Ongoing improvements

CMakeLists.txt

@@ -1,49 +1,69 @@
-cmake_minimum_required(VERSION 2.8.9)
+cmake_minimum_required(VERSION 3.5)
 
 #-----------------------------------------------------------------------------
-if(NOT Slicer_SOURCE_DIR)
-  set(EXTENSION_NAME MABMIS)
-  set(EXTENSION_HOMEPAGE "http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MABMIS")
-  set(EXTENSION_CATEGORY "Segmentation")
-  set(EXTENSION_CONTRIBUTORS "Xiaofeng Liu (GE GLobal Research), Minjeong Kim (UNC), Dinggang Shen (UNC), Jim Miller (GE GLobal Research)")
-  set(EXTENSION_ICONURL "http://wiki.slicer.org/slicerWiki/images/e/e2/MABMIS_Icon.png")
-  set(EXTENSION_DESCRIPTION "Multi-Atlas Based Group Segmentation")
-  set(EXTENSION_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/2/2c/MABMIS_trainning_GUI.png http://wiki.slicer.org/slicerWiki/images/6/64/MABMIS_testing_GUI.png http://wiki.slicer.org/slicerWiki/images/c/c3/MABMIS_algorithm.png")
-endif()
+project(MABMIS)
+set(EXTENSION_HOMEPAGE "http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MABMIS")
+set(EXTENSION_CATEGORY "Segmentation")
+set(EXTENSION_CONTRIBUTORS "Xiaofeng Liu (GE Global Research), Minjeong Kim (UNC), Dinggang Shen (UNC), Jim Miller (GE Global Research)")
+set(EXTENSION_ICONURL "http://wiki.slicer.org/slicerWiki/images/e/e2/MABMIS_Icon.png")
+set(EXTENSION_DESCRIPTION "Multi-Atlas Based Group Segmentation")
+set(EXTENSION_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/2/2c/MABMIS_trainning_GUI.png http://wiki.slicer.org/slicerWiki/images/6/64/MABMIS_testing_GUI.png http://wiki.slicer.org/slicerWiki/images/c/c3/MABMIS_algorithm.png")
+
+find_package(Slicer REQUIRED)
+include(${Slicer_USE_FILE})
+
+set(MABMIS_ITK_COMPONENTS
+  ITKIOImageBase
+  ITKTransform
+  ITKIOTransformBase
+  ITKIOXML
+  ITKImageGrid
+  ITKImageFunction
+  ITKPDEDeformableRegistration
+  ITKSmoothing
+  )
+find_package(ITK 4.6 COMPONENTS ${MABMIS_ITK_COMPONENTS} REQUIRED)
+set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # See Libs/ITKFactoryRegistration/CMakeLists.txt
+include(${ITK_USE_FILE})
 
-#-----------------------------------------------------------------------------
-if(NOT Slicer_SOURCE_DIR)
-  find_package(Slicer REQUIRED)
-  include(${Slicer_USE_FILE})
-endif()
 
 #-----------------------------------------------------------------------------
 set(MODULE_TARGET_LIBRARIES
   ${ITK_LIBRARIES}
   )
-
-#-----------------------------------------------------------------------------
-set(MODULE_NAME IGR3D_MABMIS_Training)
+message(STATUS ${MODULE_TARGET_LIBRARIES})
 
 #-----------------------------------------------------------------------------
 SEMMacroBuildCLI(
-  NAME ${MODULE_NAME}
+  NAME IGR3D_MABMIS_Training
   TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES}
   ADDITIONAL_SRCS
 	itkMABMISAtlasXMLFile.cxx
+	Training.cxx
+	commonMABMIS.cxx
   #EXECUTABLE_ONLY
   )
 
-  message(STATUS ${ITK_LIBRARIES})
 #-----------------------------------------------------------------------------
-set(MODULE_NAME IGR3D_MABMIS_Testing)
+SEMMacroBuildCLI(
+  NAME IGR3D_MABMIS_Testing
+  TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES}
+  ADDITIONAL_SRCS
+	itkMABMISAtlasXMLFile.cxx
+	Testing.cxx
+	commonMABMIS.cxx
+  #EXECUTABLE_ONLY
+  )
 
 #-----------------------------------------------------------------------------
 SEMMacroBuildCLI(
-  NAME ${MODULE_NAME}
+  NAME IGR3D_MABMIS_Direct_Invoke
   TARGET_LIBRARIES ${MODULE_TARGET_LIBRARIES}
   ADDITIONAL_SRCS
 	itkMABMISAtlasXMLFile.cxx
+	Testing.cxx
+	Training.cxx
+	commonMABMIS.cxx
   #EXECUTABLE_ONLY
   )
 
@@ -54,11 +74,5 @@ if(BUILD_TESTING)
 endif()
 
 #-----------------------------------------------------------------------------
-if(NOT Slicer_SOURCE_DIR)
-  include(${Slicer_EXTENSION_CPACK})
-endif()
-
-
-
-
-################################################
+include(${Slicer_EXTENSION_GENERATE_CONFIG})
+include(${Slicer_EXTENSION_CPACK})

Data/Input/TestData/TestData.xml

@@ -4,10 +4,10 @@
 <DataPath></DataPath>
 <NumberOfImageData>4</NumberOfImageData>
 <ImageDataSets>
-<Dataset ImageFile="UA_cbq_000.nii.gz"/>
-<Dataset ImageFile="UB_cbq_000.nii.gz"/>
-<Dataset ImageFile="VA_cbq_000.nii.gz"/>
-<Dataset ImageFile="VB_cbq_000.nii.gz"/>
+<Dataset ImageFile="UA_cbq_000.nii.gz" SegmentationFile="UA_cbq_000_seg.nii.gz"/>
+<Dataset ImageFile="UB_cbq_000.nii.gz" SegmentationFile="UB_cbq_000_seg.nii.gz"/>
+<Dataset ImageFile="VA_cbq_000.nii.gz" SegmentationFile="VA_cbq_000_seg.nii.gz"/>
+<Dataset ImageFile="VB_cbq_000.nii.gz" SegmentationFile="VB_cbq_000_seg.nii.gz"/>
 </ImageDataSets>
 
 </MABMISImageData>