ENH: update modularization scripts

.hgignore

 syntax: glob
-*~
\ No newline at end of file
+*~
+*pyc
+Scripts/modularization/logs/missingFiles.log
+Scripts/modularization/logs/newFiles.log

Scripts/modularization/manifestParser.py

@@ -362,17 +362,18 @@ def main(argv):
   printDepList(depList,cyclicDependentModules)
   #printGroupTree(groups)
   
-  """
+  
   if csvEdges:
     outputCSVEdgeList(depList,csvEdges)
   return 0
-  """
+
+  """ 
   if csvEdges and not module:
     outputDotCompleteGraph(depList,csvEdges)
   elif csvEdges and module:
     outputDotPartialGraph(depList,csvEdges,module)
   return 0
-
+  """
 
 if __name__ == "__main__":
   if len(sys.argv) < 3 :

Scripts/modularization/module-depends.csv

+Conversion,VectorDataBase
+Conversion,LabelMap
+Conversion,GdalAdapters
+Conversion,VectorDataManipulation
+Conversion,IOGDAL
+Conversion,Streaming
+Conversion,Common
+Conversion,VectorDataIO
+Conversion,ImageBase
+Conversion,Boost
+Conversion,GDAL
+ColorMap,Common
+Density,PointSet
+Density,Common
+CCOBIA,Conversion
+CCOBIA,Statistics
+CCOBIA,Projection
+CCOBIA,Moments
+CCOBIA,LabelMap
+CCOBIA,Streaming
+CCOBIA,Common
+CCOBIA,MathParser
+PointSet,Common
+PointSet,Interpolation
+Labelling,PointSet
+Labelling,ImageManipulation
+Metadata,Boost
+Metadata,Common
+Metadata,OSSIMAdapters
+Metadata,ObjectList
+DisplacementField,ImageBase
+DisplacementField,Transform
+DisplacementField,Common
+DisplacementField,OSSIMAdapters
+DisplacementField,ObjectList
+IOKML,VectorDataBase
+IOKML,Projection
+IOKML,libkml
+IOKML,OSSIMAdapters
+IOKML,Common
+IOKML,GDAL
+Path,VectorDataBase
+Path,ImageBase
+Path,Common
+Path,ObjectList
+Stereo,Statistics
+Stereo,ITKPendingPatches
+Stereo,ImageBase
+Stereo,Transform
+Stereo,Common
+Stereo,Interpolation
+Stereo,OSSIMAdapters
+Stereo,ObjectList
+UrbanArea,Indices
+UrbanArea,ImageBase
+UrbanArea,Edge
+UrbanArea,Statistics
+UrbanArea,ImageManipulation
+CommandLine,ApplicationEngine
+CommandLine,TinyXMLAdapters
+CommandLine,Common
+Simulation,Statistics
+Simulation,Metadata
+Simulation,ImageBase
+Simulation,LabelMap
+Simulation,ImageManipulation
+Simulation,Common
+Simulation,Indices
+Simulation,OpticalCalibration
+Simulation,ObjectList
+Simulation,Boost
+Simulation,Interpolation
+LearningBase,OpenCVAdapters
+LearningBase,Common
+LearningBase,SVMLearning
+ApplicationEngine,VectorDataBase
+ApplicationEngine,ImageManipulation
+ApplicationEngine,ImageIO
+ApplicationEngine,Projection
+ApplicationEngine,TinyXMLAdapters
+ApplicationEngine,VectorDataIO
+ApplicationEngine,Transform
+ApplicationEngine,Common
+ApplicationEngine,ImageBase
+ApplicationEngine,Boost
+ApplicationEngine,OSSIMAdapters
+ApplicationEngine,ObjectList
+Indices,VectorDataBase
+Indices,ImageManipulation
+Indices,ITKPendingPatches
+Indices,Common
+Indices,Fuzzy
+Indices,Path
+Indices,Metadata
+ExtendedFilename,IOGDAL
+ExtendedFilename,Boost
+GdalAdapters,BoostAdapters
+GdalAdapters,Boost
+GdalAdapters,Common
+GdalAdapters,GDAL
+EdisonMeanShift,VectorDataBase
+EdisonMeanShift,ImageBase
+EdisonMeanShift,Edison
+EdisonMeanShift,Common
+EdisonMeanShift,ObjectList
+QtWidget,ApplicationEngine
+VectorDataManipulation,VectorDataBase
+VectorDataManipulation,ImageManipulation
+VectorDataManipulation,Transform
+VectorDataManipulation,OSSIMAdapters
+VectorDataManipulation,Common
+VectorDataManipulation,GDAL
+VectorDataManipulation,Path
+VectorDataManipulation,Mapnik
+VectorDataManipulation,ObjectList
+Streaming,ImageBase
+Streaming,OSSIMAdapters
+Streaming,Common
+Streaming,ITKPendingPatches
+Streaming,ObjectList
+Corner,VectorDataBase
+Corner,Descriptors
+Corner,SpatialObjects
+Corner,VectorDataManipulation
+Corner,PointSet
+Corner,ImageManipulation
+Corner,Common
+VectorDataBase,Mapnik
+VectorDataBase,Common
+VectorDataBase,OSSIMAdapters
+VectorDataBase,GDAL
+VectorDataBase,ObjectList
+Statistics,VectorDataBase
+Statistics,ImageManipulation
+Statistics,Projection
+Statistics,ITKPendingPatches
+Statistics,ImageBase
+Statistics,LabelMap
+Statistics,Streaming
+Statistics,Common
+Statistics,ObjectList
+MorphologicalPyramid,ImageBase
+MorphologicalPyramid,PointSet
+MorphologicalPyramid,ObjectList
+MorphologicalPyramid,ImageManipulation
+MorphologicalPyramid,Common
+ImageNoise,ImageManipulation
+Wavelet,ObjectList
+Wavelet,Common
+Wavelet,ImageManipulation
+SeamCarving,Path
+SeamCarving,Common
+VectorDataIO,VectorDataBase
+VectorDataIO,VectorDataManipulation
+VectorDataIO,Common
+VectorDataIO,IOGDAL
+VectorDataIO,IOKML
+SVMLearning,VectorDataBase
+SVMLearning,ImageBase
+SVMLearning,LibSVM
+SVMLearning,LabelMap
+SVMLearning,Streaming
+SVMLearning,Common
+TinyXMLAdapters,Common
+TinyXMLAdapters,TinyXML
+EndmembersExtraction,Statistics
+EndmembersExtraction,Projection
+EndmembersExtraction,ImageBase
+EndmembersExtraction,DimensionalityReduction
+EndmembersExtraction,ImageManipulation
+EndmembersExtraction,Boost
+EndmembersExtraction,Common
+Moments,VectorDataBase
+Moments,VectorDataManipulation
+Moments,Statistics
+Moments,ImageBase
+Moments,LabelMap
+Moments,Common
+Moments,Path
+ImageBase,Common
+ImageBase,OSSIMAdapters
+ImageBase,ITKPendingPatches
+ImageBase,Metadata
+DimensionalityReduction,ImageBase
+DimensionalityReduction,Statistics
+DimensionalityReduction,ObjectList
+DimensionalityReduction,ImageManipulation
+DimensionalityReduction,Common
+ImageManipulation,ITKPendingPatches
+ImageManipulation,ImageBase
+ImageManipulation,Transform
+ImageManipulation,Streaming
+ImageManipulation,Common
+ImageManipulation,Interpolation
+ImageManipulation,OSSIMAdapters
+ImageManipulation,ObjectList
+CloudDetection,ImageManipulation
+CloudDetection,ITKPendingPatches
+IOMW,ImageBase
+IOMW,Common
+ImageIO,IORAD
+ImageIO,IOONERA
+ImageIO,IOJPEG2000
+ImageIO,ITKPendingPatches
+ImageIO,IOLUM
+ImageIO,ImageBase
+ImageIO,IOMW
+ImageIO,IOMSTAR
+ImageIO,IOBSQ
+ImageIO,IOGDAL
+ImageIO,Streaming
+ImageIO,Boost
+ImageIO,IOTileMap
+ImageIO,Common
+ImageIO,ExtendedFilename
+ImageIO,OSSIMAdapters
+ImageIO,ObjectList
+SWIG,ApplicationEngine
+Transform,ITKPendingPatches
+Transform,Common
+Transform,GDAL
+Transform,Boost
+Transform,OSSIMAdapters
+Transform,Interpolation
+Smoothing,ImageBase
+Smoothing,Common
+IOGDAL,VectorDataBase
+IOGDAL,GdalAdapters
+IOGDAL,TinyXMLAdapters
+IOGDAL,ImageBase
+IOGDAL,Common
+IOGDAL,GDAL
+IOGDAL,Boost
+IOGDAL,OSSIMAdapters
+OpenCVAdapters,OpenCV
+OpenCVAdapters,Boost
+OpenCVAdapters,Common
+ObjectDetection,VectorDataBase
+ObjectDetection,Textures
+ObjectDetection,Statistics
+ObjectDetection,Moments
+ObjectDetection,Descriptors
+ObjectDetection,Streaming
+ObjectDetection,Common
+ObjectDetection,ImageBase
+ObjectDetection,ObjectList
+ObjectDetection,ImageManipulation
+Textures,Common
+Descriptors,SiftFast
+Descriptors,ITKPendingPatches
+Descriptors,ImageBase
+Descriptors,Transform
+Descriptors,PointSet
+Descriptors,Common
+Descriptors,ObjectList
+IOBSQ,ImageBase
+IOBSQ,Common
+Fuzzy,Common
+Fuzzy,TinyXMLAdapters
+OpticalCalibration,ImageBase
+OpticalCalibration,6S
+OpticalCalibration,ImageManipulation
+OpticalCalibration,Indices
+OpticalCalibration,Common
+OpticalCalibration,Metadata
+OpticalCalibration,Boost
+OpticalCalibration,OSSIMAdapters
+OpticalCalibration,ObjectList
+Polarimetry,Common
+Polarimetry,ITKPendingPatches
+OSSIMAdapters,GDAL
+OSSIMAdapters,Common
+OSSIMAdapters,Ossim
+Edge,VectorDataBase
+Edge,Conversion
+Edge,Projection
+Edge,ITKPendingPatches
+Edge,ImageBase
+Edge,SpatialObjects
+Edge,Streaming
+Edge,ImageManipulation
+Edge,Path
+Edge,ObjectList
+Edge,Common
+MorphologicalProfiles,ImageBase
+MorphologicalProfiles,ObjectList
+MorphologicalProfiles,Common
+MorphologicalProfiles,ImageManipulation
+MathParser,VectorDataBase
+MathParser,Path
+MathParser,MuParser
+MathParser,Common
+MathParser,ImageManipulation
+Projection,VectorDataBase
+Projection,GdalAdapters
+Projection,ImageBase
+Projection,Transform
+Projection,VectorDataManipulation
+Projection,OSSIMAdapters
+Projection,ImageManipulation
+Projection,Metadata
+Projection,Boost
+Projection,GDAL
+Projection,Common
+SpatialObjects,Common
+IOONERA,ImageBase
+IOONERA,Common
+RoadExtraction,VectorDataBase
+RoadExtraction,ImageBase
+RoadExtraction,VectorDataManipulation
+RoadExtraction,ImageManipulation
+RoadExtraction,MathParser
+RoadExtraction,Path
+RoadExtraction,ObjectList
+RoadExtraction,Common
+CurlAdapters,Curl
+CurlAdapters,Common
+ObjectList,Common
+OGRProcessing,GdalAdapters
+OGRProcessing,Projection
+OGRProcessing,Conversion
+OGRProcessing,Smoothing
+OGRProcessing,Streaming
+OGRProcessing,EdisonMeanShift
+OGRProcessing,Common
+OGRProcessing,Labelling
+OGRProcessing,GDAL
+PanSharpening,ImageBase
+PanSharpening,Statistics
+PanSharpening,ImageManipulation
+PanSharpening,Convolution
+IOTileMap,IOGDAL
+IOTileMap,ImageBase
+IOTileMap,Common
+IOTileMap,CurlAdapters
+Carto,VectorDataBase
+Carto,ImageIO
+Carto,Projection
+Carto,TinyXMLAdapters
+Carto,ImageBase
+Carto,Transform
+Carto,Common
+Carto,CurlAdapters
+Carto,VectorDataIO
+Carto,ImageManipulation
+Interpolation,ImageBase
+Interpolation,Boost
+Interpolation,Common
+Interpolation,ITKPendingPatches
+IOMSTAR,ImageBase
+IOMSTAR,Common
+TestKernel,GdalAdapters
+TestKernel,ImageIO
+TestKernel,ImageBase
+TestKernel,Common
+TestKernel,GDAL
+TestKernel,OSSIMAdapters
+TestKernel,ImageManipulation
+SOM,ImageBase
+SOM,Common
+SOM,ITKPendingPatches
+Metrics,Common
+BoostAdapters,Boost
+ChangeDetection,Projection
+ChangeDetection,Statistics
+ChangeDetection,ImageManipulation
+ChangeDetection,Common
+Unmixing,DimensionalityReduction
+Unmixing,Statistics
+Unmixing,Boost
+Unmixing,Common
+Unmixing,Wavelet
+IOLUM,ImageBase
+IOLUM,Common
+MeanShift,CCOBIA
+MeanShift,Conversion
+MeanShift,Smoothing
+MeanShift,MathParser
+Common,ConfigFile
+Common,ITKPendingPatches
+Markov,Boost
+Markov,Common
+IORAD,ImageBase
+IORAD,Common
+DempsterShafer,VectorDataBase
+DempsterShafer,ImageBase
+DempsterShafer,VectorDataManipulation
+DempsterShafer,LearningBase
+DempsterShafer,Common
+DempsterShafer,MathParser
+DempsterShafer,Fuzzy
+IOJPEG2000,TinyXMLAdapters
+IOJPEG2000,ImageBase
+IOJPEG2000,OSSIMAdapters
+IOJPEG2000,Common
+IOJPEG2000,OpenJPEG
+IOJPEG2000,Boost
+IOJPEG2000,GDAL
+DisparityMap,Stereo
+DisparityMap,ITKPendingPatches
+DisparityMap,ImageBase
+DisparityMap,Transform
+DisparityMap,PointSet
+DisparityMap,Common
+Convolution,Common
+RCC8,ImageManipulation
+RCC8,ImageBase
+RCC8,RoadExtraction
+RCC8,Common
+RCC8,Path
+RCC8,Boost
+RCC8,ObjectList
+IOXML,TinyXMLAdapters
+Watersheds,Common
+KMZWriter,VectorDataBase
+KMZWriter,ImageIO
+KMZWriter,ImageBase
+KMZWriter,Transform
+KMZWriter,OSSIMAdapters
+KMZWriter,ImageManipulation
+KMZWriter,VectorDataIO
+KMZWriter,libkml
+LabelMap,VectorDataBase
+LabelMap,Common
+SARCalibration,ITKPendingPatches
+SARCalibration,Common
+SARCalibration,OSSIMAdapters
+SARCalibration,Metadata

Scripts/modularization/modulizer.py

@@ -240,11 +240,11 @@ for  moduleName in moduleList:
       cxxFiles = glob.glob(moduleDir+'/src/*.cxx')
       cxxFileList='';
       for cxxf in cxxFiles:
-          cxxFileList = cxxFileList+cxxf.split('/')[-1]+'\n'
+          cxxFileList = cxxFileList+'  '+cxxf.split('/')[-1]+'\n'
       # build list of link dependencies
       linkLibs = ""
       for dep in dependencies[moduleName]:
-        linkLibs = linkLibs + " ${OTB"+dep+"_LIBRARIES}"
+        linkLibs = linkLibs + "  ${OTB"+dep+"_LIBRARIES}" + "\n"
       if len(linkLibs) == 0:
         linkLibs = " ${OTBITK_LIBRARIES}"
       filepath = moduleDir+'/src/CMakeLists.txt'
@@ -290,16 +290,16 @@ for  moduleName in moduleList:
         # replace depend list
         dependTagPos = line.find("DEPENDS_TO_BE_REPLACED")
         if dependTagPos >= 0:
+          replacementStr = "DEPENDS"
           if len(dependencies[moduleName]) > 0:
             indentStr = ""
-            replacementStr = "DEPENDS"
             for it in range(dependTagPos+2):
               indentStr = indentStr + " "
             for dep in dependencies[moduleName]:
-              replacementStr = replacementStr + "\n" + indentStr +"OTB"+ dep  
-            line = line.replace('DEPENDS_TO_BE_REPLACED',replacementStr)
+              replacementStr = replacementStr + "\n" + indentStr +"  OTB"+ dep
           else:
-            line = line.replace('DEPENDS_TO_BE_REPLACED','')
+            replacementStr = replacementStr + "\n" + indentStr + "  OTBCommon"
+          line = line.replace('DEPENDS_TO_BE_REPLACED',replacementStr)
         # replace test_depend list
         testDependTagPos = line.find("TESTDEP_TO_BE_REPLACED")
         if testDependTagPos >= 0:
@@ -315,3 +315,11 @@ for  moduleName in moduleList:
             line = line.replace('TESTDEP_TO_BE_REPLACED','')
         o.write(line);
       o.close()
+
+# save version without patches (so that we can regenerate patches later)
+os.system( "cp -ar " + op.join(OutputDir,"OTB_Modular") + " " + op.join(OutputDir,"OTB_Modular-nopatch") )
+
+# apply patches in OTB_Modular
+curdir = os.path.dirname(__file__)
+os.system( "cd " + op.join(OutputDir,"OTB_Modular") + " && patch -p1 < " + curdir + "/patches/otbmodular.patch")
+

Scripts/modularization/patches-dump

+#!/bin/bash
+
+# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+SOURCE="$(readlink "$SOURCE")"
+[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+
+
+PATCHES_DIR=$DIR/patches
+
+MODULAR_ROOT=~/dev/src/OTB-modular-test
+UNPATCHED_SOURCES=~/dev/src/OTB-modular-test/OTB_Modular-beforepatch
+PATCHED_SOURCES=~/dev/src/OTB-modular-test/OTB_Modular
+
+cd ~/dev/src/OTB-modular-test && diff -ur OTB_Modular-beforepatch OTB_Modular > $PATCHES_DIR/otbmodular.patch
\ No newline at end of file

Scripts/modularization/patches/otbmodular.patch

+diff -ur OTB_Modular-beforepatch/Modules/Core/Common/include/otbConfigurationFile.h OTB_Modular/Modules/Core/Common/include/otbConfigurationFile.h
+--- OTB_Modular-beforepatch/Modules/Core/Common/include/otbConfigurationFile.h	2014-11-20 16:16:12.000000000 +0100
++++ OTB_Modular/Modules/Core/Common/include/otbConfigurationFile.h	2014-11-20 16:16:31.219385336 +0100
+@@ -22,7 +22,7 @@
+ 
+ #include "itkObject.h"
+ #include "itkObjectFactory.h"
+-#include "ConfigFile.h"
++#include "otb_configfile.h"
+ #include "itksys/FundamentalType.h"
+ 
+ namespace otb

Scripts/modularization/templateModule/otb-template-module/otb-module.cmake

@@ -2,9 +2,7 @@ set(DOCUMENTATION "TO BE DOCUMENTED")
 
 otb_module(otb-template-module 
   DEPENDS_TO_BE_REPLACED
-
   TESTDEP_TO_BE_REPLACED
-
   DESCRIPTION
     "${DOCUMENTATION}"
-)
+  )

Scripts/modularization/templateModule/otb-template-module/src/CMakeLists.txt

 set(otb-template-module_SRC
 LIST_OF_CXX_FILES
-)
+  )
 
 add_library(otb-template-module ${otb-template-module_SRC})
-target_link_libraries(otb-template-module LINK_LIBRARIES_TO_BE_REPLACED)
+target_link_libraries(otb-template-module 
+LINK_LIBRARIES_TO_BE_REPLACED
+  )
+
 otb_module_target(otb-template-module)