Merge branch 'develop' into s1-deburst

CMake/FindShark.cmake

@@ -26,7 +26,7 @@ find_path( SHARK_INCLUDE_DIR shark/Core/Shark.h
   PATH_SUFFIXES include include/shark shark)
 
 find_library( SHARK_LIBRARY
-  NAMES shark
+  NAMES shark shark_debug
   PATHS "${SHARK_SEARCH_PATH}"
   PATH_SUFFIXES lib
   )

CMakeLists.txt

@@ -312,7 +312,12 @@ if(OTB_WRAP_PYTHON)
 set(OTB_CONFIG_CODE "${OTB_CONFIG_CODE}
 set(OTB_PYTHONPATH \"${OTB_BINARY_DIR}/${OTB_INSTALL_PYTHON_DIR}\")")
 endif()
-
+if(OTB_HAS_CXX11)
+  if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" OR
+     "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    set(OTB_REQUIRED_CXX_FLAGS " -std=c++11")
+  endif()
+endif()
 set(OTB_CONFIG_APPLICATION_PATH "${OTB_BINARY_DIR}/${OTB_INSTALL_APP_DIR}")
 set(OTB_CONFIG_TARGETS_CONDITION " AND NOT OTB_BINARY_DIR")
 set(OTB_CONFIG_TARGETS_FILE "${OTB_BINARY_DIR}/OTBTargets.cmake")

Documentation/Cookbook/rst/Installation_Linux.txt

@@ -93,17 +93,17 @@ A: This is due to a conflict with system Qt4 (usually seen on KDE) and Qt4 + gtk
 Q: Monteverdi and Mapla applications look different from my other applications.
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-A: By default, Monteverdi, Mapla and otbapplication (otbgui\_\*) uses a default gtk theme (plastic)
-which is distributed with the OTB package!.  We do this to be on safe side, like when a user does
-not have gtk libraries installed when using our package.
+A: By default, Monteverdi, Mapla and otbapplication (otbgui\_\*) uses a the
+system gtk theme. If you can't install GTK on your system you can use the
+distributed with the OTB package. Note that using system GTK is the preferred
+way with the OTB standalone package as the distributed version of GTK do not
+work on recent Linux distributions. 
 
-gtk libraries in the package is  the reason why you are getting a default "plastic" look & feel that
-makes it look different from other GUI applications.
-To get same look and feel, you can "force"  Monteverdi and Mapla to use system GTK.
+To use the distributed GTK libraries you need to set the OTB_USE_LOCAL_GTK:
 
 ::
 
-   export OTB_USE_SYSTEM_GTK=1
+   export OTB_USE_LOCAL_GTK=1
 
 And now start ``monteverdi.sh`` or ``mapla.sh`` from OTB-|release|-Linux64
-To get back default behaviour, unset OTB_USE_SYSTEM_GTK=1 or set OTB_USE_SYSTEM_GTK=0
+To get back default behaviour, unset OTB_USE_LOCAL_GTK=1 or set OTB_USE_LOCAL_GTK=0

Documentation/Cookbook/rst/Installation_Linux_xdk.txt

+Synopsis
+--------
+
+This archive provides a development kit for the ORFEO ToolBox library which
+allows to easily compile OTB and facilitate the creation of programs based on
+OTB.
+
+It contains shared libraries of OTB dependencies and helper scripts for the
+configuration and the compilation of the library.
+
+Note that OTB sources are not included in the archive (see instructions below).
+
+Prerequisites
+-------------
+
+-  cmake (>= 3.2)
+-  gcc (>= 4.9)
+-  git
+
+Extract XDK
+-----------
+
+::
+
+    cd /opt (You can use another a directory of your own choice)
+    chmod +x OTB-|release|-xdk-Linux64.run
+    ./OTB-|release|-xdk-Linux64.run
+
+**You now will have a directory named OTB-|release|-xdk-Linux64 in \'/opt\'**
+
+Setup environment
+-----------------
+There is a helper script in package called **xdkenv.profile**. This script export
+required environments to configure and build OTB.
+
+::
+
+    cd /opt/OTB-|release|-xdk-Linux64
+    . ./xdkenv.profile
+
+Test environment setup by checking value of CMAKE_PREFIX_PATH
+
+::
+
+    echo $CMAKE_PREFIX_PATH
+
+The above command will output:
+ /opt/OTB-|release|-xdk-Linux64
+ 
+
+Download, Configure and build OTB
+---------------------------------
+
+::
+
+    mkdir -p /opt/OTB/build && cd /opt/OTB
+    git clone --depth=1 --branch=develop https://git@git.orfeo-toolbox.org/git/otb.git source
+    cd build && cmake ../source 
+    make -j2
+
+
+Notes
+~~~~~
+
+* By default, all OTB\_USE\_\* variables in OTB are set to FALSE except for 6S and SiftFast. You can check/activate them in your cmake-gui/ccmake.
+
+* If you need to activate Qt4 modules (Monteverdi, Ice, QtWidget, ApplicationEngine ..), you must set *QT_BINARY_DIR*.
+
+::
+
+    cd /opt/OTB/build && cmake -DOTB_USE_QT4=TRUE -DQT_BINARY_DIR=$CMAKE_PREFIX_PATH/bin
+
+This is because Qt tools ( moc, rcc, et al) are reported as not found by cmake due to incorrect path in "qmake -query"
+
+

Documentation/Cookbook/rst/Installation_Macx_xdk.txt

+README.md
+

Documentation/Cookbook/rst/Installation_Windows_xdk.txt

+README.md

Documentation/Cookbook/rst/Monteverdi.rst

@@ -12,22 +12,19 @@ Monteverdi is a satellite image viewer. Its main features are:
 - **Powerful**: Access to all processing application from OTB. Orthorectification,
   optical calibration, classification, SAR processing, and much more!
 
-GUI : what does it look like ?
-------------------------------
-
 .. image:: Art/MonteverdiImages/gui.png
 
-This is Monteverdi’s main window where the different functionalities are reachable:
+This is Monteverdi’s main window where the different functionalities are:
 
 #. Main menu
 
 #. Top toolbar
 
-#. Image displaying
+#. Image View
 
-#. Right side dock
+#. Widgets
 
-#. Stack layer
+#. Layer stack
 
 Main menu
 ~~~~~~~~~
@@ -92,9 +89,9 @@ In the image displaying part:
 -  CTRL+Mouse drag = Quick scroll view (rending is done after releasing
    CTRL key)
 
--  CTRL+Mouse wheel = Zoom in out
+-  Mouse wheel = Zoom
 
--  + or - = Zoom in out
+-  + or - = Zoom
 
 In the layer stack part:
 

Documentation/SoftwareGuide/CMakeLists.txt

@@ -62,7 +62,7 @@ FIND_PATH(OTB_DATA_ROOT README-OTB-Data PATHS $ENV{OTB_DATA_ROOT} ${OTB_SOURCE_D
 FIND_PATH(OTB_DATA_LARGEINPUT_ROOT OTBData.readme PATHS $ENV{OTB_DATA_LARGEINPUT_ROOT})
 
 IF( NOT OTB_DATA_LARGEINPUT_ROOT )
-  MESSAGE(FATAL_ERROR "Large input directory is not set")
+  MESSAGE(FATAL_ERROR "Large input directory is not set and is mandatory to build the Software Guide.")
 ENDIF( NOT OTB_DATA_LARGEINPUT_ROOT )
 
 # OTB_DATA_PATHS is searched recursively.. you need not enter sub-directories

Documentation/SoftwareGuide/Latex/ContributorList.tex

@@ -33,6 +33,7 @@ Julien Osman,
 Julien Radoux (UCL),
 Laurentiu Nicola (CS Romania),
 Luc Hermitte (CS),
+Ludovic Hussonnois (CS),
 Manuel Grizonnet (CNES),
 Massimo Di Stefano,
 Mathieu Deltorre (CS),

Documentation/SoftwareGuide/Latex/WriteAnApplication.tex

@@ -150,7 +150,7 @@ name of the files to write, but they also encapsulate the corresponding writers.
 \section{Composite application}
 
 The application framework has been extended to allow the implementation of composite applications :
-applications that use other applications. The concept is simple : you have two applications A and B
+\textbf{applications that use other applications}. The concept is simple : you have two applications A and B
 that you want to chain in order to build a third application C. Rather than writing C by copying
 the code of A and B, you would like to re-use applications A and B. This plain example will be
 re-used in this section for explanations.
@@ -231,7 +231,7 @@ with \code{b.in}. In this case, you have to manually call the writers of paramet
 \code{a.out}.
 \end{itemize}
 
-At the moment, the connexion of vector data parameters is not supported.
+At the moment, the in-memory connexion of vector data parameters is not supported.
 
 \subsection{Orchestration}
 
@@ -242,8 +242,17 @@ parameter update.
 
 In the \code{DoExecute()} of your composite application, you have to call \code{ExecuteInternal()}
 in order to launch each internal application. The order should be compatible with
-image parameter connexions. If you want to do "in-memory" connexions, you can to it between
-two calls to \code{ExecuteInternal()}.
+image parameter connexions. If you want to do "in-memory" connexions, you can do it between
+two calls to \code{ExecuteInternal()}, for instance :
+
+\small
+\begin{lstlisting}
+ExecuteInternal("a");
+GetInternalApplication("b")->SetParameterInputImage("in",
+  GetInternalApplication("a")->GetParameterOutputImage("out"));
+ExecuteInternal("b");
+\end{lstlisting}
+\normalsize
 
 The application BundleToPerfectSensor is a simple example of composite applications.
 For a more complex example, you can check the application TrainImagesClassifier.

Modules/Adapters/QtAdapters/src/otbQtAdapters.cxx

@@ -66,13 +66,18 @@ GetExistingDirectory( QWidget * p,
 		      const QString& dir,
 		      QFileDialog::Options options )
 {
+  QString dialogCaption(caption.isEmpty()
+    ? QObject::tr( "Select directory..." )
+    : caption);
+  QString dialogDir(dir.isEmpty()
+    ? RecentDirectory
+    : dir);
+
   QString path(
     QFileDialog::getExistingDirectory(
       p,
-      caption.isEmpty()
-      ? QObject::tr( "Select directory..." )
-      : caption,
-      dir.isEmpty() ? RecentDirectory : dir,
+      dialogCaption,
+      dialogDir,
       options
     )
   );
@@ -95,13 +100,18 @@ GetOpenFileName( QWidget * p,
 		 QString* selectedFilter,
 		 QFileDialog::Options options )
 {
+  QString dialogCaption(caption.isEmpty()
+    ? QObject::tr( "Open file..." )
+    : caption);
+  QString dialogDir(dir.isEmpty()
+    ? RecentDirectory
+    : dir);
+
   QString filename(
     QFileDialog::getOpenFileName(
       p,
-      caption.isEmpty()
-      ? QObject::tr( "Open file..." )
-      : caption,
-      dir.isEmpty() ? RecentDirectory : dir,
+      dialogCaption,
+      dialogDir,
       filter,
       selectedFilter,
       options
@@ -124,13 +134,18 @@ GetOpenFileNames( QWidget * p,
 		  QString * selectedFilter,
 		  QFileDialog::Options options )
 {
+  QString dialogCaption(caption.isEmpty()
+    ? QObject::tr( "Open file..." )
+    : caption);
+  QString dialogDir(dir.isEmpty()
+    ? RecentDirectory
+    : dir);
+
   QStringList filenames(
     QFileDialog::getOpenFileNames(
       p,
-      caption.isEmpty()
-      ? QObject::tr( "Open file..." )
-      : caption,
-      dir.isEmpty() ? RecentDirectory : dir,
+      dialogCaption,
+      dialogDir,
       filter,
       selectedFilter,
       options
@@ -153,13 +168,18 @@ GetSaveFileName( QWidget * p,
 		 QString * selectedFilter,
 		 QFileDialog::Options options )
 {
+  QString dialogCaption(caption.isEmpty()
+    ? QObject::tr( "Save file..." )
+    : caption);
+  QString dialogDir(dir.isEmpty()
+    ? RecentDirectory
+    : dir);
+
   QString filename(
     QFileDialog::getSaveFileName(
       p,
-      caption.isEmpty()
-      ? QObject::tr( "Save file..." )
-      : caption,
-      dir.isEmpty() ? RecentDirectory : dir,
+      dialogCaption,
+      dialogDir,
       filter,
       selectedFilter,
       options

Modules/Applications/AppClassification/app/otbDSFuzzyModelEstimation.cxx

@@ -140,12 +140,12 @@ private:
     AddParameter(ParameterType_String, "cri", "Criterion");
     SetParameterDescription("cri", "Dempster Shafer criterion (by default (belief+plausibility)/2)");
     MandatoryOff("cri");
-    SetParameterString("cri","((Belief + Plausibility)/2.)");
+    SetParameterString("cri","((Belief + Plausibility)/2.)", false);
 
     AddParameter(ParameterType_Float,"wgt","Weighting");
     SetParameterDescription("wgt","Coefficient between 0 and 1 to promote undetection or false detections (default 0.5)");
     MandatoryOff("wgt");
-    SetParameterFloat("wgt", 0.5);
+    SetParameterFloat("wgt",0.5, false);
 
     AddParameter(ParameterType_InputFilename,"initmod","initialization model");
     SetParameterDescription("initmod","Initialization model (xml file) to be used. If the xml initialization model is set, the descriptor list is not used (specified using the option -desclist)");
@@ -154,12 +154,12 @@ private:
     AddParameter(ParameterType_StringList, "desclist","Descriptor list");
     SetParameterDescription("desclist","List of the descriptors to be used in the model (must be specified to perform an automatic initialization)");
     MandatoryOff("desclist");
-    SetParameterString("desclist","");
+    SetParameterString("desclist","", false);
 
     AddParameter(ParameterType_Int,"maxnbit","Maximum number of iterations");
     MandatoryOff("maxnbit");
     SetParameterDescription("maxnbit","Maximum number of optimizer iteration (default 200)");
-    SetParameterInt("maxnbit", 200);
+    SetParameterInt("maxnbit",200, false);
 
     AddParameter(ParameterType_Empty,"optobs","Optimizer Observer");
     SetParameterDescription("optobs","Activate the optimizer observer");

Modules/Applications/AppClassification/app/otbKMeansClassification.cxx

@@ -245,7 +245,7 @@ private:
         {
         otbAppLogWARNING("The available RAM is too small to process this sample size of " << GetParameterInt("ts") <<
             " pixels. The sample size will be reduced to " << maxPixNb << " pixels." << std::endl);
-        this->SetParameterInt("ts", maxPixNb);
+        this->SetParameterInt("ts",maxPixNb, false);
         }
 
       this->SetMaximumParameterIntValue("ts", maxPixNb);

Modules/Applications/AppClassification/app/otbMultiImageSamplingRate.cxx

@@ -161,7 +161,7 @@ private:
     SetParameterDescription("strategy.all","Take all samples");
 
     // Default strategy : smallest
-    SetParameterString("strategy","smallest");
+    SetParameterString("strategy","smallest", false);
 
     AddParameter(ParameterType_Choice, "mim", "Multi-Image Mode");
 

Modules/Applications/AppClassification/app/otbOGRLayerClassifier.cxx

@@ -78,7 +78,7 @@ private:
 
     AddParameter(ParameterType_String,"cfield","Field containing the predicted class.");
     SetParameterDescription("cfield","Field containing the predicted class");
-    SetParameterString("cfield","predicted");
+    SetParameterString("cfield","predicted", false);
 
     // Doc example parameter settings
     SetDocExampleParameterValue("inshp", "vectorData.shp");

Modules/Applications/AppClassification/app/otbSampleExtraction.cxx

@@ -86,7 +86,7 @@ private:
     AddParameter(ParameterType_String, "outfield.prefix.name", "Output field prefix");
     SetParameterDescription("outfield.prefix.name","Prefix used to form the field names that"
       "will contain the extracted values.");
-    SetParameterString("outfield.prefix.name", "value_");
+    SetParameterString("outfield.prefix.name", "value_", false);
 
     AddChoice("outfield.list","Use the given name list");
     SetParameterDescription("outfield.list","Use the given name list");

Modules/Applications/AppClassification/app/otbSampleSelection.cxx

@@ -197,7 +197,7 @@ private:
     SetParameterDescription("strategy.all","Take all samples");
 
     // Default strategy : smallest
-    SetParameterString("strategy","smallest");
+    SetParameterString("strategy","smallest", false);
 
     AddParameter(ParameterType_ListView, "field", "Field Name");
     SetParameterDescription("field","Name of the field carrying the class name in the input vectors.");

Modules/Applications/AppClassification/app/otbTrainImagesClassifier.cxx

@@ -155,7 +155,7 @@ void DoInit() ITK_OVERRIDE
   SetParameterDescription("sample.vtr",
     "Ratio between training and validation samples (0.0 = all training, 1.0 = "
     "all validation) (default = 0.5).");
-  SetParameterFloat("sample.vtr", 0.5);
+  SetParameterFloat("sample.vtr",0.5, false);
   SetMaximumParameterFloatValue("sample.vtr",1.0);
   SetMinimumParameterFloatValue("sample.vtr",0.0);
 
@@ -214,7 +214,7 @@ void DoUpdateParameters() ITK_OVERRIDE
   if ( HasValue("io.vd") )
     {
     std::vector<std::string> vectorFileList = GetParameterStringList("io.vd");
-    GetInternalApplication("polystat")->SetParameterString("vec",vectorFileList[0]);
+    GetInternalApplication("polystat")->SetParameterString("vec",vectorFileList[0], false);
     UpdateInternalParameters("polystat");
     }
 }
@@ -289,21 +289,21 @@ void DoExecute() ITK_OVERRIDE
   for (unsigned int i=0 ; i<nbInputs ; i++)
     {
     GetInternalApplication("polystat")->SetParameterInputImage("in",imageList->GetNthElement(i));
-    GetInternalApplication("polystat")->SetParameterString("vec",vectorFileList[i]);
-    GetInternalApplication("polystat")->SetParameterString("out",polyStatTrainOutputs[i]);
+    GetInternalApplication("polystat")->SetParameterString("vec",vectorFileList[i], false);
+    GetInternalApplication("polystat")->SetParameterString("out",polyStatTrainOutputs[i], false);
     ExecuteInternal("polystat");
     // analyse polygons given for validation
     if (dedicatedValidation)
       {
-      GetInternalApplication("polystat")->SetParameterString("vec",validationVectorFileList[i]);
-      GetInternalApplication("polystat")->SetParameterString("out",polyStatValidOutputs[i]);
+      GetInternalApplication("polystat")->SetParameterString("vec",validationVectorFileList[i], false);
+      GetInternalApplication("polystat")->SetParameterString("out",polyStatValidOutputs[i], false);
       ExecuteInternal("polystat");
       }
     }
 
   // ---------------------------------------------------------------------------
   // Compute sampling rates
-  GetInternalApplication("rates")->SetParameterString("mim","proportional");
+  GetInternalApplication("rates")->SetParameterString("mim","proportional", false);
   double vtr = GetParameterFloat("sample.vtr");
   long mt = GetParameterInt("sample.mt");
   long mv = GetParameterInt("sample.mv");
@@ -348,44 +348,44 @@ void DoExecute() ITK_OVERRIDE
     }
 
   // Sampling rates for training
-  GetInternalApplication("rates")->SetParameterStringList("il",polyStatTrainOutputs);
-  GetInternalApplication("rates")->SetParameterString("out",rateTrainOut);
+  GetInternalApplication("rates")->SetParameterStringList("il",polyStatTrainOutputs, false);
+  GetInternalApplication("rates")->SetParameterString("out",rateTrainOut, false);
   if (GetParameterInt("sample.bm") != 0)
     {
-    GetInternalApplication("rates")->SetParameterString("strategy","smallest");
+    GetInternalApplication("rates")->SetParameterString("strategy","smallest", false);
     }
   else
     {
     if (fmt > -1)
       {
-      GetInternalApplication("rates")->SetParameterString("strategy","constant");
+      GetInternalApplication("rates")->SetParameterString("strategy","constant", false);
       GetInternalApplication("rates")->SetParameterInt("strategy.constant.nb",fmt);
       }
     else
       {
-      GetInternalApplication("rates")->SetParameterString("strategy","all");
+      GetInternalApplication("rates")->SetParameterString("strategy","all", false);
       }
     }
   ExecuteInternal("rates");
   // Sampling rates for validation
   if (dedicatedValidation)
     {
-    GetInternalApplication("rates")->SetParameterStringList("il",polyStatValidOutputs);
-    GetInternalApplication("rates")->SetParameterString("out",rateValidOut);
+    GetInternalApplication("rates")->SetParameterStringList("il",polyStatValidOutputs, false);
+    GetInternalApplication("rates")->SetParameterString("out",rateValidOut, false);
     if (GetParameterInt("sample.bm") != 0)
       {
-      GetInternalApplication("rates")->SetParameterString("strategy","smallest");
+      GetInternalApplication("rates")->SetParameterString("strategy","smallest", false);
       }
     else
       {
       if (fmv > -1)
         {
-        GetInternalApplication("rates")->SetParameterString("strategy","constant");
+        GetInternalApplication("rates")->SetParameterString("strategy","constant", false);
         GetInternalApplication("rates")->SetParameterInt("strategy.constant.nb",fmv);
         }
       else
         {
-        GetInternalApplication("rates")->SetParameterString("strategy","all");
+        GetInternalApplication("rates")->SetParameterString("strategy","all", false);
         }
       }
     ExecuteInternal("rates");
@@ -393,18 +393,18 @@ void DoExecute() ITK_OVERRIDE
 
   // ---------------------------------------------------------------------------
   // Select & extract samples
-  GetInternalApplication("select")->SetParameterString("sampler", "periodic");
+  GetInternalApplication("select")->SetParameterString("sampler", "periodic", false);
   GetInternalApplication("select")->SetParameterInt("sampler.periodic.jitter",50);
-  GetInternalApplication("select")->SetParameterString("strategy","byclass");
-  GetInternalApplication("extraction")->SetParameterString("outfield", "prefix");
-  GetInternalApplication("extraction")->SetParameterString("outfield.prefix.name","value_");
+  GetInternalApplication("select")->SetParameterString("strategy","byclass", false);
+  GetInternalApplication("extraction")->SetParameterString("outfield", "prefix", false);
+  GetInternalApplication("extraction")->SetParameterString("outfield.prefix.name","value_", false);
   for (unsigned int i=0 ; i<nbInputs ; i++)
     {
     GetInternalApplication("select")->SetParameterInputImage("in",imageList->GetNthElement(i));
-    GetInternalApplication("select")->SetParameterString("vec",vectorFileList[i]);
-    GetInternalApplication("select")->SetParameterString("out",sampleOutputs[i]);
-    GetInternalApplication("select")->SetParameterString("instats",polyStatTrainOutputs[i]);
-    GetInternalApplication("select")->SetParameterString("strategy.byclass.in",ratesTrainOutputs[i]);
+    GetInternalApplication("select")->SetParameterString("vec",vectorFileList[i], false);
+    GetInternalApplication("select")->SetParameterString("out",sampleOutputs[i], false);
+    GetInternalApplication("select")->SetParameterString("instats",polyStatTrainOutputs[i], false);
+    GetInternalApplication("select")->SetParameterString("strategy.byclass.in",ratesTrainOutputs[i], false);
     // select sample positions
     ExecuteInternal("select");
     // extract sample descriptors
@@ -412,10 +412,10 @@ void DoExecute() ITK_OVERRIDE
 
     if (dedicatedValidation)
       {
-      GetInternalApplication("select")->SetParameterString("vec",validationVectorFileList[i]);
-      GetInternalApplication("select")->SetParameterString("out",sampleValidOutputs[i]);
-      GetInternalApplication("select")->SetParameterString("instats",polyStatValidOutputs[i]);
-      GetInternalApplication("select")->SetParameterString("strategy.byclass.in",ratesValidOutputs[i]);
+      GetInternalApplication("select")->SetParameterString("vec",validationVectorFileList[i], false);
+      GetInternalApplication("select")->SetParameterString("out",sampleValidOutputs[i], false);
+      GetInternalApplication("select")->SetParameterString("instats",polyStatValidOutputs[i], false);
+      GetInternalApplication("select")->SetParameterString("strategy.byclass.in",ratesValidOutputs[i], false);
       // select sample positions
       ExecuteInternal("select");