Merge branch 'master' of git.creatis.insa-lyon.fr:clitk

Conflicts:
	common/clitkCoeffsToDVF.h
	tools/clitkCoeffsToDVF.cxx

diff --combined tools/CMakeLists.txt
index 5ccace9e6c41ecbf36506d1861ccf478a8edfdf7,25cd46f8d9e0eb60afd60797d53a287c1f38c035..e6126f35b225a8594bb219ca814957cddeb7d223
--- 1/tools/CMakeLists.txt
--- 2/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@@ -64,31 -64,16 +64,16 @@@ IF (CLITK_BUILD_TOOLS
    TARGET_LINK_LIBRARIES(clitkZeroVF clitkCommon  ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkZeroVF)
  
-   WRAP_GGO(clitkImageExtractLine_GGO_C clitkImageExtractLine.ggo)
-   ADD_EXECUTABLE(clitkImageExtractLine clitkImageExtractLine.cxx ${clitkImageExtractLine_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkImageExtractLine clitkCommon  ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageExtractLine)
- 
    WRAP_GGO(clitkSplitImage_GGO_C clitkSplitImage.ggo)
    ADD_EXECUTABLE(clitkSplitImage clitkSplitImage.cxx clitkSplitImageGenericFilter.cxx ${clitkSplitImage_GGO_C})
    TARGET_LINK_LIBRARIES(clitkSplitImage clitkCommon ${ITK_LIBRARIES} )
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSplitImage)
  
-   WRAP_GGO(clitkVFMerge_GGO_C clitkVFMerge.ggo)
-   ADD_EXECUTABLE(clitkVFMerge clitkVFMerge.cxx ${clitkVFMerge_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkVFMerge clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVFMerge)
- 
    WRAP_GGO(clitkWriteDicomSeries_GGO_C clitkWriteDicomSeries.ggo)
    ADD_EXECUTABLE(clitkWriteDicomSeries clitkWriteDicomSeries.cxx ${clitkWriteDicomSeries_GGO_C})
    TARGET_LINK_LIBRARIES(clitkWriteDicomSeries clitkCommon ${ITK_LIBRARIES} )
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkWriteDicomSeries)
  
-   WRAP_GGO(clitkAverageTemporalDimension_GGO_C clitkAverageTemporalDimension.ggo)
-   ADD_EXECUTABLE(clitkAverageTemporalDimension clitkAverageTemporalDimension.cxx ${clitkAverageTemporalDimension_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkAverageTemporalDimension clitkCommon ${ITK_LIBRARIES} )
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAverageTemporalDimension)
- 
    WRAP_GGO(clitkMedianTemporalDimension_GGO_C clitkMedianTemporalDimension.ggo)
    ADD_EXECUTABLE(clitkMedianTemporalDimension clitkMedianTemporalDimension.cxx
        ${clitkMedianTemporalDimension_GGO_C})
@@@ -108,19 -93,14 +93,14 @@@
    WRAP_GGO(clitkAffineTransform_GGO_C clitkAffineTransform.ggo)
    ADD_EXECUTABLE(clitkAffineTransform clitkAffineTransform.cxx ${clitkAffineTransform_GGO_C})
    TARGET_LINK_LIBRARIES(clitkAffineTransform clitkCommon ${ITK_LIBRARIES} )
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicom2Image)
+   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAffineTransform)
  
    WRAP_GGO(clitkSetBackground_GGO_C clitkSetBackground.ggo)
    ADD_EXECUTABLE(clitkSetBackground clitkSetBackground.cxx clitkSetBackgroundGenericFilter.cxx ${clitkSetBackground_GGO_C})
    TARGET_LINK_LIBRARIES(clitkSetBackground clitkCommon ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSetBackground)
  
-   WRAP_GGO(clitkGuerreroVentilation_GGO_C clitkGuerreroVentilation.ggo)
-   ADD_EXECUTABLE(clitkGuerreroVentilation clitkGuerreroVentilation.cxx clitkGuerreroVentilationGenericFilter.cxx ${clitkGuerreroVentilation_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkGuerreroVentilation clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGuerreroVentilation)
- 
-   WRAP_GGO(clitkGammaIndex_GGO_C clitkGammaIndex.ggo)
+  WRAP_GGO(clitkGammaIndex_GGO_C clitkGammaIndex.ggo)
    ADD_EXECUTABLE(clitkGammaIndex clitkGammaIndex.cxx ${clitkGammaIndex_GGO_C})
    TARGET_LINK_LIBRARIES(clitkGammaIndex clitkCommon ${VTK_LIBRARIES} ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGammaIndex)
@@@ -163,26 -143,6 +143,6 @@@
    TARGET_LINK_LIBRARIES(clitkDicomRTStruct2Image clitkDicomRTStruct clitkCommon ${ITK_LIBRARIES} )
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTStruct2Image)
  
-   # WRAP_GGO(clitkImage2DicomRTStruct_GGO_C clitkImage2DicomRTStruct.ggo)
-   # ADD_EXECUTABLE(clitkImage2DicomRTStruct clitkImage2DicomRTStruct.cxx ${clitkImage2DicomRTStruct_GGO_C})
-   # TARGET_LINK_LIBRARIES(clitkImage2DicomRTStruct clitkDicomRTStruct clitkCommon ${ITK_LIBRARIES} )
-   # SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImage2DicomRTStruct)
- 
-   WRAP_GGO(clitkImageLog_GGO_C clitkImageLog.ggo)
-   ADD_EXECUTABLE(clitkImageLog clitkImageLog.cxx ${clitkImageLog_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkImageLog  ${ITK_LIBRARIES} clitkCommon)
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageLog)
- 
-   WRAP_GGO(clitkFilter_GGO_C clitkFilter.ggo)
-   ADD_EXECUTABLE(clitkFilter clitkFilter.cxx clitkFilterGenericFilter.cxx ${clitkFilter_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkFilter ${ITK_LIBRARIES} clitkCommon)
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkFilter)
- 
-   WRAP_GGO(clitkConeBeamProjectImage_GGO_C clitkConeBeamProjectImage.ggo)
-   ADD_EXECUTABLE(clitkConeBeamProjectImage clitkConeBeamProjectImage.cxx clitkConeBeamProjectImageGenericFilter.cxx ${clitkConeBeamProjectImage_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkConeBeamProjectImage  ${ITK_LIBRARIES} clitkCommon )
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkConeBeamProjectImage)
- 
    WRAP_GGO(clitkComposeVF_GGO_C clitkComposeVF.ggo)
    ADD_EXECUTABLE(clitkComposeVF clitkComposeVFGenericFilter.cxx clitkComposeVF.cxx ${clitkComposeVF_GGO_C})
    TARGET_LINK_LIBRARIES(clitkComposeVF ${ITK_LIBRARIES} clitkCommon)
@@@ -220,63 -180,13 +180,13 @@@
    WRAP_GGO(clitkImageMoment_GGO_C clitkImageMoment.ggo)
    ADD_EXECUTABLE(clitkImageMoment clitkImageMoment.cxx clitkImageMomentGenericFilter.cxx ${clitkImageMoment_GGO_C})
    TARGET_LINK_LIBRARIES(clitkImageMoment clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicom2Image)
+   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageMoment)
  
    WRAP_GGO(clitkImageStatistics_GGO_C clitkImageStatistics.ggo)
    ADD_EXECUTABLE(clitkImageStatistics clitkImageStatistics.cxx clitkImageStatisticsGenericFilter.cxx ${clitkImageStatistics_GGO_C})
    TARGET_LINK_LIBRARIES(clitkImageStatistics clitkCommon ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageStatistics)
  
-   WRAP_GGO(clitkSetOrigin_GGO_C clitkSetOrigin.ggo)
-   ADD_EXECUTABLE(clitkSetOrigin clitkSetOrigin.cxx clitkSetOriginGenericFilter.cxx ${clitkSetOrigin_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkSetOrigin clitkCommon ${ITK_LIBRARIES} )
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSetOrigin)
-     
-   WRAP_GGO(clitkGetOrigin_GGO_C clitkGetOrigin.ggo)
-   ADD_EXECUTABLE(clitkGetOrigin clitkGetOrigin.cxx clitkGetOriginGenericFilter.cxx ${clitkGetOrigin_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkGetOrigin clitkCommon ${ITK_LIBRARIES} )
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGetOrigin)
- 
-   WRAP_GGO(clitkGetDirection_GGO_C clitkGetDirection.ggo)
-   ADD_EXECUTABLE(clitkGetDirection clitkGetDirection.cxx clitkGetDirectionGenericFilter.cxx ${clitkGetDirection_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkGetDirection clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGetDirection)
- 
-   WRAP_GGO(clitkSetDirection_GGO_C clitkSetDirection.ggo)
-   ADD_EXECUTABLE(clitkSetDirection clitkSetDirection.cxx clitkSetDirectionGenericFilter.cxx ${clitkSetDirection_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkSetDirection clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSetDirection)
- 
-   WRAP_GGO(clitkGetSize_GGO_C clitkGetSize.ggo)
-   ADD_EXECUTABLE(clitkGetSize  clitkGetSize.cxx clitkGetSizeGenericFilter.cxx ${clitkGetSize_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkGetSize  clitkCommon   ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGetSize)
- 
-   WRAP_GGO(clitkGetSpacing_GGO_C clitkGetSpacing.ggo)
-   ADD_EXECUTABLE(clitkGetSpacing  clitkGetSpacing.cxx clitkGetSpacingGenericFilter.cxx ${clitkGetSpacing_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkGetSpacing  clitkCommon   ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGetSpacing)
- 
-   WRAP_GGO(clitkSetSpacing_GGO_C clitkSetSpacing.ggo)
-   ADD_EXECUTABLE(clitkSetSpacing  clitkSetSpacing.cxx clitkSetSpacingGenericFilter.cxx ${clitkSetSpacing_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkSetSpacing  clitkCommon   ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicom2Image)
- 
-   WRAP_GGO(clitkCombineImage_GGO_C clitkCombineImage.ggo)
-   ADD_EXECUTABLE(clitkCombineImage clitkCombineImage.cxx clitkCombineImageGenericFilter.cxx ${clitkCombineImage_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkCombineImage clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCombineImage)
- 
-   WRAP_GGO(clitkPermuteAxes_GGO_C clitkPermuteAxes.ggo)
-   ADD_EXECUTABLE(clitkPermuteAxes clitkPermuteAxes.cxx clitkPermuteAxesGenericFilter.cxx ${clitkPermuteAxes_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkPermuteAxes clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkPermuteAxes)
- 
-   WRAP_GGO(clitkChangeImageOrientation_GGO_C clitkChangeImageOrientation.ggo)
-   ADD_EXECUTABLE(clitkChangeImageOrientation clitkChangeImageOrientation.cxx clitkChangeImageOrientationGenericFilter.cxx ${clitkChangeImageOrientation_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkChangeImageOrientation clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkChangeImageOrientation)
- 
    WRAP_GGO(clitkVFConvert_GGO_C clitkVFConvert.ggo)
    ADD_EXECUTABLE(clitkVFConvert clitkVFConvert.cxx clitkVFConvertGenericFilter.cxx ${clitkVFConvert_GGO_C})
    TARGET_LINK_LIBRARIES(clitkVFConvert ${ITK_LIBRARIES} clitkCommon )
@@@ -292,55 -202,15 +202,15 @@@
    TARGET_LINK_LIBRARIES(clitkVectorImageToImage  clitkCommon   ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVectorImageToImage)
  
-   WRAP_GGO(clitkBSplineCoefficientsToValues_GGO_C clitkBSplineCoefficientsToValues.ggo)
-   ADD_EXECUTABLE(clitkBSplineCoefficientsToValues  clitkBSplineCoefficientsToValues.cxx clitkBSplineCoefficientsToValuesGenericFilter.cxx ${clitkBSplineCoefficientsToValues_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkBSplineCoefficientsToValues clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBSplineCoefficientsToValues)
- 
-   WRAP_GGO(clitkValuesToBSplineCoefficients_GGO_C clitkValuesToBSplineCoefficients.ggo)
-   ADD_EXECUTABLE(clitkValuesToBSplineCoefficients  clitkValuesToBSplineCoefficients.cxx clitkValuesToBSplineCoefficientsGenericFilter.cxx ${clitkValuesToBSplineCoefficients_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkValuesToBSplineCoefficients clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkValuesToBSplineCoefficients)
- 
    ADD_EXECUTABLE(clitkMIP clitkMIP.cxx clitkMIPGenericFilter.cxx)
    TARGET_LINK_LIBRARIES(clitkMIP clitkMIPLib clitkCommon ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMIP)
  
-   WRAP_GGO(clitkRelativePosition_GGO_C clitkRelativePosition.ggo)
-   ADD_EXECUTABLE(clitkRelativePosition  clitkRelativePosition.cxx ${clitkRelativePosition_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkRelativePosition clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkRelativePosition)
- 
-   WRAP_GGO(clitkLabelImageOverlapMeasure_GGO_C clitkLabelImageOverlapMeasure.ggo)
-   ADD_EXECUTABLE(clitkLabelImageOverlapMeasure clitkLabelImageOverlapMeasure.cxx ${clitkLabelImageOverlapMeasure_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkLabelImageOverlapMeasure clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES} )
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkLabelImageOverlapMeasure)
- 
-   WRAP_GGO(clitkRelativePositionAnalyzer_GGO_C clitkRelativePositionAnalyzer.ggo)
-   ADD_EXECUTABLE(clitkRelativePositionAnalyzer ../itk/clitkRelativePositionDataBase.cxx clitkRelativePositionAnalyzer.cxx ${clitkRelativePositionAnalyzer_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkRelativePositionAnalyzer clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkRelativePositionAnalyzer)
- 
-   WRAP_GGO(clitkRelativePositionDataBaseAnalyzer_GGO_C clitkRelativePositionDataBaseAnalyzer.ggo)
-   ADD_EXECUTABLE(clitkRelativePositionDataBaseAnalyzer ../itk/clitkRelativePositionDataBase.cxx clitkRelativePositionDataBaseAnalyzer.cxx ${clitkRelativePositionDataBaseAnalyzer_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkRelativePositionDataBaseAnalyzer clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkRelativePositionDataBaseAnalyzer)
- 
-   WRAP_GGO(clitkRelativePositionDataBaseBuilder_GGO_C clitkRelativePositionDataBaseBuilder.ggo)
-   ADD_EXECUTABLE(clitkRelativePositionDataBaseBuilder ../itk/clitkRelativePositionDataBase.cxx clitkRelativePositionDataBaseBuilder.cxx ${clitkRelativePositionDataBaseBuilder_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkRelativePositionDataBaseBuilder clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkRelativePositionDataBaseBuilder)
- 
    WRAP_GGO(clitkTransformLandmarks_GGO_C clitkTransformLandmarks.ggo)
    ADD_EXECUTABLE(clitkTransformLandmarks clitkTransformLandmarks.cxx ${clitkTransformLandmarks_GGO_C})
    TARGET_LINK_LIBRARIES(clitkTransformLandmarks clitkCommon ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkTransformLandmarks)
  
-   WRAP_GGO(clitkLineProfile_GGO_C clitkLineProfile.ggo)
-   ADD_EXECUTABLE(clitkLineProfile clitkLineProfile.cxx clitkLineProfileGenericFilter.cxx ${clitkLineProfile_GGO_C})
-   TARGET_LINK_LIBRARIES(clitkLineProfile clitkCommon ${ITK_LIBRARIES})
-   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkLineProfile)
- 
    ADD_EXECUTABLE(clitkMakeSphereImage clitkMakeSphereImage.cxx) # clitkLineProfileGenericFilter.cxx ${clitkLineProfile_GGO_C})
    TARGET_LINK_LIBRARIES(clitkMakeSphereImage clitkCommon ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMakeSphereImage)
@@@ -360,6 -230,11 +230,6 @@@
    TARGET_LINK_LIBRARIES(clitkCatImage clitkCommon ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCatImage)
  
 -  WRAP_GGO(clitkCoeffsToDVF_GGO_C clitkCoeffsToDVF.ggo)
 -  ADD_EXECUTABLE(clitkCoeffsToDVF clitkCoeffsToDVF.cxx ${clitkCoeffsToDVF_GGO_C})
 -  TARGET_LINK_LIBRARIES(clitkCoeffsToDVF clitkCommon ${ITK_LIBRARIES})
 -  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCoeffsToDVF)
 -
    IF(CLITK_EXPERIMENTAL)
      WRAP_GGO(clitkBinaryImageToMesh_GGO_C clitkBinaryImageToMesh.ggo)
      ADD_EXECUTABLE(clitkBinaryImageToMesh clitkBinaryImageToMesh.cxx ${clitkBinaryImageToMesh_GGO_C})
@@@ -377,6 -252,15 +247,15 @@@
      SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshViewer)
    ENDIF(CLITK_EXPERIMENTAL)
  
+   IF(ITK_VERSION_MAJOR VERSION_LESS 4)
+     MESSAGE(WARNING "clitkDicomRTPlan2Gate is not compatible with GDCM<2 (ITK<4). It will not be build.")
+   ELSE(ITK_VERSION_MAJOR VERSION_LESS 4)
+     WRAP_GGO(clitkDicomRTPlan2Gate_GGO_C clitkDicomRTPlan2Gate.ggo)
+     ADD_EXECUTABLE(clitkDicomRTPlan2Gate clitkDicomRTPlan2Gate.cxx clitkDicomRTPlan2Gate_ggo.c)
+     TARGET_LINK_LIBRARIES(clitkDicomRTPlan2Gate clitkCommon ${ITK_LIBRARIES})
+     SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTPlan2Gate)
+   ENDIF(ITK_VERSION_MAJOR VERSION_LESS 4)
+ 
    SET_TARGET_PROPERTIES(${TOOLS_INSTALL} PROPERTIES INSTALL_RPATH "${VTK_DIR}:${ITK_DIR}" )  
    INSTALL (TARGETS ${TOOLS_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)