+ * will want to free is NBL->bricks (not each NBL->bricks[i]).
+*//*--------------------------------------------------------------------*/
+int nifti_image_load_bricks( nifti_image * nim , int nbricks,
+ const int * blist, nifti_brick_list * NBL )
+{
+ int * slist = NULL, * sindex = NULL, rv;
+ znzFile fp;
+
+ /* we can have blist == NULL */
+ if( !nim || !NBL ){
+ fprintf(stderr,"** nifti_image_load_bricks, bad params (%p,%p)\n",
+ (void *)nim, (void *)NBL);
+ return -1;
+ }
+
+ if( blist && nbricks <= 0 ){
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d load_bricks: received blist with nbricks = %d,"
+ "ignoring blist\n", nbricks);
+ blist = NULL; /* pretend nothing was passed */
+ }
+
+ if( blist && ! valid_nifti_brick_list( nim, nbricks, blist, g_opts.debug>0 ) )
+ return -1;
+
+ /* for efficiency, let's read the file in order */
+ if( blist && nifti_copynsort( nbricks, blist, &slist, &sindex ) != 0 )
+ return -1;
+
+ /* open the file and position the FILE pointer */
+ fp = nifti_image_load_prep( nim );
+ if( !fp ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** nifti_image_load_bricks, failed load_prep\n");
+ if( blist ){ free(slist); free(sindex); }
+ return -1;
+ }
+
+ /* this will flag to allocate defaults */
+ if( !blist ) nbricks = 0;
+ if( nifti_alloc_NBL_mem( nim, nbricks, NBL ) != 0 ){
+ if( blist ){ free(slist); free(sindex); }
+ znzclose(fp);
+ return -1;
+ }
+
+ rv = nifti_load_NBL_bricks(nim, slist, sindex, NBL, fp);
+
+ if( rv != 0 ){
+ nifti_free_NBL( NBL ); /* failure! */
+ NBL->nbricks = 0; /* repetative, but clear */
+ }
+
+ if( slist ){ free(slist); free(sindex); }
+
+ znzclose(fp);
+
+ return NBL->nbricks;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! nifti_free_NBL - free all pointers and clear structure
+ *
+ * note: this does not presume to free the structure pointer
+*//*--------------------------------------------------------------------*/
+void nifti_free_NBL( nifti_brick_list * NBL )
+{
+ int c;
+
+ if( NBL->bricks ){
+ for( c = 0; c < NBL->nbricks; c++ )
+ if( NBL->bricks[c] ) free(NBL->bricks[c]);
+ free(NBL->bricks);
+ NBL->bricks = NULL;
+ }
+
+ NBL->nbricks = NBL->bsize = 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * nifti_load_NBL_bricks - read the file data into the NBL struct
+ *
+ * return 0 on success, -1 on failure
+ *----------------------------------------------------------------------*/
+static int nifti_load_NBL_bricks( nifti_image * nim , int * slist, int * sindex,
+ nifti_brick_list * NBL, znzFile fp )
+{
+ int c, rv;
+ int oposn, fposn; /* orig and current file positions */
+ int prev, isrc, idest; /* previous and current sub-brick, and new index */
+
+ oposn = znztell(fp); /* store current file position */
+ fposn = oposn;
+ if( fposn < 0 ){
+ fprintf(stderr,"** load bricks: ztell failed??\n");
+ return -1;
+ }
+
+ /* first, handle the default case, no passed blist */
+ if( !slist ){
+ for( c = 0; c < NBL->nbricks; c++ ) {
+ rv = nifti_read_buffer(fp, NBL->bricks[c], NBL->bsize, nim);
+ if( rv != NBL->bsize ){
+ fprintf(stderr,"** load bricks: cannot read brick %d from '%s'\n",
+ c, nim->iname ? nim->iname : nim->fname);
+ return -1;
+ }
+ }
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d read %d default bricks from file %s\n",
+ NBL->nbricks, nim->iname ? nim->iname : nim->fname );
+ return 0;
+ }
+
+ if( !sindex ){
+ fprintf(stderr,"** load_NBL_bricks: missing index list\n");
+ return -1;
+ }
+
+ prev = -1; /* use prev for previous sub-brick */
+ for( c = 0; c < NBL->nbricks; c++ ){
+ isrc = slist[c]; /* this is original brick index (c is new one) */
+ idest = sindex[c]; /* this is the destination index for this data */
+
+ /* if this sub-brick is not the previous, we must read from disk */
+ if( isrc != prev ){
+
+ /* if we are not looking at the correct sub-brick, scan forward */
+ if( fposn != (oposn + isrc*NBL->bsize) ){
+ fposn = oposn + isrc*NBL->bsize;
+ if( znzseek(fp, fposn, SEEK_SET) < 0 ){
+ fprintf(stderr,"** failed to locate brick %d in file '%s'\n",
+ isrc, nim->iname ? nim->iname : nim->fname);
+ return -1;
+ }
+ }
+
+ /* only 10,000 lines later and we're actually reading something! */
+ rv = nifti_read_buffer(fp, NBL->bricks[idest], NBL->bsize, nim);
+ if( rv != NBL->bsize ){
+ fprintf(stderr,"** failed to read brick %d from file '%s'\n",
+ isrc, nim->iname ? nim->iname : nim->fname);
+ return -1;
+ }
+ fposn += NBL->bsize;
+ } else {
+ /* we have already read this sub-brick, just copy the previous one */
+ /* note that this works because they are sorted */
+ memcpy(NBL->bricks[idest], NBL->bricks[sindex[c-1]], NBL->bsize);
+ }
+
+ prev = isrc; /* in any case, note the now previous sub-brick */
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * nifti_alloc_NBL_mem - allocate memory for bricks
+ *
+ * return 0 on success, -1 on failure
+ *----------------------------------------------------------------------*/
+static int nifti_alloc_NBL_mem(nifti_image * nim, int nbricks,
+ nifti_brick_list * nbl)
+{
+ int c;
+
+ /* if nbricks is not specified, use the default */
+ if( nbricks > 0 ) nbl->nbricks = nbricks;
+ else nbl->nbricks = nim->nt * nim->nu * nim->nv * nim->nw;
+
+ nbl->bsize = nim->nx * nim->ny * nim->nz * nim->nbyper; /* bytes */
+ nbl->bricks = (void **)malloc(nbl->nbricks * sizeof(void *));
+
+ if( ! nbl->bricks ){
+ fprintf(stderr,"** NANM: failed to alloc %d void ptrs\n",nbricks);
+ return -1;
+ }
+
+ for( c = 0; c < nbl->nbricks; c++ ){
+ nbl->bricks[c] = (void *)malloc(nbl->bsize);
+ if( ! nbl->bricks[c] ){
+ fprintf(stderr,"** NANM: failed to alloc %d bytes for brick %d\n",
+ nbl->bsize, c);
+ /* so free and clear everything before returning */
+ while( c > 0 ){
+ c--;
+ free(nbl->bricks[c]);
+ }
+ free(nbl->bricks);
+ nbl->bricks = NULL;
+ nbl->nbricks = nbl->bsize = 0;
+ return -1;
+ }
+ }
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"+d NANM: alloc'd %d bricks of %d bytes for NBL\n",
+ nbl->nbricks, nbl->bsize);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * nifti_copynsort - copy int list, and sort with indices
+ *
+ * 1. duplicate the incoming list
+ * 2. create an sindex list, and init with 0..nbricks-1
+ * 3. do a slow insertion sort on the small slist, along with sindex list
+ * 4. check results, just to be positive
+ *
+ * So slist is sorted, and sindex hold original positions.
+ *
+ * return 0 on success, -1 on failure
+ *----------------------------------------------------------------------*/
+static int nifti_copynsort(int nbricks, const int * blist, int ** slist,
+ int ** sindex)
+{
+ int * stmp, * itmp; /* for ease of typing/reading */
+ int c1, c2, spos, tmp;
+
+ *slist = (int *)malloc(nbricks * sizeof(int));
+ *sindex = (int *)malloc(nbricks * sizeof(int));
+
+ if( !*slist || !*sindex ){
+ fprintf(stderr,"** NCS: failed to alloc %d ints for sorting\n",nbricks);
+ if(*slist) free(*slist); /* maybe one succeeded */
+ if(*sindex) free(*sindex);
+ return -1;
+ }
+
+ /* init the lists */
+ memcpy(*slist, blist, nbricks*sizeof(int));
+ for( c1 = 0; c1 < nbricks; c1++ ) (*sindex)[c1] = c1;
+
+ /* now actually sort slist */
+ stmp = *slist;
+ itmp = *sindex;
+ for( c1 = 0; c1 < nbricks-1; c1++ ) {
+ /* find smallest value, init to current */
+ spos = c1;
+ for( c2 = c1+1; c2 < nbricks; c2++ )
+ if( stmp[c2] < stmp[spos] ) spos = c2;
+ if( spos != c1 ) /* swap: fine, don't maintain sub-order, see if I care */
+ {
+ tmp = stmp[c1]; /* first swap the sorting values */
+ stmp[c1] = stmp[spos];
+ stmp[spos] = tmp;
+
+ tmp = itmp[c1]; /* then swap the index values */
+ itmp[c1] = itmp[spos];
+ itmp[spos] = tmp;
+ }
+ }
+
+ if( g_opts.debug > 2 ){
+ fprintf(stderr, "+d sorted indexing list:\n");
+ fprintf(stderr, " orig : ");
+ for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %d",blist[c1]);
+ fprintf(stderr,"\n new : ");
+ for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %d",stmp[c1]);
+ fprintf(stderr,"\n indices: ");
+ for( c1 = 0; c1 < nbricks; c1++ ) fprintf(stderr," %d",itmp[c1]);
+ fputc('\n', stderr);
+ }
+
+ /* check the sort (why not? I've got time...) */
+ for( c1 = 0; c1 < nbricks-1; c1++ ){
+ if( (stmp[c1] > stmp[c1+1]) || (blist[itmp[c1]] != stmp[c1]) ){
+ fprintf(stderr,"** sorting screw-up, way to go, rick!\n");
+ free(stmp); free(itmp); *slist = NULL; *sindex = NULL;
+ return -1;
+ }
+ }
+
+ if( g_opts.debug > 2 ) fprintf(stderr,"-d sorting is okay\n");
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! valid_nifti_brick_list - check sub-brick list for image
+ *
+ * This function verifies that nbricks and blist are appropriate
+ * for use with this nim, based on the dimensions.
+ *
+ * \param nim nifti_image to check against
+ * \param nbricks number of brick indices in blist
+ * \param blist list of brick indices to check in nim
+ * \param disp_error if this flag is set, report errors to user
+ *
+ * \return 1 if valid, 0 if not
+*//*--------------------------------------------------------------------*/
+int valid_nifti_brick_list(nifti_image * nim , int nbricks,
+ const int * blist, int disp_error)
+{
+ int c, nsubs;
+
+ if( !nim ){
+ if( disp_error || g_opts.debug > 0 )
+ fprintf(stderr,"** valid_nifti_brick_list: missing nifti image\n");
+ return 0;
+ }
+
+ if( nbricks <= 0 || !blist ){
+ if( disp_error || g_opts.debug > 1 )
+ fprintf(stderr,"** valid_nifti_brick_list: no brick list to check\n");
+ return 0;
+ }
+
+ /* nsubs sub-brick is nt*nu*nv*nw */
+ for( c = 4, nsubs = 1; c <= nim->dim[0]; c++ )
+ nsubs *= nim->dim[c];
+
+ if( nsubs <= 0 ){
+ fprintf(stderr,"** VNBL warning: bad dim list (%d,%d,%d,%d)\n",
+ nim->dim[4], nim->dim[5], nim->dim[6], nim->dim[7]);
+ return 0;
+ }
+
+ for( c = 0; c < nbricks; c++ )
+ if( (blist[c] < 0) || (blist[c] >= nsubs) ){
+ if( disp_error || g_opts.debug > 1 )
+ fprintf(stderr,
+ "-d ** bad sub-brick chooser %d (#%d), valid range is [0,%d]\n",
+ blist[c], c, nsubs-1);
+ return 0;
+ }
+
+ return 1; /* all is well */
+}
+
+#if 0
+/* set any non-positive values to 1 */
+static int int_force_positive( int * list, int nel )
+{
+ int c;
+ if( !list || nel < 0 ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** int_force_positive: bad params (%p,%d)\n",
+ (void *)list,nel);
+ return -1;
+ }
+ for( c = 0; c < nel; c++ )
+ if( list[c] <= 0 ) list[c] = 1;
+ return 0;
+}
+#endif
+/* end of new nifti_image_read_bricks() functionality */
+
+/*----------------------------------------------------------------------*/
+/*! display the orientation from the quaternian fields
+ *
+ * \param mesg if non-NULL, display this message first
+ * \param mat the matrix to convert to "nearest" orientation
+ *
+ * \return -1 if results cannot be determined, 0 if okay
+*//*--------------------------------------------------------------------*/
+int nifti_disp_matrix_orient( const char * mesg, mat44 mat )
+{
+ int i, j, k;
+
+ if ( mesg ) fputs( mesg, stderr ); /* use stdout? */
+
+ nifti_mat44_to_orientation( mat, &i,&j,&k );
+ if ( i <= 0 || j <= 0 || k <= 0 ) return -1;
+
+ /* so we have good codes */
+ fprintf(stderr, " i orientation = '%s'\n"
+ " j orientation = '%s'\n"
+ " k orientation = '%s'\n",
+ nifti_orientation_string(i),
+ nifti_orientation_string(j),
+ nifti_orientation_string(k) );
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! duplicate the given string (alloc length+1)
+ *
+ * \return allocated pointer (or NULL on failure)
+*//*--------------------------------------------------------------------*/
+char *nifti_strdup(const char *str)
+{
+ char *dup= (char *)malloc( strlen(str)+1 );
+ if (dup) strcpy(dup,str);
+ return dup;
+}
+
+
+/*---------------------------------------------------------------------------*/
+/*! Return a pointer to a string holding the name of a NIFTI datatype.
+
+ \param dt NIfTI-1 datatype
+
+ \return pointer to static string holding the datatype name
+
+ \warning Do not free() or modify this string!
+ It points to static storage.
+
+ \sa NIFTI1_DATATYPES group in nifti1.h
+*//*-------------------------------------------------------------------------*/
+char *nifti_datatype_string( int dt )
+{
+ switch( dt ){
+ case DT_UNKNOWN: return "UNKNOWN" ;
+ case DT_BINARY: return "BINARY" ;
+ case DT_INT8: return "INT8" ;
+ case DT_UINT8: return "UINT8" ;
+ case DT_INT16: return "INT16" ;
+ case DT_UINT16: return "UINT16" ;
+ case DT_INT32: return "INT32" ;
+ case DT_UINT32: return "UINT32" ;
+ case DT_INT64: return "INT64" ;
+ case DT_UINT64: return "UINT64" ;
+ case DT_FLOAT32: return "FLOAT32" ;
+ case DT_FLOAT64: return "FLOAT64" ;
+ case DT_FLOAT128: return "FLOAT128" ;
+ case DT_COMPLEX64: return "COMPLEX64" ;
+ case DT_COMPLEX128: return "COMPLEX128" ;
+ case DT_COMPLEX256: return "COMPLEX256" ;
+ case DT_RGB24: return "RGB24" ;
+ }
+ return "**ILLEGAL**" ;
+}
+
+/*----------------------------------------------------------------------*/
+/*! Determine if the datatype code dt is an integer type (1=YES, 0=NO).
+
+ \return whether the given NIfTI-1 datatype code is valid
+
+ \sa NIFTI1_DATATYPES group in nifti1.h
+*//*--------------------------------------------------------------------*/
+int nifti_is_inttype( int dt )
+{
+ switch( dt ){
+ case DT_UNKNOWN: return 0 ;
+ case DT_BINARY: return 0 ;
+ case DT_INT8: return 1 ;
+ case DT_UINT8: return 1 ;
+ case DT_INT16: return 1 ;
+ case DT_UINT16: return 1 ;
+ case DT_INT32: return 1 ;
+ case DT_UINT32: return 1 ;
+ case DT_INT64: return 1 ;
+ case DT_UINT64: return 1 ;
+ case DT_FLOAT32: return 0 ;
+ case DT_FLOAT64: return 0 ;
+ case DT_FLOAT128: return 0 ;
+ case DT_COMPLEX64: return 0 ;
+ case DT_COMPLEX128: return 0 ;
+ case DT_COMPLEX256: return 0 ;
+ case DT_RGB24: return 1 ;
+ }
+ return 0 ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Return a pointer to a string holding the name of a NIFTI units type.
+
+ \param uu NIfTI-1 unit code
+
+ \return pointer to static string for the given unit type
+
+ \warning Do not free() or modify this string!
+ It points to static storage.
+
+ \sa NIFTI1_UNITS group in nifti1.h
+*//*-------------------------------------------------------------------------*/
+char *nifti_units_string( int uu )
+{
+ switch( uu ){
+ case NIFTI_UNITS_METER: return "m" ;
+ case NIFTI_UNITS_MM: return "mm" ;
+ case NIFTI_UNITS_MICRON: return "um" ;
+ case NIFTI_UNITS_SEC: return "s" ;
+ case NIFTI_UNITS_MSEC: return "ms" ;
+ case NIFTI_UNITS_USEC: return "us" ;
+ case NIFTI_UNITS_HZ: return "Hz" ;
+ case NIFTI_UNITS_PPM: return "ppm" ;
+ case NIFTI_UNITS_RADS: return "rad/s" ;
+ }
+ return "Unknown" ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Return a pointer to a string holding the name of a NIFTI transform type.
+
+ \param xx NIfTI-1 xform code
+
+ \return pointer to static string describing xform code
+
+ \warning Do not free() or modify this string!
+ It points to static storage.
+
+ \sa NIFTI1_XFORM_CODES group in nifti1.h
+*//*-------------------------------------------------------------------------*/
+char *nifti_xform_string( int xx )
+{
+ switch( xx ){
+ case NIFTI_XFORM_SCANNER_ANAT: return "Scanner Anat" ;
+ case NIFTI_XFORM_ALIGNED_ANAT: return "Aligned Anat" ;
+ case NIFTI_XFORM_TALAIRACH: return "Talairach" ;
+ case NIFTI_XFORM_MNI_152: return "MNI_152" ;
+ }
+ return "Unknown" ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Return a pointer to a string holding the name of a NIFTI intent type.
+
+ \param ii NIfTI-1 intent code
+
+ \return pointer to static string describing code
+
+ \warning Do not free() or modify this string!
+ It points to static storage.
+
+ \sa NIFTI1_INTENT_CODES group in nifti1.h
+*//*-------------------------------------------------------------------------*/
+char *nifti_intent_string( int ii )
+{
+ switch( ii ){
+ case NIFTI_INTENT_CORREL: return "Correlation statistic" ;
+ case NIFTI_INTENT_TTEST: return "T-statistic" ;
+ case NIFTI_INTENT_FTEST: return "F-statistic" ;
+ case NIFTI_INTENT_ZSCORE: return "Z-score" ;
+ case NIFTI_INTENT_CHISQ: return "Chi-squared distribution" ;
+ case NIFTI_INTENT_BETA: return "Beta distribution" ;
+ case NIFTI_INTENT_BINOM: return "Binomial distribution" ;
+ case NIFTI_INTENT_GAMMA: return "Gamma distribution" ;
+ case NIFTI_INTENT_POISSON: return "Poisson distribution" ;
+ case NIFTI_INTENT_NORMAL: return "Normal distribution" ;
+ case NIFTI_INTENT_FTEST_NONC: return "F-statistic noncentral" ;
+ case NIFTI_INTENT_CHISQ_NONC: return "Chi-squared noncentral" ;
+ case NIFTI_INTENT_LOGISTIC: return "Logistic distribution" ;
+ case NIFTI_INTENT_LAPLACE: return "Laplace distribution" ;
+ case NIFTI_INTENT_UNIFORM: return "Uniform distribition" ;
+ case NIFTI_INTENT_TTEST_NONC: return "T-statistic noncentral" ;
+ case NIFTI_INTENT_WEIBULL: return "Weibull distribution" ;
+ case NIFTI_INTENT_CHI: return "Chi distribution" ;
+ case NIFTI_INTENT_INVGAUSS: return "Inverse Gaussian distribution" ;
+ case NIFTI_INTENT_EXTVAL: return "Extreme Value distribution" ;
+ case NIFTI_INTENT_PVAL: return "P-value" ;
+
+ case NIFTI_INTENT_LOGPVAL: return "Log P-value" ;
+ case NIFTI_INTENT_LOG10PVAL: return "Log10 P-value" ;
+
+ case NIFTI_INTENT_ESTIMATE: return "Estimate" ;
+ case NIFTI_INTENT_LABEL: return "Label index" ;
+ case NIFTI_INTENT_NEURONAME: return "NeuroNames index" ;
+ case NIFTI_INTENT_GENMATRIX: return "General matrix" ;
+ case NIFTI_INTENT_SYMMATRIX: return "Symmetric matrix" ;
+ case NIFTI_INTENT_DISPVECT: return "Displacement vector" ;
+ case NIFTI_INTENT_VECTOR: return "Vector" ;
+ case NIFTI_INTENT_POINTSET: return "Pointset" ;
+ case NIFTI_INTENT_TRIANGLE: return "Triangle" ;
+ case NIFTI_INTENT_QUATERNION: return "Quaternion" ;
+
+ case NIFTI_INTENT_DIMLESS: return "Dimensionless number" ;
+ }
+ return "Unknown" ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Return a pointer to a string holding the name of a NIFTI slice_code.
+
+ \param ss NIfTI-1 slice order code
+
+ \return pointer to static string describing code
+
+ \warning Do not free() or modify this string!
+ It points to static storage.
+
+ \sa NIFTI1_SLICE_ORDER group in nifti1.h
+*//*-------------------------------------------------------------------------*/
+char *nifti_slice_string( int ss )
+{
+ switch( ss ){
+ case NIFTI_SLICE_SEQ_INC: return "sequential_increasing" ;
+ case NIFTI_SLICE_SEQ_DEC: return "sequential_decreasing" ;
+ case NIFTI_SLICE_ALT_INC: return "alternating_increasing" ;
+ case NIFTI_SLICE_ALT_DEC: return "alternating_decreasing" ;
+ case NIFTI_SLICE_ALT_INC2: return "alternating_increasing_2" ;
+ case NIFTI_SLICE_ALT_DEC2: return "alternating_decreasing_2" ;
+ }
+ return "Unknown" ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Return a pointer to a string holding the name of a NIFTI orientation.
+
+ \param ii orientation code
+
+ \return pointer to static string holding the orientation information
+
+ \warning Do not free() or modify the return string!
+ It points to static storage.
+
+ \sa NIFTI_L2R in nifti1_io.h
+*//*-------------------------------------------------------------------------*/
+char *nifti_orientation_string( int ii )
+{
+ switch( ii ){
+ case NIFTI_L2R: return "Left-to-Right" ;
+ case NIFTI_R2L: return "Right-to-Left" ;
+ case NIFTI_P2A: return "Posterior-to-Anterior" ;
+ case NIFTI_A2P: return "Anterior-to-Posterior" ;
+ case NIFTI_I2S: return "Inferior-to-Superior" ;
+ case NIFTI_S2I: return "Superior-to-Inferior" ;
+ }
+ return "Unknown" ;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a datatype code, set number of bytes per voxel and the swapsize.
+
+ \param datatype nifti1 datatype code
+ \param nbyper pointer to return value: number of bytes per voxel
+ \param swapsize pointer to return value: size of swap blocks
+
+ \return appropriate values at nbyper and swapsize
+
+ The swapsize is set to 0 if this datatype doesn't ever need swapping.
+
+ \sa NIFTI1_DATATYPES in nifti1.h
+*//*------------------------------------------------------------------------*/
+void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize )
+{
+ int nb=0, ss=0 ;
+ switch( datatype ){
+ case DT_INT8:
+ case DT_UINT8: nb = 1 ; ss = 0 ; break ;
+
+ case DT_INT16:
+ case DT_UINT16: nb = 2 ; ss = 2 ; break ;
+
+ case DT_RGB24: nb = 3 ; ss = 0 ; break ;
+
+ case DT_INT32:
+ case DT_UINT32:
+ case DT_FLOAT32: nb = 4 ; ss = 4 ; break ;
+
+ case DT_COMPLEX64: nb = 8 ; ss = 4 ; break ;
+
+ case DT_FLOAT64:
+ case DT_INT64:
+ case DT_UINT64: nb = 8 ; ss = 8 ; break ;
+
+ case DT_FLOAT128: nb = 16 ; ss = 16 ; break ;
+
+ case DT_COMPLEX128: nb = 16 ; ss = 8 ; break ;
+
+ case DT_COMPLEX256: nb = 32 ; ss = 16 ; break ;
+ }
+
+ ASSIF(nbyper,nb) ; ASSIF(swapsize,ss) ; return ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Given the quaternion parameters (etc.), compute a transformation matrix.
+
+ See comments in nifti1.h for details.
+ - qb,qc,qd = quaternion parameters
+ - qx,qy,qz = offset parameters
+ - dx,dy,dz = grid stepsizes (non-negative inputs are set to 1.0)
+ - qfac = sign of dz step (< 0 is negative; >= 0 is positive)
+
+ <pre>
+ If qx=qy=qz=0, dx=dy=dz=1, then the output is a rotation matrix.
+ For qfac >= 0, the rotation is proper.
+ For qfac < 0, the rotation is improper.
+ </pre>
+
+ \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h
+ \see nifti_mat44_to_quatern, nifti_make_orthog_mat44,
+ nifti_mat44_to_orientation
+
+*//*-------------------------------------------------------------------------*/
+mat44 nifti_quatern_to_mat44( float qb, float qc, float qd,
+ float qx, float qy, float qz,
+ float dx, float dy, float dz, float qfac )
+{
+ mat44 R ;
+ double a,b=qb,c=qc,d=qd , xd,yd,zd ;
+
+ /* last row is always [ 0 0 0 1 ] */
+
+ R.m[3][0]=R.m[3][1]=R.m[3][2] = 0.0 ; R.m[3][3]= 1.0 ;
+
+ /* compute a parameter from b,c,d */
+
+ a = 1.0l - (b*b + c*c + d*d) ;
+ if( a < 1.e-7l ){ /* special case */
+ a = 1.0l / sqrt(b*b+c*c+d*d) ;
+ b *= a ; c *= a ; d *= a ; /* normalize (b,c,d) vector */
+ a = 0.0l ; /* a = 0 ==> 180 degree rotation */
+ } else{
+ a = sqrt(a) ; /* angle = 2*arccos(a) */
+ }
+
+ /* load rotation matrix, including scaling factors for voxel sizes */
+
+ xd = (dx > 0.0) ? dx : 1.0l ; /* make sure are positive */
+ yd = (dy > 0.0) ? dy : 1.0l ;
+ zd = (dz > 0.0) ? dz : 1.0l ;
+
+ if( qfac < 0.0 ) zd = -zd ; /* left handedness? */
+
+ R.m[0][0] = (a*a+b*b-c*c-d*d) * xd ;
+ R.m[0][1] = 2.0l * (b*c-a*d ) * yd ;
+ R.m[0][2] = 2.0l * (b*d+a*c ) * zd ;
+ R.m[1][0] = 2.0l * (b*c+a*d ) * xd ;
+ R.m[1][1] = (a*a+c*c-b*b-d*d) * yd ;
+ R.m[1][2] = 2.0l * (c*d-a*b ) * zd ;
+ R.m[2][0] = 2.0l * (b*d-a*c ) * xd ;
+ R.m[2][1] = 2.0l * (c*d+a*b ) * yd ;
+ R.m[2][2] = (a*a+d*d-c*c-b*b) * zd ;
+
+ /* load offsets */
+
+ R.m[0][3] = qx ; R.m[1][3] = qy ; R.m[2][3] = qz ;
+
+ return R ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Given the 3x4 upper corner of the matrix R, compute the quaternion
+ parameters that fit it.
+
+ - Any NULL pointer on input won't get assigned (e.g., if you don't want
+ dx,dy,dz, just pass NULL in for those pointers).
+ - If the 3 input matrix columns are NOT orthogonal, they will be
+ orthogonalized prior to calculating the parameters, using
+ the polar decomposition to find the orthogonal matrix closest
+ to the column-normalized input matrix.
+ - However, if the 3 input matrix columns are NOT orthogonal, then
+ the matrix produced by nifti_quatern_to_mat44 WILL have orthogonal
+ columns, so it won't be the same as the matrix input here.
+ This "feature" is because the NIFTI 'qform' transform is
+ deliberately not fully general -- it is intended to model a volume
+ with perpendicular axes.
+ - If the 3 input matrix columns are not even linearly independent,
+ you'll just have to take your luck, won't you?
+
+ \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h
+
+ \see nifti_quatern_to_mat44, nifti_make_orthog_mat44,
+ nifti_mat44_to_orientation
+*//*-------------------------------------------------------------------------*/
+void nifti_mat44_to_quatern( mat44 R ,
+ float *qb, float *qc, float *qd,
+ float *qx, float *qy, float *qz,
+ float *dx, float *dy, float *dz, float *qfac )
+{
+ double r11,r12,r13 , r21,r22,r23 , r31,r32,r33 ;
+ double xd,yd,zd , a,b,c,d ;
+ mat33 P,Q ;
+
+ /* offset outputs are read write out of input matrix */
+
+ ASSIF(qx,R.m[0][3]) ; ASSIF(qy,R.m[1][3]) ; ASSIF(qz,R.m[2][3]) ;
+
+ /* load 3x3 matrix into local variables */
+
+ r11 = R.m[0][0] ; r12 = R.m[0][1] ; r13 = R.m[0][2] ;
+ r21 = R.m[1][0] ; r22 = R.m[1][1] ; r23 = R.m[1][2] ;
+ r31 = R.m[2][0] ; r32 = R.m[2][1] ; r33 = R.m[2][2] ;
+
+ /* compute lengths of each column; these determine grid spacings */
+
+ xd = sqrt( r11*r11 + r21*r21 + r31*r31 ) ;
+ yd = sqrt( r12*r12 + r22*r22 + r32*r32 ) ;
+ zd = sqrt( r13*r13 + r23*r23 + r33*r33 ) ;
+
+ /* if a column length is zero, patch the trouble */
+
+ if( xd == 0.0l ){ r11 = 1.0l ; r21 = r31 = 0.0l ; xd = 1.0l ; }
+ if( yd == 0.0l ){ r22 = 1.0l ; r12 = r32 = 0.0l ; yd = 1.0l ; }
+ if( zd == 0.0l ){ r33 = 1.0l ; r13 = r23 = 0.0l ; zd = 1.0l ; }
+
+ /* assign the output lengths */
+
+ ASSIF(dx,xd) ; ASSIF(dy,yd) ; ASSIF(dz,zd) ;
+
+ /* normalize the columns */
+
+ r11 /= xd ; r21 /= xd ; r31 /= xd ;
+ r12 /= yd ; r22 /= yd ; r32 /= yd ;
+ r13 /= zd ; r23 /= zd ; r33 /= zd ;
+
+ /* At this point, the matrix has normal columns, but we have to allow
+ for the fact that the hideous user may not have given us a matrix
+ with orthogonal columns.
+
+ So, now find the orthogonal matrix closest to the current matrix.
+
+ One reason for using the polar decomposition to get this
+ orthogonal matrix, rather than just directly orthogonalizing
+ the columns, is so that inputting the inverse matrix to R
+ will result in the inverse orthogonal matrix at this point.
+ If we just orthogonalized the columns, this wouldn't necessarily hold. */
+
+ Q.m[0][0] = r11 ; Q.m[0][1] = r12 ; Q.m[0][2] = r13 ; /* load Q */
+ Q.m[1][0] = r21 ; Q.m[1][1] = r22 ; Q.m[1][2] = r23 ;
+ Q.m[2][0] = r31 ; Q.m[2][1] = r32 ; Q.m[2][2] = r33 ;
+
+ P = nifti_mat33_polar(Q) ; /* P is orthog matrix closest to Q */
+
+ r11 = P.m[0][0] ; r12 = P.m[0][1] ; r13 = P.m[0][2] ; /* unload */
+ r21 = P.m[1][0] ; r22 = P.m[1][1] ; r23 = P.m[1][2] ;
+ r31 = P.m[2][0] ; r32 = P.m[2][1] ; r33 = P.m[2][2] ;
+
+ /* [ r11 r12 r13 ] */
+ /* at this point, the matrix [ r21 r22 r23 ] is orthogonal */
+ /* [ r31 r32 r33 ] */
+
+ /* compute the determinant to determine if it is proper */
+
+ zd = r11*r22*r33-r11*r32*r23-r21*r12*r33
+ +r21*r32*r13+r31*r12*r23-r31*r22*r13 ; /* should be -1 or 1 */
+
+ if( zd > 0 ){ /* proper */
+ ASSIF(qfac,1.0) ;
+ } else { /* improper ==> flip 3rd column */
+ ASSIF(qfac,-1.0) ;
+ r13 = -r13 ; r23 = -r23 ; r33 = -r33 ;
+ }
+
+ /* now, compute quaternion parameters */
+
+ a = r11 + r22 + r33 + 1.0l ;
+
+ if( a > 0.5l ){ /* simplest case */
+ a = 0.5l * sqrt(a) ;
+ b = 0.25l * (r32-r23) / a ;
+ c = 0.25l * (r13-r31) / a ;
+ d = 0.25l * (r21-r12) / a ;
+ } else { /* trickier case */
+ xd = 1.0 + r11 - (r22+r33) ; /* 4*b*b */
+ yd = 1.0 + r22 - (r11+r33) ; /* 4*c*c */
+ zd = 1.0 + r33 - (r11+r22) ; /* 4*d*d */
+ if( xd > 1.0 ){
+ b = 0.5l * sqrt(xd) ;
+ c = 0.25l* (r12+r21) / b ;
+ d = 0.25l* (r13+r31) / b ;
+ a = 0.25l* (r32-r23) / b ;
+ } else if( yd > 1.0 ){
+ c = 0.5l * sqrt(yd) ;
+ b = 0.25l* (r12+r21) / c ;
+ d = 0.25l* (r23+r32) / c ;
+ a = 0.25l* (r13-r31) / c ;
+ } else {
+ d = 0.5l * sqrt(zd) ;
+ b = 0.25l* (r13+r31) / d ;
+ c = 0.25l* (r23+r32) / d ;
+ a = 0.25l* (r21-r12) / d ;
+ }
+ if( a < 0.0l ){ b=-b ; c=-c ; d=-d; a=-a; }
+ }
+
+ ASSIF(qb,b) ; ASSIF(qc,c) ; ASSIF(qd,d) ;
+ return ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Compute the inverse of a bordered 4x4 matrix.
+
+ <pre>
+ - Some numerical code fragments were generated by Maple 8.
+ - If a singular matrix is input, the output matrix will be all zero.
+ - You can check for this by examining the [3][3] element, which will
+ be 1.0 for the normal case and 0.0 for the bad case.
+
+ The input matrix should have the form:
+ [ r11 r12 r13 v1 ]
+ [ r21 r22 r23 v2 ]
+ [ r31 r32 r33 v3 ]
+ [ 0 0 0 1 ]
+ </pre>
+*//*-------------------------------------------------------------------------*/
+mat44 nifti_mat44_inverse( mat44 R )
+{
+ double r11,r12,r13,r21,r22,r23,r31,r32,r33,v1,v2,v3 , deti ;
+ mat44 Q ;
+ /* INPUT MATRIX IS: */
+ r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 v1 ] */
+ r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 v2 ] */
+ r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 v3 ] */
+ v1 = R.m[0][3]; v2 = R.m[1][3]; v3 = R.m[2][3]; /* [ 0 0 0 1 ] */
+
+ deti = r11*r22*r33-r11*r32*r23-r21*r12*r33
+ +r21*r32*r13+r31*r12*r23-r31*r22*r13 ;
+
+ if( deti != 0.0l ) deti = 1.0l / deti ;
+
+ Q.m[0][0] = deti*( r22*r33-r32*r23) ;
+ Q.m[0][1] = deti*(-r12*r33+r32*r13) ;
+ Q.m[0][2] = deti*( r12*r23-r22*r13) ;
+ Q.m[0][3] = deti*(-r12*r23*v3+r12*v2*r33+r22*r13*v3
+ -r22*v1*r33-r32*r13*v2+r32*v1*r23) ;
+
+ Q.m[1][0] = deti*(-r21*r33+r31*r23) ;
+ Q.m[1][1] = deti*( r11*r33-r31*r13) ;
+ Q.m[1][2] = deti*(-r11*r23+r21*r13) ;
+ Q.m[1][3] = deti*( r11*r23*v3-r11*v2*r33-r21*r13*v3
+ +r21*v1*r33+r31*r13*v2-r31*v1*r23) ;
+
+ Q.m[2][0] = deti*( r21*r32-r31*r22) ;
+ Q.m[2][1] = deti*(-r11*r32+r31*r12) ;
+ Q.m[2][2] = deti*( r11*r22-r21*r12) ;
+ Q.m[2][3] = deti*(-r11*r22*v3+r11*r32*v2+r21*r12*v3
+ -r21*r32*v1-r31*r12*v2+r31*r22*v1) ;
+
+ Q.m[3][0] = Q.m[3][1] = Q.m[3][2] = 0.0l ;
+ Q.m[3][3] = (deti == 0.0l) ? 0.0l : 1.0l ; /* failure flag if deti == 0 */
+
+ return Q ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Input 9 floats and make an orthgonal mat44 out of them.
+
+ Each row is normalized, then nifti_mat33_polar() is used to orthogonalize
+ them. If row #3 (r31,r32,r33) is input as zero, then it will be taken to
+ be the cross product of rows #1 and #2.
+
+ This function can be used to create a rotation matrix for transforming
+ an oblique volume to anatomical coordinates. For this application:
+ - row #1 (r11,r12,r13) is the direction vector along the image i-axis
+ - row #2 (r21,r22,r23) is the direction vector along the image j-axis
+ - row #3 (r31,r32,r33) is the direction vector along the slice direction
+ (if available; otherwise enter it as 0's)
+
+ The first 2 rows can be taken from the DICOM attribute (0020,0037)
+ "Image Orientation (Patient)".
+
+ After forming the rotation matrix, the complete affine transformation from
+ (i,j,k) grid indexes to (x,y,z) spatial coordinates can be computed by
+ multiplying each column by the appropriate grid spacing:
+ - column #1 (R.m[0][0],R.m[1][0],R.m[2][0]) by delta-x
+ - column #2 (R.m[0][1],R.m[1][1],R.m[2][1]) by delta-y
+ - column #3 (R.m[0][2],R.m[1][2],R.m[2][2]) by delta-z
+
+ and by then placing the center (x,y,z) coordinates of voxel (0,0,0) into
+ the column #4 (R.m[0][3],R.m[1][3],R.m[2][3]).
+
+ \sa nifti_quatern_to_mat44, nifti_mat44_to_quatern,
+ nifti_mat44_to_orientation
+*//*-------------------------------------------------------------------------*/
+mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 ,
+ float r21, float r22, float r23 ,
+ float r31, float r32, float r33 )
+{
+ mat44 R ;
+ mat33 Q , P ;
+ double val ;
+
+ R.m[3][0] = R.m[3][1] = R.m[3][2] = 0.0l ; R.m[3][3] = 1.0l ;
+
+ Q.m[0][0] = r11 ; Q.m[0][1] = r12 ; Q.m[0][2] = r13 ; /* load Q */
+ Q.m[1][0] = r21 ; Q.m[1][1] = r22 ; Q.m[1][2] = r23 ;
+ Q.m[2][0] = r31 ; Q.m[2][1] = r32 ; Q.m[2][2] = r33 ;
+
+ /* normalize row 1 */
+
+ val = Q.m[0][0]*Q.m[0][0] + Q.m[0][1]*Q.m[0][1] + Q.m[0][2]*Q.m[0][2] ;
+ if( val > 0.0l ){
+ val = 1.0l / sqrt(val) ;
+ Q.m[0][0] *= val ; Q.m[0][1] *= val ; Q.m[0][2] *= val ;
+ } else {
+ Q.m[0][0] = 1.0l ; Q.m[0][1] = 0.0l ; Q.m[0][2] = 0.0l ;
+ }
+
+ /* normalize row 2 */
+
+ val = Q.m[1][0]*Q.m[1][0] + Q.m[1][1]*Q.m[1][1] + Q.m[1][2]*Q.m[1][2] ;
+ if( val > 0.0l ){
+ val = 1.0l / sqrt(val) ;
+ Q.m[1][0] *= val ; Q.m[1][1] *= val ; Q.m[1][2] *= val ;
+ } else {
+ Q.m[1][0] = 0.0l ; Q.m[1][1] = 1.0l ; Q.m[1][2] = 0.0l ;
+ }
+
+ /* normalize row 3 */
+
+ val = Q.m[2][0]*Q.m[2][0] + Q.m[2][1]*Q.m[2][1] + Q.m[2][2]*Q.m[2][2] ;
+ if( val > 0.0l ){
+ val = 1.0l / sqrt(val) ;
+ Q.m[2][0] *= val ; Q.m[2][1] *= val ; Q.m[2][2] *= val ;
+ } else {
+ Q.m[2][0] = Q.m[0][1]*Q.m[1][2] - Q.m[0][2]*Q.m[1][1] ; /* cross */
+ Q.m[2][1] = Q.m[0][2]*Q.m[1][0] - Q.m[0][0]*Q.m[1][2] ; /* product */
+ Q.m[2][2] = Q.m[0][0]*Q.m[1][1] - Q.m[0][1]*Q.m[1][0] ;
+ }
+
+ P = nifti_mat33_polar(Q) ; /* P is orthog matrix closest to Q */
+
+ R.m[0][0] = P.m[0][0] ; R.m[0][1] = P.m[0][1] ; R.m[0][2] = P.m[0][2] ;
+ R.m[1][0] = P.m[1][0] ; R.m[1][1] = P.m[1][1] ; R.m[1][2] = P.m[1][2] ;
+ R.m[2][0] = P.m[2][0] ; R.m[2][1] = P.m[2][1] ; R.m[2][2] = P.m[2][2] ;
+
+ R.m[0][3] = R.m[1][3] = R.m[2][3] = 0.0 ; return R ;
+}
+
+/*----------------------------------------------------------------------*/
+/*! compute the inverse of a 3x3 matrix
+*//*--------------------------------------------------------------------*/
+mat33 nifti_mat33_inverse( mat33 R ) /* inverse of 3x3 matrix */
+{
+ double r11,r12,r13,r21,r22,r23,r31,r32,r33 , deti ;
+ mat33 Q ;
+ /* INPUT MATRIX: */
+ r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 ] */
+ r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 ] */
+ r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 ] */
+
+ deti = r11*r22*r33-r11*r32*r23-r21*r12*r33
+ +r21*r32*r13+r31*r12*r23-r31*r22*r13 ;
+
+ if( deti != 0.0l ) deti = 1.0l / deti ;
+
+ Q.m[0][0] = deti*( r22*r33-r32*r23) ;
+ Q.m[0][1] = deti*(-r12*r33+r32*r13) ;
+ Q.m[0][2] = deti*( r12*r23-r22*r13) ;
+
+ Q.m[1][0] = deti*(-r21*r33+r31*r23) ;
+ Q.m[1][1] = deti*( r11*r33-r31*r13) ;
+ Q.m[1][2] = deti*(-r11*r23+r21*r13) ;
+
+ Q.m[2][0] = deti*( r21*r32-r31*r22) ;
+ Q.m[2][1] = deti*(-r11*r32+r31*r12) ;
+ Q.m[2][2] = deti*( r11*r22-r21*r12) ;
+
+ return Q ;
+}
+
+/*----------------------------------------------------------------------*/
+/*! compute the determinant of a 3x3 matrix
+*//*--------------------------------------------------------------------*/
+float nifti_mat33_determ( mat33 R ) /* determinant of 3x3 matrix */
+{
+ double r11,r12,r13,r21,r22,r23,r31,r32,r33 ;
+ /* INPUT MATRIX: */
+ r11 = R.m[0][0]; r12 = R.m[0][1]; r13 = R.m[0][2]; /* [ r11 r12 r13 ] */
+ r21 = R.m[1][0]; r22 = R.m[1][1]; r23 = R.m[1][2]; /* [ r21 r22 r23 ] */
+ r31 = R.m[2][0]; r32 = R.m[2][1]; r33 = R.m[2][2]; /* [ r31 r32 r33 ] */
+
+ return r11*r22*r33-r11*r32*r23-r21*r12*r33
+ +r21*r32*r13+r31*r12*r23-r31*r22*r13 ;
+}
+
+/*----------------------------------------------------------------------*/
+/*! compute the max row norm of a 3x3 matrix
+*//*--------------------------------------------------------------------*/
+float nifti_mat33_rownorm( mat33 A ) /* max row norm of 3x3 matrix */
+{
+ float r1,r2,r3 ;
+
+ r1 = fabs(A.m[0][0])+fabs(A.m[0][1])+fabs(A.m[0][2]) ;
+ r2 = fabs(A.m[1][0])+fabs(A.m[1][1])+fabs(A.m[1][2]) ;
+ r3 = fabs(A.m[2][0])+fabs(A.m[2][1])+fabs(A.m[2][2]) ;
+ if( r1 < r2 ) r1 = r2 ;
+ if( r1 < r3 ) r1 = r3 ;
+ return r1 ;
+}
+
+/*----------------------------------------------------------------------*/
+/*! compute the max column norm of a 3x3 matrix
+*//*--------------------------------------------------------------------*/
+float nifti_mat33_colnorm( mat33 A ) /* max column norm of 3x3 matrix */
+{
+ float r1,r2,r3 ;
+
+ r1 = fabs(A.m[0][0])+fabs(A.m[1][0])+fabs(A.m[2][0]) ;
+ r2 = fabs(A.m[0][1])+fabs(A.m[1][1])+fabs(A.m[2][1]) ;
+ r3 = fabs(A.m[0][2])+fabs(A.m[1][2])+fabs(A.m[2][2]) ;
+ if( r1 < r2 ) r1 = r2 ;
+ if( r1 < r3 ) r1 = r3 ;
+ return r1 ;
+}
+
+/*----------------------------------------------------------------------*/
+/*! multiply 2 3x3 matrices
+*//*--------------------------------------------------------------------*/
+mat33 nifti_mat33_mul( mat33 A , mat33 B ) /* multiply 2 3x3 matrices */
+{
+ mat33 C ; int i,j ;
+ for( i=0 ; i < 3 ; i++ )
+ for( j=0 ; j < 3 ; j++ )
+ C.m[i][j] = A.m[i][0] * B.m[0][j]
+ + A.m[i][1] * B.m[1][j]
+ + A.m[i][2] * B.m[2][j] ;
+ return C ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! polar decomposition of a 3x3 matrix
+
+ This finds the closest orthogonal matrix to input A
+ (in both the Frobenius and L2 norms).
+
+ Algorithm is that from NJ Higham, SIAM J Sci Stat Comput, 7:1160-1174.
+*//*-------------------------------------------------------------------------*/
+mat33 nifti_mat33_polar( mat33 A )
+{
+ mat33 X , Y , Z ;
+ float alp,bet,gam,gmi , dif=1.0 ;
+ int k=0 ;
+
+ X = A ;
+
+ /* force matrix to be nonsingular */
+
+ gam = nifti_mat33_determ(X) ;
+ while( gam == 0.0 ){ /* perturb matrix */
+ gam = 0.00001 * ( 0.001 + nifti_mat33_rownorm(X) ) ;
+ X.m[0][0] += gam ; X.m[1][1] += gam ; X.m[2][2] += gam ;
+ gam = nifti_mat33_determ(X) ;
+ }
+
+ while(1){
+ Y = nifti_mat33_inverse(X) ;
+ if( dif > 0.3 ){ /* far from convergence */
+ alp = sqrt( nifti_mat33_rownorm(X) * nifti_mat33_colnorm(X) ) ;
+ bet = sqrt( nifti_mat33_rownorm(Y) * nifti_mat33_colnorm(Y) ) ;
+ gam = sqrt( bet / alp ) ;
+ gmi = 1.0 / gam ;
+ } else {
+ gam = gmi = 1.0 ; /* close to convergence */
+ }
+ Z.m[0][0] = 0.5 * ( gam*X.m[0][0] + gmi*Y.m[0][0] ) ;
+ Z.m[0][1] = 0.5 * ( gam*X.m[0][1] + gmi*Y.m[1][0] ) ;
+ Z.m[0][2] = 0.5 * ( gam*X.m[0][2] + gmi*Y.m[2][0] ) ;
+ Z.m[1][0] = 0.5 * ( gam*X.m[1][0] + gmi*Y.m[0][1] ) ;
+ Z.m[1][1] = 0.5 * ( gam*X.m[1][1] + gmi*Y.m[1][1] ) ;
+ Z.m[1][2] = 0.5 * ( gam*X.m[1][2] + gmi*Y.m[2][1] ) ;
+ Z.m[2][0] = 0.5 * ( gam*X.m[2][0] + gmi*Y.m[0][2] ) ;
+ Z.m[2][1] = 0.5 * ( gam*X.m[2][1] + gmi*Y.m[1][2] ) ;
+ Z.m[2][2] = 0.5 * ( gam*X.m[2][2] + gmi*Y.m[2][2] ) ;
+
+ dif = fabs(Z.m[0][0]-X.m[0][0])+fabs(Z.m[0][1]-X.m[0][1])
+ +fabs(Z.m[0][2]-X.m[0][2])+fabs(Z.m[1][0]-X.m[1][0])
+ +fabs(Z.m[1][1]-X.m[1][1])+fabs(Z.m[1][2]-X.m[1][2])
+ +fabs(Z.m[2][0]-X.m[2][0])+fabs(Z.m[2][1]-X.m[2][1])
+ +fabs(Z.m[2][2]-X.m[2][2]) ;
+
+ k = k+1 ;
+ if( k > 100 || dif < 3.e-6 ) break ; /* convergence or exhaustion */
+ X = Z ;
+ }
+
+ return Z ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! compute the (closest) orientation from a 4x4 ijk->xyz tranformation matrix
+
+ <pre>
+ Input: 4x4 matrix that transforms (i,j,k) indexes to (x,y,z) coordinates,
+ where +x=Right, +y=Anterior, +z=Superior.
+ (Only the upper-left 3x3 corner of R is used herein.)
+ Output: 3 orientation codes that correspond to the closest "standard"
+ anatomical orientation of the (i,j,k) axes.
+ Method: Find which permutation of (x,y,z) has the smallest angle to the
+ (i,j,k) axes directions, which are the columns of the R matrix.
+ Errors: The codes returned will be zero.
+
+ For example, an axial volume might get return values of
+ *icod = NIFTI_R2L (i axis is mostly Right to Left)
+ *jcod = NIFTI_P2A (j axis is mostly Posterior to Anterior)
+ *kcod = NIFTI_I2S (k axis is mostly Inferior to Superior)
+ </pre>
+
+ \see "QUATERNION REPRESENTATION OF ROTATION MATRIX" in nifti1.h
+
+ \see nifti_quatern_to_mat44, nifti_mat44_to_quatern,
+ nifti_make_orthog_mat44
+*//*-------------------------------------------------------------------------*/
+void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod )
+{
+ float xi,xj,xk , yi,yj,yk , zi,zj,zk , val,detQ,detP ;
+ mat33 P , Q , M ;
+ int i,j,k=0,p,q,r , ibest,jbest,kbest,pbest,qbest,rbest ;
+ float vbest ;
+
+ if( icod == NULL || jcod == NULL || kcod == NULL ) return ; /* bad */
+
+ *icod = *jcod = *kcod = 0 ; /* error returns, if sh*t happens */
+
+ /* load column vectors for each (i,j,k) direction from matrix */
+
+ /*-- i axis --*/ /*-- j axis --*/ /*-- k axis --*/
+
+ xi = R.m[0][0] ; xj = R.m[0][1] ; xk = R.m[0][2] ;
+ yi = R.m[1][0] ; yj = R.m[1][1] ; yk = R.m[1][2] ;
+ zi = R.m[2][0] ; zj = R.m[2][1] ; zk = R.m[2][2] ;
+
+ /* normalize column vectors to get unit vectors along each ijk-axis */
+
+ /* normalize i axis */
+
+ val = sqrt( xi*xi + yi*yi + zi*zi ) ;
+ if( val == 0.0 ) return ; /* stupid input */
+ xi /= val ; yi /= val ; zi /= val ;
+
+ /* normalize j axis */
+
+ val = sqrt( xj*xj + yj*yj + zj*zj ) ;
+ if( val == 0.0 ) return ; /* stupid input */
+ xj /= val ; yj /= val ; zj /= val ;
+
+ /* orthogonalize j axis to i axis, if needed */
+
+ val = xi*xj + yi*yj + zi*zj ; /* dot product between i and j */
+ if( fabs(val) > 1.e-4 ){
+ xj -= val*xi ; yj -= val*yi ; zj -= val*zi ;
+ val = sqrt( xj*xj + yj*yj + zj*zj ) ; /* must renormalize */
+ if( val == 0.0 ) return ; /* j was parallel to i? */
+ xj /= val ; yj /= val ; zj /= val ;
+ }
+
+ /* normalize k axis; if it is zero, make it the cross product i x j */
+
+ val = sqrt( xk*xk + yk*yk + zk*zk ) ;
+ if( val == 0.0 ){ xk = yi*zj-zi*yj; yk = zi*xj-zj*xi ; zk=xi*yj-yi*xj ; }
+ else { xk /= val ; yk /= val ; zk /= val ; }
+
+ /* orthogonalize k to i */
+
+ val = xi*xk + yi*yk + zi*zk ; /* dot product between i and k */
+ if( fabs(val) > 1.e-4 ){
+ xk -= val*xi ; yk -= val*yi ; zk -= val*zi ;
+ val = sqrt( xk*xk + yk*yk + zk*zk ) ;
+ if( val == 0.0 ) return ; /* bad */
+ xk /= val ; yk /= val ; zk /= val ;
+ }
+
+ /* orthogonalize k to j */
+
+ val = xj*xk + yj*yk + zj*zk ; /* dot product between j and k */
+ if( fabs(val) > 1.e-4 ){
+ xk -= val*xj ; yk -= val*yj ; zk -= val*zj ;
+ val = sqrt( xk*xk + yk*yk + zk*zk ) ;
+ if( val == 0.0 ) return ; /* bad */
+ xk /= val ; yk /= val ; zk /= val ;
+ }
+
+ Q.m[0][0] = xi ; Q.m[0][1] = xj ; Q.m[0][2] = xk ;
+ Q.m[1][0] = yi ; Q.m[1][1] = yj ; Q.m[1][2] = yk ;
+ Q.m[2][0] = zi ; Q.m[2][1] = zj ; Q.m[2][2] = zk ;
+
+ /* at this point, Q is the rotation matrix from the (i,j,k) to (x,y,z) axes */
+
+ detQ = nifti_mat33_determ( Q ) ;
+ if( detQ == 0.0 ) return ; /* shouldn't happen unless user is a DUFIS */
+
+ /* Build and test all possible +1/-1 coordinate permutation matrices P;
+ then find the P such that the rotation matrix M=PQ is closest to the
+ identity, in the sense of M having the smallest total rotation angle. */
+
+ /* Despite the formidable looking 6 nested loops, there are
+ only 3*3*3*2*2*2 = 216 passes, which will run very quickly. */
+
+ vbest = -666.0 ; ibest=pbest=qbest=rbest=1 ; jbest=2 ; kbest=3 ;
+ for( i=1 ; i <= 3 ; i++ ){ /* i = column number to use for row #1 */
+ for( j=1 ; j <= 3 ; j++ ){ /* j = column number to use for row #2 */
+ if( i == j ) continue ;
+ for( k=1 ; k <= 3 ; k++ ){ /* k = column number to use for row #3 */
+ if( i == k || j == k ) continue ;
+ P.m[0][0] = P.m[0][1] = P.m[0][2] =
+ P.m[1][0] = P.m[1][1] = P.m[1][2] =
+ P.m[2][0] = P.m[2][1] = P.m[2][2] = 0.0 ;
+ for( p=-1 ; p <= 1 ; p+=2 ){ /* p,q,r are -1 or +1 */
+ for( q=-1 ; q <= 1 ; q+=2 ){ /* and go into rows #1,2,3 */
+ for( r=-1 ; r <= 1 ; r+=2 ){
+ P.m[0][i-1] = p ; P.m[1][j-1] = q ; P.m[2][k-1] = r ;
+ detP = nifti_mat33_determ(P) ; /* sign of permutation */
+ if( detP * detQ <= 0.0 ) continue ; /* doesn't match sign of Q */
+ M = nifti_mat33_mul(P,Q) ;
+
+ /* angle of M rotation = 2.0*acos(0.5*sqrt(1.0+trace(M))) */
+ /* we want largest trace(M) == smallest angle == M nearest to I */
+
+ val = M.m[0][0] + M.m[1][1] + M.m[2][2] ; /* trace */
+ if( val > vbest ){
+ vbest = val ;
+ ibest = i ; jbest = j ; kbest = k ;
+ pbest = p ; qbest = q ; rbest = r ;
+ }
+ }}}}}}
+
+ /* At this point ibest is 1 or 2 or 3; pbest is -1 or +1; etc.
+
+ The matrix P that corresponds is the best permutation approximation
+ to Q-inverse; that is, P (approximately) takes (x,y,z) coordinates
+ to the (i,j,k) axes.
+
+ For example, the first row of P (which contains pbest in column ibest)
+ determines the way the i axis points relative to the anatomical
+ (x,y,z) axes. If ibest is 2, then the i axis is along the y axis,
+ which is direction P2A (if pbest > 0) or A2P (if pbest < 0).
+
+ So, using ibest and pbest, we can assign the output code for
+ the i axis. Mutatis mutandis for the j and k axes, of course. */
+
+ switch( ibest*pbest ){
+ case 1: i = NIFTI_L2R ; break ;
+ case -1: i = NIFTI_R2L ; break ;
+ case 2: i = NIFTI_P2A ; break ;
+ case -2: i = NIFTI_A2P ; break ;
+ case 3: i = NIFTI_I2S ; break ;
+ case -3: i = NIFTI_S2I ; break ;
+ }
+
+ switch( jbest*qbest ){
+ case 1: j = NIFTI_L2R ; break ;
+ case -1: j = NIFTI_R2L ; break ;
+ case 2: j = NIFTI_P2A ; break ;
+ case -2: j = NIFTI_A2P ; break ;
+ case 3: j = NIFTI_I2S ; break ;
+ case -3: j = NIFTI_S2I ; break ;
+ }
+
+ switch( kbest*rbest ){
+ case 1: k = NIFTI_L2R ; break ;
+ case -1: k = NIFTI_R2L ; break ;
+ case 2: k = NIFTI_P2A ; break ;
+ case -2: k = NIFTI_A2P ; break ;
+ case 3: k = NIFTI_I2S ; break ;
+ case -3: k = NIFTI_S2I ; break ;
+ }
+
+ *icod = i ; *jcod = j ; *kcod = k ; return ;
+}
+
+/*---------------------------------------------------------------------------*/
+/* Routines to swap byte arrays in various ways:
+ - 2 at a time: ab -> ba [short]
+ - 4 at a time: abcd -> dcba [int, float]
+ - 8 at a time: abcdDCBA -> ABCDdcba [long long, double]
+ - 16 at a time: abcdefghHGFEDCBA -> ABCDEFGHhgfedcba [long double]
+-----------------------------------------------------------------------------*/
+
+typedef struct { unsigned char a,b ; } twobytes ;
+
+/*----------------------------------------------------------------------*/
+/*! swap each byte pair from the given list of n pairs
+*//*--------------------------------------------------------------------*/
+void nifti_swap_2bytes( int n , void *ar ) /* 2 bytes at a time */
+{
+ register int ii ;
+ register twobytes *tb = (twobytes *)ar ;
+ register unsigned char tt ;
+
+ for( ii=0 ; ii < n ; ii++ ){
+ tt = tb[ii].a ; tb[ii].a = tb[ii].b ; tb[ii].b = tt ;
+ }
+ return ;
+}
+
+/*---------------------------------------------------------------------------*/
+
+typedef struct { unsigned char a,b,c,d ; } fourbytes ;
+
+/*----------------------------------------------------------------------*/
+/*! swap 4 bytes at a time from the given list of n sets of 4 bytes
+*//*--------------------------------------------------------------------*/
+void nifti_swap_4bytes( int n , void *ar ) /* 4 bytes at a time */
+{
+ register int ii ;
+ register fourbytes *tb = (fourbytes *)ar ;
+ register unsigned char tt ;
+
+ for( ii=0 ; ii < n ; ii++ ){
+ tt = tb[ii].a ; tb[ii].a = tb[ii].d ; tb[ii].d = tt ;
+ tt = tb[ii].b ; tb[ii].b = tb[ii].c ; tb[ii].c = tt ;
+ }
+ return ;
+}
+
+/*---------------------------------------------------------------------------*/
+
+typedef struct { unsigned char a,b,c,d , D,C,B,A ; } eightbytes ;
+
+/*----------------------------------------------------------------------*/
+/*! swap 8 bytes at a time from the given list of n sets of 8 bytes
+*//*--------------------------------------------------------------------*/
+void nifti_swap_8bytes( int n , void *ar ) /* 8 bytes at a time */
+{
+ register int ii ;
+ register eightbytes *tb = (eightbytes *)ar ;
+ register unsigned char tt ;
+
+ for( ii=0 ; ii < n ; ii++ ){
+ tt = tb[ii].a ; tb[ii].a = tb[ii].A ; tb[ii].A = tt ;
+ tt = tb[ii].b ; tb[ii].b = tb[ii].B ; tb[ii].B = tt ;
+ tt = tb[ii].c ; tb[ii].c = tb[ii].C ; tb[ii].C = tt ;
+ tt = tb[ii].d ; tb[ii].d = tb[ii].D ; tb[ii].D = tt ;
+ }
+ return ;
+}
+
+/*---------------------------------------------------------------------------*/
+
+typedef struct { unsigned char a,b,c,d,e,f,g,h ,
+ H,G,F,E,D,C,B,A ; } sixteenbytes ;
+
+/*----------------------------------------------------------------------*/
+/*! swap 16 bytes at a time from the given list of n sets of 16 bytes
+*//*--------------------------------------------------------------------*/
+void nifti_swap_16bytes( int n , void *ar ) /* 16 bytes at a time */
+{
+ register int ii ;
+ register sixteenbytes *tb = (sixteenbytes *)ar ;
+ register unsigned char tt ;
+
+ for( ii=0 ; ii < n ; ii++ ){
+ tt = tb[ii].a ; tb[ii].a = tb[ii].A ; tb[ii].A = tt ;
+ tt = tb[ii].b ; tb[ii].b = tb[ii].B ; tb[ii].B = tt ;
+ tt = tb[ii].c ; tb[ii].c = tb[ii].C ; tb[ii].C = tt ;
+ tt = tb[ii].d ; tb[ii].d = tb[ii].D ; tb[ii].D = tt ;
+
+ tt = tb[ii].e ; tb[ii].e = tb[ii].E ; tb[ii].E = tt ;
+ tt = tb[ii].f ; tb[ii].f = tb[ii].F ; tb[ii].F = tt ;
+ tt = tb[ii].g ; tb[ii].g = tb[ii].G ; tb[ii].G = tt ;
+ tt = tb[ii].h ; tb[ii].h = tb[ii].H ; tb[ii].H = tt ;
+ }
+ return ;
+}
+
+/*---------------------------------------------------------------------------*/
+
+/*----------------------------------------------------------------------*/
+/*! based on siz, call the appropriate nifti_swap_Nbytes() function
+*//*--------------------------------------------------------------------*/
+void nifti_swap_Nbytes( int n , int siz , void *ar ) /* subsuming case */
+{
+ switch( siz ){
+ case 2: nifti_swap_2bytes ( n , ar ) ; break ;
+ case 4: nifti_swap_4bytes ( n , ar ) ; break ;
+ case 8: nifti_swap_8bytes ( n , ar ) ; break ;
+ case 16: nifti_swap_16bytes( n , ar ) ; break ;
+ }
+ return ;
+}
+
+
+/*-------------------------------------------------------------------------*/
+/*! Byte swap NIFTI-1 file header in various places and ways.
+
+ If is_nifti is nonzero, will also swap the NIFTI-specific
+ components of the header; otherwise, only the components
+ common to NIFTI and ANALYZE will be swapped.
+*//*---------------------------------------------------------------------- */
+void swap_nifti_header( struct nifti_1_header *h , int is_nifti )
+{
+
+#if 0 /* ANALYZE fields not used by this software */
+ swap_4(h->sizeof_hdr) ;
+ swap_4(h->extents) ;
+ swap_2(h->session_error) ;
+ swap_4(h->compressed) ;
+ swap_4(h->glmax) ; swap_4(h->glmin) ;
+#endif
+
+ /* this stuff is always present, for ANALYZE and NIFTI */
+
+ swap_4(h->sizeof_hdr) ;
+ nifti_swap_2bytes( 8 , h->dim ) ;
+ nifti_swap_4bytes( 8 , h->pixdim ) ;
+
+ swap_2(h->datatype) ;
+ swap_2(h->bitpix) ;
+
+ swap_4(h->vox_offset); swap_4(h->cal_max); swap_4(h->cal_min);
+
+ /* this stuff is NIFTI specific */
+
+ if( is_nifti ){
+ swap_4(h->intent_p1); swap_4(h->intent_p2); swap_4(h->intent_p3);
+ swap_2(h->intent_code);
+
+ swap_2(h->slice_start); swap_2(h->slice_end);
+ swap_4(h->scl_slope); swap_4(h->scl_inter);
+ swap_4(h->slice_duration); swap_4(h->toffset);
+
+ swap_2(h->qform_code); swap_2(h->sform_code);
+ swap_4(h->quatern_b); swap_4(h->quatern_c); swap_4(h->quatern_d);
+ swap_4(h->qoffset_x); swap_4(h->qoffset_y); swap_4(h->qoffset_z);
+ nifti_swap_4bytes(4,h->srow_x);
+ nifti_swap_4bytes(4,h->srow_y);
+ nifti_swap_4bytes(4,h->srow_z);
+ }
+ return ;
+}
+
+
+#define USE_STAT
+#ifdef USE_STAT
+/*---------------------------------------------------------------------------*/
+/* Return the file length (0 if file not found or has no contents).
+ This is a Unix-specific function, since it uses stat().
+-----------------------------------------------------------------------------*/
+#include <sys/types.h>
+#include <sys/stat.h>
+
+/*---------------------------------------------------------------------------*/
+/*! return the size of a file, in bytes
+
+ \return size of file on success, -1 on error or no file
+
+ changed to return int, -1 means no file or error 20 Dec 2004 [rickr]
+*//*-------------------------------------------------------------------------*/
+int nifti_get_filesize( const char *pathname )
+{
+ struct stat buf ; int ii ;
+
+ if( pathname == NULL || *pathname == '\0' ) return -1 ;
+ ii = stat( pathname , &buf ); if( ii != 0 ) return -1 ;
+ return (unsigned int)buf.st_size ;
+}
+
+#else /*---------- non-Unix version of the above, less efficient -----------*/
+
+int nifti_get_filesize( const char *pathname )
+{
+ znzFile fp ; int len ;
+
+ if( pathname == NULL || *pathname == '\0' ) return -1 ;
+ fp = znzopen(pathname,"rb",0); if( znz_isnull(fp) ) return -1 ;
+ znzseek(fp,0L,SEEK_END) ; len = znztell(fp) ;
+ znzclose(fp) ; return len ;
+}
+
+#endif /* USE_STAT */
+
+
+/*----------------------------------------------------------------------*/
+/*! return the total volume size, in bytes
+
+ This is computed as nvox * nbyper.
+*//*--------------------------------------------------------------------*/
+size_t nifti_get_volsize(const nifti_image *nim)
+{
+ return (size_t)(nim->nbyper) * (size_t)(nim->nvox) ; /* total bytes */
+}
+
+
+/*--------------------------------------------------------------------------*/
+/* Support functions for filenames in read and write
+ - allows for gzipped files
+*/
+
+
+/*----------------------------------------------------------------------*/
+/*! simple check for file existence
+
+ \return 1 on existence, 0 otherwise
+*//*--------------------------------------------------------------------*/
+int nifti_fileexists(const char* fname)
+{
+ znzFile fp;
+ fp = znzopen( fname , "rb" , 1 ) ;
+ if( !znz_isnull(fp) ) { znzclose(fp); return 1; }
+ return 0; /* fp is NULL */
+}
+
+/*----------------------------------------------------------------------*/
+/*! return whether the filename is valid
+
+ The name is considered valid if the file basename has length greater than
+ zero, AND one of the valid nifti extensions is provided.
+ fname input | return |
+ ===============================
+ "myimage" | 0 |
+ "myimage.tif" | 0 |
+ "myimage.tif.gz" | 0 |
+ "myimage.nii" | 1 |
+ ".nii" | 0 |
+ ".myhiddenimage" | 0 |
+ ".myhiddenimage.nii" | 1 |
+*//*--------------------------------------------------------------------*/
+int nifti_is_complete_filename(const char* fname)
+{
+ char * ext;
+
+ /* check input file(s) for sanity */
+ if( fname == NULL || *fname == '\0' ){
+ if ( g_opts.debug > 1 )
+ fprintf(stderr,"-- empty filename in nifti_validfilename()\n");
+ return 0;
+ }
+
+ ext = nifti_find_file_extension(fname);
+ if ( ext == NULL ) { /*Invalid extension given */
+ if ( g_opts.debug > 0 )
+ fprintf(stderr,"-- no nifti valid extension for filename '%s'\n", fname);
+ return 0;
+ }
+
+ if ( ext && ext == fname ) { /* then no filename prefix */
+ if ( g_opts.debug > 0 )
+ fprintf(stderr,"-- no prefix for filename '%s'\n", fname);
+ return 0;
+ }
+ return 1;
+}
+
+/*----------------------------------------------------------------------*/
+/*! return whether the filename is valid
+
+ The name is considered valid if its length is positive, excluding
+ any nifti filename extension.
+ fname input | return | result of nifti_makebasename
+ ====================================================================
+ "myimage" | 1 | "myimage"
+ "myimage.tif" | 1 | "myimage.tif"
+ "myimage.tif.gz" | 1 | "myimage.tif"
+ "myimage.nii" | 1 | "myimage"
+ ".nii" | 0 | <ERROR - basename has zero length>
+ ".myhiddenimage" | 1 | ".myhiddenimage"
+ ".myhiddenimage.nii | 1 | ".myhiddenimage"
+*//*--------------------------------------------------------------------*/
+int nifti_validfilename(const char* fname)
+{
+ char * ext;
+
+ /* check input file(s) for sanity */
+ if( fname == NULL || *fname == '\0' ){
+ if ( g_opts.debug > 1 )
+ fprintf(stderr,"-- empty filename in nifti_validfilename()\n");
+ return 0;
+ }
+
+ ext = nifti_find_file_extension(fname);
+
+ if ( ext && ext == fname ) { /* then no filename prefix */
+ if ( g_opts.debug > 0 )
+ fprintf(stderr,"-- no prefix for filename '%s'\n", fname);
+ return 0;
+ }
+
+ return 1;
+}
+
+/*----------------------------------------------------------------------*/
+/*! check the end of the filename for a valid nifti extension
+
+ Valid extensions are currently .nii, .hdr, .img, .nia,
+ or any of them followed by .gz. Note that '.' is part of
+ the extension.
+
+ \return a pointer to the extension (within the filename), or NULL
+*//*--------------------------------------------------------------------*/
+char * nifti_find_file_extension( const char * name )
+{
+ char * ext;
+ int len;
+
+ if ( ! name ) return NULL;
+
+ len = strlen(name);
+ if ( len < 4 ) return NULL;
+
+ ext = (char *)name + len - 4;
+
+ if ( (strcmp(ext, ".hdr") == 0) || (strcmp(ext, ".img") == 0) ||
+ (strcmp(ext, ".nia") == 0) || (strcmp(ext, ".nii") == 0) )
+ return ext;
+
+#ifdef HAVE_ZLIB
+ if ( len < 7 ) return NULL;
+
+ ext = (char *)name + len - 7;
+
+ if ( (strcmp(ext, ".hdr.gz") == 0) || (strcmp(ext, ".img.gz") == 0) ||
+ (strcmp(ext, ".nia.gz") == 0) || (strcmp(ext, ".nii.gz") == 0) )
+ return ext;
+#endif
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"** find_file_ext: failed for name '%s'\n", name);
+
+ return NULL;
+}
+
+/*----------------------------------------------------------------------*/
+/*! return whether the filename ends in ".gz"
+*//*--------------------------------------------------------------------*/
+int nifti_is_gzfile(const char* fname)
+{
+ /* return true if the filename ends with .gz */
+ if (fname == NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ { /* just so len doesn't generate compile warning */
+ int len;
+ len = strlen(fname);
+ if (len < 3) return 0; /* so we don't search before the name */
+ if (strcmp(fname + strlen(fname) - 3,".gz")==0) { return 1; }
+ }
+#endif
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! duplicate the filename, while clearing any extension
+
+ This allocates memory for basename which should eventually be freed.
+*//*--------------------------------------------------------------------*/
+char * nifti_makebasename(const char* fname)
+{
+ char *basename, *ext;
+
+ basename=nifti_strdup(fname);
+
+ ext = nifti_find_file_extension(basename);
+ if ( ext ) *ext = '\0'; /* clear out extension */
+
+ return basename; /* in either case */
+}
+
+/*----------------------------------------------------------------------*/
+/*! set nifti's global debug level, for status reporting
+
+ - 0 : quiet, nothing is printed to the terminal, but errors
+ - 1 : normal execution (the default)
+ - 2, 3 : more details
+*//*--------------------------------------------------------------------*/
+void nifti_set_debug_level( int level )
+{
+ g_opts.debug = level;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! check current directory for existing header file
+
+ \return filename of header on success and NULL if no appropriate file
+ could be found
+
+ NB: it allocates memory for hdrname which should be freed
+ when no longer required
+*//*-------------------------------------------------------------------*/
+char * nifti_findhdrname(const char* fname)
+{
+ char *basename, *hdrname, *ext;
+ char elist[2][5] = { ".hdr", ".nii" };
+ int efirst;
+
+ /**- check input file(s) for sanity */
+ if( !nifti_validfilename(fname) ) return NULL;
+
+ basename = nifti_makebasename(fname);
+ if( !basename ) return NULL; /* only on string alloc failure */
+
+ /**- return filename if it has a valid extension and exists
+ (except if it is an .img file (and maybe .gz)) */
+ ext = nifti_find_file_extension(fname);
+ if ( ext && nifti_fileexists(fname) ) {
+ if ( strncmp(ext,".img",4) != 0 ){
+ hdrname = nifti_strdup(fname);
+ free(basename);
+ return hdrname;
+ }
+ }
+
+ /* So the requested name is a basename, contains .img, or does not exist. */
+ /* In any case, use basename. */
+
+ /**- if .img, look for .hdr, .hdr.gz, .nii, .nii.gz, in that order */
+ /**- else, look for .nii, .nii.gz, .hdr, .hdr.gz, in that order */
+
+ /* if we get more extension choices, this could be a loop */
+
+ if ( ext && strncmp(ext,".img",4) != 0 ) efirst = 0;
+ else efirst = 1;
+
+ hdrname = (char *)calloc(sizeof(char),strlen(basename)+8);
+ if( !hdrname ){
+ fprintf(stderr,"** nifti_findhdrname: failed to alloc hdrname\n");
+ free(basename);
+ return NULL;
+ }
+
+ strcpy(hdrname,basename);
+ strcat(hdrname,elist[efirst]);
+ if (nifti_fileexists(hdrname)) { free(basename); return hdrname; }
+#ifdef HAVE_ZLIB
+ strcat(hdrname,".gz");
+ if (nifti_fileexists(hdrname)) { free(basename); return hdrname; }
+#endif
+
+ /* okay, try the other possibility */
+
+ efirst = 1 - efirst;
+
+ strcpy(hdrname,basename);
+ strcat(hdrname,elist[efirst]);
+ if (nifti_fileexists(hdrname)) { free(basename); return hdrname; }
+#ifdef HAVE_ZLIB
+ strcat(hdrname,".gz");
+ if (nifti_fileexists(hdrname)) { free(basename); return hdrname; }
+#endif
+
+ /**- if nothing has been found, return NULL */
+ free(basename);
+ free(hdrname);
+ return NULL;
+}
+
+
+/*------------------------------------------------------------------------*/
+/*! check current directory for existing image file
+
+ \param fname filename to check for
+ \nifti_type nifti_type for dataset - this determines whether to
+ first check for ".nii" or ".img" (since both may exist)
+
+ \return filename of data/img file on success and NULL if no appropriate
+ file could be found
+
+ NB: it allocates memory for the image filename, which should be freed
+ when no longer required
+*//*---------------------------------------------------------------------*/
+char * nifti_findimgname(const char* fname , int nifti_type)
+{
+ char *basename, *imgname, ext[2][5] = { ".nii", ".img" };
+ int first; /* first extension to use */
+
+ /* check input file(s) for sanity */
+
+ if( !nifti_validfilename(fname) ) return NULL;
+
+ basename = nifti_makebasename(fname);
+ imgname = (char *)calloc(sizeof(char),strlen(basename)+8);
+ if( !imgname ){
+ fprintf(stderr,"** nifti_findimgname: failed to alloc imgname\n");
+ free(basename);
+ return NULL;
+ }
+
+ /**- test for .nii and .img (don't assume input type from image type) */
+ /**- if nifti_type = 1, check for .nii first, else .img first */
+
+ /* if we get 3 or more extensions, can make a loop here... */
+
+ if (nifti_type == NIFTI_FTYPE_NIFTI1_1) first = 0; /* should match .nii */
+ else first = 1; /* should match .img */
+
+ strcpy(imgname,basename);
+ strcat(imgname,ext[first]);
+ if (nifti_fileexists(imgname)) { free(basename); return imgname; }
+#ifdef HAVE_ZLIB /* then also check for .gz */
+ strcat(imgname,".gz");
+ if (nifti_fileexists(imgname)) { free(basename); return imgname; }
+#endif
+
+ /* failed to find image file with expected extension, try the other */
+
+ strcpy(imgname,basename);
+ strcat(imgname,ext[1-first]); /* can do this with only 2 choices */
+ if (nifti_fileexists(imgname)) { free(basename); return imgname; }
+#ifdef HAVE_ZLIB /* then also check for .gz */
+ strcat(imgname,".gz");
+ if (nifti_fileexists(imgname)) { free(basename); return imgname; }
+#endif
+
+ /**- if nothing has been found, return NULL */
+ free(basename);
+ free(imgname);
+ return NULL;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! creates a filename for storing the header, based on nifti_type
+
+ \param prefix - this will be copied before the suffix is added
+ \param nifti_type - determines the extension, unless one is in prefix
+ \param check - check for existence (fail condition)
+ \param comp - add .gz for compressed name
+
+ Note that if prefix provides a file suffix, nifti_type is not used.
+
+ NB: this allocates memory which should be freed
+
+ \sa nifti_set_filenames
+*//*-------------------------------------------------------------------*/
+char * nifti_makehdrname(const char * prefix, int nifti_type, int check,
+ int comp)
+{
+ char * iname, * ext;
+
+ if( !nifti_validfilename(prefix) ) return NULL;
+
+ /* add space for extension, optional ".gz", and null char */
+ iname = (char *)calloc(sizeof(char),strlen(prefix)+8);
+ if( !iname ){ fprintf(stderr,"** small malloc failure!\n"); return NULL; }
+ strcpy(iname, prefix);
+
+ /* use any valid extension */
+ if( (ext = nifti_find_file_extension(iname)) != NULL ){
+ if( strncmp(ext,".img",4) == 0 )
+ memcpy(ext,".hdr",4); /* then convert img name to hdr */
+ }
+ /* otherwise, make one up an */
+ else if( nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcat(iname, ".nii");
+ else if( nifti_type == NIFTI_FTYPE_ASCII ) strcat(iname, ".nia");
+ else strcat(iname, ".hdr");
+
+#ifdef HAVE_ZLIB /* then also check for .gz */
+ if( comp && (!ext || !strstr(iname,".gz")) ) strcat(iname,".gz");
+#endif
+
+ /* check for existence failure */
+ if( check && nifti_fileexists(iname) ){
+ fprintf(stderr,"** failure: header file '%s' already exists\n",iname);
+ free(iname);
+ return NULL;
+ }
+
+ if(g_opts.debug > 2) fprintf(stderr,"+d made header filename '%s'\n", iname);
+
+ return iname;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! creates a filename for storing the image, based on nifti_type
+
+ \param prefix - this will be copied before the suffix is added
+ \param nifti_type - determines the extension, unless provided by prefix
+ \param check - check for existence (fail condition)
+ \param comp - add .gz for compressed name
+
+ Note that if prefix provides a file suffix, nifti_type is not used.
+
+ NB: it allocates memory which should be freed
+
+ \sa nifti_set_filenames
+*//*-------------------------------------------------------------------*/
+char * nifti_makeimgname(const char * prefix, int nifti_type, int check,
+ int comp)
+{
+ char * iname, * ext;
+
+ if( !nifti_validfilename(prefix) ) return NULL;
+
+ /* add space for extension, optional ".gz", and null char */
+ iname = (char *)calloc(sizeof(char),strlen(prefix)+8);
+ if( !iname ){ fprintf(stderr,"** small malloc failure!\n"); return NULL; }
+ strcpy(iname, prefix);
+
+ /* use any valid extension */
+ if( (ext = nifti_find_file_extension(iname)) != NULL ){
+ if( strncmp(ext,".hdr",4) == 0 )
+ memcpy(ext,".img",4); /* then convert hdr name to img */
+ }
+ /* otherwise, make one up */
+ else if( nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcat(iname, ".nii");
+ else if( nifti_type == NIFTI_FTYPE_ASCII ) strcat(iname, ".nia");
+ else strcat(iname, ".img");
+
+#ifdef HAVE_ZLIB /* then also check for .gz */
+ if( comp && (!ext || !strstr(iname,".gz")) ) strcat(iname,".gz");
+#endif
+
+ /* check for existence failure */
+ if( check && nifti_fileexists(iname) ){
+ fprintf(stderr,"** failure: image file '%s' already exists\n",iname);
+ free(iname);
+ return NULL;
+ }
+
+ if( g_opts.debug > 2 ) fprintf(stderr,"+d made image filename '%s'\n",iname);
+
+ return iname;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! create and set new filenames, based on prefix and image type
+
+ \param nim pointer to nifti_image in which to set filenames
+ \param prefix (required) prefix for output filenames
+ \param check check for previous existence of filename
+ (existence is an error condition)
+ \param set_byte_order flag to set nim->byteorder here
+ (this is probably a logical place to do so)
+
+ \return 0 on successful update
+
+ \warning this will free() any existing names and create new ones
+
+ \sa nifti_makeimgname, nifti_makehdrname, nifti_type_and_names_match
+*//*--------------------------------------------------------------------*/
+int nifti_set_filenames( nifti_image * nim, const char * prefix, int check,
+ int set_byte_order )
+{
+ int comp = nifti_is_gzfile(prefix);
+
+ if( !nim || !prefix ){
+ fprintf(stderr,"** nifti_set_filenames, bad params %p, %p\n",
+ (void *)nim,prefix);
+ return -1;
+ }
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d modifying output filenames using prefix %s\n", prefix);
+
+ if( nim->fname ) free(nim->fname);
+ if( nim->iname ) free(nim->iname);
+ nim->fname = nifti_makehdrname(prefix, nim->nifti_type, check, comp);
+ nim->iname = nifti_makeimgname(prefix, nim->nifti_type, check, comp);
+ if( !nim->fname || !nim->iname ){
+ LNI_FERR("nifti_set_filename","failed to set prefix for",prefix);
+ return -1;
+ }
+
+ if( set_byte_order ) nim->byteorder = nifti_short_order() ;
+
+ if( nifti_set_type_from_names(nim) < 0 )
+ return -1;
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"+d have new filenames %s and %s\n",nim->fname,nim->iname);
+
+ return 0;
+}
+
+
+/*--------------------------------------------------------------------------*/
+/*! check whether nifti_type matches fname and iname for the nifti_image
+
+ - if type 0 or 2, expect .hdr/.img pair
+ - if type 1, expect .nii (and names must match)
+
+ \param nim given nifti_image
+ \param show_warn if set, print a warning message for any mis-match
+
+ \return
+ - 1 if the values seem to match
+ - 0 if there is a mis-match
+ - -1 if there is not sufficient information to create file(s)
+
+ \sa NIFTI_FTYPE_* codes in nifti1_io.h
+ \sa nifti_set_type_from_names, is_valid_nifti_type
+*//*------------------------------------------------------------------------*/
+int nifti_type_and_names_match( nifti_image * nim, int show_warn )
+{
+ char func[] = "nifti_type_and_names_match";
+ char * ext_h, * ext_i; /* header and image filename extensions */
+ int errs = 0; /* error counter */
+
+ /* sanity checks */
+ if( !nim ){
+ if( show_warn ) fprintf(stderr,"** %s: missing nifti_image\n", func);
+ return -1;
+ }
+ if( !nim->fname ){
+ if( show_warn ) fprintf(stderr,"** %s: missing header filename\n", func);
+ errs++;
+ }
+ if( !nim->iname ){
+ if( show_warn ) fprintf(stderr,"** %s: missing image filename\n", func);
+ errs++;
+ }
+ if( !is_valid_nifti_type(nim->nifti_type) ){
+ if( show_warn )
+ fprintf(stderr,"** %s: bad nifti_type %d\n", func, nim->nifti_type);
+ errs++;
+ }
+
+ if( errs ) return -1; /* then do not proceed */
+
+ /* get pointers to extensions */
+ ext_h = nifti_find_file_extension( nim->fname );
+ ext_i = nifti_find_file_extension( nim->iname );
+
+ /* check for filename extensions */
+ if( !ext_h ){
+ if( show_warn )
+ fprintf(stderr,"-d missing NIFTI extension in header filename, %s\n",
+ nim->fname);
+ errs++;
+ }
+ if( !ext_i ){
+ if( show_warn )
+ fprintf(stderr,"-d missing NIFTI extension in image filename, %s\n",
+ nim->iname);
+ errs++;
+ }
+
+ if( errs ) return 0; /* do not proceed, but this is just a mis-match */
+
+ /* general tests */
+ if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ){ /* .nii */
+ if( strncmp(ext_h,".nii",4) ) {
+ if( show_warn )
+ fprintf(stderr,
+ "-d NIFTI_FTYPE 1, but no .nii extension in header filename, %s\n",
+ nim->fname);
+ errs++;
+ }
+ if( strncmp(ext_i,".nii",4) ) {
+ if( show_warn )
+ fprintf(stderr,
+ "-d NIFTI_FTYPE 1, but no .nii extension in image filename, %s\n",
+ nim->iname);
+ errs++;
+ }
+ if( strcmp(nim->fname, nim->iname) != 0 ){
+ if( show_warn )
+ fprintf(stderr,
+ "-d NIFTI_FTYPE 1, but header and image filenames differ: %s, %s\n",
+ nim->fname, nim->iname);
+ errs++;
+ }
+ }
+ else if( (nim->nifti_type == NIFTI_FTYPE_NIFTI1_2) || /* .hdr/.img */
+ (nim->nifti_type == NIFTI_FTYPE_ANALYZE) )
+ {
+ if( strncmp(ext_h,".hdr",4) != 0 ){
+ if( show_warn )
+ fprintf(stderr,"-d no '.hdr' extension, but NIFTI type is %d, %s\n",
+ nim->nifti_type, nim->fname);
+ errs++;
+ }
+ if( strncmp(ext_i,".img",4) != 0 ){
+ if( show_warn )
+ fprintf(stderr,"-d no '.img' extension, but NIFTI type is %d, %s\n",
+ nim->nifti_type, nim->iname);
+ errs++;
+ }
+ }
+ /* ignore any other nifti_type */
+
+ return 1;
+}
+
+
+/*--------------------------------------------------------------------------*/
+/*! check whether the given type is on the "approved" list
+
+ The code is valid if it is non-negative, and does not exceed
+ NIFTI_MAX_FTYPE.
+
+ \return 1 if nifti_type is valid, 0 otherwise
+ \sa NIFTI_FTYPE_* codes in nifti1_io.h
+*//*------------------------------------------------------------------------*/
+int is_valid_nifti_type( int nifti_type )
+{
+ if( nifti_type >= NIFTI_FTYPE_ANALYZE && /* smallest type, 0 */
+ nifti_type <= NIFTI_MAX_FTYPE )
+ return 1;
+ return 0;
+}
+
+
+/*--------------------------------------------------------------------------*/
+/*! set the nifti_type field based on fname and iname
+
+ Note that nifti_type is changed only when it does not match
+ the filenames.
+
+ \return 0 on success, -1 on error
+
+ \sa is_valid_nifti_type, nifti_type_and_names_match
+*//*------------------------------------------------------------------------*/
+int nifti_set_type_from_names( nifti_image * nim )
+{
+ /* error checking first */
+ if( !nim ){ fprintf(stderr,"** NSTFN: no nifti_image\n"); return -1; }
+
+ if( !nim->fname || !nim->iname ){
+ fprintf(stderr,"** NSTFN: missing filename(s) fname @ %p, iname @ %p\n",
+ nim->fname, nim->iname);
+ return -1;
+ }
+
+ if( ! nifti_validfilename ( nim->fname ) ||
+ ! nifti_validfilename ( nim->iname ) ||
+ ! nifti_find_file_extension( nim->fname ) ||
+ ! nifti_find_file_extension( nim->iname )
+ ) {
+ fprintf(stderr,"** NSTFN: invalid filename(s) fname='%s', iname='%s'\n",
+ nim->fname, nim->iname);
+ return -1;
+ }
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d verify nifti_type from filenames: %d",nim->nifti_type);
+
+ /* not too picky here, do what must be done, and then verify */
+ if( strcmp(nim->fname, nim->iname) == 0 ) /* one file, type 1 */
+ nim->nifti_type = NIFTI_FTYPE_NIFTI1_1;
+ else if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ) /* cannot be type 1 */
+ nim->nifti_type = NIFTI_FTYPE_NIFTI1_2;
+
+ if( g_opts.debug > 2 ) fprintf(stderr," -> %d\n",nim->nifti_type);
+
+ if( g_opts.debug > 1 ) /* warn user about anything strange */
+ nifti_type_and_names_match(nim, 1);
+
+ if( is_valid_nifti_type(nim->nifti_type) ) return 0; /* success! */
+
+ fprintf(stderr,"** NSTFN: bad nifti_type %d, for '%s' and '%s'\n",
+ nim->nifti_type, nim->fname, nim->iname);
+
+ return -1;
+}
+
+
+/*--------------------------------------------------------------------------*/
+/*! Determine if this is a NIFTI-formatted file.
+
+ <pre>
+ \return 0 if file looks like ANALYZE 7.5 [checks sizeof_hdr field == 348]
+ 1 if file marked as NIFTI (header+data in 1 file)
+ 2 if file marked as NIFTI (header+data in 2 files)
+ -1 if it can't tell, file doesn't exist, etc.
+ </pre>
+*//*------------------------------------------------------------------------*/
+int is_nifti_file( const char *hname )
+{
+ struct nifti_1_header nhdr ;
+ znzFile fp ;
+ int ii ;
+ char *tmpname;
+
+ /* bad input name? */
+
+ if( !nifti_validfilename(hname) ) return -1 ;
+
+ /* open file */
+
+ tmpname = nifti_findhdrname(hname);
+ if( tmpname == NULL ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** no header file found for '%s'\n",hname);
+ return -1;
+ }
+ fp = znzopen( tmpname , "rb" , nifti_is_gzfile(tmpname) ) ;
+ free(tmpname);
+ if (znz_isnull(fp)) return -1 ; /* bad open? */
+
+ /* read header, close file */
+
+ ii = znzread( &nhdr , 1 , sizeof(nhdr) , fp ) ;
+ znzclose( fp ) ;
+ if( ii < (int) sizeof(nhdr) ) return -1 ; /* bad read? */
+
+ /* check for NIFTI-ness */
+
+ if( NIFTI_VERSION(nhdr) != 0 ){
+ return ( NIFTI_ONEFILE(nhdr) ) ? 1 : 2 ;
+ }
+
+ /* check for ANALYZE-ness (sizeof_hdr field == 348) */
+
+ ii = nhdr.sizeof_hdr ;
+ if( ii == (int)sizeof(nhdr) ) return 0 ; /* matches */
+
+ /* try byte-swapping header */
+
+ swap_4(ii) ;
+ if( ii == (int)sizeof(nhdr) ) return 0 ; /* matches */
+
+ return -1 ; /* not good */
+}
+
+static int print_hex_vals( const char * data, int nbytes, FILE * fp )
+{
+ int c;
+
+ if ( !data || nbytes < 1 || !fp ) return -1;
+
+ fputs("0x", fp);
+ for ( c = 0; c < nbytes; c++ )
+ fprintf(fp, " %x", data[c]);
+
+ return 0;
+}
+
+/*----------------------------------------------------------------------*/
+/*! display the contents of the nifti_1_header (send to stdout)
+
+ \param info if non-NULL, print this character string
+ \param hp pointer to nifti_1_header
+*//*--------------------------------------------------------------------*/
+int disp_nifti_1_header( const char * info, const nifti_1_header * hp )
+{
+ int c;
+
+ fputs( "-------------------------------------------------------\n", stdout );
+ if ( info ) fputs( info, stdout );
+ if ( !hp ){ fputs(" ** no nifti_1_header to display!\n",stdout); return 1; }
+
+ fprintf(stdout," nifti_1_header :\n"
+ " sizeof_hdr = %d\n"
+ " data_type[10] = ", hp->sizeof_hdr);
+ print_hex_vals(hp->data_type, 10, stdout);
+ fprintf(stdout, "\n"
+ " db_name[18] = ");
+ print_hex_vals(hp->db_name, 18, stdout);
+ fprintf(stdout, "\n"
+ " extents = %d\n"
+ " session_error = %d\n"
+ " regular = 0x%x\n"
+ " dim_info = 0x%x\n",
+ hp->extents, hp->session_error, hp->regular, hp->dim_info );
+ fprintf(stdout, " dim[8] =");
+ for ( c = 0; c < 8; c++ ) fprintf(stdout," %d", hp->dim[c]);
+ fprintf(stdout, "\n"
+ " intent_p1 = %f\n"
+ " intent_p2 = %f\n"
+ " intent_p3 = %f\n"
+ " intent_code = %d\n"
+ " datatype = %d\n"
+ " bitpix = %d\n"
+ " slice_start = %d\n"
+ " pixdim[8] =",
+ hp->intent_p1, hp->intent_p2, hp->intent_p3, hp->intent_code,
+ hp->datatype, hp->bitpix, hp->slice_start);
+ /* break pixdim over 2 lines */
+ for ( c = 0; c < 4; c++ ) fprintf(stdout," %f", hp->pixdim[c]);
+ fprintf(stdout, "\n ");
+ for ( c = 4; c < 8; c++ ) fprintf(stdout," %f", hp->pixdim[c]);
+ fprintf(stdout, "\n"
+ " vox_offset = %f\n"
+ " scl_slope = %f\n"
+ " scl_inter = %f\n"
+ " slice_end = %d\n"
+ " slice_code = %d\n"
+ " xyzt_units = 0x%x\n"
+ " cal_max = %f\n"
+ " cal_min = %f\n"
+ " slice_duration = %f\n"
+ " toffset = %f\n"
+ " glmax = %d\n"
+ " glmin = %d\n",
+ hp->vox_offset, hp->scl_slope, hp->scl_inter, hp->slice_end,
+ hp->slice_code, hp->xyzt_units, hp->cal_max, hp->cal_min,
+ hp->slice_duration, hp->toffset, hp->glmax, hp->glmin);
+ fprintf(stdout,
+ " descrip = '%.80s'\n"
+ " aux_file = '%.24s'\n"
+ " qform_code = %d\n"
+ " sform_code = %d\n"
+ " quatern_b = %f\n"
+ " quatern_c = %f\n"
+ " quatern_d = %f\n"
+ " qoffset_x = %f\n"
+ " qoffset_y = %f\n"
+ " qoffset_z = %f\n"
+ " srow_x[4] = %f, %f, %f, %f\n"
+ " srow_y[4] = %f, %f, %f, %f\n"
+ " srow_z[4] = %f, %f, %f, %f\n"
+ " intent_name = '%-.16s'\n"
+ " magic = '%-.4s'\n",
+ hp->descrip, hp->aux_file, hp->qform_code, hp->sform_code,
+ hp->quatern_b, hp->quatern_c, hp->quatern_d,
+ hp->qoffset_x, hp->qoffset_y, hp->qoffset_z,
+ hp->srow_x[0], hp->srow_x[1], hp->srow_x[2], hp->srow_x[3],
+ hp->srow_y[0], hp->srow_y[1], hp->srow_y[2], hp->srow_y[3],
+ hp->srow_z[0], hp->srow_z[1], hp->srow_z[2], hp->srow_z[3],
+ hp->intent_name, hp->magic);
+ fputs( "-------------------------------------------------------\n", stdout );
+ fflush(stdout);
+
+ return 0;
+}
+
+
+#undef ERREX
+#define ERREX(msg) \
+ do{ fprintf(stderr,"** ERROR: nifti_convert_nhdr2nim: %s\n", (msg) ) ; \
+ return NULL ; } while(0)
+
+/*----------------------------------------------------------------------*/
+/*! convert a nifti_1_header into a nift1_image
+
+ \return an allocated nifti_image, or NULL on failure
+*//*--------------------------------------------------------------------*/
+nifti_image* nifti_convert_nhdr2nim(struct nifti_1_header nhdr,
+ const char * fname)
+{
+ int ii , doswap , ioff ;
+ int is_nifti , is_onefile ;
+ nifti_image *nim;
+
+ nim = (nifti_image *) calloc( 1 , sizeof(nifti_image) ) ;
+ if( !nim ) ERREX("failed to allocate nifti image");
+
+ /* be explicit with pointers */
+ nim->fname = NULL;
+ nim->iname = NULL;
+ nim->data = NULL;
+
+ /**- check if we must swap bytes */
+
+ doswap = need_nhdr_swap(nhdr.dim[0], nhdr.sizeof_hdr); /* swap data flag */
+
+ if( doswap < 0 ){
+ if( doswap == -1 ) ERREX("bad dim[0]") ;
+ ERREX("bad sizeof_hdr") ; /* else */
+ }
+
+ /**- determine if this is a NIFTI-1 compliant header */
+
+ is_nifti = NIFTI_VERSION(nhdr) ;
+ /*
+ * before swapping header, record the Analyze75 orient code
+ */
+ if(!is_nifti)
+ {
+ /**- in analyze75, the orient code is at the same address as
+ * qform_code, but it's just one byte
+ * the qform_code will be zero, at which point you can check
+ * analyze75_orient if you care to.
+ */
+ unsigned char c = *((char *)(&nhdr.qform_code));
+ nim->analyze75_orient = (analyze_75_orient_code)c;
+ }
+ if( doswap ) {
+ if ( g_opts.debug > 3 ) disp_nifti_1_header("-d ni1 pre-swap: ", &nhdr);
+ swap_nifti_header( &nhdr , is_nifti ) ;
+ }
+
+ if ( g_opts.debug > 2 ) disp_nifti_1_header("-d nhdr2nim : ", &nhdr);
+
+ if( nhdr.datatype == DT_BINARY ||
+ nhdr.datatype == DT_UNKNOWN ) ERREX("bad datatype") ;
+
+ if( nhdr.dim[1] <= 0 ) ERREX("bad dim[1]") ;
+
+ /* fix bad dim[] values in the defined dimension range */
+ for( ii=2 ; ii <= nhdr.dim[0] ; ii++ )
+ if( nhdr.dim[ii] <= 0 ) nhdr.dim[ii] = 1 ;
+
+ /* fix any remaining bad dim[] values, so garbage does not propagate */
+ /* (only values 0 or 1 seem rational, otherwise set to arbirary 1) */
+ for( ii=nhdr.dim[0]+1 ; ii <= 7 ; ii++ )
+ if( nhdr.dim[ii] != 1 && nhdr.dim[ii] != 0) nhdr.dim[ii] = 1 ;
+
+#if 0 /* rely on dim[0], do not attempt to modify it 16 Nov 2005 [rickr] */
+
+ /**- get number of dimensions (ignoring dim[0] now) */
+ for( ii=7 ; ii >= 2 ; ii-- ) /* loop backwards until we */
+ if( nhdr.dim[ii] > 1 ) break ; /* find a dim bigger than 1 */
+ ndim = ii ;
+#endif
+
+ /**- set bad grid spacings to 1.0 */
+
+ for( ii=1 ; ii <= nhdr.dim[0] ; ii++ ){
+ if( nhdr.pixdim[ii] == 0.0 ||
+ !IS_GOOD_FLOAT(nhdr.pixdim[ii]) ) nhdr.pixdim[ii] = 1.0 ;
+ }
+
+ is_onefile = is_nifti && NIFTI_ONEFILE(nhdr) ;
+
+ if( is_nifti ) nim->nifti_type = (is_onefile) ? NIFTI_FTYPE_NIFTI1_1
+ : NIFTI_FTYPE_NIFTI1_2 ;
+ else nim->nifti_type = NIFTI_FTYPE_ANALYZE ;
+
+ ii = nifti_short_order() ;
+ if( doswap ) nim->byteorder = REVERSE_ORDER(ii) ;
+ else nim->byteorder = ii ;
+
+
+ /**- set dimensions of data array */
+
+ nim->ndim = nim->dim[0] = nhdr.dim[0];
+ nim->nx = nim->dim[1] = nhdr.dim[1];
+ nim->ny = nim->dim[2] = nhdr.dim[2];
+ nim->nz = nim->dim[3] = nhdr.dim[3];
+ nim->nt = nim->dim[4] = nhdr.dim[4];
+ nim->nu = nim->dim[5] = nhdr.dim[5];
+ nim->nv = nim->dim[6] = nhdr.dim[6];
+ nim->nw = nim->dim[7] = nhdr.dim[7];
+
+ for( ii=1, nim->nvox=1; ii <= nhdr.dim[0]; ii++ )
+ nim->nvox *= nhdr.dim[ii];
+
+ /**- set the type of data in voxels and how many bytes per voxel */
+
+ nim->datatype = nhdr.datatype ;
+
+ nifti_datatype_sizes( nim->datatype , &(nim->nbyper) , &(nim->swapsize) ) ;
+ if( nim->nbyper == 0 ){ free(nim); ERREX("bad datatype"); }
+
+ /**- set the grid spacings */
+
+ nim->dx = nim->pixdim[1] = nhdr.pixdim[1] ;
+ nim->dy = nim->pixdim[2] = nhdr.pixdim[2] ;
+ nim->dz = nim->pixdim[3] = nhdr.pixdim[3] ;
+ nim->dt = nim->pixdim[4] = nhdr.pixdim[4] ;
+ nim->du = nim->pixdim[5] = nhdr.pixdim[5] ;
+ nim->dv = nim->pixdim[6] = nhdr.pixdim[6] ;
+ nim->dw = nim->pixdim[7] = nhdr.pixdim[7] ;
+
+ /**- compute qto_xyz transformation from pixel indexes (i,j,k) to (x,y,z) */
+
+ if( !is_nifti || nhdr.qform_code <= 0 ){
+ /**- if not nifti or qform_code <= 0, use grid spacing for qto_xyz */
+
+ nim->qto_xyz.m[0][0] = nim->dx ; /* grid spacings */
+ nim->qto_xyz.m[1][1] = nim->dy ; /* along diagonal */
+ nim->qto_xyz.m[2][2] = nim->dz ;
+
+ /* off diagonal is zero */
+
+ nim->qto_xyz.m[0][1]=nim->qto_xyz.m[0][2]=nim->qto_xyz.m[0][3] = 0.0;
+ nim->qto_xyz.m[1][0]=nim->qto_xyz.m[1][2]=nim->qto_xyz.m[1][3] = 0.0;
+ nim->qto_xyz.m[2][0]=nim->qto_xyz.m[2][1]=nim->qto_xyz.m[2][3] = 0.0;
+
+ /* last row is always [ 0 0 0 1 ] */
+
+ nim->qto_xyz.m[3][0]=nim->qto_xyz.m[3][1]=nim->qto_xyz.m[3][2] = 0.0;
+ nim->qto_xyz.m[3][3]= 1.0 ;
+
+ nim->qform_code = NIFTI_XFORM_UNKNOWN ;
+
+ if( g_opts.debug > 1 ) fprintf(stderr,"-d no qform provided\n");
+ } else {
+ /**- else NIFTI: use the quaternion-specified transformation */
+
+ nim->quatern_b = FIXED_FLOAT( nhdr.quatern_b ) ;
+ nim->quatern_c = FIXED_FLOAT( nhdr.quatern_c ) ;
+ nim->quatern_d = FIXED_FLOAT( nhdr.quatern_d ) ;
+
+ nim->qoffset_x = FIXED_FLOAT(nhdr.qoffset_x) ;
+ nim->qoffset_y = FIXED_FLOAT(nhdr.qoffset_y) ;
+ nim->qoffset_z = FIXED_FLOAT(nhdr.qoffset_z) ;
+
+ nim->qfac = (nhdr.pixdim[0] < 0.0) ? -1.0 : 1.0 ; /* left-handedness? */
+
+ nim->qto_xyz = nifti_quatern_to_mat44(
+ nim->quatern_b, nim->quatern_c, nim->quatern_d,
+ nim->qoffset_x, nim->qoffset_y, nim->qoffset_z,
+ nim->dx , nim->dy , nim->dz ,
+ nim->qfac ) ;
+
+ nim->qform_code = nhdr.qform_code ;
+
+ if( g_opts.debug > 1 )
+ nifti_disp_matrix_orient("-d qform orientations:\n", nim->qto_xyz);
+ }
+
+ /**- load inverse transformation (x,y,z) -> (i,j,k) */
+
+ nim->qto_ijk = nifti_mat44_inverse( nim->qto_xyz ) ;
+
+ /**- load sto_xyz affine transformation, if present */
+
+ if( !is_nifti || nhdr.sform_code <= 0 ){
+ /**- if not nifti or sform_code <= 0, then no sto transformation */
+
+ nim->sform_code = NIFTI_XFORM_UNKNOWN ;
+
+ if( g_opts.debug > 1 ) fprintf(stderr,"-d no sform provided\n");
+
+ } else {
+ /**- else set the sto transformation from srow_*[] */
+
+ nim->sto_xyz.m[0][0] = nhdr.srow_x[0] ;
+ nim->sto_xyz.m[0][1] = nhdr.srow_x[1] ;
+ nim->sto_xyz.m[0][2] = nhdr.srow_x[2] ;
+ nim->sto_xyz.m[0][3] = nhdr.srow_x[3] ;
+
+ nim->sto_xyz.m[1][0] = nhdr.srow_y[0] ;
+ nim->sto_xyz.m[1][1] = nhdr.srow_y[1] ;
+ nim->sto_xyz.m[1][2] = nhdr.srow_y[2] ;
+ nim->sto_xyz.m[1][3] = nhdr.srow_y[3] ;
+
+ nim->sto_xyz.m[2][0] = nhdr.srow_z[0] ;
+ nim->sto_xyz.m[2][1] = nhdr.srow_z[1] ;
+ nim->sto_xyz.m[2][2] = nhdr.srow_z[2] ;
+ nim->sto_xyz.m[2][3] = nhdr.srow_z[3] ;
+
+ /* last row is always [ 0 0 0 1 ] */
+
+ nim->sto_xyz.m[3][0]=nim->sto_xyz.m[3][1]=nim->sto_xyz.m[3][2] = 0.0;
+ nim->sto_xyz.m[3][3]= 1.0 ;
+
+ nim->sto_ijk = nifti_mat44_inverse( nim->sto_xyz ) ;
+
+ nim->sform_code = nhdr.sform_code ;
+
+ if( g_opts.debug > 1 )
+ nifti_disp_matrix_orient("-d sform orientations:\n", nim->sto_xyz);
+ }
+
+ /**- set miscellaneous NIFTI stuff */
+
+ if( is_nifti ){
+ nim->scl_slope = FIXED_FLOAT( nhdr.scl_slope ) ;
+ nim->scl_inter = FIXED_FLOAT( nhdr.scl_inter ) ;
+
+ nim->intent_code = nhdr.intent_code ;
+
+ nim->intent_p1 = FIXED_FLOAT( nhdr.intent_p1 ) ;
+ nim->intent_p2 = FIXED_FLOAT( nhdr.intent_p2 ) ;
+ nim->intent_p3 = FIXED_FLOAT( nhdr.intent_p3 ) ;
+
+ nim->toffset = FIXED_FLOAT( nhdr.toffset ) ;
+
+ memcpy(nim->intent_name,nhdr.intent_name,15); nim->intent_name[15] = '\0';
+
+ nim->xyz_units = XYZT_TO_SPACE(nhdr.xyzt_units) ;
+ nim->time_units = XYZT_TO_TIME (nhdr.xyzt_units) ;
+
+ nim->freq_dim = DIM_INFO_TO_FREQ_DIM ( nhdr.dim_info ) ;
+ nim->phase_dim = DIM_INFO_TO_PHASE_DIM( nhdr.dim_info ) ;
+ nim->slice_dim = DIM_INFO_TO_SLICE_DIM( nhdr.dim_info ) ;
+
+ nim->slice_code = nhdr.slice_code ;
+ nim->slice_start = nhdr.slice_start ;
+ nim->slice_end = nhdr.slice_end ;
+ nim->slice_duration = FIXED_FLOAT(nhdr.slice_duration) ;
+ }
+
+ /**- set Miscellaneous ANALYZE stuff */
+
+ nim->cal_min = FIXED_FLOAT(nhdr.cal_min) ;
+ nim->cal_max = FIXED_FLOAT(nhdr.cal_max) ;
+
+ memcpy(nim->descrip ,nhdr.descrip ,79) ; nim->descrip [79] = '\0' ;
+ memcpy(nim->aux_file,nhdr.aux_file,23) ; nim->aux_file[23] = '\0' ;
+
+ /**- set ioff from vox_offset (but at least sizeof(header)) */
+
+ is_onefile = is_nifti && NIFTI_ONEFILE(nhdr) ;
+
+ if( is_onefile ){
+ ioff = (int)nhdr.vox_offset ;
+ if( ioff < (int) sizeof(nhdr) ) ioff = (int) sizeof(nhdr) ;
+ } else {
+ ioff = (int)nhdr.vox_offset ;
+ }
+ nim->iname_offset = ioff ;
+
+
+ /**- deal with file names if set */
+ if (fname!=NULL) {
+ nifti_set_filenames(nim,fname,0,0);
+ if (nim->iname==NULL) { ERREX("bad filename"); }
+ } else {
+ nim->fname = NULL;
+ nim->iname = NULL;
+ }
+
+ /* clear extension fields */
+ nim->num_ext = 0;
+ nim->ext_list = NULL;
+
+ return nim;
+}
+
+#undef ERREX
+#define ERREX(msg) \
+ do{ fprintf(stderr,"** ERROR: nifti_image_open(%s): %s\n", \
+ (hname != NULL) ? hname : "(null)" , (msg) ) ; \
+ return fptr ; } while(0)
+
+/***************************************************************
+ * nifti_image_open
+ ***************************************************************/
+/*! znzFile nifti_image_open( char *hname, char *opts , nifti_image **nim)
+ \brief Read in NIFTI-1 or ANALYZE-7.5 file (pair) header information into a nifti_image struct.
+
+ - The image data is not read from disk (it may be read later using
+ nifti_image_load(), for example).
+ - The image data will be stored in whatever data format the
+ input data is; no scaling will be applied.
+ - DT_BINARY data is not supported.
+ - nifti_image_free() can be used to delete the returned struct,
+ when you are done with it.
+
+ \param hname filename of dataset .hdr or .nii file
+ \param opts options string for opening the header file
+ \param nim pointer to pointer to nifti_image struct
+ (this routine allocates the nifti_image struct)
+ \return file pointer (gzippable) to the file with the image data,
+ ready for reading.
+ <br>NULL if something fails badly.
+ \sa nifti_image_load, nifti_image_free
+ */
+znzFile nifti_image_open(const char * hname, char * opts, nifti_image ** nim)
+{
+ znzFile fptr=NULL;
+ /* open the hdr and reading it in, but do not load the data */
+ *nim = nifti_image_read(hname,0);
+ /* open the image file, ready for reading (compressed works for all reads) */
+ if( ((*nim) == NULL) || ((*nim)->iname == NULL) ||
+ ((*nim)->nbyper <= 0) || ((*nim)->nvox <= 0) )
+ ERREX("bad header info") ;
+
+ /* open image data file */
+ fptr = znzopen( (*nim)->iname, opts, nifti_is_gzfile((*nim)->iname) );
+ if( znz_isnull(fptr) ) ERREX("Can't open data file") ;
+
+ return fptr;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! return an allocated and filled nifti_1_header struct
+
+ Read the binary header from disk, and swap bytes if necessary.
+
+ \return an allocated nifti_1_header struct, or NULL on failure
+
+ \param hname name of file containing header
+ \param swapped if not NULL, return whether header bytes were swapped
+ \param check flag to check for invalid nifti_1_header
+
+ \warning ASCII header type is not supported
+
+ \sa nifti_image_read, nifti_image_free, nifti_image_read_bricks
+*//*--------------------------------------------------------------------*/
+nifti_1_header * nifti_read_header(const char * hname, int * swapped, int check)
+{
+ nifti_1_header nhdr, * hptr;
+ znzFile fp;
+ int bytes, lswap;
+ char * hfile;
+ char fname[] = { "nifti_read_header" };
+
+ /* determine file name to use for header */
+ hfile = nifti_findhdrname(hname);
+ if( hfile == NULL ){
+ if( g_opts.debug > 0 )
+ LNI_FERR(fname,"failed to find header file for", hname);
+ return NULL;
+ } else if( g_opts.debug > 1 )
+ fprintf(stderr,"-d %s: found header filename '%s'\n",fname,hfile);
+
+ fp = znzopen( hfile, "rb", nifti_is_gzfile(hfile) );
+ if( znz_isnull(fp) ){
+ if( g_opts.debug > 0 ) LNI_FERR(fname,"failed to open header file",hfile);
+ free(hfile);
+ return NULL;
+ }
+
+ free(hfile); /* done with filename */
+
+ if( has_ascii_header(fp) == 1 ){
+ znzclose( fp );
+ if( g_opts.debug > 0 )
+ LNI_FERR(fname,"ASCII header type not supported",hname);
+ return NULL;
+ }
+
+ /* read the binary header */
+ bytes = znzread( &nhdr, 1, sizeof(nhdr), fp );
+ znzclose( fp ); /* we are done with the file now */
+
+ if( bytes < (int)sizeof(nhdr) ){
+ if( g_opts.debug > 0 ){
+ LNI_FERR(fname,"bad binary header read for file", hname);
+ fprintf(stderr," - read %d of %d bytes\n",bytes, (int)sizeof(nhdr));
+ }
+ return NULL;
+ }
+
+ /* now just decide on byte swapping */
+ lswap = need_nhdr_swap(nhdr.dim[0], nhdr.sizeof_hdr); /* swap data flag */
+ if( check && lswap < 0 ){
+ LNI_FERR(fname,"bad nifti_1_header for file", hname);
+ return NULL;
+ }
+
+ if( lswap ) {
+ if ( g_opts.debug > 3 ) disp_nifti_1_header("-d nhdr pre-swap: ", &nhdr);
+ swap_nifti_header( &nhdr , NIFTI_VERSION(nhdr) ) ;
+ }
+
+ if ( g_opts.debug > 2 ) disp_nifti_1_header("-d nhdr post-swap: ", &nhdr);
+
+ if ( check && ! nifti_hdr_looks_good(&nhdr) ){
+ LNI_FERR(fname,"nifti_1_header looks bad for file", hname);
+ return NULL;
+ }
+
+ /* all looks good, so allocate memory for and return the header */
+ hptr = (nifti_1_header *)malloc(sizeof(nifti_1_header));
+ if( ! hptr ){
+ fprintf(stderr,"** nifti_read_hdr: failed to alloc nifti_1_header\n");
+ return NULL;
+ }
+
+ if( swapped ) *swapped = lswap; /* only if they care <sniff!> */
+
+ memcpy(hptr, &nhdr, sizeof(nifti_1_header));
+
+ return hptr;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! decide if this nifti_1_header structure looks reasonable
+
+ Check dim[0], dim[1], sizeof_hdr, and datatype.
+ Check magic string for "n+1".
+ Maybe more tests will follow.
+
+ \return 1 if the header seems valid, 0 otherwise
+
+ \sa nifti_nim_is_valid, valid_nifti_extensions
+*//*--------------------------------------------------------------------*/
+int nifti_hdr_looks_good(const nifti_1_header * hdr)
+{
+ int nbyper, swapsize;
+ int c, errs = 0;
+
+ /* check dim[0] and sizeof_hdr */
+ if( need_nhdr_swap(hdr->dim[0], hdr->sizeof_hdr) < 0 ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** bad nhdr fields: dim0, sizeof_hdr = %d, %d\n",
+ hdr->dim[0], hdr->sizeof_hdr);
+ errs++;
+ }
+
+ /* check the valid dimension sizes (maybe dim[0] is bad) */
+ for( c = 1; c <= hdr->dim[0] && c <= 7; c++ )
+ if( hdr->dim[c] <= 0 ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** bad nhdr field: dim[%d] = %d\n",c,hdr->dim[c]);
+ errs++;
+ }
+
+ /* check the magic string */
+ if( (hdr->magic[0] != 'n') ||
+ (hdr->magic[1] != 'i' && hdr->magic[1] != '+') ||
+ (hdr->magic[2] != '1') ||
+ (hdr->magic[3] != '\0') )
+ {
+ if( g_opts.debug > 0 )
+ fprintf(stderr,
+ "** bad nhdr field: magic = '%.4s', should be \"n+1\" or \"ni1\"\n"
+ " (in hex) magic = 0x%02x%02x%02x%02x\n"
+ " should be = 0x6e2b3100 or 0x6e693100\n",
+ hdr->magic, hdr->magic[0], hdr->magic[1],
+ hdr->magic[2], hdr->magic[3]);
+ errs++;
+ }
+
+ /* check the datatype */
+ if( hdr->datatype == DT_BINARY || hdr->datatype == DT_UNKNOWN ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** bad nhdr field: datatype = %d\n",hdr->datatype);
+ errs++;
+ }
+
+ nifti_datatype_sizes(hdr->datatype, &nbyper, &swapsize);
+ if( nbyper == 0 ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** bad nhdr field: datatype = %d\n",hdr->datatype);
+ errs++;
+ }
+
+ if( errs ) return 0; /* problems */
+
+ if( g_opts.debug > 2 ) fprintf(stderr,"-d nifti header looks good\n");
+
+ return 1; /* looks good */
+}
+
+
+/*----------------------------------------------------------------------
+ * check whether byte swapping is needed
+ *
+ * dim[0] should be in [0,7], and sizeof_hdr should be accurate
+ *
+ * \returns > 0 : needs swap
+ * 0 : does not need swap
+ * < 0 : error condition
+ *----------------------------------------------------------------------*/
+static int need_nhdr_swap( short dim0, int hdrsize )
+{
+ short d0 = dim0; /* so we won't have to swap them on the stack */
+ int hsize = hdrsize;
+
+ if( d0 != 0 ){ /* then use it for the check */
+ if( d0 > 0 && d0 <= 7 ) return 0;
+
+ nifti_swap_2bytes(1, &d0); /* swap? */
+ if( d0 > 0 && d0 <= 7 ) return 1;
+
+ if( g_opts.debug > 1 ){
+ fprintf(stderr,"** bad swapped d0 = %d, unswapped = ", d0);
+ nifti_swap_2bytes(1, &d0); /* swap? */
+ fprintf(stderr,"%d\n", d0);
+ }
+
+ return -1; /* bad, naughty d0 */
+ }
+
+ /* dim[0] == 0 should not happen, but could, so try hdrsize */
+ if( hsize == sizeof(nifti_1_header) ) return 0;
+
+ nifti_swap_4bytes(1, &hsize); /* swap? */
+ if( hsize == sizeof(nifti_1_header) ) return 1;
+
+ if( g_opts.debug > 1 ){
+ fprintf(stderr,"** bad swapped hsize = %d, unswapped = ", hsize);
+ nifti_swap_4bytes(1, &hsize); /* swap? */
+ fprintf(stderr,"%d\n", hsize);
+ }
+
+ return -2; /* bad, naughty hsize */
+}
+
+
+/* use macro LNI_FILE_ERROR instead of ERREX()
+#undef ERREX
+#define ERREX(msg) \
+ do{ fprintf(stderr,"** ERROR: nifti_image_read(%s): %s\n", \
+ (hname != NULL) ? hname : "(null)" , (msg) ) ; \
+ return NULL ; } while(0)
+*/
+
+
+/***************************************************************
+ * nifti_image_read
+ ***************************************************************/
+/*! \brief Read a nifti header and optionally the data, creating a nifti_image.
+
+ - The data buffer will be byteswapped if necessary.
+ - The data buffer will not be scaled.
+ - The data buffer is allocated with calloc().
+
+ \param hname filename of the nifti dataset
+ \param read_data Flag, true=read data blob, false=don't read blob.
+ \return A pointer to the nifti_image data structure.
+
+ \sa nifti_image_free, nifti_free_extensions, nifti_image_read_bricks
+*/
+nifti_image *nifti_image_read( const char *hname , int read_data )
+{
+ struct nifti_1_header nhdr ;
+ nifti_image *nim ;
+ znzFile fp ;
+ int rv, ii , filesize, remaining;
+ char fname[] = { "nifti_image_read" };
+ char *hfile=NULL;
+
+ if( g_opts.debug > 1 ){
+ fprintf(stderr,"-d image_read from '%s', read_data = %d",hname,read_data);
+#ifdef HAVE_ZLIB
+ fprintf(stderr,", HAVE_ZLIB = 1\n");
+#else
+ fprintf(stderr,", HAVE_ZLIB = 0\n");
+#endif
+ }
+
+ /**- determine filename to use for header */
+ hfile = nifti_findhdrname(hname);
+ if( hfile == NULL ){
+ if(g_opts.debug > 0)
+ LNI_FERR(fname,"failed to find header file for", hname);
+ return NULL; /* check return */
+ } else if( g_opts.debug > 1 )
+ fprintf(stderr,"-d %s: found header filename '%s'\n",fname,hfile);
+
+ if( nifti_is_gzfile(hfile) ) filesize = -1; /* unknown */
+ else filesize = nifti_get_filesize(hfile);
+
+ fp = znzopen(hfile, "rb", nifti_is_gzfile(hfile));
+ if( znz_isnull(fp) ){
+ if( g_opts.debug > 0 ) LNI_FERR(fname,"failed to open header file",hfile);
+ free(hfile);
+ return NULL;
+ }
+
+ rv = has_ascii_header( fp );
+ if( rv < 0 ){
+ if( g_opts.debug > 0 ) LNI_FERR(fname,"short header read",hfile);
+ znzclose( fp );
+ free(hfile);
+ return NULL;
+ }
+ else if ( rv == 1 ) /* process special file type */
+ return nifti_read_ascii_image( fp, hfile, filesize, read_data );
+
+ /* else, just process normally */
+
+ /**- read binary header */
+
+ ii = znzread( &nhdr , 1 , sizeof(nhdr) , fp ) ; /* read the thing */
+
+ /* keep file open so we can check for exts. after nifti_convert_nhdr2nim() */
+
+ if( ii < sizeof(nhdr) ){
+ if( g_opts.debug > 0 ){
+ LNI_FERR(fname,"bad binary header read for file", hfile);
+ fprintf(stderr," - read %d of %d bytes\n",ii, (int)sizeof(nhdr));
+ }
+ znzclose(fp) ;
+ free(hfile);
+ return NULL;
+ }
+
+ /* create output image struct and set it up */
+
+ /**- convert all nhdr fields to nifti_image fields */
+ nim = nifti_convert_nhdr2nim(nhdr,hfile);
+
+ if( nim == NULL ){
+ znzclose( fp ) ; /* close the file */
+ if( g_opts.debug > 0 )
+ LNI_FERR(fname,"cannot create nifti image from header",hfile);
+ free(hfile); /* had to save this for debug message */
+ return NULL;
+ }
+
+ if( g_opts.debug > 3 ){
+ fprintf(stderr,"+d nifti_image_read(), have nifti image:\n");
+ if( g_opts.debug > 2 ) nifti_image_infodump(nim);
+ }
+
+ /**- check for extensions (any errors here means no extensions) */
+ if( NIFTI_ONEFILE(nhdr) ) remaining = nim->iname_offset - sizeof(nhdr);
+ else remaining = filesize - sizeof(nhdr);
+
+ (void)nifti_read_extensions(nim, fp, remaining);
+
+ znzclose( fp ) ; /* close the file */
+ free(hfile);
+
+ /**- read the data if desired, then bug out */
+ if( read_data ){
+ if( nifti_image_load( nim ) < 0 ){
+ nifti_image_free(nim); /* take ball, go home. */
+ return NULL;
+ }
+ }
+ else nim->data = NULL ;
+
+ return nim ;
+}
+
+
+/*----------------------------------------------------------------------
+ * has_ascii_header - see if the NIFTI header is an ASCII format
+ *
+ * If the file starts with the ASCII string "<nifti_image", then
+ * process the dataset as a type-3 .nia file.
+ *
+ * return: -1 on error, 1 if true, or 0 if false
+ *
+ * NOTE: this is NOT part of the NIFTI-1 standard
+ *----------------------------------------------------------------------*/
+static int has_ascii_header( znzFile fp )
+{
+ char buf[16];
+ int nread;
+
+ if( znz_isnull(fp) ) return 0;
+
+ nread = znzread( buf, 1, 12, fp );
+ buf[12] = '\0';
+
+ if( nread < 12 ) return -1;
+
+ znzrewind(fp); /* move back to the beginning, and check */
+
+ if( strcmp(buf, "<nifti_image") == 0 ) return 1;
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! nifti_read_ascii_image - process as a type-3 .nia image file
+
+ return NULL on failure
+
+ NOTE: this is NOT part of the NIFTI-1 standard
+*//*--------------------------------------------------------------------*/
+nifti_image * nifti_read_ascii_image(znzFile fp, char *fname, int flen,
+ int read_data)
+{
+ nifti_image * nim;
+ int slen, txt_size, remain, rv = 0;
+ char * sbuf, lfunc[25] = { "nifti_read_ascii_image" };
+
+ if( nifti_is_gzfile(fname) ){
+ LNI_FERR(lfunc, "compressed file with negative offset", fname);
+ free(fname); znzclose(fp); return NULL;
+ }
+ slen = flen; /* slen will be our buffer length */
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d %s: have ASCII NIFTI file of size %d\n",fname,slen);
+
+ if( slen > 65530 ) slen = 65530 ;
+ sbuf = (char *)calloc(sizeof(char),slen+1) ;
+ if( !sbuf ){
+ fprintf(stderr,"** %s: failed to alloc %d bytes for sbuf",lfunc,65530);
+ free(fname); znzclose(fp); return NULL;
+ }
+ znzread( sbuf , 1 , slen , fp ) ;
+ nim = nifti_image_from_ascii( sbuf, &txt_size ) ; free( sbuf ) ;
+ if( nim == NULL ){
+ LNI_FERR(lfunc,"failed nifti_image_from_ascii()",fname);
+ free(fname); znzclose(fp); return NULL;
+ }
+ nim->nifti_type = NIFTI_FTYPE_ASCII ;
+
+ /* compute remaining space for extensions */
+ remain = flen - txt_size - (int)nifti_get_volsize(nim);
+ if( remain > 4 ){
+ /* read extensions (reposition file pointer, first) */
+ znzseek(fp, txt_size, SEEK_SET);
+ (void) nifti_read_extensions(nim, fp, remain);
+ }
+
+ free(fname);
+ znzclose( fp ) ;
+
+ nim->iname_offset = -1 ; /* check from the end of the file */
+
+ if( read_data ) rv = nifti_image_load( nim ) ;
+ else nim->data = NULL ;
+
+ /* check for nifti_image_load() failure, maybe bail out */
+ if( read_data && rv != 0 ){
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d failed image_load, free nifti image struct\n");
+ free(nim);
+ return NULL;
+ }
+
+ return nim ;
+}
+
+
+/*----------------------------------------------------------------------
+ * Read the extensions into the nifti_image struct 08 Dec 2004 [rickr]
+ *
+ * This function is called just after the header struct is read in, and
+ * it is assumed the file pointer has not moved. The value in remain
+ * is assumed to be accurate, reflecting the bytes of space for potential
+ * extensions.
+ *
+ * return the number of extensions read in, or < 0 on error
+ *----------------------------------------------------------------------*/
+static int nifti_read_extensions( nifti_image *nim, znzFile fp, int remain )
+{
+ nifti1_extender extdr; /* defines extension existence */
+ nifti1_extension extn; /* single extension to process */
+ nifti1_extension * Elist; /* list of processed extensions */
+ int posn, count;
+
+ if( !nim || znz_isnull(fp) ) {
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** nifti_read_extensions: bad inputs (%p,%p)\n",
+ (void *)nim, (void *)fp);
+ return -1;
+ }
+
+ posn = znztell(fp);
+
+ if( (posn != sizeof(nifti_1_header)) &&
+ (nim->nifti_type != NIFTI_FTYPE_ASCII) )
+ fprintf(stderr,"** WARNING: posn not header size (%d, %d)\n",
+ posn, (int)sizeof(nifti_1_header));
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d nre: posn = %d, offset = %d, type = %d, remain = %d\n",
+ posn, nim->iname_offset, nim->nifti_type, remain);
+
+ if( remain < 16 ){
+ if( g_opts.debug > 2 ){
+ if( g_opts.skip_blank_ext )
+ fprintf(stderr,"-d no extender in '%s' is okay, as "
+ "skip_blank_ext is set\n",nim->fname);
+ else
+ fprintf(stderr,"-d no space for extensions\n");
+ }
+ return 0;
+ }
+
+ count = znzread( extdr.extension, 1, 4, fp ); /* get extender */
+
+ if( count < 4 ){
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d file '%s' is too short for an extender\n",
+ nim->fname);
+ return 0;
+ }
+
+ if( extdr.extension[0] != 1 ){
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d extender[0] (%d) shows no extensions for '%s'\n",
+ extdr.extension[0], nim->fname);
+ return 0;
+ }
+
+ remain -= 4;
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d found valid 4-byte extender, remain = %d\n", remain);
+
+ /* so we expect extensions, but have no idea of how many there may be */
+
+ count = 0;
+ Elist = NULL;
+ while (nifti_read_next_extension(&extn, nim, remain, fp) > 0)
+ {
+ if( nifti_add_exten_to_list(&extn, &Elist, count+1) < 0 ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** failed adding ext %d to list\n", count);
+ return -1;
+ }
+
+ /* we have a new extension */
+ if( g_opts.debug > 1 ){
+ fprintf(stderr,"+d found extension #%d, code = 0x%x, size = %d\n",
+ count, extn.ecode, extn.esize);
+ if( extn.ecode == NIFTI_ECODE_AFNI ) /* ~XML */
+ fprintf(stderr," AFNI extension: %.*s\n",
+ extn.esize-8,extn.edata);
+ else if( extn.ecode == NIFTI_ECODE_COMMENT ) /* TEXT */
+ fprintf(stderr," COMMENT extension: %.*s\n",
+ extn.esize-8,extn.edata);
+ }
+ remain -= extn.esize;
+ count++;
+ }
+
+ if( g_opts.debug > 2 ) fprintf(stderr,"+d found %d extension(s)\n", count);
+
+ nim->num_ext = count;
+ nim->ext_list = Elist;
+
+ return count;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! nifti_add_extension - add an extension, with a copy of the data
+
+ Add an extension to the nim->ext_list array.
+ Fill this extension with a copy of the data, noting the
+ length and extension code.
+
+ \param nim - nifti_image to add extension to
+ \param data - raw extension data
+ \param length - length of raw extension data
+ \param ecode - extension code
+
+ \sa extension codes NIFTI_ECODE_* in nifti1_io.h
+ \sa nifti_free_extensions, valid_nifti_extensions, nifti_copy_extensions
+
+ \return 0 on success, -1 on error (and free the entire list)
+*//*--------------------------------------------------------------------*/
+int nifti_add_extension(nifti_image *nim, const char * data, int len, int ecode)
+{
+ nifti1_extension ext;
+
+ /* error are printed in functions */
+ if( nifti_fill_extension(&ext, data, len, ecode) ) return -1;
+ if( nifti_add_exten_to_list(&ext, &nim->ext_list, nim->num_ext+1)) return -1;
+
+ nim->num_ext++; /* success, so increment */
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------*/
+/* nifti_add_exten_to_list - add a new nifti1_extension to the list
+
+ We will append via "malloc, copy and free", because on an error,
+ the old data pointers must all be released (sorry realloc(), only
+ quality dolphins get to become part of St@rk!st brand tunafish).
+
+ return 0 on success, -1 on error (and free the entire list)
+*//*--------------------------------------------------------------------*/
+static int nifti_add_exten_to_list( nifti1_extension * new_ext,
+ nifti1_extension ** list, int new_length )
+{
+ nifti1_extension * tmplist;
+ int count;
+
+ tmplist = *list;
+ *list = (nifti1_extension *)malloc(new_length * sizeof(nifti1_extension));
+
+ /* check for failure first */
+ if( ! *list ){
+ fprintf(stderr,"** failed to alloc %d extension structs (%d bytes)\n",
+ new_length, new_length*(int)sizeof(nifti1_extension));
+ if( !tmplist ) return -1; /* no old list to lose */
+
+ for ( count = 0; count < new_length-1; count++ )
+ if( tmplist[count].edata ) free(tmplist[count].edata);
+ free(tmplist);
+ return -1;
+ }
+
+ /* we have memory, so copy the old and insert the new */
+ memcpy(*list, tmplist, (new_length-1)*sizeof(nifti1_extension));
+
+ /* for some reason, I just don't like struct copy... */
+ (*list)[new_length-1].esize = new_ext->esize;
+ (*list)[new_length-1].ecode = new_ext->ecode;
+ (*list)[new_length-1].edata = new_ext->edata;
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"+d allocated and appended extension #%d to list\n",
+ new_length);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------*/
+/* nifti_fill_extension - given data and length, fill an extension struct
+
+ Allocate memory for data, copy data, set the size and code.
+
+ return 0 on success, -1 on error (and free the entire list)
+*//*--------------------------------------------------------------------*/
+static int nifti_fill_extension( nifti1_extension *ext, const char * data,
+ int len, int ecode)
+{
+ int esize;
+
+ if( !ext || !data || len < 0 ){
+ fprintf(stderr,"** fill_ext: bad params (%p,%p,%d)\n",
+ (void *)ext, data, len);
+ return -1;
+ } else if( ! nifti_is_valid_ecode(ecode) ){
+ fprintf(stderr,"** fill_ext: invalid ecode %d\n", ecode);
+ return -1;
+ }
+
+ /* compute esize, first : len+8, and take ceiling up to a mult of 16 */
+ esize = len+8;
+ if( esize & 0xf ) esize = (esize + 0xf) & ~0xf;
+ ext->esize = esize;
+
+ /* allocate esize-8 (maybe more than len), using calloc for fill */
+ ext->edata = (char *)calloc(esize-8, sizeof(char));
+ if( !ext->edata ){
+ fprintf(stderr,"** NFE: failed to alloc %d bytes for extension\n",len);
+ return -1;
+ }
+
+ memcpy(ext->edata, data, len); /* copy the data, using len */
+ ext->ecode = ecode; /* set the ecode */
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"+d alloc %d bytes for ext len %d, ecode %d, esize %d\n",
+ esize-8, len, ecode, esize);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * nifti_read_next_extension - read a single extension from the file
+ *
+ * return (>= 0 is okay):
+ *
+ * success : esize
+ * no extension : 0
+ * error : -1
+ *----------------------------------------------------------------------*/
+static int nifti_read_next_extension( nifti1_extension * nex, nifti_image *nim,
+ int remain, znzFile fp )
+{
+ int swap = nim->byteorder != nifti_short_order();
+ int count, size, code;
+
+ /* first clear nex */
+ nex->esize = nex->ecode = 0;
+ nex->edata = NULL;
+
+ if( remain < 16 ){
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d only %d bytes remain, so no extension\n", remain);
+ return 0;
+ }
+
+ /* must start with 4-byte size and code */
+ count = znzread( &size, 4, 1, fp );
+ if( count == 1 ) count += znzread( &code, 4, 1, fp );
+
+ if( count != 2 ){
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d current extension read failed\n");
+ znzseek(fp, -4*count, SEEK_CUR); /* back up past any read */
+ return 0; /* no extension, no error condition */
+ }
+
+ if( swap ){
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d pre-swap exts: code %d, size %d\n", code, size);
+
+ nifti_swap_4bytes(1, &size);
+ nifti_swap_4bytes(1, &code);
+ }
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d potential extension: code %d, size %d\n", code, size);
+
+ if( !nifti_check_extension(nim, size, code, remain) ){
+ if( znzseek(fp, -8, SEEK_CUR) < 0 ){ /* back up past any read */
+ fprintf(stderr,"** failure to back out of extension read!\n");
+ return -1;
+ }
+ return 0;
+ }
+
+ /* now get the actual data */
+ nex->esize = size;
+ nex->ecode = code;
+
+ size -= 8; /* subtract space for size and code in extension */
+ nex->edata = (char *)malloc(size * sizeof(char));
+ if( !nex->edata ){
+ fprintf(stderr,"** failed to allocate %d bytes for extension\n",size);
+ return -1;
+ }
+
+ count = znzread(nex->edata, 1, size, fp);
+ if( count < size ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"-d read only %d (of %d) bytes for extension\n",
+ count, size);
+ free(nex->edata);
+ nex->edata = NULL;
+ return -1;
+ }
+
+ /* success! */
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d successfully read extension, code %d, size %d\n",
+ nex->ecode, nex->esize);
+
+ return nex->esize;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! for each extension, check code, size and data pointer
+*//*--------------------------------------------------------------------*/
+int valid_nifti_extensions(const nifti_image * nim)
+{
+ nifti1_extension * ext;
+ int c, errs;
+
+ if( nim->num_ext <= 0 || nim->ext_list == NULL ){
+ if( g_opts.debug > 2 ) fprintf(stderr,"-d empty extension list\n");
+ return 0;
+ }
+
+ /* for each extension, check code, size and data pointer */
+ ext = nim->ext_list;
+ errs = 0;
+ for ( c = 0; c < nim->num_ext; c++ ){
+ if( ! nifti_is_valid_ecode(ext->ecode) ) {
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d ext %d, invalid code %d\n", c, ext->ecode);
+ errs++;
+ }
+
+ if( ext->esize <= 0 ){
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d ext %d, bad size = %d\n", c, ext->esize);
+ errs++;
+ } else if( ext->esize & 0xf ){
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d ext %d, size %d not multiple of 16\n",
+ c, ext->esize);
+ errs++;
+ }
+
+ if( ext->edata == NULL ){
+ if( g_opts.debug > 1 ) fprintf(stderr,"-d ext %d, missing data\n", c);
+ errs++;
+ }
+
+ ext++;
+ }
+
+ if( errs > 0 ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"-d had %d extension errors, none will be written\n",
+ errs);
+ return 0;
+ }
+
+ /* if we're here, we're good */
+ return 1;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! check whether the extension code is valid
+
+ \return 1 if valid, 0 otherwise
+*//*--------------------------------------------------------------------*/
+int nifti_is_valid_ecode( int ecode )
+{
+ if( ecode < NIFTI_ECODE_IGNORE || /* minimum code number (0) */
+ ecode > NIFTI_MAX_ECODE || /* maximum code number */
+ ecode & 1 ) /* cannot be odd */
+ return 0;
+
+ return 1;
+}
+
+
+/*----------------------------------------------------------------------
+ * check for valid size and code, as well as can be done
+ *----------------------------------------------------------------------*/
+static int nifti_check_extension(nifti_image *nim, int size, int code, int rem)
+{
+ /* check for bad code before bad size */
+ if( ! nifti_is_valid_ecode(code) ) {
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d invalid extension code %d\n",code);
+ return 0;
+ }
+
+ if( size < 16 ){
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d ext size %d, no extension\n",size);
+ return 0;
+ }
+
+ if( size > rem ){
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d ext size %d, space %d, no extension\n", size, rem);
+ return 0;
+ }
+
+ if( size & 0xf ){
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d nifti extension size %d not multiple of 16\n",size);
+ return 0;
+ }
+
+ if( nim->nifti_type == NIFTI_FTYPE_ASCII && size > LNI_MAX_NIA_EXT_LEN ){
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d NVE, bad nifti_type 3 size %d\n", size);
+ return 0;
+ }
+
+ return 1;
+}
+
+
+/*----------------------------------------------------------------------
+ * nifti_image_load_prep - prepare to read data
+ *
+ * Check nifti_image fields, open the file and seek to the appropriate
+ * offset for reading.
+ *
+ * return NULL on failure
+ *----------------------------------------------------------------------*/
+static znzFile nifti_image_load_prep( nifti_image *nim )
+{
+ /* set up data space, open data file and seek, then call nifti_read_buffer */
+ size_t ntot , ii , ioff;
+ znzFile fp;
+ char fname[] = { "nifti_image_load_prep" };
+
+ /**- perform sanity checks */
+ if( nim == NULL || nim->iname == NULL ||
+ nim->nbyper <= 0 || nim->nvox <= 0 )
+ {
+ if ( g_opts.debug > 0 ){
+ if( !nim ) fprintf(stderr,"** ERROR: N_image_load: no nifti image\n");
+ else fprintf(stderr,"** ERROR: N_image_load: bad params (%p,%d,%d)\n",
+ nim->iname, nim->nbyper, nim->nvox);
+ }
+ return NULL;
+ }
+
+ ntot = nifti_get_volsize(nim) ; /* total bytes to read */
+
+ /**- open image data file */
+
+ fp = znzopen(nim->iname, "rb", nifti_is_gzfile(nim->iname));
+ if( znz_isnull(fp) ){
+ if( g_opts.debug > 0 ) LNI_FERR(fname,"cannot open data file",nim->iname);
+ return NULL;
+ }
+
+ /**- get image offset: a negative offset means to figure from end of file */
+ if( nim->iname_offset < 0 ){
+ if( nifti_is_gzfile(nim->iname) ){
+ if( g_opts.debug > 0 )
+ LNI_FERR(fname,"negative offset for compressed file",nim->iname);
+ znzclose(fp);
+ return NULL;
+ }
+ ii = nifti_get_filesize( nim->iname ) ;
+ if( ii <= 0 ){
+ if( g_opts.debug > 0 ) LNI_FERR(fname,"empty data file",nim->iname);
+ znzclose(fp);
+ return NULL;
+ }
+ ioff = (ii > ntot) ? ii-ntot : 0 ;
+ } else { /* non-negative offset */
+ ioff = nim->iname_offset ; /* means use it directly */
+ }
+
+ /**- seek to the appropriate read position */
+ if( znzseek(fp , ioff , SEEK_SET) < 0 ){
+ fprintf(stderr,"** could not seek to offset %d in file '%s'\n",
+ (int)ioff, nim->iname);
+ znzclose(fp);
+ return NULL;
+ }
+
+ /**- and return the File pointer */
+ return fp;
+}
+
+
+/*----------------------------------------------------------------------
+ * nifti_image_load
+ *----------------------------------------------------------------------*/
+/*! \fn int nifti_image_load( nifti_image *nim )
+ \brief Load the image blob into a previously initialized nifti_image.
+
+ - If not yet set, the data buffer is allocated with calloc().
+ - The data buffer will be byteswapped if necessary.
+ - The data buffer will not be scaled.
+
+ This function is used to read the image from disk. It should be used
+ after a function such as nifti_image_read(), so that the nifti_image
+ structure is already initialized.
+
+ \param nim pointer to a nifti_image (previously initialized)
+ \return 0 on success, -1 on failure
+ \sa nifti_image_read, nifti_image_free, nifti_image_unload
+*/
+int nifti_image_load( nifti_image *nim )
+{
+ /* set up data space, open data file and seek, then call nifti_read_buffer */
+ size_t ntot , ii ;
+ znzFile fp ;
+
+ /**- open the file and position the FILE pointer */
+ fp = nifti_image_load_prep( nim );
+
+ if( fp == NULL ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** nifti_image_load, failed load_prep\n");
+ return -1;
+ }
+
+ ntot = nifti_get_volsize(nim);
+
+ /**- if the data pointer is not yet set, get memory space for the image */
+
+ if( nim->data == NULL )
+ {
+ nim->data = (void *)calloc(1,ntot) ; /* create image memory */
+ if( nim->data == NULL ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** failed to alloc %d bytes for image data\n",
+ (int)ntot);
+ znzclose(fp);
+ return -1;
+ }
+ }
+
+ /**- now that everything is set up, do the reading */
+ ii = nifti_read_buffer(fp,nim->data,ntot,nim);
+ if( ii < ntot ){
+ znzclose(fp) ;
+ free(nim->data) ;
+ nim->data = NULL ;
+ return -1 ; /* errors were printed in nifti_read_buffer() */
+ }
+
+ /**- close the file */
+ znzclose( fp ) ;
+
+ return 0 ;
+}
+
+
+/* 30 Nov 2004 [rickr]
+#undef ERREX
+#define ERREX(msg) \
+ do{ fprintf(stderr,"** ERROR: nifti_read_buffer: %s\n",(msg)) ; \
+ return 0; } while(0)
+*/
+
+/*----------------------------------------------------------------------*/
+/*! read ntot bytes of data from an open file and byte swaps if necessary
+
+ note that nifti_image is required for information on datatype, bsize
+ (for any needed byte swapping), etc.
+
+ This function does not allocate memory, so dataptr must be valid.
+*//*--------------------------------------------------------------------*/
+size_t nifti_read_buffer(znzFile fp, void* dataptr, size_t ntot,
+ nifti_image *nim)
+{
+ size_t ii;
+
+ if( dataptr == NULL ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** ERROR: nifti_read_buffer: NULL dataptr\n");
+ return -1;
+ }
+
+ ii = znzread( dataptr , 1 , ntot , fp ) ; /* data input */
+
+ /* if read was short, fail */
+ if( ii < ntot ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"++ WARNING: nifti_read_buffer(%s):\n"
+ " data bytes needed = %u\n"
+ " data bytes input = %u\n"
+ " number missing = %u (set to 0)\n",
+ nim->iname , (unsigned int)ntot ,
+ (unsigned int)ii , (unsigned int)(ntot-ii) ) ;
+ /* memset( (char *)(dataptr)+ii , 0 , ntot-ii ) ; now failure [rickr] */
+ return -1 ;
+ }
+
+ /* byte swap array if needed */
+
+ if( nim->swapsize > 1 && nim->byteorder != nifti_short_order() )
+ nifti_swap_Nbytes( ntot / nim->swapsize , nim->swapsize , dataptr ) ;
+
+#ifdef isfinite
+{
+ /* check input float arrays for goodness, and fix bad floats */
+ int fix_count = 0 ;
+
+ switch( nim->datatype ){
+
+ case NIFTI_TYPE_FLOAT32:
+ case NIFTI_TYPE_COMPLEX64:{
+ register float *far = (float *)dataptr ; register int jj,nj ;
+ nj = ntot / sizeof(float) ;
+ for( jj=0 ; jj < nj ; jj++ ) /* count fixes 30 Nov 2004 [rickr] */
+ if( !IS_GOOD_FLOAT(far[jj]) ){
+ far[jj] = 0 ;
+ fix_count++ ;
+ }
+ }
+ break ;
+
+ case NIFTI_TYPE_FLOAT64:
+ case NIFTI_TYPE_COMPLEX128:{
+ register double *far = (double *)dataptr ; register int jj,nj ;
+ nj = ntot / sizeof(double) ;
+ for( jj=0 ; jj < nj ; jj++ ) /* count fixes 30 Nov 2004 [rickr] */
+ if( !IS_GOOD_FLOAT(far[jj]) ){
+ far[jj] = 0 ;
+ fix_count++ ;
+ }
+ }
+ break ;
+
+ }
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d in image, %d bad floats were set to 0\n", fix_count);
+}
+#endif
+
+ return ii;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Unload the data in a nifti_image struct, but keep the metadata.
+*//*------------------------------------------------------------------------*/
+void nifti_image_unload( nifti_image *nim )
+{
+ if( nim != NULL && nim->data != NULL ){
+ free(nim->data) ; nim->data = NULL ;
+ }
+ return ;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! free 'everything' about a nifti_image struct (including the passed struct)
+
+ free (only fields which are not NULL):
+ - fname and iname
+ - data
+ - any ext_list[i].edata
+ - ext_list
+ - nim
+*//*------------------------------------------------------------------------*/
+void nifti_image_free( nifti_image *nim )
+{
+ if( nim == NULL ) return ;
+ if( nim->fname != NULL ) free(nim->fname) ;
+ if( nim->iname != NULL ) free(nim->iname) ;
+ if( nim->data != NULL ) free(nim->data ) ;
+ (void)nifti_free_extensions( nim ) ;
+ free(nim) ; return ;
+}
+
+
+/*--------------------------------------------------------------------------*/
+/*! free the nifti extensions
+
+ - If any edata pointer is set in the extension list, free() it.
+ - Free ext_list, if it is set.
+ - Clear num_ext and ext_list from nim.
+
+ \return 0 on success, -1 on error
+
+ \sa nifti_add_extension, nifti_copy_extensions
+*//*------------------------------------------------------------------------*/
+int nifti_free_extensions( nifti_image *nim )
+{
+ int c ;
+ if( nim == NULL ) return -1;
+ if( nim->num_ext > 0 && nim->ext_list ){
+ for( c = 0; c < nim->num_ext; c++ )
+ if ( nim->ext_list[c].edata ) free(nim->ext_list[c].edata);
+ free(nim->ext_list);
+ }
+ /* or if it is inconsistent, warn the user (if we are not in quiet mode) */
+ else if ( (nim->num_ext > 0 || nim->ext_list != NULL) && (g_opts.debug > 0) )
+ fprintf(stderr,"** warning: nifti extension num/ptr mismatch (%d,%p)\n",
+ nim->num_ext, (void *)nim->ext_list);
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"+d free'd %d extension(s)\n", nim->num_ext);
+
+ nim->num_ext = 0;
+ nim->ext_list = NULL;
+
+ return 0;
+}
+
+
+/*--------------------------------------------------------------------------*/
+/*! Print to stdout some info about a nifti_image struct.
+*//*------------------------------------------------------------------------*/
+void nifti_image_infodump( const nifti_image *nim )
+{
+ char *str = nifti_image_to_ascii( nim ) ;
+ /* stdout -> stderr 2 Dec 2004 [rickr] */
+ if( str != NULL ){ fputs(str,stderr) ; free(str) ; }
+ return ;
+}
+
+
+/*--------------------------------------------------------------------------
+ * nifti_write_buffer just check for a null znzFile and call znzwrite
+ *--------------------------------------------------------------------------*/
+/*! \fn size_t nifti_write_buffer(znzFile fp, void *buffer, size_t numbytes)
+ \brief write numbytes of buffer to file, fp
+
+ \param fp File pointer (from znzopen) to gzippable nifti datafile
+ \param buffer data buffer to be written
+ \param numbytes number of bytes in buffer to write
+ \return number of bytes successfully written
+*/
+size_t nifti_write_buffer(znzFile fp, const void *buffer, size_t numbytes)
+{
+ /* Write all the image data at once (no swapping here) */
+ size_t ss;
+ if (znz_isnull(fp)){
+ fprintf(stderr,"** ERROR: nifti_write_buffer: null file pointer\n");
+ return 0;
+ }
+ ss = znzwrite( (void*)buffer , 1 , numbytes , fp ) ;
+ return ss;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! write the nifti_image data to file (from nim->data or from NBL)
+
+ If NBL is not NULL, write the data from that structure. Otherwise,
+ write it out from nim->data. No swapping is done here.
+
+ \param fp : File pointer
+ \param nim : nifti_image corresponding to the data
+ \param NBL : optional source of write data (if NULL use nim->data)
+
+ \return 0 on success, -1 on failure
+
+ Note: the nifti_image byte_order is set as that of the current CPU.
+ This is because such a conversion was made to the data upon
+ reading, while byte_order was not set (so the programs would
+ know what format the data was on disk). Effectively, since
+ byte_order should match what is on disk, it should bet set to
+ that of the current CPU whenever new filenames are assigned.
+*//*--------------------------------------------------------------------*/
+int nifti_write_all_data(znzFile fp, nifti_image * nim,
+ const nifti_brick_list * NBL)
+{
+ size_t ss;
+ int bnum;
+
+ if( !NBL ){ /* just write one buffer and get out of here */
+ if( nim->data == NULL ){
+ fprintf(stderr,"** NWAD: no image data to write\n");
+ return -1;
+ }
+
+ ss = nifti_write_buffer(fp,nim->data,nim->nbyper * nim->nvox);
+ if (ss < (size_t)(nim->nbyper * nim->nvox)){
+ fprintf(stderr,
+ "** ERROR: NWAD: wrote only %d of %d bytes to file\n",
+ (int)ss, nim->nbyper * nim->nvox);
+ return -1;
+ }
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d wrote single image of %d bytes\n",(int)ss);
+ } else {
+ if( ! NBL->bricks || NBL->nbricks <= 0 || NBL->bsize <= 0 ){
+ fprintf(stderr,"** NWAD: no brick data to write (%p,%d,%d)\n",
+ (void *)NBL->bricks, NBL->nbricks, NBL->bsize);
+ return -1;
+ }
+
+ for( bnum = 0; bnum < NBL->nbricks; bnum++ ){
+ ss = nifti_write_buffer(fp, NBL->bricks[bnum], NBL->bsize);
+ if( ss < (size_t)NBL->bsize ){
+ fprintf(stderr,
+ "** NWAD ERROR: wrote %d of %d bytes of brick %d of %d to file",
+ (int)ss, NBL->bsize, bnum+1, NBL->nbricks);
+ return -1;
+ }
+ }
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d wrote image of %d brick(s), each of %d bytes\n",
+ NBL->nbricks, NBL->bsize);
+ }
+
+ /* mark as being in this CPU byte order */
+ nim->byteorder = nifti_short_order() ;
+
+ return 0;
+}
+
+/* return number of extensions written, or -1 on error */
+static int nifti_write_extensions(znzFile fp, nifti_image *nim)
+{
+ nifti1_extension * list;
+ char extdr[4] = { 0, 0, 0, 0 };
+ int c, size, ok = 1;
+
+ if( znz_isnull(fp) || !nim || nim->num_ext < 0 ){
+ if( g_opts.debug > 0 )
+ fprintf(stderr,"** nifti_write_extensions, bad params\n");
+ return -1;
+ }
+
+ /* if no extensions and user requests it, skip extender */
+ if( g_opts.skip_blank_ext && (nim->num_ext == 0 || ! nim->ext_list ) ){
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d no exts and skip_blank_ext set, "
+ "so skipping 4-byte extender\n");
+ return 0;
+ }
+
+ /* if invalid extension list, clear num_ext */
+ if( ! valid_nifti_extensions(nim) ) nim->num_ext = 0;
+
+ /* write out extender block */
+ if( nim->num_ext > 0 ) extdr[0] = 1;
+ if( nifti_write_buffer(fp, extdr, 4) != 4 ){
+ fprintf(stderr,"** failed to write extender\n");
+ return -1;
+ }
+
+ list = nim->ext_list;
+ for ( c = 0; c < nim->num_ext; c++ ){
+ size = nifti_write_buffer(fp, &list->esize, sizeof(int));
+ ok = (size == (int)sizeof(int));
+ if( ok ){
+ size = nifti_write_buffer(fp, &list->ecode, sizeof(int));
+ ok = (size == (int)sizeof(int));
+ }
+ if( ok ){
+ size = nifti_write_buffer(fp, list->edata, list->esize - 8);
+ ok = (size == list->esize - 8);
+ }
+
+ if( !ok ){
+ fprintf(stderr,"** failed while writing extension #%d\n",c);
+ return -1;
+ }
+
+ list++;
+ }
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d wrote out %d extension(s)\n", nim->num_ext);
+
+ return nim->num_ext;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! basic initialization of a nifti_image struct (to a 1x1x1 image)
+*//*--------------------------------------------------------------------*/
+nifti_image* nifti_simple_init_nim(void)
+{
+ nifti_image *nim;
+ struct nifti_1_header nhdr;
+ int nbyper, swapsize;
+
+ memset(&nhdr,0,sizeof(nhdr)) ; /* zero out header, to be safe */
+
+ nhdr.sizeof_hdr = sizeof(nhdr) ;
+ nhdr.regular = 'r' ; /* for some stupid reason */
+
+ nhdr.dim[0] = 3 ;
+ nhdr.dim[1] = 1 ; nhdr.dim[2] = 1 ; nhdr.dim[3] = 1 ;
+ nhdr.dim[4] = 0 ;
+
+ nhdr.pixdim[0] = 0.0 ;
+ nhdr.pixdim[1] = 1.0 ; nhdr.pixdim[2] = 1.0 ;
+ nhdr.pixdim[3] = 1.0 ;
+
+ nhdr.datatype = DT_FLOAT32 ;
+ nifti_datatype_sizes( nhdr.datatype , &nbyper, &swapsize );
+ nhdr.bitpix = 8 * nbyper ;
+
+ nim = nifti_convert_nhdr2nim(nhdr,NULL);
+ nim->fname = NULL;
+ nim->iname = NULL;
+ return nim;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! convert a nifti_image structure to a nifti_1_header struct
+
+ No allocation is done, this should be used via structure copy.
+ As in:
+ <pre>
+ nifti_1_header my_header;
+ my_header = nifti_convert_nim2nhdr(my_nim_pointer);
+ </pre>
+*//*--------------------------------------------------------------------*/
+struct nifti_1_header nifti_convert_nim2nhdr(const nifti_image * nim)
+{
+ struct nifti_1_header nhdr;
+
+ memset(&nhdr,0,sizeof(nhdr)) ; /* zero out header, to be safe */
+
+
+ /**- load the ANALYZE-7.5 generic parts of the header struct */
+
+ nhdr.sizeof_hdr = sizeof(nhdr) ;
+ nhdr.regular = 'r' ; /* for some stupid reason */
+
+ nhdr.dim[0] = nim->ndim ;
+ nhdr.dim[1] = nim->nx ; nhdr.dim[2] = nim->ny ; nhdr.dim[3] = nim->nz ;
+ nhdr.dim[4] = nim->nt ; nhdr.dim[5] = nim->nu ; nhdr.dim[6] = nim->nv ;
+ nhdr.dim[7] = nim->nw ;
+
+ nhdr.pixdim[0] = 0.0 ;
+ nhdr.pixdim[1] = nim->dx ; nhdr.pixdim[2] = nim->dy ;
+ nhdr.pixdim[3] = nim->dz ; nhdr.pixdim[4] = nim->dt ;
+ nhdr.pixdim[5] = nim->du ; nhdr.pixdim[6] = nim->dv ;
+ nhdr.pixdim[7] = nim->dw ;
+
+ nhdr.datatype = nim->datatype ;
+ nhdr.bitpix = 8 * nim->nbyper ;
+
+ if( nim->cal_max > nim->cal_min ){
+ nhdr.cal_max = nim->cal_max ;
+ nhdr.cal_min = nim->cal_min ;
+ }
+
+ if( nim->scl_slope != 0.0 ){
+ nhdr.scl_slope = nim->scl_slope ;
+ nhdr.scl_inter = nim->scl_inter ;
+ }
+
+ if( nim->descrip[0] != '\0' ){
+ memcpy(nhdr.descrip ,nim->descrip ,79) ; nhdr.descrip[79] = '\0' ;
+ }
+ if( nim->aux_file[0] != '\0' ){
+ memcpy(nhdr.aux_file ,nim->aux_file ,23) ; nhdr.aux_file[23] = '\0' ;
+ }
+
+ /**- Load NIFTI specific stuff into the header */
+
+ if( nim->nifti_type > NIFTI_FTYPE_ANALYZE ){ /* then not ANALYZE */
+
+ if( nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ) strcpy(nhdr.magic,"n+1") ;
+ else strcpy(nhdr.magic,"ni1") ;
+
+ nhdr.pixdim[1] = fabs(nhdr.pixdim[1]) ; nhdr.pixdim[2] = fabs(nhdr.pixdim[2]) ;
+ nhdr.pixdim[3] = fabs(nhdr.pixdim[3]) ; nhdr.pixdim[4] = fabs(nhdr.pixdim[4]) ;
+ nhdr.pixdim[5] = fabs(nhdr.pixdim[5]) ; nhdr.pixdim[6] = fabs(nhdr.pixdim[6]) ;
+ nhdr.pixdim[7] = fabs(nhdr.pixdim[7]) ;
+
+ nhdr.intent_code = nim->intent_code ;
+ nhdr.intent_p1 = nim->intent_p1 ;
+ nhdr.intent_p2 = nim->intent_p2 ;
+ nhdr.intent_p3 = nim->intent_p3 ;
+ if( nim->intent_name[0] != '\0' ){
+ memcpy(nhdr.intent_name,nim->intent_name,15) ;
+ nhdr.intent_name[15] = '\0' ;
+ }
+
+ nhdr.vox_offset = (float) nim->iname_offset ;
+ nhdr.xyzt_units = SPACE_TIME_TO_XYZT( nim->xyz_units, nim->time_units ) ;
+ nhdr.toffset = nim->toffset ;
+
+ if( nim->qform_code > 0 ){
+ nhdr.qform_code = nim->qform_code ;
+ nhdr.quatern_b = nim->quatern_b ;
+ nhdr.quatern_c = nim->quatern_c ;
+ nhdr.quatern_d = nim->quatern_d ;
+ nhdr.qoffset_x = nim->qoffset_x ;
+ nhdr.qoffset_y = nim->qoffset_y ;
+ nhdr.qoffset_z = nim->qoffset_z ;
+ nhdr.pixdim[0] = (nim->qfac >= 0.0) ? 1.0 : -1.0 ;
+ }
+
+ if( nim->sform_code > 0 ){
+ nhdr.sform_code = nim->sform_code ;
+ nhdr.srow_x[0] = nim->sto_xyz.m[0][0] ;
+ nhdr.srow_x[1] = nim->sto_xyz.m[0][1] ;
+ nhdr.srow_x[2] = nim->sto_xyz.m[0][2] ;
+ nhdr.srow_x[3] = nim->sto_xyz.m[0][3] ;
+ nhdr.srow_y[0] = nim->sto_xyz.m[1][0] ;
+ nhdr.srow_y[1] = nim->sto_xyz.m[1][1] ;
+ nhdr.srow_y[2] = nim->sto_xyz.m[1][2] ;
+ nhdr.srow_y[3] = nim->sto_xyz.m[1][3] ;
+ nhdr.srow_z[0] = nim->sto_xyz.m[2][0] ;
+ nhdr.srow_z[1] = nim->sto_xyz.m[2][1] ;
+ nhdr.srow_z[2] = nim->sto_xyz.m[2][2] ;
+ nhdr.srow_z[3] = nim->sto_xyz.m[2][3] ;
+ }
+
+ nhdr.dim_info = FPS_INTO_DIM_INFO( nim->freq_dim ,
+ nim->phase_dim , nim->slice_dim ) ;
+ nhdr.slice_code = nim->slice_code ;
+ nhdr.slice_start = nim->slice_start ;
+ nhdr.slice_end = nim->slice_end ;
+ nhdr.slice_duration = nim->slice_duration ;
+ }
+
+ return nhdr;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! \fn int nifti_copy_extensions(nifti_image * nim_dest, nifti_image * nim_src)
+ \brief copy the nifti1_extension list from src to dest
+
+ Duplicate the list of nifti1_extensions. The dest structure must
+ be clear of extensions.
+ \return 0 on success, -1 on failure
+
+ \sa nifti_add_extension, nifti_free_extensions
+*/
+int nifti_copy_extensions(nifti_image * nim_dest, const nifti_image * nim_src)
+{
+ char * data;
+ size_t bytes;
+ int c, size, old_size;
+
+ if( nim_dest->num_ext > 0 || nim_dest->ext_list != NULL ){
+ fprintf(stderr,"** will not copy extensions over existing ones\n");
+ return -1;
+ }
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d duplicating %d extension(s)\n", nim_src->num_ext);
+
+ if( nim_src->num_ext <= 0 ) return 0;
+
+ bytes = nim_src->num_ext * sizeof(nifti1_extension); /* I'm lazy */
+ nim_dest->ext_list = (nifti1_extension *)malloc(bytes);
+ if( !nim_dest->ext_list ){
+ fprintf(stderr,"** failed to allocate %d nifti1_extension structs\n",
+ nim_src->num_ext);
+ return -1;
+ }
+
+ /* copy the extension data */
+ nim_dest->num_ext = 0;
+ for( c = 0; c < nim_src->num_ext; c++ ){
+ size = old_size = nim_src->ext_list[c].esize;
+ if( size & 0xf ) size = (size + 0xf) & ~0xf; /* make multiple of 16 */
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"+d dup'ing ext #%d of size %d (from size %d)\n",
+ c, size, old_size);
+ data = (char *)calloc(size,sizeof(char)); /* calloc, maybe size > old */
+ if( !data ){
+ fprintf(stderr,"** failed to alloc %d bytes for extention\n", size);
+ if( c == 0 ) { free(nim_dest->ext_list); nim_dest->ext_list = NULL; }
+ /* otherwise, keep what we have (a.o.t. deleting them all) */
+ return -1;
+ }
+ /* finally, fill the new structure */
+ nim_dest->ext_list[c].esize = size;
+ nim_dest->ext_list[c].ecode = nim_src->ext_list[c].ecode;
+ nim_dest->ext_list[c].edata = data;
+ memcpy(data, nim_src->ext_list[c].edata, old_size);
+
+ nim_dest->num_ext++;
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! compute the total size of all extensions
+
+ \return the total of all esize fields
+
+ Note that each esize includes 4 bytes for ecode, 4 bytes for esize,
+ and the bytes used for the data. Each esize also needs to be a
+ multiple of 16, so it may be greater than the sum of its 3 parts.
+*//*--------------------------------------------------------------------*/
+int nifti_extension_size(nifti_image *nim)
+{
+ int c, size = 0;
+
+ if( !nim || nim->num_ext <= 0 ) return 0;
+
+ if( g_opts.debug > 2 ) fprintf(stderr,"-d ext sizes:");
+
+ for ( c = 0; c < nim->num_ext; c++ ){
+ size += nim->ext_list[c].esize;
+ if( g_opts.debug > 2 ) fprintf(stderr," %d",nim->ext_list[c].esize);
+ }
+
+ if( g_opts.debug > 2 ) fprintf(stderr," (total = %d)\n",size);
+
+ return size;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! set the nifti_image iname_offset field, based on nifti_type
+
+ - if writing to 2 files, set offset to 0
+ - if writing to a single NIFTI-1 file, set the offset to
+ 352 + total extension size, then align to 16-byte boundary
+ - if writing an ASCII header, set offset to -1
+*//*--------------------------------------------------------------------*/
+void nifti_set_iname_offset(nifti_image *nim)
+{
+ int offset;
+
+ switch( nim->nifti_type ){
+
+ default: /* writing into 2 files */
+ /* we only write files with 0 offset in the 2 file format */
+ nim->iname_offset = 0 ;
+ break ;
+
+ /* NIFTI-1 single binary file - always update */
+ case NIFTI_FTYPE_NIFTI1_1:
+ offset = nifti_extension_size(nim)+sizeof(struct nifti_1_header)+4;
+ /* be sure offset is aligned to a 16 byte boundary */
+ if ( ( offset % 16 ) != 0 ) offset = ((offset + 0xf) & ~0xf);
+ if( nim->iname_offset != offset ){
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d changing offset from %d to %d\n",
+ nim->iname_offset, offset);
+ nim->iname_offset = offset;
+ }
+ break ;
+
+ /* non-standard case: NIFTI-1 ASCII header + binary data (single file) */
+ case NIFTI_FTYPE_ASCII:
+ nim->iname_offset = -1 ; /* compute offset from filesize */
+ break ;
+ }
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! write the nifti_image dataset to disk, optionally including data
+
+ This is just a front-end for nifti_image_write_hdr_img2.
+
+ \param nim nifti_image to write to disk
+ \param write_data write options (see nifti_image_write_hdr_img2)
+ \param opts file open options ("wb" from nifti_image_write)
+
+ \sa nifti_image_write, nifti_image_write_hdr_img2, nifti_image_free,
+ nifti_set_filenames
+*//*--------------------------------------------------------------------*/
+znzFile nifti_image_write_hdr_img( nifti_image *nim , int write_data ,
+ const char* opts )
+{
+ return nifti_image_write_hdr_img2(nim,write_data,opts,NULL,NULL);
+}
+
+
+#undef ERREX
+#define ERREX(msg) \
+ do{ fprintf(stderr,"** ERROR: nifti_image_write_hdr_img: %s\n",(msg)) ; \
+ return fp ; } while(0)
+
+
+/* ----------------------------------------------------------------------*/
+/*! This writes the header (and optionally the image data) to file
+ *
+ * If the image data file is left open it returns a valid znzFile handle.
+ * It also uses imgfile as the open image file is not null, and modifies
+ * it inside.
+ *
+ * \param nim nifti_image to write to disk
+ * \param write_opts flags whether to write data and/or close file (see below)
+ * \param opts file-open options, probably "wb" from nifti_image_write()
+ * \param imgfile optional open znzFile struct, for writing image data
+ (may be NULL)
+ * \param NBL optional nifti_brick_list, containing the image data
+ (may be NULL)
+ *
+ * Values for write_opts mode are based on two binary flags
+ * ( 0/1 for no-write/write data, and 0/2 for close/leave-open files ) :
+ * - 0 = do not write data and close (do not open data file)
+ * - 1 = write data and close
+ * - 2 = do not write data and leave data file open
+ * - 3 = write data and leave data file open
+ *
+ * \sa nifti_image_write, nifti_image_write_hdr_img, nifti_image_free,
+ * nifti_set_filenames
+*//*---------------------------------------------------------------------*/
+znzFile nifti_image_write_hdr_img2(nifti_image *nim, int write_opts,
+ const char * opts, znzFile imgfile, const nifti_brick_list * NBL)
+{
+ struct nifti_1_header nhdr ;
+ znzFile fp=NULL;
+ size_t ss ;
+ int write_data, leave_open;
+ char func[] = { "nifti_image_write_hdr_img2" };
+
+ write_data = write_opts & 1; /* just separate the bits now */
+ leave_open = write_opts & 2;
+
+ if( ! nim ) ERREX("NULL input") ;
+ if( ! nifti_validfilename(nim->fname) ) ERREX("bad fname input") ;
+ if( write_data && ! nim->data && ! NBL ) ERREX("no image data") ;
+
+ nifti_set_iname_offset(nim);
+
+ if( g_opts.debug > 1 ){
+ fprintf(stderr,"-d writing nifti file '%s'...\n", nim->fname);
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d nifti type %d, offset %d\n",
+ nim->nifti_type, nim->iname_offset);
+ }
+
+ if( nim->nifti_type == NIFTI_FTYPE_ASCII ) /* non-standard case */
+ return nifti_write_ascii_image(nim,NBL,opts,write_data,leave_open);
+
+ nhdr = nifti_convert_nim2nhdr(nim); /* create the nifti1_header struct */
+
+ /* if writing to 2 files, make sure iname is set and different from fname */
+ if( nim->nifti_type != NIFTI_FTYPE_NIFTI1_1 ){
+ if( nim->iname && strcmp(nim->iname,nim->fname) == 0 ){
+ free(nim->iname) ; nim->iname = NULL ;
+ }
+ if( nim->iname == NULL ){ /* then make a new one */
+ nim->iname = nifti_makeimgname(nim->fname,nim->nifti_type,0,0);
+ if( nim->iname == NULL ) return NULL;
+ }
+ }
+
+ /* if we have an imgfile and will write the header there, use it */
+ if( ! znz_isnull(imgfile) && nim->nifti_type == NIFTI_FTYPE_NIFTI1_1 ){
+ if( g_opts.debug > 2 ) fprintf(stderr,"+d using passed file for hdr\n");
+ fp = imgfile;
+ }
+ else {
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"+d opening output file '%s'\n",nim->fname);
+ fp = znzopen( nim->fname , opts , nifti_is_gzfile(nim->fname) ) ;
+ if( znz_isnull(fp) ){
+ LNI_FERR(func,"cannot open output file",nim->fname);
+ return fp;
+ }
+ }
+
+ /* write the header and extensions */
+
+ ss = znzwrite(&nhdr , 1 , sizeof(nhdr) , fp); /* write header */
+ if( ss < sizeof(nhdr) ){
+ LNI_FERR(func,"bad header write to output file",nim->fname);
+ znzclose(fp); return fp;
+ }
+
+ /* partial file exists, and errors have been printed, so ignore return */
+ if( nim->nifti_type != NIFTI_FTYPE_ANALYZE )
+ (void)nifti_write_extensions(fp,nim);
+
+ /* if the header is all we want, we are done */
+ if( ! write_data && ! leave_open ){
+ if( g_opts.debug > 2 ) fprintf(stderr,"-d header is all we want: done\n");
+ znzclose(fp); return(fp);
+ }
+
+ if( nim->nifti_type != NIFTI_FTYPE_NIFTI1_1 ){ /* get a new file pointer */
+ znzclose(fp); /* first, close header file */
+ if( ! znz_isnull(imgfile) ){
+ if(g_opts.debug > 2) fprintf(stderr,"+d using passed file for img\n");
+ fp = imgfile;
+ }
+ else {
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"+d opening img file '%s'\n", nim->iname);
+ fp = znzopen( nim->iname , opts , nifti_is_gzfile(nim->iname) ) ;
+ if( znz_isnull(fp) ) ERREX("cannot open image file") ;
+ }
+ }
+
+ znzseek(fp, nim->iname_offset, SEEK_SET); /* in any case, seek to offset */
+
+ if( write_data ) nifti_write_all_data(fp,nim,NBL);
+ if( ! leave_open ) znzclose(fp);
+
+ return fp;
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! write a nifti_image to disk in ASCII format
+*//*--------------------------------------------------------------------*/
+znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL,
+ const char *opts, int write_data, int leave_open)
+{
+ znzFile fp;
+ char * hstr;
+
+ hstr = nifti_image_to_ascii( nim ) ; /* get header in ASCII form */
+ if( ! hstr ){ fprintf(stderr,"** failed image_to_ascii()\n"); return NULL; }
+
+ fp = znzopen( nim->fname , opts , nifti_is_gzfile(nim->fname) ) ;
+ if( znz_isnull(fp) ){
+ free(hstr);
+ fprintf(stderr,"** failed to open '%s' for ascii write\n",nim->fname);
+ return fp;
+ }
+
+ znzputs(hstr,fp); /* header */
+ nifti_write_extensions(fp,nim); /* extensions */
+
+ if ( write_data ) { nifti_write_all_data(fp,nim,NBL); } /* data */
+ if ( ! leave_open ) { znzclose(fp); }
+
+ return fp; /* returned but may be closed */
+}
+
+
+/*--------------------------------------------------------------------------*/
+/*! Write a nifti_image to disk.
+
+ Since data is properly byte-swapped upon reading, it is assumed
+ to be in the byte-order of the current CPU at write time. Thus,
+ nim->byte_order should match that of the current CPU. Note that
+ the nifti_set_filenames() function takes the flag, set_byte_order.
+
+ The following fields of nim affect how the output appears:
+ - nifti_type = 0 ==> ANALYZE-7.5 format file pair will be written
+ - nifti_type = 1 ==> NIFTI-1 format single file will be written
+ (data offset will be 352+extensions)
+ - nifti_type = 2 ==> NIFTI_1 format file pair will be written
+ - nifti_type = 3 ==> NIFTI_1 ASCII single file will be written
+ - fname is the name of the output file (header or header+data)
+ - if a file pair is being written, iname is the name of the data file
+ - existing files WILL be overwritten with extreme prejudice
+ - if qform_code > 0, the quatern_*, qoffset_*, and qfac fields determine
+ the qform output, NOT the qto_xyz matrix; if you want to compute these
+ fields from the qto_xyz matrix, you can use the utility function
+ nifti_mat44_to_quatern()
+
+ \sa nifti_image_write_bricks, nifti_image_free, nifti_set_filenames,
+ nifti_image_write_hdr_img
+*//*------------------------------------------------------------------------*/
+void nifti_image_write( nifti_image *nim )
+{
+ znzFile fp = nifti_image_write_hdr_img(nim,1,"wb");
+ if( fp ){
+ if( g_opts.debug > 2 ) fprintf(stderr,"-d niw: done with znzFile\n");
+ free(fp);
+ }
+ if( g_opts.debug > 1 ) fprintf(stderr,"-d nifti_image_write: done\n");
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! similar to nifti_image_write, but data is in NBL struct, not nim->data
+
+ \sa nifti_image_write, nifti_image_free, nifti_set_filenames, nifti_free_NBL
+*//*--------------------------------------------------------------------*/
+void nifti_image_write_bricks( nifti_image *nim, const nifti_brick_list * NBL )
+{
+ znzFile fp = nifti_image_write_hdr_img2(nim,1,"wb",NULL,NBL);
+ if( fp ){
+ if( g_opts.debug > 2 ) fprintf(stderr,"-d niwb: done with znzFile\n");
+ free(fp);
+ }
+ if( g_opts.debug > 1 ) fprintf(stderr,"-d niwb: done writing bricks\n");
+}
+
+
+/*----------------------------------------------------------------------*/
+/*! copy the nifti_image structure, without data
+
+ Duplicate the structure, including fname, iname and extensions.
+ Leave the data pointer as NULL.
+*//*--------------------------------------------------------------------*/
+nifti_image * nifti_copy_nim_info(const nifti_image * src)
+{
+ nifti_image *dest;
+ dest = (nifti_image *)calloc(1,sizeof(nifti_image));
+ if( !dest ){
+ fprintf(stderr,"** NCNI: failed to alloc nifti_image\n");
+ return NULL;
+ }
+ memcpy(dest, src, sizeof(nifti_image));
+ if( src->fname ) dest->fname = nifti_strdup(src->fname);
+ if( src->iname ) dest->iname = nifti_strdup(src->iname);
+
+ /* errors will be printed in NCE(), continue in either case */
+ (void)nifti_copy_extensions(dest, src);
+
+ dest->data = NULL;
+
+ return dest;
+}
+
+
+/*------------------------------------------------------------------------*/
+/* Un-escape a C string in place -- that is, convert XML escape sequences
+ back into their characters. (This can be done in place since the
+ replacement is always smaller than the input.) Escapes recognized are:
+ - < -> <
+ - > -> >
+ - " -> "
+ - ' -> '
+ - & -> &
+ Also replace CR LF pair (Microsoft), or CR alone (Macintosh) with
+ LF (Unix), per the XML standard.
+ Return value is number of replacements made (if you care).
+--------------------------------------------------------------------------*/
+
+#undef CR
+#undef LF
+#define CR 0x0D
+#define LF 0x0A
+
+static int unescape_string( char *str )
+{
+ int ii,jj , nn,ll ;
+
+ if( str == NULL ) return 0 ; /* no string? */
+ ll = strlen(str) ; if( ll == 0 ) return 0 ;
+
+ /* scan for escapes: &something; */
+
+ for( ii=jj=nn=0 ; ii<ll ; ii++,jj++ ){ /* scan at ii; results go in at jj */
+
+ if( str[ii] == '&' ){ /* start of escape? */
+
+ if( ii+3 < ll && /* < */
+ str[ii+1] == 'l' &&
+ str[ii+2] == 't' &&
+ str[ii+3] == ';' ){ str[jj] = '<' ; ii += 3 ; nn++ ; }
+
+ else if( ii+3 < ll && /* > */
+ str[ii+1] == 'g' &&
+ str[ii+2] == 't' &&
+ str[ii+3] == ';' ){ str[jj] = '>' ; ii += 3 ; nn++ ; }
+
+ else if( ii+5 < ll && /* " */
+ str[ii+1] == 'q' &&
+ str[ii+2] == 'u' &&
+ str[ii+3] == 'o' &&
+ str[ii+4] == 't' &&
+ str[ii+5] == ';' ){ str[jj] = '"' ; ii += 5 ; nn++ ; }
+
+ else if( ii+5 < ll && /* ' */
+ str[ii+1] == 'a' &&
+ str[ii+2] == 'p' &&
+ str[ii+3] == 'o' &&
+ str[ii+4] == 's' &&
+ str[ii+5] == ';' ){ str[jj] = '\'' ; ii += 5 ; nn++ ; }
+
+ else if( ii+4 < ll && /* & */
+ str[ii+1] == 'a' &&
+ str[ii+2] == 'm' &&
+ str[ii+3] == 'p' &&
+ str[ii+4] == ';' ){ str[jj] = '&' ; ii += 4 ; nn++ ; }
+
+ /* although the comments above don't mention it,
+ we also look for XML style numeric escapes
+ of the forms   (decimal) and ý (hex) */
+
+ else if( ii+3 < ll &&
+ str[ii+1] == '#' &&
+ isdigit(str[ii+2]) ){ /* &#dec; */
+
+ unsigned int val='?' ; int kk=ii+3 ;
+ while( kk < ll && kk != ';' ) kk++ ;
+ sscanf( str+ii+2 , "%u" , &val ) ;
+ str[jj] = (char) val ; ii = kk ; nn++ ;
+ }
+
+ else if( ii+4 < ll &&
+ str[ii+1] == '#' &&
+ str[ii+2] == 'x' &&
+ isxdigit(str[ii+3]) ){ /* &#hex; */
+
+ unsigned int val='?' ; int kk=ii+4 ;
+ while( kk < ll && kk != ';' ) kk++ ;
+ sscanf( str+ii+3 , "%x" , &val ) ;
+ str[jj] = (char) val ; ii = kk ; nn++ ;
+ }
+
+ /* didn't start a recognized escape, so just copy as normal */
+
+ else if( jj < ii ){ str[jj] = str[ii] ; }
+
+ } else if( str[ii] == CR ) { /* is a carriage return */
+
+ if( str[ii+1] == LF ){ str[jj] = LF ; ii++ ; nn++ ; } /* CR LF */
+ else { str[jj] = LF ; ; nn++ ; } /* CR only */
+
+ } else { /* is a normal character, just copy to output */
+
+ if( jj < ii ){ str[jj] = str[ii] ; }
+ }
+
+ /* at this point, ii=index of last character used up in scan
+ jj=index of last character written to (jj <= ii) */
+ }
+
+ if( jj < ll ) str[jj] = '\0' ; /* end string properly */
+
+ return nn ;
+}
+
+/*------------------------------------------------------------------------*/
+/* Quotize (and escapize) one string, returning a new string.
+ Approximately speaking, this is the inverse of unescape_string().
+ The result should be free()-ed when you are done with it.
+--------------------------------------------------------------------------*/
+
+static char *escapize_string( const char * str )
+{
+ int ii,jj , lstr,lout ;
+ char *out ;
+
+ if( str == NULL || (lstr=strlen(str)) == 0 ){ /* 0 length */
+ out = nifti_strdup("''") ; return out ; /* string?? */
+ }
+
+ lout = 4 ; /* initialize length of output */
+ for( ii=0 ; ii < lstr ; ii++ ){ /* count characters for output */
+ switch( str[ii] ){
+ case '&': lout += 5 ; break ; /* replace '&' with "&" */
+
+ case '<':
+ case '>': lout += 4 ; break ; /* replace '<' with "<" */
+
+ case '"' :
+ case '\'': lout += 6 ; break ; /* replace '"' with """ */
+
+ case CR:
+ case LF: lout += 6 ; break ; /* replace CR with "
"
+ LF with "
" */
+
+ default: lout++ ; break ; /* copy all other chars */
+ }
+ }
+ out = (char *)calloc(1,lout) ; /* allocate output string */
+ if( !out ){
+ fprintf(stderr,"** escapize_string: failed to alloc %d bytes\n",lout);
+ return NULL;
+ }
+ out[0] = '\'' ; /* opening quote mark */
+ for( ii=0,jj=1 ; ii < lstr ; ii++ ){
+ switch( str[ii] ){
+ default: out[jj++] = str[ii] ; break ; /* normal characters */
+
+ case '&': memcpy(out+jj,"&",5) ; jj+=5 ; break ;
+
+ case '<': memcpy(out+jj,"<",4) ; jj+=4 ; break ;
+ case '>': memcpy(out+jj,">",4) ; jj+=4 ; break ;
+
+ case '"' : memcpy(out+jj,""",6) ; jj+=6 ; break ;
+
+ case '\'': memcpy(out+jj,"'",6) ; jj+=6 ; break ;
+
+ case CR: memcpy(out+jj,"
",6) ; jj+=6 ; break ;
+ case LF: memcpy(out+jj,"
",6) ; jj+=6 ; break ;
+ }
+ }
+ out[jj++] = '\'' ; /* closing quote mark */
+ out[jj] = '\0' ; /* terminate the string */
+ return out ;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! Dump the information in a NIFTI image header to an XML-ish ASCII string
+ that can later be converted back into a NIFTI header in
+ nifti_image_from_ascii().
+
+ The resulting string can be free()-ed when you are done with it.
+*//*-------------------------------------------------------------------------*/
+char *nifti_image_to_ascii( const nifti_image *nim )
+{
+ char *buf , *ebuf ; int nbuf ;
+
+ if( nim == NULL ) return NULL ; /* stupid caller */
+
+ buf = (char *)calloc(1,65534); nbuf = 0; /* longer than needed, to be safe */
+ if( !buf ){
+ fprintf(stderr,"** NITA: failed to alloc %d bytes\n",65534);
+ return NULL;
+ }
+
+ sprintf( buf , "<nifti_image\n" ) ; /* XML-ish opener */
+
+ sprintf( buf+strlen(buf) , " nifti_type = '%s'\n" ,
+ (nim->nifti_type == NIFTI_FTYPE_NIFTI1_1) ? "NIFTI-1+"
+ :(nim->nifti_type == NIFTI_FTYPE_NIFTI1_2) ? "NIFTI-1"
+ :(nim->nifti_type == NIFTI_FTYPE_ASCII ) ? "NIFTI-1A"
+ : "ANALYZE-7.5" ) ;
+
+ /** Strings that we don't control (filenames, etc.) that might
+ contain "weird" characters (like quotes) are "escaped":
+ - A few special characters are replaced by XML-style escapes, using
+ the function escapize_string().
+ - On input, function unescape_string() reverses this process.
+ - The result is that the NIFTI ASCII-format header is XML-compliant. */
+
+ ebuf = escapize_string(nim->fname) ;
+ sprintf( buf+strlen(buf) , " header_filename = %s\n",ebuf); free(ebuf);
+
+ ebuf = escapize_string(nim->iname) ;
+ sprintf( buf+strlen(buf) , " image_filename = %s\n", ebuf); free(ebuf);
+
+ sprintf( buf+strlen(buf) , " image_offset = '%d'\n" , nim->iname_offset );
+
+ sprintf( buf+strlen(buf), " ndim = '%d'\n", nim->ndim);
+ sprintf( buf+strlen(buf), " nx = '%d'\n", nim->nx );
+ if( nim->ndim > 1 ) sprintf( buf+strlen(buf), " ny = '%d'\n", nim->ny );
+ if( nim->ndim > 2 ) sprintf( buf+strlen(buf), " nz = '%d'\n", nim->nz );
+ if( nim->ndim > 3 ) sprintf( buf+strlen(buf), " nt = '%d'\n", nim->nt );
+ if( nim->ndim > 4 ) sprintf( buf+strlen(buf), " nu = '%d'\n", nim->nu );
+ if( nim->ndim > 5 ) sprintf( buf+strlen(buf), " nv = '%d'\n", nim->nv );
+ if( nim->ndim > 6 ) sprintf( buf+strlen(buf), " nw = '%d'\n", nim->nw );
+ sprintf( buf+strlen(buf), " dx = '%g'\n", nim->dx );
+ if( nim->ndim > 1 ) sprintf( buf+strlen(buf), " dy = '%g'\n", nim->dy );
+ if( nim->ndim > 2 ) sprintf( buf+strlen(buf), " dz = '%g'\n", nim->dz );
+ if( nim->ndim > 3 ) sprintf( buf+strlen(buf), " dt = '%g'\n", nim->dt );
+ if( nim->ndim > 4 ) sprintf( buf+strlen(buf), " du = '%g'\n", nim->du );
+ if( nim->ndim > 5 ) sprintf( buf+strlen(buf), " dv = '%g'\n", nim->dv );
+ if( nim->ndim > 6 ) sprintf( buf+strlen(buf), " dw = '%g'\n", nim->dw );
+
+ sprintf( buf+strlen(buf) , " datatype = '%d'\n" , nim->datatype ) ;
+ sprintf( buf+strlen(buf) , " datatype_name = '%s'\n" ,
+ nifti_datatype_string(nim->datatype) ) ;
+
+ sprintf( buf+strlen(buf) , " nvox = '%d'\n" , nim->nvox ) ;
+ sprintf( buf+strlen(buf) , " nbyper = '%d'\n" , nim->nbyper ) ;
+
+ sprintf( buf+strlen(buf) , " byteorder = '%s'\n" ,
+ (nim->byteorder==MSB_FIRST) ? "MSB_FIRST" : "LSB_FIRST" ) ;
+
+ if( nim->cal_min < nim->cal_max ){
+ sprintf( buf+strlen(buf) , " cal_min = '%g'\n", nim->cal_min ) ;
+ sprintf( buf+strlen(buf) , " cal_max = '%g'\n", nim->cal_max ) ;
+ }
+
+ if( nim->scl_slope != 0.0 ){
+ sprintf( buf+strlen(buf) , " scl_slope = '%g'\n" , nim->scl_slope ) ;
+ sprintf( buf+strlen(buf) , " scl_inter = '%g'\n" , nim->scl_inter ) ;
+ }
+
+ if( nim->intent_code > 0 ){
+ sprintf( buf+strlen(buf) , " intent_code = '%d'\n", nim->intent_code ) ;
+ sprintf( buf+strlen(buf) , " intent_code_name = '%s'\n" ,
+ nifti_intent_string(nim->intent_code) ) ;
+ sprintf( buf+strlen(buf) , " intent_p1 = '%g'\n" , nim->intent_p1 ) ;
+ sprintf( buf+strlen(buf) , " intent_p2 = '%g'\n" , nim->intent_p2 ) ;
+ sprintf( buf+strlen(buf) , " intent_p3 = '%g'\n" , nim->intent_p3 ) ;
+
+ if( nim->intent_name[0] != '\0' ){
+ ebuf = escapize_string(nim->intent_name) ;
+ sprintf( buf+strlen(buf) , " intent_name = %s\n",ebuf) ;
+ free(ebuf) ;
+ }
+ }
+
+ if( nim->toffset != 0.0 )
+ sprintf( buf+strlen(buf) , " toffset = '%g'\n",nim->toffset ) ;
+
+ if( nim->xyz_units > 0 )
+ sprintf( buf+strlen(buf) ,
+ " xyz_units = '%d'\n"
+ " xyz_units_name = '%s'\n" ,
+ nim->xyz_units , nifti_units_string(nim->xyz_units) ) ;
+
+ if( nim->time_units > 0 )
+ sprintf( buf+strlen(buf) ,
+ " time_units = '%d'\n"
+ " time_units_name = '%s'\n" ,
+ nim->time_units , nifti_units_string(nim->time_units) ) ;
+
+ if( nim->freq_dim > 0 )
+ sprintf( buf+strlen(buf) , " freq_dim = '%d'\n",nim->freq_dim ) ;
+ if( nim->phase_dim > 0 )
+ sprintf( buf+strlen(buf) , " phase_dim = '%d'\n",nim->phase_dim ) ;
+ if( nim->slice_dim > 0 )
+ sprintf( buf+strlen(buf) , " slice_dim = '%d'\n",nim->slice_dim ) ;
+ if( nim->slice_code > 0 )
+ sprintf( buf+strlen(buf) ,
+ " slice_code = '%d'\n"
+ " slice_code_name = '%s'\n" ,
+ nim->slice_code , nifti_slice_string(nim->slice_code) ) ;
+ if( nim->slice_start >= 0 && nim->slice_end > nim->slice_start )
+ sprintf( buf+strlen(buf) ,
+ " slice_start = '%d'\n"
+ " slice_end = '%d'\n" , nim->slice_start , nim->slice_end ) ;
+ if( nim->slice_duration != 0.0 )
+ sprintf( buf+strlen(buf) , " slice_duration = '%g'\n",
+ nim->slice_duration ) ;
+
+ if( nim->descrip[0] != '\0' ){
+ ebuf = escapize_string(nim->descrip) ;
+ sprintf( buf+strlen(buf) , " descrip = %s\n",ebuf) ;
+ free(ebuf) ;
+ }
+
+ if( nim->aux_file[0] != '\0' ){
+ ebuf = escapize_string(nim->aux_file) ;
+ sprintf( buf+strlen(buf) , " aux_file = %s\n",ebuf) ;
+ free(ebuf) ;
+ }
+
+ if( nim->qform_code > 0 ){
+ int i,j,k ;
+
+ sprintf( buf+strlen(buf) ,
+ " qform_code = '%d'\n"
+ " qform_code_name = '%s'\n"
+ " qto_xyz_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" ,
+ nim->qform_code , nifti_xform_string(nim->qform_code) ,
+ nim->qto_xyz.m[0][0] , nim->qto_xyz.m[0][1] ,
+ nim->qto_xyz.m[0][2] , nim->qto_xyz.m[0][3] ,
+ nim->qto_xyz.m[1][0] , nim->qto_xyz.m[1][1] ,
+ nim->qto_xyz.m[1][2] , nim->qto_xyz.m[1][3] ,
+ nim->qto_xyz.m[2][0] , nim->qto_xyz.m[2][1] ,
+ nim->qto_xyz.m[2][2] , nim->qto_xyz.m[2][3] ,
+ nim->qto_xyz.m[3][0] , nim->qto_xyz.m[3][1] ,
+ nim->qto_xyz.m[3][2] , nim->qto_xyz.m[3][3] ) ;
+
+ sprintf( buf+strlen(buf) ,
+ " qto_ijk_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" ,
+ nim->qto_ijk.m[0][0] , nim->qto_ijk.m[0][1] ,
+ nim->qto_ijk.m[0][2] , nim->qto_ijk.m[0][3] ,
+ nim->qto_ijk.m[1][0] , nim->qto_ijk.m[1][1] ,
+ nim->qto_ijk.m[1][2] , nim->qto_ijk.m[1][3] ,
+ nim->qto_ijk.m[2][0] , nim->qto_ijk.m[2][1] ,
+ nim->qto_ijk.m[2][2] , nim->qto_ijk.m[2][3] ,
+ nim->qto_ijk.m[3][0] , nim->qto_ijk.m[3][1] ,
+ nim->qto_ijk.m[3][2] , nim->qto_ijk.m[3][3] ) ;
+
+ sprintf( buf+strlen(buf) ,
+ " quatern_b = '%g'\n"
+ " quatern_c = '%g'\n"
+ " quatern_d = '%g'\n"
+ " qoffset_x = '%g'\n"
+ " qoffset_y = '%g'\n"
+ " qoffset_z = '%g'\n"
+ " qfac = '%g'\n" ,
+ nim->quatern_b , nim->quatern_c , nim->quatern_d ,
+ nim->qoffset_x , nim->qoffset_y , nim->qoffset_z , nim->qfac ) ;
+
+ nifti_mat44_to_orientation( nim->qto_xyz , &i,&j,&k ) ;
+ if( i > 0 && j > 0 && k > 0 )
+ sprintf( buf+strlen(buf) ,
+ " qform_i_orientation = '%s'\n"
+ " qform_j_orientation = '%s'\n"
+ " qform_k_orientation = '%s'\n" ,
+ nifti_orientation_string(i) ,
+ nifti_orientation_string(j) ,
+ nifti_orientation_string(k) ) ;
+ }
+
+ if( nim->sform_code > 0 ){
+ int i,j,k ;
+
+ sprintf( buf+strlen(buf) ,
+ " sform_code = '%d'\n"
+ " sform_code_name = '%s'\n"
+ " sto_xyz_matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" ,
+ nim->sform_code , nifti_xform_string(nim->sform_code) ,
+ nim->sto_xyz.m[0][0] , nim->sto_xyz.m[0][1] ,
+ nim->sto_xyz.m[0][2] , nim->sto_xyz.m[0][3] ,
+ nim->sto_xyz.m[1][0] , nim->sto_xyz.m[1][1] ,
+ nim->sto_xyz.m[1][2] , nim->sto_xyz.m[1][3] ,
+ nim->sto_xyz.m[2][0] , nim->sto_xyz.m[2][1] ,
+ nim->sto_xyz.m[2][2] , nim->sto_xyz.m[2][3] ,
+ nim->sto_xyz.m[3][0] , nim->sto_xyz.m[3][1] ,
+ nim->sto_xyz.m[3][2] , nim->sto_xyz.m[3][3] ) ;
+
+ sprintf( buf+strlen(buf) ,
+ " sto_ijk matrix = '%g %g %g %g %g %g %g %g %g %g %g %g %g %g %g %g'\n" ,
+ nim->sto_ijk.m[0][0] , nim->sto_ijk.m[0][1] ,
+ nim->sto_ijk.m[0][2] , nim->sto_ijk.m[0][3] ,
+ nim->sto_ijk.m[1][0] , nim->sto_ijk.m[1][1] ,
+ nim->sto_ijk.m[1][2] , nim->sto_ijk.m[1][3] ,
+ nim->sto_ijk.m[2][0] , nim->sto_ijk.m[2][1] ,
+ nim->sto_ijk.m[2][2] , nim->sto_ijk.m[2][3] ,
+ nim->sto_ijk.m[3][0] , nim->sto_ijk.m[3][1] ,
+ nim->sto_ijk.m[3][2] , nim->sto_ijk.m[3][3] ) ;
+
+ nifti_mat44_to_orientation( nim->sto_xyz , &i,&j,&k ) ;
+ if( i > 0 && j > 0 && k > 0 )
+ sprintf( buf+strlen(buf) ,
+ " sform_i_orientation = '%s'\n"
+ " sform_j_orientation = '%s'\n"
+ " sform_k_orientation = '%s'\n" ,
+ nifti_orientation_string(i) ,
+ nifti_orientation_string(j) ,
+ nifti_orientation_string(k) ) ;
+ }
+
+ sprintf( buf+strlen(buf) , " num_ext = '%d'\n", nim->num_ext ) ;
+
+ sprintf( buf+strlen(buf) , "/>\n" ) ; /* XML-ish closer */
+
+ nbuf = strlen(buf) ;
+ buf = (char *)realloc((void *)buf, nbuf+1); /* cut back to proper length */
+ if( !buf ) fprintf(stderr,"** NITA: failed to realloc %d bytes\n",nbuf+1);
+ return buf ;
+}
+
+/*---------------------------------------------------------------------------*/
+
+/*----------------------------------------------------------------------*/
+/*! get the byte order for this CPU
+
+ - LSB_FIRST means least significant byte, first (little endian)
+ - MSB_FIRST means most significant byte, first (big endian)
+*//*--------------------------------------------------------------------*/
+int nifti_short_order(void) /* determine this CPU's byte order */
+{
+ union { unsigned char bb[2] ;
+ short ss ; } fred ;
+
+ fred.bb[0] = 1 ; fred.bb[1] = 0 ;
+
+ return (fred.ss == 1) ? LSB_FIRST : MSB_FIRST ;
+}
+
+/*---------------------------------------------------------------------------*/
+
+#undef QQNUM
+#undef QNUM
+#undef QSTR
+
+/* macro to check lhs string against "n1"; if it matches,
+ interpret rhs string as a number, and put it into nim->"n2" */
+
+#define QQNUM(n1,n2) if( strcmp(lhs,#n1)==0 ) nim->n2=strtod(rhs,NULL)
+
+/* same, but where "n1" == "n2" */
+
+#define QNUM(nam) QQNUM(nam,nam)
+
+/* macro to check lhs string against "nam"; if it matches,
+ put rhs string into nim->"nam" string, with max length = "ml" */
+
+#define QSTR(nam,ml) if( strcmp(lhs,#nam) == 0 ) \
+ strncpy(nim->nam,rhs,ml), nim->nam[ml]='\0'
+
+/*---------------------------------------------------------------------------*/
+/*! Take an XML-ish ASCII string and create a NIFTI image header to match.
+
+ NULL is returned if enough information isn't present in the input string.
+ - The image data can later be loaded with nifti_image_load().
+ - The struct returned here can be liberated with nifti_image_free().
+ - Not a lot of error checking is done here to make sure that the
+ input values are reasonable!
+*//*-------------------------------------------------------------------------*/
+nifti_image *nifti_image_from_ascii( const char *str, int * bytes_read )
+{
+ char lhs[1024] , rhs[1024] ;
+ int ii , spos, nn , slen ;
+ nifti_image *nim ; /* will be output */
+
+ if( str == NULL || *str == '\0' ) return NULL ; /* bad input!? */
+
+ /* scan for opening string */
+
+ spos = 0 ; slen = strlen(str) ;
+ ii = sscanf( str+spos , "%1023s%n" , lhs , &nn ) ; spos += nn ;
+ if( ii == 0 || strcmp(lhs,"<nifti_image") != 0 ) return NULL ;
+
+ /* create empty image struct */
+
+ nim = (nifti_image *) calloc( 1 , sizeof(nifti_image) ) ;
+ if( !nim ){
+ fprintf(stderr,"** NIFA: failed to alloc nifti_image\n");
+ return NULL;
+ }
+
+ nim->nx = nim->ny = nim->nz = nim->nt
+ = nim->nu = nim->nv = nim->nw = 1 ;
+ nim->dx = nim->dy = nim->dz = nim->dt
+ = nim->du = nim->dv = nim->dw = nim->qfac = 1.0 ;
+
+ nim->byteorder = nifti_short_order() ;
+
+ /* starting at str[spos], scan for "equations" of the form
+ lhs = 'rhs'
+ and assign rhs values into the struct component named by lhs */
+
+ while(1){
+
+ while( isspace(str[spos]) ) spos++ ; /* skip whitespace */
+ if( str[spos] == '\0' ) break ; /* end of string? */
+
+ /* get lhs string */
+
+ ii = sscanf( str+spos , "%1023s%n" , lhs , &nn ) ; spos += nn ;
+ if( ii == 0 || strcmp(lhs,"/>") == 0 ) break ; /* end of input? */
+
+ /* skip whitespace and the '=' marker */
+
+ while( isspace(str[spos]) || str[spos] == '=' ) spos++ ;
+ if( str[spos] == '\0' ) break ; /* end of string? */
+
+ /* if next character is a quote ', copy everything up to next '
+ otherwise, copy everything up to next nonblank */
+
+ if( str[spos] == '\'' ){
+ ii = spos+1 ;
+ while( str[ii] != '\0' && str[ii] != '\'' ) ii++ ;
+ nn = ii-spos-1 ; if( nn > 1023 ) nn = 1023 ;
+ memcpy(rhs,str+spos+1,nn) ; rhs[nn] = '\0' ;
+ spos = (str[ii] == '\'') ? ii+1 : ii ;
+ } else {
+ ii = sscanf( str+spos , "%1023s%n" , rhs , &nn ) ; spos += nn ;
+ if( ii == 0 ) break ; /* nothing found? */
+ }
+ unescape_string(rhs) ; /* remove any XML escape sequences */
+
+ /* Now can do the assignment, based on lhs string.
+ Start with special cases that don't fit the QNUM/QSTR macros. */
+
+ if( strcmp(lhs,"nifti_type") == 0 ){
+ if( strcmp(rhs,"ANALYZE-7.5") == 0 )
+ nim->nifti_type = NIFTI_FTYPE_ANALYZE ;
+ else if( strcmp(rhs,"NIFTI-1+") == 0 )
+ nim->nifti_type = NIFTI_FTYPE_NIFTI1_1 ;
+ else if( strcmp(rhs,"NIFTI-1") == 0 )
+ nim->nifti_type = NIFTI_FTYPE_NIFTI1_2 ;
+ else if( strcmp(rhs,"NIFTI-1A") == 0 )
+ nim->nifti_type = NIFTI_FTYPE_ASCII ;
+ }
+ else if( strcmp(lhs,"header_filename") == 0 ){
+ nim->fname = nifti_strdup(rhs) ;
+ }
+ else if( strcmp(lhs,"image_filename") == 0 ){
+ nim->iname = nifti_strdup(rhs) ;
+ }
+ else if( strcmp(lhs,"sto_xyz_matrix") == 0 ){
+ sscanf( rhs , "%f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f" ,
+ &(nim->sto_xyz.m[0][0]) , &(nim->sto_xyz.m[0][1]) ,
+ &(nim->sto_xyz.m[0][2]) , &(nim->sto_xyz.m[0][3]) ,
+ &(nim->sto_xyz.m[1][0]) , &(nim->sto_xyz.m[1][1]) ,
+ &(nim->sto_xyz.m[1][2]) , &(nim->sto_xyz.m[1][3]) ,
+ &(nim->sto_xyz.m[2][0]) , &(nim->sto_xyz.m[2][1]) ,
+ &(nim->sto_xyz.m[2][2]) , &(nim->sto_xyz.m[2][3]) ,
+ &(nim->sto_xyz.m[3][0]) , &(nim->sto_xyz.m[3][1]) ,
+ &(nim->sto_xyz.m[3][2]) , &(nim->sto_xyz.m[3][3]) ) ;
+ }
+ else if( strcmp(lhs,"byteorder") == 0 ){
+ if( strcmp(rhs,"MSB_FIRST") == 0 ) nim->byteorder = MSB_FIRST ;
+ if( strcmp(rhs,"LSB_FIRST") == 0 ) nim->byteorder = LSB_FIRST ;
+ }
+ else QQNUM(image_offset,iname_offset) ;
+ else QNUM(datatype) ;
+ else QNUM(ndim) ;
+ else QNUM(nx) ;
+ else QNUM(ny) ;
+ else QNUM(nz) ;
+ else QNUM(nt) ;
+ else QNUM(nu) ;
+ else QNUM(nv) ;
+ else QNUM(nw) ;
+ else QNUM(dx) ;
+ else QNUM(dy) ;
+ else QNUM(dz) ;
+ else QNUM(dt) ;
+ else QNUM(du) ;
+ else QNUM(dv) ;
+ else QNUM(dw) ;
+ else QNUM(cal_min) ;
+ else QNUM(cal_max) ;
+ else QNUM(scl_slope) ;
+ else QNUM(scl_inter) ;
+ else QNUM(intent_code) ;
+ else QNUM(intent_p1) ;
+ else QNUM(intent_p2) ;
+ else QNUM(intent_p3) ;
+ else QSTR(intent_name,15) ;
+ else QNUM(toffset) ;
+ else QNUM(xyz_units) ;
+ else QNUM(time_units) ;
+ else QSTR(descrip,79) ;
+ else QSTR(aux_file,23) ;
+ else QNUM(qform_code) ;
+ else QNUM(quatern_b) ;
+ else QNUM(quatern_c) ;
+ else QNUM(quatern_d) ;
+ else QNUM(qoffset_x) ;
+ else QNUM(qoffset_y) ;
+ else QNUM(qoffset_z) ;
+ else QNUM(qfac) ;
+ else QNUM(sform_code) ;
+ else QNUM(freq_dim) ;
+ else QNUM(phase_dim) ;
+ else QNUM(slice_dim) ;
+ else QNUM(slice_code) ;
+ else QNUM(slice_start) ;
+ else QNUM(slice_end) ;
+ else QNUM(slice_duration) ;
+ else QNUM(num_ext) ;
+
+ } /* end of while loop */
+
+ if( bytes_read ) *bytes_read = spos+1; /* "process" last '\n' */
+
+ /* do miscellaneous checking and cleanup */
+
+ if( nim->ndim <= 0 ){ nifti_image_free(nim); return NULL; } /* bad! */
+
+ nifti_datatype_sizes( nim->datatype, &(nim->nbyper), &(nim->swapsize) );
+ if( nim->nbyper == 0 ){ nifti_image_free(nim); return NULL; } /* bad! */
+
+ nim->dim[0] = nim->ndim ;
+ nim->dim[1] = nim->nx ; nim->pixdim[1] = nim->dx ;
+ nim->dim[2] = nim->ny ; nim->pixdim[2] = nim->dy ;
+ nim->dim[3] = nim->nz ; nim->pixdim[3] = nim->dz ;
+ nim->dim[4] = nim->nt ; nim->pixdim[4] = nim->dt ;
+ nim->dim[5] = nim->nu ; nim->pixdim[5] = nim->du ;
+ nim->dim[6] = nim->nv ; nim->pixdim[6] = nim->dv ;
+ nim->dim[7] = nim->nw ; nim->pixdim[7] = nim->dw ;
+
+ nim->nvox = nim->nx * nim->ny * nim->nz
+ * nim->nt * nim->nu * nim->nv * nim->nw ;
+
+ if( nim->qform_code > 0 )
+ nim->qto_xyz = nifti_quatern_to_mat44(
+ nim->quatern_b, nim->quatern_c, nim->quatern_d,
+ nim->qoffset_x, nim->qoffset_y, nim->qoffset_z,
+ nim->dx , nim->dy , nim->dz ,
+ nim->qfac ) ;
+ else
+ nim->qto_xyz = nifti_quatern_to_mat44(
+ 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 ,
+ nim->dx , nim->dy , nim->dz , 0.0 ) ;
+
+
+ nim->qto_ijk = nifti_mat44_inverse( nim->qto_xyz ) ;
+
+ if( nim->sform_code > 0 )
+ nim->sto_ijk = nifti_mat44_inverse( nim->sto_xyz ) ;
+
+ return nim ;
+}
+
+
+/*---------------------------------------------------------------------------*/
+/*! validate the nifti_image
+
+ \return 1 if the structure seems valid, otherwise 0
+
+ \sa nifti_nim_has_valid_dims, nifti_hdr_looks_good
+*//*-------------------------------------------------------------------------*/
+int nifti_nim_is_valid(nifti_image * nim, int complain)
+{
+ int errs = 0;
+
+ if( !nim ){
+ fprintf(stderr,"** is_valid_nim: nim is NULL\n");
+ return 0;
+ }
+
+ if( g_opts.debug > 2 ) fprintf(stderr,"-d nim_is_valid check...\n");
+
+ /**- check that dim[] matches the individual values ndim, nx, ny, ... */
+ if( ! nifti_nim_has_valid_dims(nim,complain) ){
+ if( !complain ) return 0;
+ errs++;
+ }
+
+ /* might check nbyper, pixdim, q/sforms, swapsize, nifti_type, ... */
+
+ /**- be explicit in return of 0 or 1 */
+ if( errs > 0 ) return 0;
+ else return 1;
+}
+
+/*---------------------------------------------------------------------------*/
+/*! validate nifti dimensions
+
+ \return 1 if valid, 0 if not
+
+ \sa nifti_nim_is_valid, nifti_hdr_looks_good
+
+ rely on dim[] as the master
+*//*-------------------------------------------------------------------------*/
+int nifti_nim_has_valid_dims(nifti_image * nim, int complain)
+{
+ int c, prod, errs = 0;
+
+ /**- start with dim[0]: failure here is considered terminal */
+ if( nim->dim[0] <= 0 || nim->dim[0] > 7 ){
+ errs++;
+ if( complain )
+ fprintf(stderr,"** NVd: dim[0] (%d) out of range [1,7]\n",nim->dim[0]);
+ return 0;
+ }
+
+ /**- check whether ndim equals dim[0] */
+ if( nim->ndim != nim->dim[0] ){
+ errs++;
+ if( ! complain ) return 0;
+ fprintf(stderr,"** NVd: ndim != dim[0] (%d,%d)\n",nim->ndim,nim->dim[0]);
+ }
+
+ /**- compare each dim[i] to the proper nx, ny, ... */
+ if( ( (nim->dim[0] >= 1) && (nim->dim[1] != nim->nx) ) ||
+ ( (nim->dim[0] >= 2) && (nim->dim[2] != nim->ny) ) ||
+ ( (nim->dim[0] >= 3) && (nim->dim[3] != nim->nz) ) ||
+ ( (nim->dim[0] >= 4) && (nim->dim[4] != nim->nt) ) ||
+ ( (nim->dim[0] >= 5) && (nim->dim[5] != nim->nu) ) ||
+ ( (nim->dim[0] >= 6) && (nim->dim[6] != nim->nv) ) ||
+ ( (nim->dim[0] >= 7) && (nim->dim[7] != nim->nw) ) ){
+ errs++;
+ if( !complain ) return 0;
+ fprintf(stderr,"** NVd mismatch: dims = %d,%d,%d,%d,%d,%d,%d\n"
+ " nxyz... = %d,%d,%d,%d,%d,%d,%d\n",
+ nim->dim[1], nim->dim[2], nim->dim[3],
+ nim->dim[4], nim->dim[5], nim->dim[6], nim->dim[7],
+ nim->nx, nim->ny, nim->nz,
+ nim->nt, nim->nu, nim->nv, nim->nw );
+ }
+
+ /**- check the dimensions, and that their product matches nvox */
+ prod = 1;
+ for( c = 1; c <= nim->dim[0]; c++ ){
+ if( nim->dim[c] > 0)
+ prod *= nim->dim[c];
+ else if( nim->dim[c] <= 0 ){
+ if( !complain ) return 0;
+ fprintf(stderr,"** NVd: dim[%d] (=%d) <= 0\n",c, nim->dim[c]);
+ errs++;
+ }
+ }
+ if( prod != nim->nvox ){
+ if( ! complain ) return 0;
+ fprintf(stderr,"** NVd: nvox does not match dimension product (%d, %d)\n",
+ nim->nvox, prod);
+ errs++;
+ }
+
+ /**- if debug, warn about any remaining dim that is neither 0, nor 1 */
+ /* (values in dims above dim[0] are undefined, as reminded by Cinly
+ Ooi and Alle Meije Wink) 16 Nov 2005 [rickr] */
+ if( g_opts.debug > 1 )
+ for( c = nim->dim[0]+1; c <= 7; c++ )
+ if( nim->dim[c] != 0 && nim->dim[c] != 1 )
+ fprintf(stderr,"** NVd warning: dim[%d] = %d, but ndim = %d\n",
+ c, nim->dim[c], nim->dim[0]);
+
+ if( g_opts.debug > 2 )
+ fprintf(stderr,"-d nim_has_valid_dims check, errs = %d\n", errs);
+
+ /**- return invalid or valid */
+ if( errs > 0 ) return 0;
+ else return 1;
+}
+
+
+/*---------------------------------------------------------------------------*/
+/*! read a nifti image, collapsed across dimensions according to dims[8] <pre>
+
+ This function may be used to read parts of a nifti dataset, such as
+ the time series for a single voxel, or perhaps a slice. It is similar
+ to nifti_image_load(), though the passed 'data' parameter is used for
+ returning the image, not nim->data.
+
+ \param nim given nifti_image struct, corresponding to the data file
+ \param dims given list of dimensions (see below)
+ \param data pointer to data pointer (if *data is NULL, data will be
+ allocated, otherwise not)
+
+ Here, dims is an array of 8 ints, similar to nim->dim[8]. While dims[0]
+ is unused at this point, the other indices specify which dimensions to
+ collapse (and at which index), and which not to collapse. If dims[i] is
+ set to -1, then that entire dimension will be read in, from index 0 to
+ index (nim->dim[i] - 1). If dims[i] >= 0, then only that index will be
+ read in (so dims[i] must also be < nim->dim[i]).
+
+ Example: given nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 } (4-D dataset)
+
+ if dims[8] = { 0, 5, 4, 17, -1, -1, -1, -1 }
+ -> read time series for voxel i,j,k = 5,4,17
+
+ if dims[8] = { 0, -1, -1, -1, 17, -1, -1, -1 }
+ -> read single volume at time point 17
+
+ Example: given nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 } (6-D dataset)
+
+ if dims[8] = { 0, 5, 4, 17, -1, 2, 1, 0 }
+ -> read time series for the voxel i,j,k = 5,4,17, and dim 5,6 = 2,1
+
+ if dims[8] = { 0, 5, 4, -1, -1, 0, 0, 0 }
+ -> read time series for slice at i,j = 5,4, and dim 5,6,7 = 0,0,0
+ (note that dims[7] is not relevant, but must be 0 or -1)
+
+ If *data is NULL, then *data will be set as a pointer to new memory,
+ allocated here for the resulting collapsed image data.
+
+ e.g. { int dims[8] = { 0, 5, 4, 17, -1, -1, -1, -1 };
+ void * data = NULL;
+ ret_val = nifti_read_collapsed_image(nim, dims, &data);
+ if( ret_val > 0 ){
+ process_time_series(data);
+ if( data != NULL ) free(data);
+ }
+ }
+
+ NOTE: If *data is not NULL, then it will be assumed that it points to
+ valid memory, sufficient to hold the results. This is done for
+ speed and possibly repeated calls to this function.
+
+ e.g. { int dims[8] = { 0, -1, -1, -1, -1, -1, -1, -1 };
+ void * data = NULL;
+ for( zslice = 0; zslice < nzslices; zslice++ ){
+ dims[3] = zslice;
+ ret_val = nifti_read_collapsed_image(nim, dims, &data);
+ if( ret_val > 0 ) process_slice(zslice, data);
+ }
+ if( data != NULL ) free(data);
+ }
+
+ \return
+ - the total number of bytes read, or < 0 on failure
+ - the read and byte-swapped data, in 'data' </pre>
+
+ \sa nifti_image_read, nifti_image_free, nifti_image_read_bricks
+ nifti_image_load
+*//*-------------------------------------------------------------------------*/
+int nifti_read_collapsed_image( nifti_image * nim, const int dims [8],
+ void ** data )
+{
+ znzFile fp;
+ int pivots[8], prods[8], nprods; /* sizes are bounded by dims[], so 8 */
+ int c, bytes;
+
+ /** - check pointers for sanity */
+ if( !nim || !dims || !data ){
+ fprintf(stderr,"** nifti_RCI: bad params %p, %p, %p\n",
+ (void *)nim, (void *)dims, (void *)data);
+ return -1;
+ }
+
+ if( g_opts.debug > 2 ){
+ fprintf(stderr,"-d read_collapsed_image:\n dims =");
+ for(c = 0; c < 8; c++) fprintf(stderr," %3d", dims[c]);
+ fprintf(stderr,"\n nim->dims =");
+ for(c = 0; c < 8; c++) fprintf(stderr," %3d", nim->dim[c]);
+ fputc('\n', stderr);
+ }
+
+ /** - verify that dim[] makes sense */
+ if( ! nifti_nim_is_valid(nim, g_opts.debug > 0) ){
+ fprintf(stderr,"** invalid nim (file is '%s')\n", nim->fname );
+ return -1;
+ }
+
+ /** - verify that dims[] makes sense for this dataset */
+ for( c = 1; c <= nim->dim[0]; c++ ){
+ if( dims[c] >= nim->dim[c] ){
+ fprintf(stderr,"** nifti_RCI: dims[%d] >= nim->dim[%d] (%d,%d)\n",
+ c, c, dims[c], nim->dim[c]);
+ return -1;
+ }
+ }
+
+ /** - prepare pivot list - pivots are fixed indices */
+ if( make_pivot_list(nim, dims, pivots, prods, &nprods) < 0 ) return -1;
+
+ bytes = rci_alloc_mem(data, prods, nprods, nim->nbyper);
+ if( bytes < 0 ) return -1;
+
+ /** - open the image file for reading at the appropriate offset */
+ fp = nifti_image_load_prep( nim );
+ if( ! fp ){ free(*data); *data = NULL; return -1; } /* failure */
+
+ /** - call the recursive reading function, passing nim, the pivot info,
+ location to store memory, and file pointer and position */
+ c = rci_read_data(nim, pivots,prods,nprods,dims,
+ (char *)*data, fp, znztell(fp));
+ znzclose(fp); /* in any case, close the file */
+ if( c < 0 ){ free(*data); *data = NULL; return -1; } /* failure */
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d read %d bytes of collapsed image from %s\n",
+ bytes, nim->fname);
+
+ return bytes;
+}
+
+
+/* read the data from the file pointed to by fp
+
+ - this a recursive function, so start with the base case
+ - data is now (char *) for easy incrementing
+
+ return 0 on success, < 0 on failure
+*/
+static int rci_read_data(nifti_image * nim, int * pivots, int * prods,
+ int nprods, const int dims[], char * data, znzFile fp, int base_offset)
+{
+ int c, sublen, offset, read_size;
+
+ /* bad check first - base_offset may not have been checked */
+ if( base_offset < 0 || nprods <= 0 ){
+ fprintf(stderr,"** rci_read_data, bad params, %d,%d\n",
+ nprods, base_offset);
+ return -1;
+ }
+
+ /* base case: actually read the data */
+ if( nprods == 1 ){
+ int nread, bytes;
+
+ /* make sure things look good here */
+ if( *pivots != 0 ){
+ fprintf(stderr,"** rciRD: final pivot == %d!\n", *pivots);
+ return -1;
+ }
+
+ /* so just seek and read (prods[0] * nbyper) bytes from the file */
+ znzseek(fp, base_offset, SEEK_SET);
+ bytes = prods[0] * nim->nbyper;
+ nread = nifti_read_buffer(fp, data, bytes, nim);
+ if( nread != bytes ){
+ fprintf(stderr,"** rciRD: read only %d of %d bytes from '%s'\n",
+ nread, bytes, nim->fname);
+ return -1;
+ } else if( g_opts.debug > 3 )
+ fprintf(stderr,"+d successful read of %d bytes at offset %d\n",
+ bytes, base_offset);
+
+ return 0; /* done with base case - return success */
+ }
+
+ /* not the base case, so do a set of reduced reads */
+
+ /* compute size of sub-brick: all dimensions below pivot */
+ for( c = 1, sublen = 1; c < *pivots; c++ ) sublen *= nim->dim[c];
+
+ /* compute number of values to read, i.e. remaining prods */
+ for( c = 1, read_size = 1; c < nprods; c++ ) read_size *= prods[c];
+ read_size *= nim->nbyper; /* and multiply by bytes per voxel */
+
+ /* now repeatedly compute offsets, and recursively read */
+ for( c = 0; c < prods[0]; c++ ){
+ /* offset is (c * sub-block size (including pivot dim)) */
+ /* + (dims[] index into pivot sub-block) */
+ /* the unneeded multiplication is to make this more clear */
+ offset = c * sublen * nim->dim[*pivots] + sublen * dims[*pivots];
+ offset *= nim->nbyper;
+
+ if( g_opts.debug > 3 )
+ fprintf(stderr,"-d reading %d bytes, foff %d + %d, doff %d\n",
+ read_size, base_offset, offset, c*read_size);
+
+ /* now read the next level down, adding this offset */
+ if( rci_read_data(nim, pivots+1, prods+1, nprods-1, dims,
+ data + c * read_size, fp, base_offset + offset) < 0 )
+ return -1;
+ }
+
+ return 0;
+}
+
+
+/* allocate memory for all collapsed image data
+
+ If *data is already set, do not allocate, but still calculate
+ size for debug report.
+
+ return total size on success, and < 0 on failure
+*/
+static int rci_alloc_mem(void ** data, int prods[8], int nprods, int nbyper )
+{
+ int size, index;
+
+ if( nbyper < 0 || nprods < 1 || nprods > 8 ){
+ fprintf(stderr,"** rci_am: bad params, %d, %d\n", nbyper, nprods);
+ return -1;
+ }
+
+ for( index = 0, size = 1; index < nprods; index++ )
+ size *= prods[index];
+
+ size *= nbyper;
+
+ if( ! *data ){ /* then allocate what is needed */
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"+d alloc %d (= %d x %d) bytes for collapsed image\n",
+ size, size/nbyper, nbyper);
+
+ *data = malloc(size); /* actually allocate the memory */
+ if( ! *data ){
+ fprintf(stderr,"** rci_am: failed to alloc %d bytes for data\n", size);
+ return -1;
+ }
+ } else if( g_opts.debug > 1 )
+ fprintf(stderr,"-d rci_am: *data already set, need %d (%d x %d) bytes\n",
+ size, size/nbyper, nbyper);
+
+ return size;
+}
+
+
+/* prepare a pivot list for reading
+
+ The pivot points are the indices into dims where the calling function
+ wants to collapse a dimension. The last pivot should always be zero
+ (note that we have space for that in the lists).
+*/
+static int make_pivot_list(nifti_image * nim, const int dims[], int pivots[],
+ int prods[], int * nprods )
+{
+ int len, index;
+
+ len = 0;
+ index = nim->dim[0];
+ while( index > 0 ){
+ prods[len] = 1;
+ while( index > 0 && (nim->dim[index] == 1 || dims[index] == -1) ){
+ prods[len] *= nim->dim[index];
+ index--;
+ }
+ pivots[len] = index;
+ len++;
+ index--; /* fine, let it drop out at -1 */
+ }
+
+ /* make sure to include 0 as a pivot (instead of just 1, if it is) */
+ if( pivots[len-1] != 0 ){
+ pivots[len] = 0;
+ prods[len] = 1;
+ len++;
+ }
+
+ *nprods = len;
+
+ if( g_opts.debug > 2 ){
+ fprintf(stderr,"+d pivot list created, pivots :");
+ for(index = 0; index < len; index++) fprintf(stderr," %d", pivots[index]);
+ fprintf(stderr,", prods :");
+ for(index = 0; index < len; index++) fprintf(stderr," %d", prods[index]);
+ fputc('\n',stderr);
+ }
+
+ return 0;
+}
+
+
+#undef ISEND
+#define ISEND(c) ( (c)==']' || (c)=='}' || (c)=='\0' )
+
+/*---------------------------------------------------------------------*/
+/*! Get an integer list in the range 0..(nvals-1), from the
+ character string str. If we call the output pointer fred,
+ then fred[0] = number of integers in the list (> 0), and
+ fred[i] = i-th integer in the list for i=1..fred[0].
+ If on return, fred == NULL or fred[0] == 0, then something is
+ wrong, and the caller must deal with that.
+
+ Syntax of input string:
+ - initial '{' or '[' is skipped, if present
+ - ends when '}' or ']' or end of string is found
+ - contains entries separated by commas
+ - entries have one of these forms:
+ - a single number
+ - a dollar sign '$', which means nvals-1
+ - a sequence of consecutive numbers in the form "a..b" or
+ "a-b", where "a" and "b" are single numbers (or '$')
+ - a sequence of evenly spaced numbers in the form
+ "a..b(c)" or "a-b(c)", where "c" encodes the step
+ - Example: "[2,7..4,3..9(2)]" decodes to the list
+ 2 7 6 5 4 3 5 7 9
+ - entries should be in the range 0..nvals-1
+
+ (borrowed, with permission, from thd_intlist.c)
+*//*-------------------------------------------------------------------*/
+int * nifti_get_intlist( int nvals , const char * str )
+{
+ int *subv = NULL ;
+ int ii , ipos , nout , slen ;
+ int ibot,itop,istep , nused ;
+ char *cpt ;
+
+ /* Meaningless input? */
+ if( nvals < 1 ) return NULL ;
+
+ /* No selection list? */
+ if( str == NULL || str[0] == '\0' ) return NULL ;
+
+ /* skip initial '[' or '{' */
+ subv = (int *) malloc( sizeof(int) * 2 ) ;
+ subv[0] = nout = 0 ;
+
+ ipos = 0 ;
+ if( str[ipos] == '[' || str[ipos] == '{' ) ipos++ ;
+
+ if( g_opts.debug > 1 )
+ fprintf(stderr,"-d making int_list (vals = %d) from '%s'\n", nvals, str);
+
+ /**- for each sub-selector until end of input... */
+
+ slen = strlen(str) ;
+ while( ipos < slen && !ISEND(str[ipos]) ){
+
+ while( isspace(str[ipos]) ) ipos++ ; /* skip blanks */
+ if( ISEND(str[ipos]) ) break ; /* done */
+
+ /**- get starting value */
+
+ if( str[ipos] == '$' ){ /* special case */
+ ibot = nvals-1 ; ipos++ ;
+ } else { /* decode an integer */
+ ibot = strtol( str+ipos , &cpt , 10 ) ;
+ if( ibot < 0 ){
+ fprintf(stderr,"** ERROR: list index %d is out of range 0..%d\n",
+ ibot,nvals-1) ;
+ free(subv) ; return NULL ;
+ }
+ if( ibot >= nvals ){
+ fprintf(stderr,"** ERROR: list index %d is out of range 0..%d\n",
+ ibot,nvals-1) ;
+ free(subv) ; return NULL ;
+ }
+ nused = (cpt-(str+ipos)) ;
+ if( ibot == 0 && nused == 0 ){
+ fprintf(stderr,"** ERROR: list syntax error '%s'\n",str+ipos) ;
+ free(subv) ; return NULL ;
+ }
+ ipos += nused ;
+ }
+
+ while( isspace(str[ipos]) ) ipos++ ; /* skip blanks */
+
+ /**- if that's it for this sub-selector, add one value to list */
+
+ if( str[ipos] == ',' || ISEND(str[ipos]) ){
+ nout++ ;
+ subv = (int *) realloc( (char *)subv , sizeof(int) * (nout+1) ) ;
+ subv[0] = nout ;
+ subv[nout] = ibot ;
+ if( ISEND(str[ipos]) ) break ; /* done */
+ ipos++ ; continue ; /* re-start loop at next sub-selector */
+ }
+
+ /**- otherwise, must have '..' or '-' as next inputs */
+
+ if( str[ipos] == '-' ){
+ ipos++ ;
+ } else if( str[ipos] == '.' && str[ipos+1] == '.' ){
+ ipos++ ; ipos++ ;
+ } else {
+ fprintf(stderr,"** ERROR: index list syntax is bad: '%s'\n",
+ str+ipos) ;
+ free(subv) ; return NULL ;
+ }
+
+ /**- get ending value for loop now */
+
+ if( str[ipos] == '$' ){ /* special case */
+ itop = nvals-1 ; ipos++ ;
+ } else { /* decode an integer */
+ itop = strtol( str+ipos , &cpt , 10 ) ;
+ if( itop < 0 ){
+ fprintf(stderr,"** ERROR: index %d is out of range 0..%d\n",
+ itop,nvals-1) ;
+ free(subv) ; return NULL ;
+ }
+ if( itop >= nvals ){
+ fprintf(stderr,"** ERROR: index %d is out of range 0..%d\n",
+ itop,nvals-1) ;
+ free(subv) ; return NULL ;
+ }
+ nused = (cpt-(str+ipos)) ;
+ if( itop == 0 && nused == 0 ){
+ fprintf(stderr,"** ERROR: index list syntax error '%s'\n",str+ipos) ;
+ free(subv) ; return NULL ;
+ }
+ ipos += nused ;
+ }
+
+ /**- set default loop step */
+
+ istep = (ibot <= itop) ? 1 : -1 ;
+
+ while( isspace(str[ipos]) ) ipos++ ; /* skip blanks */
+
+ /**- check if we have a non-default loop step */
+
+ if( str[ipos] == '(' ){ /* decode an integer */
+ ipos++ ;
+ istep = strtol( str+ipos , &cpt , 10 ) ;
+ if( istep == 0 ){
+ fprintf(stderr,"** ERROR: index loop step is 0!\n") ;
+ free(subv) ; return NULL ;
+ }
+ nused = (cpt-(str+ipos)) ;
+ ipos += nused ;
+ if( str[ipos] == ')' ) ipos++ ;
+ if( (ibot-itop)*istep > 0 ){
+ fprintf(stderr,"** WARNING: index list '%d..%d(%d)' means nothing\n",
+ ibot,itop,istep ) ;
+ }
+ }
+
+ /**- add values to output */
+
+ for( ii=ibot ; (ii-itop)*istep <= 0 ; ii += istep ){
+ nout++ ;
+ subv = (int *) realloc( (char *)subv , sizeof(int) * (nout+1) ) ;
+ subv[0] = nout ;
+ subv[nout] = ii ;
+ }
+
+ /**- check if we have a comma to skip over */
+
+ while( isspace(str[ipos]) ) ipos++ ; /* skip blanks */
+ if( str[ipos] == ',' ) ipos++ ; /* skip commas */
+
+ } /* end of loop through selector string */
+
+ if( g_opts.debug > 1 ) {
+ fprintf(stderr,"+d int_list (vals = %d): ", subv[0]);
+ for( ii = 1; ii <= subv[0]; ii++ ) fprintf(stderr,"%d ", subv[ii]);
+ fputc('\n',stderr);
+ }
+
+ if( subv[0] == 0 ){ free(subv); subv = NULL; }
+ return subv ;
+}
diff --git a/Utilities/ITK/Utilities/nifti/niftilib/nifti1_io.h b/Utilities/ITK/Utilities/nifti/niftilib/nifti1_io.h
new file mode 100644
index 0000000000000000000000000000000000000000..a14a45b7cbb846e69317dae89d7aad82532ac344
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/niftilib/nifti1_io.h
@@ -0,0 +1,434 @@
+/** \file nifti1_io.h
+ \brief Data structures for using nifti1_io API.
+ - Written by Bob Cox, SSCC NIMH
+ - Revisions by Rick Reynolds, SSCC NIMH
+ */
+#ifndef _NIFTI_IO_HEADER_
+#define _NIFTI_IO_HEADER_
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include <ctype.h>
+
+#ifndef DONT_INCLUDE_ANALYZE_STRUCT
+#define DONT_INCLUDE_ANALYZE_STRUCT /*** not needed herein ***/
+#endif
+#include "nifti1.h" /*** NIFTI-1 header specification ***/
+
+#include <znzlib.h>
+
+/*=================*/
+#ifdef __cplusplus
+extern "C" {
+#endif
+/*=================*/
+
+/*****===================================================================*****/
+/***** File nifti1_io.h == Declarations for nifti1_io.c *****/
+/*****...................................................................*****/
+/***** This code is released to the public domain. *****/
+/*****...................................................................*****/
+/***** Author: Robert W Cox, SSCC/DIRP/NIMH/NIH/DHHS/USA/EARTH *****/
+/***** Date: August 2003 *****/
+/*****...................................................................*****/
+/***** Neither the National Institutes of Health (NIH), nor any of its *****/
+/***** employees imply any warranty of usefulness of this software for *****/
+/***** any purpose, and do not assume any liability for damages, *****/
+/***** incidental or otherwise, caused by any use of this document. *****/
+/*****===================================================================*****/
+
+/*
+ Modified by: Mark Jenkinson (FMRIB Centre, University of Oxford, UK)
+ Date: July/August 2004
+
+ Mainly adding low-level IO and changing things to allow gzipped files
+ to be read and written
+ Full backwards compatability should have been maintained
+
+ Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health)
+ Date: December 2004
+
+ Modified and added many routines for I/O.
+*/
+
+/********************** Some sample data structures **************************/
+
+typedef struct { /** 4x4 matrix struct **/
+ float m[4][4] ;
+} mat44 ;
+
+typedef struct { /** 3x3 matrix struct **/
+ float m[3][3] ;
+} mat33 ;
+
+/*...........................................................................*/
+
+/*! \enum analyze_75_orient_code
+ * \brief Old-style analyze75 orientation
+ * codes.
+ */
+typedef enum _analyze75_orient_code
+ {
+ a75_transverse_unflipped = 0,
+ a75_coronal_unflipped = 1,
+ a75_sagittal_unflipped = 2,
+ a75_transverse_flipped = 3,
+ a75_coronal_flipped = 4,
+ a75_sagittal_flipped = 5,
+ a75_orient_unknown = 6
+ }
+ analyze_75_orient_code;
+
+/*! \struct nifti_image
+ \brief High level data structure for open nifti datasets in the
+ nifti1_io API. Note that this structure is not part of the
+ nifti1 format definition; it is used to implement one API
+ for reading/writing formats in the nifti1 format.
+ */
+typedef struct { /*!< Image storage struct **/
+
+ int ndim ; /*!< last dimension greater than 1 (1..7) */
+ int nx ; /*!< dimensions of grid array */
+ int ny ; /*!< dimensions of grid array */
+ int nz ; /*!< dimensions of grid array */
+ int nt ; /*!< dimensions of grid array */
+ int nu ; /*!< dimensions of grid array */
+ int nv ; /*!< dimensions of grid array */
+ int nw ; /*!< dimensions of grid array */
+ int dim[8] ; /*!< dim[0]=ndim, dim[1]=nx, etc. */
+ int nvox ; /*!< number of voxels = nx*ny*nz*...*nw */
+ int nbyper ; /*!< bytes per voxel, matches datatype */
+ int datatype ; /*!< type of data in voxels: DT_* code */
+
+ float dx ; /*!< grid spacings */
+ float dy ; /*!< grid spacings */
+ float dz ; /*!< grid spacings */
+ float dt ; /*!< grid spacings */
+ float du ; /*!< grid spacings */
+ float dv ; /*!< grid spacings */
+ float dw ; /*!< grid spacings */
+ float pixdim[8] ; /*!< pixdim[1]=dx, etc. */
+
+ float scl_slope ; /*!< scaling parameter - slope */
+ float scl_inter ; /*!< scaling parameter - intercept */
+
+ float cal_min ; /*!< calibration parameter, minimum */
+ float cal_max ; /*!< calibration parameter, maximum */
+
+ int qform_code ; /*!< codes for (x,y,z) space meaning */
+ int sform_code ; /*!< codes for (x,y,z) space meaning */
+
+ int freq_dim ; /*!< indexes (1,2,3, or 0) for MRI */
+ int phase_dim ; /*!< directions in dim[]/pixdim[] */
+ int slice_dim ; /*!< directions in dim[]/pixdim[] */
+
+ int slice_code ; /*!< code for slice timing pattern */
+ int slice_start ; /*!< index for start of slices */
+ int slice_end ; /*!< index for end of slices */
+ float slice_duration ; /*!< time between individual slices */
+
+ /*! quaternion transform parameters
+ [when writing a dataset, these are used for qform, NOT qto_xyz] */
+ float quatern_b , quatern_c , quatern_d ,
+ qoffset_x , qoffset_y , qoffset_z ,
+ qfac ;
+
+ mat44 qto_xyz ; /*!< qform: transform (i,j,k) to (x,y,z) */
+ mat44 qto_ijk ; /*!< qform: transform (x,y,z) to (i,j,k) */
+
+ mat44 sto_xyz ; /*!< sform: transform (i,j,k) to (x,y,z) */
+ mat44 sto_ijk ; /*!< sform: transform (x,y,z) to (i,j,k) */
+
+ float toffset ; /*!< time coordinate offset */
+
+ int xyz_units ; /*!< dx,dy,dz units: NIFTI_UNITS_* code */
+ int time_units ; /*!< dt units: NIFTI_UNITS_* code */
+
+ int nifti_type ; /*!< 0==ANALYZE, 1==NIFTI-1 (1 file),
+ 2==NIFTI-1 (2 files),
+ 3==NIFTI-ASCII (1 file) */
+ int intent_code ; /*!< statistic type (or something) */
+ float intent_p1 ; /*!< intent parameters */
+ float intent_p2 ; /*!< intent parameters */
+ float intent_p3 ; /*!< intent parameters */
+ char intent_name[16] ; /*!< optional description of intent data */
+
+ char descrip[80] ; /*!< optional text to describe dataset */
+ char aux_file[24] ; /*!< auxiliary filename */
+
+ char *fname ; /*!< header filename (.hdr or .nii) */
+ char *iname ; /*!< image filename (.img or .nii) */
+ int iname_offset ; /*!< offset into iname where data starts */
+ int swapsize ; /*!< swap unit in image data (might be 0) */
+ int byteorder ; /*!< byte order on disk (MSB_ or LSB_FIRST) */
+ void *data ; /*!< pointer to data: nbyper*nvox bytes */
+
+ int num_ext ; /*!< number of extensions in ext_list */
+ nifti1_extension * ext_list ; /*!< array of extension structs (with data) */
+ analyze_75_orient_code analyze75_orient; /*!< for old analyze files, orient */
+} nifti_image ;
+
+
+
+/* struct for return from nifti_image_read_bricks() */
+typedef struct {
+ int nbricks; /* the number of allocated pointers in 'bricks' */
+ int bsize; /* the length of each data block, in bytes */
+ void ** bricks; /* array of pointers to data blocks */
+} nifti_brick_list;
+
+
+/*****************************************************************************/
+/*--------------- Prototypes of functions defined in this file --------------*/
+
+char *nifti_datatype_string ( int dt ) ;
+char *nifti_units_string ( int uu ) ;
+char *nifti_intent_string ( int ii ) ;
+char *nifti_xform_string ( int xx ) ;
+char *nifti_slice_string ( int ss ) ;
+char *nifti_orientation_string( int ii ) ;
+
+int nifti_is_inttype( int dt ) ;
+
+mat44 nifti_mat44_inverse( mat44 R ) ;
+
+mat33 nifti_mat33_inverse( mat33 R ) ;
+mat33 nifti_mat33_polar ( mat33 A ) ;
+float nifti_mat33_rownorm( mat33 A ) ;
+float nifti_mat33_colnorm( mat33 A ) ;
+float nifti_mat33_determ ( mat33 R ) ;
+mat33 nifti_mat33_mul ( mat33 A , mat33 B ) ;
+
+void nifti_swap_2bytes ( int n , void *ar ) ;
+void nifti_swap_4bytes ( int n , void *ar ) ;
+void nifti_swap_8bytes ( int n , void *ar ) ;
+void nifti_swap_16bytes( int n , void *ar ) ;
+void nifti_swap_Nbytes ( int n , int siz , void *ar ) ;
+
+void swap_nifti_header ( struct nifti_1_header *h , int is_nifti ) ;
+int nifti_get_filesize( const char *pathname ) ;
+
+/* main read/write routines */
+
+nifti_image *nifti_image_read_bricks(const char *hname , int nbricks,
+ const int *blist, nifti_brick_list * NBL);
+int nifti_image_load_bricks(nifti_image *nim , int nbricks,
+ const int *blist, nifti_brick_list * NBL);
+void nifti_free_NBL( nifti_brick_list * NBL );
+
+nifti_image *nifti_image_read ( const char *hname , int read_data ) ;
+int nifti_image_load ( nifti_image *nim ) ;
+void nifti_image_unload ( nifti_image *nim ) ;
+void nifti_image_free ( nifti_image *nim ) ;
+
+int nifti_read_collapsed_image( nifti_image * nim, const int dims [8],
+ void ** data );
+
+void nifti_image_write ( nifti_image * nim ) ;
+void nifti_image_write_bricks(nifti_image * nim,
+ const nifti_brick_list * NBL);
+void nifti_image_infodump( const nifti_image * nim ) ;
+
+void nifti_disp_lib_hist( void ) ; /* to display library history */
+void nifti_disp_lib_version( void ) ; /* to display library version */
+int nifti_disp_matrix_orient( const char * mesg, mat44 mat );
+
+char * nifti_image_to_ascii ( const nifti_image * nim ) ;
+nifti_image *nifti_image_from_ascii( const char * str, int * bytes_read ) ;
+
+size_t nifti_get_volsize(const nifti_image *nim) ;
+
+/* basic file operations */
+int nifti_set_filenames(nifti_image * nim, const char * prefix, int check,
+ int set_byte_order);
+char * nifti_makehdrname (const char * prefix, int nifti_type, int check,
+ int comp);
+char * nifti_makeimgname (const char * prefix, int nifti_type, int check,
+ int comp);
+int is_nifti_file (const char *hname);
+char * nifti_find_file_extension(const char * name);
+int nifti_is_complete_filename(const char* fname);
+int nifti_validfilename(const char* fname);
+
+int disp_nifti_1_header(const char * info, const nifti_1_header * hp ) ;
+void nifti_set_debug_level( int level ) ;
+void nifti_set_skip_blank_ext( int skip ) ;
+
+int valid_nifti_brick_list(nifti_image * nim , int nbricks,
+ const int * blist, int disp_error);
+
+/* znzFile operations */
+znzFile nifti_image_open(const char * hname, char * opts, nifti_image ** nim);
+znzFile nifti_image_write_hdr_img(nifti_image *nim, int write_data,
+ const char* opts);
+znzFile nifti_image_write_hdr_img2( nifti_image *nim , int write_opts ,
+ const char* opts, znzFile imgfile, const nifti_brick_list * NBL);
+size_t nifti_read_buffer(znzFile fp, void* datatptr, size_t ntot,
+ nifti_image *nim);
+int nifti_write_all_data(znzFile fp, nifti_image * nim,
+ const nifti_brick_list * NBL);
+size_t nifti_write_buffer(znzFile fp, const void * buffer, size_t numbytes);
+nifti_image *nifti_read_ascii_image(znzFile fp, char *fname, int flen,
+ int read_data);
+znzFile nifti_write_ascii_image(nifti_image *nim, const nifti_brick_list * NBL,
+ const char * opts, int write_data, int leave_open);
+
+
+void nifti_datatype_sizes( int datatype , int *nbyper, int *swapsize ) ;
+
+void nifti_mat44_to_quatern( mat44 R ,
+ float *qb, float *qc, float *qd,
+ float *qx, float *qy, float *qz,
+ float *dx, float *dy, float *dz, float *qfac ) ;
+
+mat44 nifti_quatern_to_mat44( float qb, float qc, float qd,
+ float qx, float qy, float qz,
+ float dx, float dy, float dz, float qfac );
+
+mat44 nifti_make_orthog_mat44( float r11, float r12, float r13 ,
+ float r21, float r22, float r23 ,
+ float r31, float r32, float r33 ) ;
+
+int nifti_short_order(void) ; /* CPU byte order */
+
+
+/* Orientation codes that might be returned from nifti_mat44_to_orientation().*/
+
+#define NIFTI_L2R 1 /* Left to Right */
+#define NIFTI_R2L 2 /* Right to Left */
+#define NIFTI_P2A 3 /* Posterior to Anterior */
+#define NIFTI_A2P 4 /* Anterior to Posterior */
+#define NIFTI_I2S 5 /* Inferior to Superior */
+#define NIFTI_S2I 6 /* Superior to Inferior */
+
+void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod ) ;
+
+/*--------------------- Low level IO routines ------------------------------*/
+
+char * nifti_findhdrname (const char* fname);
+char * nifti_findimgname (const char* fname , int nifti_type);
+int nifti_is_gzfile (const char* fname);
+
+char * nifti_makebasename(const char* fname);
+
+
+/* other routines */
+struct nifti_1_header nifti_convert_nim2nhdr(const nifti_image* nim);
+nifti_1_header * nifti_read_header(const char *hname, int *swapped, int check);
+nifti_image * nifti_copy_nim_info(const nifti_image * src);
+nifti_image * nifti_simple_init_nim(void);
+nifti_image * nifti_convert_nhdr2nim(struct nifti_1_header nhdr,
+ const char * fname);
+
+int nifti_hdr_looks_good (const nifti_1_header * hdr);
+int nifti_is_valid_ecode (int ecode);
+int nifti_nim_is_valid (nifti_image * nim, int complain);
+int nifti_nim_has_valid_dims (nifti_image * nim, int complain);
+int is_valid_nifti_type (int nifti_type);
+int nifti_type_and_names_match (nifti_image * nim, int show_warn);
+int nifti_update_dims_from_array(nifti_image * nim);
+void nifti_set_iname_offset (nifti_image *nim);
+int nifti_set_type_from_names (nifti_image * nim);
+int nifti_add_extension(nifti_image * nim, const char * data, int len,
+ int ecode );
+int nifti_copy_extensions (nifti_image *nim_dest,const nifti_image *nim_src);
+int nifti_free_extensions (nifti_image *nim);
+int * nifti_get_intlist (int nvals , const char *str);
+char * nifti_strdup (const char *str);
+int valid_nifti_extensions(const nifti_image *nim);
+
+
+/*-------------------- Some C convenience macros ----------------------------*/
+
+/* NIfTI-1.1 extension codes:
+ see http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q21 */
+
+#define NIFTI_ECODE_IGNORE 0 /* changed from UNKNOWN, 29 June 2005 */
+
+#define NIFTI_ECODE_DICOM 2 /* intended for raw DICOM attributes */
+
+#define NIFTI_ECODE_AFNI 4 /* Robert W Cox: rwcox@nih.gov
+ http://afni.nimh.nih.gov/afni */
+
+#define NIFTI_ECODE_COMMENT 6 /* plain ASCII text only */
+
+#define NIFTI_ECODE_XCEDE 8 /* David B Keator: dbkeator@uci.edu
+ http://www.nbirn.net/Resources
+ /Users/Applications/
+ /xcede/index.htm */
+
+#define NIFTI_ECODE_JIMDIMINFO 10 /* Mark A Horsfield:
+ mah5@leicester.ac.uk
+ http://someplace/something */
+
+#define NIFTI_ECODE_WORKFLOW_FWDS 12 /* Kate Fissell: fissel+@pitt.edu
+ http://kraepelin.wpic.pitt.edu
+ /~fissell/NIFTI_ECODE_WORKFLOW_FWDS
+ /NIFTI_ECODE_WORKFLOW_FWDS.html */
+
+#define NIFTI_MAX_ECODE 12 /******* maximum extension code *******/
+
+/* nifti_type file codes */
+#define NIFTI_FTYPE_ANALYZE 0
+#define NIFTI_FTYPE_NIFTI1_1 1
+#define NIFTI_FTYPE_NIFTI1_2 2
+#define NIFTI_FTYPE_ASCII 3
+#define NIFTI_MAX_FTYPE 3 /* this should match the maximum code */
+
+/*------------------------------------------------------------------------*/
+/*-- the rest of these apply only to nifti1_io.c, check for _NIFTI1_IO_C_ */
+/* Feb 9, 2005 [rickr] */
+#ifdef _NIFTI1_IO_C_
+
+typedef struct {
+ int debug; /*!< debug level for status reports */
+ int skip_blank_ext; /*!< skip extender if no extensions */
+} nifti_global_options;
+
+#undef LNI_FERR /* local nifti file error, to be compact and repetative */
+#define LNI_FERR(func,msg,file) \
+ fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file)
+
+#undef swap_2
+#undef swap_4
+#define swap_2(s) nifti_swap_2bytes(1,&(s)) /* s: 2-byte short; swap in place */
+#define swap_4(v) nifti_swap_4bytes(1,&(v)) /* v: 4-byte value; swap in place */
+
+ /***** isfinite() is a C99 macro, which is
+ present in many C implementations already *****/
+
+#undef IS_GOOD_FLOAT
+#undef FIXED_FLOAT
+
+#ifdef isfinite /* use isfinite() to check floats/doubles for goodness */
+# define IS_GOOD_FLOAT(x) isfinite(x) /* check if x is a "good" float */
+# define FIXED_FLOAT(x) (isfinite(x) ? (x) : 0) /* fixed if bad */
+#else
+# define IS_GOOD_FLOAT(x) 1 /* don't check it */
+# define FIXED_FLOAT(x) (x) /* don't fix it */
+#endif
+
+#undef ASSIF /* assign v to *p, if possible */
+#define ASSIF(p,v) if( (p)!=NULL ) *(p) = (v)
+
+#undef MSB_FIRST
+#undef LSB_FIRST
+#undef REVERSE_ORDER
+#define LSB_FIRST 1
+#define MSB_FIRST 2
+#define REVERSE_ORDER(x) (3-(x)) /* convert MSB_FIRST <--> LSB_FIRST */
+
+#define LNI_MAX_NIA_EXT_LEN 100000 /* consider a longer extension invalid */
+
+#endif /* _NIFTI1_IO_C_ section */
+/*------------------------------------------------------------------------*/
+
+/*=================*/
+#ifdef __cplusplus
+}
+#endif
+/*=================*/
+
+#endif /* _NIFTI_IO_HEADER_ */
diff --git a/Utilities/ITK/Utilities/nifti/real_easy/nifti1_read_write.c b/Utilities/ITK/Utilities/nifti/real_easy/nifti1_read_write.c
new file mode 100644
index 0000000000000000000000000000000000000000..6dcaa9ae0d334b94fa5bbc64b9916d1e7525c97c
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/real_easy/nifti1_read_write.c
@@ -0,0 +1,360 @@
+/*********************************************************************
+ *
+ * Very simple code snippets to read/write nifti1 files
+ * This code is placed in the public domain.
+ *
+ * If you are the type who doesn't want to use a file format unless
+ * you can write your own i/o code in less than 30minutes, this
+ * example is for you.
+ *
+ * This code does not deal with wrong-endian data, compressed data,
+ * the new qform/sform orientation codes, parsing filesnames, volume-
+ * wise or timecourse-wise data access or any of a million other very useful
+ * things that are in the niftilib i/o reference libraries.
+ * We encourage people to use the niftilib reference library and send
+ * feedback/suggestions, see http://niftilib.sourceforge.net/
+ * But, if that is too much to tackle and you just want to jump in, this
+ * code is a starting point.
+ * This code was written for maximum readability, not for the greatest
+ * coding style.
+ *
+ *
+ * If you are already a little familiar with reading/writing Analyze
+ * files of some flavor, and maybe even have some of your own code, here
+ * are the most important things to be aware of in transitioning to nifti1:
+ *
+ * 1. nii vs .hdr/.img
+ * nifti1 datasets can be stored either in .hdr/.img pairs of files
+ * or in 1 .nii file. In a .nii file the data will start at the byte
+ * specified by the vox_offset field, which will be 352 if no extensions
+ * have been added. And, nifti1 really does like that magic field set
+ * to "n+1" for .nii and "ni1" for .img/.hdr
+ *
+ * 2. scaling
+ * nifti1 datasets can contain a scaling factor. You need to check the
+ * scl_slope field and if that isn't 0, scale your data by
+ * Y * scl_slope + scl_inter
+ *
+ * 3. extensions
+ * nifti1 datasets can have some "extension data" stuffed after the
+ * regular header. You can just ignore it, but, be aware that a
+ * .hdr file may be longer than 348 bytes, and, in a .nii file
+ * you can't just jump to byte 352, you need to use the vox_offset
+ * field to get the start of the image data.
+ *
+ * 4. new datatypes
+ * nifti1 added a few new datatypes that were not in the Analyze 7.5
+ * format from which nifti1 is derived. If you're just working with
+ * your own data this is not an issue but if you get a foreign nifti1
+ * file, be aware of exotic datatypes like DT_COMPLEX256 and mundane
+ * things like DT_UINT16.
+ *
+ * 5. other stuff
+ * nifti1 really does like the dim[0] field set to the number of
+ * dimensions of the dataset. Other Analyze flavors might not
+ * have been so scrupulous about that.
+ * nifti1 has a bunch of other new fields such as intent codes,
+ * qform/sform, etc. but, if you just want to get your hands on
+ * the data blob you can ignore these.
+ *
+ *
+ *
+ * To compile:
+ * You need to put a copy of the nifti1.h header file in this directory.
+ * It can be obtained from the NIFTI homepage http://nifti.nimh.nih.gov/
+ * or from the niftilib SourceForge site http://niftilib.sourceforge.net/
+ *
+ * cc -o nifti1_read_write nifti1_read_write.c
+ *
+ *
+ * To run:
+ * nifti1_read_write -w abc.nii abc.nii
+ * nifti1_read_write -r abc.nii abc.nii
+ *
+ *
+ * The read method is hardcoded to read float32 data. To change
+ * to your datatype, just change the line:
+ * typedef float MY_DATATYPE;
+ *
+ * The write method is hardcoded to write float32 data. To change
+ * to your datatype, change the line:
+ * typedef float MY_DATATYPE;
+ * and change the lines:
+ * hdr.datatype = NIFTI_TYPE_FLOAT32;
+ * hdr.bitpix = 32;
+ *
+ *
+ * Written by Kate Fissell, University of Pittsburgh, May 2005.
+ *
+ *********************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "nifti1.h"
+
+typedef float MY_DATATYPE;
+
+#define MIN_HEADER_SIZE 348
+#define NII_HEADER_SIZE 352
+
+
+main(argc,argv)
+int argc;
+char *argv[];
+{
+
+char *hdr_file, *data_file;
+short do_read=0;
+short do_write=0;
+
+
+/********** process commandline parameters */
+if (argc != 4) {
+ fprintf(stderr, "\nUsage: %s <-r|-w> <header file> <data file>\n",argv[0]);
+ exit(1);
+}
+
+if (!strncmp(argv[1],"-r",2))
+ do_read=1;
+else if (!strncmp(argv[1],"-w",2))
+ do_write=1;
+else {
+ fprintf(stderr, "\nUsage: %s <-r|-w> <header file> <data file>\n",argv[0]);
+ exit(1);
+}
+
+hdr_file = argv[2];
+data_file = argv[3];
+
+
+
+/********** do the simple read or write */
+if (do_read)
+ read_nifti_file(hdr_file, data_file);
+else if (do_write)
+ write_nifti_file(hdr_file, data_file);
+
+
+exit(0);
+}
+
+/**********************************************************************
+ *
+ * read_nifti_file
+ *
+ **********************************************************************/
+int read_nifti_file(hdr_file, data_file)
+char *hdr_file, *data_file;
+{
+nifti_1_header hdr;
+FILE *fp;
+int ret,i;
+double total;
+MY_DATATYPE *data=NULL;
+
+
+/********** open and read header */
+fp = fopen(hdr_file,"r");
+if (fp == NULL) {
+ fprintf(stderr, "\nError opening header file %s\n",hdr_file);
+ exit(1);
+}
+ret = fread(&hdr, MIN_HEADER_SIZE, 1, fp);
+if (ret != 1) {
+ fprintf(stderr, "\nError reading header file %s\n",hdr_file);
+ exit(1);
+}
+fclose(fp);
+
+
+/********** print a little header information */
+fprintf(stderr, "\n%s header information:",hdr_file);
+fprintf(stderr, "\nXYZT dimensions: %d %d %d %d",hdr.dim[1],hdr.dim[2],hdr.dim[3],hdr.dim[4]);
+fprintf(stderr, "\nDatatype code and bits/pixel: %d %d",hdr.datatype,hdr.bitpix);
+fprintf(stderr, "\nScaling slope and intercept: %.6f %.6f",hdr.scl_slope,hdr.scl_inter);
+fprintf(stderr, "\nByte offset to data in datafile: %ld",(long)(hdr.vox_offset));
+fprintf(stderr, "\n");
+
+
+/********** open the datafile, jump to data offset */
+fp = fopen(data_file,"r");
+if (fp == NULL) {
+ fprintf(stderr, "\nError opening data file %s\n",data_file);
+ exit(1);
+}
+
+ret = fseek(fp, (long)(hdr.vox_offset), SEEK_SET);
+if (ret != 0) {
+ fprintf(stderr, "\nError doing fseek() to %ld in data file %s\n",(long)(hdr.vox_offset), data_file);
+ exit(1);
+}
+
+
+/********** allocate buffer and read first 3D volume from data file */
+data = (MY_DATATYPE *) malloc(sizeof(MY_DATATYPE) * hdr.dim[1]*hdr.dim[2]*hdr.dim[3]);
+if (data == NULL) {
+ fprintf(stderr, "\nError allocating data buffer for %s\n",data_file);
+ exit(1);
+}
+ret = fread(data, sizeof(MY_DATATYPE), hdr.dim[1]*hdr.dim[2]*hdr.dim[3], fp);
+if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]) {
+ fprintf(stderr, "\nError reading volume 1 from %s (%d)\n",data_file,ret);
+ exit(1);
+}
+fclose(fp);
+
+
+/********** scale the data buffer */
+if (hdr.scl_slope != 0) {
+ for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]; i++)
+ data[i] = (data[i] * hdr.scl_slope) + hdr.scl_inter;
+}
+
+
+/********** print mean of data */
+total = 0;
+for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]; i++)
+ total += data[i];
+total /= (hdr.dim[1]*hdr.dim[2]*hdr.dim[3]);
+fprintf(stderr, "\nMean of volume 1 in %s is %.3f\n",data_file,total);
+
+
+return(0);
+}
+
+
+/**********************************************************************
+ *
+ * write_nifti_file
+ *
+ * write a sample nifti1 (.nii) data file
+ * datatype is float32
+ * XYZT size is 64x64x16x10
+ * XYZ voxel size is 1mm
+ * TR is 1500ms
+ *
+ **********************************************************************/
+int write_nifti_file(hdr_file, data_file)
+char *hdr_file, *data_file;
+{
+nifti_1_header hdr;
+nifti1_extender pad={0,0,0,0};
+FILE *fp;
+int ret,i;
+MY_DATATYPE *data=NULL;
+short do_nii;
+
+
+/********** make sure user specified .hdr/.img or .nii/.nii */
+if ( (strlen(hdr_file) < 4) || (strlen(data_file) < 4) ) {
+ fprintf(stderr, "\nError: write files must end with .hdr/.img or .nii/.nii extension\n");
+ exit(1);
+}
+
+if ( (!strncmp(hdr_file+(strlen(hdr_file)-4), ".hdr",4)) &&
+ (!strncmp(data_file+(strlen(data_file)-4), ".img",4)) ) {
+ do_nii = 0;
+}
+else if ( (!strncmp(hdr_file+(strlen(hdr_file)-4), ".nii",4)) &&
+ (!strncmp(data_file+(strlen(data_file)-4), ".nii",4)) ) {
+ do_nii = 1;
+}
+else {
+ fprintf(stderr, "\nError: file(s) to be written must end with .hdr/.img or .nii/.nii extension\n");
+ exit(1);
+}
+
+
+/********** fill in the minimal default header fields */
+bzero((void *)&hdr, sizeof(hdr));
+hdr.sizeof_hdr = MIN_HEADER_SIZE;
+hdr.dim[0] = 4;
+hdr.dim[1] = 64;
+hdr.dim[2] = 64;
+hdr.dim[3] = 16;
+hdr.dim[4] = 10;
+hdr.datatype = NIFTI_TYPE_FLOAT32;
+hdr.bitpix = 32;
+hdr.pixdim[1] = 1.0;
+hdr.pixdim[2] = 1.0;
+hdr.pixdim[3] = 1.0;
+hdr.pixdim[4] = 1.5;
+if (do_nii)
+ hdr.vox_offset = (float) NII_HEADER_SIZE;
+else
+ hdr.vox_offset = (float)0;
+hdr.scl_slope = 100.0;
+hdr.xyzt_units = NIFTI_UNITS_MM | NIFTI_UNITS_SEC;
+if (do_nii)
+ strncpy(hdr.magic, "n+1\0", 4);
+else
+ strncpy(hdr.magic, "ni1\0", 4);
+
+
+/********** allocate buffer and fill with dummy data */
+data = (MY_DATATYPE *) malloc(sizeof(MY_DATATYPE) * hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]);
+if (data == NULL) {
+ fprintf(stderr, "\nError allocating data buffer for %s\n",data_file);
+ exit(1);
+}
+
+for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]; i++)
+ data[i] = i / hdr.scl_slope;
+
+
+/********** write first 348 bytes of header */
+fp = fopen(hdr_file,"w");
+if (fp == NULL) {
+ fprintf(stderr, "\nError opening header file %s for write\n",hdr_file);
+ exit(1);
+}
+ret = fwrite(&hdr, MIN_HEADER_SIZE, 1, fp);
+if (ret != 1) {
+ fprintf(stderr, "\nError writing header file %s\n",hdr_file);
+ exit(1);
+}
+
+
+/********** if nii, write extender pad and image data */
+if (do_nii == 1) {
+
+ ret = fwrite(&pad, 4, 1, fp);
+ if (ret != 1) {
+ fprintf(stderr, "\nError writing header file extension pad %s\n",hdr_file);
+ exit(1);
+ }
+
+ ret = fwrite(data, (size_t)(hdr.bitpix/8), hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4], fp);
+ if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]) {
+ fprintf(stderr, "\nError writing data to %s\n",hdr_file);
+ exit(1);
+ }
+
+ fclose(fp);
+}
+
+
+/********** if hdr/img, close .hdr and write image data to .img */
+else {
+
+ fclose(fp); /* close .hdr file */
+
+ fp = fopen(data_file,"w");
+ if (fp == NULL) {
+ fprintf(stderr, "\nError opening data file %s for write\n",data_file);
+ exit(1);
+ }
+ ret = fwrite(data, (size_t)(hdr.bitpix/8), hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4], fp);
+ if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]) {
+ fprintf(stderr, "\nError writing data to %s\n",data_file);
+ exit(1);
+ }
+
+ fclose(fp);
+}
+
+
+
+return(0);
+}
diff --git a/Utilities/ITK/Utilities/nifti/utils/CMakeLists.txt b/Utilities/ITK/Utilities/nifti/utils/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2218043413de1feeec7ae888f4f62893b5a1bb93
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/utils/CMakeLists.txt
@@ -0,0 +1,42 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(NIFTIUTILS)
+
+INCLUDE_DIRECTORIES(${NIFTILIB_SOURCE_DIR} ${ZNZLIB_SOURCE_DIR})
+
+ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti_stats nifti_stats.c)
+ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti_tool nifti_tool.c)
+ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti1_test nifti1_test.c)
+TARGET_LINK_LIBRARIES( nifti_stats ${PACKAGE_PREFIX}niftiio)
+TARGET_LINK_LIBRARIES( nifti_tool ${PACKAGE_PREFIX}niftiio)
+TARGET_LINK_LIBRARIES( nifti1_test ${PACKAGE_PREFIX}niftiio)
+
+INSTALL_TARGETS(/bin ${PACKAGE_PREFIX}nifti_stats ${PACKAGE_PREFIX}nifti_tool ${PACKAGE_PREFIX}nifti1_test)
+INSTALL_FILES(/include "(\\.h)$")
+
+
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_help ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test)
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_n1 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -n1 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/n1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_n2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -n2 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/n2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_a2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -a2 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/a2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_zn1 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -zn1 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/zn1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_zn2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -zn2 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/zn2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_za2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -za2 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/za2 )
+
+#The help screens always return 1; ADD_TEST(${PACKAGE_PREFIX}nifti_tool_help ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool)
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_n1 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/n1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_n2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/n2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_a2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/a2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_zn1 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/zn1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_zn2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/zn2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_za2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/za2 )
+
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_diff_hdr ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -diff_hdr -infiles ${NIFTIUTILS_BINARY_DIR}/n1 ${NIFTIUTILS_BINARY_DIR}/n1 )
+
+FOREACH(DISTRIBUTION CORREL TTEST FTEST ZSCORE CHISQ BETA BINOM GAMMA POISSON NORMAL FTEST_NONC CHISQ_NONC LOGISTIC LAPLACE UNIFORM TTEST_NONC WEIBULL CHI INVGAUSS EXTVAL PVAL LOGPVAL LOG10PVAL )
+ ADD_TEST(${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats 0:4:1 ${DISTRIBUTION})
+ENDFOREACH(DISTRIBUTION)
+
+
+
+
diff --git a/Utilities/ITK/Utilities/nifti/utils/Makefile b/Utilities/ITK/Utilities/nifti/utils/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..5693eb3a21f1452045c110308e9f0819fe4e9d02
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/utils/Makefile
@@ -0,0 +1,44 @@
+CC = gcc
+CFLAGS = -ansi -pedantic
+
+FSLIO_INCS = -I../include
+NIFTI_INCS = -I../include
+ZNZ_INCS = -I/usr/include
+
+FSLIO_LIBS = -L../lib -lfslio
+NIFTI_LIBS = -L../lib -lniftiio
+ZNZ_LIBS = -L/usr/lib -L../lib -lznz -lm -lz
+
+
+
+## SGI 32bit
+ifeq ($(ARCH),SGI)
+ZNZ_INCS = -I/usr/freeware/include
+ZNZ_LIBS = -L/usr/freeware/lib32 -L../lib -lznz -lm -lz
+endif
+
+
+
+## Redhat Fedora Linux
+##ZNZ_INCS = -I/usr/include
+##ZNZ_LIBS = -L/usr/lib -L../lib -lznz -lm -lz
+
+
+UTILS_PROGS = nifti_stats nifti_tool nifti1_test
+
+
+
+all: $(UTILS_PROGS)
+
+clean:
+ rm -f $(UTILS_PROGS)
+
+
+nifti_stats: nifti_stats.c
+ $(CC) $(CFLAGS) -o nifti_stats nifti_stats.c $(NIFTI_INCS) $(ZNZ_INCS) $(NIFTI_LIBS) $(ZNZ_LIBS)
+
+nifti_tool: nifti_tool.c nifti_tool.h
+ $(CC) $(CFLAGS) -Wall -o nifti_tool nifti_tool.c $(NIFTI_INCS) $(ZNZ_INCS) $(NIFTI_LIBS) $(ZNZ_LIBS)
+
+nifti1_test: nifti1_test.c
+ $(CC) $(CFLAGS) -o nifti1_test nifti1_test.c $(NIFTI_INCS) $(ZNZ_INCS) $(NIFTI_LIBS) $(ZNZ_LIBS)
diff --git a/Utilities/ITK/Utilities/nifti/utils/nifti1_test.c b/Utilities/ITK/Utilities/nifti/utils/nifti1_test.c
new file mode 100644
index 0000000000000000000000000000000000000000..dce66d8c78330f0f85f5c93aada9d30dc7a04c14
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/utils/nifti1_test.c
@@ -0,0 +1,95 @@
+#include <nifti1_io.h> /* directly include I/O library functions */
+
+/*-----------------------------------------------*/
+/* cc -o nifti1_test -O2 nifti1_test.c -lm */
+/*-----------------------------------------------*/
+
+/****************************************************************************/
+
+int main( int argc , char *argv[] )
+{
+ nifti_image *nim ;
+ int iarg=1 , outmode=1 , ll , argn=1, usegzip=0;
+ char *tmpstr;
+
+ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
+ printf("Usage: nifti1_test [-n2|-n1|-na|-a2] infile [prefix]\n"
+ "\n"
+ " If prefix is given, then the options mean:\n"
+ " -a2 ==> write an ANALYZE 7.5 file pair: prefix.hdr/prefix.img\n"
+ " -n2 ==> write a NIFTI-1 file pair: prefix.hdr/prefix.img\n"
+ " -n1 ==> write a NIFTI-1 single file: prefix.nii\n"
+ " -na ==> write a NIFTI-1 ASCII+binary file: prefix.nia\n");
+ printf(" -za2 => write an ANALYZE 7.5 file pair:\n"
+ " prefix.hdr.gz/prefix.img.gz\n"
+ " -zn2 => write a NIFTI-1 file pair: prefix.hdr.gz/prefix.img.gz\n"
+ " -zn1 => write a NIFTI-1 single file: prefix.nii.gz\n"
+ " -zna => write a NIFTI-1 ASCII+binary file: prefix.nia.gz\n");
+ printf(" The default is '-n1'.\n"
+ "\n"
+ " If prefix is not given, then the header info from infile\n"
+ " file is printed to stdout.\n"
+ "\n"
+ " Please note that the '.nia' format is NOT part of the\n"
+ " NIFTI-1 specification, but is provided mostly for ease\n"
+ " of visualization (e.g., you can edit a .nia file and\n"
+ " change some header fields, then rewrite it as .nii)\n"
+ ) ;
+ printf("\nsizeof(nifti_1_header)=%u\n",
+ (unsigned int)sizeof(nifti_1_header)) ;
+ exit(0) ;
+ }
+
+ if( argv[1][0] == '-' ){
+ argn=1;
+ if (argv[1][1] == 'z' ) {
+ usegzip = 1;
+ argn=2;
+ }
+ if( argv[1][argn] == 'a' ){
+ outmode = 0 ;
+ } else if( argv[1][argn] == 'n' ){
+ switch( argv[1][argn+1] ){
+ case '1': outmode = 1 ; break ;
+ default: outmode = 2 ; break ;
+ case 'a': outmode = 3 ; break ;
+ }
+ }
+ iarg++ ;
+ }
+
+ if( iarg >= argc ){
+ fprintf(stderr,"** ERROR: no input file on command line!?\n"); exit(1);
+ }
+
+ nim = nifti_image_read( argv[iarg++] , 1 ) ;
+ if( nim == NULL ) exit(1) ;
+
+ if( iarg >= argc ){ nifti_image_infodump(nim); exit(0); }
+
+ nim->nifti_type = outmode ;
+ if( nim->fname != NULL ) free(nim->fname) ;
+ if( nim->iname != NULL ) free(nim->iname) ;
+
+ ll = strlen(argv[iarg]) ;
+ tmpstr = nifti_makebasename(argv[iarg]);
+ nim->fname = (char *)calloc(1,ll+8) ; strcpy(nim->fname,tmpstr) ;
+ nim->iname = (char *)calloc(1,ll+8) ; strcpy(nim->iname,tmpstr) ;
+ free(tmpstr);
+ if( nim->nifti_type == 1 ){
+ strcat(nim->fname,".nii") ;
+ strcat(nim->iname,".nii") ;
+ } else if ( nim->nifti_type == 3 ){
+ strcat(nim->fname,".nia") ;
+ strcat(nim->iname,".nia") ;
+ } else {
+ strcat(nim->fname,".hdr") ;
+ strcat(nim->iname,".img") ;
+ }
+ if (usegzip) {
+ strcat(nim->fname,".gz");
+ strcat(nim->iname,".gz");
+ }
+ nifti_image_write( nim ) ;
+ exit(0) ;
+}
diff --git a/Utilities/ITK/Utilities/nifti/utils/nifti_stats.c b/Utilities/ITK/Utilities/nifti/utils/nifti_stats.c
new file mode 100644
index 0000000000000000000000000000000000000000..84ce7d0ee06f89ebc9b2334ba72aadbe799636c4
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/utils/nifti_stats.c
@@ -0,0 +1,11318 @@
+
+ /************************************************************************/
+ /** Functions to compute cumulative distributions and their inverses **/
+ /** for the NIfTI-1 statistical types. Much of this code is taken **/
+ /** from other sources. In particular, the cdflib functions by **/
+ /** Brown and Lovato make up the bulk of this file. That code **/
+ /** was placed in the public domain. The code by K. Krishnamoorthy **/
+ /** is also released for unrestricted use. Finally, the other parts **/
+ /** of this file (by RW Cox) are released to the public domain. **/
+ /** **/
+ /** Most of this file comprises a set of "static" functions, to be **/
+ /** called by the user-level functions at the very end of the file. **/
+ /** At the end of the file is a simple main program to drive these **/
+ /** functions. **/
+ /** **/
+ /** To find the user-level functions, search forward for the string **/
+ /** "nifti_", which will be at about line 11000. **/
+ /************************************************************************/
+ /*****==============================================================*****/
+ /***** Neither the National Institutes of Health (NIH), the DFWG, *****/
+ /***** nor any of the members or employees of these institutions *****/
+ /***** imply any warranty of usefulness of this material for any *****/
+ /***** purpose, and do not assume any liability for damages, *****/
+ /***** incidental or otherwise, caused by any use of this document. *****/
+ /***** If these conditions are not acceptable, do not use this! *****/
+ /*****==============================================================*****/
+ /************************************************************************/
+
+ /*.......................................................................
+ To compile with gcc, for example:
+
+ gcc -O3 -ffast-math -o nifti_stats nifti_stats.c -lm
+
+ To avoid compilation of the main() program, define OMIT_MAIN, as in
+
+ gcc -O3 -ffast-math -c nifti_stats.c -DOMIT_MAIN
+ ........................................................................*/
+
+#include "nifti1.h" /* for the NIFTI_INTENT_* constants */
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+
+ /************************************************************************/
+ /************ Include all the cdflib functions here and now *************/
+ /************ [about 9900 lines of code below here] *************/
+ /************************************************************************/
+
+/** Prototypes for cdflib functions **/
+
+static double algdiv(double*,double*);
+static double alngam(double*);
+static double alnrel(double*);
+static double apser(double*,double*,double*,double*);
+static double basym(double*,double*,double*,double*);
+static double bcorr(double*,double*);
+static double betaln(double*,double*);
+static double bfrac(double*,double*,double*,double*,double*,double*);
+static void bgrat(double*,double*,double*,double*,double*,double*,int*i);
+static double bpser(double*,double*,double*,double*);
+static void bratio(double*,double*,double*,double*,double*,double*,int*);
+static double brcmp1(int*,double*,double*,double*,double*);
+static double brcomp(double*,double*,double*,double*);
+static double bup(double*,double*,double*,double*,int*,double*);
+static void cdfbet(int*,double*,double*,double*,double*,double*,double*,
+ int*,double*);
+static void cdfbin(int*,double*,double*,double*,double*,double*,double*,
+ int*,double*);
+static void cdfchi(int*,double*,double*,double*,double*,int*,double*);
+static void cdfchn(int*,double*,double*,double*,double*,double*,int*,double*);
+static void cdff(int*,double*,double*,double*,double*,double*,int*,double*);
+static void cdffnc(int*,double*,double*,double*,double*,double*,double*,
+ int*s,double*);
+static void cdfgam(int*,double*,double*,double*,double*,double*,int*,double*);
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+static void cdfnbn(int*,double*,double*,double*,double*,double*,double*,
+ int*,double*);
+static void cdfnor(int*,double*,double*,double*,double*,double*,int*,double*);
+#endif /*defined(__COMPILE_UNUSED_FUNCTIONS__)*/
+static void cdfpoi(int*,double*,double*,double*,double*,int*,double*);
+static void cdft(int*,double*,double*,double*,double*,int*,double*);
+static void cumbet(double*,double*,double*,double*,double*,double*);
+static void cumbin(double*,double*,double*,double*,double*,double*);
+static void cumchi(double*,double*,double*,double*);
+static void cumchn(double*,double*,double*,double*,double*);
+static void cumf(double*,double*,double*,double*,double*);
+static void cumfnc(double*,double*,double*,double*,double*,double*);
+static void cumgam(double*,double*,double*,double*);
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+static void cumnbn(double*,double*,double*,double*,double*,double*);
+#endif /*defined(__COMPILE_UNUSED_FUNCTIONS__)*/
+static void cumnor(double*,double*,double*);
+static void cumpoi(double*,double*,double*,double*);
+static void cumt(double*,double*,double*,double*);
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+static double dbetrm(double*,double*);
+#endif /*defined(__COMPILE_UNUSED_FUNCTIONS__)*/
+static double devlpl(double [],int*,double*);
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+static double dexpm1(double*);
+static double dinvnr(double *p,double *q);
+#endif /*defined(__COMPILE_UNUSED_FUNCTIONS__)*/
+static void E0000(int,int*,double*,double*,unsigned long*,
+ unsigned long*,double*,double*,double*,
+ double*,double*,double*,double*);
+static void dinvr(int*,double*,double*,unsigned long*,unsigned long*);
+static void dstinv(double*,double*,double*,double*,double*,double*,
+ double*);
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+static double dlanor(double*);
+static double dln1mx(double*);
+static double dln1px(double*);
+static double dlnbet(double*,double*);
+static double dlngam(double*);
+static double dstrem(double*);
+#endif /*defined(__COMPILE_UNUSED_FUNCTIONS__)*/
+static double dt1(double*,double*,double*);
+static void E0001(int,int*,double*,double*,double*,double*,
+ unsigned long*,unsigned long*,double*,double*,
+ double*,double*);
+static void dzror(int*,double*,double*,double*,double *,
+ unsigned long*,unsigned long*);
+static void dstzr(double *zxlo,double *zxhi,double *zabstl,double *zreltl);
+static double erf1(double*);
+static double erfc1(int*,double*);
+static double esum(int*,double*);
+static double exparg(int*);
+static double fpser(double*,double*,double*,double*);
+static double gam1(double*);
+static void gaminv(double*,double*,double*,double*,double*,int*);
+static double gamln(double*);
+static double gamln1(double*);
+static double Xgamm(double*);
+static void grat1(double*,double*,double*,double*,double*,double*);
+static void gratio(double*,double*,double*,double*,int*);
+static double gsumln(double*,double*);
+static double psi(double*);
+static double rcomp(double*,double*);
+static double rexp(double*);
+static double rlog(double*);
+static double rlog1(double*);
+static double spmpar(int*);
+static double stvaln(double*);
+static double fifdint(double);
+static double fifdmax1(double,double);
+static double fifdmin1(double,double);
+static double fifdsign(double,double);
+static long fifidint(double);
+static long fifmod(long,long);
+static void ftnstop(char*);
+static int ipmpar(int*);
+
+/***=====================================================================***/
+static double algdiv(double *a,double *b)
+/*
+-----------------------------------------------------------------------
+
+ COMPUTATION OF LN(GAMMA(B)/GAMMA(A+B)) WHEN B .GE. 8
+
+ --------
+
+ IN THIS ALGORITHM, DEL(X) IS THE FUNCTION DEFINED BY
+ LN(GAMMA(X)) = (X - 0.5)*LN(X) - X + 0.5*LN(2*PI) + DEL(X).
+
+-----------------------------------------------------------------------
+*/
+{
+static double c0 = .833333333333333e-01;
+static double c1 = -.277777777760991e-02;
+static double c2 = .793650666825390e-03;
+static double c3 = -.595202931351870e-03;
+static double c4 = .837308034031215e-03;
+static double c5 = -.165322962780713e-02;
+static double algdiv,c,d,h,s11,s3,s5,s7,s9,t,u,v,w,x,x2,T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(*a <= *b) goto S10;
+ h = *b/ *a;
+ c = 1.0e0/(1.0e0+h);
+ x = h/(1.0e0+h);
+ d = *a+(*b-0.5e0);
+ goto S20;
+S10:
+ h = *a/ *b;
+ c = h/(1.0e0+h);
+ x = 1.0e0/(1.0e0+h);
+ d = *b+(*a-0.5e0);
+S20:
+/*
+ SET SN = (1 - X**N)/(1 - X)
+*/
+ x2 = x*x;
+ s3 = 1.0e0+(x+x2);
+ s5 = 1.0e0+(x+x2*s3);
+ s7 = 1.0e0+(x+x2*s5);
+ s9 = 1.0e0+(x+x2*s7);
+ s11 = 1.0e0+(x+x2*s9);
+/*
+ SET W = DEL(B) - DEL(A + B)
+*/
+ t = pow(1.0e0/ *b,2.0);
+ w = ((((c5*s11*t+c4*s9)*t+c3*s7)*t+c2*s5)*t+c1*s3)*t+c0;
+ w *= (c/ *b);
+/*
+ COMBINE THE RESULTS
+*/
+ T1 = *a/ *b;
+ u = d*alnrel(&T1);
+ v = *a*(log(*b)-1.0e0);
+ if(u <= v) goto S30;
+ algdiv = w-v-u;
+ return algdiv;
+S30:
+ algdiv = w-u-v;
+ return algdiv;
+} /* END */
+
+/***=====================================================================***/
+static double alngam(double *x)
+/*
+**********************************************************************
+
+ double alngam(double *x)
+ double precision LN of the GAMma function
+
+
+ Function
+
+
+ Returns the natural logarithm of GAMMA(X).
+
+
+ Arguments
+
+
+ X --> value at which scaled log gamma is to be returned
+ X is DOUBLE PRECISION
+
+
+ Method
+
+
+ If X .le. 6.0, then use recursion to get X below 3
+ then apply rational approximation number 5236 of
+ Hart et al, Computer Approximations, John Wiley and
+ Sons, NY, 1968.
+
+ If X .gt. 6.0, then use recursion to get X to at least 12 and
+ then use formula 5423 of the same source.
+
+**********************************************************************
+*/
+{
+#define hln2pi 0.91893853320467274178e0
+static double coef[5] = {
+ 0.83333333333333023564e-1,-0.27777777768818808e-2,0.79365006754279e-3,
+ -0.594997310889e-3,0.8065880899e-3
+};
+static double scoefd[4] = {
+ 0.62003838007126989331e2,0.9822521104713994894e1,-0.8906016659497461257e1,
+ 0.1000000000000000000e1
+};
+static double scoefn[9] = {
+ 0.62003838007127258804e2,0.36036772530024836321e2,0.20782472531792126786e2,
+ 0.6338067999387272343e1,0.215994312846059073e1,0.3980671310203570498e0,
+ 0.1093115956710439502e0,0.92381945590275995e-2,0.29737866448101651e-2
+};
+static int K1 = 9;
+static int K3 = 4;
+static int K5 = 5;
+static double alngam,offset,prod,xx;
+static int i,n;
+static double T2,T4,T6;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(!(*x <= 6.0e0)) goto S70;
+ prod = 1.0e0;
+ xx = *x;
+ if(!(*x > 3.0e0)) goto S30;
+S10:
+ if(!(xx > 3.0e0)) goto S20;
+ xx -= 1.0e0;
+ prod *= xx;
+ goto S10;
+S30:
+S20:
+ if(!(*x < 2.0e0)) goto S60;
+S40:
+ if(!(xx < 2.0e0)) goto S50;
+ prod /= xx;
+ xx += 1.0e0;
+ goto S40;
+S60:
+S50:
+ T2 = xx-2.0e0;
+ T4 = xx-2.0e0;
+ alngam = devlpl(scoefn,&K1,&T2)/devlpl(scoefd,&K3,&T4);
+/*
+ COMPUTE RATIONAL APPROXIMATION TO GAMMA(X)
+*/
+ alngam *= prod;
+ alngam = log(alngam);
+ goto S110;
+S70:
+ offset = hln2pi;
+/*
+ IF NECESSARY MAKE X AT LEAST 12 AND CARRY CORRECTION IN OFFSET
+*/
+ n = fifidint(12.0e0-*x);
+ if(!(n > 0)) goto S90;
+ prod = 1.0e0;
+ for(i=1; i<=n; i++) prod *= (*x+(double)(i-1));
+ offset -= log(prod);
+ xx = *x+(double)n;
+ goto S100;
+S90:
+ xx = *x;
+S100:
+/*
+ COMPUTE POWER SERIES
+*/
+ T6 = 1.0e0/pow(xx,2.0);
+ alngam = devlpl(coef,&K5,&T6)/xx;
+ alngam += (offset+(xx-0.5e0)*log(xx)-xx);
+S110:
+ return alngam;
+#undef hln2pi
+} /* END */
+
+/***=====================================================================***/
+static double alnrel(double *a)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF THE FUNCTION LN(1 + A)
+-----------------------------------------------------------------------
+*/
+{
+static double p1 = -.129418923021993e+01;
+static double p2 = .405303492862024e+00;
+static double p3 = -.178874546012214e-01;
+static double q1 = -.162752256355323e+01;
+static double q2 = .747811014037616e+00;
+static double q3 = -.845104217945565e-01;
+static double alnrel,t,t2,w,x;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(fabs(*a) > 0.375e0) goto S10;
+ t = *a/(*a+2.0e0);
+ t2 = t*t;
+ w = (((p3*t2+p2)*t2+p1)*t2+1.0e0)/(((q3*t2+q2)*t2+q1)*t2+1.0e0);
+ alnrel = 2.0e0*t*w;
+ return alnrel;
+S10:
+ x = 1.e0+*a;
+ alnrel = log(x);
+ return alnrel;
+} /* END */
+
+/***=====================================================================***/
+static double apser(double *a,double *b,double *x,double *eps)
+/*
+-----------------------------------------------------------------------
+ APSER YIELDS THE INCOMPLETE BETA RATIO I(SUB(1-X))(B,A) FOR
+ A .LE. MIN(EPS,EPS*B), B*X .LE. 1, AND X .LE. 0.5. USED WHEN
+ A IS VERY SMALL. USE ONLY IF ABOVE INEQUALITIES ARE SATISFIED.
+-----------------------------------------------------------------------
+*/
+{
+static double g = .577215664901533e0;
+static double apser,aj,bx,c,j,s,t,tol;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ bx = *b**x;
+ t = *x-bx;
+ if(*b**eps > 2.e-2) goto S10;
+ c = log(*x)+psi(b)+g+t;
+ goto S20;
+S10:
+ c = log(bx)+g+t;
+S20:
+ tol = 5.0e0**eps*fabs(c);
+ j = 1.0e0;
+ s = 0.0e0;
+S30:
+ j += 1.0e0;
+ t *= (*x-bx/j);
+ aj = t/j;
+ s += aj;
+ if(fabs(aj) > tol) goto S30;
+ apser = -(*a*(c+s));
+ return apser;
+} /* END */
+
+/***=====================================================================***/
+static double basym(double *a,double *b,double *lambda,double *eps)
+/*
+-----------------------------------------------------------------------
+ ASYMPTOTIC EXPANSION FOR IX(A,B) FOR LARGE A AND B.
+ LAMBDA = (A + B)*Y - B AND EPS IS THE TOLERANCE USED.
+ IT IS ASSUMED THAT LAMBDA IS NONNEGATIVE AND THAT
+ A AND B ARE GREATER THAN OR EQUAL TO 15.
+-----------------------------------------------------------------------
+*/
+{
+static double e0 = 1.12837916709551e0;
+static double e1 = .353553390593274e0;
+static int num = 20;
+/*
+------------------------
+ ****** NUM IS THE MAXIMUM VALUE THAT N CAN TAKE IN THE DO LOOP
+ ENDING AT STATEMENT 50. IT IS REQUIRED THAT NUM BE EVEN.
+ THE ARRAYS A0, B0, C, D HAVE DIMENSION NUM + 1.
+------------------------
+ E0 = 2/SQRT(PI)
+ E1 = 2**(-3/2)
+------------------------
+*/
+static int K3 = 1;
+static double basym,bsum,dsum,f,h,h2,hn,j0,j1,r,r0,r1,s,sum,t,t0,t1,u,w,w0,z,z0,
+ z2,zn,znm1;
+static int i,im1,imj,j,m,mm1,mmj,n,np1;
+static double a0[21],b0[21],c[21],d[21],T1,T2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ basym = 0.0e0;
+ if(*a >= *b) goto S10;
+ h = *a/ *b;
+ r0 = 1.0e0/(1.0e0+h);
+ r1 = (*b-*a)/ *b;
+ w0 = 1.0e0/sqrt(*a*(1.0e0+h));
+ goto S20;
+S10:
+ h = *b/ *a;
+ r0 = 1.0e0/(1.0e0+h);
+ r1 = (*b-*a)/ *a;
+ w0 = 1.0e0/sqrt(*b*(1.0e0+h));
+S20:
+ T1 = -(*lambda/ *a);
+ T2 = *lambda/ *b;
+ f = *a*rlog1(&T1)+*b*rlog1(&T2);
+ t = exp(-f);
+ if(t == 0.0e0) return basym;
+ z0 = sqrt(f);
+ z = 0.5e0*(z0/e1);
+ z2 = f+f;
+ a0[0] = 2.0e0/3.0e0*r1;
+ c[0] = -(0.5e0*a0[0]);
+ d[0] = -c[0];
+ j0 = 0.5e0/e0*erfc1(&K3,&z0);
+ j1 = e1;
+ sum = j0+d[0]*w0*j1;
+ s = 1.0e0;
+ h2 = h*h;
+ hn = 1.0e0;
+ w = w0;
+ znm1 = z;
+ zn = z2;
+ for(n=2; n<=num; n+=2) {
+ hn = h2*hn;
+ a0[n-1] = 2.0e0*r0*(1.0e0+h*hn)/((double)n+2.0e0);
+ np1 = n+1;
+ s += hn;
+ a0[np1-1] = 2.0e0*r1*s/((double)n+3.0e0);
+ for(i=n; i<=np1; i++) {
+ r = -(0.5e0*((double)i+1.0e0));
+ b0[0] = r*a0[0];
+ for(m=2; m<=i; m++) {
+ bsum = 0.0e0;
+ mm1 = m-1;
+ for(j=1; j<=mm1; j++) {
+ mmj = m-j;
+ bsum += (((double)j*r-(double)mmj)*a0[j-1]*b0[mmj-1]);
+ }
+ b0[m-1] = r*a0[m-1]+bsum/(double)m;
+ }
+ c[i-1] = b0[i-1]/((double)i+1.0e0);
+ dsum = 0.0e0;
+ im1 = i-1;
+ for(j=1; j<=im1; j++) {
+ imj = i-j;
+ dsum += (d[imj-1]*c[j-1]);
+ }
+ d[i-1] = -(dsum+c[i-1]);
+ }
+ j0 = e1*znm1+((double)n-1.0e0)*j0;
+ j1 = e1*zn+(double)n*j1;
+ znm1 = z2*znm1;
+ zn = z2*zn;
+ w = w0*w;
+ t0 = d[n-1]*w*j0;
+ w = w0*w;
+ t1 = d[np1-1]*w*j1;
+ sum += (t0+t1);
+ if(fabs(t0)+fabs(t1) <= *eps*sum) goto S80;
+ }
+S80:
+ u = exp(-bcorr(a,b));
+ basym = e0*t*u*sum;
+ return basym;
+} /* END */
+
+/***=====================================================================***/
+static double bcorr(double *a0,double *b0)
+/*
+-----------------------------------------------------------------------
+
+ EVALUATION OF DEL(A0) + DEL(B0) - DEL(A0 + B0) WHERE
+ LN(GAMMA(A)) = (A - 0.5)*LN(A) - A + 0.5*LN(2*PI) + DEL(A).
+ IT IS ASSUMED THAT A0 .GE. 8 AND B0 .GE. 8.
+
+-----------------------------------------------------------------------
+*/
+{
+static double c0 = .833333333333333e-01;
+static double c1 = -.277777777760991e-02;
+static double c2 = .793650666825390e-03;
+static double c3 = -.595202931351870e-03;
+static double c4 = .837308034031215e-03;
+static double c5 = -.165322962780713e-02;
+static double bcorr,a,b,c,h,s11,s3,s5,s7,s9,t,w,x,x2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ a = fifdmin1(*a0,*b0);
+ b = fifdmax1(*a0,*b0);
+ h = a/b;
+ c = h/(1.0e0+h);
+ x = 1.0e0/(1.0e0+h);
+ x2 = x*x;
+/*
+ SET SN = (1 - X**N)/(1 - X)
+*/
+ s3 = 1.0e0+(x+x2);
+ s5 = 1.0e0+(x+x2*s3);
+ s7 = 1.0e0+(x+x2*s5);
+ s9 = 1.0e0+(x+x2*s7);
+ s11 = 1.0e0+(x+x2*s9);
+/*
+ SET W = DEL(B) - DEL(A + B)
+*/
+ t = pow(1.0e0/b,2.0);
+ w = ((((c5*s11*t+c4*s9)*t+c3*s7)*t+c2*s5)*t+c1*s3)*t+c0;
+ w *= (c/b);
+/*
+ COMPUTE DEL(A) + W
+*/
+ t = pow(1.0e0/a,2.0);
+ bcorr = (((((c5*t+c4)*t+c3)*t+c2)*t+c1)*t+c0)/a+w;
+ return bcorr;
+} /* END */
+
+/***=====================================================================***/
+static double betaln(double *a0,double *b0)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF THE LOGARITHM OF THE BETA FUNCTION
+-----------------------------------------------------------------------
+ E = 0.5*LN(2*PI)
+--------------------------
+*/
+{
+static double e = .918938533204673e0;
+static double betaln,a,b,c,h,u,v,w,z;
+static int i,n;
+static double T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ a = fifdmin1(*a0,*b0);
+ b = fifdmax1(*a0,*b0);
+ if(a >= 8.0e0) goto S100;
+ if(a >= 1.0e0) goto S20;
+/*
+-----------------------------------------------------------------------
+ PROCEDURE WHEN A .LT. 1
+-----------------------------------------------------------------------
+*/
+ if(b >= 8.0e0) goto S10;
+ T1 = a+b;
+ betaln = gamln(&a)+(gamln(&b)-gamln(&T1));
+ return betaln;
+S10:
+ betaln = gamln(&a)+algdiv(&a,&b);
+ return betaln;
+S20:
+/*
+-----------------------------------------------------------------------
+ PROCEDURE WHEN 1 .LE. A .LT. 8
+-----------------------------------------------------------------------
+*/
+ if(a > 2.0e0) goto S40;
+ if(b > 2.0e0) goto S30;
+ betaln = gamln(&a)+gamln(&b)-gsumln(&a,&b);
+ return betaln;
+S30:
+ w = 0.0e0;
+ if(b < 8.0e0) goto S60;
+ betaln = gamln(&a)+algdiv(&a,&b);
+ return betaln;
+S40:
+/*
+ REDUCTION OF A WHEN B .LE. 1000
+*/
+ if(b > 1000.0e0) goto S80;
+ n = a-1.0e0;
+ w = 1.0e0;
+ for(i=1; i<=n; i++) {
+ a -= 1.0e0;
+ h = a/b;
+ w *= (h/(1.0e0+h));
+ }
+ w = log(w);
+ if(b < 8.0e0) goto S60;
+ betaln = w+gamln(&a)+algdiv(&a,&b);
+ return betaln;
+S60:
+/*
+ REDUCTION OF B WHEN B .LT. 8
+*/
+ n = b-1.0e0;
+ z = 1.0e0;
+ for(i=1; i<=n; i++) {
+ b -= 1.0e0;
+ z *= (b/(a+b));
+ }
+ betaln = w+log(z)+(gamln(&a)+(gamln(&b)-gsumln(&a,&b)));
+ return betaln;
+S80:
+/*
+ REDUCTION OF A WHEN B .GT. 1000
+*/
+ n = a-1.0e0;
+ w = 1.0e0;
+ for(i=1; i<=n; i++) {
+ a -= 1.0e0;
+ w *= (a/(1.0e0+a/b));
+ }
+ betaln = log(w)-(double)n*log(b)+(gamln(&a)+algdiv(&a,&b));
+ return betaln;
+S100:
+/*
+-----------------------------------------------------------------------
+ PROCEDURE WHEN A .GE. 8
+-----------------------------------------------------------------------
+*/
+ w = bcorr(&a,&b);
+ h = a/b;
+ c = h/(1.0e0+h);
+ u = -((a-0.5e0)*log(c));
+ v = b*alnrel(&h);
+ if(u <= v) goto S110;
+ betaln = -(0.5e0*log(b))+e+w-v-u;
+ return betaln;
+S110:
+ betaln = -(0.5e0*log(b))+e+w-u-v;
+ return betaln;
+} /* END */
+
+/***=====================================================================***/
+static double bfrac(double *a,double *b,double *x,double *y,double *lambda,
+ double *eps)
+/*
+-----------------------------------------------------------------------
+ CONTINUED FRACTION EXPANSION FOR IX(A,B) WHEN A,B .GT. 1.
+ IT IS ASSUMED THAT LAMBDA = (A + B)*Y - B.
+-----------------------------------------------------------------------
+*/
+{
+static double bfrac,alpha,an,anp1,beta,bn,bnp1,c,c0,c1,e,n,p,r,r0,s,t,w,yp1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ bfrac = brcomp(a,b,x,y);
+ if(bfrac == 0.0e0) return bfrac;
+ c = 1.0e0+*lambda;
+ c0 = *b/ *a;
+ c1 = 1.0e0+1.0e0/ *a;
+ yp1 = *y+1.0e0;
+ n = 0.0e0;
+ p = 1.0e0;
+ s = *a+1.0e0;
+ an = 0.0e0;
+ bn = anp1 = 1.0e0;
+ bnp1 = c/c1;
+ r = c1/c;
+S10:
+/*
+ CONTINUED FRACTION CALCULATION
+*/
+ n += 1.0e0;
+ t = n/ *a;
+ w = n*(*b-n)**x;
+ e = *a/s;
+ alpha = p*(p+c0)*e*e*(w**x);
+ e = (1.0e0+t)/(c1+t+t);
+ beta = n+w/s+e*(c+n*yp1);
+ p = 1.0e0+t;
+ s += 2.0e0;
+/*
+ UPDATE AN, BN, ANP1, AND BNP1
+*/
+ t = alpha*an+beta*anp1;
+ an = anp1;
+ anp1 = t;
+ t = alpha*bn+beta*bnp1;
+ bn = bnp1;
+ bnp1 = t;
+ r0 = r;
+ r = anp1/bnp1;
+ if(fabs(r-r0) <= *eps*r) goto S20;
+/*
+ RESCALE AN, BN, ANP1, AND BNP1
+*/
+ an /= bnp1;
+ bn /= bnp1;
+ anp1 = r;
+ bnp1 = 1.0e0;
+ goto S10;
+S20:
+/*
+ TERMINATION
+*/
+ bfrac *= r;
+ return bfrac;
+} /* END */
+
+/***=====================================================================***/
+static void bgrat(double *a,double *b,double *x,double *y,double *w,
+ double *eps,int *ierr)
+/*
+-----------------------------------------------------------------------
+ ASYMPTOTIC EXPANSION FOR IX(A,B) WHEN A IS LARGER THAN B.
+ THE RESULT OF THE EXPANSION IS ADDED TO W. IT IS ASSUMED
+ THAT A .GE. 15 AND B .LE. 1. EPS IS THE TOLERANCE USED.
+ IERR IS A VARIABLE THAT REPORTS THE STATUS OF THE RESULTS.
+-----------------------------------------------------------------------
+*/
+{
+static double bm1,bp2n,cn,coef,dj,j,l,lnx,n2,nu,p,q,r,s,sum,t,t2,u,v,z;
+static int i,n,nm1;
+static double c[30],d[30],T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ bm1 = *b-0.5e0-0.5e0;
+ nu = *a+0.5e0*bm1;
+ if(*y > 0.375e0) goto S10;
+ T1 = -*y;
+ lnx = alnrel(&T1);
+ goto S20;
+S10:
+ lnx = log(*x);
+S20:
+ z = -(nu*lnx);
+ if(*b*z == 0.0e0) goto S70;
+/*
+ COMPUTATION OF THE EXPANSION
+ SET R = EXP(-Z)*Z**B/GAMMA(B)
+*/
+ r = *b*(1.0e0+gam1(b))*exp(*b*log(z));
+ r *= (exp(*a*lnx)*exp(0.5e0*bm1*lnx));
+ u = algdiv(b,a)+*b*log(nu);
+ u = r*exp(-u);
+ if(u == 0.0e0) goto S70;
+ grat1(b,&z,&r,&p,&q,eps);
+ v = 0.25e0*pow(1.0e0/nu,2.0);
+ t2 = 0.25e0*lnx*lnx;
+ l = *w/u;
+ j = q/r;
+ sum = j;
+ t = cn = 1.0e0;
+ n2 = 0.0e0;
+ for(n=1; n<=30; n++) {
+ bp2n = *b+n2;
+ j = (bp2n*(bp2n+1.0e0)*j+(z+bp2n+1.0e0)*t)*v;
+ n2 += 2.0e0;
+ t *= t2;
+ cn /= (n2*(n2+1.0e0));
+ c[n-1] = cn;
+ s = 0.0e0;
+ if(n == 1) goto S40;
+ nm1 = n-1;
+ coef = *b-(double)n;
+ for(i=1; i<=nm1; i++) {
+ s += (coef*c[i-1]*d[n-i-1]);
+ coef += *b;
+ }
+S40:
+ d[n-1] = bm1*cn+s/(double)n;
+ dj = d[n-1]*j;
+ sum += dj;
+ if(sum <= 0.0e0) goto S70;
+ if(fabs(dj) <= *eps*(sum+l)) goto S60;
+ }
+S60:
+/*
+ ADD THE RESULTS TO W
+*/
+ *ierr = 0;
+ *w += (u*sum);
+ return;
+S70:
+/*
+ THE EXPANSION CANNOT BE COMPUTED
+*/
+ *ierr = 1;
+ return;
+} /* END */
+
+/***=====================================================================***/
+static double bpser(double *a,double *b,double *x,double *eps)
+/*
+-----------------------------------------------------------------------
+ POWER SERIES EXPANSION FOR EVALUATING IX(A,B) WHEN B .LE. 1
+ OR B*X .LE. 0.7. EPS IS THE TOLERANCE USED.
+-----------------------------------------------------------------------
+*/
+{
+static double bpser,a0,apb,b0,c,n,sum,t,tol,u,w,z;
+static int i,m;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ bpser = 0.0e0;
+ if(*x == 0.0e0) return bpser;
+/*
+-----------------------------------------------------------------------
+ COMPUTE THE FACTOR X**A/(A*BETA(A,B))
+-----------------------------------------------------------------------
+*/
+ a0 = fifdmin1(*a,*b);
+ if(a0 < 1.0e0) goto S10;
+ z = *a*log(*x)-betaln(a,b);
+ bpser = exp(z)/ *a;
+ goto S100;
+S10:
+ b0 = fifdmax1(*a,*b);
+ if(b0 >= 8.0e0) goto S90;
+ if(b0 > 1.0e0) goto S40;
+/*
+ PROCEDURE FOR A0 .LT. 1 AND B0 .LE. 1
+*/
+ bpser = pow(*x,*a);
+ if(bpser == 0.0e0) return bpser;
+ apb = *a+*b;
+ if(apb > 1.0e0) goto S20;
+ z = 1.0e0+gam1(&apb);
+ goto S30;
+S20:
+ u = *a+*b-1.e0;
+ z = (1.0e0+gam1(&u))/apb;
+S30:
+ c = (1.0e0+gam1(a))*(1.0e0+gam1(b))/z;
+ bpser *= (c*(*b/apb));
+ goto S100;
+S40:
+/*
+ PROCEDURE FOR A0 .LT. 1 AND 1 .LT. B0 .LT. 8
+*/
+ u = gamln1(&a0);
+ m = b0-1.0e0;
+ if(m < 1) goto S60;
+ c = 1.0e0;
+ for(i=1; i<=m; i++) {
+ b0 -= 1.0e0;
+ c *= (b0/(a0+b0));
+ }
+ u = log(c)+u;
+S60:
+ z = *a*log(*x)-u;
+ b0 -= 1.0e0;
+ apb = a0+b0;
+ if(apb > 1.0e0) goto S70;
+ t = 1.0e0+gam1(&apb);
+ goto S80;
+S70:
+ u = a0+b0-1.e0;
+ t = (1.0e0+gam1(&u))/apb;
+S80:
+ bpser = exp(z)*(a0/ *a)*(1.0e0+gam1(&b0))/t;
+ goto S100;
+S90:
+/*
+ PROCEDURE FOR A0 .LT. 1 AND B0 .GE. 8
+*/
+ u = gamln1(&a0)+algdiv(&a0,&b0);
+ z = *a*log(*x)-u;
+ bpser = a0/ *a*exp(z);
+S100:
+ if(bpser == 0.0e0 || *a <= 0.1e0**eps) return bpser;
+/*
+-----------------------------------------------------------------------
+ COMPUTE THE SERIES
+-----------------------------------------------------------------------
+*/
+ sum = n = 0.0e0;
+ c = 1.0e0;
+ tol = *eps/ *a;
+S110:
+ n += 1.0e0;
+ c *= ((0.5e0+(0.5e0-*b/n))**x);
+ w = c/(*a+n);
+ sum += w;
+ if(fabs(w) > tol) goto S110;
+ bpser *= (1.0e0+*a*sum);
+ return bpser;
+} /* END */
+
+/***=====================================================================***/
+static void bratio(double *a,double *b,double *x,double *y,double *w,
+ double *w1,int *ierr)
+/*
+-----------------------------------------------------------------------
+
+ EVALUATION OF THE INCOMPLETE BETA FUNCTION IX(A,B)
+
+ --------------------
+
+ IT IS ASSUMED THAT A AND B ARE NONNEGATIVE, AND THAT X .LE. 1
+ AND Y = 1 - X. BRATIO ASSIGNS W AND W1 THE VALUES
+
+ W = IX(A,B)
+ W1 = 1 - IX(A,B)
+
+ IERR IS A VARIABLE THAT REPORTS THE STATUS OF THE RESULTS.
+ IF NO INPUT ERRORS ARE DETECTED THEN IERR IS SET TO 0 AND
+ W AND W1 ARE COMPUTED. OTHERWISE, IF AN ERROR IS DETECTED,
+ THEN W AND W1 ARE ASSIGNED THE VALUE 0 AND IERR IS SET TO
+ ONE OF THE FOLLOWING VALUES ...
+
+ IERR = 1 IF A OR B IS NEGATIVE
+ IERR = 2 IF A = B = 0
+ IERR = 3 IF X .LT. 0 OR X .GT. 1
+ IERR = 4 IF Y .LT. 0 OR Y .GT. 1
+ IERR = 5 IF X + Y .NE. 1
+ IERR = 6 IF X = A = 0
+ IERR = 7 IF Y = B = 0
+
+--------------------
+ WRITTEN BY ALFRED H. MORRIS, JR.
+ NAVAL SURFACE WARFARE CENTER
+ DAHLGREN, VIRGINIA
+ REVISED ... NOV 1991
+-----------------------------------------------------------------------
+*/
+{
+static int K1 = 1;
+static double a0,b0,eps,lambda,t,x0,y0,z;
+static int ierr1,ind,n;
+static double T2,T3,T4,T5;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ ****** EPS IS A MACHINE DEPENDENT CONSTANT. EPS IS THE SMALLEST
+ FLOATING POINT NUMBER FOR WHICH 1.0 + EPS .GT. 1.0
+*/
+ eps = spmpar(&K1);
+ *w = *w1 = 0.0e0;
+ if(*a < 0.0e0 || *b < 0.0e0) goto S270;
+ if(*a == 0.0e0 && *b == 0.0e0) goto S280;
+ if(*x < 0.0e0 || *x > 1.0e0) goto S290;
+ if(*y < 0.0e0 || *y > 1.0e0) goto S300;
+ z = *x+*y-0.5e0-0.5e0;
+ if(fabs(z) > 3.0e0*eps) goto S310;
+ *ierr = 0;
+ if(*x == 0.0e0) goto S210;
+ if(*y == 0.0e0) goto S230;
+ if(*a == 0.0e0) goto S240;
+ if(*b == 0.0e0) goto S220;
+ eps = fifdmax1(eps,1.e-15);
+ if(fifdmax1(*a,*b) < 1.e-3*eps) goto S260;
+ ind = 0;
+ a0 = *a;
+ b0 = *b;
+ x0 = *x;
+ y0 = *y;
+ if(fifdmin1(a0,b0) > 1.0e0) goto S40;
+/*
+ PROCEDURE FOR A0 .LE. 1 OR B0 .LE. 1
+*/
+ if(*x <= 0.5e0) goto S10;
+ ind = 1;
+ a0 = *b;
+ b0 = *a;
+ x0 = *y;
+ y0 = *x;
+S10:
+ if(b0 < fifdmin1(eps,eps*a0)) goto S90;
+ if(a0 < fifdmin1(eps,eps*b0) && b0*x0 <= 1.0e0) goto S100;
+ if(fifdmax1(a0,b0) > 1.0e0) goto S20;
+ if(a0 >= fifdmin1(0.2e0,b0)) goto S110;
+ if(pow(x0,a0) <= 0.9e0) goto S110;
+ if(x0 >= 0.3e0) goto S120;
+ n = 20;
+ goto S140;
+S20:
+ if(b0 <= 1.0e0) goto S110;
+ if(x0 >= 0.3e0) goto S120;
+ if(x0 >= 0.1e0) goto S30;
+ if(pow(x0*b0,a0) <= 0.7e0) goto S110;
+S30:
+ if(b0 > 15.0e0) goto S150;
+ n = 20;
+ goto S140;
+S40:
+/*
+ PROCEDURE FOR A0 .GT. 1 AND B0 .GT. 1
+*/
+ if(*a > *b) goto S50;
+ lambda = *a-(*a+*b)**x;
+ goto S60;
+S50:
+ lambda = (*a+*b)**y-*b;
+S60:
+ if(lambda >= 0.0e0) goto S70;
+ ind = 1;
+ a0 = *b;
+ b0 = *a;
+ x0 = *y;
+ y0 = *x;
+ lambda = fabs(lambda);
+S70:
+ if(b0 < 40.0e0 && b0*x0 <= 0.7e0) goto S110;
+ if(b0 < 40.0e0) goto S160;
+ if(a0 > b0) goto S80;
+ if(a0 <= 100.0e0) goto S130;
+ if(lambda > 0.03e0*a0) goto S130;
+ goto S200;
+S80:
+ if(b0 <= 100.0e0) goto S130;
+ if(lambda > 0.03e0*b0) goto S130;
+ goto S200;
+S90:
+/*
+ EVALUATION OF THE APPROPRIATE ALGORITHM
+*/
+ *w = fpser(&a0,&b0,&x0,&eps);
+ *w1 = 0.5e0+(0.5e0-*w);
+ goto S250;
+S100:
+ *w1 = apser(&a0,&b0,&x0,&eps);
+ *w = 0.5e0+(0.5e0-*w1);
+ goto S250;
+S110:
+ *w = bpser(&a0,&b0,&x0,&eps);
+ *w1 = 0.5e0+(0.5e0-*w);
+ goto S250;
+S120:
+ *w1 = bpser(&b0,&a0,&y0,&eps);
+ *w = 0.5e0+(0.5e0-*w1);
+ goto S250;
+S130:
+ T2 = 15.0e0*eps;
+ *w = bfrac(&a0,&b0,&x0,&y0,&lambda,&T2);
+ *w1 = 0.5e0+(0.5e0-*w);
+ goto S250;
+S140:
+ *w1 = bup(&b0,&a0,&y0,&x0,&n,&eps);
+ b0 += (double)n;
+S150:
+ T3 = 15.0e0*eps;
+ bgrat(&b0,&a0,&y0,&x0,w1,&T3,&ierr1);
+ *w = 0.5e0+(0.5e0-*w1);
+ goto S250;
+S160:
+ n = b0;
+ b0 -= (double)n;
+ if(b0 != 0.0e0) goto S170;
+ n -= 1;
+ b0 = 1.0e0;
+S170:
+ *w = bup(&b0,&a0,&y0,&x0,&n,&eps);
+ if(x0 > 0.7e0) goto S180;
+ *w += bpser(&a0,&b0,&x0,&eps);
+ *w1 = 0.5e0+(0.5e0-*w);
+ goto S250;
+S180:
+ if(a0 > 15.0e0) goto S190;
+ n = 20;
+ *w += bup(&a0,&b0,&x0,&y0,&n,&eps);
+ a0 += (double)n;
+S190:
+ T4 = 15.0e0*eps;
+ bgrat(&a0,&b0,&x0,&y0,w,&T4,&ierr1);
+ *w1 = 0.5e0+(0.5e0-*w);
+ goto S250;
+S200:
+ T5 = 100.0e0*eps;
+ *w = basym(&a0,&b0,&lambda,&T5);
+ *w1 = 0.5e0+(0.5e0-*w);
+ goto S250;
+S210:
+/*
+ TERMINATION OF THE PROCEDURE
+*/
+ if(*a == 0.0e0) goto S320;
+S220:
+ *w = 0.0e0;
+ *w1 = 1.0e0;
+ return;
+S230:
+ if(*b == 0.0e0) goto S330;
+S240:
+ *w = 1.0e0;
+ *w1 = 0.0e0;
+ return;
+S250:
+ if(ind == 0) return;
+ t = *w;
+ *w = *w1;
+ *w1 = t;
+ return;
+S260:
+/*
+ PROCEDURE FOR A AND B .LT. 1.E-3*EPS
+*/
+ *w = *b/(*a+*b);
+ *w1 = *a/(*a+*b);
+ return;
+S270:
+/*
+ ERROR RETURN
+*/
+ *ierr = 1;
+ return;
+S280:
+ *ierr = 2;
+ return;
+S290:
+ *ierr = 3;
+ return;
+S300:
+ *ierr = 4;
+ return;
+S310:
+ *ierr = 5;
+ return;
+S320:
+ *ierr = 6;
+ return;
+S330:
+ *ierr = 7;
+ return;
+} /* END */
+
+/***=====================================================================***/
+static double brcmp1(int *mu,double *a,double *b,double *x,double *y)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF EXP(MU) * (X**A*Y**B/BETA(A,B))
+-----------------------------------------------------------------------
+*/
+{
+static double Const = .398942280401433e0;
+static double brcmp1,a0,apb,b0,c,e,h,lambda,lnx,lny,t,u,v,x0,y0,z;
+static int i,n;
+/*
+-----------------
+ CONST = 1/SQRT(2*PI)
+-----------------
+*/
+static double T1,T2,T3,T4;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ a0 = fifdmin1(*a,*b);
+ if(a0 >= 8.0e0) goto S130;
+ if(*x > 0.375e0) goto S10;
+ lnx = log(*x);
+ T1 = -*x;
+ lny = alnrel(&T1);
+ goto S30;
+S10:
+ if(*y > 0.375e0) goto S20;
+ T2 = -*y;
+ lnx = alnrel(&T2);
+ lny = log(*y);
+ goto S30;
+S20:
+ lnx = log(*x);
+ lny = log(*y);
+S30:
+ z = *a*lnx+*b*lny;
+ if(a0 < 1.0e0) goto S40;
+ z -= betaln(a,b);
+ brcmp1 = esum(mu,&z);
+ return brcmp1;
+S40:
+/*
+-----------------------------------------------------------------------
+ PROCEDURE FOR A .LT. 1 OR B .LT. 1
+-----------------------------------------------------------------------
+*/
+ b0 = fifdmax1(*a,*b);
+ if(b0 >= 8.0e0) goto S120;
+ if(b0 > 1.0e0) goto S70;
+/*
+ ALGORITHM FOR B0 .LE. 1
+*/
+ brcmp1 = esum(mu,&z);
+ if(brcmp1 == 0.0e0) return brcmp1;
+ apb = *a+*b;
+ if(apb > 1.0e0) goto S50;
+ z = 1.0e0+gam1(&apb);
+ goto S60;
+S50:
+ u = *a+*b-1.e0;
+ z = (1.0e0+gam1(&u))/apb;
+S60:
+ c = (1.0e0+gam1(a))*(1.0e0+gam1(b))/z;
+ brcmp1 = brcmp1*(a0*c)/(1.0e0+a0/b0);
+ return brcmp1;
+S70:
+/*
+ ALGORITHM FOR 1 .LT. B0 .LT. 8
+*/
+ u = gamln1(&a0);
+ n = b0-1.0e0;
+ if(n < 1) goto S90;
+ c = 1.0e0;
+ for(i=1; i<=n; i++) {
+ b0 -= 1.0e0;
+ c *= (b0/(a0+b0));
+ }
+ u = log(c)+u;
+S90:
+ z -= u;
+ b0 -= 1.0e0;
+ apb = a0+b0;
+ if(apb > 1.0e0) goto S100;
+ t = 1.0e0+gam1(&apb);
+ goto S110;
+S100:
+ u = a0+b0-1.e0;
+ t = (1.0e0+gam1(&u))/apb;
+S110:
+ brcmp1 = a0*esum(mu,&z)*(1.0e0+gam1(&b0))/t;
+ return brcmp1;
+S120:
+/*
+ ALGORITHM FOR B0 .GE. 8
+*/
+ u = gamln1(&a0)+algdiv(&a0,&b0);
+ T3 = z-u;
+ brcmp1 = a0*esum(mu,&T3);
+ return brcmp1;
+S130:
+/*
+-----------------------------------------------------------------------
+ PROCEDURE FOR A .GE. 8 AND B .GE. 8
+-----------------------------------------------------------------------
+*/
+ if(*a > *b) goto S140;
+ h = *a/ *b;
+ x0 = h/(1.0e0+h);
+ y0 = 1.0e0/(1.0e0+h);
+ lambda = *a-(*a+*b)**x;
+ goto S150;
+S140:
+ h = *b/ *a;
+ x0 = 1.0e0/(1.0e0+h);
+ y0 = h/(1.0e0+h);
+ lambda = (*a+*b)**y-*b;
+S150:
+ e = -(lambda/ *a);
+ if(fabs(e) > 0.6e0) goto S160;
+ u = rlog1(&e);
+ goto S170;
+S160:
+ u = e-log(*x/x0);
+S170:
+ e = lambda/ *b;
+ if(fabs(e) > 0.6e0) goto S180;
+ v = rlog1(&e);
+ goto S190;
+S180:
+ v = e-log(*y/y0);
+S190:
+ T4 = -(*a*u+*b*v);
+ z = esum(mu,&T4);
+ brcmp1 = Const*sqrt(*b*x0)*z*exp(-bcorr(a,b));
+ return brcmp1;
+} /* END */
+
+/***=====================================================================***/
+static double brcomp(double *a,double *b,double *x,double *y)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF X**A*Y**B/BETA(A,B)
+-----------------------------------------------------------------------
+*/
+{
+static double Const = .398942280401433e0;
+static double brcomp,a0,apb,b0,c,e,h,lambda,lnx,lny,t,u,v,x0,y0,z;
+static int i,n;
+/*
+-----------------
+ CONST = 1/SQRT(2*PI)
+-----------------
+*/
+static double T1,T2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ brcomp = 0.0e0;
+ if(*x == 0.0e0 || *y == 0.0e0) return brcomp;
+ a0 = fifdmin1(*a,*b);
+ if(a0 >= 8.0e0) goto S130;
+ if(*x > 0.375e0) goto S10;
+ lnx = log(*x);
+ T1 = -*x;
+ lny = alnrel(&T1);
+ goto S30;
+S10:
+ if(*y > 0.375e0) goto S20;
+ T2 = -*y;
+ lnx = alnrel(&T2);
+ lny = log(*y);
+ goto S30;
+S20:
+ lnx = log(*x);
+ lny = log(*y);
+S30:
+ z = *a*lnx+*b*lny;
+ if(a0 < 1.0e0) goto S40;
+ z -= betaln(a,b);
+ brcomp = exp(z);
+ return brcomp;
+S40:
+/*
+-----------------------------------------------------------------------
+ PROCEDURE FOR A .LT. 1 OR B .LT. 1
+-----------------------------------------------------------------------
+*/
+ b0 = fifdmax1(*a,*b);
+ if(b0 >= 8.0e0) goto S120;
+ if(b0 > 1.0e0) goto S70;
+/*
+ ALGORITHM FOR B0 .LE. 1
+*/
+ brcomp = exp(z);
+ if(brcomp == 0.0e0) return brcomp;
+ apb = *a+*b;
+ if(apb > 1.0e0) goto S50;
+ z = 1.0e0+gam1(&apb);
+ goto S60;
+S50:
+ u = *a+*b-1.e0;
+ z = (1.0e0+gam1(&u))/apb;
+S60:
+ c = (1.0e0+gam1(a))*(1.0e0+gam1(b))/z;
+ brcomp = brcomp*(a0*c)/(1.0e0+a0/b0);
+ return brcomp;
+S70:
+/*
+ ALGORITHM FOR 1 .LT. B0 .LT. 8
+*/
+ u = gamln1(&a0);
+ n = b0-1.0e0;
+ if(n < 1) goto S90;
+ c = 1.0e0;
+ for(i=1; i<=n; i++) {
+ b0 -= 1.0e0;
+ c *= (b0/(a0+b0));
+ }
+ u = log(c)+u;
+S90:
+ z -= u;
+ b0 -= 1.0e0;
+ apb = a0+b0;
+ if(apb > 1.0e0) goto S100;
+ t = 1.0e0+gam1(&apb);
+ goto S110;
+S100:
+ u = a0+b0-1.e0;
+ t = (1.0e0+gam1(&u))/apb;
+S110:
+ brcomp = a0*exp(z)*(1.0e0+gam1(&b0))/t;
+ return brcomp;
+S120:
+/*
+ ALGORITHM FOR B0 .GE. 8
+*/
+ u = gamln1(&a0)+algdiv(&a0,&b0);
+ brcomp = a0*exp(z-u);
+ return brcomp;
+S130:
+/*
+-----------------------------------------------------------------------
+ PROCEDURE FOR A .GE. 8 AND B .GE. 8
+-----------------------------------------------------------------------
+*/
+ if(*a > *b) goto S140;
+ h = *a/ *b;
+ x0 = h/(1.0e0+h);
+ y0 = 1.0e0/(1.0e0+h);
+ lambda = *a-(*a+*b)**x;
+ goto S150;
+S140:
+ h = *b/ *a;
+ x0 = 1.0e0/(1.0e0+h);
+ y0 = h/(1.0e0+h);
+ lambda = (*a+*b)**y-*b;
+S150:
+ e = -(lambda/ *a);
+ if(fabs(e) > 0.6e0) goto S160;
+ u = rlog1(&e);
+ goto S170;
+S160:
+ u = e-log(*x/x0);
+S170:
+ e = lambda/ *b;
+ if(fabs(e) > 0.6e0) goto S180;
+ v = rlog1(&e);
+ goto S190;
+S180:
+ v = e-log(*y/y0);
+S190:
+ z = exp(-(*a*u+*b*v));
+ brcomp = Const*sqrt(*b*x0)*z*exp(-bcorr(a,b));
+ return brcomp;
+} /* END */
+
+/***=====================================================================***/
+static double bup(double *a,double *b,double *x,double *y,int *n,double *eps)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF IX(A,B) - IX(A+N,B) WHERE N IS A POSITIVE INTEGER.
+ EPS IS THE TOLERANCE USED.
+-----------------------------------------------------------------------
+*/
+{
+static int K1 = 1;
+static int K2 = 0;
+static double bup,ap1,apb,d,l,r,t,w;
+static int i,k,kp1,mu,nm1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ OBTAIN THE SCALING FACTOR EXP(-MU) AND
+ EXP(MU)*(X**A*Y**B/BETA(A,B))/A
+*/
+ apb = *a+*b;
+ ap1 = *a+1.0e0;
+ mu = 0;
+ d = 1.0e0;
+ if(*n == 1 || *a < 1.0e0) goto S10;
+ if(apb < 1.1e0*ap1) goto S10;
+ mu = fabs(exparg(&K1));
+ k = exparg(&K2);
+ if(k < mu) mu = k;
+ t = mu;
+ d = exp(-t);
+S10:
+ bup = brcmp1(&mu,a,b,x,y)/ *a;
+ if(*n == 1 || bup == 0.0e0) return bup;
+ nm1 = *n-1;
+ w = d;
+/*
+ LET K BE THE INDEX OF THE MAXIMUM TERM
+*/
+ k = 0;
+ if(*b <= 1.0e0) goto S50;
+ if(*y > 1.e-4) goto S20;
+ k = nm1;
+ goto S30;
+S20:
+ r = (*b-1.0e0)**x/ *y-*a;
+ if(r < 1.0e0) goto S50;
+ k = t = nm1;
+ if(r < t) k = r;
+S30:
+/*
+ ADD THE INCREASING TERMS OF THE SERIES
+*/
+ for(i=1; i<=k; i++) {
+ l = i-1;
+ d = (apb+l)/(ap1+l)**x*d;
+ w += d;
+ }
+ if(k == nm1) goto S70;
+S50:
+/*
+ ADD THE REMAINING TERMS OF THE SERIES
+*/
+ kp1 = k+1;
+ for(i=kp1; i<=nm1; i++) {
+ l = i-1;
+ d = (apb+l)/(ap1+l)**x*d;
+ w += d;
+ if(d <= *eps*w) goto S70;
+ }
+S70:
+/*
+ TERMINATE THE PROCEDURE
+*/
+ bup *= w;
+ return bup;
+} /* END */
+
+/***=====================================================================***/
+static void cdfbet(int *which,double *p,double *q,double *x,double *y,
+ double *a,double *b,int *status,double *bound)
+/**********************************************************************
+
+ void cdfbet(int *which,double *p,double *q,double *x,double *y,
+ double *a,double *b,int *status,double *bound)
+
+ Cumulative Distribution Function
+ BETa Distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the beta distribution given
+ values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next four argument
+ values is to be calculated from the others.
+ Legal range: 1..4
+ iwhich = 1 : Calculate P and Q from X,Y,A and B
+ iwhich = 2 : Calculate X and Y from P,Q,A and B
+ iwhich = 3 : Calculate A from P,Q,X,Y and B
+ iwhich = 4 : Calculate B from P,Q,X,Y and A
+
+ P <--> The integral from 0 to X of the chi-square
+ distribution.
+ Input range: [0, 1].
+
+ Q <--> 1-P.
+ Input range: [0, 1].
+ P + Q = 1.0.
+
+ X <--> Upper limit of integration of beta density.
+ Input range: [0,1].
+ Search range: [0,1]
+
+ Y <--> 1-X.
+ Input range: [0,1].
+ Search range: [0,1]
+ X + Y = 1.0.
+
+ A <--> The first parameter of the beta density.
+ Input range: (0, +infinity).
+ Search range: [1D-300,1D300]
+
+ B <--> The second parameter of the beta density.
+ Input range: (0, +infinity).
+ Search range: [1D-300,1D300]
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+ 4 if X + Y .ne. 1
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Cumulative distribution function (P) is calculated directly by
+ code associated with the following reference.
+
+ DiDinato, A. R. and Morris, A. H. Algorithm 708: Significant
+ Digit Computation of the Incomplete Beta Function Ratios. ACM
+ Trans. Math. Softw. 18 (1993), 360-373.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+
+ Note
+
+
+ The beta density is proportional to
+ t^(A-1) * (1-t)^(B-1)
+
+**********************************************************************/
+{
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define zero (1.0e-300)
+#define inf 1.0e300
+#define one 1.0e0
+static int K1 = 1;
+static double K2 = 0.0e0;
+static double K3 = 1.0e0;
+static double K8 = 0.5e0;
+static double K9 = 5.0e0;
+static double fx,xhi,xlo,cum,ccum,xy,pq;
+static unsigned long qhi,qleft,qporq;
+static double T4,T5,T6,T7,T10,T11,T12,T13,T14,T15;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 4)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 4.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q < 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q < 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 2) goto S150;
+/*
+ X
+*/
+ if(!(*x < 0.0e0 || *x > 1.0e0)) goto S140;
+ if(!(*x < 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ goto S130;
+S120:
+ *bound = 1.0e0;
+S130:
+ *status = -4;
+ return;
+S150:
+S140:
+ if(*which == 2) goto S190;
+/*
+ Y
+*/
+ if(!(*y < 0.0e0 || *y > 1.0e0)) goto S180;
+ if(!(*y < 0.0e0)) goto S160;
+ *bound = 0.0e0;
+ goto S170;
+S160:
+ *bound = 1.0e0;
+S170:
+ *status = -5;
+ return;
+S190:
+S180:
+ if(*which == 3) goto S210;
+/*
+ A
+*/
+ if(!(*a <= 0.0e0)) goto S200;
+ *bound = 0.0e0;
+ *status = -6;
+ return;
+S210:
+S200:
+ if(*which == 4) goto S230;
+/*
+ B
+*/
+ if(!(*b <= 0.0e0)) goto S220;
+ *bound = 0.0e0;
+ *status = -7;
+ return;
+S230:
+S220:
+ if(*which == 1) goto S270;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S260;
+ if(!(pq < 0.0e0)) goto S240;
+ *bound = 0.0e0;
+ goto S250;
+S240:
+ *bound = 1.0e0;
+S250:
+ *status = 3;
+ return;
+S270:
+S260:
+ if(*which == 2) goto S310;
+/*
+ X + Y
+*/
+ xy = *x+*y;
+ if(!(fabs(xy-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S300;
+ if(!(xy < 0.0e0)) goto S280;
+ *bound = 0.0e0;
+ goto S290;
+S280:
+ *bound = 1.0e0;
+S290:
+ *status = 4;
+ return;
+S310:
+S300:
+ if(!(*which == 1)) qporq = *p <= *q;
+/*
+ Select the minimum of P or Q
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P and Q
+*/
+ cumbet(x,y,a,b,p,q);
+ *status = 0;
+ }
+ else if(2 == *which) {
+/*
+ Calculating X and Y
+*/
+ T4 = atol;
+ T5 = tol;
+ dstzr(&K2,&K3,&T4,&T5);
+ if(!qporq) goto S340;
+ *status = 0;
+ dzror(status,x,&fx,&xlo,&xhi,&qleft,&qhi);
+ *y = one-*x;
+S320:
+ if(!(*status == 1)) goto S330;
+ cumbet(x,y,a,b,&cum,&ccum);
+ fx = cum-*p;
+ dzror(status,x,&fx,&xlo,&xhi,&qleft,&qhi);
+ *y = one-*x;
+ goto S320;
+S330:
+ goto S370;
+S340:
+ *status = 0;
+ dzror(status,y,&fx,&xlo,&xhi,&qleft,&qhi);
+ *x = one-*y;
+S350:
+ if(!(*status == 1)) goto S360;
+ cumbet(x,y,a,b,&cum,&ccum);
+ fx = ccum-*q;
+ dzror(status,y,&fx,&xlo,&xhi,&qleft,&qhi);
+ *x = one-*y;
+ goto S350;
+S370:
+S360:
+ if(!(*status == -1)) goto S400;
+ if(!qleft) goto S380;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S390;
+S380:
+ *status = 2;
+ *bound = 1.0e0;
+S400:
+S390:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Computing A
+*/
+ *a = 5.0e0;
+ T6 = zero;
+ T7 = inf;
+ T10 = atol;
+ T11 = tol;
+ dstinv(&T6,&T7,&K8,&K8,&K9,&T10,&T11);
+ *status = 0;
+ dinvr(status,a,&fx,&qleft,&qhi);
+S410:
+ if(!(*status == 1)) goto S440;
+ cumbet(x,y,a,b,&cum,&ccum);
+ if(!qporq) goto S420;
+ fx = cum-*p;
+ goto S430;
+S420:
+ fx = ccum-*q;
+S430:
+ dinvr(status,a,&fx,&qleft,&qhi);
+ goto S410;
+S440:
+ if(!(*status == -1)) goto S470;
+ if(!qleft) goto S450;
+ *status = 1;
+ *bound = zero;
+ goto S460;
+S450:
+ *status = 2;
+ *bound = inf;
+S470:
+S460:
+ ;
+ }
+ else if(4 == *which) {
+/*
+ Computing B
+*/
+ *b = 5.0e0;
+ T12 = zero;
+ T13 = inf;
+ T14 = atol;
+ T15 = tol;
+ dstinv(&T12,&T13,&K8,&K8,&K9,&T14,&T15);
+ *status = 0;
+ dinvr(status,b,&fx,&qleft,&qhi);
+S480:
+ if(!(*status == 1)) goto S510;
+ cumbet(x,y,a,b,&cum,&ccum);
+ if(!qporq) goto S490;
+ fx = cum-*p;
+ goto S500;
+S490:
+ fx = ccum-*q;
+S500:
+ dinvr(status,b,&fx,&qleft,&qhi);
+ goto S480;
+S510:
+ if(!(*status == -1)) goto S540;
+ if(!qleft) goto S520;
+ *status = 1;
+ *bound = zero;
+ goto S530;
+S520:
+ *status = 2;
+ *bound = inf;
+S530:
+ ;
+ }
+S540:
+ return;
+#undef tol
+#undef atol
+#undef zero
+#undef inf
+#undef one
+} /* END */
+
+/***=====================================================================***/
+static void cdfbin(int *which,double *p,double *q,double *s,double *xn,
+ double *pr,double *ompr,int *status,double *bound)
+/**********************************************************************
+
+ void cdfbin(int *which,double *p,double *q,double *s,double *xn,
+ double *pr,double *ompr,int *status,double *bound)
+
+ Cumulative Distribution Function
+ BINomial distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the binomial
+ distribution given values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next four argument
+ values is to be calculated from the others.
+ Legal range: 1..4
+ iwhich = 1 : Calculate P and Q from S,XN,PR and OMPR
+ iwhich = 2 : Calculate S from P,Q,XN,PR and OMPR
+ iwhich = 3 : Calculate XN from P,Q,S,PR and OMPR
+ iwhich = 4 : Calculate PR and OMPR from P,Q,S and XN
+
+ P <--> The cumulation from 0 to S of the binomial distribution.
+ (Probablility of S or fewer successes in XN trials each
+ with probability of success PR.)
+ Input range: [0,1].
+
+ Q <--> 1-P.
+ Input range: [0, 1].
+ P + Q = 1.0.
+
+ S <--> The number of successes observed.
+ Input range: [0, XN]
+ Search range: [0, XN]
+
+ XN <--> The number of binomial trials.
+ Input range: (0, +infinity).
+ Search range: [1E-300, 1E300]
+
+ PR <--> The probability of success in each binomial trial.
+ Input range: [0,1].
+ Search range: [0,1]
+
+ OMPR <--> 1-PR
+ Input range: [0,1].
+ Search range: [0,1]
+ PR + OMPR = 1.0
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+ 4 if PR + OMPR .ne. 1
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Formula 26.5.24 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to reduce the binomial
+ distribution to the cumulative incomplete beta distribution.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+
+**********************************************************************/
+{
+#define atol (1.0e-50)
+#define tol (1.0e-8)
+#define zero (1.0e-300)
+#define inf 1.0e300
+#define one 1.0e0
+static int K1 = 1;
+static double K2 = 0.0e0;
+static double K3 = 0.5e0;
+static double K4 = 5.0e0;
+static double K11 = 1.0e0;
+static double fx,xhi,xlo,cum,ccum,pq,prompr;
+static unsigned long qhi,qleft,qporq;
+static double T5,T6,T7,T8,T9,T10,T12,T13;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 && *which > 4)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 4.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q < 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q < 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 3) goto S130;
+/*
+ XN
+*/
+ if(!(*xn <= 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S130:
+S120:
+ if(*which == 2) goto S170;
+/*
+ S
+*/
+ if(!( *s < 0.0e0 || ( *which != 3 && *s > *xn ))) goto S160;
+ if(!(*s < 0.0e0)) goto S140;
+ *bound = 0.0e0;
+ goto S150;
+S140:
+ *bound = *xn;
+S150:
+ *status = -4;
+ return;
+S170:
+S160:
+ if(*which == 4) goto S210;
+/*
+ PR
+*/
+ if(!(*pr < 0.0e0 || *pr > 1.0e0)) goto S200;
+ if(!(*pr < 0.0e0)) goto S180;
+ *bound = 0.0e0;
+ goto S190;
+S180:
+ *bound = 1.0e0;
+S190:
+ *status = -6;
+ return;
+S210:
+S200:
+ if(*which == 4) goto S250;
+/*
+ OMPR
+*/
+ if(!(*ompr < 0.0e0 || *ompr > 1.0e0)) goto S240;
+ if(!(*ompr < 0.0e0)) goto S220;
+ *bound = 0.0e0;
+ goto S230;
+S220:
+ *bound = 1.0e0;
+S230:
+ *status = -7;
+ return;
+S250:
+S240:
+ if(*which == 1) goto S290;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S280;
+ if(!(pq < 0.0e0)) goto S260;
+ *bound = 0.0e0;
+ goto S270;
+S260:
+ *bound = 1.0e0;
+S270:
+ *status = 3;
+ return;
+S290:
+S280:
+ if(*which == 4) goto S330;
+/*
+ PR + OMPR
+*/
+ prompr = *pr+*ompr;
+ if(!(fabs(prompr-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S320;
+ if(!(prompr < 0.0e0)) goto S300;
+ *bound = 0.0e0;
+ goto S310;
+S300:
+ *bound = 1.0e0;
+S310:
+ *status = 4;
+ return;
+S330:
+S320:
+ if(!(*which == 1)) qporq = *p <= *q;
+/*
+ Select the minimum of P or Q
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P
+*/
+ cumbin(s,xn,pr,ompr,p,q);
+ *status = 0;
+ }
+ else if(2 == *which) {
+/*
+ Calculating S
+*/
+ *s = 5.0e0;
+ T5 = atol;
+ T6 = tol;
+ dstinv(&K2,xn,&K3,&K3,&K4,&T5,&T6);
+ *status = 0;
+ dinvr(status,s,&fx,&qleft,&qhi);
+S340:
+ if(!(*status == 1)) goto S370;
+ cumbin(s,xn,pr,ompr,&cum,&ccum);
+ if(!qporq) goto S350;
+ fx = cum-*p;
+ goto S360;
+S350:
+ fx = ccum-*q;
+S360:
+ dinvr(status,s,&fx,&qleft,&qhi);
+ goto S340;
+S370:
+ if(!(*status == -1)) goto S400;
+ if(!qleft) goto S380;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S390;
+S380:
+ *status = 2;
+ *bound = *xn;
+S400:
+S390:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Calculating XN
+*/
+ *xn = 5.0e0;
+ T7 = zero;
+ T8 = inf;
+ T9 = atol;
+ T10 = tol;
+ dstinv(&T7,&T8,&K3,&K3,&K4,&T9,&T10);
+ *status = 0;
+ dinvr(status,xn,&fx,&qleft,&qhi);
+S410:
+ if(!(*status == 1)) goto S440;
+ cumbin(s,xn,pr,ompr,&cum,&ccum);
+ if(!qporq) goto S420;
+ fx = cum-*p;
+ goto S430;
+S420:
+ fx = ccum-*q;
+S430:
+ dinvr(status,xn,&fx,&qleft,&qhi);
+ goto S410;
+S440:
+ if(!(*status == -1)) goto S470;
+ if(!qleft) goto S450;
+ *status = 1;
+ *bound = zero;
+ goto S460;
+S450:
+ *status = 2;
+ *bound = inf;
+S470:
+S460:
+ ;
+ }
+ else if(4 == *which) {
+/*
+ Calculating PR and OMPR
+*/
+ T12 = atol;
+ T13 = tol;
+ dstzr(&K2,&K11,&T12,&T13);
+ if(!qporq) goto S500;
+ *status = 0;
+ dzror(status,pr,&fx,&xlo,&xhi,&qleft,&qhi);
+ *ompr = one-*pr;
+S480:
+ if(!(*status == 1)) goto S490;
+ cumbin(s,xn,pr,ompr,&cum,&ccum);
+ fx = cum-*p;
+ dzror(status,pr,&fx,&xlo,&xhi,&qleft,&qhi);
+ *ompr = one-*pr;
+ goto S480;
+S490:
+ goto S530;
+S500:
+ *status = 0;
+ dzror(status,ompr,&fx,&xlo,&xhi,&qleft,&qhi);
+ *pr = one-*ompr;
+S510:
+ if(!(*status == 1)) goto S520;
+ cumbin(s,xn,pr,ompr,&cum,&ccum);
+ fx = ccum-*q;
+ dzror(status,ompr,&fx,&xlo,&xhi,&qleft,&qhi);
+ *pr = one-*ompr;
+ goto S510;
+S530:
+S520:
+ if(!(*status == -1)) goto S560;
+ if(!qleft) goto S540;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S550;
+S540:
+ *status = 2;
+ *bound = 1.0e0;
+S550:
+ ;
+ }
+S560:
+ return;
+#undef atol
+#undef tol
+#undef zero
+#undef inf
+#undef one
+} /* END */
+
+/***=====================================================================***/
+static void cdfchi(int *which,double *p,double *q,double *x,double *df,
+ int *status,double *bound)
+/**********************************************************************
+
+ void cdfchi(int *which,double *p,double *q,double *x,double *df,
+ int *status,double *bound)
+
+ Cumulative Distribution Function
+ CHI-Square distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the chi-square
+ distribution given values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next three argument
+ values is to be calculated from the others.
+ Legal range: 1..3
+ iwhich = 1 : Calculate P and Q from X and DF
+ iwhich = 2 : Calculate X from P,Q and DF
+ iwhich = 3 : Calculate DF from P,Q and X
+
+ P <--> The integral from 0 to X of the chi-square
+ distribution.
+ Input range: [0, 1].
+
+ Q <--> 1-P.
+ Input range: (0, 1].
+ P + Q = 1.0.
+
+ X <--> Upper limit of integration of the non-central
+ chi-square distribution.
+ Input range: [0, +infinity).
+ Search range: [0,1E300]
+
+ DF <--> Degrees of freedom of the
+ chi-square distribution.
+ Input range: (0, +infinity).
+ Search range: [ 1E-300, 1E300]
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+ 10 indicates error returned from cumgam. See
+ references in cdfgam
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Formula 26.4.19 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to reduce the chisqure
+ distribution to the incomplete distribution.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+**********************************************************************/
+{
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define zero (1.0e-300)
+#define inf 1.0e300
+static int K1 = 1;
+static double K2 = 0.0e0;
+static double K4 = 0.5e0;
+static double K5 = 5.0e0;
+static double fx,cum,ccum,pq,porq;
+static unsigned long qhi,qleft,qporq;
+static double T3,T6,T7,T8,T9,T10,T11;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 3)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 3.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q <= 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q <= 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 2) goto S130;
+/*
+ X
+*/
+ if(!(*x < 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -4;
+ return;
+S130:
+S120:
+ if(*which == 3) goto S150;
+/*
+ DF
+*/
+ if(!(*df <= 0.0e0)) goto S140;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S150:
+S140:
+ if(*which == 1) goto S190;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S180;
+ if(!(pq < 0.0e0)) goto S160;
+ *bound = 0.0e0;
+ goto S170;
+S160:
+ *bound = 1.0e0;
+S170:
+ *status = 3;
+ return;
+S190:
+S180:
+ if(*which == 1) goto S220;
+/*
+ Select the minimum of P or Q
+*/
+ qporq = *p <= *q;
+ if(!qporq) goto S200;
+ porq = *p;
+ goto S210;
+S200:
+ porq = *q;
+S220:
+S210:
+/*
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P and Q
+*/
+ *status = 0;
+ cumchi(x,df,p,q);
+ if(porq > 1.5e0) {
+ *status = 10;
+ return;
+ }
+ }
+ else if(2 == *which) {
+/*
+ Calculating X
+*/
+ *x = 5.0e0;
+ T3 = inf;
+ T6 = atol;
+ T7 = tol;
+ dstinv(&K2,&T3,&K4,&K4,&K5,&T6,&T7);
+ *status = 0;
+ dinvr(status,x,&fx,&qleft,&qhi);
+S230:
+ if(!(*status == 1)) goto S270;
+ cumchi(x,df,&cum,&ccum);
+ if(!qporq) goto S240;
+ fx = cum-*p;
+ goto S250;
+S240:
+ fx = ccum-*q;
+S250:
+ if(!(fx+porq > 1.5e0)) goto S260;
+ *status = 10;
+ return;
+S260:
+ dinvr(status,x,&fx,&qleft,&qhi);
+ goto S230;
+S270:
+ if(!(*status == -1)) goto S300;
+ if(!qleft) goto S280;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S290;
+S280:
+ *status = 2;
+ *bound = inf;
+S300:
+S290:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Calculating DF
+*/
+ *df = 5.0e0;
+ T8 = zero;
+ T9 = inf;
+ T10 = atol;
+ T11 = tol;
+ dstinv(&T8,&T9,&K4,&K4,&K5,&T10,&T11);
+ *status = 0;
+ dinvr(status,df,&fx,&qleft,&qhi);
+S310:
+ if(!(*status == 1)) goto S350;
+ cumchi(x,df,&cum,&ccum);
+ if(!qporq) goto S320;
+ fx = cum-*p;
+ goto S330;
+S320:
+ fx = ccum-*q;
+S330:
+ if(!(fx+porq > 1.5e0)) goto S340;
+ *status = 10;
+ return;
+S340:
+ dinvr(status,df,&fx,&qleft,&qhi);
+ goto S310;
+S350:
+ if(!(*status == -1)) goto S380;
+ if(!qleft) goto S360;
+ *status = 1;
+ *bound = zero;
+ goto S370;
+S360:
+ *status = 2;
+ *bound = inf;
+S370:
+ ;
+ }
+S380:
+ return;
+#undef tol
+#undef atol
+#undef zero
+#undef inf
+} /* END */
+
+/***=====================================================================***/
+static void cdfchn(int *which,double *p,double *q,double *x,double *df,
+ double *pnonc,int *status,double *bound)
+/**********************************************************************
+
+ void cdfchn(int *which,double *p,double *q,double *x,double *df,
+ double *pnonc,int *status,double *bound)
+
+ Cumulative Distribution Function
+ Non-central Chi-Square
+
+
+ Function
+
+
+ Calculates any one parameter of the non-central chi-square
+ distribution given values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next three argument
+ values is to be calculated from the others.
+ Input range: 1..4
+ iwhich = 1 : Calculate P and Q from X and DF
+ iwhich = 2 : Calculate X from P,DF and PNONC
+ iwhich = 3 : Calculate DF from P,X and PNONC
+ iwhich = 3 : Calculate PNONC from P,X and DF
+
+ P <--> The integral from 0 to X of the non-central chi-square
+ distribution.
+ Input range: [0, 1-1E-16).
+
+ Q <--> 1-P.
+ Q is not used by this subroutine and is only included
+ for similarity with other cdf* routines.
+
+ X <--> Upper limit of integration of the non-central
+ chi-square distribution.
+ Input range: [0, +infinity).
+ Search range: [0,1E300]
+
+ DF <--> Degrees of freedom of the non-central
+ chi-square distribution.
+ Input range: (0, +infinity).
+ Search range: [ 1E-300, 1E300]
+
+ PNONC <--> Non-centrality parameter of the non-central
+ chi-square distribution.
+ Input range: [0, +infinity).
+ Search range: [0,1E4]
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Formula 26.4.25 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to compute the cumulative
+ distribution function.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+
+ WARNING
+
+ The computation time required for this routine is proportional
+ to the noncentrality parameter (PNONC). Very large values of
+ this parameter can consume immense computer resources. This is
+ why the search range is bounded by 10,000.
+
+**********************************************************************/
+{
+#define tent4 1.0e4
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define zero (1.0e-300)
+#define one (1.0e0-1.0e-16)
+#define inf 1.0e300
+static double K1 = 0.0e0;
+static double K3 = 0.5e0;
+static double K4 = 5.0e0;
+static double fx,cum,ccum;
+static unsigned long qhi,qleft;
+static double T2,T5,T6,T7,T8,T9,T10,T11,T12,T13;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 4)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 4.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > one)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = one;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 2) goto S90;
+/*
+ X
+*/
+ if(!(*x < 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ *status = -4;
+ return;
+S90:
+S80:
+ if(*which == 3) goto S110;
+/*
+ DF
+*/
+ if(!(*df <= 0.0e0)) goto S100;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S110:
+S100:
+ if(*which == 4) goto S130;
+/*
+ PNONC
+*/
+ if(!(*pnonc < 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -6;
+ return;
+S130:
+S120:
+/*
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P and Q
+*/
+ cumchn(x,df,pnonc,p,q);
+ *status = 0;
+ }
+ else if(2 == *which) {
+/*
+ Calculating X
+*/
+ *x = 5.0e0;
+ T2 = inf;
+ T5 = atol;
+ T6 = tol;
+ dstinv(&K1,&T2,&K3,&K3,&K4,&T5,&T6);
+ *status = 0;
+ dinvr(status,x,&fx,&qleft,&qhi);
+S140:
+ if(!(*status == 1)) goto S150;
+ cumchn(x,df,pnonc,&cum,&ccum);
+ fx = cum-*p;
+ dinvr(status,x,&fx,&qleft,&qhi);
+ goto S140;
+S150:
+ if(!(*status == -1)) goto S180;
+ if(!qleft) goto S160;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S170;
+S160:
+ *status = 2;
+ *bound = inf;
+S180:
+S170:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Calculating DF
+*/
+ *df = 5.0e0;
+ T7 = zero;
+ T8 = inf;
+ T9 = atol;
+ T10 = tol;
+ dstinv(&T7,&T8,&K3,&K3,&K4,&T9,&T10);
+ *status = 0;
+ dinvr(status,df,&fx,&qleft,&qhi);
+S190:
+ if(!(*status == 1)) goto S200;
+ cumchn(x,df,pnonc,&cum,&ccum);
+ fx = cum-*p;
+ dinvr(status,df,&fx,&qleft,&qhi);
+ goto S190;
+S200:
+ if(!(*status == -1)) goto S230;
+ if(!qleft) goto S210;
+ *status = 1;
+ *bound = zero;
+ goto S220;
+S210:
+ *status = 2;
+ *bound = inf;
+S230:
+S220:
+ ;
+ }
+ else if(4 == *which) {
+/*
+ Calculating PNONC
+*/
+ *pnonc = 5.0e0;
+ T11 = tent4;
+ T12 = atol;
+ T13 = tol;
+ dstinv(&K1,&T11,&K3,&K3,&K4,&T12,&T13);
+ *status = 0;
+ dinvr(status,pnonc,&fx,&qleft,&qhi);
+S240:
+ if(!(*status == 1)) goto S250;
+ cumchn(x,df,pnonc,&cum,&ccum);
+ fx = cum-*p;
+ dinvr(status,pnonc,&fx,&qleft,&qhi);
+ goto S240;
+S250:
+ if(!(*status == -1)) goto S280;
+ if(!qleft) goto S260;
+ *status = 1;
+ *bound = zero;
+ goto S270;
+S260:
+ *status = 2;
+ *bound = tent4;
+S270:
+ ;
+ }
+S280:
+ return;
+#undef tent4
+#undef tol
+#undef atol
+#undef zero
+#undef one
+#undef inf
+} /* END */
+
+/***=====================================================================***/
+static void cdff(int *which,double *p,double *q,double *f,double *dfn,
+ double *dfd,int *status,double *bound)
+/**********************************************************************
+
+ void cdff(int *which,double *p,double *q,double *f,double *dfn,
+ double *dfd,int *status,double *bound)
+
+ Cumulative Distribution Function
+ F distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the F distribution
+ given values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next four argument
+ values is to be calculated from the others.
+ Legal range: 1..4
+ iwhich = 1 : Calculate P and Q from F,DFN and DFD
+ iwhich = 2 : Calculate F from P,Q,DFN and DFD
+ iwhich = 3 : Calculate DFN from P,Q,F and DFD
+ iwhich = 4 : Calculate DFD from P,Q,F and DFN
+
+ P <--> The integral from 0 to F of the f-density.
+ Input range: [0,1].
+
+ Q <--> 1-P.
+ Input range: (0, 1].
+ P + Q = 1.0.
+
+ F <--> Upper limit of integration of the f-density.
+ Input range: [0, +infinity).
+ Search range: [0,1E300]
+
+ DFN < --> Degrees of freedom of the numerator sum of squares.
+ Input range: (0, +infinity).
+ Search range: [ 1E-300, 1E300]
+
+ DFD < --> Degrees of freedom of the denominator sum of squares.
+ Input range: (0, +infinity).
+ Search range: [ 1E-300, 1E300]
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Formula 26.6.2 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to reduce the computation
+ of the cumulative distribution function for the F variate to
+ that of an incomplete beta.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+ WARNING
+
+ The value of the cumulative F distribution is not necessarily
+ monotone in either degrees of freedom. There thus may be two
+ values that provide a given CDF value. This routine assumes
+ monotonicity and will find an arbitrary one of the two values.
+
+**********************************************************************/
+{
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define zero (1.0e-300)
+#define inf 1.0e300
+static int K1 = 1;
+static double K2 = 0.0e0;
+static double K4 = 0.5e0;
+static double K5 = 5.0e0;
+static double pq,fx,cum,ccum;
+static unsigned long qhi,qleft,qporq;
+static double T3,T6,T7,T8,T9,T10,T11,T12,T13,T14,T15;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 4)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 4.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q <= 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q <= 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 2) goto S130;
+/*
+ F
+*/
+ if(!(*f < 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -4;
+ return;
+S130:
+S120:
+ if(*which == 3) goto S150;
+/*
+ DFN
+*/
+ if(!(*dfn <= 0.0e0)) goto S140;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S150:
+S140:
+ if(*which == 4) goto S170;
+/*
+ DFD
+*/
+ if(!(*dfd <= 0.0e0)) goto S160;
+ *bound = 0.0e0;
+ *status = -6;
+ return;
+S170:
+S160:
+ if(*which == 1) goto S210;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S200;
+ if(!(pq < 0.0e0)) goto S180;
+ *bound = 0.0e0;
+ goto S190;
+S180:
+ *bound = 1.0e0;
+S190:
+ *status = 3;
+ return;
+S210:
+S200:
+ if(!(*which == 1)) qporq = *p <= *q;
+/*
+ Select the minimum of P or Q
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P
+*/
+ cumf(f,dfn,dfd,p,q);
+ *status = 0;
+ }
+ else if(2 == *which) {
+/*
+ Calculating F
+*/
+ *f = 5.0e0;
+ T3 = inf;
+ T6 = atol;
+ T7 = tol;
+ dstinv(&K2,&T3,&K4,&K4,&K5,&T6,&T7);
+ *status = 0;
+ dinvr(status,f,&fx,&qleft,&qhi);
+S220:
+ if(!(*status == 1)) goto S250;
+ cumf(f,dfn,dfd,&cum,&ccum);
+ if(!qporq) goto S230;
+ fx = cum-*p;
+ goto S240;
+S230:
+ fx = ccum-*q;
+S240:
+ dinvr(status,f,&fx,&qleft,&qhi);
+ goto S220;
+S250:
+ if(!(*status == -1)) goto S280;
+ if(!qleft) goto S260;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S270;
+S260:
+ *status = 2;
+ *bound = inf;
+S280:
+S270:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Calculating DFN
+*/
+ *dfn = 5.0e0;
+ T8 = zero;
+ T9 = inf;
+ T10 = atol;
+ T11 = tol;
+ dstinv(&T8,&T9,&K4,&K4,&K5,&T10,&T11);
+ *status = 0;
+ dinvr(status,dfn,&fx,&qleft,&qhi);
+S290:
+ if(!(*status == 1)) goto S320;
+ cumf(f,dfn,dfd,&cum,&ccum);
+ if(!qporq) goto S300;
+ fx = cum-*p;
+ goto S310;
+S300:
+ fx = ccum-*q;
+S310:
+ dinvr(status,dfn,&fx,&qleft,&qhi);
+ goto S290;
+S320:
+ if(!(*status == -1)) goto S350;
+ if(!qleft) goto S330;
+ *status = 1;
+ *bound = zero;
+ goto S340;
+S330:
+ *status = 2;
+ *bound = inf;
+S350:
+S340:
+ ;
+ }
+ else if(4 == *which) {
+/*
+ Calculating DFD
+*/
+ *dfd = 5.0e0;
+ T12 = zero;
+ T13 = inf;
+ T14 = atol;
+ T15 = tol;
+ dstinv(&T12,&T13,&K4,&K4,&K5,&T14,&T15);
+ *status = 0;
+ dinvr(status,dfd,&fx,&qleft,&qhi);
+S360:
+ if(!(*status == 1)) goto S390;
+ cumf(f,dfn,dfd,&cum,&ccum);
+ if(!qporq) goto S370;
+ fx = cum-*p;
+ goto S380;
+S370:
+ fx = ccum-*q;
+S380:
+ dinvr(status,dfd,&fx,&qleft,&qhi);
+ goto S360;
+S390:
+ if(!(*status == -1)) goto S420;
+ if(!qleft) goto S400;
+ *status = 1;
+ *bound = zero;
+ goto S410;
+S400:
+ *status = 2;
+ *bound = inf;
+S410:
+ ;
+ }
+S420:
+ return;
+#undef tol
+#undef atol
+#undef zero
+#undef inf
+} /* END */
+
+/***=====================================================================***/
+static void cdffnc(int *which,double *p,double *q,double *f,double *dfn,
+ double *dfd,double *phonc,int *status,double *bound)
+/**********************************************************************
+
+ void cdffnc(int *which,double *p,double *q,double *f,double *dfn,
+ double *dfd,double *phonc,int *status,double *bound)
+
+ Cumulative Distribution Function
+ Non-central F distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the Non-central F
+ distribution given values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next five argument
+ values is to be calculated from the others.
+ Legal range: 1..5
+ iwhich = 1 : Calculate P and Q from F,DFN,DFD and PNONC
+ iwhich = 2 : Calculate F from P,Q,DFN,DFD and PNONC
+ iwhich = 3 : Calculate DFN from P,Q,F,DFD and PNONC
+ iwhich = 4 : Calculate DFD from P,Q,F,DFN and PNONC
+ iwhich = 5 : Calculate PNONC from P,Q,F,DFN and DFD
+
+ P <--> The integral from 0 to F of the non-central f-density.
+ Input range: [0,1-1E-16).
+
+ Q <--> 1-P.
+ Q is not used by this subroutine and is only included
+ for similarity with other cdf* routines.
+
+ F <--> Upper limit of integration of the non-central f-density.
+ Input range: [0, +infinity).
+ Search range: [0,1E300]
+
+ DFN < --> Degrees of freedom of the numerator sum of squares.
+ Input range: (0, +infinity).
+ Search range: [ 1E-300, 1E300]
+
+ DFD < --> Degrees of freedom of the denominator sum of squares.
+ Must be in range: (0, +infinity).
+ Input range: (0, +infinity).
+ Search range: [ 1E-300, 1E300]
+
+ PNONC <-> The non-centrality parameter
+ Input range: [0,infinity)
+ Search range: [0,1E4]
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Formula 26.6.20 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to compute the cumulative
+ distribution function.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+ WARNING
+
+ The computation time required for this routine is proportional
+ to the noncentrality parameter (PNONC). Very large values of
+ this parameter can consume immense computer resources. This is
+ why the search range is bounded by 10,000.
+
+ WARNING
+
+ The value of the cumulative noncentral F distribution is not
+ necessarily monotone in either degrees of freedom. There thus
+ may be two values that provide a given CDF value. This routine
+ assumes monotonicity and will find an arbitrary one of the two
+ values.
+
+**********************************************************************/
+{
+#define tent4 1.0e4
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define zero (1.0e-300)
+#define one (1.0e0-1.0e-16)
+#define inf 1.0e300
+static double K1 = 0.0e0;
+static double K3 = 0.5e0;
+static double K4 = 5.0e0;
+static double fx,cum,ccum;
+static unsigned long qhi,qleft;
+static double T2,T5,T6,T7,T8,T9,T10,T11,T12,T13,T14,T15,T16,T17;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 5)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 5.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > one)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = one;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 2) goto S90;
+/*
+ F
+*/
+ if(!(*f < 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ *status = -4;
+ return;
+S90:
+S80:
+ if(*which == 3) goto S110;
+/*
+ DFN
+*/
+ if(!(*dfn <= 0.0e0)) goto S100;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S110:
+S100:
+ if(*which == 4) goto S130;
+/*
+ DFD
+*/
+ if(!(*dfd <= 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -6;
+ return;
+S130:
+S120:
+ if(*which == 5) goto S150;
+/*
+ PHONC
+*/
+ if(!(*phonc < 0.0e0)) goto S140;
+ *bound = 0.0e0;
+ *status = -7;
+ return;
+S150:
+S140:
+/*
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P
+*/
+ cumfnc(f,dfn,dfd,phonc,p,q);
+ *status = 0;
+ }
+ else if(2 == *which) {
+/*
+ Calculating F
+*/
+ *f = 5.0e0;
+ T2 = inf;
+ T5 = atol;
+ T6 = tol;
+ dstinv(&K1,&T2,&K3,&K3,&K4,&T5,&T6);
+ *status = 0;
+ dinvr(status,f,&fx,&qleft,&qhi);
+S160:
+ if(!(*status == 1)) goto S170;
+ cumfnc(f,dfn,dfd,phonc,&cum,&ccum);
+ fx = cum-*p;
+ dinvr(status,f,&fx,&qleft,&qhi);
+ goto S160;
+S170:
+ if(!(*status == -1)) goto S200;
+ if(!qleft) goto S180;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S190;
+S180:
+ *status = 2;
+ *bound = inf;
+S200:
+S190:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Calculating DFN
+*/
+ *dfn = 5.0e0;
+ T7 = zero;
+ T8 = inf;
+ T9 = atol;
+ T10 = tol;
+ dstinv(&T7,&T8,&K3,&K3,&K4,&T9,&T10);
+ *status = 0;
+ dinvr(status,dfn,&fx,&qleft,&qhi);
+S210:
+ if(!(*status == 1)) goto S220;
+ cumfnc(f,dfn,dfd,phonc,&cum,&ccum);
+ fx = cum-*p;
+ dinvr(status,dfn,&fx,&qleft,&qhi);
+ goto S210;
+S220:
+ if(!(*status == -1)) goto S250;
+ if(!qleft) goto S230;
+ *status = 1;
+ *bound = zero;
+ goto S240;
+S230:
+ *status = 2;
+ *bound = inf;
+S250:
+S240:
+ ;
+ }
+ else if(4 == *which) {
+/*
+ Calculating DFD
+*/
+ *dfd = 5.0e0;
+ T11 = zero;
+ T12 = inf;
+ T13 = atol;
+ T14 = tol;
+ dstinv(&T11,&T12,&K3,&K3,&K4,&T13,&T14);
+ *status = 0;
+ dinvr(status,dfd,&fx,&qleft,&qhi);
+S260:
+ if(!(*status == 1)) goto S270;
+ cumfnc(f,dfn,dfd,phonc,&cum,&ccum);
+ fx = cum-*p;
+ dinvr(status,dfd,&fx,&qleft,&qhi);
+ goto S260;
+S270:
+ if(!(*status == -1)) goto S300;
+ if(!qleft) goto S280;
+ *status = 1;
+ *bound = zero;
+ goto S290;
+S280:
+ *status = 2;
+ *bound = inf;
+S300:
+S290:
+ ;
+ }
+ else if(5 == *which) {
+/*
+ Calculating PHONC
+*/
+ *phonc = 5.0e0;
+ T15 = tent4;
+ T16 = atol;
+ T17 = tol;
+ dstinv(&K1,&T15,&K3,&K3,&K4,&T16,&T17);
+ *status = 0;
+ dinvr(status,phonc,&fx,&qleft,&qhi);
+S310:
+ if(!(*status == 1)) goto S320;
+ cumfnc(f,dfn,dfd,phonc,&cum,&ccum);
+ fx = cum-*p;
+ dinvr(status,phonc,&fx,&qleft,&qhi);
+ goto S310;
+S320:
+ if(!(*status == -1)) goto S350;
+ if(!qleft) goto S330;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S340;
+S330:
+ *status = 2;
+ *bound = tent4;
+S340:
+ ;
+ }
+S350:
+ return;
+#undef tent4
+#undef tol
+#undef atol
+#undef zero
+#undef one
+#undef inf
+} /* END */
+
+/***=====================================================================***/
+static void cdfgam(int *which,double *p,double *q,double *x,double *shape,
+ double *scale,int *status,double *bound)
+/**********************************************************************
+
+ void cdfgam(int *which,double *p,double *q,double *x,double *shape,
+ double *scale,int *status,double *bound)
+
+ Cumulative Distribution Function
+ GAMma Distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the gamma
+ distribution given values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next four argument
+ values is to be calculated from the others.
+ Legal range: 1..4
+ iwhich = 1 : Calculate P and Q from X,SHAPE and SCALE
+ iwhich = 2 : Calculate X from P,Q,SHAPE and SCALE
+ iwhich = 3 : Calculate SHAPE from P,Q,X and SCALE
+ iwhich = 4 : Calculate SCALE from P,Q,X and SHAPE
+
+ P <--> The integral from 0 to X of the gamma density.
+ Input range: [0,1].
+
+ Q <--> 1-P.
+ Input range: (0, 1].
+ P + Q = 1.0.
+
+ X <--> The upper limit of integration of the gamma density.
+ Input range: [0, +infinity).
+ Search range: [0,1E300]
+
+ SHAPE <--> The shape parameter of the gamma density.
+ Input range: (0, +infinity).
+ Search range: [1E-300,1E300]
+
+ SCALE <--> The scale parameter of the gamma density.
+ Input range: (0, +infinity).
+ Search range: (1E-300,1E300]
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+ 10 if the gamma or inverse gamma routine cannot
+ compute the answer. Usually happens only for
+ X and SHAPE very large (gt 1E10 or more)
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Cumulative distribution function (P) is calculated directly by
+ the code associated with:
+
+ DiDinato, A. R. and Morris, A. H. Computation of the incomplete
+ gamma function ratios and their inverse. ACM Trans. Math.
+ Softw. 12 (1986), 377-393.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+
+ Note
+
+
+
+ The gamma density is proportional to
+ T**(SHAPE - 1) * EXP(- SCALE * T)
+
+**********************************************************************/
+{
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define zero (1.0e-300)
+#define inf 1.0e300
+static int K1 = 1;
+static double K5 = 0.5e0;
+static double K6 = 5.0e0;
+static double xx,fx,xscale,cum,ccum,pq,porq;
+static int ierr;
+static unsigned long qhi,qleft,qporq;
+static double T2,T3,T4,T7,T8,T9;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 4)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 4.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q <= 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q <= 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 2) goto S130;
+/*
+ X
+*/
+ if(!(*x < 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -4;
+ return;
+S130:
+S120:
+ if(*which == 3) goto S150;
+/*
+ SHAPE
+*/
+ if(!(*shape <= 0.0e0)) goto S140;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S150:
+S140:
+ if(*which == 4) goto S170;
+/*
+ SCALE
+*/
+ if(!(*scale <= 0.0e0)) goto S160;
+ *bound = 0.0e0;
+ *status = -6;
+ return;
+S170:
+S160:
+ if(*which == 1) goto S210;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S200;
+ if(!(pq < 0.0e0)) goto S180;
+ *bound = 0.0e0;
+ goto S190;
+S180:
+ *bound = 1.0e0;
+S190:
+ *status = 3;
+ return;
+S210:
+S200:
+ if(*which == 1) goto S240;
+/*
+ Select the minimum of P or Q
+*/
+ qporq = *p <= *q;
+ if(!qporq) goto S220;
+ porq = *p;
+ goto S230;
+S220:
+ porq = *q;
+S240:
+S230:
+/*
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P
+*/
+ *status = 0;
+ xscale = *x**scale;
+ cumgam(&xscale,shape,p,q);
+ if(porq > 1.5e0) *status = 10;
+ }
+ else if(2 == *which) {
+/*
+ Computing X
+*/
+ T2 = -1.0e0;
+ gaminv(shape,&xx,&T2,p,q,&ierr);
+ if(ierr < 0.0e0) {
+ *status = 10;
+ return;
+ }
+ else {
+ *x = xx/ *scale;
+ *status = 0;
+ }
+ }
+ else if(3 == *which) {
+/*
+ Computing SHAPE
+*/
+ *shape = 5.0e0;
+ xscale = *x**scale;
+ T3 = zero;
+ T4 = inf;
+ T7 = atol;
+ T8 = tol;
+ dstinv(&T3,&T4,&K5,&K5,&K6,&T7,&T8);
+ *status = 0;
+ dinvr(status,shape,&fx,&qleft,&qhi);
+S250:
+ if(!(*status == 1)) goto S290;
+ cumgam(&xscale,shape,&cum,&ccum);
+ if(!qporq) goto S260;
+ fx = cum-*p;
+ goto S270;
+S260:
+ fx = ccum-*q;
+S270:
+ if(!(( qporq && cum > 1.5e0 ) || (!qporq && ccum > 1.5e0 ))) goto S280;
+ *status = 10;
+ return;
+S280:
+ dinvr(status,shape,&fx,&qleft,&qhi);
+ goto S250;
+S290:
+ if(!(*status == -1)) goto S320;
+ if(!qleft) goto S300;
+ *status = 1;
+ *bound = zero;
+ goto S310;
+S300:
+ *status = 2;
+ *bound = inf;
+S320:
+S310:
+ ;
+ }
+ else if(4 == *which) {
+/*
+ Computing SCALE
+*/
+ T9 = -1.0e0;
+ gaminv(shape,&xx,&T9,p,q,&ierr);
+ if(ierr < 0.0e0) {
+ *status = 10;
+ return;
+ }
+ else {
+ *scale = xx/ *x;
+ *status = 0;
+ }
+ }
+ return;
+#undef tol
+#undef atol
+#undef zero
+#undef inf
+} /* END */
+
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+/***=====================================================================***/
+static void cdfnbn(int *which,double *p,double *q,double *s,double *xn,
+ double *pr,double *ompr,int *status,double *bound)
+/**********************************************************************
+
+ void cdfnbn(int *which,double *p,double *q,double *s,double *xn,
+ double *pr,double *ompr,int *status,double *bound)
+
+ Cumulative Distribution Function
+ Negative BiNomial distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the negative binomial
+ distribution given values for the others.
+
+ The cumulative negative binomial distribution returns the
+ probability that there will be F or fewer failures before the
+ XNth success in binomial trials each of which has probability of
+ success PR.
+
+ The individual term of the negative binomial is the probability of
+ S failures before XN successes and is
+ Choose( S, XN+S-1 ) * PR^(XN) * (1-PR)^S
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next four argument
+ values is to be calculated from the others.
+ Legal range: 1..4
+ iwhich = 1 : Calculate P and Q from S,XN,PR and OMPR
+ iwhich = 2 : Calculate S from P,Q,XN,PR and OMPR
+ iwhich = 3 : Calculate XN from P,Q,S,PR and OMPR
+ iwhich = 4 : Calculate PR and OMPR from P,Q,S and XN
+
+ P <--> The cumulation from 0 to S of the negative
+ binomial distribution.
+ Input range: [0,1].
+
+ Q <--> 1-P.
+ Input range: (0, 1].
+ P + Q = 1.0.
+
+ S <--> The upper limit of cumulation of the binomial distribution.
+ There are F or fewer failures before the XNth success.
+ Input range: [0, +infinity).
+ Search range: [0, 1E300]
+
+ XN <--> The number of successes.
+ Input range: [0, +infinity).
+ Search range: [0, 1E300]
+
+ PR <--> The probability of success in each binomial trial.
+ Input range: [0,1].
+ Search range: [0,1].
+
+ OMPR <--> 1-PR
+ Input range: [0,1].
+ Search range: [0,1]
+ PR + OMPR = 1.0
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+ 4 if PR + OMPR .ne. 1
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Formula 26.5.26 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to reduce calculation of
+ the cumulative distribution function to that of an incomplete
+ beta.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+**********************************************************************/
+{
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define inf 1.0e300
+#define one 1.0e0
+static int K1 = 1;
+static double K2 = 0.0e0;
+static double K4 = 0.5e0;
+static double K5 = 5.0e0;
+static double K11 = 1.0e0;
+static double fx,xhi,xlo,pq,prompr,cum,ccum;
+static unsigned long qhi,qleft,qporq;
+static double T3,T6,T7,T8,T9,T10,T12,T13;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 4)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 4.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q <= 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q <= 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 2) goto S130;
+/*
+ S
+*/
+ if(!(*s < 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -4;
+ return;
+S130:
+S120:
+ if(*which == 3) goto S150;
+/*
+ XN
+*/
+ if(!(*xn < 0.0e0)) goto S140;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S150:
+S140:
+ if(*which == 4) goto S190;
+/*
+ PR
+*/
+ if(!(*pr < 0.0e0 || *pr > 1.0e0)) goto S180;
+ if(!(*pr < 0.0e0)) goto S160;
+ *bound = 0.0e0;
+ goto S170;
+S160:
+ *bound = 1.0e0;
+S170:
+ *status = -6;
+ return;
+S190:
+S180:
+ if(*which == 4) goto S230;
+/*
+ OMPR
+*/
+ if(!(*ompr < 0.0e0 || *ompr > 1.0e0)) goto S220;
+ if(!(*ompr < 0.0e0)) goto S200;
+ *bound = 0.0e0;
+ goto S210;
+S200:
+ *bound = 1.0e0;
+S210:
+ *status = -7;
+ return;
+S230:
+S220:
+ if(*which == 1) goto S270;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S260;
+ if(!(pq < 0.0e0)) goto S240;
+ *bound = 0.0e0;
+ goto S250;
+S240:
+ *bound = 1.0e0;
+S250:
+ *status = 3;
+ return;
+S270:
+S260:
+ if(*which == 4) goto S310;
+/*
+ PR + OMPR
+*/
+ prompr = *pr+*ompr;
+ if(!(fabs(prompr-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S300;
+ if(!(prompr < 0.0e0)) goto S280;
+ *bound = 0.0e0;
+ goto S290;
+S280:
+ *bound = 1.0e0;
+S290:
+ *status = 4;
+ return;
+S310:
+S300:
+ if(!(*which == 1)) qporq = *p <= *q;
+/*
+ Select the minimum of P or Q
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P
+*/
+ cumnbn(s,xn,pr,ompr,p,q);
+ *status = 0;
+ }
+ else if(2 == *which) {
+/*
+ Calculating S
+*/
+ *s = 5.0e0;
+ T3 = inf;
+ T6 = atol;
+ T7 = tol;
+ dstinv(&K2,&T3,&K4,&K4,&K5,&T6,&T7);
+ *status = 0;
+ dinvr(status,s,&fx,&qleft,&qhi);
+S320:
+ if(!(*status == 1)) goto S350;
+ cumnbn(s,xn,pr,ompr,&cum,&ccum);
+ if(!qporq) goto S330;
+ fx = cum-*p;
+ goto S340;
+S330:
+ fx = ccum-*q;
+S340:
+ dinvr(status,s,&fx,&qleft,&qhi);
+ goto S320;
+S350:
+ if(!(*status == -1)) goto S380;
+ if(!qleft) goto S360;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S370;
+S360:
+ *status = 2;
+ *bound = inf;
+S380:
+S370:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Calculating XN
+*/
+ *xn = 5.0e0;
+ T8 = inf;
+ T9 = atol;
+ T10 = tol;
+ dstinv(&K2,&T8,&K4,&K4,&K5,&T9,&T10);
+ *status = 0;
+ dinvr(status,xn,&fx,&qleft,&qhi);
+S390:
+ if(!(*status == 1)) goto S420;
+ cumnbn(s,xn,pr,ompr,&cum,&ccum);
+ if(!qporq) goto S400;
+ fx = cum-*p;
+ goto S410;
+S400:
+ fx = ccum-*q;
+S410:
+ dinvr(status,xn,&fx,&qleft,&qhi);
+ goto S390;
+S420:
+ if(!(*status == -1)) goto S450;
+ if(!qleft) goto S430;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S440;
+S430:
+ *status = 2;
+ *bound = inf;
+S450:
+S440:
+ ;
+ }
+ else if(4 == *which) {
+/*
+ Calculating PR and OMPR
+*/
+ T12 = atol;
+ T13 = tol;
+ dstzr(&K2,&K11,&T12,&T13);
+ if(!qporq) goto S480;
+ *status = 0;
+ dzror(status,pr,&fx,&xlo,&xhi,&qleft,&qhi);
+ *ompr = one-*pr;
+S460:
+ if(!(*status == 1)) goto S470;
+ cumnbn(s,xn,pr,ompr,&cum,&ccum);
+ fx = cum-*p;
+ dzror(status,pr,&fx,&xlo,&xhi,&qleft,&qhi);
+ *ompr = one-*pr;
+ goto S460;
+S470:
+ goto S510;
+S480:
+ *status = 0;
+ dzror(status,ompr,&fx,&xlo,&xhi,&qleft,&qhi);
+ *pr = one-*ompr;
+S490:
+ if(!(*status == 1)) goto S500;
+ cumnbn(s,xn,pr,ompr,&cum,&ccum);
+ fx = ccum-*q;
+ dzror(status,ompr,&fx,&xlo,&xhi,&qleft,&qhi);
+ *pr = one-*ompr;
+ goto S490;
+S510:
+S500:
+ if(!(*status == -1)) goto S540;
+ if(!qleft) goto S520;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S530;
+S520:
+ *status = 2;
+ *bound = 1.0e0;
+S530:
+ ;
+ }
+S540:
+ return;
+#undef tol
+#undef atol
+#undef inf
+#undef one
+} /* END */
+
+/***=====================================================================***/
+static void cdfnor(int *which,double *p,double *q,double *x,double *mean,
+ double *sd,int *status,double *bound)
+/**********************************************************************
+
+ void cdfnor(int *which,double *p,double *q,double *x,double *mean,
+ double *sd,int *status,double *bound)
+
+ Cumulative Distribution Function
+ NORmal distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the normal
+ distribution given values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which of the next parameter
+ values is to be calculated using values of the others.
+ Legal range: 1..4
+ iwhich = 1 : Calculate P and Q from X,MEAN and SD
+ iwhich = 2 : Calculate X from P,Q,MEAN and SD
+ iwhich = 3 : Calculate MEAN from P,Q,X and SD
+ iwhich = 4 : Calculate SD from P,Q,X and MEAN
+
+ P <--> The integral from -infinity to X of the normal density.
+ Input range: (0,1].
+
+ Q <--> 1-P.
+ Input range: (0, 1].
+ P + Q = 1.0.
+
+ X < --> Upper limit of integration of the normal-density.
+ Input range: ( -infinity, +infinity)
+
+ MEAN <--> The mean of the normal density.
+ Input range: (-infinity, +infinity)
+
+ SD <--> Standard Deviation of the normal density.
+ Input range: (0, +infinity).
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+
+
+ A slightly modified version of ANORM from
+
+ Cody, W.D. (1993). "ALGORITHM 715: SPECFUN - A Portabel FORTRAN
+ Package of Special Function Routines and Test Drivers"
+ acm Transactions on Mathematical Software. 19, 22-32.
+
+ is used to calulate the cumulative standard normal distribution.
+
+ The rational functions from pages 90-95 of Kennedy and Gentle,
+ Statistical Computing, Marcel Dekker, NY, 1980 are used as
+ starting values to Newton's Iterations which compute the inverse
+ standard normal. Therefore no searches are necessary for any
+ parameter.
+
+ For X < -15, the asymptotic expansion for the normal is used as
+ the starting value in finding the inverse standard normal.
+ This is formula 26.2.12 of Abramowitz and Stegun.
+
+
+ Note
+
+
+ The normal density is proportional to
+ exp( - 0.5 * (( X - MEAN)/SD)**2)
+
+**********************************************************************/
+{
+static int K1 = 1;
+static double z,pq;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ *status = 0;
+ if(!(*which < 1 || *which > 4)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 4.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p <= 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p <= 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q <= 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q <= 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 1) goto S150;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S140;
+ if(!(pq < 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ goto S130;
+S120:
+ *bound = 1.0e0;
+S130:
+ *status = 3;
+ return;
+S150:
+S140:
+ if(*which == 4) goto S170;
+/*
+ SD
+*/
+ if(!(*sd <= 0.0e0)) goto S160;
+ *bound = 0.0e0;
+ *status = -6;
+ return;
+S170:
+S160:
+/*
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Computing P
+*/
+ z = (*x-*mean)/ *sd;
+ cumnor(&z,p,q);
+ }
+ else if(2 == *which) {
+/*
+ Computing X
+*/
+ z = dinvnr(p,q);
+ *x = *sd*z+*mean;
+ }
+ else if(3 == *which) {
+/*
+ Computing the MEAN
+*/
+ z = dinvnr(p,q);
+ *mean = *x-*sd*z;
+ }
+ else if(4 == *which) {
+/*
+ Computing SD
+*/
+ z = dinvnr(p,q);
+ *sd = (*x-*mean)/z;
+ }
+ return;
+} /* END */
+#endif /* defined(__COMPILE_UNUSED_FUNCTIONS__) */
+
+/***=====================================================================***/
+static void cdfpoi(int *which,double *p,double *q,double *s,double *xlam,
+ int *status,double *bound)
+/**********************************************************************
+
+ void cdfpoi(int *which,double *p,double *q,double *s,double *xlam,
+ int *status,double *bound)
+
+ Cumulative Distribution Function
+ POIsson distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the Poisson
+ distribution given values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which argument
+ value is to be calculated from the others.
+ Legal range: 1..3
+ iwhich = 1 : Calculate P and Q from S and XLAM
+ iwhich = 2 : Calculate A from P,Q and XLAM
+ iwhich = 3 : Calculate XLAM from P,Q and S
+
+ P <--> The cumulation from 0 to S of the poisson density.
+ Input range: [0,1].
+
+ Q <--> 1-P.
+ Input range: (0, 1].
+ P + Q = 1.0.
+
+ S <--> Upper limit of cumulation of the Poisson.
+ Input range: [0, +infinity).
+ Search range: [0,1E300]
+
+ XLAM <--> Mean of the Poisson distribution.
+ Input range: [0, +infinity).
+ Search range: [0,1E300]
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Formula 26.4.21 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to reduce the computation
+ of the cumulative distribution function to that of computing a
+ chi-square, hence an incomplete gamma function.
+
+ Cumulative distribution function (P) is calculated directly.
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+**********************************************************************/
+{
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define inf 1.0e300
+static int K1 = 1;
+static double K2 = 0.0e0;
+static double K4 = 0.5e0;
+static double K5 = 5.0e0;
+static double fx,cum,ccum,pq;
+static unsigned long qhi,qleft,qporq;
+static double T3,T6,T7,T8,T9,T10;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 3)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 3.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p < 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p < 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q <= 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q <= 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 2) goto S130;
+/*
+ S
+*/
+ if(!(*s < 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -4;
+ return;
+S130:
+S120:
+ if(*which == 3) goto S150;
+/*
+ XLAM
+*/
+ if(!(*xlam < 0.0e0)) goto S140;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S150:
+S140:
+ if(*which == 1) goto S190;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S180;
+ if(!(pq < 0.0e0)) goto S160;
+ *bound = 0.0e0;
+ goto S170;
+S160:
+ *bound = 1.0e0;
+S170:
+ *status = 3;
+ return;
+S190:
+S180:
+ if(!(*which == 1)) qporq = *p <= *q;
+/*
+ Select the minimum of P or Q
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Calculating P
+*/
+ cumpoi(s,xlam,p,q);
+ *status = 0;
+ }
+ else if(2 == *which) {
+/*
+ Calculating S
+*/
+ *s = 5.0e0;
+ T3 = inf;
+ T6 = atol;
+ T7 = tol;
+ dstinv(&K2,&T3,&K4,&K4,&K5,&T6,&T7);
+ *status = 0;
+ dinvr(status,s,&fx,&qleft,&qhi);
+S200:
+ if(!(*status == 1)) goto S230;
+ cumpoi(s,xlam,&cum,&ccum);
+ if(!qporq) goto S210;
+ fx = cum-*p;
+ goto S220;
+S210:
+ fx = ccum-*q;
+S220:
+ dinvr(status,s,&fx,&qleft,&qhi);
+ goto S200;
+S230:
+ if(!(*status == -1)) goto S260;
+ if(!qleft) goto S240;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S250;
+S240:
+ *status = 2;
+ *bound = inf;
+S260:
+S250:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Calculating XLAM
+*/
+ *xlam = 5.0e0;
+ T8 = inf;
+ T9 = atol;
+ T10 = tol;
+ dstinv(&K2,&T8,&K4,&K4,&K5,&T9,&T10);
+ *status = 0;
+ dinvr(status,xlam,&fx,&qleft,&qhi);
+S270:
+ if(!(*status == 1)) goto S300;
+ cumpoi(s,xlam,&cum,&ccum);
+ if(!qporq) goto S280;
+ fx = cum-*p;
+ goto S290;
+S280:
+ fx = ccum-*q;
+S290:
+ dinvr(status,xlam,&fx,&qleft,&qhi);
+ goto S270;
+S300:
+ if(!(*status == -1)) goto S330;
+ if(!qleft) goto S310;
+ *status = 1;
+ *bound = 0.0e0;
+ goto S320;
+S310:
+ *status = 2;
+ *bound = inf;
+S320:
+ ;
+ }
+S330:
+ return;
+#undef tol
+#undef atol
+#undef inf
+} /* END */
+
+/***=====================================================================***/
+static void cdft(int *which,double *p,double *q,double *t,double *df,
+ int *status,double *bound)
+/**********************************************************************
+
+ void cdft(int *which,double *p,double *q,double *t,double *df,
+ int *status,double *bound)
+
+ Cumulative Distribution Function
+ T distribution
+
+
+ Function
+
+
+ Calculates any one parameter of the t distribution given
+ values for the others.
+
+
+ Arguments
+
+
+ WHICH --> Integer indicating which argument
+ values is to be calculated from the others.
+ Legal range: 1..3
+ iwhich = 1 : Calculate P and Q from T and DF
+ iwhich = 2 : Calculate T from P,Q and DF
+ iwhich = 3 : Calculate DF from P,Q and T
+
+ P <--> The integral from -infinity to t of the t-density.
+ Input range: (0,1].
+
+ Q <--> 1-P.
+ Input range: (0, 1].
+ P + Q = 1.0.
+
+ T <--> Upper limit of integration of the t-density.
+ Input range: ( -infinity, +infinity).
+ Search range: [ -1E300, 1E300 ]
+
+ DF <--> Degrees of freedom of the t-distribution.
+ Input range: (0 , +infinity).
+ Search range: [1e-300, 1E10]
+
+ STATUS <-- 0 if calculation completed correctly
+ -I if input parameter number I is out of range
+ 1 if answer appears to be lower than lowest
+ search bound
+ 2 if answer appears to be higher than greatest
+ search bound
+ 3 if P + Q .ne. 1
+
+ BOUND <-- Undefined if STATUS is 0
+
+ Bound exceeded by parameter number I if STATUS
+ is negative.
+
+ Lower search bound if STATUS is 1.
+
+ Upper search bound if STATUS is 2.
+
+
+ Method
+
+
+ Formula 26.5.27 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to reduce the computation
+ of the cumulative distribution function to that of an incomplete
+ beta.
+
+ Computation of other parameters involve a seach for a value that
+ produces the desired value of P. The search relies on the
+ monotinicity of P with the other parameter.
+
+**********************************************************************/
+{
+#define tol (1.0e-8)
+#define atol (1.0e-50)
+#define zero (1.0e-300)
+#define inf 1.0e300
+#define maxdf 1.0e10
+static int K1 = 1;
+static double K4 = 0.5e0;
+static double K5 = 5.0e0;
+static double fx,cum,ccum,pq;
+static unsigned long qhi,qleft,qporq;
+static double T2,T3,T6,T7,T8,T9,T10,T11;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Check arguments
+*/
+ if(!(*which < 1 || *which > 3)) goto S30;
+ if(!(*which < 1)) goto S10;
+ *bound = 1.0e0;
+ goto S20;
+S10:
+ *bound = 3.0e0;
+S20:
+ *status = -1;
+ return;
+S30:
+ if(*which == 1) goto S70;
+/*
+ P
+*/
+ if(!(*p <= 0.0e0 || *p > 1.0e0)) goto S60;
+ if(!(*p <= 0.0e0)) goto S40;
+ *bound = 0.0e0;
+ goto S50;
+S40:
+ *bound = 1.0e0;
+S50:
+ *status = -2;
+ return;
+S70:
+S60:
+ if(*which == 1) goto S110;
+/*
+ Q
+*/
+ if(!(*q <= 0.0e0 || *q > 1.0e0)) goto S100;
+ if(!(*q <= 0.0e0)) goto S80;
+ *bound = 0.0e0;
+ goto S90;
+S80:
+ *bound = 1.0e0;
+S90:
+ *status = -3;
+ return;
+S110:
+S100:
+ if(*which == 3) goto S130;
+/*
+ DF
+*/
+ if(!(*df <= 0.0e0)) goto S120;
+ *bound = 0.0e0;
+ *status = -5;
+ return;
+S130:
+S120:
+ if(*which == 1) goto S170;
+/*
+ P + Q
+*/
+ pq = *p+*q;
+ if(!(fabs(pq-0.5e0-0.5e0) > 3.0e0*spmpar(&K1))) goto S160;
+ if(!(pq < 0.0e0)) goto S140;
+ *bound = 0.0e0;
+ goto S150;
+S140:
+ *bound = 1.0e0;
+S150:
+ *status = 3;
+ return;
+S170:
+S160:
+ if(!(*which == 1)) qporq = *p <= *q;
+/*
+ Select the minimum of P or Q
+ Calculate ANSWERS
+*/
+ if(1 == *which) {
+/*
+ Computing P and Q
+*/
+ cumt(t,df,p,q);
+ *status = 0;
+ }
+ else if(2 == *which) {
+/*
+ Computing T
+ .. Get initial approximation for T
+*/
+ *t = dt1(p,q,df);
+ T2 = -inf;
+ T3 = inf;
+ T6 = atol;
+ T7 = tol;
+ dstinv(&T2,&T3,&K4,&K4,&K5,&T6,&T7);
+ *status = 0;
+ dinvr(status,t,&fx,&qleft,&qhi);
+S180:
+ if(!(*status == 1)) goto S210;
+ cumt(t,df,&cum,&ccum);
+ if(!qporq) goto S190;
+ fx = cum-*p;
+ goto S200;
+S190:
+ fx = ccum-*q;
+S200:
+ dinvr(status,t,&fx,&qleft,&qhi);
+ goto S180;
+S210:
+ if(!(*status == -1)) goto S240;
+ if(!qleft) goto S220;
+ *status = 1;
+ *bound = -inf;
+ goto S230;
+S220:
+ *status = 2;
+ *bound = inf;
+S240:
+S230:
+ ;
+ }
+ else if(3 == *which) {
+/*
+ Computing DF
+*/
+ *df = 5.0e0;
+ T8 = zero;
+ T9 = maxdf;
+ T10 = atol;
+ T11 = tol;
+ dstinv(&T8,&T9,&K4,&K4,&K5,&T10,&T11);
+ *status = 0;
+ dinvr(status,df,&fx,&qleft,&qhi);
+S250:
+ if(!(*status == 1)) goto S280;
+ cumt(t,df,&cum,&ccum);
+ if(!qporq) goto S260;
+ fx = cum-*p;
+ goto S270;
+S260:
+ fx = ccum-*q;
+S270:
+ dinvr(status,df,&fx,&qleft,&qhi);
+ goto S250;
+S280:
+ if(!(*status == -1)) goto S310;
+ if(!qleft) goto S290;
+ *status = 1;
+ *bound = zero;
+ goto S300;
+S290:
+ *status = 2;
+ *bound = maxdf;
+S300:
+ ;
+ }
+S310:
+ return;
+#undef tol
+#undef atol
+#undef zero
+#undef inf
+#undef maxdf
+} /* END */
+
+/***=====================================================================***/
+static void cumbet(double *x,double *y,double *a,double *b,double *cum,
+ double *ccum)
+/*
+**********************************************************************
+
+ void cumbet(double *x,double *y,double *a,double *b,double *cum,
+ double *ccum)
+
+ Double precision cUMulative incomplete BETa distribution
+
+
+ Function
+
+
+ Calculates the cdf to X of the incomplete beta distribution
+ with parameters a and b. This is the integral from 0 to x
+ of (1/B(a,b))*f(t)) where f(t) = t**(a-1) * (1-t)**(b-1)
+
+
+ Arguments
+
+
+ X --> Upper limit of integration.
+ X is DOUBLE PRECISION
+
+ Y --> 1 - X.
+ Y is DOUBLE PRECISION
+
+ A --> First parameter of the beta distribution.
+ A is DOUBLE PRECISION
+
+ B --> Second parameter of the beta distribution.
+ B is DOUBLE PRECISION
+
+ CUM <-- Cumulative incomplete beta distribution.
+ CUM is DOUBLE PRECISION
+
+ CCUM <-- Compliment of Cumulative incomplete beta distribution.
+ CCUM is DOUBLE PRECISION
+
+
+ Method
+
+
+ Calls the routine BRATIO.
+
+ References
+
+ Didonato, Armido R. and Morris, Alfred H. Jr. (1992) Algorithim
+ 708 Significant Digit Computation of the Incomplete Beta Function
+ Ratios. ACM ToMS, Vol.18, No. 3, Sept. 1992, 360-373.
+
+**********************************************************************
+*/
+{
+static int ierr;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(!(*x <= 0.0e0)) goto S10;
+ *cum = 0.0e0;
+ *ccum = 1.0e0;
+ return;
+S10:
+ if(!(*y <= 0.0e0)) goto S20;
+ *cum = 1.0e0;
+ *ccum = 0.0e0;
+ return;
+S20:
+ bratio(a,b,x,y,cum,ccum,&ierr);
+/*
+ Call bratio routine
+*/
+ return;
+} /* END */
+
+/***=====================================================================***/
+static void cumbin(double *s,double *xn,double *pr,double *ompr,
+ double *cum,double *ccum)
+/*
+**********************************************************************
+
+ void cumbin(double *s,double *xn,double *pr,double *ompr,
+ double *cum,double *ccum)
+
+ CUmulative BINomial distribution
+
+
+ Function
+
+
+ Returns the probability of 0 to S successes in XN binomial
+ trials, each of which has a probability of success, PBIN.
+
+
+ Arguments
+
+
+ S --> The upper limit of cumulation of the binomial distribution.
+ S is DOUBLE PRECISION
+
+ XN --> The number of binomial trials.
+ XN is DOUBLE PRECISIO
+
+ PBIN --> The probability of success in each binomial trial.
+ PBIN is DOUBLE PRECIS
+
+ OMPR --> 1 - PBIN
+ OMPR is DOUBLE PRECIS
+
+ CUM <-- Cumulative binomial distribution.
+ CUM is DOUBLE PRECISI
+
+ CCUM <-- Compliment of Cumulative binomial distribution.
+ CCUM is DOUBLE PRECIS
+
+
+ Method
+
+
+ Formula 26.5.24 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to reduce the binomial
+ distribution to the cumulative beta distribution.
+
+**********************************************************************
+*/
+{
+static double T1,T2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(!(*s < *xn)) goto S10;
+ T1 = *s+1.0e0;
+ T2 = *xn-*s;
+ cumbet(pr,ompr,&T1,&T2,ccum,cum);
+ goto S20;
+S10:
+ *cum = 1.0e0;
+ *ccum = 0.0e0;
+S20:
+ return;
+} /* END */
+
+/***=====================================================================***/
+static void cumchi(double *x,double *df,double *cum,double *ccum)
+/*
+**********************************************************************
+
+ void cumchi(double *x,double *df,double *cum,double *ccum)
+ CUMulative of the CHi-square distribution
+
+
+ Function
+
+
+ Calculates the cumulative chi-square distribution.
+
+
+ Arguments
+
+
+ X --> Upper limit of integration of the
+ chi-square distribution.
+ X is DOUBLE PRECISION
+
+ DF --> Degrees of freedom of the
+ chi-square distribution.
+ DF is DOUBLE PRECISION
+
+ CUM <-- Cumulative chi-square distribution.
+ CUM is DOUBLE PRECISIO
+
+ CCUM <-- Compliment of Cumulative chi-square distribution.
+ CCUM is DOUBLE PRECISI
+
+
+ Method
+
+
+ Calls incomplete gamma function (CUMGAM)
+
+**********************************************************************
+*/
+{
+static double a,xx;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ a = *df*0.5e0;
+ xx = *x*0.5e0;
+ cumgam(&xx,&a,cum,ccum);
+ return;
+} /* END */
+
+/***=====================================================================***/
+static void cumchn(double *x,double *df,double *pnonc,double *cum,
+ double *ccum)
+/*
+**********************************************************************
+
+ void cumchn(double *x,double *df,double *pnonc,double *cum,
+ double *ccum)
+
+ CUMulative of the Non-central CHi-square distribution
+
+
+ Function
+
+
+ Calculates the cumulative non-central chi-square
+ distribution, i.e., the probability that a random variable
+ which follows the non-central chi-square distribution, with
+ non-centrality parameter PNONC and continuous degrees of
+ freedom DF, is less than or equal to X.
+
+
+ Arguments
+
+
+ X --> Upper limit of integration of the non-central
+ chi-square distribution.
+ X is DOUBLE PRECISION
+
+ DF --> Degrees of freedom of the non-central
+ chi-square distribution.
+ DF is DOUBLE PRECISION
+
+ PNONC --> Non-centrality parameter of the non-central
+ chi-square distribution.
+ PNONC is DOUBLE PRECIS
+
+ CUM <-- Cumulative non-central chi-square distribution.
+ CUM is DOUBLE PRECISIO
+
+ CCUM <-- Compliment of Cumulative non-central chi-square distribut
+ CCUM is DOUBLE PRECISI
+
+
+ Method
+
+
+ Uses formula 26.4.25 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions, US NBS (1966) to calculate the
+ non-central chi-square.
+
+
+ Variables
+
+
+ EPS --- Convergence criterion. The sum stops when a
+ term is less than EPS*SUM.
+ EPS is DOUBLE PRECISIO
+
+ NTIRED --- Maximum number of terms to be evaluated
+ in each sum.
+ NTIRED is INTEGER
+
+ QCONV --- .TRUE. if convergence achieved -
+ i.e., program did not stop on NTIRED criterion.
+ QCONV is LOGICAL
+
+ CCUM <-- Compliment of Cumulative non-central
+ chi-square distribution.
+ CCUM is DOUBLE PRECISI
+
+**********************************************************************
+*/
+{
+#define dg(i) (*df+2.0e0*(double)(i))
+#define qsmall(xx) (int)(sum < 1.0e-20 || (xx) < eps*sum)
+#define qtired(i) (int)((i) > ntired)
+static double eps = 1.0e-5;
+static int ntired = 1000;
+static double adj,centaj,centwt,chid2,dfd2,lcntaj,lcntwt,lfact,pcent,pterm,sum,
+ sumadj,term,wt,xnonc;
+static int i,icent,iterb,iterf;
+static double T1,T2,T3;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(!(*x <= 0.0e0)) goto S10;
+ *cum = 0.0e0;
+ *ccum = 1.0e0;
+ return;
+S10:
+ if(!(*pnonc <= 1.0e-10)) goto S20;
+/*
+ When non-centrality parameter is (essentially) zero,
+ use cumulative chi-square distribution
+*/
+ cumchi(x,df,cum,ccum);
+ return;
+S20:
+ xnonc = *pnonc/2.0e0;
+/*
+**********************************************************************
+ The following code calcualtes the weight, chi-square, and
+ adjustment term for the central term in the infinite series.
+ The central term is the one in which the poisson weight is
+ greatest. The adjustment term is the amount that must
+ be subtracted from the chi-square to move up two degrees
+ of freedom.
+**********************************************************************
+*/
+ icent = fifidint(xnonc);
+ if(icent == 0) icent = 1;
+ chid2 = *x/2.0e0;
+/*
+ Calculate central weight term
+*/
+ T1 = (double)(icent+1);
+ lfact = alngam(&T1);
+ lcntwt = -xnonc+(double)icent*log(xnonc)-lfact;
+ centwt = exp(lcntwt);
+/*
+ Calculate central chi-square
+*/
+ T2 = dg(icent);
+ cumchi(x,&T2,&pcent,ccum);
+/*
+ Calculate central adjustment term
+*/
+ dfd2 = dg(icent)/2.0e0;
+ T3 = 1.0e0+dfd2;
+ lfact = alngam(&T3);
+ lcntaj = dfd2*log(chid2)-chid2-lfact;
+ centaj = exp(lcntaj);
+ sum = centwt*pcent;
+/*
+**********************************************************************
+ Sum backwards from the central term towards zero.
+ Quit whenever either
+ (1) the zero term is reached, or
+ (2) the term gets small relative to the sum, or
+ (3) More than NTIRED terms are totaled.
+**********************************************************************
+*/
+ iterb = 0;
+ sumadj = 0.0e0;
+ adj = centaj;
+ wt = centwt;
+ i = icent;
+ goto S40;
+S30:
+ if(qtired(iterb) || qsmall(term) || i == 0) goto S50;
+S40:
+ dfd2 = dg(i)/2.0e0;
+/*
+ Adjust chi-square for two fewer degrees of freedom.
+ The adjusted value ends up in PTERM.
+*/
+ adj = adj*dfd2/chid2;
+ sumadj += adj;
+ pterm = pcent+sumadj;
+/*
+ Adjust poisson weight for J decreased by one
+*/
+ wt *= ((double)i/xnonc);
+ term = wt*pterm;
+ sum += term;
+ i -= 1;
+ iterb += 1;
+ goto S30;
+S50:
+ iterf = 0;
+/*
+**********************************************************************
+ Now sum forward from the central term towards infinity.
+ Quit when either
+ (1) the term gets small relative to the sum, or
+ (2) More than NTIRED terms are totaled.
+**********************************************************************
+*/
+ sumadj = adj = centaj;
+ wt = centwt;
+ i = icent;
+ goto S70;
+S60:
+ if(qtired(iterf) || qsmall(term)) goto S80;
+S70:
+/*
+ Update weights for next higher J
+*/
+ wt *= (xnonc/(double)(i+1));
+/*
+ Calculate PTERM and add term to sum
+*/
+ pterm = pcent-sumadj;
+ term = wt*pterm;
+ sum += term;
+/*
+ Update adjustment term for DF for next iteration
+*/
+ i += 1;
+ dfd2 = dg(i)/2.0e0;
+ adj = adj*chid2/dfd2;
+ sumadj += adj;
+ iterf += 1;
+ goto S60;
+S80:
+ *cum = sum;
+ *ccum = 0.5e0+(0.5e0-*cum);
+ return;
+#undef dg
+#undef qsmall
+#undef qtired
+} /* END */
+
+/***=====================================================================***/
+static void cumf(double *f,double *dfn,double *dfd,double *cum,double *ccum)
+/*
+**********************************************************************
+
+ void cumf(double *f,double *dfn,double *dfd,double *cum,double *ccum)
+ CUMulative F distribution
+
+
+ Function
+
+
+ Computes the integral from 0 to F of the f-density with DFN
+ and DFD degrees of freedom.
+
+
+ Arguments
+
+
+ F --> Upper limit of integration of the f-density.
+ F is DOUBLE PRECISION
+
+ DFN --> Degrees of freedom of the numerator sum of squares.
+ DFN is DOUBLE PRECISI
+
+ DFD --> Degrees of freedom of the denominator sum of squares.
+ DFD is DOUBLE PRECISI
+
+ CUM <-- Cumulative f distribution.
+ CUM is DOUBLE PRECISI
+
+ CCUM <-- Compliment of Cumulative f distribution.
+ CCUM is DOUBLE PRECIS
+
+
+ Method
+
+
+ Formula 26.5.28 of Abramowitz and Stegun is used to reduce
+ the cumulative F to a cumulative beta distribution.
+
+
+ Note
+
+
+ If F is less than or equal to 0, 0 is returned.
+
+**********************************************************************
+*/
+{
+#define half 0.5e0
+#define done 1.0e0
+static double dsum,prod,xx,yy;
+static int ierr;
+static double T1,T2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(!(*f <= 0.0e0)) goto S10;
+ *cum = 0.0e0;
+ *ccum = 1.0e0;
+ return;
+S10:
+ prod = *dfn**f;
+/*
+ XX is such that the incomplete beta with parameters
+ DFD/2 and DFN/2 evaluated at XX is 1 - CUM or CCUM
+ YY is 1 - XX
+ Calculate the smaller of XX and YY accurately
+*/
+ dsum = *dfd+prod;
+ xx = *dfd/dsum;
+ if(xx > half) {
+ yy = prod/dsum;
+ xx = done-yy;
+ }
+ else yy = done-xx;
+ T1 = *dfd*half;
+ T2 = *dfn*half;
+ bratio(&T1,&T2,&xx,&yy,ccum,cum,&ierr);
+ return;
+#undef half
+#undef done
+} /* END */
+
+/***=====================================================================***/
+static void cumfnc(double *f,double *dfn,double *dfd,double *pnonc,
+ double *cum,double *ccum)
+/*
+**********************************************************************
+
+ F -NON- -C-ENTRAL F DISTRIBUTION
+
+
+
+ Function
+
+
+ COMPUTES NONCENTRAL F DISTRIBUTION WITH DFN AND DFD
+ DEGREES OF FREEDOM AND NONCENTRALITY PARAMETER PNONC
+
+
+ Arguments
+
+
+ X --> UPPER LIMIT OF INTEGRATION OF NONCENTRAL F IN EQUATION
+
+ DFN --> DEGREES OF FREEDOM OF NUMERATOR
+
+ DFD --> DEGREES OF FREEDOM OF DENOMINATOR
+
+ PNONC --> NONCENTRALITY PARAMETER.
+
+ CUM <-- CUMULATIVE NONCENTRAL F DISTRIBUTION
+
+ CCUM <-- COMPLIMENT OF CUMMULATIVE
+
+
+ Method
+
+
+ USES FORMULA 26.6.20 OF REFERENCE FOR INFINITE SERIES.
+ SERIES IS CALCULATED BACKWARD AND FORWARD FROM J = LAMBDA/2
+ (THIS IS THE TERM WITH THE LARGEST POISSON WEIGHT) UNTIL
+ THE CONVERGENCE CRITERION IS MET.
+
+ FOR SPEED, THE INCOMPLETE BETA FUNCTIONS ARE EVALUATED
+ BY FORMULA 26.5.16.
+
+
+ REFERENCE
+
+
+ HANDBOOD OF MATHEMATICAL FUNCTIONS
+ EDITED BY MILTON ABRAMOWITZ AND IRENE A. STEGUN
+ NATIONAL BUREAU OF STANDARDS APPLIED MATEMATICS SERIES - 55
+ MARCH 1965
+ P 947, EQUATIONS 26.6.17, 26.6.18
+
+
+ Note
+
+
+ THE SUM CONTINUES UNTIL A SUCCEEDING TERM IS LESS THAN EPS
+ TIMES THE SUM (OR THE SUM IS LESS THAN 1.0E-20). EPS IS
+ SET TO 1.0E-4 IN A DATA STATEMENT WHICH CAN BE CHANGED.
+
+**********************************************************************
+*/
+{
+#define qsmall(x) (int)(sum < 1.0e-20 || (x) < eps*sum)
+#define half 0.5e0
+#define done 1.0e0
+static double eps = 1.0e-4;
+static double dsum,dummy,prod,xx,yy,adn,aup,b,betdn,betup,centwt,dnterm,sum,
+ upterm,xmult,xnonc;
+static int i,icent,ierr;
+static double T1,T2,T3,T4,T5,T6;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(!(*f <= 0.0e0)) goto S10;
+ *cum = 0.0e0;
+ *ccum = 1.0e0;
+ return;
+S10:
+ if(!(*pnonc < 1.0e-10)) goto S20;
+/*
+ Handle case in which the non-centrality parameter is
+ (essentially) zero.
+*/
+ cumf(f,dfn,dfd,cum,ccum);
+ return;
+S20:
+ xnonc = *pnonc/2.0e0;
+/*
+ Calculate the central term of the poisson weighting factor.
+*/
+ icent = xnonc;
+ if(icent == 0) icent = 1;
+/*
+ Compute central weight term
+*/
+ T1 = (double)(icent+1);
+ centwt = exp(-xnonc+(double)icent*log(xnonc)-alngam(&T1));
+/*
+ Compute central incomplete beta term
+ Assure that minimum of arg to beta and 1 - arg is computed
+ accurately.
+*/
+ prod = *dfn**f;
+ dsum = *dfd+prod;
+ yy = *dfd/dsum;
+ if(yy > half) {
+ xx = prod/dsum;
+ yy = done-xx;
+ }
+ else xx = done-yy;
+ T2 = *dfn*half+(double)icent;
+ T3 = *dfd*half;
+ bratio(&T2,&T3,&xx,&yy,&betdn,&dummy,&ierr);
+ adn = *dfn/2.0e0+(double)icent;
+ aup = adn;
+ b = *dfd/2.0e0;
+ betup = betdn;
+ sum = centwt*betdn;
+/*
+ Now sum terms backward from icent until convergence or all done
+*/
+ xmult = centwt;
+ i = icent;
+ T4 = adn+b;
+ T5 = adn+1.0e0;
+ dnterm = exp(alngam(&T4)-alngam(&T5)-alngam(&b)+adn*log(xx)+b*log(yy));
+S30:
+ if(qsmall(xmult*betdn) || i <= 0) goto S40;
+ xmult *= ((double)i/xnonc);
+ i -= 1;
+ adn -= 1.0;
+ dnterm = (adn+1.0)/((adn+b)*xx)*dnterm;
+ betdn += dnterm;
+ sum += (xmult*betdn);
+ goto S30;
+S40:
+ i = icent+1;
+/*
+ Now sum forwards until convergence
+*/
+ xmult = centwt;
+ if(aup-1.0+b == 0) upterm = exp(-alngam(&aup)-alngam(&b)+(aup-1.0)*log(xx)+
+ b*log(yy));
+ else {
+ T6 = aup-1.0+b;
+ upterm = exp(alngam(&T6)-alngam(&aup)-alngam(&b)+(aup-1.0)*log(xx)+b*
+ log(yy));
+ }
+ goto S60;
+S50:
+ if(qsmall(xmult*betup)) goto S70;
+S60:
+ xmult *= (xnonc/(double)i);
+ i += 1;
+ aup += 1.0;
+ upterm = (aup+b-2.0e0)*xx/(aup-1.0)*upterm;
+ betup -= upterm;
+ sum += (xmult*betup);
+ goto S50;
+S70:
+ *cum = sum;
+ *ccum = 0.5e0+(0.5e0-*cum);
+ return;
+#undef qsmall
+#undef half
+#undef done
+} /* END */
+
+/***=====================================================================***/
+static void cumgam(double *x,double *a,double *cum,double *ccum)
+/*
+**********************************************************************
+
+ void cumgam(double *x,double *a,double *cum,double *ccum)
+ Double precision cUMulative incomplete GAMma distribution
+
+
+ Function
+
+
+ Computes the cumulative of the incomplete gamma
+ distribution, i.e., the integral from 0 to X of
+ (1/GAM(A))*EXP(-T)*T**(A-1) DT
+ where GAM(A) is the complete gamma function of A, i.e.,
+ GAM(A) = integral from 0 to infinity of
+ EXP(-T)*T**(A-1) DT
+
+
+ Arguments
+
+
+ X --> The upper limit of integration of the incomplete gamma.
+ X is DOUBLE PRECISION
+
+ A --> The shape parameter of the incomplete gamma.
+ A is DOUBLE PRECISION
+
+ CUM <-- Cumulative incomplete gamma distribution.
+ CUM is DOUBLE PRECISION
+
+ CCUM <-- Compliment of Cumulative incomplete gamma distribution.
+ CCUM is DOUBLE PRECISIO
+
+
+ Method
+
+
+ Calls the routine GRATIO.
+
+**********************************************************************
+*/
+{
+static int K1 = 0;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(!(*x <= 0.0e0)) goto S10;
+ *cum = 0.0e0;
+ *ccum = 1.0e0;
+ return;
+S10:
+ gratio(a,x,cum,ccum,&K1);
+/*
+ Call gratio routine
+*/
+ return;
+} /* END */
+
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+/***=====================================================================***/
+static void cumnbn(double *s,double *xn,double *pr,double *ompr,
+ double *cum,double *ccum)
+/*
+**********************************************************************
+
+ void cumnbn(double *s,double *xn,double *pr,double *ompr,
+ double *cum,double *ccum)
+
+ CUmulative Negative BINomial distribution
+
+
+ Function
+
+
+ Returns the probability that it there will be S or fewer failures
+ before there are XN successes, with each binomial trial having
+ a probability of success PR.
+
+ Prob(# failures = S | XN successes, PR) =
+ ( XN + S - 1 )
+ ( ) * PR^XN * (1-PR)^S
+ ( S )
+
+
+ Arguments
+
+
+ S --> The number of failures
+ S is DOUBLE PRECISION
+
+ XN --> The number of successes
+ XN is DOUBLE PRECISIO
+
+ PR --> The probability of success in each binomial trial.
+ PR is DOUBLE PRECISIO
+
+ OMPR --> 1 - PR
+ OMPR is DOUBLE PRECIS
+
+ CUM <-- Cumulative negative binomial distribution.
+ CUM is DOUBLE PRECISI
+
+ CCUM <-- Compliment of Cumulative negative binomial distribution.
+ CCUM is DOUBLE PRECIS
+
+
+ Method
+
+
+ Formula 26.5.26 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions (1966) is used to reduce the negative
+ binomial distribution to the cumulative beta distribution.
+
+**********************************************************************
+*/
+{
+static double T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ T1 = *s+1.e0;
+ cumbet(pr,ompr,xn,&T1,cum,ccum);
+ return;
+} /* END */
+#endif /*defined(__COMPILE_UNUSED_FUNCTIONS__)*/
+
+/***=====================================================================***/
+static void cumnor(double *arg,double *result,double *ccum)
+/*
+**********************************************************************
+
+ void cumnor(double *arg,double *result,double *ccum)
+
+
+ Function
+
+
+ Computes the cumulative of the normal distribution, i.e.,
+ the integral from -infinity to x of
+ (1/sqrt(2*pi)) exp(-u*u/2) du
+
+ X --> Upper limit of integration.
+ X is DOUBLE PRECISION
+
+ RESULT <-- Cumulative normal distribution.
+ RESULT is DOUBLE PRECISION
+
+ CCUM <-- Compliment of Cumulative normal distribution.
+ CCUM is DOUBLE PRECISION
+
+ Renaming of function ANORM from:
+
+ Cody, W.D. (1993). "ALGORITHM 715: SPECFUN - A Portabel FORTRAN
+ Package of Special Function Routines and Test Drivers"
+ acm Transactions on Mathematical Software. 19, 22-32.
+
+ with slight modifications to return ccum and to deal with
+ machine constants.
+
+**********************************************************************
+ Original Comments:
+------------------------------------------------------------------
+
+ This function evaluates the normal distribution function:
+
+ / x
+ 1 | -t*t/2
+ P(x) = ----------- | e dt
+ sqrt(2 pi) |
+ /-oo
+
+ The main computation evaluates near-minimax approximations
+ derived from those in "Rational Chebyshev approximations for
+ the error function" by W. J. Cody, Math. Comp., 1969, 631-637.
+ This transportable program uses rational functions that
+ theoretically approximate the normal distribution function to
+ at least 18 significant decimal digits. The accuracy achieved
+ depends on the arithmetic system, the compiler, the intrinsic
+ functions, and proper selection of the machine-dependent
+ constants.
+
+*******************************************************************
+*******************************************************************
+
+ Explanation of machine-dependent constants.
+
+ MIN = smallest machine representable number.
+
+ EPS = argument below which anorm(x) may be represented by
+ 0.5 and above which x*x will not underflow.
+ A conservative value is the largest machine number X
+ such that 1.0 + X = 1.0 to machine precision.
+*******************************************************************
+*******************************************************************
+
+ Error returns
+
+ The program returns ANORM = 0 for ARG .LE. XLOW.
+
+
+ Intrinsic functions required are:
+
+ ABS, AINT, EXP
+
+
+ Author: W. J. Cody
+ Mathematics and Computer Science Division
+ Argonne National Laboratory
+ Argonne, IL 60439
+
+ Latest modification: March 15, 1992
+
+------------------------------------------------------------------
+*/
+{
+static double a[5] = {
+ 2.2352520354606839287e00,1.6102823106855587881e02,1.0676894854603709582e03,
+ 1.8154981253343561249e04,6.5682337918207449113e-2
+};
+static double b[4] = {
+ 4.7202581904688241870e01,9.7609855173777669322e02,1.0260932208618978205e04,
+ 4.5507789335026729956e04
+};
+static double c[9] = {
+ 3.9894151208813466764e-1,8.8831497943883759412e00,9.3506656132177855979e01,
+ 5.9727027639480026226e02,2.4945375852903726711e03,6.8481904505362823326e03,
+ 1.1602651437647350124e04,9.8427148383839780218e03,1.0765576773720192317e-8
+};
+static double d[8] = {
+ 2.2266688044328115691e01,2.3538790178262499861e02,1.5193775994075548050e03,
+ 6.4855582982667607550e03,1.8615571640885098091e04,3.4900952721145977266e04,
+ 3.8912003286093271411e04,1.9685429676859990727e04
+};
+static double half = 0.5e0;
+static double p[6] = {
+ 2.1589853405795699e-1,1.274011611602473639e-1,2.2235277870649807e-2,
+ 1.421619193227893466e-3,2.9112874951168792e-5,2.307344176494017303e-2
+};
+static double one = 1.0e0;
+static double q[5] = {
+ 1.28426009614491121e00,4.68238212480865118e-1,6.59881378689285515e-2,
+ 3.78239633202758244e-3,7.29751555083966205e-5
+};
+static double sixten = 1.60e0;
+static double sqrpi = 3.9894228040143267794e-1;
+static double thrsh = 0.66291e0;
+static double root32 = 5.656854248e0;
+static double zero = 0.0e0;
+static int K1 = 1;
+static int K2 = 2;
+static int i;
+static double del,eps,temp,x,xden,xnum,y,xsq,min;
+/*
+------------------------------------------------------------------
+ Machine dependent constants
+------------------------------------------------------------------
+*/
+ eps = spmpar(&K1)*0.5e0;
+ min = spmpar(&K2);
+ x = *arg;
+ y = fabs(x);
+ if(y <= thrsh) {
+/*
+------------------------------------------------------------------
+ Evaluate anorm for |X| <= 0.66291
+------------------------------------------------------------------
+*/
+ xsq = zero;
+ if(y > eps) xsq = x*x;
+ xnum = a[4]*xsq;
+ xden = xsq;
+ for(i=0; i<3; i++) {
+ xnum = (xnum+a[i])*xsq;
+ xden = (xden+b[i])*xsq;
+ }
+ *result = x*(xnum+a[3])/(xden+b[3]);
+ temp = *result;
+ *result = half+temp;
+ *ccum = half-temp;
+ }
+/*
+------------------------------------------------------------------
+ Evaluate anorm for 0.66291 <= |X| <= sqrt(32)
+------------------------------------------------------------------
+*/
+ else if(y <= root32) {
+ xnum = c[8]*y;
+ xden = y;
+ for(i=0; i<7; i++) {
+ xnum = (xnum+c[i])*y;
+ xden = (xden+d[i])*y;
+ }
+ *result = (xnum+c[7])/(xden+d[7]);
+ xsq = fifdint(y*sixten)/sixten;
+ del = (y-xsq)*(y+xsq);
+ *result = exp(-(xsq*xsq*half))*exp(-(del*half))**result;
+ *ccum = one-*result;
+ if(x > zero) {
+ temp = *result;
+ *result = *ccum;
+ *ccum = temp;
+ }
+ }
+/*
+------------------------------------------------------------------
+ Evaluate anorm for |X| > sqrt(32)
+------------------------------------------------------------------
+*/
+ else {
+ *result = zero;
+ xsq = one/(x*x);
+ xnum = p[5]*xsq;
+ xden = xsq;
+ for(i=0; i<4; i++) {
+ xnum = (xnum+p[i])*xsq;
+ xden = (xden+q[i])*xsq;
+ }
+ *result = xsq*(xnum+p[4])/(xden+q[4]);
+ *result = (sqrpi-*result)/y;
+ xsq = fifdint(x*sixten)/sixten;
+ del = (x-xsq)*(x+xsq);
+ *result = exp(-(xsq*xsq*half))*exp(-(del*half))**result;
+ *ccum = one-*result;
+ if(x > zero) {
+ temp = *result;
+ *result = *ccum;
+ *ccum = temp;
+ }
+ }
+ if(*result < min) *result = 0.0e0;
+/*
+------------------------------------------------------------------
+ Fix up for negative argument, erf, etc.
+------------------------------------------------------------------
+----------Last card of ANORM ----------
+*/
+ if(*ccum < min) *ccum = 0.0e0;
+} /* END */
+
+/***=====================================================================***/
+static void cumpoi(double *s,double *xlam,double *cum,double *ccum)
+/*
+**********************************************************************
+
+ void cumpoi(double *s,double *xlam,double *cum,double *ccum)
+ CUMulative POIsson distribution
+
+
+ Function
+
+
+ Returns the probability of S or fewer events in a Poisson
+ distribution with mean XLAM.
+
+
+ Arguments
+
+
+ S --> Upper limit of cumulation of the Poisson.
+ S is DOUBLE PRECISION
+
+ XLAM --> Mean of the Poisson distribution.
+ XLAM is DOUBLE PRECIS
+
+ CUM <-- Cumulative poisson distribution.
+ CUM is DOUBLE PRECISION
+
+ CCUM <-- Compliment of Cumulative poisson distribution.
+ CCUM is DOUBLE PRECIS
+
+
+ Method
+
+
+ Uses formula 26.4.21 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions to reduce the cumulative Poisson to
+ the cumulative chi-square distribution.
+
+**********************************************************************
+*/
+{
+static double chi,df;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ df = 2.0e0*(*s+1.0e0);
+ chi = 2.0e0**xlam;
+ cumchi(&chi,&df,ccum,cum);
+ return;
+} /* END */
+
+/***=====================================================================***/
+static void cumt(double *t,double *df,double *cum,double *ccum)
+/*
+**********************************************************************
+
+ void cumt(double *t,double *df,double *cum,double *ccum)
+ CUMulative T-distribution
+
+
+ Function
+
+
+ Computes the integral from -infinity to T of the t-density.
+
+
+ Arguments
+
+
+ T --> Upper limit of integration of the t-density.
+ T is DOUBLE PRECISION
+
+ DF --> Degrees of freedom of the t-distribution.
+ DF is DOUBLE PRECISIO
+
+ CUM <-- Cumulative t-distribution.
+ CCUM is DOUBLE PRECIS
+
+ CCUM <-- Compliment of Cumulative t-distribution.
+ CCUM is DOUBLE PRECIS
+
+
+ Method
+
+
+ Formula 26.5.27 of Abramowitz and Stegun, Handbook of
+ Mathematical Functions is used to reduce the t-distribution
+ to an incomplete beta.
+
+**********************************************************************
+*/
+{
+static double K2 = 0.5e0;
+static double xx,a,oma,tt,yy,dfptt,T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ tt = *t**t;
+ dfptt = *df+tt;
+ xx = *df/dfptt;
+ yy = tt/dfptt;
+ T1 = 0.5e0**df;
+ cumbet(&xx,&yy,&T1,&K2,&a,&oma);
+ if(!(*t <= 0.0e0)) goto S10;
+ *cum = 0.5e0*a;
+ *ccum = oma+*cum;
+ goto S20;
+S10:
+ *ccum = 0.5e0*a;
+ *cum = oma+*ccum;
+S20:
+ return;
+} /* END */
+
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+/***=====================================================================***/
+static double dbetrm(double *a,double *b)
+/*
+**********************************************************************
+
+ double dbetrm(double *a,double *b)
+ Double Precision Sterling Remainder for Complete
+ Beta Function
+
+
+ Function
+
+
+ Log(Beta(A,B)) = Lgamma(A) + Lgamma(B) - Lgamma(A+B)
+ where Lgamma is the log of the (complete) gamma function
+
+ Let ZZ be approximation obtained if each log gamma is approximated
+ by Sterling's formula, i.e.,
+ Sterling(Z) = LOG( SQRT( 2*PI ) ) + ( Z-0.5 ) * LOG( Z ) - Z
+
+ Returns Log(Beta(A,B)) - ZZ
+
+
+ Arguments
+
+
+ A --> One argument of the Beta
+ DOUBLE PRECISION A
+
+ B --> The other argument of the Beta
+ DOUBLE PRECISION B
+
+**********************************************************************
+*/
+{
+static double dbetrm,T1,T2,T3;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ Try to sum from smallest to largest
+*/
+ T1 = *a+*b;
+ dbetrm = -dstrem(&T1);
+ T2 = fifdmax1(*a,*b);
+ dbetrm += dstrem(&T2);
+ T3 = fifdmin1(*a,*b);
+ dbetrm += dstrem(&T3);
+ return dbetrm;
+} /* END */
+#endif /* defined(__COMPILE_UNUSED_FUNCTIONS__) */
+
+/***=====================================================================***/
+static double devlpl(double a[],int *n,double *x)
+/*
+**********************************************************************
+
+ double devlpl(double a[],int *n,double *x)
+ Double precision EVALuate a PoLynomial at X
+
+
+ Function
+
+
+ returns
+ A(1) + A(2)*X + ... + A(N)*X**(N-1)
+
+
+ Arguments
+
+
+ A --> Array of coefficients of the polynomial.
+ A is DOUBLE PRECISION(N)
+
+ N --> Length of A, also degree of polynomial - 1.
+ N is INTEGER
+
+ X --> Point at which the polynomial is to be evaluated.
+ X is DOUBLE PRECISION
+
+**********************************************************************
+*/
+{
+static double devlpl,term;
+static int i;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ term = a[*n-1];
+ for(i= *n-1-1; i>=0; i--) term = a[i]+term**x;
+ devlpl = term;
+ return devlpl;
+} /* END */
+
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+/***=====================================================================***/
+static double dexpm1(double *x)
+/*
+**********************************************************************
+
+ double dexpm1(double *x)
+ Evaluation of the function EXP(X) - 1
+
+
+ Arguments
+
+
+ X --> Argument at which exp(x)-1 desired
+ DOUBLE PRECISION X
+
+
+ Method
+
+
+ Renaming of function rexp from code of:
+
+ DiDinato, A. R. and Morris, A. H. Algorithm 708: Significant
+ Digit Computation of the Incomplete Beta Function Ratios. ACM
+ Trans. Math. Softw. 18 (1993), 360-373.
+
+**********************************************************************
+*/
+{
+static double p1 = .914041914819518e-09;
+static double p2 = .238082361044469e-01;
+static double q1 = -.499999999085958e+00;
+static double q2 = .107141568980644e+00;
+static double q3 = -.119041179760821e-01;
+static double q4 = .595130811860248e-03;
+static double dexpm1,w;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(fabs(*x) > 0.15e0) goto S10;
+ dexpm1 = *x*(((p2**x+p1)**x+1.0e0)/((((q4**x+q3)**x+q2)**x+q1)**x+1.0e0));
+ return dexpm1;
+S10:
+ w = exp(*x);
+ if(*x > 0.0e0) goto S20;
+ dexpm1 = w-0.5e0-0.5e0;
+ return dexpm1;
+S20:
+ dexpm1 = w*(0.5e0+(0.5e0-1.0e0/w));
+ return dexpm1;
+} /* END */
+#endif /*defined(__COMPILE_UNUSED_FUNCTIONS__)*/
+
+/***=====================================================================***/
+static double dinvnr(double *p,double *q)
+/*
+**********************************************************************
+
+ double dinvnr(double *p,double *q)
+ Double precision NoRmal distribution INVerse
+
+
+ Function
+
+
+ Returns X such that CUMNOR(X) = P, i.e., the integral from -
+ infinity to X of (1/SQRT(2*PI)) EXP(-U*U/2) dU is P
+
+
+ Arguments
+
+
+ P --> The probability whose normal deviate is sought.
+ P is DOUBLE PRECISION
+
+ Q --> 1-P
+ P is DOUBLE PRECISION
+
+
+ Method
+
+
+ The rational function on page 95 of Kennedy and Gentle,
+ Statistical Computing, Marcel Dekker, NY , 1980 is used as a start
+ value for the Newton method of finding roots.
+
+
+ Note
+
+
+ If P or Q .lt. machine EPS returns +/- DINVNR(EPS)
+
+**********************************************************************
+*/
+{
+#define maxit 100
+#define eps (1.0e-13)
+#define r2pi 0.3989422804014326e0
+#define nhalf (-0.5e0)
+#define dennor(x) (r2pi*exp(nhalf*(x)*(x)))
+static double dinvnr,strtx,xcur,cum,ccum,pp,dx;
+static int i;
+static unsigned long qporq;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ FIND MINIMUM OF P AND Q
+*/
+ qporq = *p <= *q;
+ if(!qporq) goto S10;
+ pp = *p;
+ goto S20;
+S10:
+ pp = *q;
+S20:
+/*
+ INITIALIZATION STEP
+*/
+ strtx = stvaln(&pp);
+ xcur = strtx;
+/*
+ NEWTON INTERATIONS
+*/
+ for(i=1; i<=maxit; i++) {
+ cumnor(&xcur,&cum,&ccum);
+ dx = (cum-pp)/dennor(xcur);
+ xcur -= dx;
+ if(fabs(dx/xcur) < eps) goto S40;
+ }
+ dinvnr = strtx;
+/*
+ IF WE GET HERE, NEWTON HAS FAILED
+*/
+ if(!qporq) dinvnr = -dinvnr;
+ return dinvnr;
+S40:
+/*
+ IF WE GET HERE, NEWTON HAS SUCCEDED
+*/
+ dinvnr = xcur;
+ if(!qporq) dinvnr = -dinvnr;
+ return dinvnr;
+#undef maxit
+#undef eps
+#undef r2pi
+#undef nhalf
+#undef dennor
+} /* END */
+
+/***=====================================================================***/
+static void E0000(int IENTRY,int *status,double *x,double *fx,
+ unsigned long *qleft,unsigned long *qhi,double *zabsst,
+ double *zabsto,double *zbig,double *zrelst,
+ double *zrelto,double *zsmall,double *zstpmu)
+{
+#define qxmon(zx,zy,zz) (int)((zx) <= (zy) && (zy) <= (zz))
+static double absstp,abstol,big,fbig,fsmall,relstp,reltol,small,step,stpmul,xhi,
+ xlb,xlo,xsave,xub,yy;
+static int i99999;
+static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup;
+ switch(IENTRY){case 0: goto DINVR; case 1: goto DSTINV;}
+DINVR:
+ if(*status > 0) goto S310;
+ qcond = !qxmon(small,*x,big);
+ if(qcond){ ftnstop("SMALL,X,BIG nonmonotone in E0000"); *status=-1; return;}
+ xsave = *x;
+/*
+ See that SMALL and BIG bound the zero and set QINCR
+*/
+ *x = small;
+/*
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 1;
+ goto S300;
+S10:
+ fsmall = *fx;
+ *x = big;
+/*
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 2;
+ goto S300;
+S20:
+ fbig = *fx;
+ qincr = fbig > fsmall;
+ if(!qincr) goto S50;
+ if(fsmall <= 0.0e0) goto S30;
+ *status = -1;
+ *qleft = *qhi = 1;
+ return;
+S30:
+ if(fbig >= 0.0e0) goto S40;
+ *status = -1;
+ *qleft = *qhi = 0;
+ return;
+S40:
+ goto S80;
+S50:
+ if(fsmall >= 0.0e0) goto S60;
+ *status = -1;
+ *qleft = 1;
+ *qhi = 0;
+ return;
+S60:
+ if(fbig <= 0.0e0) goto S70;
+ *status = -1;
+ *qleft = 0;
+ *qhi = 1;
+ return;
+S80:
+S70:
+ *x = xsave;
+ step = fifdmax1(absstp,relstp*fabs(*x));
+/*
+ YY = F(X) - Y
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 3;
+ goto S300;
+S90:
+ yy = *fx;
+ if(!(yy == 0.0e0)) goto S100;
+ *status = 0;
+ qok = 1;
+ return;
+S100:
+ qup = ( qincr && yy < 0.0e0 ) || ( !qincr && yy > 0.0e0 );
+/*
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ HANDLE CASE IN WHICH WE MUST STEP HIGHER
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+*/
+ if(!qup) goto S170;
+ xlb = xsave;
+ xub = fifdmin1(xlb+step,big);
+ goto S120;
+S110:
+ if(qcond) goto S150;
+S120:
+/*
+ YY = F(XUB) - Y
+*/
+ *x = xub;
+/*
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 4;
+ goto S300;
+S130:
+ yy = *fx;
+ qbdd = ( qincr && yy >= 0.0e0 ) || (!qincr && yy <= 0.0e0 );
+ qlim = xub >= big;
+ qcond = qbdd || qlim;
+ if(qcond) goto S140;
+ step = stpmul*step;
+ xlb = xub;
+ xub = fifdmin1(xlb+step,big);
+S140:
+ goto S110;
+S150:
+ if(!(qlim && !qbdd)) goto S160;
+ *status = -1;
+ *qleft = 0;
+ *qhi = !qincr;
+ *x = big;
+ return;
+S160:
+ goto S240;
+S170:
+/*
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ HANDLE CASE IN WHICH WE MUST STEP LOWER
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+*/
+ xub = xsave;
+ xlb = fifdmax1(xub-step,small);
+ goto S190;
+S180:
+ if(qcond) goto S220;
+S190:
+/*
+ YY = F(XLB) - Y
+*/
+ *x = xlb;
+/*
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 5;
+ goto S300;
+S200:
+ yy = *fx;
+ qbdd = ( qincr && yy <= 0.0e0 ) || (!qincr && yy >= 0.0e0 );
+ qlim = xlb <= small;
+ qcond = qbdd || qlim;
+ if(qcond) goto S210;
+ step = stpmul*step;
+ xub = xlb;
+ xlb = fifdmax1(xub-step,small);
+S210:
+ goto S180;
+S220:
+ if(!(qlim && !qbdd)) goto S230;
+ *status = -1;
+ *qleft = 1;
+ *qhi = qincr;
+ *x = small;
+ return;
+S240:
+S230:
+ dstzr(&xlb,&xub,&abstol,&reltol);
+/*
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ IF WE REACH HERE, XLB AND XUB BOUND THE ZERO OF F.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+*/
+ *status = 0;
+ goto S260;
+S250:
+ if(!(*status == 1)) goto S290;
+S260:
+ dzror(status,x,fx,&xlo,&xhi,&qdum1,&qdum2);
+ if(!(*status == 1)) goto S280;
+/*
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 6;
+ goto S300;
+S280:
+S270:
+ goto S250;
+S290:
+ *x = xlo;
+ *status = 0;
+ return;
+DSTINV:
+ small = *zsmall;
+ big = *zbig;
+ absstp = *zabsst;
+ relstp = *zrelst;
+ stpmul = *zstpmu;
+ abstol = *zabsto;
+ reltol = *zrelto;
+ return;
+S300:
+/*
+ TO GET-FUNCTION-VALUE
+*/
+ *status = 1;
+ return;
+S310:
+ switch((int)i99999){case 1: goto S10;case 2: goto S20;case 3: goto S90;case
+ 4: goto S130;case 5: goto S200;case 6: goto S270;default: break;}
+#undef qxmon
+} /* END */
+
+/***=====================================================================***/
+static void dinvr(int *status,double *x,double *fx,
+ unsigned long *qleft,unsigned long *qhi)
+/*
+**********************************************************************
+
+ void dinvr(int *status,double *x,double *fx,
+ unsigned long *qleft,unsigned long *qhi)
+
+ Double precision
+ bounds the zero of the function and invokes zror
+ Reverse Communication
+
+
+ Function
+
+
+ Bounds the function and invokes ZROR to perform the zero
+ finding. STINVR must have been called before this routine
+ in order to set its parameters.
+
+
+ Arguments
+
+
+ STATUS <--> At the beginning of a zero finding problem, STATUS
+ should be set to 0 and INVR invoked. (The value
+ of parameters other than X will be ignored on this cal
+
+ When INVR needs the function evaluated, it will set
+ STATUS to 1 and return. The value of the function
+ should be set in FX and INVR again called without
+ changing any of its other parameters.
+
+ When INVR has finished without error, it will return
+ with STATUS 0. In that case X is approximately a root
+ of F(X).
+
+ If INVR cannot bound the function, it returns status
+ -1 and sets QLEFT and QHI.
+ INTEGER STATUS
+
+ X <-- The value of X at which F(X) is to be evaluated.
+ DOUBLE PRECISION X
+
+ FX --> The value of F(X) calculated when INVR returns with
+ STATUS = 1.
+ DOUBLE PRECISION FX
+
+ QLEFT <-- Defined only if QMFINV returns .FALSE. In that
+ case it is .TRUE. If the stepping search terminated
+ unsucessfully at SMALL. If it is .FALSE. the search
+ terminated unsucessfully at BIG.
+ QLEFT is LOGICAL
+
+ QHI <-- Defined only if QMFINV returns .FALSE. In that
+ case it is .TRUE. if F(X) .GT. Y at the termination
+ of the search and .FALSE. if F(X) .LT. Y at the
+ termination of the search.
+ QHI is LOGICAL
+
+**********************************************************************
+*/
+{
+ E0000(0,status,x,fx,qleft,qhi,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
+} /* END */
+
+/***=====================================================================***/
+static void dstinv(double *zsmall,double *zbig,double *zabsst,
+ double *zrelst,double *zstpmu,double *zabsto,
+ double *zrelto)
+/*
+**********************************************************************
+ void dstinv(double *zsmall,double *zbig,double *zabsst,
+ double *zrelst,double *zstpmu,double *zabsto,
+ double *zrelto)
+
+ Double Precision - SeT INverse finder - Reverse Communication
+ Function
+ Concise Description - Given a monotone function F finds X
+ such that F(X) = Y. Uses Reverse communication -- see invr.
+ This routine sets quantities needed by INVR.
+ More Precise Description of INVR -
+ F must be a monotone function, the results of QMFINV are
+ otherwise undefined. QINCR must be .TRUE. if F is non-
+ decreasing and .FALSE. if F is non-increasing.
+ QMFINV will return .TRUE. if and only if F(SMALL) and
+ F(BIG) bracket Y, i. e.,
+ QINCR is .TRUE. and F(SMALL).LE.Y.LE.F(BIG) or
+ QINCR is .FALSE. and F(BIG).LE.Y.LE.F(SMALL)
+ if QMFINV returns .TRUE., then the X returned satisfies
+ the following condition. let
+ TOL(X) = MAX(ABSTOL,RELTOL*ABS(X))
+ then if QINCR is .TRUE.,
+ F(X-TOL(X)) .LE. Y .LE. F(X+TOL(X))
+ and if QINCR is .FALSE.
+ F(X-TOL(X)) .GE. Y .GE. F(X+TOL(X))
+ Arguments
+ SMALL --> The left endpoint of the interval to be
+ searched for a solution.
+ SMALL is DOUBLE PRECISION
+ BIG --> The right endpoint of the interval to be
+ searched for a solution.
+ BIG is DOUBLE PRECISION
+ ABSSTP, RELSTP --> The initial step size in the search
+ is MAX(ABSSTP,RELSTP*ABS(X)). See algorithm.
+ ABSSTP is DOUBLE PRECISION
+ RELSTP is DOUBLE PRECISION
+ STPMUL --> When a step doesn't bound the zero, the step
+ size is multiplied by STPMUL and another step
+ taken. A popular value is 2.0
+ DOUBLE PRECISION STPMUL
+ ABSTOL, RELTOL --> Two numbers that determine the accuracy
+ of the solution. See function for a precise definition.
+ ABSTOL is DOUBLE PRECISION
+ RELTOL is DOUBLE PRECISION
+ Method
+ Compares F(X) with Y for the input value of X then uses QINCR
+ to determine whether to step left or right to bound the
+ desired x. the initial step size is
+ MAX(ABSSTP,RELSTP*ABS(S)) for the input value of X.
+ Iteratively steps right or left until it bounds X.
+ At each step which doesn't bound X, the step size is doubled.
+ The routine is careful never to step beyond SMALL or BIG. If
+ it hasn't bounded X at SMALL or BIG, QMFINV returns .FALSE.
+ after setting QLEFT and QHI.
+ If X is successfully bounded then Algorithm R of the paper
+ 'Two Efficient Algorithms with Guaranteed Convergence for
+ Finding a Zero of a Function' by J. C. P. Bus and
+ T. J. Dekker in ACM Transactions on Mathematical
+ Software, Volume 1, No. 4 page 330 (DEC. '75) is employed
+ to find the zero of the function F(X)-Y. This is routine
+ QRZERO.
+**********************************************************************
+*/
+{
+ E0000(1,NULL,NULL,NULL,NULL,NULL,zabsst,zabsto,zbig,zrelst,zrelto,zsmall,
+ zstpmu);
+} /* END */
+
+#if defined(__COMPILE_UNUSED_FUNCTIONS__)
+/***=====================================================================***/
+static double dlanor(double *x)
+/*
+**********************************************************************
+
+ double dlanor(double *x)
+ Double precision Logarith of the Asymptotic Normal
+
+
+ Function
+
+
+ Computes the logarithm of the cumulative normal distribution
+ from abs( x ) to infinity for abs( x ) >= 5.
+
+
+ Arguments
+
+
+ X --> Value at which cumulative normal to be evaluated
+ DOUBLE PRECISION X
+
+
+ Method
+
+
+ 23 term expansion of formula 26.2.12 of Abramowitz and Stegun.
+ The relative error at X = 5 is about 0.5E-5.
+
+
+ Note
+
+
+ ABS(X) must be >= 5 else there is an error stop.
+
+**********************************************************************
+*/
+{
+#define dlsqpi 0.91893853320467274177e0
+static double coef[12] = {
+ -1.0e0,3.0e0,-15.0e0,105.0e0,-945.0e0,10395.0e0,-135135.0e0,2027025.0e0,
+ -34459425.0e0,654729075.0e0,-13749310575.e0,316234143225.0e0
+};
+static int K1 = 12;
+static double dlanor,approx,correc,xx,xx2,T2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ xx = fabs(*x);
+ if(xx < 5.0e0){ ftnstop("Argument too small in DLANOR"); return 66.6; }
+ approx = -dlsqpi-0.5e0*xx*xx-log(xx);
+ xx2 = xx*xx;
+ T2 = 1.0e0/xx2;
+ correc = devlpl(coef,&K1,&T2)/xx2;
+ correc = dln1px(&correc);
+ dlanor = approx+correc;
+ return dlanor;
+#undef dlsqpi
+} /* END */
+
+/***=====================================================================***/
+static double dln1mx(double *x)
+/*
+**********************************************************************
+
+ double dln1mx(double *x)
+ Double precision LN(1-X)
+
+
+ Function
+
+
+ Returns ln(1-x) for small x (good accuracy if x .le. 0.1).
+ Note that the obvious code of
+ LOG(1.0-X)
+ won't work for small X because 1.0-X loses accuracy
+
+
+ Arguments
+
+
+ X --> Value for which ln(1-x) is desired.
+ X is DOUBLE PRECISION
+
+
+ Method
+
+
+ If X > 0.1, the obvious code above is used ELSE
+ The Taylor series for 1-x is expanded to 20 terms.
+
+**********************************************************************
+*/
+{
+static double dln1mx,T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ T1 = -*x;
+ dln1mx = dln1px(&T1);
+ return dln1mx;
+} /* END */
+
+/***=====================================================================***/
+static double dln1px(double *a)
+/*
+**********************************************************************
+
+ double dln1px(double *a)
+ Double precision LN(1+X)
+
+
+ Function
+
+
+ Returns ln(1+x)
+ Note that the obvious code of
+ LOG(1.0+X)
+ won't work for small X because 1.0+X loses accuracy
+
+
+ Arguments
+
+
+ X --> Value for which ln(1-x) is desired.
+ X is DOUBLE PRECISION
+
+
+ Method
+
+
+ Renames ALNREL from:
+ DiDinato, A. R. and Morris, A. H. Algorithm 708: Significant
+ Digit Computation of the Incomplete Beta Function Ratios. ACM
+ Trans. Math. Softw. 18 (1993), 360-373.
+
+**********************************************************************
+-----------------------------------------------------------------------
+ EVALUATION OF THE FUNCTION LN(1 + A)
+-----------------------------------------------------------------------
+*/
+{
+static double p1 = -.129418923021993e+01;
+static double p2 = .405303492862024e+00;
+static double p3 = -.178874546012214e-01;
+static double q1 = -.162752256355323e+01;
+static double q2 = .747811014037616e+00;
+static double q3 = -.845104217945565e-01;
+static double dln1px,t,t2,w,x;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(fabs(*a) > 0.375e0) goto S10;
+ t = *a/(*a+2.0e0);
+ t2 = t*t;
+ w = (((p3*t2+p2)*t2+p1)*t2+1.0e0)/(((q3*t2+q2)*t2+q1)*t2+1.0e0);
+ dln1px = 2.0e0*t*w;
+ return dln1px;
+S10:
+ x = 1.e0+*a;
+ dln1px = log(x);
+ return dln1px;
+} /* END */
+
+/***=====================================================================***/
+static double dlnbet(double *a0,double *b0)
+/*
+**********************************************************************
+
+ double dlnbet(a0,b0)
+ Double precision LN of the complete BETa
+
+
+ Function
+
+
+ Returns the natural log of the complete beta function,
+ i.e.,
+
+ ln( Gamma(a)*Gamma(b) / Gamma(a+b)
+
+
+ Arguments
+
+
+ A,B --> The (symmetric) arguments to the complete beta
+ DOUBLE PRECISION A, B
+
+
+ Method
+
+
+ Renames BETALN from:
+ DiDinato, A. R. and Morris, A. H. Algorithm 708: Significant
+ Digit Computation of the Incomplete Beta Function Ratios. ACM
+ Trans. Math. Softw. 18 (1993), 360-373.
+
+**********************************************************************
+-----------------------------------------------------------------------
+ EVALUATION OF THE LOGARITHM OF THE BETA FUNCTION
+-----------------------------------------------------------------------
+ E = 0.5*LN(2*PI)
+--------------------------
+*/
+{
+static double e = .918938533204673e0;
+static double dlnbet,a,b,c,h,u,v,w,z;
+static int i,n;
+static double T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ a = fifdmin1(*a0,*b0);
+ b = fifdmax1(*a0,*b0);
+ if(a >= 8.0e0) goto S100;
+ if(a >= 1.0e0) goto S20;
+/*
+-----------------------------------------------------------------------
+ PROCEDURE WHEN A .LT. 1
+-----------------------------------------------------------------------
+*/
+ if(b >= 8.0e0) goto S10;
+ T1 = a+b;
+ dlnbet = gamln(&a)+(gamln(&b)-gamln(&T1));
+ return dlnbet;
+S10:
+ dlnbet = gamln(&a)+algdiv(&a,&b);
+ return dlnbet;
+S20:
+/*
+-----------------------------------------------------------------------
+ PROCEDURE WHEN 1 .LE. A .LT. 8
+-----------------------------------------------------------------------
+*/
+ if(a > 2.0e0) goto S40;
+ if(b > 2.0e0) goto S30;
+ dlnbet = gamln(&a)+gamln(&b)-gsumln(&a,&b);
+ return dlnbet;
+S30:
+ w = 0.0e0;
+ if(b < 8.0e0) goto S60;
+ dlnbet = gamln(&a)+algdiv(&a,&b);
+ return dlnbet;
+S40:
+/*
+ REDUCTION OF A WHEN B .LE. 1000
+*/
+ if(b > 1000.0e0) goto S80;
+ n = a-1.0e0;
+ w = 1.0e0;
+ for(i=1; i<=n; i++) {
+ a -= 1.0e0;
+ h = a/b;
+ w *= (h/(1.0e0+h));
+ }
+ w = log(w);
+ if(b < 8.0e0) goto S60;
+ dlnbet = w+gamln(&a)+algdiv(&a,&b);
+ return dlnbet;
+S60:
+/*
+ REDUCTION OF B WHEN B .LT. 8
+*/
+ n = b-1.0e0;
+ z = 1.0e0;
+ for(i=1; i<=n; i++) {
+ b -= 1.0e0;
+ z *= (b/(a+b));
+ }
+ dlnbet = w+log(z)+(gamln(&a)+(gamln(&b)-gsumln(&a,&b)));
+ return dlnbet;
+S80:
+/*
+ REDUCTION OF A WHEN B .GT. 1000
+*/
+ n = a-1.0e0;
+ w = 1.0e0;
+ for(i=1; i<=n; i++) {
+ a -= 1.0e0;
+ w *= (a/(1.0e0+a/b));
+ }
+ dlnbet = log(w)-(double)n*log(b)+(gamln(&a)+algdiv(&a,&b));
+ return dlnbet;
+S100:
+/*
+-----------------------------------------------------------------------
+ PROCEDURE WHEN A .GE. 8
+-----------------------------------------------------------------------
+*/
+ w = bcorr(&a,&b);
+ h = a/b;
+ c = h/(1.0e0+h);
+ u = -((a-0.5e0)*log(c));
+ v = b*alnrel(&h);
+ if(u <= v) goto S110;
+ dlnbet = -(0.5e0*log(b))+e+w-v-u;
+ return dlnbet;
+S110:
+ dlnbet = -(0.5e0*log(b))+e+w-u-v;
+ return dlnbet;
+} /* END */
+
+/***=====================================================================***/
+static double dlngam(double *a)
+/*
+**********************************************************************
+
+ double dlngam(double *a)
+ Double precision LN of the GAMma function
+
+
+ Function
+
+
+ Returns the natural logarithm of GAMMA(X).
+
+
+ Arguments
+
+
+ X --> value at which scaled log gamma is to be returned
+ X is DOUBLE PRECISION
+
+
+ Method
+
+
+ Renames GAMLN from:
+ DiDinato, A. R. and Morris, A. H. Algorithm 708: Significant
+ Digit Computation of the Incomplete Beta Function Ratios. ACM
+ Trans. Math. Softw. 18 (1993), 360-373.
+
+**********************************************************************
+-----------------------------------------------------------------------
+ EVALUATION OF LN(GAMMA(A)) FOR POSITIVE A
+-----------------------------------------------------------------------
+ WRITTEN BY ALFRED H. MORRIS
+ NAVAL SURFACE WARFARE CENTER
+ DAHLGREN, VIRGINIA
+--------------------------
+ D = 0.5*(LN(2*PI) - 1)
+--------------------------
+*/
+{
+static double c0 = .833333333333333e-01;
+static double c1 = -.277777777760991e-02;
+static double c2 = .793650666825390e-03;
+static double c3 = -.595202931351870e-03;
+static double c4 = .837308034031215e-03;
+static double c5 = -.165322962780713e-02;
+static double d = .418938533204673e0;
+static double dlngam,t,w;
+static int i,n;
+static double T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(*a > 0.8e0) goto S10;
+ dlngam = gamln1(a)-log(*a);
+ return dlngam;
+S10:
+ if(*a > 2.25e0) goto S20;
+ t = *a-0.5e0-0.5e0;
+ dlngam = gamln1(&t);
+ return dlngam;
+S20:
+ if(*a >= 10.0e0) goto S40;
+ n = *a-1.25e0;
+ t = *a;
+ w = 1.0e0;
+ for(i=1; i<=n; i++) {
+ t -= 1.0e0;
+ w = t*w;
+ }
+ T1 = t-1.0e0;
+ dlngam = gamln1(&T1)+log(w);
+ return dlngam;
+S40:
+ t = pow(1.0e0/ *a,2.0);
+ w = (((((c5*t+c4)*t+c3)*t+c2)*t+c1)*t+c0)/ *a;
+ dlngam = d+w+(*a-0.5e0)*(log(*a)-1.0e0);
+ return dlngam;
+} /* END */
+
+/***=====================================================================***/
+static double dstrem(double *z)
+{
+/*
+**********************************************************************
+ double dstrem(double *z)
+ Double precision Sterling Remainder
+ Function
+ Returns Log(Gamma(Z)) - Sterling(Z) where Sterling(Z) is
+ Sterling's Approximation to Log(Gamma(Z))
+ Sterling(Z) = LOG( SQRT( 2*PI ) ) + ( Z-0.5 ) * LOG( Z ) - Z
+ Arguments
+ Z --> Value at which Sterling remainder calculated
+ Must be positive.
+ DOUBLE PRECISION Z
+ Method
+ If Z >= 6 uses 9 terms of series in Bernoulli numbers
+ (Values calculated using Maple)
+ Otherwise computes difference explicitly
+**********************************************************************
+*/
+#define hln2pi 0.91893853320467274178e0
+#define ncoef 10
+static double coef[ncoef] = {
+ 0.0e0,0.0833333333333333333333333333333e0,
+ -0.00277777777777777777777777777778e0,0.000793650793650793650793650793651e0,
+ -0.000595238095238095238095238095238e0,
+ 0.000841750841750841750841750841751e0,-0.00191752691752691752691752691753e0,
+ 0.00641025641025641025641025641026e0,-0.0295506535947712418300653594771e0,
+ 0.179644372368830573164938490016e0
+};
+static int K1 = 10;
+static double dstrem,sterl,T2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ For information, here are the next 11 coefficients of the
+ remainder term in Sterling's formula
+ -1.39243221690590111642743221691
+ 13.4028640441683919944789510007
+ -156.848284626002017306365132452
+ 2193.10333333333333333333333333
+ -36108.7712537249893571732652192
+ 691472.268851313067108395250776
+ -0.152382215394074161922833649589D8
+ 0.382900751391414141414141414141D9
+ -0.108822660357843910890151491655D11
+ 0.347320283765002252252252252252D12
+ -0.123696021422692744542517103493D14
+*/
+ if(*z <= 0.0e0){ ftnstop("nonpositive argument in DSTREM"); return 66.6; }
+ if(!(*z > 6.0e0)) goto S10;
+ T2 = 1.0e0/pow(*z,2.0);
+ dstrem = devlpl(coef,&K1,&T2)**z;
+ goto S20;
+S10:
+ sterl = hln2pi+(*z-0.5e0)*log(*z)-*z;
+ dstrem = dlngam(z)-sterl;
+S20:
+ return dstrem;
+#undef hln2pi
+#undef ncoef
+} /* END */
+#endif /*defined(__COMPILE_UNUSED_FUNCTIONS__)*/
+
+/***=====================================================================***/
+static double dt1(double *p,double *q,double *df)
+/*
+**********************************************************************
+
+ double dt1(double *p,double *q,double *df)
+ Double precision Initalize Approximation to
+ INVerse of the cumulative T distribution
+
+
+ Function
+
+
+ Returns the inverse of the T distribution function, i.e.,
+ the integral from 0 to INVT of the T density is P. This is an
+ initial approximation
+
+
+ Arguments
+
+
+ P --> The p-value whose inverse from the T distribution is
+ desired.
+ P is DOUBLE PRECISION
+
+ Q --> 1-P.
+ Q is DOUBLE PRECISION
+
+ DF --> Degrees of freedom of the T distribution.
+ DF is DOUBLE PRECISION
+
+**********************************************************************
+*/
+{
+static double coef[4][5] = {
+ {1.0e0,1.0e0,0.0e0,0.0e0,0.0e0},
+ {3.0e0,16.0e0,5.0e0,0.0e0,0.0e0},
+ {-15.0e0,17.0e0,19.0e0,3.0e0,0.0e0},
+ {-945.0e0,-1920.0e0,1482.0e0,776.0e0,79.0e0}
+};
+static double denom[4] = {
+ 4.0e0,96.0e0,384.0e0,92160.0e0
+};
+static int ideg[4] = {
+ 2,3,4,5
+};
+static double dt1,denpow,sum,term,x,xp,xx;
+static int i;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ x = fabs(dinvnr(p,q));
+ xx = x*x;
+ sum = x;
+ denpow = 1.0e0;
+ for(i=0; i<4; i++) {
+ term = devlpl(&coef[i][0],&ideg[i],&xx)*x;
+ denpow *= *df;
+ sum += (term/(denpow*denom[i]));
+ }
+ if(!(*p >= 0.5e0)) goto S20;
+ xp = sum;
+ goto S30;
+S20:
+ xp = -sum;
+S30:
+ dt1 = xp;
+ return dt1;
+} /* END */
+
+/***=====================================================================***/
+static void E0001(int IENTRY,int *status,double *x,double *fx,
+ double *xlo,double *xhi,unsigned long *qleft,
+ unsigned long *qhi,double *zabstl,double *zreltl,
+ double *zxhi,double *zxlo)
+{
+#define ftol(zx) (0.5e0*fifdmax1(abstol,reltol*fabs((zx))))
+static double a,abstol,b,c,d,fa,fb,fc,fd,fda,fdb,m,mb,p,q,reltol,tol,w,xxhi,xxlo;
+static int ext,i99999;
+static unsigned long first,qrzero;
+ switch(IENTRY){case 0: goto DZROR; case 1: goto DSTZR;}
+DZROR:
+ if(*status > 0) goto S280;
+ *xlo = xxlo;
+ *xhi = xxhi;
+ b = *x = *xlo;
+/*
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 1;
+ goto S270;
+S10:
+ fb = *fx;
+ *xlo = *xhi;
+ a = *x = *xlo;
+/*
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 2;
+ goto S270;
+S20:
+/*
+ Check that F(ZXLO) < 0 < F(ZXHI) or
+ F(ZXLO) > 0 > F(ZXHI)
+*/
+ if(!(fb < 0.0e0)) goto S40;
+ if(!(*fx < 0.0e0)) goto S30;
+ *status = -1;
+ *qleft = *fx < fb;
+ *qhi = 0;
+ return;
+S40:
+S30:
+ if(!(fb > 0.0e0)) goto S60;
+ if(!(*fx > 0.0e0)) goto S50;
+ *status = -1;
+ *qleft = *fx > fb;
+ *qhi = 1;
+ return;
+S60:
+S50:
+ fa = *fx;
+ first = 1;
+S70:
+ c = a;
+ fc = fa;
+ ext = 0;
+S80:
+ if(!(fabs(fc) < fabs(fb))) goto S100;
+ if(!(c != a)) goto S90;
+ d = a;
+ fd = fa;
+S90:
+ a = b;
+ fa = fb;
+ *xlo = c;
+ b = *xlo;
+ fb = fc;
+ c = a;
+ fc = fa;
+S100:
+ tol = ftol(*xlo);
+ m = (c+b)*.5e0;
+ mb = m-b;
+ if(!(fabs(mb) > tol)) goto S240;
+ if(!(ext > 3)) goto S110;
+ w = mb;
+ goto S190;
+S110:
+ tol = fifdsign(tol,mb);
+ p = (b-a)*fb;
+ if(!first) goto S120;
+ q = fa-fb;
+ first = 0;
+ goto S130;
+S120:
+ fdb = (fd-fb)/(d-b);
+ fda = (fd-fa)/(d-a);
+ p = fda*p;
+ q = fdb*fa-fda*fb;
+S130:
+ if(!(p < 0.0e0)) goto S140;
+ p = -p;
+ q = -q;
+S140:
+ if(ext == 3) p *= 2.0e0;
+ if(!(p*1.0e0 == 0.0e0 || p <= q*tol)) goto S150;
+ w = tol;
+ goto S180;
+S150:
+ if(!(p < mb*q)) goto S160;
+ w = p/q;
+ goto S170;
+S160:
+ w = mb;
+S190:
+S180:
+S170:
+ d = a;
+ fd = fa;
+ a = b;
+ fa = fb;
+ b += w;
+ *xlo = b;
+ *x = *xlo;
+/*
+ GET-FUNCTION-VALUE
+*/
+ i99999 = 3;
+ goto S270;
+S200:
+ fb = *fx;
+ if(!(fc*fb >= 0.0e0)) goto S210;
+ goto S70;
+S210:
+ if(!(w == mb)) goto S220;
+ ext = 0;
+ goto S230;
+S220:
+ ext += 1;
+S230:
+ goto S80;
+S240:
+ *xhi = c;
+ qrzero = ((fc >= 0.0e0 && fb <= 0.0e0 ) || (fc < 0.0e0 && fb >= 0.0e0));
+ if(!qrzero) goto S250;
+ *status = 0;
+ goto S260;
+S250:
+ *status = -1;
+S260:
+ return;
+DSTZR:
+ xxlo = *zxlo;
+ xxhi = *zxhi;
+ abstol = *zabstl;
+ reltol = *zreltl;
+ return;
+S270:
+/*
+ TO GET-FUNCTION-VALUE
+*/
+ *status = 1;
+ return;
+S280:
+ switch((int)i99999){case 1: goto S10;case 2: goto S20;case 3: goto S200;
+ default: break;}
+#undef ftol
+} /* END */
+
+/***=====================================================================***/
+static void dzror(int *status,double *x,double *fx,double *xlo,
+ double *xhi,unsigned long *qleft,unsigned long *qhi)
+/*
+**********************************************************************
+
+ void dzror(int *status,double *x,double *fx,double *xlo,
+ double *xhi,unsigned long *qleft,unsigned long *qhi)
+
+ Double precision ZeRo of a function -- Reverse Communication
+
+
+ Function
+
+
+ Performs the zero finding. STZROR must have been called before
+ this routine in order to set its parameters.
+
+
+ Arguments
+
+
+ STATUS <--> At the beginning of a zero finding problem, STATUS
+ should be set to 0 and ZROR invoked. (The value
+ of other parameters will be ignored on this call.)
+
+ When ZROR needs the function evaluated, it will set
+ STATUS to 1 and return. The value of the function
+ should be set in FX and ZROR again called without
+ changing any of its other parameters.
+
+ When ZROR has finished without error, it will return
+ with STATUS 0. In that case (XLO,XHI) bound the answe
+
+ If ZROR finds an error (which implies that F(XLO)-Y an
+ F(XHI)-Y have the same sign, it returns STATUS -1. In
+ this case, XLO and XHI are undefined.
+ INTEGER STATUS
+
+ X <-- The value of X at which F(X) is to be evaluated.
+ DOUBLE PRECISION X
+
+ FX --> The value of F(X) calculated when ZROR returns with
+ STATUS = 1.
+ DOUBLE PRECISION FX
+
+ XLO <-- When ZROR returns with STATUS = 0, XLO bounds the
+ inverval in X containing the solution below.
+ DOUBLE PRECISION XLO
+
+ XHI <-- When ZROR returns with STATUS = 0, XHI bounds the
+ inverval in X containing the solution above.
+ DOUBLE PRECISION XHI
+
+ QLEFT <-- .TRUE. if the stepping search terminated unsucessfully
+ at XLO. If it is .FALSE. the search terminated
+ unsucessfully at XHI.
+ QLEFT is LOGICAL
+
+ QHI <-- .TRUE. if F(X) .GT. Y at the termination of the
+ search and .FALSE. if F(X) .LT. Y at the
+ termination of the search.
+ QHI is LOGICAL
+
+**********************************************************************
+*/
+{
+ E0001(0,status,x,fx,xlo,xhi,qleft,qhi,NULL,NULL,NULL,NULL);
+} /* END */
+
+/***=====================================================================***/
+static void dstzr(double *zxlo,double *zxhi,double *zabstl,double *zreltl)
+/*
+**********************************************************************
+ void dstzr(double *zxlo,double *zxhi,double *zabstl,double *zreltl)
+ Double precision SeT ZeRo finder - Reverse communication version
+ Function
+ Sets quantities needed by ZROR. The function of ZROR
+ and the quantities set is given here.
+ Concise Description - Given a function F
+ find XLO such that F(XLO) = 0.
+ More Precise Description -
+ Input condition. F is a double precision function of a single
+ double precision argument and XLO and XHI are such that
+ F(XLO)*F(XHI) .LE. 0.0
+ If the input condition is met, QRZERO returns .TRUE.
+ and output values of XLO and XHI satisfy the following
+ F(XLO)*F(XHI) .LE. 0.
+ ABS(F(XLO) .LE. ABS(F(XHI)
+ ABS(XLO-XHI) .LE. TOL(X)
+ where
+ TOL(X) = MAX(ABSTOL,RELTOL*ABS(X))
+ If this algorithm does not find XLO and XHI satisfying
+ these conditions then QRZERO returns .FALSE. This
+ implies that the input condition was not met.
+ Arguments
+ XLO --> The left endpoint of the interval to be
+ searched for a solution.
+ XLO is DOUBLE PRECISION
+ XHI --> The right endpoint of the interval to be
+ for a solution.
+ XHI is DOUBLE PRECISION
+ ABSTOL, RELTOL --> Two numbers that determine the accuracy
+ of the solution. See function for a
+ precise definition.
+ ABSTOL is DOUBLE PRECISION
+ RELTOL is DOUBLE PRECISION
+ Method
+ Algorithm R of the paper 'Two Efficient Algorithms with
+ Guaranteed Convergence for Finding a Zero of a Function'
+ by J. C. P. Bus and T. J. Dekker in ACM Transactions on
+ Mathematical Software, Volume 1, no. 4 page 330
+ (Dec. '75) is employed to find the zero of F(X)-Y.
+**********************************************************************
+*/
+{
+ E0001(1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,zabstl,zreltl,zxhi,zxlo);
+} /* END */
+
+/***=====================================================================***/
+static double erf1(double *x)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF THE REAL ERROR FUNCTION
+-----------------------------------------------------------------------
+*/
+{
+static double c = .564189583547756e0;
+static double a[5] = {
+ .771058495001320e-04,-.133733772997339e-02,.323076579225834e-01,
+ .479137145607681e-01,.128379167095513e+00
+};
+static double b[3] = {
+ .301048631703895e-02,.538971687740286e-01,.375795757275549e+00
+};
+static double p[8] = {
+ -1.36864857382717e-07,5.64195517478974e-01,7.21175825088309e+00,
+ 4.31622272220567e+01,1.52989285046940e+02,3.39320816734344e+02,
+ 4.51918953711873e+02,3.00459261020162e+02
+};
+static double q[8] = {
+ 1.00000000000000e+00,1.27827273196294e+01,7.70001529352295e+01,
+ 2.77585444743988e+02,6.38980264465631e+02,9.31354094850610e+02,
+ 7.90950925327898e+02,3.00459260956983e+02
+};
+static double r[5] = {
+ 2.10144126479064e+00,2.62370141675169e+01,2.13688200555087e+01,
+ 4.65807828718470e+00,2.82094791773523e-01
+};
+static double s[4] = {
+ 9.41537750555460e+01,1.87114811799590e+02,9.90191814623914e+01,
+ 1.80124575948747e+01
+};
+static double erf1,ax,bot,t,top,x2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ ax = fabs(*x);
+ if(ax > 0.5e0) goto S10;
+ t = *x**x;
+ top = (((a[0]*t+a[1])*t+a[2])*t+a[3])*t+a[4]+1.0e0;
+ bot = ((b[0]*t+b[1])*t+b[2])*t+1.0e0;
+ erf1 = *x*(top/bot);
+ return erf1;
+S10:
+ if(ax > 4.0e0) goto S20;
+ top = ((((((p[0]*ax+p[1])*ax+p[2])*ax+p[3])*ax+p[4])*ax+p[5])*ax+p[6])*ax+p[
+ 7];
+ bot = ((((((q[0]*ax+q[1])*ax+q[2])*ax+q[3])*ax+q[4])*ax+q[5])*ax+q[6])*ax+q[
+ 7];
+ erf1 = 0.5e0+(0.5e0-exp(-(*x**x))*top/bot);
+ if(*x < 0.0e0) erf1 = -erf1;
+ return erf1;
+S20:
+ if(ax >= 5.8e0) goto S30;
+ x2 = *x**x;
+ t = 1.0e0/x2;
+ top = (((r[0]*t+r[1])*t+r[2])*t+r[3])*t+r[4];
+ bot = (((s[0]*t+s[1])*t+s[2])*t+s[3])*t+1.0e0;
+ erf1 = (c-top/(x2*bot))/ax;
+ erf1 = 0.5e0+(0.5e0-exp(-x2)*erf1);
+ if(*x < 0.0e0) erf1 = -erf1;
+ return erf1;
+S30:
+ erf1 = fifdsign(1.0e0,*x);
+ return erf1;
+} /* END */
+
+/***=====================================================================***/
+static double erfc1(int *ind,double *x)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF THE COMPLEMENTARY ERROR FUNCTION
+
+ ERFC1(IND,X) = ERFC(X) IF IND = 0
+ ERFC1(IND,X) = EXP(X*X)*ERFC(X) OTHERWISE
+-----------------------------------------------------------------------
+*/
+{
+static double c = .564189583547756e0;
+static double a[5] = {
+ .771058495001320e-04,-.133733772997339e-02,.323076579225834e-01,
+ .479137145607681e-01,.128379167095513e+00
+};
+static double b[3] = {
+ .301048631703895e-02,.538971687740286e-01,.375795757275549e+00
+};
+static double p[8] = {
+ -1.36864857382717e-07,5.64195517478974e-01,7.21175825088309e+00,
+ 4.31622272220567e+01,1.52989285046940e+02,3.39320816734344e+02,
+ 4.51918953711873e+02,3.00459261020162e+02
+};
+static double q[8] = {
+ 1.00000000000000e+00,1.27827273196294e+01,7.70001529352295e+01,
+ 2.77585444743988e+02,6.38980264465631e+02,9.31354094850610e+02,
+ 7.90950925327898e+02,3.00459260956983e+02
+};
+static double r[5] = {
+ 2.10144126479064e+00,2.62370141675169e+01,2.13688200555087e+01,
+ 4.65807828718470e+00,2.82094791773523e-01
+};
+static double s[4] = {
+ 9.41537750555460e+01,1.87114811799590e+02,9.90191814623914e+01,
+ 1.80124575948747e+01
+};
+static int K1 = 1;
+static double erfc1,ax,bot,e,t,top,w;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ ABS(X) .LE. 0.5
+*/
+ ax = fabs(*x);
+ if(ax > 0.5e0) goto S10;
+ t = *x**x;
+ top = (((a[0]*t+a[1])*t+a[2])*t+a[3])*t+a[4]+1.0e0;
+ bot = ((b[0]*t+b[1])*t+b[2])*t+1.0e0;
+ erfc1 = 0.5e0+(0.5e0-*x*(top/bot));
+ if(*ind != 0) erfc1 = exp(t)*erfc1;
+ return erfc1;
+S10:
+/*
+ 0.5 .LT. ABS(X) .LE. 4
+*/
+ if(ax > 4.0e0) goto S20;
+ top = ((((((p[0]*ax+p[1])*ax+p[2])*ax+p[3])*ax+p[4])*ax+p[5])*ax+p[6])*ax+p[
+ 7];
+ bot = ((((((q[0]*ax+q[1])*ax+q[2])*ax+q[3])*ax+q[4])*ax+q[5])*ax+q[6])*ax+q[
+ 7];
+ erfc1 = top/bot;
+ goto S40;
+S20:
+/*
+ ABS(X) .GT. 4
+*/
+ if(*x <= -5.6e0) goto S60;
+ if(*ind != 0) goto S30;
+ if(*x > 100.0e0) goto S70;
+ if(*x**x > -exparg(&K1)) goto S70;
+S30:
+ t = pow(1.0e0/ *x,2.0);
+ top = (((r[0]*t+r[1])*t+r[2])*t+r[3])*t+r[4];
+ bot = (((s[0]*t+s[1])*t+s[2])*t+s[3])*t+1.0e0;
+ erfc1 = (c-t*top/bot)/ax;
+S40:
+/*
+ FINAL ASSEMBLY
+*/
+ if(*ind == 0) goto S50;
+ if(*x < 0.0e0) erfc1 = 2.0e0*exp(*x**x)-erfc1;
+ return erfc1;
+S50:
+ w = *x**x;
+ t = w;
+ e = w-t;
+ erfc1 = (0.5e0+(0.5e0-e))*exp(-t)*erfc1;
+ if(*x < 0.0e0) erfc1 = 2.0e0-erfc1;
+ return erfc1;
+S60:
+/*
+ LIMIT VALUE FOR LARGE NEGATIVE X
+*/
+ erfc1 = 2.0e0;
+ if(*ind != 0) erfc1 = 2.0e0*exp(*x**x);
+ return erfc1;
+S70:
+/*
+ LIMIT VALUE FOR LARGE POSITIVE X
+ WHEN IND = 0
+*/
+ erfc1 = 0.0e0;
+ return erfc1;
+} /* END */
+
+/***=====================================================================***/
+static double esum(int *mu,double *x)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF EXP(MU + X)
+-----------------------------------------------------------------------
+*/
+{
+static double esum,w;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(*x > 0.0e0) goto S10;
+ if(*mu < 0) goto S20;
+ w = (double)*mu+*x;
+ if(w > 0.0e0) goto S20;
+ esum = exp(w);
+ return esum;
+S10:
+ if(*mu > 0) goto S20;
+ w = (double)*mu+*x;
+ if(w < 0.0e0) goto S20;
+ esum = exp(w);
+ return esum;
+S20:
+ w = *mu;
+ esum = exp(w)*exp(*x);
+ return esum;
+} /* END */
+
+/***=====================================================================***/
+static double exparg(int *l)
+/*
+--------------------------------------------------------------------
+ IF L = 0 THEN EXPARG(L) = THE LARGEST POSITIVE W FOR WHICH
+ EXP(W) CAN BE COMPUTED.
+
+ IF L IS NONZERO THEN EXPARG(L) = THE LARGEST NEGATIVE W FOR
+ WHICH THE COMPUTED VALUE OF EXP(W) IS NONZERO.
+
+ NOTE... ONLY AN APPROXIMATE VALUE FOR EXPARG(L) IS NEEDED.
+--------------------------------------------------------------------
+*/
+{
+static int K1 = 4;
+static int K2 = 9;
+static int K3 = 10;
+static double exparg,lnb;
+static int b,m;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ b = ipmpar(&K1);
+ if(b != 2) goto S10;
+ lnb = .69314718055995e0;
+ goto S40;
+S10:
+ if(b != 8) goto S20;
+ lnb = 2.0794415416798e0;
+ goto S40;
+S20:
+ if(b != 16) goto S30;
+ lnb = 2.7725887222398e0;
+ goto S40;
+S30:
+ lnb = log((double)b);
+S40:
+ if(*l == 0) goto S50;
+ m = ipmpar(&K2)-1;
+ exparg = 0.99999e0*((double)m*lnb);
+ return exparg;
+S50:
+ m = ipmpar(&K3);
+ exparg = 0.99999e0*((double)m*lnb);
+ return exparg;
+} /* END */
+
+/***=====================================================================***/
+static double fpser(double *a,double *b,double *x,double *eps)
+/*
+-----------------------------------------------------------------------
+
+ EVALUATION OF I (A,B)
+ X
+
+ FOR B .LT. MIN(EPS,EPS*A) AND X .LE. 0.5.
+
+-----------------------------------------------------------------------
+
+ SET FPSER = X**A
+*/
+{
+static int K1 = 1;
+static double fpser,an,c,s,t,tol;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ fpser = 1.0e0;
+ if(*a <= 1.e-3**eps) goto S10;
+ fpser = 0.0e0;
+ t = *a*log(*x);
+ if(t < exparg(&K1)) return fpser;
+ fpser = exp(t);
+S10:
+/*
+ NOTE THAT 1/B(A,B) = B
+*/
+ fpser = *b/ *a*fpser;
+ tol = *eps/ *a;
+ an = *a+1.0e0;
+ t = *x;
+ s = t/an;
+S20:
+ an += 1.0e0;
+ t = *x*t;
+ c = t/an;
+ s += c;
+ if(fabs(c) > tol) goto S20;
+ fpser *= (1.0e0+*a*s);
+ return fpser;
+} /* END */
+
+/***=====================================================================***/
+static double gam1(double *a)
+/*
+ ------------------------------------------------------------------
+ COMPUTATION OF 1/GAMMA(A+1) - 1 FOR -0.5 .LE. A .LE. 1.5
+ ------------------------------------------------------------------
+*/
+{
+static double s1 = .273076135303957e+00;
+static double s2 = .559398236957378e-01;
+static double p[7] = {
+ .577215664901533e+00,-.409078193005776e+00,-.230975380857675e+00,
+ .597275330452234e-01,.766968181649490e-02,-.514889771323592e-02,
+ .589597428611429e-03
+};
+static double q[5] = {
+ .100000000000000e+01,.427569613095214e+00,.158451672430138e+00,
+ .261132021441447e-01,.423244297896961e-02
+};
+static double r[9] = {
+ -.422784335098468e+00,-.771330383816272e+00,-.244757765222226e+00,
+ .118378989872749e+00,.930357293360349e-03,-.118290993445146e-01,
+ .223047661158249e-02,.266505979058923e-03,-.132674909766242e-03
+};
+static double gam1,bot,d,t,top,w,T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ t = *a;
+ d = *a-0.5e0;
+ if(d > 0.0e0) t = d-0.5e0;
+ T1 = t;
+ if(T1 < 0) goto S40;
+ else if(T1 == 0) goto S10;
+ else goto S20;
+S10:
+ gam1 = 0.0e0;
+ return gam1;
+S20:
+ top = (((((p[6]*t+p[5])*t+p[4])*t+p[3])*t+p[2])*t+p[1])*t+p[0];
+ bot = (((q[4]*t+q[3])*t+q[2])*t+q[1])*t+1.0e0;
+ w = top/bot;
+ if(d > 0.0e0) goto S30;
+ gam1 = *a*w;
+ return gam1;
+S30:
+ gam1 = t/ *a*(w-0.5e0-0.5e0);
+ return gam1;
+S40:
+ top = (((((((r[8]*t+r[7])*t+r[6])*t+r[5])*t+r[4])*t+r[3])*t+r[2])*t+r[1])*t+
+ r[0];
+ bot = (s2*t+s1)*t+1.0e0;
+ w = top/bot;
+ if(d > 0.0e0) goto S50;
+ gam1 = *a*(w+0.5e0+0.5e0);
+ return gam1;
+S50:
+ gam1 = t*w/ *a;
+ return gam1;
+} /* END */
+
+/***=====================================================================***/
+static void gaminv(double *a,double *x,double *x0,double *p,double *q,
+ int *ierr)
+/*
+ ----------------------------------------------------------------------
+ INVERSE INCOMPLETE GAMMA RATIO FUNCTION
+
+ GIVEN POSITIVE A, AND NONEGATIVE P AND Q WHERE P + Q = 1.
+ THEN X IS COMPUTED WHERE P(A,X) = P AND Q(A,X) = Q. SCHRODER
+ ITERATION IS EMPLOYED. THE ROUTINE ATTEMPTS TO COMPUTE X
+ TO 10 SIGNIFICANT DIGITS IF THIS IS POSSIBLE FOR THE
+ PARTICULAR COMPUTER ARITHMETIC BEING USED.
+
+ ------------
+
+ X IS A VARIABLE. IF P = 0 THEN X IS ASSIGNED THE VALUE 0,
+ AND IF Q = 0 THEN X IS SET TO THE LARGEST FLOATING POINT
+ NUMBER AVAILABLE. OTHERWISE, GAMINV ATTEMPTS TO OBTAIN
+ A SOLUTION FOR P(A,X) = P AND Q(A,X) = Q. IF THE ROUTINE
+ IS SUCCESSFUL THEN THE SOLUTION IS STORED IN X.
+
+ X0 IS AN OPTIONAL INITIAL APPROXIMATION FOR X. IF THE USER
+ DOES NOT WISH TO SUPPLY AN INITIAL APPROXIMATION, THEN SET
+ X0 .LE. 0.
+
+ IERR IS A VARIABLE THAT REPORTS THE STATUS OF THE RESULTS.
+ WHEN THE ROUTINE TERMINATES, IERR HAS ONE OF THE FOLLOWING
+ VALUES ...
+
+ IERR = 0 THE SOLUTION WAS OBTAINED. ITERATION WAS
+ NOT USED.
+ IERR.GT.0 THE SOLUTION WAS OBTAINED. IERR ITERATIONS
+ WERE PERFORMED.
+ IERR = -2 (INPUT ERROR) A .LE. 0
+ IERR = -3 NO SOLUTION WAS OBTAINED. THE RATIO Q/A
+ IS TOO LARGE.
+ IERR = -4 (INPUT ERROR) P + Q .NE. 1
+ IERR = -6 20 ITERATIONS WERE PERFORMED. THE MOST
+ RECENT VALUE OBTAINED FOR X IS GIVEN.
+ THIS CANNOT OCCUR IF X0 .LE. 0.
+ IERR = -7 ITERATION FAILED. NO VALUE IS GIVEN FOR X.
+ THIS MAY OCCUR WHEN X IS APPROXIMATELY 0.
+ IERR = -8 A VALUE FOR X HAS BEEN OBTAINED, BUT THE
+ ROUTINE IS NOT CERTAIN OF ITS ACCURACY.
+ ITERATION CANNOT BE PERFORMED IN THIS
+ CASE. IF X0 .LE. 0, THIS CAN OCCUR ONLY
+ WHEN P OR Q IS APPROXIMATELY 0. IF X0 IS
+ POSITIVE THEN THIS CAN OCCUR WHEN A IS
+ EXCEEDINGLY CLOSE TO X AND A IS EXTREMELY
+ LARGE (SAY A .GE. 1.E20).
+ ----------------------------------------------------------------------
+ WRITTEN BY ALFRED H. MORRIS, JR.
+ NAVAL SURFACE WEAPONS CENTER
+ DAHLGREN, VIRGINIA
+ -------------------
+*/
+{
+static double a0 = 3.31125922108741e0;
+static double a1 = 11.6616720288968e0;
+static double a2 = 4.28342155967104e0;
+static double a3 = .213623493715853e0;
+static double b1 = 6.61053765625462e0;
+static double b2 = 6.40691597760039e0;
+static double b3 = 1.27364489782223e0;
+static double b4 = .036117081018842e0;
+static double c = .577215664901533e0;
+static double ln10 = 2.302585e0;
+static double tol = 1.e-5;
+static double amin[2] = {
+ 500.0e0,100.0e0
+};
+static double bmin[2] = {
+ 1.e-28,1.e-13
+};
+static double dmin[2] = {
+ 1.e-06,1.e-04
+};
+static double emin[2] = {
+ 2.e-03,6.e-03
+};
+static double eps0[2] = {
+ 1.e-10,1.e-08
+};
+static int K1 = 1;
+static int K2 = 2;
+static int K3 = 3;
+static int K8 = 0;
+static double am1,amax,ap1,ap2,ap3,apn,b,c1,c2,c3,c4,c5,d,e,e2,eps,g,h,pn,qg,qn,
+ r,rta,s,s2,sum,t,u,w,xmax,xmin,xn,y,z;
+static int iop;
+static double T4,T5,T6,T7,T9;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ ****** E, XMIN, AND XMAX ARE MACHINE DEPENDENT CONSTANTS.
+ E IS THE SMALLEST NUMBER FOR WHICH 1.0 + E .GT. 1.0.
+ XMIN IS THE SMALLEST POSITIVE NUMBER AND XMAX IS THE
+ LARGEST POSITIVE NUMBER.
+*/
+ e = spmpar(&K1);
+ xmin = spmpar(&K2);
+ xmax = spmpar(&K3);
+ *x = 0.0e0;
+ if(*a <= 0.0e0) goto S300;
+ t = *p+*q-1.e0;
+ if(fabs(t) > e) goto S320;
+ *ierr = 0;
+ if(*p == 0.0e0) return;
+ if(*q == 0.0e0) goto S270;
+ if(*a == 1.0e0) goto S280;
+ e2 = 2.0e0*e;
+ amax = 0.4e-10/(e*e);
+ iop = 1;
+ if(e > 1.e-10) iop = 2;
+ eps = eps0[iop-1];
+ xn = *x0;
+ if(*x0 > 0.0e0) goto S160;
+/*
+ SELECTION OF THE INITIAL APPROXIMATION XN OF X
+ WHEN A .LT. 1
+*/
+ if(*a > 1.0e0) goto S80;
+ T4 = *a+1.0e0;
+ g = Xgamm(&T4);
+ qg = *q*g;
+ if(qg == 0.0e0) goto S360;
+ b = qg/ *a;
+ if(qg > 0.6e0**a) goto S40;
+ if(*a >= 0.30e0 || b < 0.35e0) goto S10;
+ t = exp(-(b+c));
+ u = t*exp(t);
+ xn = t*exp(u);
+ goto S160;
+S10:
+ if(b >= 0.45e0) goto S40;
+ if(b == 0.0e0) goto S360;
+ y = -log(b);
+ s = 0.5e0+(0.5e0-*a);
+ z = log(y);
+ t = y-s*z;
+ if(b < 0.15e0) goto S20;
+ xn = y-s*log(t)-log(1.0e0+s/(t+1.0e0));
+ goto S220;
+S20:
+ if(b <= 0.01e0) goto S30;
+ u = ((t+2.0e0*(3.0e0-*a))*t+(2.0e0-*a)*(3.0e0-*a))/((t+(5.0e0-*a))*t+2.0e0);
+ xn = y-s*log(t)-log(u);
+ goto S220;
+S30:
+ c1 = -(s*z);
+ c2 = -(s*(1.0e0+c1));
+ c3 = s*((0.5e0*c1+(2.0e0-*a))*c1+(2.5e0-1.5e0**a));
+ c4 = -(s*(((c1/3.0e0+(2.5e0-1.5e0**a))*c1+((*a-6.0e0)**a+7.0e0))*c1+(
+ (11.0e0**a-46.0)**a+47.0e0)/6.0e0));
+ c5 = -(s*((((-(c1/4.0e0)+(11.0e0**a-17.0e0)/6.0e0)*c1+((-(3.0e0**a)+13.0e0)*
+ *a-13.0e0))*c1+0.5e0*(((2.0e0**a-25.0e0)**a+72.0e0)**a-61.0e0))*c1+((
+ (25.0e0**a-195.0e0)**a+477.0e0)**a-379.0e0)/12.0e0));
+ xn = (((c5/y+c4)/y+c3)/y+c2)/y+c1+y;
+ if(*a > 1.0e0) goto S220;
+ if(b > bmin[iop-1]) goto S220;
+ *x = xn;
+ return;
+S40:
+ if(b**q > 1.e-8) goto S50;
+ xn = exp(-(*q/ *a+c));
+ goto S70;
+S50:
+ if(*p <= 0.9e0) goto S60;
+ T5 = -*q;
+ xn = exp((alnrel(&T5)+gamln1(a))/ *a);
+ goto S70;
+S60:
+ xn = exp(log(*p*g)/ *a);
+S70:
+ if(xn == 0.0e0) goto S310;
+ t = 0.5e0+(0.5e0-xn/(*a+1.0e0));
+ xn /= t;
+ goto S160;
+S80:
+/*
+ SELECTION OF THE INITIAL APPROXIMATION XN OF X
+ WHEN A .GT. 1
+*/
+ if(*q <= 0.5e0) goto S90;
+ w = log(*p);
+ goto S100;
+S90:
+ w = log(*q);
+S100:
+ t = sqrt(-(2.0e0*w));
+ s = t-(((a3*t+a2)*t+a1)*t+a0)/((((b4*t+b3)*t+b2)*t+b1)*t+1.0e0);
+ if(*q > 0.5e0) s = -s;
+ rta = sqrt(*a);
+ s2 = s*s;
+ xn = *a+s*rta+(s2-1.0e0)/3.0e0+s*(s2-7.0e0)/(36.0e0*rta)-((3.0e0*s2+7.0e0)*
+ s2-16.0e0)/(810.0e0**a)+s*((9.0e0*s2+256.0e0)*s2-433.0e0)/(38880.0e0**a*
+ rta);
+ xn = fifdmax1(xn,0.0e0);
+ if(*a < amin[iop-1]) goto S110;
+ *x = xn;
+ d = 0.5e0+(0.5e0-*x/ *a);
+ if(fabs(d) <= dmin[iop-1]) return;
+S110:
+ if(*p <= 0.5e0) goto S130;
+ if(xn < 3.0e0**a) goto S220;
+ y = -(w+gamln(a));
+ d = fifdmax1(2.0e0,*a*(*a-1.0e0));
+ if(y < ln10*d) goto S120;
+ s = 1.0e0-*a;
+ z = log(y);
+ goto S30;
+S120:
+ t = *a-1.0e0;
+ T6 = -(t/(xn+1.0e0));
+ xn = y+t*log(xn)-alnrel(&T6);
+ T7 = -(t/(xn+1.0e0));
+ xn = y+t*log(xn)-alnrel(&T7);
+ goto S220;
+S130:
+ ap1 = *a+1.0e0;
+ if(xn > 0.70e0*ap1) goto S170;
+ w += gamln(&ap1);
+ if(xn > 0.15e0*ap1) goto S140;
+ ap2 = *a+2.0e0;
+ ap3 = *a+3.0e0;
+ *x = exp((w+*x)/ *a);
+ *x = exp((w+*x-log(1.0e0+*x/ap1*(1.0e0+*x/ap2)))/ *a);
+ *x = exp((w+*x-log(1.0e0+*x/ap1*(1.0e0+*x/ap2)))/ *a);
+ *x = exp((w+*x-log(1.0e0+*x/ap1*(1.0e0+*x/ap2*(1.0e0+*x/ap3))))/ *a);
+ xn = *x;
+ if(xn > 1.e-2*ap1) goto S140;
+ if(xn <= emin[iop-1]*ap1) return;
+ goto S170;
+S140:
+ apn = ap1;
+ t = xn/apn;
+ sum = 1.0e0+t;
+S150:
+ apn += 1.0e0;
+ t *= (xn/apn);
+ sum += t;
+ if(t > 1.e-4) goto S150;
+ t = w-log(sum);
+ xn = exp((xn+t)/ *a);
+ xn *= (1.0e0-(*a*log(xn)-xn-t)/(*a-xn));
+ goto S170;
+S160:
+/*
+ SCHRODER ITERATION USING P
+*/
+ if(*p > 0.5e0) goto S220;
+S170:
+ if(*p <= 1.e10*xmin) goto S350;
+ am1 = *a-0.5e0-0.5e0;
+S180:
+ if(*a <= amax) goto S190;
+ d = 0.5e0+(0.5e0-xn/ *a);
+ if(fabs(d) <= e2) goto S350;
+S190:
+ if(*ierr >= 20) goto S330;
+ *ierr += 1;
+ gratio(a,&xn,&pn,&qn,&K8);
+ if(pn == 0.0e0 || qn == 0.0e0) goto S350;
+ r = rcomp(a,&xn);
+ if(r == 0.0e0) goto S350;
+ t = (pn-*p)/r;
+ w = 0.5e0*(am1-xn);
+ if(fabs(t) <= 0.1e0 && fabs(w*t) <= 0.1e0) goto S200;
+ *x = xn*(1.0e0-t);
+ if(*x <= 0.0e0) goto S340;
+ d = fabs(t);
+ goto S210;
+S200:
+ h = t*(1.0e0+w*t);
+ *x = xn*(1.0e0-h);
+ if(*x <= 0.0e0) goto S340;
+ if(fabs(w) >= 1.0e0 && fabs(w)*t*t <= eps) return;
+ d = fabs(h);
+S210:
+ xn = *x;
+ if(d > tol) goto S180;
+ if(d <= eps) return;
+ if(fabs(*p-pn) <= tol**p) return;
+ goto S180;
+S220:
+/*
+ SCHRODER ITERATION USING Q
+*/
+ if(*q <= 1.e10*xmin) goto S350;
+ am1 = *a-0.5e0-0.5e0;
+S230:
+ if(*a <= amax) goto S240;
+ d = 0.5e0+(0.5e0-xn/ *a);
+ if(fabs(d) <= e2) goto S350;
+S240:
+ if(*ierr >= 20) goto S330;
+ *ierr += 1;
+ gratio(a,&xn,&pn,&qn,&K8);
+ if(pn == 0.0e0 || qn == 0.0e0) goto S350;
+ r = rcomp(a,&xn);
+ if(r == 0.0e0) goto S350;
+ t = (*q-qn)/r;
+ w = 0.5e0*(am1-xn);
+ if(fabs(t) <= 0.1e0 && fabs(w*t) <= 0.1e0) goto S250;
+ *x = xn*(1.0e0-t);
+ if(*x <= 0.0e0) goto S340;
+ d = fabs(t);
+ goto S260;
+S250:
+ h = t*(1.0e0+w*t);
+ *x = xn*(1.0e0-h);
+ if(*x <= 0.0e0) goto S340;
+ if(fabs(w) >= 1.0e0 && fabs(w)*t*t <= eps) return;
+ d = fabs(h);
+S260:
+ xn = *x;
+ if(d > tol) goto S230;
+ if(d <= eps) return;
+ if(fabs(*q-qn) <= tol**q) return;
+ goto S230;
+S270:
+/*
+ SPECIAL CASES
+*/
+ *x = xmax;
+ return;
+S280:
+ if(*q < 0.9e0) goto S290;
+ T9 = -*p;
+ *x = -alnrel(&T9);
+ return;
+S290:
+ *x = -log(*q);
+ return;
+S300:
+/*
+ ERROR RETURN
+*/
+ *ierr = -2;
+ return;
+S310:
+ *ierr = -3;
+ return;
+S320:
+ *ierr = -4;
+ return;
+S330:
+ *ierr = -6;
+ return;
+S340:
+ *ierr = -7;
+ return;
+S350:
+ *x = xn;
+ *ierr = -8;
+ return;
+S360:
+ *x = xmax;
+ *ierr = -8;
+ return;
+} /* END */
+
+/***=====================================================================***/
+static double gamln(double *a)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF LN(GAMMA(A)) FOR POSITIVE A
+-----------------------------------------------------------------------
+ WRITTEN BY ALFRED H. MORRIS
+ NAVAL SURFACE WARFARE CENTER
+ DAHLGREN, VIRGINIA
+--------------------------
+ D = 0.5*(LN(2*PI) - 1)
+--------------------------
+*/
+{
+static double c0 = .833333333333333e-01;
+static double c1 = -.277777777760991e-02;
+static double c2 = .793650666825390e-03;
+static double c3 = -.595202931351870e-03;
+static double c4 = .837308034031215e-03;
+static double c5 = -.165322962780713e-02;
+static double d = .418938533204673e0;
+static double gamln,t,w;
+static int i,n;
+static double T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(*a > 0.8e0) goto S10;
+ gamln = gamln1(a)-log(*a);
+ return gamln;
+S10:
+ if(*a > 2.25e0) goto S20;
+ t = *a-0.5e0-0.5e0;
+ gamln = gamln1(&t);
+ return gamln;
+S20:
+ if(*a >= 10.0e0) goto S40;
+ n = *a-1.25e0;
+ t = *a;
+ w = 1.0e0;
+ for(i=1; i<=n; i++) {
+ t -= 1.0e0;
+ w = t*w;
+ }
+ T1 = t-1.0e0;
+ gamln = gamln1(&T1)+log(w);
+ return gamln;
+S40:
+ t = pow(1.0e0/ *a,2.0);
+ w = (((((c5*t+c4)*t+c3)*t+c2)*t+c1)*t+c0)/ *a;
+ gamln = d+w+(*a-0.5e0)*(log(*a)-1.0e0);
+ return gamln;
+} /* END */
+
+/***=====================================================================***/
+static double gamln1(double *a)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF LN(GAMMA(1 + A)) FOR -0.2 .LE. A .LE. 1.25
+-----------------------------------------------------------------------
+*/
+{
+static double p0 = .577215664901533e+00;
+static double p1 = .844203922187225e+00;
+static double p2 = -.168860593646662e+00;
+static double p3 = -.780427615533591e+00;
+static double p4 = -.402055799310489e+00;
+static double p5 = -.673562214325671e-01;
+static double p6 = -.271935708322958e-02;
+static double q1 = .288743195473681e+01;
+static double q2 = .312755088914843e+01;
+static double q3 = .156875193295039e+01;
+static double q4 = .361951990101499e+00;
+static double q5 = .325038868253937e-01;
+static double q6 = .667465618796164e-03;
+static double r0 = .422784335098467e+00;
+static double r1 = .848044614534529e+00;
+static double r2 = .565221050691933e+00;
+static double r3 = .156513060486551e+00;
+static double r4 = .170502484022650e-01;
+static double r5 = .497958207639485e-03;
+static double s1 = .124313399877507e+01;
+static double s2 = .548042109832463e+00;
+static double s3 = .101552187439830e+00;
+static double s4 = .713309612391000e-02;
+static double s5 = .116165475989616e-03;
+static double gamln1,w,x;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(*a >= 0.6e0) goto S10;
+ w = ((((((p6**a+p5)**a+p4)**a+p3)**a+p2)**a+p1)**a+p0)/((((((q6**a+q5)**a+
+ q4)**a+q3)**a+q2)**a+q1)**a+1.0e0);
+ gamln1 = -(*a*w);
+ return gamln1;
+S10:
+ x = *a-0.5e0-0.5e0;
+ w = (((((r5*x+r4)*x+r3)*x+r2)*x+r1)*x+r0)/(((((s5*x+s4)*x+s3)*x+s2)*x+s1)*x
+ +1.0e0);
+ gamln1 = x*w;
+ return gamln1;
+} /* END */
+
+/***=====================================================================***/
+static double Xgamm(double *a)
+/*
+-----------------------------------------------------------------------
+
+ EVALUATION OF THE GAMMA FUNCTION FOR REAL ARGUMENTS
+
+ -----------
+
+ GAMMA(A) IS ASSIGNED THE VALUE 0 WHEN THE GAMMA FUNCTION CANNOT
+ BE COMPUTED.
+
+-----------------------------------------------------------------------
+ WRITTEN BY ALFRED H. MORRIS, JR.
+ NAVAL SURFACE WEAPONS CENTER
+ DAHLGREN, VIRGINIA
+-----------------------------------------------------------------------
+*/
+{
+static double d = .41893853320467274178e0;
+static double pi = 3.1415926535898e0;
+static double r1 = .820756370353826e-03;
+static double r2 = -.595156336428591e-03;
+static double r3 = .793650663183693e-03;
+static double r4 = -.277777777770481e-02;
+static double r5 = .833333333333333e-01;
+static double p[7] = {
+ .539637273585445e-03,.261939260042690e-02,.204493667594920e-01,
+ .730981088720487e-01,.279648642639792e+00,.553413866010467e+00,1.0e0
+};
+static double q[7] = {
+ -.832979206704073e-03,.470059485860584e-02,.225211131035340e-01,
+ -.170458969313360e+00,-.567902761974940e-01,.113062953091122e+01,1.0e0
+};
+static int K2 = 3;
+static int K3 = 0;
+static double Xgamm,bot,g,lnx,s,t,top,w,x,z;
+static int i,j,m,n,T1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ Xgamm = 0.0e0;
+ x = *a;
+ if(fabs(*a) >= 15.0e0) goto S110;
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF GAMMA(A) FOR ABS(A) .LT. 15
+-----------------------------------------------------------------------
+*/
+ t = 1.0e0;
+ m = fifidint(*a)-1;
+/*
+ LET T BE THE PRODUCT OF A-J WHEN A .GE. 2
+*/
+ T1 = m;
+ if(T1 < 0) goto S40;
+ else if(T1 == 0) goto S30;
+ else goto S10;
+S10:
+ for(j=1; j<=m; j++) {
+ x -= 1.0e0;
+ t = x*t;
+ }
+S30:
+ x -= 1.0e0;
+ goto S80;
+S40:
+/*
+ LET T BE THE PRODUCT OF A+J WHEN A .LT. 1
+*/
+ t = *a;
+ if(*a > 0.0e0) goto S70;
+ m = -m-1;
+ if(m == 0) goto S60;
+ for(j=1; j<=m; j++) {
+ x += 1.0e0;
+ t = x*t;
+ }
+S60:
+ x += (0.5e0+0.5e0);
+ t = x*t;
+ if(t == 0.0e0) return Xgamm;
+S70:
+/*
+ THE FOLLOWING CODE CHECKS IF 1/T CAN OVERFLOW. THIS
+ CODE MAY BE OMITTED IF DESIRED.
+*/
+ if(fabs(t) >= 1.e-30) goto S80;
+ if(fabs(t)*spmpar(&K2) <= 1.0001e0) return Xgamm;
+ Xgamm = 1.0e0/t;
+ return Xgamm;
+S80:
+/*
+ COMPUTE GAMMA(1 + X) FOR 0 .LE. X .LT. 1
+*/
+ top = p[0];
+ bot = q[0];
+ for(i=1; i<7; i++) {
+ top = p[i]+x*top;
+ bot = q[i]+x*bot;
+ }
+ Xgamm = top/bot;
+/*
+ TERMINATION
+*/
+ if(*a < 1.0e0) goto S100;
+ Xgamm *= t;
+ return Xgamm;
+S100:
+ Xgamm /= t;
+ return Xgamm;
+S110:
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF GAMMA(A) FOR ABS(A) .GE. 15
+-----------------------------------------------------------------------
+*/
+ if(fabs(*a) >= 1.e3) return Xgamm;
+ if(*a > 0.0e0) goto S120;
+ x = -*a;
+ n = x;
+ t = x-(double)n;
+ if(t > 0.9e0) t = 1.0e0-t;
+ s = sin(pi*t)/pi;
+ if(fifmod(n,2) == 0) s = -s;
+ if(s == 0.0e0) return Xgamm;
+S120:
+/*
+ COMPUTE THE MODIFIED ASYMPTOTIC SUM
+*/
+ t = 1.0e0/(x*x);
+ g = ((((r1*t+r2)*t+r3)*t+r4)*t+r5)/x;
+/*
+ ONE MAY REPLACE THE NEXT STATEMENT WITH LNX = ALOG(X)
+ BUT LESS ACCURACY WILL NORMALLY BE OBTAINED.
+*/
+ lnx = log(x);
+/*
+ FINAL ASSEMBLY
+*/
+ z = x;
+ g = d+g+(z-0.5e0)*(lnx-1.e0);
+ w = g;
+ t = g-w;
+ if(w > 0.99999e0*exparg(&K3)) return Xgamm;
+ Xgamm = exp(w)*(1.0e0+t);
+ if(*a < 0.0e0) Xgamm = 1.0e0/(Xgamm*s)/x;
+ return Xgamm;
+} /* END */
+
+/***=====================================================================***/
+static void grat1(double *a,double *x,double *r,double *p,double *q,
+ double *eps)
+{
+static int K2 = 0;
+static double a2n,a2nm1,am0,an,an0,b2n,b2nm1,c,cma,g,h,j,l,sum,t,tol,w,z,T1,T3;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF THE INCOMPLETE GAMMA RATIO FUNCTIONS
+ P(A,X) AND Q(A,X)
+ IT IS ASSUMED THAT A .LE. 1. EPS IS THE TOLERANCE TO BE USED.
+ THE INPUT ARGUMENT R HAS THE VALUE E**(-X)*X**A/GAMMA(A).
+-----------------------------------------------------------------------
+*/
+ if(*a**x == 0.0e0) goto S120;
+ if(*a == 0.5e0) goto S100;
+ if(*x < 1.1e0) goto S10;
+ goto S60;
+S10:
+/*
+ TAYLOR SERIES FOR P(A,X)/X**A
+*/
+ an = 3.0e0;
+ c = *x;
+ sum = *x/(*a+3.0e0);
+ tol = 0.1e0**eps/(*a+1.0e0);
+S20:
+ an += 1.0e0;
+ c = -(c*(*x/an));
+ t = c/(*a+an);
+ sum += t;
+ if(fabs(t) > tol) goto S20;
+ j = *a**x*((sum/6.0e0-0.5e0/(*a+2.0e0))**x+1.0e0/(*a+1.0e0));
+ z = *a*log(*x);
+ h = gam1(a);
+ g = 1.0e0+h;
+ if(*x < 0.25e0) goto S30;
+ if(*a < *x/2.59e0) goto S50;
+ goto S40;
+S30:
+ if(z > -.13394e0) goto S50;
+S40:
+ w = exp(z);
+ *p = w*g*(0.5e0+(0.5e0-j));
+ *q = 0.5e0+(0.5e0-*p);
+ return;
+S50:
+ l = rexp(&z);
+ w = 0.5e0+(0.5e0+l);
+ *q = (w*j-l)*g-h;
+ if(*q < 0.0e0) goto S90;
+ *p = 0.5e0+(0.5e0-*q);
+ return;
+S60:
+/*
+ CONTINUED FRACTION EXPANSION
+*/
+ a2nm1 = a2n = 1.0e0;
+ b2nm1 = *x;
+ b2n = *x+(1.0e0-*a);
+ c = 1.0e0;
+S70:
+ a2nm1 = *x*a2n+c*a2nm1;
+ b2nm1 = *x*b2n+c*b2nm1;
+ am0 = a2nm1/b2nm1;
+ c += 1.0e0;
+ cma = c-*a;
+ a2n = a2nm1+cma*a2n;
+ b2n = b2nm1+cma*b2n;
+ an0 = a2n/b2n;
+ if(fabs(an0-am0) >= *eps*an0) goto S70;
+ *q = *r*an0;
+ *p = 0.5e0+(0.5e0-*q);
+ return;
+S80:
+/*
+ SPECIAL CASES
+*/
+ *p = 0.0e0;
+ *q = 1.0e0;
+ return;
+S90:
+ *p = 1.0e0;
+ *q = 0.0e0;
+ return;
+S100:
+ if(*x >= 0.25e0) goto S110;
+ T1 = sqrt(*x);
+ *p = erf1(&T1);
+ *q = 0.5e0+(0.5e0-*p);
+ return;
+S110:
+ T3 = sqrt(*x);
+ *q = erfc1(&K2,&T3);
+ *p = 0.5e0+(0.5e0-*q);
+ return;
+S120:
+ if(*x <= *a) goto S80;
+ goto S90;
+} /* END */
+
+/***=====================================================================***/
+static void gratio(double *a,double *x,double *ans,double *qans,int *ind)
+/*
+ ----------------------------------------------------------------------
+ EVALUATION OF THE INCOMPLETE GAMMA RATIO FUNCTIONS
+ P(A,X) AND Q(A,X)
+
+ ----------
+
+ IT IS ASSUMED THAT A AND X ARE NONNEGATIVE, WHERE A AND X
+ ARE NOT BOTH 0.
+
+ ANS AND QANS ARE VARIABLES. GRATIO ASSIGNS ANS THE VALUE
+ P(A,X) AND QANS THE VALUE Q(A,X). IND MAY BE ANY INTEGER.
+ IF IND = 0 THEN THE USER IS REQUESTING AS MUCH ACCURACY AS
+ POSSIBLE (UP TO 14 SIGNIFICANT DIGITS). OTHERWISE, IF
+ IND = 1 THEN ACCURACY IS REQUESTED TO WITHIN 1 UNIT OF THE
+ 6-TH SIGNIFICANT DIGIT, AND IF IND .NE. 0,1 THEN ACCURACY
+ IS REQUESTED TO WITHIN 1 UNIT OF THE 3RD SIGNIFICANT DIGIT.
+
+ ERROR RETURN ...
+ ANS IS ASSIGNED THE VALUE 2 WHEN A OR X IS NEGATIVE,
+ WHEN A*X = 0, OR WHEN P(A,X) AND Q(A,X) ARE INDETERMINANT.
+ P(A,X) AND Q(A,X) ARE COMPUTATIONALLY INDETERMINANT WHEN
+ X IS EXCEEDINGLY CLOSE TO A AND A IS EXTREMELY LARGE.
+ ----------------------------------------------------------------------
+ WRITTEN BY ALFRED H. MORRIS, JR.
+ NAVAL SURFACE WEAPONS CENTER
+ DAHLGREN, VIRGINIA
+ --------------------
+*/
+{
+static double alog10 = 2.30258509299405e0;
+static double d10 = -.185185185185185e-02;
+static double d20 = .413359788359788e-02;
+static double d30 = .649434156378601e-03;
+static double d40 = -.861888290916712e-03;
+static double d50 = -.336798553366358e-03;
+static double d60 = .531307936463992e-03;
+static double d70 = .344367606892378e-03;
+static double rt2pin = .398942280401433e0;
+static double rtpi = 1.77245385090552e0;
+static double third = .333333333333333e0;
+static double acc0[3] = {
+ 5.e-15,5.e-7,5.e-4
+};
+static double big[3] = {
+ 20.0e0,14.0e0,10.0e0
+};
+static double d0[13] = {
+ .833333333333333e-01,-.148148148148148e-01,.115740740740741e-02,
+ .352733686067019e-03,-.178755144032922e-03,.391926317852244e-04,
+ -.218544851067999e-05,-.185406221071516e-05,.829671134095309e-06,
+ -.176659527368261e-06,.670785354340150e-08,.102618097842403e-07,
+ -.438203601845335e-08
+};
+static double d1[12] = {
+ -.347222222222222e-02,.264550264550265e-02,-.990226337448560e-03,
+ .205761316872428e-03,-.401877572016461e-06,-.180985503344900e-04,
+ .764916091608111e-05,-.161209008945634e-05,.464712780280743e-08,
+ .137863344691572e-06,-.575254560351770e-07,.119516285997781e-07
+};
+static double d2[10] = {
+ -.268132716049383e-02,.771604938271605e-03,.200938786008230e-05,
+ -.107366532263652e-03,.529234488291201e-04,-.127606351886187e-04,
+ .342357873409614e-07,.137219573090629e-05,-.629899213838006e-06,
+ .142806142060642e-06
+};
+static double d3[8] = {
+ .229472093621399e-03,-.469189494395256e-03,.267720632062839e-03,
+ -.756180167188398e-04,-.239650511386730e-06,.110826541153473e-04,
+ -.567495282699160e-05,.142309007324359e-05
+};
+static double d4[6] = {
+ .784039221720067e-03,-.299072480303190e-03,-.146384525788434e-05,
+ .664149821546512e-04,-.396836504717943e-04,.113757269706784e-04
+};
+static double d5[4] = {
+ -.697281375836586e-04,.277275324495939e-03,-.199325705161888e-03,
+ .679778047793721e-04
+};
+static double d6[2] = {
+ -.592166437353694e-03,.270878209671804e-03
+};
+static double e00[3] = {
+ .25e-3,.25e-1,.14e0
+};
+static double x00[3] = {
+ 31.0e0,17.0e0,9.7e0
+};
+static int K1 = 1;
+static int K2 = 0;
+static double a2n,a2nm1,acc,am0,amn,an,an0,apn,b2n,b2nm1,c,c0,c1,c2,c3,c4,c5,c6,
+ cma,e,e0,g,h,j,l,r,rta,rtx,s,sum,t,t1,tol,twoa,u,w,x0,y,z;
+static int i,iop,m,max,n;
+static double wk[20],T3;
+static int T4,T5;
+static double T6,T7;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+ --------------------
+ ****** E IS A MACHINE DEPENDENT CONSTANT. E IS THE SMALLEST
+ FLOATING POINT NUMBER FOR WHICH 1.0 + E .GT. 1.0 .
+*/
+ e = spmpar(&K1);
+ if(*a < 0.0e0 || *x < 0.0e0) goto S430;
+ if(*a == 0.0e0 && *x == 0.0e0) goto S430;
+ if(*a**x == 0.0e0) goto S420;
+ iop = *ind+1;
+ if(iop != 1 && iop != 2) iop = 3;
+ acc = fifdmax1(acc0[iop-1],e);
+ e0 = e00[iop-1];
+ x0 = x00[iop-1];
+/*
+ SELECT THE APPROPRIATE ALGORITHM
+*/
+ if(*a >= 1.0e0) goto S10;
+ if(*a == 0.5e0) goto S390;
+ if(*x < 1.1e0) goto S160;
+ t1 = *a*log(*x)-*x;
+ u = *a*exp(t1);
+ if(u == 0.0e0) goto S380;
+ r = u*(1.0e0+gam1(a));
+ goto S250;
+S10:
+ if(*a >= big[iop-1]) goto S30;
+ if(*a > *x || *x >= x0) goto S20;
+ twoa = *a+*a;
+ m = fifidint(twoa);
+ if(twoa != (double)m) goto S20;
+ i = m/2;
+ if(*a == (double)i) goto S210;
+ goto S220;
+S20:
+ t1 = *a*log(*x)-*x;
+ r = exp(t1)/Xgamm(a);
+ goto S40;
+S30:
+ l = *x/ *a;
+ if(l == 0.0e0) goto S370;
+ s = 0.5e0+(0.5e0-l);
+ z = rlog(&l);
+ if(z >= 700.0e0/ *a) goto S410;
+ y = *a*z;
+ rta = sqrt(*a);
+ if(fabs(s) <= e0/rta) goto S330;
+ if(fabs(s) <= 0.4e0) goto S270;
+ t = pow(1.0e0/ *a,2.0);
+ t1 = (((0.75e0*t-1.0e0)*t+3.5e0)*t-105.0e0)/(*a*1260.0e0);
+ t1 -= y;
+ r = rt2pin*rta*exp(t1);
+S40:
+ if(r == 0.0e0) goto S420;
+ if(*x <= fifdmax1(*a,alog10)) goto S50;
+ if(*x < x0) goto S250;
+ goto S100;
+S50:
+/*
+ TAYLOR SERIES FOR P/R
+*/
+ apn = *a+1.0e0;
+ t = *x/apn;
+ wk[0] = t;
+ for(n=2; n<=20; n++) {
+ apn += 1.0e0;
+ t *= (*x/apn);
+ if(t <= 1.e-3) goto S70;
+ wk[n-1] = t;
+ }
+ n = 20;
+S70:
+ sum = t;
+ tol = 0.5e0*acc;
+S80:
+ apn += 1.0e0;
+ t *= (*x/apn);
+ sum += t;
+ if(t > tol) goto S80;
+ max = n-1;
+ for(m=1; m<=max; m++) {
+ n -= 1;
+ sum += wk[n-1];
+ }
+ *ans = r/ *a*(1.0e0+sum);
+ *qans = 0.5e0+(0.5e0-*ans);
+ return;
+S100:
+/*
+ ASYMPTOTIC EXPANSION
+*/
+ amn = *a-1.0e0;
+ t = amn/ *x;
+ wk[0] = t;
+ for(n=2; n<=20; n++) {
+ amn -= 1.0e0;
+ t *= (amn/ *x);
+ if(fabs(t) <= 1.e-3) goto S120;
+ wk[n-1] = t;
+ }
+ n = 20;
+S120:
+ sum = t;
+S130:
+ if(fabs(t) <= acc) goto S140;
+ amn -= 1.0e0;
+ t *= (amn/ *x);
+ sum += t;
+ goto S130;
+S140:
+ max = n-1;
+ for(m=1; m<=max; m++) {
+ n -= 1;
+ sum += wk[n-1];
+ }
+ *qans = r/ *x*(1.0e0+sum);
+ *ans = 0.5e0+(0.5e0-*qans);
+ return;
+S160:
+/*
+ TAYLOR SERIES FOR P(A,X)/X**A
+*/
+ an = 3.0e0;
+ c = *x;
+ sum = *x/(*a+3.0e0);
+ tol = 3.0e0*acc/(*a+1.0e0);
+S170:
+ an += 1.0e0;
+ c = -(c*(*x/an));
+ t = c/(*a+an);
+ sum += t;
+ if(fabs(t) > tol) goto S170;
+ j = *a**x*((sum/6.0e0-0.5e0/(*a+2.0e0))**x+1.0e0/(*a+1.0e0));
+ z = *a*log(*x);
+ h = gam1(a);
+ g = 1.0e0+h;
+ if(*x < 0.25e0) goto S180;
+ if(*a < *x/2.59e0) goto S200;
+ goto S190;
+S180:
+ if(z > -.13394e0) goto S200;
+S190:
+ w = exp(z);
+ *ans = w*g*(0.5e0+(0.5e0-j));
+ *qans = 0.5e0+(0.5e0-*ans);
+ return;
+S200:
+ l = rexp(&z);
+ w = 0.5e0+(0.5e0+l);
+ *qans = (w*j-l)*g-h;
+ if(*qans < 0.0e0) goto S380;
+ *ans = 0.5e0+(0.5e0-*qans);
+ return;
+S210:
+/*
+ FINITE SUMS FOR Q WHEN A .GE. 1
+ AND 2*A IS AN INTEGER
+*/
+ sum = exp(-*x);
+ t = sum;
+ n = 1;
+ c = 0.0e0;
+ goto S230;
+S220:
+ rtx = sqrt(*x);
+ sum = erfc1(&K2,&rtx);
+ t = exp(-*x)/(rtpi*rtx);
+ n = 0;
+ c = -0.5e0;
+S230:
+ if(n == i) goto S240;
+ n += 1;
+ c += 1.0e0;
+ t = *x*t/c;
+ sum += t;
+ goto S230;
+S240:
+ *qans = sum;
+ *ans = 0.5e0+(0.5e0-*qans);
+ return;
+S250:
+/*
+ CONTINUED FRACTION EXPANSION
+*/
+ tol = fifdmax1(5.0e0*e,acc);
+ a2nm1 = a2n = 1.0e0;
+ b2nm1 = *x;
+ b2n = *x+(1.0e0-*a);
+ c = 1.0e0;
+S260:
+ a2nm1 = *x*a2n+c*a2nm1;
+ b2nm1 = *x*b2n+c*b2nm1;
+ am0 = a2nm1/b2nm1;
+ c += 1.0e0;
+ cma = c-*a;
+ a2n = a2nm1+cma*a2n;
+ b2n = b2nm1+cma*b2n;
+ an0 = a2n/b2n;
+ if(fabs(an0-am0) >= tol*an0) goto S260;
+ *qans = r*an0;
+ *ans = 0.5e0+(0.5e0-*qans);
+ return;
+S270:
+/*
+ GENERAL TEMME EXPANSION
+*/
+ if(fabs(s) <= 2.0e0*e && *a*e*e > 3.28e-3) goto S430;
+ c = exp(-y);
+ T3 = sqrt(y);
+ w = 0.5e0*erfc1(&K1,&T3);
+ u = 1.0e0/ *a;
+ z = sqrt(z+z);
+ if(l < 1.0e0) z = -z;
+ T4 = iop-2;
+ if(T4 < 0) goto S280;
+ else if(T4 == 0) goto S290;
+ else goto S300;
+S280:
+ if(fabs(s) <= 1.e-3) goto S340;
+ c0 = ((((((((((((d0[12]*z+d0[11])*z+d0[10])*z+d0[9])*z+d0[8])*z+d0[7])*z+d0[
+ 6])*z+d0[5])*z+d0[4])*z+d0[3])*z+d0[2])*z+d0[1])*z+d0[0])*z-third;
+ c1 = (((((((((((d1[11]*z+d1[10])*z+d1[9])*z+d1[8])*z+d1[7])*z+d1[6])*z+d1[5]
+ )*z+d1[4])*z+d1[3])*z+d1[2])*z+d1[1])*z+d1[0])*z+d10;
+ c2 = (((((((((d2[9]*z+d2[8])*z+d2[7])*z+d2[6])*z+d2[5])*z+d2[4])*z+d2[3])*z+
+ d2[2])*z+d2[1])*z+d2[0])*z+d20;
+ c3 = (((((((d3[7]*z+d3[6])*z+d3[5])*z+d3[4])*z+d3[3])*z+d3[2])*z+d3[1])*z+
+ d3[0])*z+d30;
+ c4 = (((((d4[5]*z+d4[4])*z+d4[3])*z+d4[2])*z+d4[1])*z+d4[0])*z+d40;
+ c5 = (((d5[3]*z+d5[2])*z+d5[1])*z+d5[0])*z+d50;
+ c6 = (d6[1]*z+d6[0])*z+d60;
+ t = ((((((d70*u+c6)*u+c5)*u+c4)*u+c3)*u+c2)*u+c1)*u+c0;
+ goto S310;
+S290:
+ c0 = (((((d0[5]*z+d0[4])*z+d0[3])*z+d0[2])*z+d0[1])*z+d0[0])*z-third;
+ c1 = (((d1[3]*z+d1[2])*z+d1[1])*z+d1[0])*z+d10;
+ c2 = d2[0]*z+d20;
+ t = (c2*u+c1)*u+c0;
+ goto S310;
+S300:
+ t = ((d0[2]*z+d0[1])*z+d0[0])*z-third;
+S310:
+ if(l < 1.0e0) goto S320;
+ *qans = c*(w+rt2pin*t/rta);
+ *ans = 0.5e0+(0.5e0-*qans);
+ return;
+S320:
+ *ans = c*(w-rt2pin*t/rta);
+ *qans = 0.5e0+(0.5e0-*ans);
+ return;
+S330:
+/*
+ TEMME EXPANSION FOR L = 1
+*/
+ if(*a*e*e > 3.28e-3) goto S430;
+ c = 0.5e0+(0.5e0-y);
+ w = (0.5e0-sqrt(y)*(0.5e0+(0.5e0-y/3.0e0))/rtpi)/c;
+ u = 1.0e0/ *a;
+ z = sqrt(z+z);
+ if(l < 1.0e0) z = -z;
+ T5 = iop-2;
+ if(T5 < 0) goto S340;
+ else if(T5 == 0) goto S350;
+ else goto S360;
+S340:
+ c0 = ((((((d0[6]*z+d0[5])*z+d0[4])*z+d0[3])*z+d0[2])*z+d0[1])*z+d0[0])*z-
+ third;
+ c1 = (((((d1[5]*z+d1[4])*z+d1[3])*z+d1[2])*z+d1[1])*z+d1[0])*z+d10;
+ c2 = ((((d2[4]*z+d2[3])*z+d2[2])*z+d2[1])*z+d2[0])*z+d20;
+ c3 = (((d3[3]*z+d3[2])*z+d3[1])*z+d3[0])*z+d30;
+ c4 = (d4[1]*z+d4[0])*z+d40;
+ c5 = (d5[1]*z+d5[0])*z+d50;
+ c6 = d6[0]*z+d60;
+ t = ((((((d70*u+c6)*u+c5)*u+c4)*u+c3)*u+c2)*u+c1)*u+c0;
+ goto S310;
+S350:
+ c0 = (d0[1]*z+d0[0])*z-third;
+ c1 = d1[0]*z+d10;
+ t = (d20*u+c1)*u+c0;
+ goto S310;
+S360:
+ t = d0[0]*z-third;
+ goto S310;
+S370:
+/*
+ SPECIAL CASES
+*/
+ *ans = 0.0e0;
+ *qans = 1.0e0;
+ return;
+S380:
+ *ans = 1.0e0;
+ *qans = 0.0e0;
+ return;
+S390:
+ if(*x >= 0.25e0) goto S400;
+ T6 = sqrt(*x);
+ *ans = erf1(&T6);
+ *qans = 0.5e0+(0.5e0-*ans);
+ return;
+S400:
+ T7 = sqrt(*x);
+ *qans = erfc1(&K2,&T7);
+ *ans = 0.5e0+(0.5e0-*qans);
+ return;
+S410:
+ if(fabs(s) <= 2.0e0*e) goto S430;
+S420:
+ if(*x <= *a) goto S370;
+ goto S380;
+S430:
+/*
+ ERROR RETURN
+*/
+ *ans = 2.0e0;
+ return;
+} /* END */
+
+/***=====================================================================***/
+static double gsumln(double *a,double *b)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF THE FUNCTION LN(GAMMA(A + B))
+ FOR 1 .LE. A .LE. 2 AND 1 .LE. B .LE. 2
+-----------------------------------------------------------------------
+*/
+{
+static double gsumln,x,T1,T2;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ x = *a+*b-2.e0;
+ if(x > 0.25e0) goto S10;
+ T1 = 1.0e0+x;
+ gsumln = gamln1(&T1);
+ return gsumln;
+S10:
+ if(x > 1.25e0) goto S20;
+ gsumln = gamln1(&x)+alnrel(&x);
+ return gsumln;
+S20:
+ T2 = x-1.0e0;
+ gsumln = gamln1(&T2)+log(x*(1.0e0+x));
+ return gsumln;
+} /* END */
+
+/***=====================================================================***/
+static double psi(double *xx)
+/*
+---------------------------------------------------------------------
+
+ EVALUATION OF THE DIGAMMA FUNCTION
+
+ -----------
+
+ PSI(XX) IS ASSIGNED THE VALUE 0 WHEN THE DIGAMMA FUNCTION CANNOT
+ BE COMPUTED.
+
+ THE MAIN COMPUTATION INVOLVES EVALUATION OF RATIONAL CHEBYSHEV
+ APPROXIMATIONS PUBLISHED IN MATH. COMP. 27, 123-127(1973) BY
+ CODY, STRECOK AND THACHER.
+
+---------------------------------------------------------------------
+ PSI WAS WRITTEN AT ARGONNE NATIONAL LABORATORY FOR THE FUNPACK
+ PACKAGE OF SPECIAL FUNCTION SUBROUTINES. PSI WAS MODIFIED BY
+ A.H. MORRIS (NSWC).
+---------------------------------------------------------------------
+*/
+{
+static double dx0 = 1.461632144968362341262659542325721325e0;
+static double piov4 = .785398163397448e0;
+static double p1[7] = {
+ .895385022981970e-02,.477762828042627e+01,.142441585084029e+03,
+ .118645200713425e+04,.363351846806499e+04,.413810161269013e+04,
+ .130560269827897e+04
+};
+static double p2[4] = {
+ -.212940445131011e+01,-.701677227766759e+01,-.448616543918019e+01,
+ -.648157123766197e+00
+};
+static double q1[6] = {
+ .448452573429826e+02,.520752771467162e+03,.221000799247830e+04,
+ .364127349079381e+04,.190831076596300e+04,.691091682714533e-05
+};
+static double q2[4] = {
+ .322703493791143e+02,.892920700481861e+02,.546117738103215e+02,
+ .777788548522962e+01
+};
+static int K1 = 3;
+static int K2 = 1;
+static double psi,aug,den,sgn,upper,w,x,xmax1,xmx0,xsmall,z;
+static int i,m,n,nq;
+/*
+ ..
+ .. Executable Statements ..
+*/
+/*
+---------------------------------------------------------------------
+ MACHINE DEPENDENT CONSTANTS ...
+ XMAX1 = THE SMALLEST POSITIVE FLOATING POINT CONSTANT
+ WITH ENTIRELY INTEGER REPRESENTATION. ALSO USED
+ AS NEGATIVE OF LOWER BOUND ON ACCEPTABLE NEGATIVE
+ ARGUMENTS AND AS THE POSITIVE ARGUMENT BEYOND WHICH
+ PSI MAY BE REPRESENTED AS ALOG(X).
+ XSMALL = ABSOLUTE ARGUMENT BELOW WHICH PI*COTAN(PI*X)
+ MAY BE REPRESENTED BY 1/X.
+---------------------------------------------------------------------
+*/
+ xmax1 = ipmpar(&K1);
+ xmax1 = fifdmin1(xmax1,1.0e0/spmpar(&K2));
+ xsmall = 1.e-9;
+ x = *xx;
+ aug = 0.0e0;
+ if(x >= 0.5e0) goto S50;
+/*
+---------------------------------------------------------------------
+ X .LT. 0.5, USE REFLECTION FORMULA
+ PSI(1-X) = PSI(X) + PI * COTAN(PI*X)
+---------------------------------------------------------------------
+*/
+ if(fabs(x) > xsmall) goto S10;
+ if(x == 0.0e0) goto S100;
+/*
+---------------------------------------------------------------------
+ 0 .LT. ABS(X) .LE. XSMALL. USE 1/X AS A SUBSTITUTE
+ FOR PI*COTAN(PI*X)
+---------------------------------------------------------------------
+*/
+ aug = -(1.0e0/x);
+ goto S40;
+S10:
+/*
+---------------------------------------------------------------------
+ REDUCTION OF ARGUMENT FOR COTAN
+---------------------------------------------------------------------
+*/
+ w = -x;
+ sgn = piov4;
+ if(w > 0.0e0) goto S20;
+ w = -w;
+ sgn = -sgn;
+S20:
+/*
+---------------------------------------------------------------------
+ MAKE AN ERROR EXIT IF X .LE. -XMAX1
+---------------------------------------------------------------------
+*/
+ if(w >= xmax1) goto S100;
+ nq = fifidint(w);
+ w -= (double)nq;
+ nq = fifidint(w*4.0e0);
+ w = 4.0e0*(w-(double)nq*.25e0);
+/*
+---------------------------------------------------------------------
+ W IS NOW RELATED TO THE FRACTIONAL PART OF 4.0 * X.
+ ADJUST ARGUMENT TO CORRESPOND TO VALUES IN FIRST
+ QUADRANT AND DETERMINE SIGN
+---------------------------------------------------------------------
+*/
+ n = nq/2;
+ if(n+n != nq) w = 1.0e0-w;
+ z = piov4*w;
+ m = n/2;
+ if(m+m != n) sgn = -sgn;
+/*
+---------------------------------------------------------------------
+ DETERMINE FINAL VALUE FOR -PI*COTAN(PI*X)
+---------------------------------------------------------------------
+*/
+ n = (nq+1)/2;
+ m = n/2;
+ m += m;
+ if(m != n) goto S30;
+/*
+---------------------------------------------------------------------
+ CHECK FOR SINGULARITY
+---------------------------------------------------------------------
+*/
+ if(z == 0.0e0) goto S100;
+/*
+---------------------------------------------------------------------
+ USE COS/SIN AS A SUBSTITUTE FOR COTAN, AND
+ SIN/COS AS A SUBSTITUTE FOR TAN
+---------------------------------------------------------------------
+*/
+ aug = sgn*(cos(z)/sin(z)*4.0e0);
+ goto S40;
+S30:
+ aug = sgn*(sin(z)/cos(z)*4.0e0);
+S40:
+ x = 1.0e0-x;
+S50:
+ if(x > 3.0e0) goto S70;
+/*
+---------------------------------------------------------------------
+ 0.5 .LE. X .LE. 3.0
+---------------------------------------------------------------------
+*/
+ den = x;
+ upper = p1[0]*x;
+ for(i=1; i<=5; i++) {
+ den = (den+q1[i-1])*x;
+ upper = (upper+p1[i+1-1])*x;
+ }
+ den = (upper+p1[6])/(den+q1[5]);
+ xmx0 = x-dx0;
+ psi = den*xmx0+aug;
+ return psi;
+S70:
+/*
+---------------------------------------------------------------------
+ IF X .GE. XMAX1, PSI = LN(X)
+---------------------------------------------------------------------
+*/
+ if(x >= xmax1) goto S90;
+/*
+---------------------------------------------------------------------
+ 3.0 .LT. X .LT. XMAX1
+---------------------------------------------------------------------
+*/
+ w = 1.0e0/(x*x);
+ den = w;
+ upper = p2[0]*w;
+ for(i=1; i<=3; i++) {
+ den = (den+q2[i-1])*w;
+ upper = (upper+p2[i+1-1])*w;
+ }
+ aug = upper/(den+q2[3])-0.5e0/x+aug;
+S90:
+ psi = aug+log(x);
+ return psi;
+S100:
+/*
+---------------------------------------------------------------------
+ ERROR RETURN
+---------------------------------------------------------------------
+*/
+ psi = 0.0e0;
+ return psi;
+} /* END */
+
+/***=====================================================================***/
+static double rcomp(double *a,double *x)
+/*
+ -------------------
+ EVALUATION OF EXP(-X)*X**A/GAMMA(A)
+ -------------------
+ RT2PIN = 1/SQRT(2*PI)
+ -------------------
+*/
+{
+static double rt2pin = .398942280401433e0;
+static double rcomp,t,t1,u;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ rcomp = 0.0e0;
+ if(*a >= 20.0e0) goto S20;
+ t = *a*log(*x)-*x;
+ if(*a >= 1.0e0) goto S10;
+ rcomp = *a*exp(t)*(1.0e0+gam1(a));
+ return rcomp;
+S10:
+ rcomp = exp(t)/Xgamm(a);
+ return rcomp;
+S20:
+ u = *x/ *a;
+ if(u == 0.0e0) return rcomp;
+ t = pow(1.0e0/ *a,2.0);
+ t1 = (((0.75e0*t-1.0e0)*t+3.5e0)*t-105.0e0)/(*a*1260.0e0);
+ t1 -= (*a*rlog(&u));
+ rcomp = rt2pin*sqrt(*a)*exp(t1);
+ return rcomp;
+} /* END */
+
+/***=====================================================================***/
+static double rexp(double *x)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF THE FUNCTION EXP(X) - 1
+-----------------------------------------------------------------------
+*/
+{
+static double p1 = .914041914819518e-09;
+static double p2 = .238082361044469e-01;
+static double q1 = -.499999999085958e+00;
+static double q2 = .107141568980644e+00;
+static double q3 = -.119041179760821e-01;
+static double q4 = .595130811860248e-03;
+static double rexp,w;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(fabs(*x) > 0.15e0) goto S10;
+ rexp = *x*(((p2**x+p1)**x+1.0e0)/((((q4**x+q3)**x+q2)**x+q1)**x+1.0e0));
+ return rexp;
+S10:
+ w = exp(*x);
+ if(*x > 0.0e0) goto S20;
+ rexp = w-0.5e0-0.5e0;
+ return rexp;
+S20:
+ rexp = w*(0.5e0+(0.5e0-1.0e0/w));
+ return rexp;
+} /* END */
+
+/***=====================================================================***/
+static double rlog(double *x)
+/*
+ -------------------
+ COMPUTATION OF X - 1 - LN(X)
+ -------------------
+*/
+{
+static double a = .566749439387324e-01;
+static double b = .456512608815524e-01;
+static double p0 = .333333333333333e+00;
+static double p1 = -.224696413112536e+00;
+static double p2 = .620886815375787e-02;
+static double q1 = -.127408923933623e+01;
+static double q2 = .354508718369557e+00;
+static double rlog,r,t,u,w,w1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(*x < 0.61e0 || *x > 1.57e0) goto S40;
+ if(*x < 0.82e0) goto S10;
+ if(*x > 1.18e0) goto S20;
+/*
+ ARGUMENT REDUCTION
+*/
+ u = *x-0.5e0-0.5e0;
+ w1 = 0.0e0;
+ goto S30;
+S10:
+ u = *x-0.7e0;
+ u /= 0.7e0;
+ w1 = a-u*0.3e0;
+ goto S30;
+S20:
+ u = 0.75e0**x-1.e0;
+ w1 = b+u/3.0e0;
+S30:
+/*
+ SERIES EXPANSION
+*/
+ r = u/(u+2.0e0);
+ t = r*r;
+ w = ((p2*t+p1)*t+p0)/((q2*t+q1)*t+1.0e0);
+ rlog = 2.0e0*t*(1.0e0/(1.0e0-r)-r*w)+w1;
+ return rlog;
+S40:
+ r = *x-0.5e0-0.5e0;
+ rlog = r-log(*x);
+ return rlog;
+} /* END */
+
+/***=====================================================================***/
+static double rlog1(double *x)
+/*
+-----------------------------------------------------------------------
+ EVALUATION OF THE FUNCTION X - LN(1 + X)
+-----------------------------------------------------------------------
+*/
+{
+static double a = .566749439387324e-01;
+static double b = .456512608815524e-01;
+static double p0 = .333333333333333e+00;
+static double p1 = -.224696413112536e+00;
+static double p2 = .620886815375787e-02;
+static double q1 = -.127408923933623e+01;
+static double q2 = .354508718369557e+00;
+static double rlog1,h,r,t,w,w1;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(*x < -0.39e0 || *x > 0.57e0) goto S40;
+ if(*x < -0.18e0) goto S10;
+ if(*x > 0.18e0) goto S20;
+/*
+ ARGUMENT REDUCTION
+*/
+ h = *x;
+ w1 = 0.0e0;
+ goto S30;
+S10:
+ h = *x+0.3e0;
+ h /= 0.7e0;
+ w1 = a-h*0.3e0;
+ goto S30;
+S20:
+ h = 0.75e0**x-0.25e0;
+ w1 = b+h/3.0e0;
+S30:
+/*
+ SERIES EXPANSION
+*/
+ r = h/(h+2.0e0);
+ t = r*r;
+ w = ((p2*t+p1)*t+p0)/((q2*t+q1)*t+1.0e0);
+ rlog1 = 2.0e0*t*(1.0e0/(1.0e0-r)-r*w)+w1;
+ return rlog1;
+S40:
+ w = *x+0.5e0+0.5e0;
+ rlog1 = *x-log(w);
+ return rlog1;
+} /* END */
+
+/***=====================================================================***/
+static double spmpar(int *i)
+/*
+-----------------------------------------------------------------------
+
+ SPMPAR PROVIDES THE SINGLE PRECISION MACHINE CONSTANTS FOR
+ THE COMPUTER BEING USED. IT IS ASSUMED THAT THE ARGUMENT
+ I IS AN INTEGER HAVING ONE OF THE VALUES 1, 2, OR 3. IF THE
+ SINGLE PRECISION ARITHMETIC BEING USED HAS M BASE B DIGITS AND
+ ITS SMALLEST AND LARGEST EXPONENTS ARE EMIN AND EMAX, THEN
+
+ SPMPAR(1) = B**(1 - M), THE MACHINE PRECISION,
+
+ SPMPAR(2) = B**(EMIN - 1), THE SMALLEST MAGNITUDE,
+
+ SPMPAR(3) = B**EMAX*(1 - B**(-M)), THE LARGEST MAGNITUDE.
+
+-----------------------------------------------------------------------
+ WRITTEN BY
+ ALFRED H. MORRIS, JR.
+ NAVAL SURFACE WARFARE CENTER
+ DAHLGREN VIRGINIA
+-----------------------------------------------------------------------
+-----------------------------------------------------------------------
+ MODIFIED BY BARRY W. BROWN TO RETURN DOUBLE PRECISION MACHINE
+ CONSTANTS FOR THE COMPUTER BEING USED. THIS MODIFICATION WAS
+ MADE AS PART OF CONVERTING BRATIO TO DOUBLE PRECISION
+-----------------------------------------------------------------------
+*/
+{
+static int K1 = 4;
+static int K2 = 8;
+static int K3 = 9;
+static int K4 = 10;
+static double spmpar,b,binv,bm1,one,w,z;
+static int emax,emin,ibeta,m;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(*i > 1) goto S10;
+ b = ipmpar(&K1);
+ m = ipmpar(&K2);
+ spmpar = pow(b,(double)(1-m));
+ return spmpar;
+S10:
+ if(*i > 2) goto S20;
+ b = ipmpar(&K1);
+ emin = ipmpar(&K3);
+ one = 1.0;
+ binv = one/b;
+ w = pow(b,(double)(emin+2));
+ spmpar = w*binv*binv*binv;
+ return spmpar;
+S20:
+ ibeta = ipmpar(&K1);
+ m = ipmpar(&K2);
+ emax = ipmpar(&K4);
+ b = ibeta;
+ bm1 = ibeta-1;
+ one = 1.0;
+ z = pow(b,(double)(m-1));
+ w = ((z-one)*b+bm1)/(b*z);
+ z = pow(b,(double)(emax-2));
+ spmpar = w*z*b*b;
+ return spmpar;
+} /* END */
+
+/***=====================================================================***/
+static double stvaln(double *p)
+/*
+**********************************************************************
+
+ double stvaln(double *p)
+ STarting VALue for Neton-Raphon
+ calculation of Normal distribution Inverse
+
+
+ Function
+
+
+ Returns X such that CUMNOR(X) = P, i.e., the integral from -
+ infinity to X of (1/SQRT(2*PI)) EXP(-U*U/2) dU is P
+
+
+ Arguments
+
+
+ P --> The probability whose normal deviate is sought.
+ P is DOUBLE PRECISION
+
+
+ Method
+
+
+ The rational function on page 95 of Kennedy and Gentle,
+ Statistical Computing, Marcel Dekker, NY , 1980.
+
+**********************************************************************
+*/
+{
+static double xden[5] = {
+ 0.993484626060e-1,0.588581570495e0,0.531103462366e0,0.103537752850e0,
+ 0.38560700634e-2
+};
+static double xnum[5] = {
+ -0.322232431088e0,-1.000000000000e0,-0.342242088547e0,-0.204231210245e-1,
+ -0.453642210148e-4
+};
+static int K1 = 5;
+static double stvaln,sign,y,z;
+/*
+ ..
+ .. Executable Statements ..
+*/
+ if(!(*p <= 0.5e0)) goto S10;
+ sign = -1.0e0;
+ z = *p;
+ goto S20;
+S10:
+ sign = 1.0e0;
+ z = 1.0e0-*p;
+S20:
+ y = sqrt(-(2.0e0*log(z)));
+ stvaln = y+devlpl(xnum,&K1,&y)/devlpl(xden,&K1,&y);
+ stvaln = sign*stvaln;
+ return stvaln;
+} /* END */
+
+/***=====================================================================***/
+static double fifdint(double a)
+/************************************************************************
+FIFDINT:
+Truncates a double precision number to an integer and returns the
+value in a double.
+************************************************************************/
+/* a - number to be truncated */
+{
+ return (double) ((int) a);
+} /* END */
+
+/***=====================================================================***/
+static double fifdmax1(double a,double b)
+/************************************************************************
+FIFDMAX1:
+returns the maximum of two numbers a and b
+************************************************************************/
+/* a - first number */
+/* b - second number */
+{
+ if (a < b) return b;
+ else return a;
+} /* END */
+
+/***=====================================================================***/
+static double fifdmin1(double a,double b)
+/************************************************************************
+FIFDMIN1:
+returns the minimum of two numbers a and b
+************************************************************************/
+/* a - first number */
+/* b - second number */
+{
+ if (a < b) return a;
+ else return b;
+} /* END */
+
+/***=====================================================================***/
+static double fifdsign(double mag,double sign)
+/************************************************************************
+FIFDSIGN:
+transfers the sign of the variable "sign" to the variable "mag"
+************************************************************************/
+/* mag - magnitude */
+/* sign - sign to be transfered */
+{
+ if (mag < 0) mag = -mag;
+ if (sign < 0) mag = -mag;
+ return mag;
+
+} /* END */
+
+/***=====================================================================***/
+static long fifidint(double a)
+/************************************************************************
+FIFIDINT:
+Truncates a double precision number to a long integer
+************************************************************************/
+/* a - number to be truncated */
+{
+ if (a < 1.0) return (long) 0;
+ else return (long) a;
+} /* END */
+
+/***=====================================================================***/
+static long fifmod(long a,long b)
+/************************************************************************
+FIFMOD:
+returns the modulo of a and b
+************************************************************************/
+/* a - numerator */
+/* b - denominator */
+{
+ return a % b;
+} /* END */
+
+/***=====================================================================***/
+static void ftnstop(char* msg)
+/************************************************************************
+FTNSTOP:
+Prints msg to standard error and then exits
+************************************************************************/
+/* msg - error message */
+{
+ if (msg != NULL) fprintf(stderr,"*** CDFLIB ERROR: %s\n",msg);
+ /** exit(1); **/ /** RWCox - DON'T EXIT */
+} /* END */
+
+/***=====================================================================***/
+static int ipmpar(int *i)
+/*
+-----------------------------------------------------------------------
+
+ IPMPAR PROVIDES THE INTEGER MACHINE CONSTANTS FOR THE COMPUTER
+ THAT IS USED. IT IS ASSUMED THAT THE ARGUMENT I IS AN INTEGER
+ HAVING ONE OF THE VALUES 1-10. IPMPAR(I) HAS THE VALUE ...
+
+ INTEGERS.
+
+ ASSUME INTEGERS ARE REPRESENTED IN THE N-DIGIT, BASE-A FORM
+
+ SIGN ( X(N-1)*A**(N-1) + ... + X(1)*A + X(0) )
+
+ WHERE 0 .LE. X(I) .LT. A FOR I=0,...,N-1.
+
+ IPMPAR(1) = A, THE BASE.
+
+ IPMPAR(2) = N, THE NUMBER OF BASE-A DIGITS.
+
+ IPMPAR(3) = A**N - 1, THE LARGEST MAGNITUDE.
+
+ FLOATING-POINT NUMBERS.
+
+ IT IS ASSUMED THAT THE SINGLE AND DOUBLE PRECISION FLOATING
+ POINT ARITHMETICS HAVE THE SAME BASE, SAY B, AND THAT THE
+ NONZERO NUMBERS ARE REPRESENTED IN THE FORM
+
+ SIGN (B**E) * (X(1)/B + ... + X(M)/B**M)
+
+ WHERE X(I) = 0,1,...,B-1 FOR I=1,...,M,
+ X(1) .GE. 1, AND EMIN .LE. E .LE. EMAX.
+
+ IPMPAR(4) = B, THE BASE.
+
+ SINGLE-PRECISION
+
+ IPMPAR(5) = M, THE NUMBER OF BASE-B DIGITS.
+
+ IPMPAR(6) = EMIN, THE SMALLEST EXPONENT E.
+
+ IPMPAR(7) = EMAX, THE LARGEST EXPONENT E.
+
+ DOUBLE-PRECISION
+
+ IPMPAR(8) = M, THE NUMBER OF BASE-B DIGITS.
+
+ IPMPAR(9) = EMIN, THE SMALLEST EXPONENT E.
+
+ IPMPAR(10) = EMAX, THE LARGEST EXPONENT E.
+
+-----------------------------------------------------------------------
+
+ TO DEFINE THIS FUNCTION FOR THE COMPUTER BEING USED REMOVE
+ THE COMMENT DELIMITORS FROM THE DEFINITIONS DIRECTLY BELOW THE NAME
+ OF THE MACHINE
+
+*** RWCox: at this time, the IEEE parameters are enabled.
+
+-----------------------------------------------------------------------
+
+ IPMPAR IS AN ADAPTATION OF THE FUNCTION I1MACH, WRITTEN BY
+ P.A. FOX, A.D. HALL, AND N.L. SCHRYER (BELL LABORATORIES).
+ IPMPAR WAS FORMED BY A.H. MORRIS (NSWC). THE CONSTANTS ARE
+ FROM BELL LABORATORIES, NSWC, AND OTHER SOURCES.
+
+-----------------------------------------------------------------------
+ .. Scalar Arguments ..
+*/
+{
+static int imach[11];
+static int outval ;
+/* MACHINE CONSTANTS FOR AMDAHL MACHINES. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 16;
+ imach[5] = 6;
+ imach[6] = -64;
+ imach[7] = 63;
+ imach[8] = 14;
+ imach[9] = -64;
+ imach[10] = 63;
+*/
+/* MACHINE CONSTANTS FOR THE AT&T 3B SERIES, AT&T
+ PC 7300, AND AT&T 6300. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -125;
+ imach[7] = 128;
+ imach[8] = 53;
+ imach[9] = -1021;
+ imach[10] = 1024;
+*/
+/* MACHINE CONSTANTS FOR THE BURROUGHS 1700 SYSTEM. */
+/*
+ imach[1] = 2;
+ imach[2] = 33;
+ imach[3] = 8589934591;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -256;
+ imach[7] = 255;
+ imach[8] = 60;
+ imach[9] = -256;
+ imach[10] = 255;
+*/
+/* MACHINE CONSTANTS FOR THE BURROUGHS 5700 SYSTEM. */
+/*
+ imach[1] = 2;
+ imach[2] = 39;
+ imach[3] = 549755813887;
+ imach[4] = 8;
+ imach[5] = 13;
+ imach[6] = -50;
+ imach[7] = 76;
+ imach[8] = 26;
+ imach[9] = -50;
+ imach[10] = 76;
+*/
+/* MACHINE CONSTANTS FOR THE BURROUGHS 6700/7700 SYSTEMS. */
+/*
+ imach[1] = 2;
+ imach[2] = 39;
+ imach[3] = 549755813887;
+ imach[4] = 8;
+ imach[5] = 13;
+ imach[6] = -50;
+ imach[7] = 76;
+ imach[8] = 26;
+ imach[9] = -32754;
+ imach[10] = 32780;
+*/
+/* MACHINE CONSTANTS FOR THE CDC 6000/7000 SERIES
+ 60 BIT ARITHMETIC, AND THE CDC CYBER 995 64 BIT
+ ARITHMETIC (NOS OPERATING SYSTEM). */
+/*
+ imach[1] = 2;
+ imach[2] = 48;
+ imach[3] = 281474976710655;
+ imach[4] = 2;
+ imach[5] = 48;
+ imach[6] = -974;
+ imach[7] = 1070;
+ imach[8] = 95;
+ imach[9] = -926;
+ imach[10] = 1070;
+*/
+/* MACHINE CONSTANTS FOR THE CDC CYBER 995 64 BIT
+ ARITHMETIC (NOS/VE OPERATING SYSTEM). */
+/*
+ imach[1] = 2;
+ imach[2] = 63;
+ imach[3] = 9223372036854775807;
+ imach[4] = 2;
+ imach[5] = 48;
+ imach[6] = -4096;
+ imach[7] = 4095;
+ imach[8] = 96;
+ imach[9] = -4096;
+ imach[10] = 4095;
+*/
+/* MACHINE CONSTANTS FOR THE CRAY 1, XMP, 2, AND 3. */
+/*
+ imach[1] = 2;
+ imach[2] = 63;
+ imach[3] = 9223372036854775807;
+ imach[4] = 2;
+ imach[5] = 47;
+ imach[6] = -8189;
+ imach[7] = 8190;
+ imach[8] = 94;
+ imach[9] = -8099;
+ imach[10] = 8190;
+*/
+/* MACHINE CONSTANTS FOR THE DATA GENERAL ECLIPSE S/200. */
+/*
+ imach[1] = 2;
+ imach[2] = 15;
+ imach[3] = 32767;
+ imach[4] = 16;
+ imach[5] = 6;
+ imach[6] = -64;
+ imach[7] = 63;
+ imach[8] = 14;
+ imach[9] = -64;
+ imach[10] = 63;
+*/
+/* MACHINE CONSTANTS FOR THE HARRIS 220. */
+/*
+ imach[1] = 2;
+ imach[2] = 23;
+ imach[3] = 8388607;
+ imach[4] = 2;
+ imach[5] = 23;
+ imach[6] = -127;
+ imach[7] = 127;
+ imach[8] = 38;
+ imach[9] = -127;
+ imach[10] = 127;
+*/
+/* MACHINE CONSTANTS FOR THE HONEYWELL 600/6000
+ AND DPS 8/70 SERIES. */
+/*
+ imach[1] = 2;
+ imach[2] = 35;
+ imach[3] = 34359738367;
+ imach[4] = 2;
+ imach[5] = 27;
+ imach[6] = -127;
+ imach[7] = 127;
+ imach[8] = 63;
+ imach[9] = -127;
+ imach[10] = 127;
+*/
+/* MACHINE CONSTANTS FOR THE HP 2100
+ 3 WORD DOUBLE PRECISION OPTION WITH FTN4 */
+/*
+ imach[1] = 2;
+ imach[2] = 15;
+ imach[3] = 32767;
+ imach[4] = 2;
+ imach[5] = 23;
+ imach[6] = -128;
+ imach[7] = 127;
+ imach[8] = 39;
+ imach[9] = -128;
+ imach[10] = 127;
+*/
+/* MACHINE CONSTANTS FOR THE HP 2100
+ 4 WORD DOUBLE PRECISION OPTION WITH FTN4 */
+/*
+ imach[1] = 2;
+ imach[2] = 15;
+ imach[3] = 32767;
+ imach[4] = 2;
+ imach[5] = 23;
+ imach[6] = -128;
+ imach[7] = 127;
+ imach[8] = 55;
+ imach[9] = -128;
+ imach[10] = 127;
+*/
+/* MACHINE CONSTANTS FOR THE HP 9000. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -126;
+ imach[7] = 128;
+ imach[8] = 53;
+ imach[9] = -1021;
+ imach[10] = 1024;
+*/
+/* MACHINE CONSTANTS FOR THE IBM 360/370 SERIES,
+ THE ICL 2900, THE ITEL AS/6, THE XEROX SIGMA
+ 5/7/9 AND THE SEL SYSTEMS 85/86. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 16;
+ imach[5] = 6;
+ imach[6] = -64;
+ imach[7] = 63;
+ imach[8] = 14;
+ imach[9] = -64;
+ imach[10] = 63;
+*/
+/* MACHINE CONSTANTS FOR THE IBM PC. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -125;
+ imach[7] = 128;
+ imach[8] = 53;
+ imach[9] = -1021;
+ imach[10] = 1024;
+*/
+/* MACHINE CONSTANTS FOR THE MACINTOSH II - ABSOFT
+ MACFORTRAN II. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -125;
+ imach[7] = 128;
+ imach[8] = 53;
+ imach[9] = -1021;
+ imach[10] = 1024;
+*/
+/* MACHINE CONSTANTS FOR THE MICROVAX - VMS FORTRAN. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -127;
+ imach[7] = 127;
+ imach[8] = 56;
+ imach[9] = -127;
+ imach[10] = 127;
+*/
+/* MACHINE CONSTANTS FOR THE PDP-10 (KA PROCESSOR). */
+/*
+ imach[1] = 2;
+ imach[2] = 35;
+ imach[3] = 34359738367;
+ imach[4] = 2;
+ imach[5] = 27;
+ imach[6] = -128;
+ imach[7] = 127;
+ imach[8] = 54;
+ imach[9] = -101;
+ imach[10] = 127;
+*/
+/* MACHINE CONSTANTS FOR THE PDP-10 (KI PROCESSOR). */
+/*
+ imach[1] = 2;
+ imach[2] = 35;
+ imach[3] = 34359738367;
+ imach[4] = 2;
+ imach[5] = 27;
+ imach[6] = -128;
+ imach[7] = 127;
+ imach[8] = 62;
+ imach[9] = -128;
+ imach[10] = 127;
+*/
+/* MACHINE CONSTANTS FOR THE PDP-11 FORTRAN SUPPORTING
+ 32-BIT INTEGER ARITHMETIC. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -127;
+ imach[7] = 127;
+ imach[8] = 56;
+ imach[9] = -127;
+ imach[10] = 127;
+*/
+/* MACHINE CONSTANTS FOR THE SEQUENT BALANCE 8000. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -125;
+ imach[7] = 128;
+ imach[8] = 53;
+ imach[9] = -1021;
+ imach[10] = 1024;
+*/
+/* MACHINE CONSTANTS FOR THE SILICON GRAPHICS IRIS-4D
+ SERIES (MIPS R3000 PROCESSOR). */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -125;
+ imach[7] = 128;
+ imach[8] = 53;
+ imach[9] = -1021;
+ imach[10] = 1024;
+*/
+/* MACHINE CONSTANTS FOR IEEE ARITHMETIC MACHINES, SUCH AS THE AT&T
+ 3B SERIES, MOTOROLA 68000 BASED MACHINES (E.G. SUN 3 AND AT&T
+ PC 7300), AND 8087 BASED MICROS (E.G. IBM PC AND AT&T 6300). */
+
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -125;
+ imach[7] = 128;
+ imach[8] = 53;
+ imach[9] = -1021;
+ imach[10] = 1024;
+
+/* MACHINE CONSTANTS FOR THE UNIVAC 1100 SERIES. */
+/*
+ imach[1] = 2;
+ imach[2] = 35;
+ imach[3] = 34359738367;
+ imach[4] = 2;
+ imach[5] = 27;
+ imach[6] = -128;
+ imach[7] = 127;
+ imach[8] = 60;
+ imach[9] = -1024;
+ imach[10] = 1023;
+*/
+/* MACHINE CONSTANTS FOR THE VAX 11/780. */
+/*
+ imach[1] = 2;
+ imach[2] = 31;
+ imach[3] = 2147483647;
+ imach[4] = 2;
+ imach[5] = 24;
+ imach[6] = -127;
+ imach[7] = 127;
+ imach[8] = 56;
+ imach[9] = -127;
+ imach[10] = 127;
+*/
+ outval = imach[*i];
+ return outval ;
+}
+
+/*************************************************************************/
+/*************************************************************************/
+/************************ End of cdflib inclusion ************************/
+/*************************************************************************/
+/*************************************************************************/
+
+/*-----------------------------------------------------------------------*/
+typedef struct { double p,q ; } pqpair ; /* for returning p=cdf q=1-cdf */
+/*-----------------------------------------------------------------------*/
+#undef BIGG
+#define BIGG 9.99e+37 /* a really big number (duh) */
+/*-----------------------------------------------------------------------*/
+
+/*************************************************************************/
+/******** Internal functions for various statistical computations ********/
+/*************************************************************************/
+
+/*---------------------------------------------------------------
+ F statistic
+-----------------------------------------------------------------*/
+
+static double fstat_pq2s( pqpair pq , double dofnum , double dofden )
+{
+ int which , status ;
+ double p , q , f , dfn , dfd , bound ;
+
+ which = 2 ;
+ p = pq.p ; if( p <= 0.0 ) return 0.0 ;
+ q = pq.q ; if( q <= 0.0 ) return BIGG ;
+ f = 0.0 ;
+ dfn = dofnum ;
+ dfd = dofden ;
+
+ cdff( &which , &p , &q , &f , &dfn , &dfd , &status , &bound ) ;
+ return f ;
+}
+
+/*------------------------------*/
+
+static pqpair fstat_s2pq( double ff , double dofnum , double dofden )
+{
+ int which , status ;
+ double p , q , f , dfn , dfd , bound ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ f = ff ; if( f <= 0.0 ) return pq;
+ dfn = dofnum ; if( dfn <= 0.0 ) return pq ;
+ dfd = dofden ; if( dfd <= 0.0 ) return pq ;
+
+ cdff( &which , &p , &q , &f , &dfn , &dfd , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*---------------------------------------------------------------
+ noncentral F statistic
+-----------------------------------------------------------------*/
+
+static double fnonc_pq2s( pqpair pq , double dofnum , double dofden , double nonc )
+{
+ int which , status ;
+ double p , q , f , dfn , dfd , bound , pnonc ;
+
+ which = 2 ;
+ p = pq.p ; if( p <= 0.0 ) return 0.0 ;
+ q = pq.q ; if( q <= 0.0 ) return BIGG ;
+ f = 0.0 ;
+ dfn = dofnum ;
+ dfd = dofden ;
+ pnonc = nonc ;
+
+ cdffnc( &which , &p , &q , &f , &dfn , &dfd , &pnonc , &status , &bound ) ;
+ return f ;
+}
+
+/*------------------------------*/
+
+static pqpair fnonc_s2pq( double ff , double dofnum , double dofden , double nonc )
+{
+ int which , status ;
+ double p , q , f , dfn , dfd , bound , pnonc ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ f = ff ; if( f <= 0.0 ) return pq ;
+ dfn = dofnum ; if( dfn <= 0.0 ) return pq ;
+ dfd = dofden ; if( dfd <= 0.0 ) return pq ;
+ pnonc = nonc ; if( pnonc < 0.0 ) return pq ;
+
+ cdffnc( &which , &p , &q , &f , &dfn , &dfd , &pnonc , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*---------------------------------------------------------------
+ Standard Normal distribution
+-----------------------------------------------------------------*/
+
+static pqpair normal_s2pq( double zz )
+{
+ double p , q , x=zz ;
+ pqpair pq ;
+
+ cumnor( &x, &p, &q ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+static double normal_pq2s( pqpair pq )
+{
+ double p=pq.p , q=pq.q ;
+
+ if( p <= 0.0 ) return -BIGG ;
+ if( q <= 0.0 ) return BIGG ;
+ return dinvnr( &p,&q ) ;
+}
+
+/*----------------------------------------------------------------
+ Chi-square
+------------------------------------------------------------------*/
+
+static pqpair chisq_s2pq( double xx , double dof )
+{
+ int which , status ;
+ double p,q,x,df,bound ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ x = xx ; if( x <= 0.0 ) return pq ;
+ df = dof ; if( dof <= 0.0 ) return pq ;
+
+ cdfchi( &which , &p , &q , &x , &df , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+static double chisq_pq2s( pqpair pq , double dof )
+{
+ int which , status ;
+ double p,q,x,df,bound ;
+
+ which = 2 ;
+ p = pq.p ; if( p <= 0.0 ) return 0.0 ;
+ q = pq.q ; if( q <= 0.0 ) return BIGG ;
+ x = 0.0 ;
+ df = dof ;
+
+ cdfchi( &which , &p , &q , &x , &df , &status , &bound ) ;
+ return x ;
+}
+
+/*----------------------------------------------------------------
+ noncentral Chi-square
+------------------------------------------------------------------*/
+
+static pqpair chsqnonc_s2pq( double xx , double dof , double nonc )
+{
+ int which , status ;
+ double p,q,x,df,bound , pnonc ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ x = xx ; if( x <= 0.0 ) return pq ;
+ df = dof ; if( df <= 0.0 ) return pq ;
+ pnonc = nonc ; if( pnonc < 0.0 ) return pq ;
+
+ cdfchn( &which , &p , &q , &x , &df , &pnonc , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+static double chsqnonc_pq2s( pqpair pq , double dof , double nonc )
+{
+ int which , status ;
+ double p,q,x,df,bound , pnonc ;
+
+ which = 2 ;
+ p = pq.p ; if( p <= 0.0 ) return 0.0 ;
+ q = pq.q ; if( q <= 0.0 ) return BIGG ;
+ x = 0.0 ;
+ df = dof ;
+ pnonc = nonc ;
+
+ cdfchn( &which , &p , &q , &x , &df , &pnonc , &status , &bound ) ;
+ return x ;
+}
+
+/*----------------------------------------------------------------
+ Beta distribution
+------------------------------------------------------------------*/
+
+static pqpair beta_s2pq( double xx , double aa , double bb )
+{
+ int which , status ;
+ double p,q,x,y,a,b,bound ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ x = xx ; if( x <= 0.0 ) return pq ;
+ y = 1.0 - xx ; if( y <= 0.0 ){ pq.p=1.0; pq.q=0.0; return pq; }
+ a = aa ; if( a < 0.0 ) return pq ;
+ b = bb ; if( b < 0.0 ) return pq ;
+
+ cdfbet( &which , &p , &q , &x , &y , &a , &b , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+static double beta_pq2s( pqpair pq , double aa , double bb )
+{
+ int which , status ;
+ double p,q,x,y,a,b,bound ;
+
+ which = 2 ;
+ p = pq.p ; if( p <= 0.0 ) return 0.0 ;
+ q = pq.q ; if( q <= 0.0 ) return 1.0 ;
+ x = 0.0 ;
+ y = 1.0 ;
+ a = aa ;
+ b = bb ;
+
+ cdfbet( &which , &p , &q , &x , &y , &a , &b , &status , &bound ) ;
+ return x ;
+}
+
+/*----------------------------------------------------------------
+ Binomial distribution
+ (that is, the probability that more than ss out of ntrial
+ trials were successful).
+------------------------------------------------------------------*/
+
+static pqpair binomial_s2pq( double ss , double ntrial , double ptrial )
+{
+ int which , status ;
+ double p,q, s,xn,pr,ompr,bound ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ s = ss ; if( s < 0.0 ) return pq ;
+ xn = ntrial ; if( xn <= 0.0 ) return pq ;
+ pr = ptrial ; if( pr < 0.0 ) return pq ;
+ ompr = 1.0 - ptrial ;
+
+ cdfbin( &which , &p , &q , &s , &xn , &pr , &ompr , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+static double binomial_pq2s( pqpair pq , double ntrial , double ptrial )
+{
+ int which , status ;
+ double p,q, s,xn,pr,ompr,bound ;
+
+ which = 2 ;
+ p = pq.p ;
+ q = pq.q ;
+ s = 0.0 ;
+ xn = ntrial ;
+ pr = ptrial ;
+ ompr = 1.0 - ptrial ;
+
+ cdfbin( &which , &p , &q , &s , &xn , &pr , &ompr , &status , &bound ) ;
+ return s ;
+}
+
+/*----------------------------------------------------------------
+ Gamma distribution.
+------------------------------------------------------------------*/
+
+static pqpair gamma_s2pq( double xx , double sh , double sc )
+{
+ int which , status ;
+ double p,q, x,shape,scale,bound ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ x = xx ; if( x <= 0.0 ) return pq ;
+ shape = sh ; if( shape <= 0.0 ) return pq ;
+ scale = sc ; if( scale <= 0.0 ) return pq ;
+
+ cdfgam( &which , &p , &q , &x , &shape , &scale , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+static double gamma_pq2s( pqpair pq , double sh , double sc )
+{
+ int which , status ;
+ double p,q, x,shape,scale,bound ;
+
+ which = 2 ;
+ p = pq.p ; if( p <= 0.0 ) return 0.0 ;
+ q = pq.q ; if( q <= 0.0 ) return BIGG ;
+ x = 0.0 ;
+ shape = sh ;
+ scale = sc ;
+
+ cdfgam( &which , &p , &q , &x , &shape , &scale , &status , &bound ) ;
+ return x ;
+}
+
+/*----------------------------------------------------------------
+ Poisson distribution
+------------------------------------------------------------------*/
+
+static pqpair poisson_s2pq( double xx , double lambda )
+{
+ int which , status ;
+ double p,q, s,xlam,bound ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ s = xx ; if( s < 0.0 ) return pq ;
+ xlam = lambda ; if( xlam < 0.0 ) return pq ;
+
+ cdfpoi( &which , &p , &q , &s , &xlam , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+static double poisson_pq2s( pqpair pq , double lambda )
+{
+ int which , status ;
+ double p,q, s,xlam,bound ;
+
+ which = 2 ;
+ p = pq.p ;
+ q = pq.q ;
+ s = 0.0 ;
+ xlam = lambda ;
+
+ cdfpoi( &which , &p , &q , &s , &xlam , &status , &bound ) ;
+ return s ;
+}
+
+/*----------------------------------------------------------------
+ T distribution.
+------------------------------------------------------------------*/
+
+static pqpair student_s2pq( double xx , double dof )
+{
+ int which , status ;
+ double p,q, s,xlam,bound ;
+ pqpair pq={0.0,1.0} ;
+
+ which = 1 ;
+ p = 0.0 ;
+ q = 1.0 ;
+ s = xx ;
+ xlam = dof ; if( xlam <= 0.0 ) return pq ;
+
+ cdft( &which , &p , &q , &s , &xlam , &status , &bound ) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+double student_pq2s( pqpair pq , double dof )
+{
+ int which , status ;
+ double p,q, s,xlam,bound ;
+
+ which = 2 ;
+ p = pq.p ;
+ q = pq.q ;
+ s = 0.0 ;
+ xlam = dof ;
+
+ cdft( &which , &p , &q , &s , &xlam , &status , &bound ) ;
+ return s ;
+}
+
+/****************************************************************************/
+/* For the distributions below here, cdflib can't do what we want directly. */
+/****************************************************************************/
+
+/*----------------------------------------------------------------
+ Null correlation distribution.
+ Let x = (rr+1)/2; then x is Beta(dof/2,dof/2).
+------------------------------------------------------------------*/
+
+static pqpair correl_s2pq( double rr , double dof ) /* fake it with cdflib */
+{
+ return beta_s2pq( 0.5*(rr+1.0) , 0.5*dof , 0.5*dof ) ;
+}
+
+/*------------------------------*/
+
+static double correl_pq2s( pqpair pq , double dof )
+{
+ double xx = beta_pq2s( pq , 0.5*dof , 0.5*dof ) ;
+ return (2.0*xx-1.0) ;
+}
+
+/*----------------------------------------------------------------
+ Uniform U(0,1) distribution.
+------------------------------------------------------------------*/
+
+static pqpair uniform_s2pq( double xx ) /* this isn't too hard */
+{
+ pqpair pq ;
+ if( xx <= 0.0 ) pq.p = 0.0 ;
+ else if( xx >= 1.0 ) pq.p = 1.0 ;
+ else pq.p = xx ;
+ pq.q = 1.0-xx ; return pq ;
+}
+
+/*------------------------------*/
+
+static double uniform_pq2s( pqpair pq )
+{
+ return pq.p ; /* that was easy */
+}
+
+/*----------------------------------------------------------------
+ standard Logistic distribution.
+------------------------------------------------------------------*/
+
+static pqpair logistic_s2pq( double xx ) /* this isn't hard, either */
+{
+ pqpair pq ;
+ if( xx >= 0.0 ){ pq.q = 1.0/(1.0+exp( xx)); pq.p = 1.0-pq.q; }
+ else { pq.p = 1.0/(1.0+exp(-xx)); pq.q = 1.0-pq.p; }
+ return pq ;
+}
+
+/*------------------------------*/
+
+static double logistic_pq2s( pqpair pq )
+{
+ if( pq.p <= 0.0 ) return -BIGG ;
+ else if( pq.q <= 0.0 ) return BIGG ;
+
+ if( pq.p < pq.q ) return -log(1.0/pq.p-1.0) ;
+ else return log(1.0/pq.q-1.0) ;
+}
+
+/*----------------------------------------------------------------
+ standard Laplace distribution.
+------------------------------------------------------------------*/
+
+static pqpair laplace_s2pq( double xx ) /* easy */
+{
+ pqpair pq ;
+
+ if( xx >= 0.0 ){ pq.q = 0.5*exp(-xx) ; pq.p = 1.0-pq.q ; }
+ else { pq.p = 0.5*exp( xx) ; pq.q = 1.0-pq.p ; }
+ return pq ;
+}
+
+/*------------------------------*/
+
+static double laplace_pq2s( pqpair pq )
+{
+ if( pq.p <= 0.0 ) return -BIGG ;
+ else if( pq.q <= 0.0 ) return BIGG ;
+
+ if( pq.p < pq.q ) return log(2.0*pq.p) ;
+ else return -log(2.0*pq.q) ;
+}
+
+/*----------------------------------------------------------------
+ noncentral T distribution = hard calculation
+------------------------------------------------------------------*/
+
+/****************************************************************************
+ Noncentral t distribution function by
+ Professor K. Krishnamoorthy
+ Department of Mathematics
+ University of Louisiana at Lafayette
+ Manually translated from Fortran by RWC.
+*****************************************************************************/
+
+#if 0
+static double alng( double x ) /* log(Gamma(x)) from K */
+{
+ int indx ;
+ double xx,fterm,sum,valg ;
+ double b[9] = { 0.0 ,
+ 8.33333333333333e-2, 3.33333333333333e-2,
+ 2.52380952380952e-1, 5.25606469002695e-1,
+ 1.01152306812684e0, 1.51747364915329e0,
+ 2.26948897420496e0, 3.00991738325940e0 } ;
+
+ if( x < 8.0 ){ xx = x + 8.0 ; indx = 1 ; }
+ else { xx = x ; indx = 0 ; }
+
+ fterm = (xx-0.5)*log(xx) - xx + 9.1893853320467e-1 ;
+ sum = b[1]/(xx+b[2]/(xx+b[3]/(xx+b[4]/(xx+b[5]/(xx+b[6]/
+ (xx+b[7]/(xx+b[8]))))))) ;
+ valg = sum + fterm ;
+ if(indx)
+ valg = valg-log(x+7.0)-log(x+6.0)-log(x+5.0)
+ -log(x+4.0)-log(x+3.0)-log(x+2.0)-log(x+1.0)-log(x) ;
+ return valg ;
+}
+#else
+static double alng( double x ) /*-- replace with cdflib function --*/
+{
+ double xx=x ; return alngam( &xx ) ;
+}
+#endif
+
+/*---------------------------------------------------------------------------*/
+
+#if 0
+static double gaudf( double x ) /* N(0,1) cdf from K */
+{
+ static double p0=913.16744211475570 , p1=1024.60809538333800,
+ p2=580.109897562908800, p3=202.102090717023000,
+ p4=46.0649519338751400, p5=6.81311678753268400,
+ p6=6.047379926867041e-1,p7=2.493381293151434e-2 ;
+ static double q0=1826.33488422951125, q1=3506.420597749092,
+ q2=3044.77121163622200, q3=1566.104625828454,
+ q4=523.596091947383490, q5=116.9795245776655,
+ q6=17.1406995062577800, q7=1.515843318555982,
+ q8=6.25e-2 ;
+ static double sqr2pi=2.506628274631001 ;
+ int check ;
+ double reslt,z , first,phi ;
+
+ if(x > 0.0){ z = x ; check = 1 ; }
+ else { z =-x ; check = 0 ; }
+
+ if( z > 32.0 ) return (x > 0.0) ? 1.0 : 0.0 ;
+
+ first = exp(-0.5*z*z) ;
+ phi = first/sqr2pi ;
+
+ if (z < 7.0)
+ reslt = first* (((((((p7*z+p6)*z+p5)*z+p4)*z+p3)*z+p2)*z+p1)*z+p0)
+ /((((((((q8*z+q7)*z+q6)*z+q5)*z+q4)*z+q3)*z+q2)*z+q1)*z+q0);
+ else
+ reslt = phi/(z+1.0/(z+2.0/(z+3.0/(z+4.0/(z+6.0/(z+7.0)))))) ;
+
+ if(check) reslt = 1.0 - reslt ;
+ return reslt ;
+}
+#else
+static double gaudf( double x ) /*-- replace with cdflib func --*/
+{
+ double xx=x , p,q ;
+ cumnor( &xx, &p, &q ); return p;
+}
+#endif
+
+/*---------------------------------------------------------------------------*/
+
+#if 0
+static double betadf( double x , double p , double q ) /* Beta cdf from K */
+{
+ int check , ns ;
+ double result,betf,psq,xx,cx,pp,qq ;
+ double term,ai,rx,temp ;
+
+ if( x >= 1.0 ) return 1.0 ;
+ if( x <= 0.0 ) return 0.0 ;
+
+ betf = alng(p)+alng(q)-alng(p+q) ;
+ result=x ;
+ psq=p+q ;
+ cx=1.0-x ;
+ if(p < psq*x){ xx=cx ; cx=x ; pp=q ; qq=p ; check=1 ; }
+ else { xx=x ; pp=p ; qq=q ; check=0 ; }
+
+ term=1.0 ;
+ ai=1.0 ;
+ result=1.0 ;
+ ns=(int)(qq+cx*psq) ;
+ rx=xx/cx ;
+L3:
+ temp=qq-ai ;
+ if(ns == 0) rx=xx ;
+L4:
+ term=term*temp*rx/(pp+ai) ;
+ result=result+term ;
+ temp=fabs(term) ;
+ if(temp <= 1.e-14 && temp <= 1.e-14*result) goto L5 ;
+ ai=ai+1.0 ;
+ ns=ns-1 ;
+ if(ns >= 0) goto L3 ;
+ temp=psq ;
+ psq=psq+1.0 ;
+ goto L4 ;
+
+L5:
+ result=result*exp(pp*log(xx)+(qq-1.0)*log(cx)-betf)/pp ;
+ if(check) result=1.0-result ;
+ return result ;
+}
+#else
+static double betadf( double x , double p , double q ) /*-- cdflib func --*/
+{
+ double xx=x,yy=1.0-x , aa=p,bb=q , pp,qq ;
+ cumbet( &xx,&yy , &aa,&bb , &pp,&qq ) ; return pp ;
+}
+#endif
+
+/*---------------------------------------------------------------------------*/
+/* Krishnamoorthy's function for cdf of noncentral t, for df > 0,
+ translated into C by RW Cox [Mar 2004].
+ Note the original fails for delta=0, so we call the cdflib func for this.
+ A couple of other minor fixes are also included.
+-----------------------------------------------------------------------------*/
+
+static pqpair tnonc_s2pq( double t , double df , double delta )
+{
+ int indx , k , i ;
+ double x,del,tnd,ans,y,dels,a,b,c ;
+ double pkf,pkb,qkf,qkb , pgamf,pgamb,qgamf,qgamb ;
+ double pbetaf,pbetab,qbetaf,qbetab ;
+ double ptermf,qtermf,ptermb,qtermb,term ;
+ double rempois,delosq2,sum,cons,error ;
+
+ pqpair pq={0.0,1.0} ; /* will be return value */
+ double ab1 ;
+
+ /*-- stupid user? --*/
+
+ if( df <= 0.0 ) return pq ;
+
+ /*-- non-centrality = 0? --*/
+
+ if( fabs(delta) < 1.e-8 ) return student_s2pq(t,df) ;
+
+ /*-- start K's code here --*/
+
+ if( t < 0.0 ){ x = -t ; del = -delta ; indx = 1 ; } /* x will be */
+ else { x = t ; del = delta ; indx = 0 ; } /* positive */
+
+ ans = gaudf(-del) ; /* prob that x <= 0 = Normal cdf */
+
+ /*-- the nearly trivial case of x=0 --*/
+
+ if( x == 0.0 ){ pq.p = ans; pq.q = 1.0-ans; return pq; }
+
+ if( df == 1.0 ) df = 1.0000001 ; /** df=1 is BAD **/
+
+ y = x*x/(df+x*x) ; /* between 0 and 1 */
+ dels = 0.5*del*del ; /* will be positive */
+ k = (int)dels ; /* 0, 1, 2, ... */
+ a = k+0.5 ; /* might be as small as 0.5 */
+ c = k+1.0 ;
+ b = 0.5*df ; /* might be as small as 0.0 */
+
+ pkf = exp(-dels+k*log(dels)-alng(k+1.0)) ;
+ pkb = pkf ;
+ qkf = exp(-dels+k*log(dels)-alng(k+1.0+0.5)) ;
+ qkb = qkf ;
+
+ pbetaf = betadf(y, a, b) ;
+ pbetab = pbetaf ;
+ qbetaf = betadf(y, c, b) ;
+ qbetab = qbetaf ;
+
+ ab1 = a+b-1.0 ; /* might be as small as -0.5 */
+
+ /*-- RWCox: if a+b-1 < 0, log(Gamma(a+b-1)) won't work;
+ instead, use Gamma(a+b-1)=Gamma(a+b)/(a+b-1) --*/
+
+ if( ab1 > 0.0 )
+ pgamf = exp(alng(ab1)-alng(a)-alng(b)+(a-1.0)*log(y)+b*log(1.0-y)) ;
+ else
+ pgamf = exp(alng(a+b)-alng(a)-alng(b)+(a-1.0)*log(y)+b*log(1.0-y))/ab1 ;
+
+ pgamb = pgamf*y*(ab1)/a ;
+
+ /*-- we can't have c+b-1 < 0, so the above patchup isn't needed --*/
+
+ qgamf = exp(alng(c+b-1.0)-alng(c)-alng(b)+(c-1.0)*log(y) + b*log(1.0-y)) ;
+ qgamb = qgamf*y*(c+b-1.0)/c ;
+
+ rempois = 1.0 - pkf ;
+ delosq2 = del/1.4142135623731 ;
+ sum = pkf*pbetaf+delosq2*qkf*qbetaf ;
+ cons = 0.5*(1.0 + 0.5*fabs(delta)) ;
+ i = 0 ;
+L1:
+ i = i + 1 ;
+ pgamf = pgamf*y*(a+b+i-2.0)/(a+i-1.0) ;
+ pbetaf = pbetaf - pgamf ;
+ pkf = pkf*dels/(k+i) ;
+ ptermf = pkf*pbetaf ;
+ qgamf = qgamf*y*(c+b+i-2.0)/(c+i-1.0) ;
+ qbetaf = qbetaf - qgamf ;
+ qkf = qkf*dels/(k+i-1.0+1.5) ;
+ qtermf = qkf*qbetaf ;
+ term = ptermf + delosq2*qtermf ;
+ sum = sum + term ;
+ error = rempois*cons*pbetaf ;
+ rempois = rempois - pkf ;
+
+ if( i > k ){
+ if( error <= 1.e-12 || i >= 9999 ) goto L2 ;
+ goto L1 ;
+ } else {
+ pgamb = pgamb*(a-i+1.0)/(y*(a+b-i)) ;
+ pbetab = pbetab + pgamb ;
+ pkb = (k-i+1.0)*pkb/dels ;
+ ptermb = pkb*pbetab ;
+ qgamb = qgamb*(c-i+1.0)/(y*(c+b-i)) ;
+ qbetab = qbetab + qgamb ;
+ qkb = (k-i+1.0+0.5)*qkb/dels ;
+ qtermb = qkb*qbetab ;
+ term = ptermb + delosq2*qtermb ;
+ sum = sum + term ;
+ rempois = rempois - pkb ;
+ if (rempois <= 1.e-12 || i >= 9999) goto L2 ;
+ goto L1 ;
+ }
+L2:
+ tnd = 0.5*sum + ans ;
+
+ /*-- return a pqpair, not just the cdf --*/
+
+ if( indx ){ pq.p = 1.0-tnd; pq.q = tnd ; }
+ else { pq.p = tnd ; pq.q = 1.0-tnd; }
+ return pq ;
+}
+
+/*------------------------------*/
+/* Inverse to above function;
+ uses cdflib dstinv()/dinvr()
+ to solve the equation.
+--------------------------------*/
+
+static double tnonc_pq2s( pqpair pq , double dof , double nonc )
+{
+ double t ; /* will be result */
+ double tbot,ttop , dt ;
+ double T6=1.e-50,T7=1.e-8 ;
+ double K4=0.5,K5=5.0 ;
+ double fx ;
+ unsigned long qhi,qleft ;
+ int status , qporq , ite ;
+ pqpair tpq ;
+
+ if( dof <= 0.0 ) return BIGG ; /* bad user */
+ if( pq.p <= 0.0 ) return -BIGG ;
+ if( pq.q <= 0.0 ) return BIGG ;
+
+ t = student_pq2s(pq,dof) ; /* initial guess */
+
+ if( fabs(nonc) < 1.e-8 ) return t ;
+
+ t += 0.5*nonc ; /* adjust up or down */
+
+ dt = 0.1 * fabs(t) ; if( dt < 1.0 ) dt = 1.0 ; /* stepsize */
+
+ /* scan down for lower bound, below which cdf is < p */
+
+ tbot = t ;
+ for( ite=0 ; ite < 1000 ; ite++ ){
+ tpq = tnonc_s2pq( tbot , dof , nonc ) ;
+ if( tpq.p <= pq.p ) break ;
+ tbot -= dt ;
+ }
+ if( ite >= 1000 ) return -BIGG ;
+
+ /* scan up for upper bound, above which cdf is > p */
+
+ ttop = tbot+0.5*dt ;
+ for( ite=0 ; ite < 1000 ; ite++ ){
+ tpq = tnonc_s2pq( ttop , dof , nonc ) ;
+ if( tpq.p >= pq.p ) break ;
+ ttop += dt ;
+ }
+ if( ite >= 1000 ) return BIGG ;
+
+ t = 0.5*(tbot+ttop) ; /* initial guess in middle */
+
+ /* initialize searching parameters */
+
+ dstinv(&tbot,&ttop,&K4,&K4,&K5,&T6,&T7);
+
+ status = 0 ; qporq = (pq.p <= pq.q) ;
+
+ while(1){
+
+ dinvr(&status,&t,&fx,&qleft,&qhi) ;
+
+ if( status != 1 ) return t ; /* done! */
+
+ tpq = tnonc_s2pq( t , dof , nonc ) ; /* get cdf */
+
+ /* goal of dinvr is to drive fx to zero */
+
+ fx = (qporq) ? pq.p-tpq.p : pq.q-tpq.q ;
+ }
+
+ return BIGG ; /* unreachable */
+}
+
+/*----------------------------------------------------------------
+ Chi distribution (sqrt of chi-squared, duh).
+------------------------------------------------------------------*/
+
+static pqpair chi_s2pq( double xx , double dof )
+{
+ pqpair pq={0.0,1.0} ;
+
+ if( xx <= 0.0 || dof <= 0.0 ) return pq ;
+ return chisq_s2pq( xx*xx , dof ) ;
+}
+
+/*------------------------------*/
+
+static double chi_pq2s( pqpair pq , double dof )
+{
+ if( pq.p <= 0.0 ) return 0.0 ;
+ if( pq.q <= 0.0 ) return BIGG ;
+ return sqrt(chisq_pq2s(pq,dof)) ;
+}
+
+/*----------------------------------------------------------------
+ Extreme value type I: cdf(x) = exp(-exp(-x)).
+------------------------------------------------------------------*/
+
+static pqpair extval1_s2pq( double x )
+{
+ double p,q,y ; pqpair pq ;
+
+ if( x > -5.0 ){ y = exp(-x) ; p = exp(-y) ; }
+ else { y = 1.0 ; p = 0.0 ; }
+
+ if( y >= 1.e-4 ) q = 1.0-p ;
+ else q = y*(1.0+y*(-0.5+y*(1.0/6.0-y/24.0))) ;
+ pq.p = p ; pq.q = q ; return pq ;
+}
+
+/*------------------------------*/
+
+static double extval1_pq2s( pqpair pq )
+{
+ if( pq.p <= 0.0 ) return -BIGG ;
+ else if( pq.p >= 1.0 ) return BIGG ;
+ return -log(-log(pq.p)) ;
+}
+
+/*----------------------------------------------------------------
+ Weibull distribution: cdf(x) = 1 - exp( -x^c ) for x>0 and c>0.
+------------------------------------------------------------------*/
+
+static pqpair weibull_s2pq( double x , double c )
+{
+ double y ;
+ pqpair pq={0.0,1.0} ;
+
+ if( x <= 0.0 || c <= 0.0 ) return pq ;
+
+ y = pow(x,c) ; pq.q = exp(-y) ;
+ if( y >= 1.e-4 ) pq.p = 1.0-pq.q ;
+ else pq.p = y*(1.0+y*(-0.5+y*(1.0/6.0-y/24.0))) ;
+ return pq ;
+}
+
+/*------------------------------*/
+
+static double weibull_pq2s( pqpair pq , double c )
+{
+ if( pq.p <= 0.0 || c <= 0.0 ) return 0.0 ;
+ else if( pq.q <= 0.0 ) return BIGG ;
+ return pow( -log(pq.q) , 1.0/c ) ;
+}
+
+/*----------------------------------------------------------------
+ Inverse Gaussian:
+ density proportional to exp(-0.5*c(x+1/x))/x^1.5 (x,c >0).
+------------------------------------------------------------------*/
+
+static pqpair invgauss_s2pq( double x, double c )
+{
+ double y , p1,q1 , p2,q2 , v ;
+ pqpair pq={0.0,1.0} ;
+
+ if( x <= 0.0 || c <= 0.0 ) return pq ;
+
+ y = sqrt(c/x) ;
+ v = y*(x-1.0) ; cumnor( &v , &p1,&q1 ) ;
+ v = -y*(x+1.0) ; cumnor( &v , &p2,&q2 ) ;
+ pq.p = p1 ;
+ if( p2 > 0.0 ) pq.p += exp(2.0*c+log(p2)) ;
+ pq.q = 1.0-pq.p ; return pq ;
+}
+
+/*------------------------------*/
+/* Inverse to above function;
+ uses cdflib dstinv()/dinvr()
+ to solve the equation.
+--------------------------------*/
+
+static double invgauss_pq2s( pqpair pq , double c )
+{
+ double t ; /* will be result */
+ double tbot,ttop , dt ;
+ double T6=1.e-50,T7=1.e-8 ;
+ double K4=0.5,K5=5.0 ;
+ double fx ;
+ unsigned long qhi,qleft ;
+ int status , qporq , ite ;
+ pqpair tpq ;
+
+ if( c <= 0.0 ) return BIGG ; /* bad user */
+ if( pq.p <= 0.0 ) return 0.0 ;
+ if( pq.q <= 0.0 ) return BIGG ;
+
+ /* initial guess is t=1; scan down for lower bound */
+
+ tbot = 1.01 ; dt = 0.9 ;
+ for( ite=0 ; ite < 1000 ; ite++ ){
+ tpq = invgauss_s2pq( tbot , c ) ;
+ if( tpq.p <= pq.p ) break ;
+ tbot *= dt ;
+ }
+ if( ite >= 1000 ) return 0.0 ;
+
+ /* scan up for upper bound */
+
+ dt = 1.1 ; ttop = tbot*dt ;
+ for( ite=0 ; ite < 1000 ; ite++ ){
+ tpq = invgauss_s2pq( ttop , c ) ;
+ if( tpq.p >= pq.p ) break ;
+ ttop *= dt ;
+ }
+ if( ite >= 1000 ) return BIGG ;
+
+ t = sqrt(tbot*ttop) ; /* start at geometric mean */
+
+ /* initialize searching parameters */
+
+ dstinv(&tbot,&ttop,&K4,&K4,&K5,&T6,&T7);
+
+ status = 0 ; qporq = (pq.p <= pq.q) ;
+
+ while(1){
+
+ dinvr(&status,&t,&fx,&qleft,&qhi) ;
+
+ if( status != 1 ) return t ; /* done! */
+
+ tpq = invgauss_s2pq( t , c ) ;
+
+ /* goal is to drive fx to zero */
+
+ fx = (qporq) ? pq.p-tpq.p : pq.q-tpq.q ;
+ }
+
+ return BIGG ; /* unreachable */
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a value, calculate both its cdf and reversed cdf (1.0-cdf).
+ - If an error occurs, you'll probably get back {0.0,1.0}.
+ - All the actual work is done in utility functions for each distribution.
+----------------------------------------------------------------------------*/
+
+static pqpair stat2pq( double val, int code, double p1,double p2,double p3 )
+{
+ pqpair pq={0.0,1.0} ;
+
+ switch( code ){
+
+ case NIFTI_INTENT_CORREL: pq = correl_s2pq ( val, p1 ) ; break;
+ case NIFTI_INTENT_TTEST: pq = student_s2pq ( val, p1 ) ; break;
+ case NIFTI_INTENT_FTEST: pq = fstat_s2pq ( val, p1,p2 ) ; break;
+ case NIFTI_INTENT_ZSCORE: pq = normal_s2pq ( val ) ; break;
+ case NIFTI_INTENT_CHISQ: pq = chisq_s2pq ( val, p1 ) ; break;
+ case NIFTI_INTENT_BETA: pq = beta_s2pq ( val, p1,p2 ) ; break;
+ case NIFTI_INTENT_BINOM: pq = binomial_s2pq( val, p1,p2 ) ; break;
+ case NIFTI_INTENT_GAMMA: pq = gamma_s2pq ( val, p1,p2 ) ; break;
+ case NIFTI_INTENT_POISSON: pq = poisson_s2pq ( val, p1 ) ; break;
+ case NIFTI_INTENT_FTEST_NONC: pq = fnonc_s2pq ( val, p1,p2,p3 ); break;
+ case NIFTI_INTENT_CHISQ_NONC: pq = chsqnonc_s2pq( val, p1,p2 ); break;
+ case NIFTI_INTENT_TTEST_NONC: pq = tnonc_s2pq ( val, p1,p2 ) ; break;
+ case NIFTI_INTENT_CHI: pq = chi_s2pq ( val, p1 ) ; break;
+
+ /* these distributions are shifted and scaled copies of a standard case */
+
+ case NIFTI_INTENT_INVGAUSS:
+ if( p1 > 0.0 && p2 > 0.0 ) pq = invgauss_s2pq( val/p1,p2/p1 ) ; break;
+
+ case NIFTI_INTENT_WEIBULL:
+ if( p2 > 0.0 && p3 > 0.0 ) pq = weibull_s2pq ((val-p1)/p2,p3) ; break;
+
+ case NIFTI_INTENT_EXTVAL:
+ if( p2 > 0.0 ) pq = extval1_s2pq ( (val-p1)/p2 ) ; break;
+
+ case NIFTI_INTENT_NORMAL:
+ if( p2 > 0.0 ) pq = normal_s2pq ( (val-p1)/p2 ) ; break;
+
+ case NIFTI_INTENT_LOGISTIC:
+ if( p2 > 0.0 ) pq = logistic_s2pq( (val-p1)/p2 ) ; break;
+
+ case NIFTI_INTENT_LAPLACE:
+ if( p2 > 0.0 ) pq = laplace_s2pq ( (val-p1)/p2 ) ; break;
+
+ case NIFTI_INTENT_UNIFORM:
+ if( p2 > p1 ) pq = uniform_s2pq((val-p1)/(p2-p1)); break;
+
+ /* these cases are trivial (note what is called 'p' is really 'q') */
+
+ case NIFTI_INTENT_PVAL:
+ if( val >= 0.0 && val <= 1.0 ) pq.q = val ;
+ pq.p = 1.0-pq.q; break;
+ case NIFTI_INTENT_LOGPVAL:
+ pq.q = exp(-abs(val)) ; pq.p = 1.0-pq.q; break;
+ case NIFTI_INTENT_LOG10PVAL:
+ pq.q = pow(10.,-abs(val)); pq.p = 1.0-pq.q; break;
+ }
+
+ return pq ;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a pq value (cdf and 1-cdf), compute the value that gives this.
+ - If an error occurs, you'll probably get back a BIGG number.
+ - All the actual work is done in utility functions for each distribution.
+ - Note that for the LOGPVAL and LOG10PVAL cases, the returned value
+ will be -log(q) and -log10(q).
+----------------------------------------------------------------------------*/
+
+static double pq2stat( pqpair pq, int code, double p1,double p2,double p3 )
+{
+ double val=BIGG ;
+
+ if( pq.p < 0.0 || pq.q < 0.0 || pq.p > 1.0 || pq.q > 1.0 ) return val ;
+
+ switch( code ){
+
+ case NIFTI_INTENT_CORREL: val = correl_pq2s ( pq , p1 ) ; break;
+ case NIFTI_INTENT_TTEST: val = student_pq2s ( pq , p1 ) ; break;
+ case NIFTI_INTENT_FTEST: val = fstat_pq2s ( pq , p1,p2 ) ; break;
+ case NIFTI_INTENT_ZSCORE: val = normal_pq2s ( pq ) ; break;
+ case NIFTI_INTENT_CHISQ: val = chisq_pq2s ( pq , p1 ) ; break;
+ case NIFTI_INTENT_BETA: val = beta_pq2s ( pq , p1,p2 ) ; break;
+ case NIFTI_INTENT_BINOM: val = binomial_pq2s( pq , p1,p2 ) ; break;
+ case NIFTI_INTENT_GAMMA: val = gamma_pq2s ( pq , p1,p2 ) ; break;
+ case NIFTI_INTENT_POISSON: val = poisson_pq2s ( pq , p1 ) ; break;
+ case NIFTI_INTENT_FTEST_NONC: val = fnonc_pq2s ( pq , p1,p2,p3 ); break;
+ case NIFTI_INTENT_CHISQ_NONC: val = chsqnonc_pq2s( pq , p1,p2 ); break;
+ case NIFTI_INTENT_TTEST_NONC: val = tnonc_pq2s ( pq , p1,p2 ) ; break;
+ case NIFTI_INTENT_CHI: val = chi_pq2s ( pq , p1 ) ; break;
+
+ /* these distributions are shifted and scaled copies of a standard case */
+
+ case NIFTI_INTENT_INVGAUSS:
+ if( p1 > 0.0 && p2 > 0.0 ) val = p1*invgauss_pq2s ( pq,p2/p1); break;
+
+ case NIFTI_INTENT_WEIBULL:
+ if( p2 > 0.0 && p3 > 0.0 ) val = p1+p2*weibull_pq2s ( pq, p3 ) ; break;
+
+ case NIFTI_INTENT_EXTVAL:
+ if( p2 > 0.0 ) val = p1+p2*extval1_pq2s ( pq ) ; break;
+
+ case NIFTI_INTENT_NORMAL:
+ if( p2 > 0.0 ) val = p1+p2*normal_pq2s ( pq ) ; break;
+
+ case NIFTI_INTENT_LOGISTIC:
+ if( p2 > 0.0 ) val = p1+p2*logistic_pq2s( pq ) ; break;
+
+ case NIFTI_INTENT_LAPLACE:
+ if( p2 > 0.0 ) val = p1+p2*laplace_pq2s ( pq ) ; break;
+
+ case NIFTI_INTENT_UNIFORM:
+ if( p2 > p1 ) val = p1+(p2-p1)*uniform_pq2s(pq) ; break;
+
+ /* these cases are trivial */
+
+ case NIFTI_INTENT_PVAL: val = pq.q ; break;
+ case NIFTI_INTENT_LOGPVAL: val = (pq.q > 0.0) ? -log(pq.q)
+ : BIGG ; break;
+ case NIFTI_INTENT_LOG10PVAL: val = (pq.q > 0.0) ? -log10(pq.q)
+ : BIGG ; break;
+ }
+
+ return val ;
+}
+
+/****************************************************************************/
+/*[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]*/
+/*..........................................................................*/
+/*............. AT LAST! Functions to be called by the user! ..............*/
+/*..........................................................................*/
+/*[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]*/
+/****************************************************************************/
+
+/****************************************************************************
+ Statistical codes implemented here:
+
+ NIFTI_INTENT_CORREL = correlation statistic
+ NIFTI_INTENT_TTEST = t statistic (central)
+ NIFTI_INTENT_FTEST = F statistic (central)
+ NIFTI_INTENT_ZSCORE = N(0,1) statistic
+ NIFTI_INTENT_CHISQ = Chi-squared (central)
+ NIFTI_INTENT_BETA = Beta variable (central)
+ NIFTI_INTENT_BINOM = Binomial variable
+ NIFTI_INTENT_GAMMA = Gamma distribution
+ NIFTI_INTENT_POISSON = Poisson distribution
+ NIFTI_INTENT_FTEST_NONC = noncentral F statistic
+ NIFTI_INTENT_CHISQ_NONC = noncentral chi-squared
+ NIFTI_INTENT_TTEST_NONC = noncentral t statistic
+ NIFTI_INTENT_CHI = Chi statistic (central)
+ NIFTI_INTENT_INVGAUSS = inverse Gaussian variable
+ NIFTI_INTENT_WEIBULL = Weibull distribution
+ NIFTI_INTENT_EXTVAL = Extreme value type I
+ NIFTI_INTENT_NORMAL = N(mu,variance) normal
+ NIFTI_INTENT_LOGISTIC = Logistic distribution
+ NIFTI_INTENT_LAPLACE = Laplace distribution
+ NIFTI_INTENT_UNIFORM = Uniform distribution
+ NIFTI_INTENT_PVAL = "p-value"
+ NIFTI_INTENT_LOGPVAL = -ln(p)
+ NIFTI_INTENT_LOG10PVAL = -log10(p)
+*****************************************************************************/
+
+static char *inam[]={ NULL , NULL ,
+ "CORREL" , "TTEST" , "FTEST" , "ZSCORE" ,
+ "CHISQ" , "BETA" , "BINOM" , "GAMMA" ,
+ "POISSON" , "NORMAL" , "FTEST_NONC" , "CHISQ_NONC" ,
+ "LOGISTIC" , "LAPLACE" , "UNIFORM" , "TTEST_NONC" ,
+ "WEIBULL" , "CHI" , "INVGAUSS" , "EXTVAL" ,
+ "PVAL" , "LOGPVAL" , "LOG10PVAL" ,
+ NULL } ;
+
+#include <ctype.h>
+#include <string.h>
+
+/*--------------------------------------------------------------------------*/
+/*! Given a string name for a statistic, return its integer code.
+ - Input string can be any case.
+ - Returns -1 if name isn't found in the table.
+----------------------------------------------------------------------------*/
+
+int nifti_intent_code( char *name )
+{
+ char *unam , *upt ;
+ int ii ;
+
+ if( name == NULL || *name == '\0' ) return -1 ;
+
+ unam = (char *)malloc(strlen(name)+1);
+ strcpy(unam,name);
+ for( upt=unam ; *upt != '\0' ; upt++ ) *upt = (char)toupper(*upt) ;
+
+ for( ii=NIFTI_FIRST_STATCODE ; ii <= NIFTI_LAST_STATCODE ; ii++ )
+ if( strcmp(inam[ii],unam) == 0 ) break ;
+
+ free(unam) ;
+ return (ii <= NIFTI_LAST_STATCODE) ? ii : -1 ;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a value, return its cumulative distribution function (cdf):
+ - val = statistic
+ - code = NIFTI_INTENT_* statistical code
+ - p1,p2,p3 = parameters of the distribution
+
+ If an error occurs, you'll probably get back 0.0.
+----------------------------------------------------------------------------*/
+
+double nifti_stat2cdf( double val, int code, double p1,double p2,double p3 )
+{
+ pqpair pq ;
+ pq = stat2pq( val, code, p1,p2,p3 ) ;
+ return pq.p ;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a value, return its reversed cumulative distribution function
+ (1-cdf):
+ - val = statistic
+ - code = NIFTI_INTENT_* statistical code
+ - p1,p2,p3 = parameters of the distribution
+
+ If an error transpires, you'll probably get back 1.0.
+----------------------------------------------------------------------------*/
+
+double nifti_stat2rcdf( double val, int code, double p1,double p2,double p3 )
+{
+ pqpair pq ;
+ pq = stat2pq( val, code, p1,p2,p3 ) ;
+ return pq.q ;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a cdf probability, find the value that gave rise to it.
+ - p = cdf; 0 < p < 1
+ - code = NIFTI_INTENT_* statistical code
+ - p1,p2,p3 = parameters of the distribution
+
+ If an error transpires, you'll probably get back a BIGG number.
+----------------------------------------------------------------------------*/
+
+double nifti_cdf2stat( double p , int code, double p1,double p2,double p3 )
+{
+ pqpair pq ;
+ pq.p = p ; pq.q = 1.0-p ;
+ return pq2stat(pq,code,p1,p2,p3) ;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a reversed cdf probability, find the value that gave rise to it.
+ - q = 1-cdf; 0 < q < 1
+ - code = NIFTI_INTENT_* statistical code
+ - p1,p2,p3 = parameters of the distribution
+
+ If an error transpires, you'll probably get back a BIGG number.
+----------------------------------------------------------------------------*/
+
+double nifti_rcdf2stat( double q , int code, double p1,double p2,double p3 )
+{
+ pqpair pq ;
+ pq.p = 1.0-q ; pq.q = q ;
+ return pq2stat(pq,code,p1,p2,p3) ;
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a statistic, compute a z-score from it. That is, the output
+ is z such that cdf(z) of a N(0,1) variable is the same as the cdf
+ of the given distribution at val.
+----------------------------------------------------------------------------*/
+
+double nifti_stat2zscore( double val , int code, double p1,double p2,double p3 )
+{
+ pqpair pq ;
+
+ if( code == NIFTI_INTENT_ZSCORE ) return val ; /* trivial */
+ if( code == NIFTI_INTENT_NORMAL ) return (val-p1)/p2 ; /* almost so */
+
+ pq = stat2pq( val, code, p1,p2,p3 ) ; /* find cdf */
+ return normal_pq2s( pq ) ; /* find z */
+}
+
+/*--------------------------------------------------------------------------*/
+/*! Given a statistic, compute a half-z-score from it. That is, the output
+ is z such that cdf(z) of a half-N(0,1) variable is the same as the cdf
+ of the given distribution at val. A half-N(0,1) variable has density
+ zero for z < 0 and twice the usual N(0,1) density for z > 0.
+----------------------------------------------------------------------------*/
+
+double nifti_stat2hzscore( double val, int code, double p1,double p2,double p3 )
+{
+ pqpair pq ;
+
+ pq = stat2pq( val, code, p1,p2,p3 ) ; /* find cdf */
+ pq.q = 0.5*(1.0-pq.p) ; pq.p = 0.5*(1.0+pq.p) ; /* mangle it */
+ return normal_pq2s( pq ) ; /* find z */
+}
+
+/****************************************************************************/
+/*[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]*/
+/****************************************************************************/
+
+/*--------------------------------------------------------------------------*/
+/* Sample program to test the above functions. Otherwise unimportant.
+----------------------------------------------------------------------------*/
+
+#ifndef OMIT_MAIN
+int main( int argc , char *argv[] )
+{
+ double val , p , p1=0.0,p2=0.0,p3=0.0 ;
+ double vbot,vtop,vdel ;
+ int code , iarg=1 , doq=0 , dod=0 , doi=0 , doz=0 , doh=0 ;
+
+ /*-- print some help for the pitiful user --*/
+
+ if( argc < 3 || strstr(argv[1],"help") != NULL ){
+ int ii ;
+ printf("\n") ;
+ printf("Demo program for computing NIfTI statistical functions.\n") ;
+ printf("Usage: nifti_stats [-q|-d|-1|-z] val CODE [p1 p2 p3]\n") ;
+ printf(" val can be a single number or in the form bot:top:step.\n") ;
+ printf(" default ==> output p = Prob(statistic < val).\n") ;
+ printf(" -q ==> output is 1-p.\n") ;
+ printf(" -d ==> output is density.\n") ;
+ printf(" -1 ==> output is x such that Prob(statistic < x) = val.\n") ;
+ printf(" -z ==> output is z such that Normal cdf(z) = p(val).\n") ;
+ printf(" -h ==> output is z such that 1/2-Normal cdf(z) = p(val).\n");
+ printf(" Allowable CODEs:\n") ;
+ for( ii=NIFTI_FIRST_STATCODE ; ii <= NIFTI_LAST_STATCODE ; ii++ ){
+ printf(" %-10s",inam[ii]); if((ii-NIFTI_FIRST_STATCODE)%6==5)printf("\n");
+ }
+ printf("\n") ;
+ printf(" Following CODE are distributional parameters, as needed.\n");
+ printf("\n") ;
+ printf("Results are written to stdout, 1 number per output line.\n") ;
+ printf("Example (piping output into AFNI program 1dplot):\n") ;
+ printf(" nifti_stats -d 0:4:.001 INVGAUSS 1 3 | 1dplot -dx 0.001 -stdin\n");
+ printf("\n") ;
+ printf("Author - RW Cox - SSCC/NIMH/NIH/DHHS/USA/EARTH - March 2004\n") ;
+ printf("\n") ;
+ exit(0) ;
+ }
+
+ /*-- check first arg to see if it is an output option;
+ if so, set the appropriate output flag to determine what to compute --*/
+
+ if( strcmp(argv[iarg],"-q") == 0 ){ doq = 1 ; iarg++ ; }
+ else if( strcmp(argv[iarg],"-d") == 0 ){ dod = 1 ; iarg++ ; }
+ else if( strcmp(argv[iarg],"-1") == 0 ){ doi = 1 ; iarg++ ; }
+ else if( strcmp(argv[iarg],"-z") == 0 ){ doz = 1 ; iarg++ ; }
+ else if( strcmp(argv[iarg],"-h") == 0 ){ doh = 1 ; iarg++ ; }
+
+ /*-- get the value(s) to process --*/
+
+ vbot=vtop=vdel = 0.0 ;
+ sscanf( argv[iarg++] , "%lf:%lf:%lf" , &vbot,&vtop,&vdel ) ;
+ if( vbot >= vtop ) vdel = 0.0 ;
+ if( vdel <= 0.0 ) vtop = vbot ;
+
+ /*-- decode the CODE into the integer signifying the distribution --*/
+
+ code = nifti_intent_code(argv[iarg++]) ;
+ if( code < 0 ){ fprintf(stderr,"illegal code=%s\n",argv[iarg-1]); exit(1); }
+
+ /*-- get the parameters, if present (defaults are 0) --*/
+
+ if( argc > iarg ) p1 = strtod(argv[iarg++],NULL) ;
+ if( argc > iarg ) p2 = strtod(argv[iarg++],NULL) ;
+ if( argc > iarg ) p3 = strtod(argv[iarg++],NULL) ;
+
+ /*-- loop over input value(s), compute output, write to stdout --*/
+
+ for( val=vbot ; val <= vtop ; val += vdel ){
+ if( doq ) /* output = 1-cdf */
+ p = nifti_stat2rcdf( val , code,p1,p2,p3 ) ;
+ else if( dod ) /* output = density */
+ p = 1000.0*( nifti_stat2cdf(val+.001,code,p1,p2,p3)
+ -nifti_stat2cdf(val ,code,p1,p2,p3)) ;
+ else if( doi ) /* output = inverse */
+ p = nifti_cdf2stat( val , code,p1,p2,p3 ) ;
+ else if( doz ) /* output = z score */
+ p = nifti_stat2zscore( val , code,p1,p2,p3 ) ;
+ else if( doh ) /* output = halfz score */
+ p = nifti_stat2hzscore( val , code,p1,p2,p3 ) ;
+ else /* output = cdf */
+ p = nifti_stat2cdf( val , code,p1,p2,p3 ) ;
+
+ printf("%.9g\n",p) ;
+ if( vdel <= 0.0 ) break ; /* the case of just 1 value */
+ }
+
+ /*-- terminus est --*/
+
+ exit(0) ;
+}
+#endif /* OMIT_MAIN */
diff --git a/Utilities/ITK/Utilities/nifti/utils/nifti_tool.c b/Utilities/ITK/Utilities/nifti/utils/nifti_tool.c
new file mode 100644
index 0000000000000000000000000000000000000000..848cfac9727cbc5595ceb7e6408c86efc5dc9a7d
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/utils/nifti_tool.c
@@ -0,0 +1,3374 @@
+/*--------------------------------------------------------------------------*/
+/*! \file nifti_tool.c
+ * \brief a tool for nifti file perusal, manipulation and copying
+ * written by Rick Reynolds, SSCC, NIMH, January 2005
+ * <pre>
+ *
+ * usage: nifti_tool [options] -infiles files...
+ *
+ * Via this tool, one should be able to:
+ *
+ * - copy a set of volumes (sub-bricks) from one dataset to another
+ * - copy a dataset, restricting some dimensions to given indices
+ *
+ * - display the contents of a nifti_image (or various fields)
+ * - display the contents of a nifti1_header (or various fields)
+ * - display AFNI extensions (they are text)
+ * - display the time series at coordinates i,j,k
+ * - display the data from any collapsed image
+ *
+ * - do a diff on two nifti_image structs (or various fields)
+ * - do a diff on two nifti1_header structs (or various fields)
+ *
+ * - add an AFNI extension
+ * - remove any extension
+ *
+ * - modify any field(s) of a nifti_image
+ * - modify any field(s) of a nifti1_struct
+ *
+ * usage forms:
+ *
+ * nifti_tool -help
+ * nifti_tool -help_hdr
+ * nifti_tool -help_nim
+ * nifti_tool -hist
+ * nifti_tool -ver
+ * nifti_tool -nifti_hist
+ * nifti_tool -nifti_ver
+ *
+ * nifti_tool -check_hdr -infiles f1 ...
+ * nifti_tool -check_nim -infiles f1 ...
+
+ * nifti_tool -disp_exts -infiles f1 ...
+ * nifti_tool -disp_hdr [-field fieldname] [...] -infiles f1 ...
+ * nifti_tool -disp_nim [-field fieldname] [...] -infiles f1 ...
+ * nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...
+ * nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...
+ *
+ * nifti_tool -diff_hdr [-field fieldname] [...] -infiles f1 f2
+ * nifti_tool -diff_nim [-field fieldname] [...] -infiles f1 f2
+ *
+ * nifti_tool -add_afni_ext "extension in quotes" -infiles f1 ...
+ * nifti_tool -add_comment_ext "extension in quotes" -infiles f1 ...
+ * nifti_tool -rm_ext ext_index -infiles f1 ...
+ *
+ * nifti_tool -mod_hdr [-mod_field fieldname new_val] [...] -infiles f1 ...
+ * nifti_tool -mod_nim [-mod_field fieldname new_val] [...] -infiles f1 ...
+ *
+ * </pre> */
+/*-------------------------------------------------------------------------*/
+
+/*! module history */
+static char * g_history[] =
+{
+ "----------------------------------------------------------------------\n"
+ "nifti_tool modification history:\n"
+ "\n",
+ "0.1 30 December 2004 [rickr]\n"
+ " (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n"
+ " - skeleton version: options read and printed\n"
+ "\n",
+ "1.0 07 January 2005 [rickr]\n"
+ " - initial release version\n"
+ "\n",
+ "1.1 14 January 2005 [rickr]\n"
+ " - changed all non-error/non-debug output from stderr to stdout\n"
+ " note: creates a mis-match between normal output and debug messages\n"
+ " - modified act_diff_hdrs and act_diff_nims to do the processing in\n"
+ " lower-level functions\n",
+ " - added functions diff_hdrs, diff_hdrs_list, diff_nims, diff_nims_list\n"
+ " - added function get_field, to return a struct pointer via a fieldname\n"
+ " - made 'quiet' output more quiet (no description on output)\n"
+ " - made hdr and nim_fields arrays global, so do not pass in main()\n"
+ " - return (from main()) after first act_diff() difference\n"
+ "\n",
+ "1.2 9 February 2005 [rickr] - minor\n"
+ " - defined a local NTL_FERR macro (so it does not come from nifti1_io.h)\n"
+ " - added new set_byte_order parameter to nifti_set_filenames\n"
+ "\n",
+ "1.3 23 February 2005 [rickr] - sourceforge.net merge\n"
+ " - moved to utils directory\n"
+ " - added simple casts of 3 pointers for -pedantic warnings\n"
+ " - added a doxygen comment for the file\n"
+ "\n",
+ "1.4 02 March 2005 [rickr] - small update\n"
+ " - no validation in nifti_read_header calls\n"
+ "\n",
+ "1.5 05 April 2005 [rickr] - small update\n"
+ " - refuse mod_hdr for gzipped files (we cannot do partial overwrites)\n"
+ "\n",
+ "1.6 08 April 2005 [rickr] - added cbl, cci and dts functionality\n"
+ " - added -cbl: 'copy brick list' dataset copy functionality\n"
+ " - added -ccd: 'copy collapsed data' dataset copy functionality\n"
+ " - added -disp_ts: 'disp time series' data display functionality\n"
+ " - moved raw data display to disp_raw_data()\n"
+ "\n",
+ "1.7 14 April 2005 [rickr] - added data display functionality\n"
+ " - added -dci: 'display collapsed image' functionality\n"
+ " - modified -dts to use -dci\n"
+ " - modified and updated the help in use_full()\n"
+ " - changed copy_collapsed_dims to copy_collapsed_image, etc.\n",
+ " - fixed problem in disp_raw_data() for printing NT_DT_CHAR_PTR\n"
+ " - modified act_disp_ci():\n"
+ " o was act_disp_ts(), now displays arbitrary collapsed image data\n"
+ " o added missed debug filename act_disp_ci()\n"
+ " o can now save free() of data pointer for end of file loop\n",
+ " - modified disp_raw_data()\n"
+ " o takes a flag for whether to print newline\n"
+ " o trailing spaces and zeros are removed from printing floats\n"
+ " - added clear_float_zeros(), to remove trailing zeros\n"
+ "\n",
+ "1.8 19 April 2005 [rickr] - COMMENT extensions\n"
+ " - added int_list struct, and keep_hist,etypes,command fields to nt_opts\n"
+ " - added -add_comment_ext action\n"
+ " - allowed for removal of multiple extensions, including option of ALL\n"
+ " - added -keep_hist option, to store the command as a COMMENT extension\n",
+ " (includes fill_cmd_string() and add_int(), is done for all actions)\n"
+ " - added remove_ext_list(), for removing a list of extensions by indices\n"
+ " - added -strip action, to strip all extensions and descrip fields\n"
+ "\n",
+ "1.9 25 August 2005 [rickr] - const/string cleanup for warnings\n"
+ "\n",
+ "1.10 18 November 2005 [rickr] - added check_hdr and check_nim actions\n"
+ "----------------------------------------------------------------------\n"
+};
+static char g_version[] = "version 1.10 (November 18, 2005)";
+static int g_debug = 1;
+
+#define _NIFTI_TOOL_C_
+#include "nifti1_io.h"
+#include "nifti_tool.h"
+
+#define NTL_FERR(func,msg,file) \
+ fprintf(stderr,"** ERROR (%s): %s '%s'\n",func,msg,file)
+
+/* these are effectively constant, and are built only for verification */
+field_s g_hdr_fields[NT_HDR_NUM_FIELDS]; /* nifti_1_header fields */
+field_s g_nim_fields[NT_NIM_NUM_FIELDS]; /* nifti_image fields */
+
+int main( int argc, char * argv[] )
+{
+ nt_opts opts;
+ int rv;
+
+ if( (rv = process_opts(argc, argv, &opts)) != 0)
+ return rv;
+
+ if( (rv = verify_opts(&opts, argv[0])) != 0 )
+ return rv;
+
+ /* now perform the requested action(s) */
+
+ if( (rv = fill_hdr_field_array(g_hdr_fields)) != 0 )
+ return rv;
+
+ if( (rv = fill_nim_field_array(g_nim_fields)) != 0 )
+ return rv;
+
+ /* 'check' functions, first */
+ if( opts.check_hdr || opts.check_nim ) /* allow for both */
+ return act_check_hdrs(&opts);
+
+ /* copy or dts functions */
+ if( opts.cbl ) return act_cbl(&opts); /* just return */
+ if( opts.cci ) return act_cci(&opts);
+ if( opts.dts || opts.dci ) return act_disp_ci(&opts);
+
+ /* perform modifications early, in case we allow multiple actions */
+ if( opts.strip && ((rv = act_strip (&opts)) != 0) ) return rv;
+
+ if( opts.add_exts && ((rv = act_add_exts (&opts)) != 0) ) return rv;
+ if( opts.rm_exts && ((rv = act_rm_ext (&opts)) != 0) ) return rv;
+
+ if( opts.mod_hdr && ((rv = act_mod_hdrs (&opts)) != 0) ) return rv;
+ if( opts.mod_nim && ((rv = act_mod_nims (&opts)) != 0) ) return rv;
+
+ /* if a diff, return wither a difference exists (like the UNIX command) */
+ if( opts.diff_hdr && ((rv = act_diff_hdrs(&opts)) != 0) ) return rv;
+ if( opts.diff_nim && ((rv = act_diff_nims(&opts)) != 0) ) return rv;
+
+ /* last action type is display */
+ if( opts.disp_exts && ((rv = act_disp_exts(&opts)) != 0) ) return rv;
+ if( opts.disp_hdr && ((rv = act_disp_hdrs(&opts)) != 0) ) return rv;
+ if( opts.disp_nim && ((rv = act_disp_nims(&opts)) != 0) ) return rv;
+
+ return 0;
+}
+
+/*----------------------------------------------------------------------
+ * process user options, return 0 on success
+ *----------------------------------------------------------------------*/
+int process_opts( int argc, char * argv[], nt_opts * opts )
+{
+ int ac;
+
+ memset(opts, 0, sizeof(*opts));
+
+ opts->prefix = NULL;
+ opts->debug = 1; /* init debug level to basic output */
+
+ if( argc < 2 ) return usage(argv[0], USE_SHORT);
+
+ /* terminal options are first, the rest are sorted */
+ for( ac = 1; ac < argc; ac++ )
+ {
+ if( ! strncmp(argv[ac], "-help_hdr", 9) )
+ return usage(argv[0], USE_FIELD_HDR);
+ if( ! strncmp(argv[ac], "-help_nim", 9) )
+ return usage(argv[0], USE_FIELD_NIM);
+ if( ! strncmp(argv[ac], "-help", 5) )
+ return usage(argv[0], USE_FULL);
+ else if( ! strncmp(argv[ac], "-hist", 5) )
+ return usage(argv[0], USE_HIST);
+ else if( ! strncmp(argv[ac], "-ver", 2) )
+ return usage(argv[0], USE_VERSION);
+ else if( ! strncmp(argv[ac], "-nifti_hist", 11) )
+ {
+ nifti_disp_lib_hist();
+ return 1;
+ }
+ else if( ! strncmp(argv[ac], "-nifti_ver", 10) )
+ {
+ nifti_disp_lib_version();
+ return 1;
+ }
+
+ /* begin normal execution options... */
+ else if( ! strncmp(argv[ac], "-add_afni_ext", 9) )
+ {
+ ac++;
+ CHECK_NEXT_OPT(ac, argc, "-add_afni_ext");
+ if( add_string(&opts->elist, argv[ac]) ) return 1; /* add extension */
+ if( add_int(&opts->etypes, NIFTI_ECODE_AFNI) ) return 1;
+ opts->add_exts = 1;
+ }
+ else if( ! strncmp(argv[ac], "-add_comment_ext", 9) )
+ {
+ ac++;
+ CHECK_NEXT_OPT(ac, argc, "-add_comment_ext");
+ if( add_string(&opts->elist, argv[ac]) ) return 1; /* add extension */
+ if( add_int(&opts->etypes, NIFTI_ECODE_COMMENT) ) return 1;
+ opts->add_exts = 1;
+ }
+ else if( ! strncmp(argv[ac], "-check_hdr", 10) )
+ opts->check_hdr = 1;
+ else if( ! strncmp(argv[ac], "-check_nim", 10) )
+ opts->check_nim = 1;
+ else if( ! strncmp(argv[ac], "-copy_brick_list", 11) ||
+ ! strncmp(argv[ac], "-cbl", 4) )
+ {
+ opts->cbl = 1;
+ }
+ else if( ! strncmp(argv[ac], "-copy_collapsed_image", 10) ||
+ ! strncmp(argv[ac], "-cci", 4) )
+ {
+ /* we need to read in the 7 dimension values */
+ int index;
+ opts->ci_dims[0] = 0;
+ for( index = 1; index < 8; index++ )
+ {
+ ac++;
+ CHECK_NEXT_OPT_MSG(ac,argc,"-cci","7 dimension values are requred");
+ if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){
+ fprintf(stderr,"** -cci param %d (= '%s') is not a valid\n"
+ " consider: 'nifti_tool -help'\n",index,argv[ac]);
+ return 1;
+ }
+ opts->ci_dims[index] = atoi(argv[ac]);
+ }
+
+ opts->cci = 1;
+ }
+ else if( ! strncmp(argv[ac], "-debug", 6) )
+ {
+ ac++;
+ CHECK_NEXT_OPT(ac, argc, "-debug");
+ opts->debug = atoi(argv[ac]);
+ }
+ else if( ! strncmp(argv[ac], "-diff_hdr", 8) )
+ opts->diff_hdr = 1;
+ else if( ! strncmp(argv[ac], "-diff_nim", 8) )
+ opts->diff_nim = 1;
+ else if( ! strncmp(argv[ac], "-disp_exts", 7) )
+ opts->disp_exts = 1;
+ else if( ! strncmp(argv[ac], "-disp_hdr", 8) )
+ opts->disp_hdr = 1;
+ else if( ! strncmp(argv[ac], "-disp_nim", 8) )
+ opts->disp_nim = 1;
+ else if( ! strncmp(argv[ac], "-dci_lines", 6) || /* before -dts */
+ ! strncmp(argv[ac], "-dts_lines", 6) )
+ {
+ opts->dci_lines = 1;
+ }
+ else if( ! strncmp(argv[ac], "-disp_collapsed_image", 10) ||
+ ! strncmp(argv[ac], "-disp_ci", 8) )
+ {
+ /* we need to read in the 7 dimension values */
+ int index;
+ opts->ci_dims[0] = 0;
+ for( index = 1; index < 8; index++ )
+ {
+ ac++;
+ CHECK_NEXT_OPT_MSG(ac,argc,"-disp_ci",
+ "7 dimension values are requred");
+ if( ! isdigit(argv[ac][0]) && strcmp(argv[ac],"-1") ){
+ fprintf(stderr,"** -disp_ci param %d (= '%s') is not a valid\n"
+ " consider: 'nifti_tool -help'\n",index,argv[ac]);
+ return 1;
+ }
+ opts->ci_dims[index] = atoi(argv[ac]);
+ }
+
+ opts->dci = 1;
+ }
+ else if( ! strncmp(argv[ac], "-disp_ts", 10) ||
+ ! strncmp(argv[ac], "-dts", 4) )
+ {
+ /* we need to read in the ijk indices into the ci_dims array */
+ int index;
+ for( index = 1; index <= 3; index++ )
+ {
+ ac++;
+ CHECK_NEXT_OPT_MSG(ac,argc,"-dts","i,j,k indices are requied\n");
+ if( ! isdigit(argv[ac][0]) ){
+ fprintf(stderr,"** -dts param %d (= '%s') is not a number\n"
+ " consider: 'nifti_tool -help'\n",index,argv[ac]);
+ return 1;
+ }
+ opts->ci_dims[index] = atoi(argv[ac]);
+ }
+ /* and fill the rest of the array */
+ opts->ci_dims[0] = 0;
+ for( index = 4; index < 8; index++ ) opts->ci_dims[index] = -1;
+
+ opts->dts = 1;
+ }
+ else if( ! strncmp(argv[ac], "-field", 2) )
+ {
+ ac++;
+ CHECK_NEXT_OPT(ac, argc, "-field");
+ if( add_string(&opts->flist, argv[ac]) ) return 1; /* add field */
+ }
+ else if( ! strncmp(argv[ac], "-infiles", 3) )
+ {
+ int count;
+ /* for -infiles, get all next arguments until a '-' or done */
+ ac++;
+ for( count = 0; (ac < argc) && (argv[ac][0] != '-'); ac++, count++ )
+ if( add_string(&opts->infiles, argv[ac]) ) return 1; /* add field */
+ if( count > 0 && ac < argc ) ac--; /* more options to process */
+ if( g_debug > 2 ) fprintf(stderr,"+d have %d file names\n", count);
+ }
+ else if( ! strncmp(argv[ac], "-mod_field", 6) )
+ {
+ ac++;
+ CHECK_NEXT_OPT(ac, argc, "-mod_field");
+ if( add_string(&opts->flist, argv[ac]) ) return 1; /* add field */
+ ac++;
+ CHECK_NEXT_OPT(ac, argc, "-mod_field (2)");
+ if( add_string(&opts->vlist, argv[ac]) ) return 1; /* add value */
+ }
+ else if( ! strncmp(argv[ac], "-mod_hdr", 7) )
+ opts->mod_hdr = 1;
+ else if( ! strncmp(argv[ac], "-mod_nim", 7) )
+ opts->mod_nim = 1;
+ else if( ! strncmp(argv[ac], "-keep_hist", 5) )
+ opts->keep_hist = 1;
+ else if( ! strncmp(argv[ac], "-overwrite", 6) )
+ opts->overwrite = 1;
+ else if( ! strncmp(argv[ac], "-prefix", 4) )
+ {
+ ac++;
+ CHECK_NEXT_OPT(ac, argc, "-prefix");
+ opts->prefix = argv[ac];
+ }
+ else if( ! strncmp(argv[ac], "-quiet", 3) )
+ opts->debug = 0;
+ else if( ! strncmp(argv[ac], "-rm_ext", 7) )
+ {
+ ac++;
+ CHECK_NEXT_OPT(ac, argc, "-rm_ext");
+ if( strcmp(argv[ac],"ALL") == 0 ) /* special case, pass -1 */
+ {
+ if( add_string(&opts->elist, "-1") ) return 1;
+ }
+ else
+ {
+ int index = atoi(argv[ac]);
+ if( (index != -1) && ((index > 1000) || !isdigit(*argv[ac])) ){
+ fprintf(stderr,
+ "** '-rm_ext' requires an extension index (read '%s')\n",
+ argv[ac]);
+ return 1;
+ }
+ if( add_string(&opts->elist, argv[ac]) ) return 1;
+ }
+ opts->rm_exts = 1;
+ }
+ else if( ! strncmp(argv[ac], "-strip_extras", 6) )
+ opts->strip = 1;
+ else
+ {
+ fprintf(stderr,"** unknown option: '%s'\n", argv[ac]);
+ return 1;
+ }
+ }
+
+ /* verify for programming purposes */
+ if( opts->add_exts && ( opts->elist.len != opts->etypes.len ) )
+ {
+ fprintf(stderr,"** ext list length (%d) != etype length (%d)\n",
+ opts->elist.len, opts->etypes.len);
+ return 1;
+ }
+
+ g_debug = opts->debug;
+ nifti_set_debug_level(g_debug);
+
+ fill_cmd_string(opts, argc, argv); /* copy this command */
+
+ if( g_debug > 2 ) disp_nt_opts("options read: ", opts);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * verify that the options make sense
+ *----------------------------------------------------------------------*/
+int verify_opts( nt_opts * opts, char * prog )
+{
+ int ac, errs = 0; /* number of requested action types */
+
+ /* check that only one of disp, diff, mod or add_*_ext is used */
+ ac = (opts->check_hdr || opts->check_nim ) ? 1 : 0;
+ ac += (opts->diff_hdr || opts->diff_nim ) ? 1 : 0;
+ ac += (opts->disp_hdr || opts->disp_nim || opts->disp_exts) ? 1 : 0;
+ ac += (opts->mod_hdr || opts->mod_nim ) ? 1 : 0;
+ ac += (opts->add_exts || opts->rm_exts ) ? 1 : 0;
+ ac += (opts->strip ) ? 1 : 0;
+ ac += (opts->cbl ) ? 1 : 0;
+ ac += (opts->cci ) ? 1 : 0;
+ ac += (opts->dts || opts->dci ) ? 1 : 0;
+
+ if( ac < 1 )
+ {
+ fprintf(stderr,
+ "** no action option, so nothing to do...\n"
+ " (try one of '-add...', '-diff...', '-disp...' or '-mod...')\n"
+ " (see '%s -help' for details)\n", prog);
+ return 1;
+ }
+ else if( ac > 1 )
+ {
+ fprintf(stderr,
+ "** only one action option is allowed, please use only one of:\n"
+ " '-add_...', '-check_...', '-diff_...', '-disp_...',\n"
+ " '-mod_...', '-strip', '-dts', '-cbl' or '-cci'\n"
+ " (see '%s -help' for details)\n", prog);
+ return 1;
+ }
+
+ /* can modify nifti_1_header or nifti_image, but not both */
+ if( opts->mod_hdr && opts->mod_nim )
+ {
+ fprintf(stderr,"** cannot use both '-mod_hdr' and '-mod_nim'\n");
+ return 1;
+ }
+
+ /* can add or remove extensions, but not both */
+ if( opts->add_exts && opts->rm_exts )
+ {
+ fprintf(stderr,"** cannot use both '-add_*_ext' and '-rm_ext'\n");
+ return 1;
+ }
+ if( (opts->add_exts || opts->rm_exts) && opts->elist.len <= 0 )
+ {
+ fprintf(stderr,"** missing extensions to add or remove\n");
+ return 1;
+ }
+
+ /* if modify, then we need fields and corresponding values */
+ if( opts->mod_hdr || opts->mod_nim )
+ {
+ if( opts->flist.len <= 0 )
+ {
+ fprintf(stderr,"** missing field to modify (need '-mod_field' opt)\n");
+ return 1;
+ }
+ if( opts->flist.len != opts->vlist.len )
+ {
+ fprintf(stderr,"** error: modifying %d fields with %d values\n",
+ opts->flist.len, opts->vlist.len);
+ return 1;
+ }
+ }
+
+ /* verify the number of files given for each of 4 action types */
+
+ /* -diff_... : require nfiles == 2 */
+ if( opts->diff_hdr || opts->diff_nim )
+ {
+ if( opts->infiles.len != 2 )
+ {
+ fprintf(stderr,"** '-diff_XXX' options require exactly 2 inputs files\n");
+ return 1;
+ }
+ }
+ /* if we are making changes, but not overwriting... */
+ else if( (opts->elist.len > 0 || opts->mod_hdr || opts->mod_nim) &&
+ !opts->overwrite )
+ {
+ if( opts->infiles.len > 1 )
+ {
+ fprintf(stderr,"** without -overwrite, only one input file may be"
+ " modified at a time\n");
+ errs++;
+ }
+ if( ! opts->prefix )
+ {
+ fprintf(stderr,"** missing -prefix for output file\n");
+ errs++;
+ }
+ }
+
+ if( opts->dci_lines && ! opts->dts && ! opts->dci )
+ {
+ fprintf(stderr,"** option '-dci_lines' must only be used with '-dts'\n");
+ errs++;
+ }
+
+ if( opts->infiles.len <= 0 ) /* in any case */
+ {
+ fprintf(stderr,"** missing input files (see -infiles option)\n");
+ errs++;
+ }
+
+ if ( opts->overwrite && opts->prefix )
+ {
+ fprintf(stderr, "** please specify only one of -prefix and -overwrite\n");
+ errs++;
+ }
+
+ if( errs ) return 1;
+
+ if( g_debug > 1 ) fprintf(stderr,"+d options seem valid\n");
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * re-assemble the command string into opts->command
+ *----------------------------------------------------------------------*/
+int fill_cmd_string( nt_opts * opts, int argc, char * argv[])
+{
+ char * cp;
+ int len, remain = NT_CMD_LEN; /* NT_CMD_LEN is max command len */
+ int c, ac;
+ int has_space; /* arguments containing space must be quoted */
+ int skip = 0; /* counter to skip some of the arguments */
+
+ /* get the first argument separately */
+ len = sprintf( opts->command, "\n command: %s", argv[0] );
+ cp = opts->command + len;
+ remain -= len;
+
+ /* get the rest, with special attention to input files */
+ for( ac = 1; ac < argc; ac++ )
+ {
+ if( skip ){ skip--; continue; } /* then skip these arguments */
+
+ len = strlen(argv[ac]);
+ if( len + 3 >= remain ) { /* extra 3 for space and possible '' */
+ fprintf(stderr,"FCS: no space remaining for command, continuing...\n");
+ return 1;
+ }
+
+ /* put the argument in, possibly with '' */
+
+ has_space = 0;
+ for( c = 0; c < len-1; c++ )
+ if( isspace(argv[ac][c]) ){ has_space = 1; break; }
+ if( has_space ) len = sprintf(cp, " '%s'", argv[ac]);
+ else len = sprintf(cp, " %s", argv[ac]);
+
+ remain -= len;
+
+ /* infiles is okay, but after the *next* argument, we may skip files */
+ /* (danger, will robinson! hack alert!) */
+ if( !strncmp(argv[ac-1],"-infiles",3) )
+ {
+ /* if more than 4 (just to be arbitrary) input files,
+ include only the first and last */
+ if( opts->infiles.len > 4 )
+ skip = opts->infiles.len - 2;
+ }
+
+ cp += len;
+ }
+
+ if( g_debug > 1 ){
+ fprintf(stderr,"+d filled command string, %d args, %d bytes\n",
+ argc, (int)(cp - opts->command));
+ if( g_debug > 2 ) fprintf(stderr,"%s\n", opts->command);
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * - only bother to alloc one pointer at a time (don't need efficiency here)
+ * - return 0 on success
+ *----------------------------------------------------------------------*/
+int add_int(int_list * ilist, int val)
+{
+ if( ilist->len == 0 ) ilist->list = NULL; /* just to be safe */
+ ilist->len++;
+ ilist->list = (int *)realloc(ilist->list,ilist->len*sizeof(int));
+ if( ! ilist->list ){
+ fprintf(stderr,"** failed to alloc %d (int *) elements\n",ilist->len);
+ return -1;
+ }
+
+ ilist->list[ilist->len-1] = val;
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * - do not duplicate the string
+ * - only bother to alloc one pointer at a time (don't need efficiency here)
+ * - return 0 on success
+ *----------------------------------------------------------------------*/
+int add_string(str_list * slist, char * str)
+{
+ if( slist->len == 0 ) slist->list = NULL; /* just to be safe */
+ slist->len++;
+ slist->list = (char **)realloc(slist->list,slist->len*sizeof(char *));
+ if( ! slist->list ){
+ fprintf(stderr,"** failed to alloc %d (char *) elements\n",slist->len);
+ return -1;
+ }
+
+ slist->list[slist->len-1] = str;
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * display information on using the program
+ *----------------------------------------------------------------------*/
+int usage(char * prog, int level)
+{
+ int c, len;
+ if( level == USE_SHORT )
+ {
+ fprintf(stdout,"usage %s [options] -infiles files...\n", prog);
+ fprintf(stdout,"usage %s -help\n", prog);
+ }
+ else if( level == USE_FULL )
+ use_full("nifti_tool"); /* let's not allow paths in here */
+ else if( level == USE_HIST )
+ {
+ len = sizeof(g_history)/sizeof(char *);
+ for( c = 0; c < len; c++)
+ fputs(g_history[c], stdout);
+ }
+ else if( level == USE_FIELD_HDR )
+ {
+ field_s nhdr_fields[NT_HDR_NUM_FIELDS]; /* just do it all here */
+
+ fill_hdr_field_array(nhdr_fields);
+ disp_field_s_list("nifti_1_header: ", nhdr_fields, NT_HDR_NUM_FIELDS);
+ }
+ else if( level == USE_FIELD_NIM )
+ {
+ field_s nim_fields[NT_NIM_NUM_FIELDS];
+
+ fill_nim_field_array(nim_fields);
+ disp_field_s_list("nifti_image: ", nim_fields, NT_NIM_NUM_FIELDS);
+ }
+ else if( level == USE_VERSION )
+ fprintf(stdout, "%s, %s\n", prog, g_version);
+ else
+ fprintf(stdout,"** illegal level for usage(): %d\n", level);
+
+ return 1;
+}
+
+
+/*----------------------------------------------------------------------
+ * full usage
+ *----------------------------------------------------------------------*/
+int use_full(char * prog)
+{
+ printf(
+ "nifti_tool\n"
+ "\n"
+ " - display, modify or compare nifti structures in datasets\n"
+ " - copy a dataset by selecting a list of volumes from the original\n"
+ " - copy a dataset, collapsing any dimensions, each to a single index\n"
+ " - display a time series for a voxel, or more generally, the data\n"
+ " from any collapsed image, in ASCII text\n");
+ printf(
+ "\n"
+ " This program can be used to display information from nifti datasets,\n"
+ " to modify information in nifti datasets, to look for differences\n"
+ " between two nifti datasets (like the UNIX 'diff' command), and to copy\n"
+ " a dataset to a new one, either by restricting any dimensions, or by\n"
+ " copying a list of volumes (the time dimension) from a dataset.\n"
+ "\n");
+ printf(
+ " Only one action type is allowed, e.g. one cannot modify a dataset\n"
+ " and then take a 'diff'.\n"
+ "\n");
+ printf(
+ " one can display - any or all fields in the nifti_1_header structure\n"
+ " - any or all fields in the nifti_image structure\n"
+ " - the extensions in the nifti_image structure\n"
+ " - the time series from a 4-D dataset, given i,j,k\n"
+ " - the data from any collapsed image, given dims. list\n"
+ "\n");
+ printf(
+ " one can check - perform internal check on the nifti_1_header struct\n"
+ " (by nifti_hdr_looks_good())\n"
+ " - perform internal check on the nifti_image struct\n"
+ " (by nifti_nim_is_valid())\n"
+ "\n");
+ printf(
+ " one can modify - any or all fields in the nifti_1_header structure\n"
+ " - any or all fields in the nifti_image structure\n"
+ " add/rm - any or all extensions in the nifti_image structure\n"
+ " remove - all extensions and descriptions from the datasets\n"
+ "\n");
+ printf(
+ " one can compare - any or all field pairs of nifti_1_header structures\n"
+ " - any or all field pairs of nifti_image structures\n"
+ "\n"
+ " one can copy - an arbitrary list of dataset volumes (time points)\n"
+ " - a dataset, collapsing across arbitrary dimensions\n"
+ " (restricting those dimensions to the given indices)\n"
+ "\n");
+ printf(
+ " Note: to learn about which fields exist in either of the structures,\n"
+ " or to learn a field's type, size of each element, or the number\n"
+ " of elements in the field, use either the '-help_hdr' option, or\n"
+ " the '-help_nim' option. No further options are required.\n"
+ " ------------------------------\n");
+ printf(
+ "\n"
+ " usage styles:\n"
+ "\n"
+ " nifti_tool -help : show this help\n"
+ " nifti_tool -help_hdr : show nifti_1_header field info\n"
+ " nifti_tool -help_nim : show nifti_image field info\n"
+ "\n");
+ printf(
+ " nifti_tool -ver : show the current version\n"
+ " nifti_tool -hist : show the modification history\n"
+ " nifti_tool -nifti_ver : show the nifti library version\n"
+ " nifti_tool -nifti_hist : show the nifti library history\n"
+ "\n"
+ "\n");
+ printf(
+ " nifti_tool -check_hdr -infiles f1 ...\n"
+ " nifti_tool -check_nim -infiles f1 ...\n"
+ "\n");
+ printf(
+ " nifti_tool -copy_brick_list -infiles f1'[indices...]'\n"
+ " nifti_tool -copy_collapsed_image I J K T U V W -infiles f1\n"
+ "\n");
+ printf(
+ " nifti_tool -disp_hdr [-field FIELDNAME] [...] -infiles f1 ...\n"
+ " nifti_tool -disp_nim [-field FIELDNAME] [...] -infiles f1 ...\n"
+ " nifti_tool -disp_exts -infiles f1 ...\n"
+ " nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...\n"
+ " nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...\n"
+ "\n");
+ printf(
+ " nifti_tool -mod_hdr [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1\n"
+ " nifti_tool -mod_nim [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1\n"
+ "\n"
+ " nifti_tool -add_afni_ext 'extension in quotes' [...] -infiles f1\n"
+ " nifti_tool -add_comment_ext 'extension in quotes' [...] -infiles f1\n"
+ " nifti_tool -rm_ext INDEX [...] -infiles f1 ...\n"
+ " nifti_tool -strip_extras -infiles f1 ...\n"
+ "\n");
+ printf(
+ " nifti_tool -diff_hdr [-field FIELDNAME] [...] -infiles f1 f2\n"
+ " nifti_tool -diff_nim [-field FIELDNAME] [...] -infiles f1 f2\n"
+ "\n"
+ " ------------------------------\n");
+
+ printf(
+ "\n"
+ " selected examples:\n"
+ "\n"
+ " checks header (for problems):\n"
+ "\n"
+ " nifti_tool -check_hdr -infiles dset0.nii dset1.nii\n"
+ " nifti_tool -check_hdr -infiles *.nii *.hdr\n"
+ " nifti_tool -check_hdr -quiet -infiles *.nii *.hdr\n"
+ "\n");
+ printf(
+ " show header differences:\n"
+ "\n"
+ " nifti_tool -diff_hdr -field dim -field intent_code \\\n"
+ " -infiles dset0.nii dset1.nii \n"
+ "\n"
+ " display structures or fields:\n"
+ "\n");
+ printf(
+ " nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii\n"
+ " nifti_tool -disp_hdr -field dim -field descrip -infiles dset0.nii\n"
+ "\n"
+ " nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii\n"
+ "\n"
+ " nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii\n"
+ "\n"
+ " nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii\n"
+ "\n");
+ printf(
+ " copy brick list, or copy collapsed image:\n"
+ "\n"
+ " nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'\n"
+ " nifti_tool -cbl -prefix new_partial.nii \\\n"
+ " -infiles dset0.nii'[3..$(2)]'\n"
+ "\n"
+ " nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii\n"
+ " nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \\\n"
+ " -prefix new_5_0_17_2.nii\n"
+ "\n");
+ printf(
+ " modify the header:\n"
+ "\n"
+ " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
+ " -mod_field dim '4 64 64 20 30 1 1 1 1'\n"
+ " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
+ " -mod_field descrip 'beer, brats and cheese, mmmmm...'\n"
+ "\n");
+ printf(
+ " strip, add or remove extensions:\n"
+ "\n"
+ " nifti_tool -strip -overwrite -infiles *.nii\n"
+ "\n"
+ " nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \\\n"
+ " -prefix dnew -infiles dset0.nii\n"
+ "\n");
+ printf(
+ " nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii\n"
+ " nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \\\n"
+ " -infiles dset0.nii\n"
+ "\n"
+ " ------------------------------\n");
+ printf(
+ "\n"
+ " options for check actions:\n"
+ "\n");
+ printf(
+ " -check_hdr : check for a valid nifti_1_header struct\n"
+ "\n"
+ " This action is used to check the nifti_1_header structure for\n"
+ " problems. The nifti_hdr_looks_good() function is used for the\n"
+ " test, and currently checks:\n"
+ " \n"
+ " dim[], sizeof_hdr, magic, datatype\n"
+ " \n"
+ " More tests can be requested of the author.\n"
+ "\n");
+ printf(
+ " e.g. perform checks on the headers of some datasets\n"
+ " nifti_tool -check_hdr -infiles dset0.nii dset1.nii\n"
+ " nifti_tool -check_hdr -infiles *.nii *.hdr\n"
+ " \n"
+ " e.g. add the -quiet option, so that only erros are reported\n"
+ " nifti_tool -check_hdr -quiet -infiles *.nii *.hdr\n"
+ "\n");
+ printf(
+ " -check_nim : check for a valid nifti_image struct\n"
+ "\n"
+ " This action is used to check the nifti_image structure for\n"
+ " problems. This is tested via both nifti_convert_nhdr2nim()\n"
+ " and nifti_nim_is_valid(), though other functions are called\n"
+ " below them, of course. Current checks are:\n"
+ "\n");
+ printf(
+ " dim[], sizeof_hdr, datatype, fname, iname, nifti_type\n"
+ " \n"
+ " Note that creation of a nifti_image structure depends on good\n"
+ " header fields. So errors are terminal, meaning this check would\n"
+ " probably report at most one error, even if more exist. The\n"
+ " -check_hdr action is more complete.\n"
+ "\n");
+ printf(
+ " More tests can be requested of the author.\n"
+ "\n");
+ printf(
+ " e.g. nifti_tool -check_nim -infiles dset0.nii dset1.nii\n"
+ " e.g. nifti_tool -check_nim -infiles *.nii *.hdr\n"
+ "\n");
+ printf(
+ " ------------------------------\n");
+
+ printf(
+ "\n"
+ " options for copy actions:\n"
+ "\n"
+ " -copy_brick_list : copy a list of volumes to a new dataset\n"
+ " -cbl : (a shorter, alternative form)\n"
+ "\n");
+ printf(
+ " This action allows the user to copy a list of volumes (over time)\n"
+ " from one dataset to another. The listed volumes can be in any\n"
+ " order and contain repeats, but are of course restricted to\n"
+ " the set of values {1, 2, ..., nt-1}, from dimension 4.\n"
+ "\n");
+ printf(
+ " This option is a flag. The index list is specified with the input\n"
+ " dataset, contained in square brackets. Note that square brackets\n"
+ " are special to most UNIX shells, so they should be contained\n"
+ " within single quotes. Syntax of an index list:\n"
+ "\n"
+ " notes:\n"
+ "\n");
+ printf(
+ " - indices start at zero\n"
+ " - indices end at nt-1, which has the special symbol '$'\n"
+ " - single indices should be separated with commas, ','\n"
+ " e.g. -infiles dset0.nii'[0,3,8,5,2,2,2]'\n"
+ " - ranges may be specified using '..' or '-' \n");
+ printf(
+ " e.g. -infiles dset0.nii'[2..95]'\n"
+ " e.g. -infiles dset0.nii'[2..$]'\n"
+ " - ranges may have step values, specified in ()\n"
+ " example: 2 through 95 with a step of 3, i.e. {2,5,8,11,...,95}\n"
+ " e.g. -infiles dset0.nii'[2..95(3)]'\n"
+ "\n");
+ printf(
+ " This functionality applies only to 4-dimensional datasets.\n"
+ "\n"
+ " e.g. to copy sub-bricks 0 and 7:\n"
+ " nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'\n"
+ "\n"
+ " e.g. to copy an entire dataset:\n"
+ " nifti_tool -cbl -prefix new_all.nii -infiles dset0.nii'[0..$]'\n"
+ "\n");
+ printf(
+ " e.g. to copy every other time point, skipping the first three:\n"
+ " nifti_tool -cbl -prefix new_partial.nii \\\n"
+ " -infiles dset0.nii'[3..$(2)]'\n"
+ "\n"
+ "\n"
+ " -copy_collapsed_image ... : copy a list of volumes to a new dataset\n"
+ " -cci I J K T U V W : (a shorter, alternative form)\n"
+ "\n");
+ printf(
+ " This action allows the user to copy a collapsed dataset, where\n"
+ " some dimensions are collapsed to a given index. For instance, the\n"
+ " X dimension could be collapsed to i=42, and the time dimensions\n"
+ " could be collapsed to t=17. To collapse a dimension, set Di to\n"
+ " the desired index, where i is in {0..ni-1}. Any dimension that\n"
+ " should not be collapsed must be listed as -1.\n"
+ "\n");
+ printf(
+ " Any number (of valid) dimensions can be collapsed, even down to a\n"
+ " a single value, by specifying enough valid indices. The resulting\n"
+ " dataset will then have a reduced number of non-trivial dimensions.\n"
+ "\n"
+ " Assume dset0.nii has nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 }.\n"
+ " Note that this is a 4-dimensional dataset.\n"
+ "\n");
+ printf(
+ " e.g. copy the time series for voxel i,j,k = 5,4,17\n"
+ " nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii\n"
+ "\n"
+ " e.g. read the single volume at time point 26\n"
+ " nifti_tool -cci -1 -1 -1 26 -1 -1 -1 -prefix new_t26.nii\n"
+ "\n");
+ printf(
+ " Assume dset1.nii has nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 }.\n"
+ " Note that this is a 6-dimensional dataset.\n"
+ "\n"
+ " e.g. copy all time series for voxel i,j,k = 5,0,17, with v=2\n"
+ " (and add the command to the history)\n"
+ " nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \\\n"
+ " -prefix new_5_0_17_2.nii\n"
+ "\n");
+ printf(
+ " e.g. copy all data where i=3, j=19 and v=2\n"
+ " (I do not claim to know a good reason to do this)\n"
+ " nifti_tool -cci 3 19 -1 -1 -1 2 -1 -prefix new_mess.nii\n"
+ "\n"
+ " See '-disp_ci' for more information (which displays/prints the\n"
+ " data, instead of copying it to a new dataset).\n"
+ "\n"
+ " ------------------------------\n");
+
+ printf(
+ "\n"
+ " options for display actions:\n"
+ "\n"
+ " -disp_hdr : display nifti_1_header fields for datasets\n"
+ "\n"
+ " This flag means the user wishes to see some of the nifti_1_header\n"
+ " fields in one or more nifti datasets. The user may want to specify\n"
+ " mutliple '-field' options along with this. This option requires\n"
+ " one or more files input, via '-infiles'.\n"
+ "\n");
+ printf(
+ " If no '-field' option is present, all fields will be displayed.\n"
+ "\n"
+ " e.g. to display the contents of all fields:\n"
+ " nifti_tool -disp_hdr -infiles dset0.nii\n"
+ " nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii\n"
+ "\n"
+ " e.g. to display the contents of select fields:\n"
+ " nifti_tool -disp_hdr -field dim -infiles dset0.nii\n"
+ " nifti_tool -disp_hdr -field dim -field descrip -infiles dset0.nii\n"
+ "\n");
+ printf(
+ " -disp_nim : display nifti_image fields for datasets\n"
+ "\n"
+ " This flag option works the same way as the '-disp_hdr' option,\n"
+ " except that the fields in question are from the nifti_image\n"
+ " structure.\n"
+ "\n");
+ printf(
+ " -disp_exts : display all AFNI-type extensions\n"
+ "\n"
+ " This flag option is used to display all nifti_1_extension data,\n"
+ " for only those extensions of type AFNI (code = 4). The only\n"
+ " other option used will be '-infiles'.\n"
+ "\n");
+ printf(
+ " e.g. to display the extensions in datasets:\n"
+ " nifti_tool -disp_exts -infiles dset0.nii\n"
+ " nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii\n"
+ "\n");
+ printf(
+ " -disp_ts I J K : display ASCII time series at i,j,k = I,J,K\n"
+ "\n"
+ " This option is used to display the time series data for the voxel\n"
+ " at i,j,k indices I,J,K. The data is displayed in text, either all\n"
+ " on one line (the default), or as one number per line (via the\n"
+ " '-dci_lines' option).\n"
+ "\n");
+ printf(
+ " Notes:\n"
+ "\n"
+ " o This function applies only to 4-dimensional datasets.\n"
+ " o The '-quiet' option can be used to suppress the text header,\n"
+ " leaving only the data.\n"
+ " o This option is short for using '-disp_ci' (display collapsed\n"
+ " image), restricted to 4-dimensional datasets. i.e. :\n"
+ " -disp_ci I J K -1 -1 -1 -1\n"
+ "\n");
+ printf(
+ " e.g. to display the time series at voxel 23, 0, 172:\n"
+ " nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii\n"
+ " nifti_tool -disp_ts 23 0 172 -dci_lines -infiles dset1_time.nii\n"
+ " nifti_tool -disp_ts 23 0 172 -quiet -infiles dset1_time.nii\n"
+ "\n");
+ printf(
+ " -disp_collapsed_image : display ASCII values for collapsed dataset\n"
+ " -disp_ci I J K T U V W : (a shorter, alternative form)\n"
+ "\n"
+ " This option is used to display all of the data from a collapsed\n"
+ " image, given the dimension list. The data is displayed in text,\n"
+ " either all on one line (the default), or as one number per line\n"
+ " (by using the '-dci_lines' flag).\n"
+ "\n");
+ printf(
+ " The '-quiet' option can be used to suppress the text header.\n"
+ "\n"
+ " e.g. to display the time series at voxel 23, 0, 172:\n"
+ " nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii\n"
+ "\n"
+ " e.g. to display z-slice 14, at time t=68:\n"
+ " nifti_tool -disp_ci -1 -1 14 68 0 0 0 -infiles dset1_time.nii\n"
+ "\n"
+ " See '-ccd' for more information, which copies such data to a new\n"
+ " dataset, instead of printing it to the terminal window.\n"
+ "\n"
+ " ------------------------------\n");
+ printf(
+ "\n"
+ " options for modification actions:\n"
+ "\n"
+ " -mod_hdr : modify nifti_1_header fields for datasets\n"
+ "\n"
+ " This action is used to modify some of the nifti_1_header fields in\n"
+ " one or more datasets. The user must specify a list of fields to\n"
+ " modify via one or more '-mod_field' options, which include field\n"
+ " names, along with the new (set of) values.\n"
+ "\n");
+ printf(
+ " The user can modify a dataset in place, or use '-prefix' to\n"
+ " produce a new dataset, to which the changes have been applied.\n"
+ " It is recommended to normally use the '-prefix' option, so as not\n"
+ " to ruin a dataset.\n"
+ "\n");
+ printf(
+ " Note that some fields have a length greater than 1, meaning that\n"
+ " the field is an array of numbers, or a string of characters. In\n"
+ " order to modify an array of numbers, the user must provide the\n"
+ " correct number of values, and contain those values in quotes, so\n"
+ " that they are seen as a single option.\n"
+ "\n");
+ printf(
+ " To modify a string field, put the string in quotes.\n"
+ "\n"
+ " The '-mod_field' option takes a field_name and a list of values.\n"
+ "\n"
+ " e.g. to modify the contents of various fields:\n"
+ "\n");
+ printf(
+ " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
+ " -mod_field qoffset_x -17.325\n"
+ " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
+ " -mod_field dim '4 64 64 20 30 1 1 1 1'\n"
+ " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
+ " -mod_field descrip 'beer, brats and cheese, mmmmm...'\n"
+ "\n");
+ printf(
+ " e.g. to modify the contents of multiple fields:\n"
+ " nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \\\n"
+ " -mod_field qoffset_x -17.325 -mod_field slice_start 1\n"
+ "\n"
+ " e.g. to modify the contents of multiple files (must overwrite):\n"
+ " nifti_tool -mod_hdr -overwrite -mod_field qoffset_x -17.325 \\\n"
+ " -infiles dset0.nii dset1.nii\n"
+ "\n");
+ printf(
+ " -mod_nim : modify nifti_image fields for datasets\n"
+ "\n"
+ " This action option is used the same way that '-mod_hdr' is used,\n"
+ " except that the fields in question are from the nifti_image\n"
+ " structure.\n"
+ "\n");
+ printf(
+ " -strip_extras : remove extensions and descriptions from datasets\n"
+ "\n"
+ " This action is used to attempt to 'clean' a dataset of general\n"
+ " text, in order to make it more anonymous. Extensions and the\n"
+ " nifti_image descrip field are cleared by this action.\n"
+ "\n");
+ printf(
+ " e.g. to strip all *.nii datasets in this directory:\n"
+ " nifti_tool -strip -overwrite -infiles *.nii\n"
+ "\n"
+ " ------------------------------\n");
+ printf(
+ "\n"
+ " options for adding/removing extensions:\n"
+ "\n"
+ " -add_afni_ext EXT : add an AFNI extension to the dataset\n"
+ "\n"
+ " This option is used to add AFNI-type extensions to one or more\n"
+ " datasets. This option may be used more than once to add more than\n"
+ " one extension.\n"
+ "\n");
+ printf(
+ " The '-prefix' option is recommended, to create a new dataset.\n"
+ " In such a case, only a single file may be taken as input. Using\n"
+ " '-overwrite' allows the user to overwrite the current file, or\n"
+ " to add the extension(s) to multiple files, overwriting them.\n"
+ "\n");
+ printf(
+ " e.g. to add a generic AFNI extension:\n"
+ " nifti_tool -add_afni_ext 'wow, my first extension' -prefix dnew \\\n"
+ " -infiles dset0.nii\n"
+ "\n"
+ " e.g. to add multiple AFNI extensions:\n"
+ " nifti_tool -add_afni_ext 'wow, my first extension :)' \\\n"
+ " -add_afni_ext 'look, my second...' \\\n"
+ " -prefix dnew -infiles dset0.nii\n"
+ "\n");
+ printf(
+ " e.g. to add an extension, and overwrite the dataset:\n"
+ " nifti_tool -add_afni_ext 'some AFNI extension' -overwrite \\\n"
+ " -infiles dset0.nii dset1.nii \n"
+ "\n");
+ printf(
+ " -add_comment_ext EXT : add a COMMENT extension to the dataset\n"
+ "\n"
+ " This option is used to add COMMENT-type extensions to one or more\n"
+ " datasets. This option may be used more than once to add more than\n"
+ " one extension. This option may also be used with '-add_afni_ext'.\n"
+ "\n");
+ printf(
+ " The '-prefix' option is recommended, to create a new dataset.\n"
+ " In such a case, only a single file may be taken as input. Using\n"
+ " '-overwrite' allows the user to overwrite the current file, or\n"
+ " to add the extension(s) to multiple files, overwriting them.\n"
+ "\n");
+ printf(
+ " e.g. to add a comment about the dataset:\n"
+ " nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \\\n"
+ " -prefix dnew \\\n"
+ " -infiles dset0.nii\n"
+ "\n");
+ printf(
+ " e.g. to add multiple extensions:\n"
+ " nifti_tool -add_comment 'add a comment extension' \\\n"
+ " -add_afni_ext 'and an AFNI XML style extension' \\\n"
+ " -add_comment 'dataset copied from dset0.nii' \\\n"
+ " -prefix dnew -infiles dset0.nii\n"
+ "\n");
+ printf(
+ " -rm_ext INDEX : remove the extension given by INDEX\n"
+ "\n"
+ " This option is used to remove any single extension from the\n"
+ " dataset. Multiple extensions require multiple options.\n"
+ "\n"
+ " notes - extension indices begin with 0 (zero)\n"
+ " - to view the current extensions, see '-disp_exts'\n"
+ " - all exensions can be removed using ALL or -1 for INDEX\n"
+ "\n");
+ printf(
+ " e.g. to remove the extension #0:\n"
+ " nifti_tool -rm_ext 0 -overwrite -infiles dset0.nii\n"
+ "\n"
+ " e.g. to remove ALL extensions:\n"
+ " nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii\n"
+ " nifti_tool -rm_ext -1 -prefix dset1 -infiles dset0.nii\n"
+ "\n");
+ printf(
+ " e.g. to remove the extensions #2, #3 and #5:\n"
+ " nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \\\n"
+ " -infiles dset0.nii\n"
+ "\n"
+ " ------------------------------\n");
+
+ printf(
+ "\n"
+ " options for showing differences:\n"
+ "\n"
+ " -diff_hdr : display header field diffs between two datasets\n"
+ "\n"
+ " This option is used to find differences between two datasets.\n"
+ " If any fields are different, the contents of those fields is\n"
+ " displayed (unless the '-quiet' option is used).\n"
+ "\n");
+ printf(
+ " A list of fields can be specified by using multiple '-field'\n"
+ " options. If no '-field' option is given, all fields will be\n"
+ " checked.\n"
+ "\n"
+ " Exactly two dataset names must be provided via '-infiles'.\n"
+ "\n"
+ " e.g. to display all nifti_1_header field differences:\n"
+ " nifti_tool -diff_hdr -infiles dset0.nii dset1.nii\n"
+ "\n");
+ printf(
+ " e.g. to display selected nifti_1_header field differences:\n"
+ " nifti_tool -diff_hdr -field dim -field intent_code \\\n"
+ " -infiles dset0.nii dset1.nii \n"
+ "\n"
+ " -diff_nim : display nifti_image field diffs between datasets\n"
+ "\n"
+ " This option works the same as '-diff_hdr', except that the fields\n"
+ " in question are from the nifti_image structure.\n"
+ "\n"
+ " ------------------------------\n");
+
+ printf(
+ "\n"
+ " miscellaneous options:\n"
+ "\n"
+ " -debug LEVEL : set the debugging level\n"
+ "\n"
+ " Level 0 will attempt to operate with no screen output, but errors.\n"
+ " Level 1 is the default.\n"
+ " Levels 2 and 3 give progressively more infomation.\n"
+ "\n"
+ " e.g. -debug 2\n"
+ "\n");
+ printf(
+ " -field FIELDNAME : provide a field to work with\n"
+ "\n"
+ " This option is used to provide a field to display, modify or\n"
+ " compare. This option can be used along with one of the action\n"
+ " options presented above.\n"
+ "\n"
+ " See '-disp_hdr', above, for complete examples.\n"
+ "\n"
+ " e.g. nifti_tool -field descrip\n"
+ " e.g. nifti_tool -field descrip -field dim\n"
+ "\n");
+ printf(
+ " -infiles file0... : provide a list of files to work with\n"
+ "\n"
+ " This parameter is required for any of the actions, in order to\n"
+ " provide a list of files to process. If input filenames do not\n"
+ " have an extension, the directory we be searched for any\n"
+ " appropriate files (such as .nii or .hdr).\n"
+ "\n");
+ printf(
+ " See '-mod_hdr', above, for complete examples.\n"
+ "\n"
+ " e.g. nifti_tool -infiles file0.nii\n"
+ " e.g. nifti_tool -infiles file1.nii file2 file3.hdr\n"
+ "\n");
+ printf(
+ " -mod_field NAME 'VALUE_LIST' : provide new values for a field\n"
+ "\n"
+ " This parameter is required for any the modification actions.\n"
+ " If the user wants to modify any fields of a dataset, this is\n"
+ " where the fields and values are specified.\n"
+ "\n");
+ printf(
+ " NAME is a field name (in either the nifti_1_header structure or\n"
+ " the nifti_image structure). If the action option is '-mod_hdr',\n"
+ " then NAME must be the name of a nifti_1_header field. If the\n"
+ " action is '-mod_nim', NAME must be from a nifti_image structure.\n"
+ "\n");
+ printf(
+ " VALUE_LIST must be one or more values, as many as are required\n"
+ " for the field, contained in quotes if more than one is provided.\n"
+ "\n"
+ " Use 'nifti_tool -help_hdr' to get a list of nifti_1_header fields\n"
+ " Use 'nifti_tool -help_nim' to get a list of nifti_image fields\n"
+ "\n"
+ " See '-mod_hdr', above, for complete examples.\n"
+ "\n");
+ printf(
+ " e.g. modifying nifti_1_header fields:\n"
+ " -mod_field descrip 'toga, toga, toga'\n"
+ " -mod_field qoffset_x 19.4 -mod_field qoffset_z -11\n"
+ " -mod_field pixdim '1 0.9375 0.9375 1.2 1 1 1 1'\n"
+ "\n");
+ printf(
+ " -keep_hist : add the command as COMMENT (to the 'history')\n"
+ "\n"
+ " When this option is used, the current command will be added\n"
+ " as a NIFTI_ECODE_COMMENT type extension. This provides the\n"
+ " ability to keep a history of commands affecting a dataset.\n"
+ "\n"
+ " e.g. -keep_hist\n"
+ "\n");
+ printf(
+ " -overwrite : any modifications will be made to input files\n"
+ "\n"
+ " This option is used so that all field modifications, including\n"
+ " extension additions or deletions, will be made to the files that\n"
+ " are input.\n"
+ "\n");
+ printf(
+ " In general, the user is recommended to use the '-prefix' option\n"
+ " to create new files. But if overwriting the contents of the\n"
+ " input files is prefered, this is how to do it.\n"
+ "\n"
+ " See '-mod_hdr' or '-add_afni_ext', above, for complete examples.\n"
+ "\n"
+ " e.g. -overwrite\n"
+ "\n");
+ printf(
+ " -prefix : specify an output file to write change into\n"
+ "\n"
+ " This option is used to specify an output file to write, after\n"
+ " modifications have been made. If modifications are being made,\n"
+ " then either '-prefix' or '-overwrite' is required.\n"
+ "\n"
+ " If no extension is given, the output extension will be '.nii'.\n"
+ "\n");
+ printf(
+ " e.g. -prefix new_dset\n"
+ " e.g. -prefix new_dset.nii\n"
+ " e.g. -prefix new_dset.hdr\n"
+ "\n"
+ " -quiet : report only errors or requested information\n"
+ "\n"
+ " This option is equivalent to '-debug 0'.\n"
+ "\n"
+ " ------------------------------\n");
+
+ printf(
+ "\n"
+ " basic help options:\n"
+ "\n"
+ " -help : show this help\n"
+ "\n"
+ " e.g. nifti_tool -help\n"
+ "\n"
+ " -help_hdr : show nifti_1_header field info\n"
+ "\n"
+ " e.g. nifti_tool -help_hdr\n"
+ "\n"
+ " -help_nim : show nifti_image field info\n"
+ "\n"
+ " e.g. nifti_tool -help_nim\n");
+
+ printf(
+ "\n"
+ " -ver : show the program version number\n"
+ "\n"
+ " e.g. nifti_tool -ver\n"
+ "\n"
+ " -hist : show the program modification history\n"
+ "\n"
+ " e.g. nifti_tool -hist\n"
+ "\n");
+ printf(
+ " -nifti_ver : show the nifti library version number\n"
+ "\n"
+ " e.g. nifti_tool -nifti_ver\n"
+ "\n"
+ " -nifti_hist : show the nifti library modification history\n"
+ "\n"
+ " e.g. nifti_tool -nifti_hist\n"
+ "\n"
+ " ------------------------------\n"
+ "\n"
+ " R. Reynolds\n"
+ " compiled: %s\n"
+ " %s\n\n",
+ __DATE__, g_version );
+
+ return 1;
+}
+
+
+/*----------------------------------------------------------------------
+ * display the contents of the struct and all lists
+ *----------------------------------------------------------------------*/
+int disp_nt_opts(char * mesg, nt_opts * opts)
+{
+ int c;
+
+ if( mesg ) fputs(mesg, stderr);
+ if( ! opts )
+ {
+ fprintf(stderr,"** disp_nt_opts: missing opts\n");
+ return -1;
+ }
+
+ fprintf(stderr,"nt_opts @ %p\n"
+ " check_hdr, check_nim = %d, %d\n"
+ " diff_hdr, diff_nim = %d, %d\n"
+ " disp_hdr, disp_nim = %d, %d\n"
+ " disp_exts = %d\n"
+ " add_exts, rm_exts = %d, %d\n"
+ " mod_hdr, mod_nim = %d, %d\n"
+ " cbl, cci = %d, %d\n"
+ " dts, dci_lines = %d, %d\n",
+ (void *)opts,
+ opts->check_hdr, opts->check_nim,
+ opts->diff_hdr, opts->diff_nim, opts->disp_hdr, opts->disp_nim,
+ opts->disp_exts, opts->add_exts, opts->rm_exts,
+ opts->mod_hdr, opts->mod_nim, opts->cbl, opts->cci,
+ opts->dts, opts->dci_lines );
+
+ fprintf(stderr," ci_dims[8] = ");
+ disp_raw_data(opts->ci_dims, DT_INT32, 8, ' ', 1);
+
+ fprintf(stderr,"\n"
+ " debug, keep_hist = %d, %d\n"
+ " overwrite = %d\n"
+ " prefix = '%s'\n",
+ opts->debug, opts->keep_hist, opts->overwrite,
+ opts->prefix ? opts->prefix : "(NULL)" );
+
+ fprintf(stderr," elist (length %d) :\n", opts->elist.len);
+ for( c = 0; c < opts->elist.len; c++ )
+ fprintf(stderr," %d : %s\n", c, opts->elist.list[c]);
+
+ fprintf(stderr," etypes (length %d) : ", opts->etypes.len);
+ disp_raw_data(opts->etypes.list, DT_INT32, opts->etypes.len, ' ', 0);
+ fputc('\n',stderr);
+
+ fprintf(stderr," flist (length %d) :\n", opts->flist.len);
+ for( c = 0; c < opts->flist.len; c++ )
+ fprintf(stderr," %d : %s\n", c, opts->flist.list[c]);
+
+ fprintf(stderr," vlist (length %d) :\n", opts->vlist.len);
+ for( c = 0; c < opts->vlist.len; c++ )
+ fprintf(stderr," %d : %s\n", c, opts->vlist.list[c]);
+
+ fprintf(stderr," infiles (length %d) :\n", opts->infiles.len);
+ for( c = 0; c < opts->infiles.len; c++ )
+ fprintf(stderr," %d : %s\n", c, opts->infiles.list[c]);
+
+ fprintf(stderr," command len : %d\n",(int)strlen(opts->command));
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * For each file, add all extensions with type NIFTI_ECODE_AFNI.
+ * Though it should not matter, copy the trailing null characters.
+ *----------------------------------------------------------------------*/
+int act_add_exts( nt_opts * opts )
+{
+ nifti_image * nim;
+ int fc, ec;
+
+ if( g_debug > 2 ){
+ fprintf(stderr,"+d adding %d extensions to %d files...\n"
+ " extension types are: ",
+ opts->elist.len, opts->infiles.len);
+ disp_raw_data(opts->etypes.list, DT_INT32, opts->etypes.len, ' ', 1);
+ }
+
+ if( opts->prefix && opts->infiles.len != 1 ){
+ fprintf(stderr,"** error: we have a prefix but %d files\n",
+ opts->infiles.len);
+ return 1;
+ }
+
+ if( opts->elist.len <= 0 ) return 0;
+
+ for( fc = 0; fc < opts->infiles.len; fc++ )
+ {
+ nim = nifti_image_read( opts->infiles.list[fc], 1 );
+ if( !nim ) return 1; /* errors come from the library */
+
+ for( ec = 0; ec < opts->elist.len; ec++ ){
+ if( nifti_add_extension(nim, opts->elist.list[ec],
+ strlen(opts->elist.list[ec]), opts->etypes.list[ec]) ){
+ nifti_image_free(nim);
+ return 1;
+ }
+ }
+
+ if( opts->keep_hist && nifti_add_extension(nim, opts->command,
+ strlen(opts->command), NIFTI_ECODE_COMMENT) )
+ fprintf(stderr,"** failed to add command to image as extension\n");
+
+ if( opts->prefix &&
+ nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) )
+ {
+ nifti_image_free(nim);
+ return 1;
+ }
+
+ if( g_debug > 1 )
+ fprintf(stderr,"+d writing %s with %d new extension(s)\n",
+ opts->infiles.list[fc], opts->elist.len);
+
+ nifti_image_write(nim);
+ nifti_image_free(nim);
+ }
+
+ if( g_debug > 0 )
+ fprintf(stderr,"+d added %d extension(s) to %d files\n",
+ opts->elist.len, opts->infiles.len);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * For each file, strip the extra fields.
+ *
+ * Clear extensions and descrip field. No other generic strings will get
+ * passed to nifti_1_header struct.
+ *
+ * - this may make the datasets more anonymous
+ * - no history is appended here
+ *----------------------------------------------------------------------*/
+int act_strip( nt_opts * opts )
+{
+ nifti_image * nim;
+ int fc;
+
+ if( g_debug > 2 )
+ fprintf(stderr,"+d stripping extras from %d files\n", opts->infiles.len);
+
+ if( opts->prefix && opts->infiles.len != 1 ){
+ fprintf(stderr,"** error: we have a prefix but %d files\n",
+ opts->infiles.len);
+ return 1;
+ }
+
+ for( fc = 0; fc < opts->infiles.len; fc++ )
+ {
+ nim = nifti_image_read( opts->infiles.list[fc], 1 );
+ if( !nim ) return 1; /* errors come from the library */
+
+ /* now remove the extensions */
+ nifti_free_extensions(nim);
+ memset(nim->descrip, 0, 80);
+
+ if( opts->prefix &&
+ nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ){
+ nifti_image_free(nim);
+ return 1;
+ }
+
+ if( g_debug > 1 )
+ fprintf(stderr,"+d writing %s without extensions or 'descrip'\n",
+ nim->fname);
+
+ nifti_image_write(nim);
+
+ if( g_debug > 3 ) nifti_image_infodump(nim);
+ nifti_image_free(nim);
+ }
+
+ if( g_debug > 0 )
+ fprintf(stderr,"+d stripped extras from %d files\n", opts->infiles.len);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * For each file, remove the given extension for the given indices.
+ *
+ * Note that index = -1 means to remove them all.
+ *----------------------------------------------------------------------*/
+int act_rm_ext( nt_opts * opts )
+{
+ nifti_image * nim;
+ int fc, ext_ind, num_ext;
+
+ if( g_debug > 2 )
+ fprintf(stderr,"+d removing %d extensions from %d files...\n",
+ opts->elist.len, opts->infiles.len);
+
+ if( opts->elist.len <= 0 ) return 0;
+
+ if( opts->prefix && opts->infiles.len != 1 ){
+ fprintf(stderr,"** error: we have a prefix but %d files\n",
+ opts->infiles.len);
+ return 1;
+ }
+ else if( opts->overwrite && opts->infiles.len != 1 &&
+ strcmp(opts->elist.list[0], "-1") ) {
+ fprintf(stderr,"** error: for multiple files, can only delete ALL\n");
+ return 1;
+ }
+
+ ext_ind = atoi(opts->elist.list[0]);
+ if( ext_ind < -1 ){
+ fprintf(stderr,"** bad extension index to remove: %d\n", ext_ind);
+ return 1;
+ }
+
+ if( g_debug > 1 ) fprintf(stderr,"+d removing extension index %d\n",ext_ind);
+
+ for( fc = 0; fc < opts->infiles.len; fc++ )
+ {
+ nim = nifti_image_read( opts->infiles.list[fc], 1 );
+ if( !nim ) return 1; /* errors come from the library */
+
+ /* now remove the extensions */
+ if( remove_ext_list(nim, opts->elist.list, opts->elist.len) )
+ return 1;
+
+ if( opts->keep_hist && nifti_add_extension(nim, opts->command,
+ strlen(opts->command), NIFTI_ECODE_COMMENT) )
+ fprintf(stderr,"** failed to add command to image as extension\n");
+
+ if( opts->prefix &&
+ nifti_set_filenames(nim, opts->prefix, !opts->overwrite, 1) ){
+ nifti_image_free(nim);
+ return 1;
+ }
+
+ if( g_debug > 1 )
+ fprintf(stderr,"+d writing %s with %d fewer extension(s)\n",
+ nim->fname, ext_ind == -1 ? num_ext : opts->elist.len);
+
+ nifti_image_write(nim);
+ nifti_image_free(nim);
+ }
+
+ if( g_debug > 0 )
+ fprintf(stderr,"+d removed %s extension(s) from %d files\n",
+ ext_ind == -1 ? "ALL" : "1", opts->infiles.len);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * remove extensions by index
+ *
+ * return: 0 on success, -1 on failure
+ *----------------------------------------------------------------------*/
+int remove_ext_list( nifti_image * nim, char ** elist, int len )
+{
+ int * marks;
+ int c, ec, extval;
+
+ if( len > nim->num_ext ){
+ fprintf(stderr, "** cannot remove %d exts from image '%s' with only %d\n",
+ len, nim->fname, nim->num_ext);
+ return -1;
+ }
+
+ if( len <= 0 ){
+ fprintf(stderr,"** REL: (%d) no extensions to remove?\n",len);
+ return -1;
+ }
+
+ extval = atoi(elist[0]); /* check the first value */
+
+ /* first special case, elist[0] == -1 */
+ if( extval == -1 )
+ {
+ if( g_debug > 1 )
+ fprintf(stderr,"+d removing ALL (%d) extensions from '%s'\n",
+ nim->num_ext, nim->fname );
+ nifti_free_extensions(nim);
+ return 0;
+ }
+
+ if( g_debug > 2 )
+ fprintf(stderr,"+d removing %d exts from '%s'\n", len, nim->fname );
+
+ if( ! (marks = (int *)calloc(nim->num_ext, sizeof(int))) ) {
+ fprintf(stderr,"** failed to alloc %d marks\n",nim->num_ext);
+ return -1;
+ }
+
+ /* mark all extensions for removal */
+ for( ec = 0; ec < len; ec++ )
+ {
+ extval = atoi(elist[ec]);
+
+ if( extval < 0 || extval >= nim->num_ext ){
+ fprintf(stderr,"** ext #%d (= %d) is out of range [0,%d] for %s\n",
+ ec, extval, nim->num_ext-1, nim->fname);
+ free(marks); return -1;
+ }
+
+ if( marks[extval] ){
+ fprintf(stderr,"** ext #%d (= %d) is a duplicate", ec, extval);
+ free(marks); return -1;
+ }
+
+ marks[extval]++;
+ }
+
+ /* now remove them - count from top down to do lazy programming */
+ for( ec = nim->num_ext-1; ec >= 0; ec-- )
+ {
+ if( !marks[ec] ) continue; /* do not delete this one */
+
+ if( g_debug > 2 )
+ disp_nifti1_extension("+d removing ext: ",nim->ext_list+ec,-1);
+
+ /* delete this data, and shift the list down (yeah, inefficient) */
+ if( nim->ext_list[ec].edata ) free( nim->ext_list[ec].edata );
+
+ /* move anything above down one */
+ for( c = ec+1; c < nim->num_ext; c++ )
+ nim->ext_list[c-1] = nim->ext_list[c];
+
+ nim->num_ext--;
+ }
+
+ if( g_debug > 3 ) fprintf(stderr,"-d done removing extensions\n");
+
+ if( nim->num_ext == 0 ){ /* did we trash the only extension? */
+ if( g_debug > 1 )
+ fprintf(stderr,"-d removed ALL extensions from %s\n",nim->fname);
+ free(nim->ext_list);
+ nim->ext_list = NULL;
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * check for diffs between all fields in opts->flist, or in the
+ * entire nifti_1_header
+ *
+ * if quiet mode (debug == 0) return on first diff
+ *
+ * return: 1 if diffs exist, 0 otherwise
+ *----------------------------------------------------------------------*/
+int act_diff_hdrs( nt_opts * opts )
+{
+ nifti_1_header * nhdr0, * nhdr1;
+ int diffs = 0;
+
+ if( opts->infiles.len != 2 ){
+ fprintf(stderr,"** -diff_hdr requires 2 -infiles, have %d\n",
+ opts->infiles.len);
+ return 1;
+ }
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d nifti_1_header diff between %s and %s...\n",
+ opts->infiles.list[0], opts->infiles.list[1]);
+
+ /* get the nifiti headers (but do not validate them) */
+
+ nhdr0 = nifti_read_header(opts->infiles.list[0], NULL, 0);
+ if( ! nhdr0 ) return 1; /* errors have been printed */
+
+ nhdr1 = nifti_read_header(opts->infiles.list[1], NULL, 0);
+ if( ! nhdr1 ){ free(nhdr0); return 1; }
+
+ if( g_debug > 1 )
+ fprintf(stderr,"\n-d nifti_1_header diffs between '%s' and '%s'...\n",
+ opts->infiles.list[0], opts->infiles.list[1]);
+
+ if( opts->flist.len <= 0 )
+ diffs = diff_hdrs(nhdr0, nhdr1, g_debug > 0);
+ else
+ diffs = diff_hdrs_list(nhdr0, nhdr1, &opts->flist, g_debug > 0);
+
+ if( diffs == 0 && g_debug > 1 )
+ fprintf(stderr,"+d no differences found\n");
+ else if ( g_debug > 2 )
+ fprintf(stderr,"+d %d differences found\n", diffs);
+
+ free(nhdr0);
+ free(nhdr1);
+
+ return (diffs > 0);
+}
+
+
+/*----------------------------------------------------------------------
+ * check for diffs between all fields in opts->flist, or in the
+ * entire nifti_image
+ *
+ * if quiet mode (debug == 0) return on first diff
+ *
+ * return: 1 if diffs exist, 0 otherwise
+ *----------------------------------------------------------------------*/
+int act_diff_nims( nt_opts * opts )
+{
+ nifti_image * nim0, * nim1;
+ int diffs = 0;
+
+ if( opts->infiles.len != 2 ){
+ fprintf(stderr,"** -diff_nim requires 2 -infiles, have %d\n",
+ opts->infiles.len);
+ return 1;
+ }
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d nifti_image diff between %s and %s...\n",
+ opts->infiles.list[0], opts->infiles.list[1]);
+
+ /* get the nifiti images */
+
+ nim0 = nifti_image_read(opts->infiles.list[0], 0);
+ if( ! nim0 ) return 1; /* errors have been printed */
+
+ nim1 = nifti_image_read(opts->infiles.list[1], 0);
+ if( ! nim1 ){ free(nim0); return 1; }
+
+ if( g_debug > 1 )
+ fprintf(stderr,"\n-d nifti_image diffs between '%s' and '%s'...\n",
+ opts->infiles.list[0], opts->infiles.list[1]);
+
+ if( opts->flist.len <= 0 )
+ diffs = diff_nims(nim0, nim1, g_debug > 0);
+ else
+ diffs = diff_nims_list(nim0, nim1, &opts->flist, g_debug > 0);
+
+ if( diffs == 0 && g_debug > 1 )
+ fprintf(stderr,"+d no differences found\n");
+ else if ( g_debug > 2 )
+ fprintf(stderr,"+d %d differences found\n", diffs);
+
+ nifti_image_free(nim0);
+ nifti_image_free(nim1);
+
+ return (diffs > 0);
+}
+
+
+/*----------------------------------------------------------------------
+ * for each file, read nifti1_header
+ * if checking header, check it
+ * if checking nifti_image, convert and check it
+ *----------------------------------------------------------------------*/
+int act_check_hdrs( nt_opts * opts )
+{
+ nifti_1_header * nhdr;
+ nifti_image * nim;
+ int filenum, rv;
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d checking hdrs/nims for %d nifti datasets...\n",
+ opts->infiles.len);
+
+ for( filenum = 0; filenum < opts->infiles.len; filenum++ )
+ {
+ /* do not validate the header structure */
+ nhdr = nifti_read_header(opts->infiles.list[filenum], NULL, 0);
+ if( !nhdr ) continue; /* errors are printed from library */
+
+ if( opts->check_hdr )
+ {
+ if( g_debug > 1 )
+ fprintf(stdout,"\nchecking nifti_1_header for file '%s'\n",
+ opts->infiles.list[filenum]);
+
+ rv = nifti_hdr_looks_good(nhdr);
+
+ if( rv && g_debug > 0 ) /* if quiet, no GOOD response */
+ printf("header IS GOOD for file %s\n",opts->infiles.list[filenum]);
+ else if( ! rv )
+ printf("header FAILURE for file %s\n",opts->infiles.list[filenum]);
+ }
+
+ if( opts->check_nim )
+ {
+ nim = nifti_convert_nhdr2nim(*nhdr, opts->infiles.list[filenum]);
+ if( !nim ) continue; /* errors are printed from library */
+
+ if( g_debug > 1 )
+ fprintf(stdout,"\nchecking nifti_image for file '%s'\n",
+ opts->infiles.list[filenum]);
+
+ rv = nifti_nim_is_valid(nim, 1); /* complain about errors */
+
+ if( rv && g_debug > 0 ) /* if quiet, no GOOD response */
+ printf("nifti_image IS GOOD for file %s\n",
+ opts->infiles.list[filenum]);
+ else if( ! rv )
+ printf("nifti_image FAILURE for file %s\n",
+ opts->infiles.list[filenum]);
+
+ free(nim);
+ }
+
+ free(nhdr);
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * display all extensions for each dataset
+ *----------------------------------------------------------------------*/
+int act_disp_exts( nt_opts * opts )
+{
+ nifti_image * nim;
+ char mesg[32];
+ int ec, fc;
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d displaying all extensions for %d files...\n",
+ opts->infiles.len);
+
+ for( fc = 0; fc < opts->infiles.len; fc++ )
+ {
+ nim = nifti_image_read(opts->infiles.list[fc], 0);
+ if( !nim ) return 1; /* errors are printed from library */
+
+ if( g_debug > 0 )
+ fprintf(stdout,"header file '%s', num_ext = %d\n",
+ nim->fname, nim->num_ext);
+ for( ec = 0; ec < nim->num_ext; ec++ )
+ {
+ sprintf(mesg, " ext #%d : ", ec);
+ disp_nifti1_extension(mesg, nim->ext_list + ec, -1);
+ }
+
+ nifti_image_free(nim);
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * for each file, read nifti1_header and display all fields
+ *----------------------------------------------------------------------*/
+int act_disp_hdrs( nt_opts * opts )
+{
+ nifti_1_header * nhdr;
+ field_s * fnhdr;
+ char ** sptr;
+ int nfields, filenum, fc;
+
+ /* set the number of fields to display */
+ nfields = opts->flist.len > 0 ? opts->flist.len : NT_HDR_NUM_FIELDS;
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n",
+ nfields, opts->infiles.len);
+
+ for( filenum = 0; filenum < opts->infiles.len; filenum++ )
+ {
+ /* do not validate the header structure */
+ nhdr = nifti_read_header(opts->infiles.list[filenum], NULL, 0);
+ if( !nhdr ) return 1; /* errors are printed from library */
+
+ if( g_debug > 0 )
+ fprintf(stdout,"\nheader file '%s', num_fields = %d\n",
+ opts->infiles.list[filenum], nfields);
+ if( g_debug > 1 )
+ fprintf(stderr,"-d header is: %s\n",
+ nifti_hdr_looks_good(nhdr) ? "valid" : "invalid");
+
+ if( opts->flist.len <= 0 ) /* then display all fields */
+ disp_field("\nall fields:\n", g_hdr_fields, nhdr, nfields, g_debug>0);
+ else /* print only the requested fields... */
+ {
+ /* must locate each field before printing it */
+ sptr = opts->flist.list;
+ for( fc = 0; fc < opts->flist.len; fc++ )
+ {
+ fnhdr = get_hdr_field(*sptr, filenum == 0);
+ if( fnhdr ) disp_field(NULL, fnhdr, nhdr, 1, g_debug>0 && fc == 0);
+ sptr++;
+ }
+ }
+
+ free(nhdr);
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * for each file, get nifti_image and display all fields
+ *----------------------------------------------------------------------*/
+int act_disp_nims( nt_opts * opts )
+{
+ nifti_image * nim;
+ field_s * fnim;
+ char ** sptr;
+ int nfields, filenum, fc;
+
+ /* set the number of fields to display */
+ nfields = opts->flist.len > 0 ? opts->flist.len : NT_NIM_NUM_FIELDS;
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d displaying %d fields for %d nifti datasets...\n",
+ nfields, opts->infiles.len);
+
+ for( filenum = 0; filenum < opts->infiles.len; filenum++ )
+ {
+ nim = nifti_image_read(opts->infiles.list[filenum], 0);
+ if( !nim ) return 1; /* errors are printed from library */
+
+ if( g_debug > 0 )
+ fprintf(stdout,"\nheader file '%s', num_fields = %d, fields:\n\n",
+ nim->fname, nfields);
+
+ if( opts->flist.len <= 0 ) /* then display all fields */
+ disp_field("all fields:\n", g_nim_fields, nim, nfields, g_debug > 0);
+ else /* print only the requested fields... */
+ {
+ /* must locate each field before printing it */
+ sptr = opts->flist.list;
+ for( fc = 0; fc < opts->flist.len; fc++ )
+ {
+ fnim = get_nim_field(*sptr, filenum == 0);
+ if( fnim ) disp_field(NULL, fnim, nim, 1, g_debug > 0 && fc == 0);
+ sptr++;
+ }
+ }
+
+ nifti_image_free(nim);
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * - read header
+ * - modify header
+ * - if -prefix duplicate file
+ * - else if swapped, swap back
+ * - overwrite file header (allows (danger-of) no evaluation of data)
+ *----------------------------------------------------------------------*/
+int act_mod_hdrs( nt_opts * opts )
+{
+ nifti_1_header * nhdr;
+ nifti_image * nim; /* for reading/writing entire datasets */
+ int filec, swap;
+ char * fname, * dupname;
+ char func[] = { "act_mod_hdrs" };
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d modifying %d fields for %d nifti headers...\n",
+ opts->flist.len, opts->infiles.len);
+ if( opts->flist.len <= 0 || opts->infiles.len <= 0 ) return 0;
+
+ for( filec = 0; filec < opts->infiles.len; filec++ )
+ {
+ fname = opts->infiles.list[filec]; /* for convenience and mod file */
+
+ if( nifti_is_gzfile(fname) ){
+ fprintf(stderr,"** sorry, cannot modify a zipped file: %s\n", fname);
+ continue;
+ }
+
+ /* do not validate the header structure */
+ nhdr = nifti_read_header(fname, &swap, 0);
+ if( !nhdr ) return 1;
+
+ if( g_debug > 1 )
+ {
+ fprintf(stderr,"-d modifying %d fields of '%s' header\n",
+ opts->flist.len, fname);
+ fprintf(stderr,"-d header is: %s\n",
+ nifti_hdr_looks_good(nhdr) ? "valid" : "invalid");
+ }
+
+ /* okay, let's actually trash the data fields */
+ if( modify_all_fields(nhdr, opts, g_hdr_fields, NT_HDR_NUM_FIELDS) )
+ {
+ free(nhdr);
+ return 1;
+ }
+
+ dupname = NULL; /* unless we duplicate file */
+
+ /* possibly duplicate the current dataset before writing new header */
+ if( opts->prefix )
+ {
+ nim = nifti_image_read(fname, 1); /* get data */
+ if( !nim ) {
+ fprintf(stderr,"** failed to dup file '%s' before modifying\n",
+ fname);
+ return 1;
+ }
+ if( opts->keep_hist && nifti_add_extension(nim, opts->command,
+ strlen(opts->command), NIFTI_ECODE_COMMENT) )
+ fprintf(stderr,"** failed to add command to image as exten\n");
+ if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
+ {
+ NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix);
+ nifti_image_free(nim);
+ return 1;
+ }
+ dupname = nifti_strdup(nim->fname); /* so we know to free it */
+ fname = dupname;
+ nifti_image_write(nim); /* create the duplicate file */
+ /* if we added a history note, get the new offset into the header */
+ if( opts->keep_hist ) nhdr->vox_offset = nim->iname_offset;
+ nifti_image_free(nim);
+ }
+ else if ( swap )
+ swap_nifti_header(nhdr, NIFTI_VERSION(*nhdr));
+
+ /* if all is well, overwrite header in fname dataset */
+ (void)write_hdr_to_file(nhdr, fname); /* errors printed in function */
+
+ if( dupname ) free(dupname);
+ free(nhdr);
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * - read image w/data, modify and write
+ *----------------------------------------------------------------------*/
+int act_mod_nims( nt_opts * opts )
+{
+ nifti_image * nim; /* for reading/writing entire datasets */
+ int filec;
+ char func[] = { "act_mod_nims" };
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d modifying %d fields for %d nifti images...\n",
+ opts->flist.len, opts->infiles.len);
+ if( opts->flist.len <= 0 || opts->infiles.len <= 0 ) return 0;
+
+ for( filec = 0; filec < opts->infiles.len; filec++ )
+ {
+ nim = nifti_image_read(opts->infiles.list[filec], 1); /* with data */
+
+ if( g_debug > 1 )
+ fprintf(stderr,"-d modifying %d fields from '%s' image\n",
+ opts->flist.len, opts->infiles.list[filec]);
+
+ /* okay, let's actually trash the data fields */
+ if( modify_all_fields(nim, opts, g_nim_fields, NT_NIM_NUM_FIELDS) )
+ {
+ nifti_image_free(nim);
+ return 1;
+ }
+
+ /* add command as COMMENT extension */
+ if( opts->keep_hist && nifti_add_extension(nim, opts->command,
+ strlen(opts->command), NIFTI_ECODE_COMMENT) )
+ fprintf(stderr,"** failed to add command to image as extension\n");
+
+ /* possibly duplicate the current dataset before writing new header */
+ if( opts->prefix )
+ if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
+ {
+ NTL_FERR(func,"failed to set prefix for new file: ",opts->prefix);
+ nifti_image_free(nim);
+ return 1;
+ }
+
+ nifti_image_write(nim); /* and write it out, piece of cake :) */
+ nifti_image_free(nim);
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * overwrite nifti_1_header in the given file
+ *----------------------------------------------------------------------*/
+int write_hdr_to_file( nifti_1_header * nhdr, char * fname )
+{
+ znzFile fp;
+ size_t bytes;
+ char func[] = { "write_hdr_to_file" };
+ int rv = 0;
+
+ fp = znzopen(fname,"r+b",nifti_is_gzfile(fname));
+ if( znz_isnull(fp) ){
+ NTL_FERR(func, "failed to re-open mod file", fname);
+ return 1;
+ }
+
+ bytes = znzwrite(nhdr, 1, sizeof(nifti_1_header), fp);
+ if( bytes != sizeof(nifti_1_header)){
+ NTL_FERR(func, "failed to write header to file",fname);
+ fprintf(stderr," - wrote %d of %d bytes\n",
+ (int)bytes,(int)sizeof(nifti_1_header));
+ rv = 1;
+ }
+
+ if( g_debug > 3 )
+ disp_nifti_1_header("+d writing new header to file : ", nhdr);
+
+ znzclose(fp);
+
+ return rv;
+}
+
+
+/*----------------------------------------------------------------------
+ * modify all fields in the list
+ *----------------------------------------------------------------------*/
+int modify_all_fields( void * basep, nt_opts * opts, field_s * fields, int flen)
+{
+ field_s * fp;
+ int fc, lc; /* field and list counters */
+
+ if( opts->flist.len <= 0 ) return 0;
+ if( opts->flist.len != opts->vlist.len ){
+ fprintf(stderr,"** have %d fields but %d new values\n",
+ opts->flist.len, opts->vlist.len);
+ return 1;
+ }
+
+ for( lc = 0; lc < opts->flist.len; lc++ )
+ {
+ /* is it in the list? */
+ fp = fields;
+ for( fc = 0; fc < flen; fc++, fp++ )
+ if( strcmp(opts->flist.list[lc], fp->name) == 0 ) break;
+
+ if( fc == flen ) /* do no modifications on failure */
+ {
+ fprintf(stderr,"** field '%s' not found in structure\n",
+ opts->flist.list[lc]);
+ return 1;
+ }
+
+ if( modify_field( basep, fp, opts->vlist.list[lc]) )
+ return 1;
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * modify a single field with the given value field
+ *
+ * pointer fields are not allowed here
+ *----------------------------------------------------------------------*/
+int modify_field(void * basep, field_s * field, char * data)
+{
+ float fval;
+ char * posn = data;
+ int val, max, fc, nchars;
+
+ if( g_debug > 1 )
+ fprintf(stderr,"+d modifying field '%s' with '%s'\n", field->name, data);
+
+ if( !data || strlen(data) == 0 )
+ {
+ fprintf(stderr,"** no data for '%s' field modification\n",field->name);
+ return 1;
+ }
+
+ switch( field->type )
+ {
+ case DT_UNKNOWN:
+ case NT_DT_POINTER:
+ case NT_DT_CHAR_PTR:
+ case NT_DT_EXT_PTR:
+ default:
+ fprintf(stderr,"** refusing to modify a pointer field, '%s'\n",
+ field->name);
+ return 1;
+
+ case DT_INT8:
+ {
+ max = 127;
+ for( fc = 0; fc < field->len; fc++ )
+ {
+ if( sscanf(posn, " %d%n", &val, &nchars) != 1 )
+ {
+ fprintf(stderr,"** found %d of %d modify values\n",
+ fc,field->len);
+ return 1;
+ }
+ if( val > max || val < -(max+1) )
+ {
+ fprintf(stderr,
+ "** mod val #%d (= %d) outside byte range [-%d,%d]\n",
+ fc, val, max+1, max);
+ return 1;
+ }
+ /* otherwise, we're good */
+ (((char *)basep + field->offset))[fc] = (char)val;
+ if( g_debug > 1 )
+ fprintf(stderr,"+d setting posn %d of '%s' to %d\n",
+ fc, field->name, val);
+ posn += nchars;
+ }
+ }
+ break;
+
+ case DT_INT16:
+ {
+ max = 32767;
+ for( fc = 0; fc < field->len; fc++ )
+ {
+ if( sscanf(posn, " %d%n", &val, &nchars) != 1 )
+ {
+ fprintf(stderr,"** found %d of %d modify values\n",
+ fc,field->len);
+ return 1;
+ }
+ if( val > max || val < -(max+1) )
+ {
+ fprintf(stderr,
+ "** mod val #%d (= %d) outside byte range [-%d,%d]\n",
+ fc, val, max+1, max);
+ return 1;
+ }
+ /* otherwise, we're good */
+ ((short *)((char *)basep + field->offset))[fc] = (short)val;
+ if( g_debug > 1 )
+ fprintf(stderr,"+d setting posn %d of '%s' to %d\n",
+ fc, field->name, val);
+ posn += nchars;
+ }
+ }
+ break;
+
+ case DT_INT32:
+ {
+ for( fc = 0; fc < field->len; fc++ )
+ {
+ if( sscanf(posn, " %d%n", &val, &nchars) != 1 )
+ {
+ fprintf(stderr,"** found %d of %d modify values\n",
+ fc,field->len);
+ return 1;
+ }
+ ((int *)((char *)basep + field->offset))[fc] = val;
+ if( g_debug > 1 )
+ fprintf(stderr,"+d setting posn %d of '%s' to %d\n",
+ fc, field->name, val);
+ posn += nchars;
+ }
+ }
+ break;
+
+ case DT_FLOAT32:
+ {
+ for( fc = 0; fc < field->len; fc++ )
+ {
+ if( sscanf(posn, " %f%n", &fval, &nchars) != 1 )
+ {
+ fprintf(stderr,"** found %d of %d modify values\n",
+ fc,field->len);
+ return 1;
+ }
+ /* otherwise, we're good */
+ ((float *)((char *)basep + field->offset))[fc] = fval;
+ if( g_debug > 1 )
+ fprintf(stderr,"+d setting posn %d of '%s' to %f\n",
+ fc, field->name, fval);
+ posn += nchars;
+ }
+ }
+ break;
+
+ case NT_DT_STRING:
+ {
+ char * dest = (char *)basep + field->offset;
+ nchars = strlen(data);
+ strncpy(dest, data, field->len);
+ if( nchars < field->len ) /* clear the rest */
+ memset(dest+nchars, '\0', field->len-nchars);
+ }
+ break;
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * fill the nifti_1_header field list
+ *----------------------------------------------------------------------*/
+int fill_hdr_field_array( field_s * nh_fields )
+{
+ nifti_1_header nhdr;
+ field_s * nhf = nh_fields;
+ int rv, errs;
+
+ memset(nhf, 0, NT_HDR_NUM_FIELDS*sizeof(field_s));
+
+ /* this macro takes (TYPE, NAME, NUM) and does:
+ fill_field(nhdr, TYPE, NT_OFF(nhdr,NAME), NUM, "NAME");
+ nhf++;
+ */
+ errs = 0;
+ NT_SFILL(nhdr, nhf, DT_INT32, sizeof_hdr, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, NT_DT_STRING, data_type, 10, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, NT_DT_STRING, db_name, 18, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT32, extents, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT16, session_error, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, NT_DT_STRING, regular, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT8, dim_info, 1, rv); errs += rv;
+
+ NT_SFILL(nhdr, nhf, DT_INT16, dim, 8, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p1, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p2, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, intent_p3, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT16, intent_code, 1, rv); errs += rv;
+
+ NT_SFILL(nhdr, nhf, DT_INT16, datatype, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT16, bitpix, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT16, slice_start, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, pixdim, 8, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, vox_offset, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, scl_slope, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, scl_inter, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT16, slice_end, 1, rv); errs += rv;
+
+ NT_SFILL(nhdr, nhf, DT_INT8, slice_code, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT8, xyzt_units, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, cal_max, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, cal_min, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, slice_duration, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, toffset, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT32, glmax, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT32, glmin, 1, rv); errs += rv;
+
+ NT_SFILL(nhdr, nhf, NT_DT_STRING, descrip, 80, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, NT_DT_STRING, aux_file, 24, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT16, qform_code, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_INT16, sform_code, 1, rv); errs += rv;
+
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_b, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_c, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, quatern_d, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_x, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_y, 1, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, qoffset_z, 1, rv); errs += rv;
+
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_x, 4, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_y, 4, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, DT_FLOAT32, srow_z, 4, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, NT_DT_STRING, intent_name, 16, rv); errs += rv;
+ NT_SFILL(nhdr, nhf, NT_DT_STRING, magic, 4, rv); errs += rv;
+
+ if( errs > 0 ){
+ fprintf(stderr, "** %d fill_fields errors!\n", errs);
+ return 1;
+ }
+
+ /* failure here is a serious problem */
+ if( check_total_size("nifti_1_header test: ", nh_fields,
+ NT_HDR_NUM_FIELDS, sizeof(nhdr)) )
+ return 1;
+
+ if( g_debug > 3 )
+ disp_field_s_list("nh_fields: ", nh_fields, NT_HDR_NUM_FIELDS);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * fill the nifti_image field list
+ *----------------------------------------------------------------------*/
+int fill_nim_field_array( field_s * nim_fields )
+{
+ nifti_image nim;
+ field_s * nif = nim_fields;
+ int rv, errs;
+
+ memset(nif, 0, NT_NIM_NUM_FIELDS*sizeof(field_s));
+
+ errs = 0;
+
+ NT_SFILL(nim, nif, DT_INT32, ndim, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nx, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, ny, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nz, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nt, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nu, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nv, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nw, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, dim, 8, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nvox, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nbyper, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, datatype, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, dx, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, dy, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, dz, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, dt, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, du, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, dv, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, dw, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, pixdim, 8, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, scl_slope, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, scl_inter, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, cal_min, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, cal_max, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, qform_code, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, sform_code, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, freq_dim, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, phase_dim, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, slice_dim, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, slice_code, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, slice_start, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, slice_end, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, slice_duration, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, quatern_b, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, quatern_c, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, quatern_d, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, qoffset_x, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, qoffset_y, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, qoffset_z, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, qfac, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, qto_xyz, 16, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, qto_ijk, 16, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, sto_xyz, 16, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, sto_ijk, 16, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, toffset, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, xyz_units, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, time_units, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, nifti_type, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, intent_code, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, intent_p1, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, intent_p2, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_FLOAT32, intent_p3, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, NT_DT_STRING, intent_name, 16, rv); errs += rv;
+ NT_SFILL(nim, nif, NT_DT_STRING, descrip, 80, rv); errs += rv;
+ NT_SFILL(nim, nif, NT_DT_STRING, aux_file, 24, rv); errs += rv;
+ NT_SFILL(nim, nif, NT_DT_CHAR_PTR, fname, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, NT_DT_CHAR_PTR, iname, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, iname_offset, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, swapsize, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, byteorder, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, NT_DT_POINTER, data, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, DT_INT32, num_ext, 1, rv); errs += rv;
+ NT_SFILL(nim, nif, NT_DT_EXT_PTR, ext_list, 1, rv); errs += rv;
+
+ if( errs > 0 ){
+ fprintf(stderr, "** %d fill_fields errors "
+ "(note that pointers get aligned)\n", errs);
+ return 1;
+ }
+
+ if( g_debug > 3 ) /* failure here is not an error condition */
+ check_total_size("nifti_image test: ", nim_fields,
+ NT_NIM_NUM_FIELDS, sizeof(nim));
+
+ if( g_debug > 3 )
+ disp_field_s_list("nim_fields: ", nim_fields, NT_NIM_NUM_FIELDS);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * compare sizes to offset, including total
+ *----------------------------------------------------------------------*/
+int check_total_size( char * mesg, field_s * fields, int nfields, int tot_size )
+{
+ field_s * fp;
+ int c, total;
+ int bad_offs;
+
+ total = 0;
+ bad_offs = 0;
+ for( c = 0, fp = fields; c < nfields; c++, fp++ ){
+ if( fp->offset != total ){
+ if( g_debug > 2 )
+ fprintf(stderr,"** bad offset for field '%s'\n"
+ " offset = %d, total = %d\n",
+ fp->name, fp->offset, total);
+ bad_offs++;
+ }
+
+ total += fp->size * fp->len;
+ }
+
+ if( g_debug > 1 || (g_debug > 0 && bad_offs > 0) ){
+ fputs(mesg, stderr); c = 0;
+ if( bad_offs > 0 ){
+ fprintf(stderr,"** found %d bad offsets\n", bad_offs); c++; }
+ if( total != tot_size ){
+ fprintf(stderr,"** computed total %d not equal to struct size %d\n",
+ total, tot_size); c++; }
+ if( c == 0 ) fputs("... okay\n", stderr);
+ }
+
+ if( bad_offs > 0 ) return 1;
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * fill the field structure with the given data
+ *----------------------------------------------------------------------*/
+int fill_field( field_s * fp, int type, int offset, int num, char * name )
+{
+ fp->type = type;
+ fp->offset = offset;
+ fp->size = 1; /* init before check */
+ fp->len = num;
+
+ strncpy(fp->name, name, NT_FIELD_NAME_LEN-1);
+
+ switch( type ){
+ case DT_UNKNOWN:
+ case DT_INT8:
+ case NT_DT_STRING:
+ fp->size = 1;
+ break;
+
+ case DT_INT16:
+ fp->size = 2;
+ break;
+
+ case DT_INT32:
+ case DT_FLOAT32:
+ fp->size = 4;
+ break;
+
+ case NT_DT_POINTER:
+ case NT_DT_CHAR_PTR:
+ case NT_DT_EXT_PTR:
+ fp->size = (int)sizeof(void *);
+ break;
+
+ default:
+ fprintf(stderr,"** fill_field: invalid type %d\n", type );
+ return 1;
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * display the contents of all of the field structures
+ *----------------------------------------------------------------------*/
+char * field_type_str( int type )
+{
+ if( type == DT_INT8 ) return "DT_INT8";
+ if( type == DT_INT16 ) return "DT_INT16";
+ if( type == DT_INT32 ) return "DT_INT32";
+ if( type == DT_FLOAT32 ) return "DT_FLOAT32";
+ if( type == NT_DT_STRING ) return "NT_DT_STRING";
+ if( type == NT_DT_POINTER ) return "NT_DT_POINTER";
+ if( type == NT_DT_CHAR_PTR ) return "NT_DT_CHAR_PTR"; /* longest: 14 */
+ if( type == NT_DT_EXT_PTR ) return "NT_DT_EXT_PTR";
+
+ return "DT_UNKNOWN"; /* for DT_UNKNOWN, or as an else */
+}
+
+#define NT_MAX_DT_STR_LEN 14
+
+/*----------------------------------------------------------------------
+ * display the contents of all of the field structures
+ *----------------------------------------------------------------------*/
+int disp_field_s_list( char * mesg, field_s * fp, int nfields )
+{
+ int c;
+
+ if( mesg ) fputs(mesg, stdout);
+
+ fprintf(stdout," %d fields:\n"
+ " name size len offset type\n"
+ " ------------------- ---- --- ------ --------------\n",
+ nfields);
+
+ for( c = 0; c < nfields; c++, fp++ )
+ fprintf(stdout," %-*s %4d %3d %4d %-14s\n",
+ NT_FIELD_NAME_LEN-1, fp->name, fp->size, fp->len,
+ fp->offset, field_type_str(fp->type));
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * display the contents of all of the field structures
+ *----------------------------------------------------------------------*/
+int disp_field(char *mesg, field_s *fieldp, void * str, int nfields, int header)
+{
+ field_s * fp;
+ int c;
+
+ if( mesg ) fputs(mesg, stdout);
+
+ if( header && g_debug > 0 ){
+ fprintf(stdout, " name offset nvals values\n");
+ fprintf(stdout, " ------------------- ------ ----- ------\n");
+ }
+
+ fp = fieldp;
+ for( c = 0; c < nfields; c++, fp++ )
+ {
+ /* start by displaying the field information */
+ if( g_debug > 0 )
+ fprintf(stdout, " %-*.*s %4d %3d ",
+ NT_FIELD_NAME_LEN-1, NT_FIELD_NAME_LEN-1, fp->name,
+ fp->offset, fp->len);
+
+ /* now, print the value(s), depending on the type */
+ switch( fp->type ){
+ case DT_UNKNOWN:
+ default:
+ fprintf(stdout,"(unknown data type)\n");
+ break;
+
+ case DT_INT8: case DT_UINT8:
+ case DT_INT16: case DT_UINT16:
+ case DT_INT32: case DT_UINT32:
+ case DT_FLOAT32: case DT_FLOAT64:
+ disp_raw_data((char *)str+fp->offset, fp->type, fp->len, ' ', 1);
+ break;
+
+ case NT_DT_POINTER:
+ fprintf(stdout,"(raw data of unknown type)\n");
+ break;
+
+ case NT_DT_CHAR_PTR: /* look for string of length <= 40 */
+ {
+ char * sp;
+ int len;
+
+ /* start by sucking the pointer stored here */
+ sp = *(char **)((char *)str + fp->offset);
+
+ if( ! sp ){ fprintf(stdout,"(NULL)\n"); break; } /* anything? */
+
+ /* see if we have a printable string here */
+ for(len = 0; len <= 40 && *sp && isprint(*sp); len++, sp++ )
+ ;
+ if( len > 40 )
+ fprintf(stdout,"(apparent long string)\n");
+ else if ( len == 0 )
+ fprintf(stdout,"(empty string)\n");
+ else if( *sp && !isprint(*sp) ) /* if no termination, it's bad */
+ fprintf(stdout,"(non-printable string)\n");
+ else /* woohoo! a good string */
+ fprintf(stdout,"'%.40s'\n",*(char **)((char *)str + fp->offset));
+ break;
+ }
+
+ case NT_DT_EXT_PTR:
+ {
+ nifti1_extension * extp;
+
+ /* yank the address sitting there into extp */
+ extp = *(nifti1_extension **)((char *)str + fp->offset);
+
+ /* the user may use -disp_exts to display all of them */
+ if( extp ) disp_nifti1_extension(NULL, extp, 6);
+ else fprintf(stdout,"(NULL)\n");
+ break;
+ }
+
+ case NT_DT_STRING:
+ {
+ char * charp = (char *)str + fp->offset;
+ fprintf(stdout,"%.*s\n", fp->len, charp);
+ break;
+ }
+ }
+ }
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * no display, just return whether any fields differ
+ *----------------------------------------------------------------------*/
+int diff_field(field_s *fieldp, void * str0, void * str1, int nfields)
+{
+ field_s * fp;
+ char * cp0, * cp1;
+ int fnum, c, size;
+
+ fp = fieldp;
+ for( fnum = 0; fnum < nfields; fnum++, fp++ )
+ {
+ switch( fp->type ){
+ case DT_UNKNOWN: /* all basic types are easy */
+ case DT_INT8:
+ case DT_INT16:
+ case DT_INT32:
+ case DT_FLOAT32:
+ case NT_DT_STRING:
+ size = fp->size * fp->len; /* total field size */
+ cp0 = (char *)str0 + fp->offset;
+ cp1 = (char *)str1 + fp->offset;
+ for( c = 0; c < size; c++, cp0++, cp1++ )
+ if( *cp0 != *cp1 ) break;
+
+ if(c < size) return 1; /* found a diff */
+
+ break;
+
+ case NT_DT_POINTER: /* let's pass on these - no diff */
+ case NT_DT_CHAR_PTR:
+
+ break;
+
+ case NT_DT_EXT_PTR:
+ {
+ nifti1_extension * ext0, * ext1;
+
+ ext0 = *(nifti1_extension **)((char *)str0 + fp->offset);
+ ext1 = *(nifti1_extension **)((char *)str1 + fp->offset);
+
+ if( ! ext0 && ! ext1 ) break; /* continue on */
+
+ if( ext0 && ! ext1 ) return 1; /* pointer diff is diff */
+ if( ! ext0 && ext1 ) return 1;
+
+ /* just check size and type for a single extension */
+ if( ext0->esize != ext1->esize ) return 1;
+ if( ext0->ecode != ext1->ecode ) return 1;
+
+ break;
+ }
+ }
+ }
+
+ return 0; /* no diffs found */
+}
+
+
+/*----------------------------------------------------------------------
+ * display a single extension
+ *----------------------------------------------------------------------*/
+int disp_nifti1_extension(char *mesg, nifti1_extension * ext, int maxlen)
+{
+ int len;
+ if( mesg ) fputs(mesg, stdout);
+
+ if( !ext )
+ {
+ fprintf(stderr,"** no extension to display\n");
+ return 1;
+ }
+
+ fprintf(stdout,"ecode = %d, esize = %d, edata = ",
+ ext->ecode, ext->esize);
+
+ if( !ext->edata )
+ fprintf(stdout,"(NULL)\n");
+ else if ( ext->ecode == NIFTI_ECODE_AFNI ||
+ ext->ecode == NIFTI_ECODE_COMMENT )
+ {
+ len = ext->esize-8;
+ if( maxlen >= 0 && len > maxlen ) len = maxlen;
+ fprintf(stdout,"%.*s\n", len, (char *)ext->edata);
+ }
+ else
+ fprintf(stdout,"(unknown data type)\n");
+
+ fflush(stdout);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * return the appropritate pointer into the g_hdr_fields struct
+ *----------------------------------------------------------------------*/
+field_s * get_hdr_field( char * fname, int show_fail )
+{
+ field_s * fp;
+ int c;
+
+ if( ! fname || *fname == '\0' ) return NULL;
+
+ fp = g_hdr_fields;
+ for( c = 0; c < NT_HDR_NUM_FIELDS; c++, fp++ )
+ if( strcmp(fname, fp->name) == 0 ) break;
+
+ if( c == NT_HDR_NUM_FIELDS )
+ {
+ if( show_fail > 0 )
+ fprintf(stderr,"** get_hdr_field: field not found in hdr: %s\n",fname);
+ return NULL;
+ }
+
+ return fp;
+}
+
+
+/*----------------------------------------------------------------------
+ * return the appropritate pointer into the g_hdr_fields struct
+ *----------------------------------------------------------------------*/
+field_s * get_nim_field( char * fname, int show_fail )
+{
+ field_s * fp;
+ int c;
+
+ if( ! fname || *fname == '\0' ) return NULL;
+
+ fp = g_nim_fields;
+ for( c = 0; c < NT_NIM_NUM_FIELDS; c++, fp++ )
+ if( strcmp(fname, fp->name) == 0 ) break;
+
+ if( c == NT_NIM_NUM_FIELDS )
+ {
+ if( show_fail > 0 )
+ fprintf(stderr,"** get_nim_field: field not found in hdr: %s\n",fname);
+ return NULL;
+ }
+
+ return fp;
+}
+
+
+/*----------------------------------------------------------------------
+ * return the number of fields that differ
+ *----------------------------------------------------------------------*/
+int diff_hdrs( nifti_1_header * s0, nifti_1_header * s1, int display )
+{
+ field_s * fp = g_hdr_fields;
+ int c, ndiff = 0;
+
+ for( c = 0; c < NT_HDR_NUM_FIELDS; c++, fp++ )
+ if( diff_field(fp, s0, s1, 1) )
+ {
+ if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0);
+ if( display ) disp_field(NULL, fp, s1, 1, 0);
+ ndiff++;
+ }
+
+ return ndiff;
+}
+
+
+/*----------------------------------------------------------------------
+ * return the number of fields that differ
+ *----------------------------------------------------------------------*/
+int diff_nims( nifti_image * s0, nifti_image * s1, int display )
+{
+ field_s * fp = g_nim_fields;
+ int c, ndiff = 0;
+
+ for( c = 0; c < NT_NIM_NUM_FIELDS; c++, fp++ )
+ if( diff_field(fp, s0, s1, 1) )
+ {
+ if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0);
+ if( display ) disp_field(NULL, fp, s1, 1, 0);
+ ndiff++;
+ }
+
+ return ndiff;
+}
+
+
+/*----------------------------------------------------------------------
+ * return the number of fields that differ
+ *----------------------------------------------------------------------*/
+int diff_hdrs_list( nifti_1_header * s0, nifti_1_header * s1, str_list * slist,
+ int display )
+{
+ field_s * fp;
+ char ** sptr;
+ int c, ndiff = 0;
+
+ sptr = slist->list;
+ for( c = 0; c < slist->len; c++ )
+ {
+ fp = get_hdr_field(*sptr, 1); /* "not found" displayed in func */
+ if( fp && diff_field(fp, s0, s1, 1) )
+ {
+ if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0);
+ if( display ) disp_field(NULL, fp, s1, 1, 0);
+ ndiff++;
+ }
+ sptr++;
+ }
+
+ return ndiff;
+}
+
+
+/*----------------------------------------------------------------------
+ * return the number of fields that differ
+ *----------------------------------------------------------------------*/
+int diff_nims_list( nifti_image * s0, nifti_image * s1, str_list * slist,
+ int display )
+{
+ field_s * fp;
+ char ** sptr;
+ int c, ndiff = 0;
+
+ sptr = slist->list;
+ for( c = 0; c < slist->len; c++ )
+ {
+ fp = get_nim_field(*sptr, 1); /* "not found" displayed in func */
+ if( fp && diff_field(fp, s0, s1, 1) )
+ {
+ if( display ) disp_field(NULL, fp, s0, 1, ndiff == 0);
+ if( display ) disp_field(NULL, fp, s1, 1, 0);
+ ndiff++;
+ }
+ sptr++;
+ }
+
+ return ndiff;
+}
+
+
+/*----------------------------------------------------------------------
+ * display data from collapsed_image
+ *----------------------------------------------------------------------*/
+int act_disp_ci( nt_opts * opts )
+{
+ nifti_image * nim;
+ void * data = NULL;
+ char space = ' '; /* use space or newline */
+ int filenum, len, err;
+
+ if( opts->dci_lines ) space = '\n'; /* then use newlines as separators */
+
+ if( g_debug > 2 && opts->dts )
+ {
+ fprintf(stderr,"-d displaying time series at (i,j,k) = (%d,%d,%d)\n"
+ " for %d nifti datasets...\n\n", opts->ci_dims[1],
+ opts->ci_dims[2], opts->ci_dims[3], opts->infiles.len);
+ }
+ else if ( g_debug > 2 ) /* the general collapsed image form */
+ {
+ fprintf(stderr,"-d displaying collapsed image for %d datasets...\n\n"
+ " dims = ", opts->infiles.len);
+ disp_raw_data(opts->ci_dims, DT_INT32, 8, ' ', 1);
+ }
+
+ for( filenum = 0; filenum < opts->infiles.len; filenum++ )
+ {
+ err = 0;
+ nim = nifti_image_read(opts->infiles.list[filenum], 0);
+ if( !nim ) continue; /* errors are printed from library */
+ if( opts->dts && nim->ndim != 4 )
+ {
+ fprintf(stderr,"** error: dataset '%s' is not 4-dimensional\n",
+ nim->fname);
+ err++;
+ }
+
+ switch( nim->datatype )
+ {
+ case DT_INT8: case DT_INT16: case DT_INT32:
+ case DT_UINT8: case DT_UINT16: case DT_UINT32:
+ case DT_FLOAT32: case DT_FLOAT64:
+ if( g_debug > 1 )
+ fprintf(stderr,"-d datatype %d of size %d\n",
+ nim->datatype, nim->nbyper);
+ break;
+ default:
+ fprintf(stderr,"** dataset '%s' has unknown type %d\n",
+ nim->fname, nim->datatype);
+ err++;
+ break;
+ }
+
+ if( err ) { nifti_image_free(nim); continue; }
+
+ len = nifti_read_collapsed_image(nim, opts->ci_dims, &data);
+ if( len < 0 || !data )
+ {
+ fprintf(stderr,"** FAILURE for dataset '%s'\n", nim->fname);
+ if( data ) free(data);
+ err++;
+ }
+ else if( len != (nim->nt * nim->nbyper) )
+ {
+ fprintf(stderr,"** dset read '%s', returned length %d instead of %d\n",
+ nim->fname, len, nim->nt * nim->nbyper);
+ free(data); data = NULL;
+ err++;
+ }
+
+ if( err ){ nifti_image_free(nim); continue; }
+
+ /* now just print the results */
+ if( g_debug > 0 )
+ {
+ fprintf(stdout,"\ndataset '%s' @ (", nim->fname);
+ if( opts->dts ) disp_raw_data(opts->ci_dims+1, DT_INT32, 3, ' ', 0);
+ else disp_raw_data(opts->ci_dims+1, DT_INT32, 7, ' ', 0);
+ fprintf(stdout,")\n");
+ }
+
+ disp_raw_data(data, nim->datatype, len / nim->nbyper, space, 1);
+
+ nifti_image_free(nim);
+ }
+
+ if( data ) free(data);
+
+ return 0;
+}
+
+
+int disp_raw_data( void * data, int type, int nvals, char space, int newline )
+{
+ char * dp, fbuf[32];
+ int c, size;
+
+ nifti_datatype_sizes( type, &size, NULL ); /* get nbyper */
+
+ for( c = 0, dp = (char *)data; c < nvals; c++, dp += size )
+ {
+ switch( type )
+ {
+ case DT_INT8:
+ printf("%d", *(char *)dp);
+ break;
+ case DT_INT16:
+ printf("%d", *(short *)dp);
+ break;
+ case DT_INT32:
+ printf("%d", *(int *)dp);
+ break;
+ case DT_UINT8:
+ printf("%u", *(unsigned char *)dp);
+ break;
+ case DT_UINT16:
+ printf("%u", *(unsigned short *)dp);
+ break;
+ case DT_UINT32:
+ printf("%u", *(unsigned int *)dp);
+ break;
+ case DT_FLOAT32:
+ {
+ sprintf(fbuf,"%f", *(float *)dp);
+ clear_float_zeros(fbuf);
+ printf("%s", fbuf);
+ break;
+ }
+ case DT_FLOAT64:
+ {
+ sprintf(fbuf,"%f", *(double *)dp);
+ clear_float_zeros(fbuf);
+ printf("%s", fbuf);
+ break;
+ }
+ default:
+ fprintf(stderr,"** disp_raw_data: unknown type %d\n", type);
+ return 1;
+ }
+ if( c < nvals - 1 ) fputc(space,stdout);
+ }
+
+ if ( newline ) fputc('\n',stdout);
+
+ return 0;
+}
+
+/*----------------------------------------------------------------------
+ * remove trailing zeros from string of printed float
+ * return 1 if something was cleared
+ * 0 if not
+ *----------------------------------------------------------------------*/
+int clear_float_zeros( char * str )
+{
+ char * dp = strchr(str, '.'), * valp;
+ int len;
+
+ if( !dp ) return 0; /* nothing to clear */
+
+ len = strlen(dp);
+
+ /* never clear what is just to the right of '.' */
+ for( valp = dp+len-1; (valp > dp+1) && (*valp==' ' || *valp=='0'); valp-- )
+ *valp = '\0'; /* clear, so we don't worry about break conditions */
+
+ if( valp < dp + len - 1 ) return 1;
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * create a new dataset using sub-brick selection
+ *----------------------------------------------------------------------*/
+int act_cbl( nt_opts * opts )
+{
+ nifti_brick_list NBL;
+ nifti_image * nim;
+ char * fname, * selstr, * cp;
+ int * blist;
+ int err = 0;
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d copying file info from '%s' to '%s'\n",
+ opts->infiles.list[0], opts->prefix);
+
+ /* sanity checks */
+ if( ! opts->prefix ) {
+ fprintf(stderr,"** error: -prefix is required with -cbl function\n");
+ return 1;
+ } else if( opts->infiles.len > 1 ) {
+ fprintf(stderr,"** sorry, at the moment -cbl allows only 1 input\n");
+ return 1;
+ }
+
+ /* remove selector from fname, and copy selector string */
+ fname = nifti_strdup(opts->infiles.list[0]);
+ cp = strchr(fname,'['); if( !cp ) cp = strchr(fname,'{');
+
+ if( !cp ) {
+ if( g_debug > 1 )
+ fprintf(stderr,"-d using -cbl without brick list in '%s'\n",fname);
+ selstr = nifti_strdup("[0..$]");
+ } else {
+ selstr = nifti_strdup(cp);
+ *cp = '\0'; /* remove selection string from fname */
+ }
+
+ if( g_debug > 1 )
+ fprintf(stderr,"+d -cbl: using '%s' for selection string\n", selstr);
+
+ nim = nifti_image_read(fname, 0); /* get image */
+ if( !nim ) return 1;
+
+ blist = nifti_get_intlist(nim->nt, selstr);
+ nifti_image_free(nim); /* throw away, will re-load */
+ if( !blist ){
+ fprintf(stderr,"** failed sub-brick selection using '%s'\n",selstr);
+ free(fname); free(selstr); return 1;
+ }
+
+ nim = nifti_image_read_bricks(fname, blist[0], blist+1, &NBL);
+ free(blist); /* with this */
+ if( !nim ){ free(fname); free(selstr); return 1; }
+
+ if( g_debug > 1 ) fprintf(stderr,"+d sub-bricks loaded\n");
+
+ /* add command as COMMENT extension */
+ if( opts->keep_hist && nifti_add_extension(nim, opts->command,
+ strlen(opts->command), NIFTI_ECODE_COMMENT) )
+ fprintf(stderr,"** failed to add command to image as extension\n");
+
+ /* replace filenames using prefix */
+ if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
+ {
+ fprintf(stderr,"** failed to set names, prefix = '%s'\n",opts->prefix);
+ err++;
+ }
+
+ if(g_debug>2) disp_field("new nim:\n",g_nim_fields,nim,NT_NIM_NUM_FIELDS,1);
+
+ /* and finally, write out results */
+ if( err == 0 && nifti_nim_is_valid(nim, g_debug) )
+ nifti_image_write_bricks(nim, &NBL);
+
+ nifti_image_free(nim);
+ nifti_free_NBL(&NBL);
+ free(fname);
+ free(selstr);
+
+ return 0;
+}
+
+
+/*----------------------------------------------------------------------
+ * create a new dataset using read_collapsed_image
+ *----------------------------------------------------------------------*/
+int act_cci( nt_opts * opts )
+{
+ nifti_image * nim;
+ int c;
+
+ if( g_debug > 2 )
+ fprintf(stderr,"-d collapsing file info from '%s' to '%s'\n",
+ opts->infiles.list[0], opts->prefix);
+
+ /* sanity checks */
+ if( ! opts->prefix ) {
+ fprintf(stderr,"** error: -prefix is required with -cci function\n");
+ return 1;
+ } else if( opts->infiles.len > 1 ) {
+ fprintf(stderr,"** sorry, at the moment -cci allows only 1 input\n");
+ return 1;
+ }
+
+ nim = nifti_image_read(opts->infiles.list[0], 0);
+ if( !nim ) return 1;
+ nim->data = NULL; /* just to be sure */
+
+ if( nifti_read_collapsed_image(nim, opts->ci_dims, &nim->data) < 0 )
+ {
+ nifti_image_free(nim);
+ return 1;
+ }
+
+ /* add command as COMMENT extension */
+ if( opts->keep_hist && nifti_add_extension(nim, opts->command,
+ strlen(opts->command), NIFTI_ECODE_COMMENT) )
+ fprintf(stderr,"** failed to add command to image as extension\n");
+
+ /* replace filenames using prefix */
+ if( nifti_set_filenames(nim, opts->prefix, 1, 1) )
+ {
+ fprintf(stderr,"** failed to set names, prefix = '%s'\n",opts->prefix);
+ nifti_image_free(nim);
+ return 1;
+ }
+
+ for( c = 1; c < 8; c++ ) /* nuke any collapsed dimension */
+ if( opts->ci_dims[c] >= 0 ) nim->dim[c] = 1;
+
+ nifti_update_dims_from_array(nim);
+
+ if(g_debug>2) disp_field("new nim:\n",g_nim_fields,nim,NT_NIM_NUM_FIELDS,1);
+
+ /* and finally, write out results */
+ if( nifti_nim_is_valid(nim, g_debug) ) nifti_image_write(nim);
+
+ nifti_image_free(nim);
+
+ return 0;
+}
+
diff --git a/Utilities/ITK/Utilities/nifti/utils/nifti_tool.h b/Utilities/ITK/Utilities/nifti/utils/nifti_tool.h
new file mode 100644
index 0000000000000000000000000000000000000000..d6d3bdcce9995acd9f30b7f6b4c84faa5a84b8f9
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/utils/nifti_tool.h
@@ -0,0 +1,144 @@
+#ifndef _NIFTI_TOOL_H_
+#define _NIFTI_TOOL_H_
+
+#define NT_CMD_LEN 2048
+
+typedef struct{
+ int len;
+ char ** list;
+} str_list;
+
+typedef struct{
+ int len;
+ int * list;
+} int_list;
+
+typedef struct{
+ /* action options (flags) */
+ int check_hdr, check_nim;
+ int diff_hdr, diff_nim;
+ int disp_hdr, disp_nim;
+ int disp_exts, add_exts, rm_exts;
+ int mod_hdr, mod_nim;
+
+ int strip; /* strip extras from dataset(s) */
+ int cbl, cci; /* -copy_XXX option flags */
+ int dts, dci, dci_lines; /* display collapsed img flags */
+ int ci_dims[8]; /* user dims list (last 7 valid) */
+ int debug, keep_hist; /* debug level and history flag */
+ int overwrite; /* overwrite flag */
+ char * prefix; /* for output file */
+ str_list elist; /* extension strings */
+ int_list etypes; /* extension type list */
+ str_list flist; /* fields (to display or modify) */
+ str_list vlist; /* values (to set fields to) */
+ str_list infiles; /* input files */
+ char command[NT_CMD_LEN]; /* for inserting the command */
+} nt_opts;
+
+#define USE_SHORT 1
+#define USE_FULL 2
+#define USE_HIST 3
+#define USE_FIELD_HDR 4
+#define USE_FIELD_NIM 5
+#define USE_VERSION 6
+
+#define CHECK_NEXT_OPT(n,m,str) \
+ do { if ( (n) >= (m) ) { \
+ fprintf(stderr,"** option '%s': missing parameter\n",str); \
+ fprintf(stderr," consider: 'nifti_tool -help'\n"); \
+ return 1; } \
+ } while(0)
+
+#define CHECK_NEXT_OPT_MSG(n,m,str,msg) \
+ do { if ( (n) >= (m) ) { \
+ fprintf(stderr,"** option '%s': %s\n",str,msg); \
+ fprintf(stderr," consider: 'nifti_tool -help'\n"); \
+ return 1; } \
+ } while(0)
+
+/*----------------------------------------------------------------------
+ * this structure and definitions will be used to process the nifti_1_header
+ * and nifti_image structure fields (actions disp, diff, mod)
+ *----------------------------------------------------------------------*/
+
+#define NT_FIELD_NAME_LEN 20 /* more than length of longest name */
+#define NT_HDR_NUM_FIELDS 43 /* in the nifti_1_header struct */
+#define NT_NIM_NUM_FIELDS 63 /* in the nifti_image struct */
+#define NT_DT_STRING -0xfff /* some strange number to abuse... */
+#define NT_DT_POINTER -0xfef /* some strange number to abuse... */
+#define NT_DT_CHAR_PTR -0xfee /* another... */
+#define NT_DT_EXT_PTR -0xfed /* and another... */
+
+typedef struct {
+ int type; /* one of the DT_* types from nifti1.h */
+ int offset; /* bytes from the start of the struct */
+ int size; /* size of one element type */
+ int len; /* number of elements */
+ char name[NT_FIELD_NAME_LEN]; /* actual structure name used */
+} field_s;
+
+/* for computing the offset from the start of the struct */
+#define NT_OFF(str,field) ((int)( ((char *)&str.field) - ((char *)&str) ))
+
+/* call fill_field() for a single type, name and number of elements */
+/* nstr is the base struct, and fldp is a field pointer */
+#define NT_SFILL(nstr,fldp,type,name,num,rv) do{ \
+ rv=fill_field(fldp,type,NT_OFF(nstr,name),num,#name); \
+ fldp++; } while (0)
+
+/*----------------------------------------------------------------------*/
+/*----- prototypes ---------------------------------------------------*/
+/*----------------------------------------------------------------------*/
+int act_add_exts ( nt_opts * opts );
+int act_cbl ( nt_opts * opts ); /* copy brick list */
+int act_cci ( nt_opts * opts ); /* copy collapsed dimensions */
+int act_check_hdrs ( nt_opts * opts ); /* check for valid hdr or nim */
+int act_diff_hdrs ( nt_opts * opts );
+int act_diff_nims ( nt_opts * opts );
+int act_disp_ci ( nt_opts * opts ); /* display general collapsed data */
+int act_disp_exts ( nt_opts * opts );
+int act_disp_hdrs ( nt_opts * opts );
+int act_disp_nims ( nt_opts * opts );
+int act_disp_ts ( nt_opts * opts ); /* display time series */
+int act_mod_hdrs ( nt_opts * opts );
+int act_mod_nims ( nt_opts * opts );
+int act_rm_ext ( nt_opts * opts );
+int act_strip ( nt_opts * opts ); /* strip extras from datasets */
+
+field_s * get_hdr_field( char * fname, int show_fail );
+field_s * get_nim_field( char * fname, int show_fail );
+char * field_type_str (int type);
+
+int diff_hdrs (nifti_1_header *s0, nifti_1_header *s1, int display);
+int diff_hdrs_list(nifti_1_header *s0, nifti_1_header *s1, str_list *slist,
+ int display);
+int diff_nims (nifti_image *s0,nifti_image *s1, int display);
+int diff_nims_list(nifti_image *s0,nifti_image *s1,str_list *slist,int display);
+
+int add_int (int_list * ilist, int val);
+int add_string (str_list * slist, char * str);
+int check_total_size (char *mesg, field_s *fields, int nfields, int tot_size);
+int clear_float_zeros( char * str );
+int diff_field (field_s *fieldp, void * str0, void * str1, int nfields);
+int disp_nifti1_extension(char *mesg, nifti1_extension * ext, int maxlen);
+int disp_field (char *mesg,field_s *fp,void *str,int nfields,int header);
+int disp_field_s_list(char * mesg, field_s *, int nfields);
+int disp_nt_opts (char * mesg, nt_opts * opts);
+int disp_raw_data (void * data, int type, int nvals, char space,int newline);
+int fill_cmd_string (nt_opts * opts, int argc, char * argv[]);
+int fill_field (field_s *fp, int type, int offset, int num, char *name);
+int fill_hdr_field_array(field_s * nh_fields);
+int fill_nim_field_array(field_s * nim_fields);
+int modify_all_fields(void *basep, nt_opts *opts, field_s *fields, int flen);
+int modify_field (void * basep, field_s * field, char * data);
+int process_opts (int argc, char * argv[], nt_opts * opts);
+int remove_ext_list (nifti_image * nim, char ** elist, int len);
+int usage (char * prog, int level);
+int use_full (char * prog);
+int verify_opts (nt_opts * opts, char * prog);
+int write_hdr_to_file(nifti_1_header * nhdr, char * fname);
+
+
+
+#endif /* _NIFTI_TOOL_H_ */
diff --git a/Utilities/ITK/Utilities/nifti/znzlib/CMakeLists.txt b/Utilities/ITK/Utilities/nifti/znzlib/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..687fbc973f4b2ab381035058306a88ff3b691c1a
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/znzlib/CMakeLists.txt
@@ -0,0 +1,10 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(ZNZLIB)
+SET(ZNZLIB_SRC znzlib.c)
+
+ADD_LIBRARY(${PACKAGE_PREFIX}znz ${ZNZLIB_SRC} )
+TARGET_LINK_LIBRARIES( ${PACKAGE_PREFIX}znz ${NIFTI_ZLIB_LIBRARIES} )
+INSTALL_TARGETS(${LIB_INSTALL_DIR} ${PACKAGE_PREFIX}znz)
+INSTALL_FILES(${INCLUDE_INSTALL_DIR} "(\\.h)$")
+
diff --git a/Utilities/ITK/Utilities/nifti/znzlib/Makefile b/Utilities/ITK/Utilities/nifti/znzlib/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..0952a39f05536b09e43326ef7fd8baba6b3e68b4
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/znzlib/Makefile
@@ -0,0 +1,33 @@
+include ../Makefile
+
+PROJNAME = znzlib
+
+INCFLAGS = $(ZLIB_INC)
+
+SRCS=znzlib.c
+OBJS=znzlib.o
+
+TESTXFILES = testprog
+
+depend:
+ $(RM) -f depend.mk
+ $(MAKE) depend.mk
+
+depend.mk:
+ $(CC) $(DEPENDFLAGS) $(INCFLAGS) $(SRCS) >> depend.mk
+
+lib: libznz.a
+
+test: $(TESTXFILES)
+
+znzlib.o: znzlib.c znzlib.h
+ $(CC) -c $(CFLAGS) $(USEZLIB) $(INCFLAGS) $<
+
+libznz.a: $(OBJS)
+ $(AR) -r libznz.a $(OBJS)
+ $(RANLIB) $@
+
+testprog: libznz.a testprog.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o testprog testprog.c $(ZLIB_LIBS)
+
+include depend.mk
diff --git a/Utilities/ITK/Utilities/nifti/znzlib/config.h b/Utilities/ITK/Utilities/nifti/znzlib/config.h
new file mode 100644
index 0000000000000000000000000000000000000000..bd67b7e3d41e5118b301f4d1813a8f815b26e2fe
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/znzlib/config.h
@@ -0,0 +1,34 @@
+#ifndef _ZNZCONFIG_H_
+#define _ZNZCONFIG_H_
+
+/*
+config.h - for znzlib
+
+
+***** This code is released to the public domain. *****
+
+***** Author: Mark Jenkinson, FMRIB Centre, University of Oxford *****
+***** Date: September 2004 *****
+
+***** Neither the FMRIB Centre, the University of Oxford, nor any of *****
+***** its employees imply any warranty of usefulness of this software *****
+***** for any purpose, and do not assume any liability for damages, *****
+***** incidental or otherwise, caused by any use of this document. *****
+
+*/
+
+/*
+
+This file contains all the configuration variables for znzlib
+
+*/
+
+
+/* comment out the following line if compression support is not wanted */
+/* #define HAVE_ZLIB -- this is now defined via -DHAVE_ZLIB in Makefile */
+
+/* uncomment the following line is fdopen() exists for your compiler and compiler options */
+/* #define HAVE_FDOPEN */
+
+/* for _ZNZCONFIG_H */
+#endif
diff --git a/Utilities/ITK/Utilities/nifti/znzlib/znzlib.c b/Utilities/ITK/Utilities/nifti/znzlib/znzlib.c
new file mode 100644
index 0000000000000000000000000000000000000000..da8644de4527b94610071ce8c68cbb0b8cfb2d8a
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/znzlib/znzlib.c
@@ -0,0 +1,274 @@
+/** \file znzlib.c
+ \brief Low level i/o interface to compressed and noncompressed files.
+ Written by Mark Jenkinson, FMRIB
+
+This library provides an interface to both compressed (gzip/zlib) and
+uncompressed (normal) file IO. The functions are written to have the
+same interface as the standard file IO functions.
+
+To use this library instead of normal file IO, the following changes
+are required:
+ - replace all instances of FILE* with znzFile
+ - change the name of all function calls, replacing the initial character
+ f with the znz (e.g. fseek becomes znzseek)
+ one exception is rewind() -> znzrewind()
+ - add a third parameter to all calls to znzopen (previously fopen)
+ that specifies whether to use compression (1) or not (0)
+ - use znz_isnull rather than any (pointer == NULL) comparisons in the code
+ for znzfile types (normally done after a return from znzopen)
+
+NB: seeks for writable files with compression are quite restricted
+
+ */
+
+#include "znzlib.h"
+
+/*
+znzlib.c (zipped or non-zipped library)
+
+***** This code is released to the public domain. *****
+
+***** Author: Mark Jenkinson, FMRIB Centre, University of Oxford *****
+***** Date: September 2004 *****
+
+***** Neither the FMRIB Centre, the University of Oxford, nor any of *****
+***** its employees imply any warranty of usefulness of this software *****
+***** for any purpose, and do not assume any liability for damages, *****
+***** incidental or otherwise, caused by any use of this document. *****
+
+*/
+
+
+/* Note extra argument (use_compression) where
+ use_compression==0 is no compression
+ use_compression!=0 uses zlib (gzip) compression
+*/
+
+znzFile znzopen(const char *path, const char *mode, int use_compression)
+{
+ znzFile file;
+ file = (znzFile) calloc(1,sizeof(struct znzptr));
+ if( file == NULL ){
+ fprintf(stderr,"** ERROR: znzopen failed to alloc znzptr\n");
+ return NULL;
+ }
+
+ file->nzfptr = NULL;
+
+#ifdef HAVE_ZLIB
+ file->zfptr = NULL;
+
+ if (use_compression) {
+ file->withz = 1;
+ if((file->zfptr = gzopen(path,mode)) == NULL) {
+ free(file);
+ file = NULL;
+ }
+ } else {
+#endif
+
+ file->withz = 0;
+ if((file->nzfptr = fopen(path,mode)) == NULL) {
+ free(file);
+ file = NULL;
+ }
+
+#ifdef HAVE_ZLIB
+ }
+#endif
+
+ return file;
+}
+
+
+znzFile znzdopen(int fd, const char *mode, int use_compression)
+{
+ znzFile file;
+ file = (znzFile) calloc(1,sizeof(struct znzptr));
+ if( file == NULL ){
+ fprintf(stderr,"** ERROR: znzdopen failed to alloc znzptr\n");
+ return NULL;
+ }
+#ifdef HAVE_ZLIB
+ if (use_compression) {
+ file->withz = 1;
+ file->zfptr = gzdopen(fd,mode);
+ file->nzfptr = NULL;
+ } else {
+#endif
+ file->withz = 0;
+#ifdef HAVE_FDOPEN
+ file->nzfptr = fdopen(fd,mode);
+#endif
+#ifdef HAVE_ZLIB
+ file->zfptr = NULL;
+ };
+#endif
+ return file;
+}
+
+
+int Xznzclose(znzFile * file)
+{
+ int retval = 0;
+ if (*file!=NULL) {
+#ifdef HAVE_ZLIB
+ if ((*file)->zfptr!=NULL) { retval = gzclose((*file)->zfptr); }
+#endif
+ if ((*file)->nzfptr!=NULL) { retval = fclose((*file)->nzfptr); }
+
+ free(*file);
+ *file = NULL;
+ }
+ return retval;
+}
+
+
+size_t znzread(void* buf, size_t size, size_t nmemb, znzFile file)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL)
+ return (size_t) (gzread(file->zfptr,buf,((int) size)*((int) nmemb)) / size);
+#endif
+ return fread(buf,size,nmemb,file->nzfptr);
+}
+
+size_t znzwrite(const void* buf, size_t size, size_t nmemb, znzFile file)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL)
+ {
+ /* NOTE: We must typecast const away from the buffer because
+ gzwrite does not have complete const specification */
+ return (size_t) ( gzwrite(file->zfptr,(void *)buf,size*nmemb) / size );
+ }
+#endif
+ return fwrite(buf,size,nmemb,file->nzfptr);
+}
+
+long znzseek(znzFile file, long offset, int whence)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL) return (long) gzseek(file->zfptr,offset,whence);
+#endif
+ return fseek(file->nzfptr,offset,whence);
+}
+
+int znzrewind(znzFile stream)
+{
+ if (stream==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ /* On some systems, gzrewind() fails for uncompressed files.
+ Use gzseek(), instead. 10, May 2005 [rickr]
+
+ if (stream->zfptr!=NULL) return gzrewind(stream->zfptr);
+ */
+
+ if (stream->zfptr!=NULL) return (int)gzseek(stream->zfptr, 0L, SEEK_SET);
+#endif
+ rewind(stream->nzfptr);
+ return 0;
+}
+
+long znztell(znzFile file)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL) return (long) gztell(file->zfptr);
+#endif
+ return ftell(file->nzfptr);
+}
+
+int znzputs(const char * str, znzFile file)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL) return gzputs(file->zfptr,str);
+#endif
+ return fputs(str,file->nzfptr);
+}
+
+
+char * znzgets(char* str, int size, znzFile file)
+{
+ if (file==NULL) { return NULL; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL) return gzgets(file->zfptr,str,size);
+#endif
+ return fgets(str,size,file->nzfptr);
+}
+
+
+int znzflush(znzFile file)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL) return gzflush(file->zfptr,Z_SYNC_FLUSH);
+#endif
+ return fflush(file->nzfptr);
+}
+
+
+int znzeof(znzFile file)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL) return gzeof(file->zfptr);
+#endif
+ return feof(file->nzfptr);
+}
+
+
+int znzputc(int c, znzFile file)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL) return gzputc(file->zfptr,c);
+#endif
+ return fputc(c,file->nzfptr);
+}
+
+
+int znzgetc(znzFile file)
+{
+ if (file==NULL) { return 0; }
+#ifdef HAVE_ZLIB
+ if (file->zfptr!=NULL) return gzgetc(file->zfptr);
+#endif
+ return fgetc(file->nzfptr);
+}
+
+#if !defined (WIN32)
+int znzprintf(znzFile stream, const char *format, ...)
+{
+ int retval=0;
+ char *tmpstr;
+ va_list va;
+ if (stream==NULL) { return 0; }
+ va_start(va, format);
+#ifdef HAVE_ZLIB
+ if (stream->zfptr!=NULL) {
+ int size; /* local to HAVE_ZLIB block */
+ size = strlen(format) + 1000000; /* overkill I hope */
+ tmpstr = (char *)calloc(1, size);
+ if( tmpstr == NULL ){
+ fprintf(stderr,"** ERROR: znzprintf failed to alloc %d bytes\n", size);
+ return retval;
+ }
+ vsprintf(tmpstr,format,va);
+ retval=gzprintf(stream->zfptr,"%s",tmpstr);
+ free(tmpstr);
+ } else
+#endif
+ {
+ retval=vfprintf(stream->nzfptr,format,va);
+ }
+ va_end(va);
+ return retval;
+}
+
+#endif
+
diff --git a/Utilities/ITK/Utilities/nifti/znzlib/znzlib.h b/Utilities/ITK/Utilities/nifti/znzlib/znzlib.h
new file mode 100644
index 0000000000000000000000000000000000000000..14f92bf3e695a87875f7501f4a50c690f9840f19
--- /dev/null
+++ b/Utilities/ITK/Utilities/nifti/znzlib/znzlib.h
@@ -0,0 +1,113 @@
+#ifndef _ZNZLIB_H_
+#define _ZNZLIB_H_
+
+/*
+znzlib.h (zipped or non-zipped library)
+
+***** This code is released to the public domain. *****
+
+***** Author: Mark Jenkinson, FMRIB Centre, University of Oxford *****
+***** Date: September 2004 *****
+
+***** Neither the FMRIB Centre, the University of Oxford, nor any of *****
+***** its employees imply any warranty of usefulness of this software *****
+***** for any purpose, and do not assume any liability for damages, *****
+***** incidental or otherwise, caused by any use of this document. *****
+
+*/
+
+/*
+
+This library provides an interface to both compressed (gzip/zlib) and
+uncompressed (normal) file IO. The functions are written to have the
+same interface as the standard file IO functions.
+
+To use this library instead of normal file IO, the following changes
+are required:
+ - replace all instances of FILE* with znzFile
+ - change the name of all function calls, replacing the initial character
+ f with the znz (e.g. fseek becomes znzseek)
+ - add a third parameter to all calls to znzopen (previously fopen)
+ that specifies whether to use compression (1) or not (0)
+ - use znz_isnull rather than any (pointer == NULL) comparisons in the code
+
+NB: seeks for writable files with compression are quite restricted
+
+*/
+
+
+/*=================*/
+#ifdef __cplusplus
+extern "C" {
+#endif
+/*=================*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdarg.h>
+
+#include "config.h"
+
+#ifdef HAVE_ZLIB
+#include "zlib.h"
+#endif
+
+
+struct znzptr {
+ int withz;
+ FILE* nzfptr;
+#ifdef HAVE_ZLIB
+ gzFile zfptr;
+#endif
+} ;
+
+/* the type for all file pointers */
+typedef struct znzptr * znzFile;
+
+
+/* int znz_isnull(znzFile f); */
+/* int znzclose(znzFile f); */
+#define znz_isnull(f) ((f) == NULL)
+#define znzclose(f) Xznzclose(&(f))
+
+/* Note extra argument (use_compression) where
+ use_compression==0 is no compression
+ use_compression!=0 uses zlib (gzip) compression
+*/
+
+znzFile znzopen(const char *path, const char *mode, int use_compression);
+
+znzFile znzdopen(int fd, const char *mode, int use_compression);
+
+int Xznzclose(znzFile * file);
+
+size_t znzread(void* buf, size_t size, size_t nmemb, znzFile file);
+
+size_t znzwrite(const void* buf, size_t size, size_t nmemb, znzFile file);
+
+long znzseek(znzFile file, long offset, int whence);
+
+int znzrewind(znzFile stream);
+
+long znztell(znzFile file);
+
+int znzputs(const char *str, znzFile file);
+
+char * znzgets(char* str, int size, znzFile file);
+
+int znzputc(int c, znzFile file);
+
+int znzgetc(znzFile file);
+
+#if !defined(WIN32)
+int znzprintf(znzFile stream, const char *format, ...);
+#endif
+
+/*=================*/
+#ifdef __cplusplus
+}
+#endif
+/*=================*/
+
+#endif