Merge branch 'master' of https://github.com/stnava/ANTs

ANTS.cmake

@@ -34,7 +34,7 @@ endif()
 
 option( ${PROJECT_NAME}_BUILD_DISTRIBUTE "Remove '-g#####' from version. ( for official distribution only )" OFF )
 mark_as_advanced( ${PROJECT_NAME}_BUILD_DISTRIBUTE )
-if( NOT ${PROJECT_NAME}_BUILD_DISTRIBUTE )
+if( NOT ${PROJECT_NAME}_BUILD_DISTRIBUTE AND NOT ${PROJECT_NAME}_VERSION_HASH STREQUAL "GITDIR-NOTFOUND")
   set(${PROJECT_NAME}_VERSION "${${PROJECT_NAME}_VERSION}-g${${PROJECT_NAME}_VERSION_HASH}")
 endif()
 

CMake/ProjectSourceVersion.cmake

@@ -32,10 +32,8 @@ include(GetGitRevisionDescription)
 get_git_head_revision(GIT_REFVAR _GIT_VERSION_HASH)
 
 # if there is not git directory we should be in a distributed package
-# which should contain this additional cmake file with the
-# _GIT_VERSION variables
+# we will use version provided in Version.cmake
 if(_GIT_VERSION_HASH STREQUAL "GITDIR-NOTFOUND")
-  include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/ProjectSourceVersionVars.cmake" )
   return()
 endif()
 

Examples/antsJointFusion.cxx

@@ -114,7 +114,6 @@ int antsJointFusion( itk::ants::CommandLineParser *parser )
   typename FusionFilterType::Pointer fusionFilter = FusionFilterType::New();
   typedef typename LabelImageType::PixelType                   LabelType;
 
-
   // Get the alpha and beta parameters
 
   RealType alpha = 0.1;
@@ -137,45 +136,48 @@ int antsJointFusion( itk::ants::CommandLineParser *parser )
   // Get the search and patch radii
   typename OptionType::Pointer searchRadiusOption = parser->GetOption( "search-radius" );
 
-  // try reading the search radius as an image first.
-  try
-    {
-    std::string searchRadiusString = searchRadiusOption->GetFunction( 0 )->GetName();
-    typedef typename FusionFilterType::RadiusImageType  RadiusImageType;
-    typename RadiusImageType::Pointer searchRadiusImage;
-    ReadImage<RadiusImageType>( searchRadiusImage, searchRadiusString.c_str() );
-
-    fusionFilter->SetSearchNeighborhoodRadiusImage( searchRadiusImage );
-    }
-  catch( ... )
+  if( searchRadiusOption && searchRadiusOption->GetNumberOfFunctions() )
     {
-    std::vector<unsigned int> searchRadius;
-    searchRadius.push_back( 3 );
-    if( searchRadiusOption && searchRadiusOption->GetNumberOfFunctions() )
+    // try reading the search radius as an image first.
+    try
       {
-      searchRadius = parser->ConvertVector<unsigned int>( searchRadiusOption->GetFunction( 0 )->GetName() );
+      std::string searchRadiusString = searchRadiusOption->GetFunction( 0 )->GetName();
+      typedef typename FusionFilterType::RadiusImageType  RadiusImageType;
+      typename RadiusImageType::Pointer searchRadiusImage;
+      ReadImage<RadiusImageType>( searchRadiusImage, searchRadiusString.c_str() );
+
+      fusionFilter->SetSearchNeighborhoodRadiusImage( searchRadiusImage );
       }
-    if( searchRadius.size() == 1 )
+    catch( ... )
       {
-      for( unsigned int d = 1; d < ImageDimension; d++ )
+      std::vector<unsigned int> searchRadius;
+      searchRadius.push_back( 3 );
+      if( searchRadiusOption && searchRadiusOption->GetNumberOfFunctions() )
         {
-        searchRadius.push_back( searchRadius[0] );
+        searchRadius = parser->ConvertVector<unsigned int>( searchRadiusOption->GetFunction( 0 )->GetName() );
         }
-      }
-    if( searchRadius.size() != ImageDimension )
-      {
-      if( verbose )
+      if( searchRadius.size() == 1 )
         {
-        std::cerr << "Search radius specified incorrectly.  Please see usage options." << std::endl;
+        for( unsigned int d = 1; d < ImageDimension; d++ )
+          {
+          searchRadius.push_back( searchRadius[0] );
+          }
         }
-      return EXIT_FAILURE;
-      }
-    typename FusionFilterType::NeighborhoodRadiusType searchNeighborhoodRadius;
-    for( unsigned int d = 0; d < ImageDimension; d++ )
-      {
-      searchNeighborhoodRadius[d] = searchRadius[d];
+      if( searchRadius.size() != ImageDimension )
+        {
+        if( verbose )
+          {
+          std::cerr << "Search radius specified incorrectly.  Please see usage options." << std::endl;
+          }
+        return EXIT_FAILURE;
+        }
+      typename FusionFilterType::NeighborhoodRadiusType searchNeighborhoodRadius;
+      for( unsigned int d = 0; d < ImageDimension; d++ )
+        {
+        searchNeighborhoodRadius[d] = searchRadius[d];
+        }
+      fusionFilter->SetSearchNeighborhoodRadius( searchNeighborhoodRadius );
       }
-    fusionFilter->SetSearchNeighborhoodRadius( searchNeighborhoodRadius );
     }
 
   std::vector<unsigned int> patchRadius;

ExternalApplications/MALF/CMakeLists.txt

@@ -10,15 +10,15 @@ project(PICSL_MALF)
 include_directories(${CMAKE_CURRENT_BINARY_DIR})
 
 add_executable(jointfusion ./JointFusion/LabelFusion.cxx)
-add_executable(sa ./CorrectiveLearning/segAdapter.cxx)
+add_executable(adaBoostSegmentationRefinement ./CorrectiveLearning/segAdapter.cxx)
 add_executable(bl ./CorrectiveLearning/BiasLearn.cxx)
 
 target_link_libraries(jointfusion antsUtilities ${ITK_LIBRARIES} )
-target_link_libraries(sa ${ITK_LIBRARIES} )
+target_link_libraries(adaBoostSegmentationRefinement ${ITK_LIBRARIES} )
 target_link_libraries(bl ${ITK_LIBRARIES} )
 
 
-install(TARGETS jointfusion sa bl
+install(TARGETS jointfusion adaBoostSegmentationRefinement bl
         RUNTIME DESTINATION bin
         LIBRARY DESTINATION lib
         ARCHIVE DESTINATION lib)

ExternalApplications/MALF/README.md

@@ -40,9 +40,9 @@ make
 to complie and build the executable files. Our program uses ITK's I/O functions to handle image input
 and output. Hence, it requries prebuilt ITK. The following three executable files will be built,
 
-jointfusion : joint label fusion
-bl          : learning classifiers for correcting systematic errors
-sa          : apply the learned classifiers to correct systematic segmentation errors on testing images
+jointfusion                    : joint label fusion
+bl                             : learning classifiers for correcting systematic errors
+adaBoostSegmentationRefinement : apply the learned classifiers to correct systematic segmentation errors on testing images
 
 Type each command to see details on how to use them.