Merge pull request #206 from SCIInstitute/itk_upgrade

Itk upgrade

Superbuild/CMakeLists.txt

@@ -1,21 +1,21 @@
 #  For more information, please see: http://software.sci.utah.edu
-# 
+#
 #  The MIT License
-# 
+#
 #  Copyright (c) 2016 Scientific Computing and Imaging Institute,
 #  University of Utah.
-# 
-#  
+#
+#
 #  Permission is hereby granted, free of charge, to any person obtaining a
 #  copy of this software and associated documentation files (the "Software"),
 #  to deal in the Software without restriction, including without limitation
 #  the rights to use, copy, modify, merge, publish, distribute, sublicense,
 #  and/or sell copies of the Software, and to permit persons to whom the
 #  Software is furnished to do so, subject to the following conditions:
-# 
+#
 #  The above copyright notice and this permission notice shall be included
-#  in all copies or substantial portions of the Software. 
-# 
+#  in all copies or substantial portions of the Software.
+#
 #  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 #  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 #  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
@@ -28,8 +28,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8.9 FATAL_ERROR)
 #CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12 FATAL_ERROR)
 #CMAKE_MINIMUM_REQUIRED(VERSION 3.0 FATAL_ERROR)
 IF(POLICY CMP0053)
-  # TODO: revisit on ITK upgrade
-  CMAKE_POLICY(SET CMP0053 OLD)
+   CMAKE_POLICY(SET CMP0053 OLD)
 ENDIF()
 IF(POLICY CMP0054)
   CMAKE_POLICY(SET CMP0054 NEW)

Superbuild/ITKExternal.cmake

@@ -46,18 +46,36 @@ ENDIF()
 SET(itk_CACHE_ARGS
   "-DCMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}"
   "-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}"
+  "-DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>"
   "-DITK_BUILD_DEFAULT_MODULES:BOOL=OFF"
-  "-DITK_INSTALL_NO_LIBRARIES:BOOL=ON"
-  "-DITK_INSTALL_NO_DEVELOPMENT:BOOL=ON"
-  "-DITK_INSTALL_NO_RUNTIME:BOOL=ON"
-  "-DITK_INSTALL_NO_DOCUMENTATION:BOOL=ON"
-  "-DGDCM_INSTALL_NO_DEVELOPMENT:BOOL=ON"
-  "-DGDCM_INSTALL_NO_RUNTIME:BOOL=ON"
-  "-DGDCM_INSTALL_NO_DOCUMENTATION:BOOL=ON"
-  "-DHDF5_INSTALL_NO_DEVELOPMENT:BOOL=ON"
-  "-DModule_ITKReview:BOOL=ON"
-  "-DModule_ITKDeprecated:BOOL=ON"
   "-DITKV3_COMPATIBILITY:BOOL=ON"
+#  "-DITK_INSTALL_NO_LIBRARIES:BOOL=ON"
+#  "-DITK_INSTALL_NO_DEVELOPMENT:BOOL=ON"
+#  "-DITK_INSTALL_NO_RUNTIME:BOOL=ON"
+#  "-DITK_INSTALL_NO_DOCUMENTATION:BOOL=ON"
+#  "-DGDCM_INSTALL_NO_DEVELOPMENT:BOOL=ON"
+#  "-DGDCM_INSTALL_NO_RUNTIME:BOOL=ON"
+#  "-DGDCM_INSTALL_NO_DOCUMENTATION:BOOL=ON"
+#  "-DHDF5_INSTALL_NO_DEVELOPMENT:BOOL=ON"
+#  "-DModule_ITKReview:BOOL=ON"
+  "-DModule_ITKRegistrationCommon:BOOL=ON"
+  "-DModule_ITKSmoothing:BOOL=ON"
+  "-DModule_ITKAnisotropicSmoothing:BOOL=ON"
+  "-DModule_ITKRegionGrowing:BOOL=ON"
+  "-DModule_ITKMathematicalMorphology:BOOL=ON"
+  "-DModule_ITKBinaryMathematicalMorphology:BOOL=ON"
+  "-DModule_ITKDistanceMap:BOOL=ON"
+  "-DModule_ITKLevelSets:BOOL=ON"
+  "-DModule_ITKWatersheds:BOOL=ON"
+  "-DModule_ITKImageFusion:BOOL=ON"
+  "-DModule_ITKHDF5:BOOL=ON"
+  "-DModule_ITKIOHDF5:BOOL=ON"
+  "-DModule_ITKIOLSM:BOOL=ON"
+  "-DModule_ITKIOJPEG:BOOL=ON"
+  "-DModule_ITKIOGIPL:BOOL=ON"
+  "-DModule_IITKIOMeta:BOOL=ON"
+  "-DModule_ITKIONRRD:BOOL=ON"
+  "-DModule_ITKDeprecated:BOOL=ON"
   "-DCMAKE_CXX_FLAGS:STATIC=${CMAKE_CXX_FLAGS}"
   "-DCMAKE_CXX_FLAGS_DEBUG:STATIC=${CMAKE_CXX_FLAGS_DEBUG}"
   "-DCMAKE_C_FLAGS:STATIC=${CMAKE_C_FLAGS}"
@@ -66,29 +84,29 @@ SET(itk_CACHE_ARGS
 )
 
 IF(BUILD_MOSAIC_TOOLS)
-  #SET(ITK_USE_FFTWD ON CACHE BOOL "" FORCE)
-  #SET(ITK_USE_FFTWF ON CACHE BOOL "" FORCE)
   LIST(APPEND itk_CACHE_ARGS
     "-DITK_USE_FFTWD:BOOL=ON"
     "-DITK_USE_FFTWF:BOOL=ON"
+    "-DModule_ITKImageIntensity:BOOL=ON"
+    "-DModule_ITKThresholding:BOOL=ON"
+    "-DModule_ITKTransformFactory:BOOL=ON"
   )
 ENDIF()
 
-SET(itk_GIT_TAG "origin/vtkio_fix")
+SET(itk_GIT_TAG "origin/master")
 
 # If CMake ever allows overriding the checkout command or adding flags,
 # git checkout -q will silence message about detached head (harmless).
 ExternalProject_Add(ITK_external
   GIT_REPOSITORY "https://github.com/CIBC-Internal/itk.git"
   GIT_TAG ${itk_GIT_TAG}
   PATCH_COMMAND ""
-  INSTALL_DIR ""
-  INSTALL_COMMAND ""
   CMAKE_ARGS ${itk_ARGS}
   CMAKE_CACHE_ARGS ${itk_CACHE_ARGS}
 )
 
-ExternalProject_Get_Property(ITK_external BINARY_DIR)
-SET(ITK_DIR ${BINARY_DIR} CACHE PATH "")
+# hardcoded, since we need this before ITK's configure step
+ExternalProject_Get_Property(ITK_external INSTALL_DIR)
+SET(ITK_DIR "${INSTALL_DIR}/lib/cmake/ITK-4.10" CACHE PATH "")
 
 MESSAGE(STATUS "ITK_DIR=${ITK_DIR}")

src/Application/Filters/Actions/ActionAndFilter.h

@@ -65,9 +65,9 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
   virtual bool run( Core::ActionContextHandle& context, 
-    Core::ActionResultHandle& result );
+    Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionArithmeticFilter.h

@@ -64,8 +64,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
 private:
   ActionArithmeticFilterPrivateHandle private_;

src/Application/Filters/Actions/ActionCannyEdgeDetectionFilter.h

@@ -69,8 +69,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionConfidenceConnectedFilter.h

@@ -71,8 +71,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionConnectedComponentFilter.h

@@ -72,8 +72,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionConnectedComponentSizeFilter.h

@@ -64,8 +64,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionCrop.h

@@ -62,8 +62,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
 private:
   ActionCropPrivateHandle private_;

src/Application/Filters/Actions/ActionCurvatureAnisotropicDiffusionFilter.h

@@ -73,8 +73,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionDilateErodeFilter.h

@@ -85,8 +85,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionDilateFilter.h

@@ -80,8 +80,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionDiscreteGaussianFilter.h

@@ -67,8 +67,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionDistanceFilter.h

@@ -69,8 +69,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionErodeFilter.h

@@ -83,8 +83,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionFillHolesFilter.h

@@ -68,8 +68,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionGradientAnisotropicDiffusionFilter.h

@@ -74,8 +74,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionGradientMagnitudeFilter.h

@@ -70,8 +70,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionHistogramEqualizationFilter.h

@@ -72,8 +72,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionImplicitModel.h

@@ -70,12 +70,12 @@ CORE_ACTION(
   // Each action needs to be validated just before it is posted. This way we
   // enforce that every action that hits the main post_action signal will be
   // a valid action to execute.
-  virtual bool validate( Core::ActionContextHandle& context );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
 
   // RUN:
   // Each action needs to have this piece implemented. It spells out how the
   // action is run. It returns whether the action was successful or not.
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
   bool run_threshold( Core::ActionContextHandle& context );
 
 private:

src/Application/Filters/Actions/ActionIntensityCorrectionFilter.h

@@ -74,8 +74,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionInvert.h

@@ -64,8 +64,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionIterativeDilateErodeFilter.h

@@ -85,8 +85,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionIterativeDilateFilter.h

@@ -82,8 +82,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionIterativeErodeFilter.h

@@ -83,8 +83,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private:

src/Application/Filters/Actions/ActionMaskDataFilter.h

@@ -71,8 +71,8 @@ CORE_ACTION(
 
   // -- Functions that describe action --
 public:
-  virtual bool validate( Core::ActionContextHandle& context );
-  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result );
+  virtual bool validate( Core::ActionContextHandle& context ) override;
+  virtual bool run( Core::ActionContextHandle& context, Core::ActionResultHandle& result ) override;
 
   // -- Action parameters --
 private: