Merge remote branch 'origin/master' into fixRegistrationRandomSeed

Conflicts:
	Examples/itkantsRegistrationHelper.h

.travis.yml

@@ -22,8 +22,12 @@ addons:
       - cmake-data
 
 before_install:
+  - if [ "$TRAVIS_OS_NAME" == "linux" ];  then  CMAKE_INSTALLER=install-cmake.sh && curl -sSL https://cmake.org/files/v3.11/cmake-3.11.3-Linux-x86_64.sh -o ${CMAKE_INSTALLER} &&  chmod +x ${CMAKE_INSTALLER} && sudo ./${CMAKE_INSTALLER} --prefix=/usr/local --skip-license; fi
+  - alias cmake=/usr/local/bin/cmake
+  - export PATH=/usr/local/bin/cmake/bin:/usr/local/bin:${PATH}
   - if [ "$TRAVIS_OS_NAME" == "osx" ];  then echo "need cmake 3.2"; fi
   - if [ "$TRAVIS_OS_NAME" == "osx" ]; then brew update && brew install ccache; fi
+  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then brew upgrade cmake; fi
   - if [ "$TRAVIS_OS_NAME" == "osx" ]; then export PATH="/usr/local/opt/ccache/libexec:$PATH"; fi
   - mkdir antsbin
   - cd antsbin

ANTS.cmake

@@ -42,7 +42,7 @@ message(STATUS "Building ${PROJECT_NAME} version \"${${PROJECT_NAME}_VERSION}\""
 
 
 # Set up ITK
-find_package(ITK 4 REQUIRED)
+find_package(ITK 5 REQUIRED)
 include(${ITK_USE_FILE})
 
 

CTestCustom.cmake

@@ -303,7 +303,7 @@ set(CTEST_CUSTOM_WARNING_EXCEPTION
   ".*OpenCV.*"
   ".*VTK.*"
   ".*has no symbols."
-  "ITKv4"
+  "ITKv5"
   "SlicerExecutionModel"
   "SimpleITK"
 
@@ -352,7 +352,7 @@ set(CTEST_CUSTOM_ERROR_EXCEPTION
   ".*OpenCV.*"
   ".*VTK.*"
   ".*has no symbols."
-  "ITKv4"
+  "ITKv5"
   "SlicerExecutionModel"
   "SimpleITK"
 

Common.cmake

@@ -35,10 +35,10 @@ set(ANTS_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
 # endif("${isSystemDir}" STREQUAL "-1")
 #####################################################################################################
 
-set(USE_ITKv4 ON)
-set(ITK_VERSION_MAJOR 4 CACHE STRING "Choose the expected ITK major version to build ANTS only version 4 allowed.")
+set(USE_ITKv5 ON)
+set(ITK_VERSION_MAJOR 5 CACHE STRING "Choose the expected ITK major version to build ANTS only version 5 allowed.")
 # Set the possible values of ITK major version for cmake-gui
-set_property(CACHE ITK_VERSION_MAJOR PROPERTY STRINGS "4")
+set_property(CACHE ITK_VERSION_MAJOR PROPERTY STRINGS "5")
 set(expected_ITK_VERSION_MAJOR ${ITK_VERSION_MAJOR})
 if(${ITK_VERSION_MAJOR} VERSION_LESS ${expected_ITK_VERSION_MAJOR})
   # Note: Since ITKv3 doesn't include a ITKConfigVersion.cmake file, let's check the version
@@ -158,4 +158,3 @@ if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
   endif()
 endif()
-

Examples/CreateDTICohort.cxx

@@ -596,8 +596,7 @@ int CreateDTICohort( itk::ants::CommandLineParser *parser )
     duplicator->SetInputImage( inputAtlas );
     duplicator->Update();
 
-    typename TensorImageType::Pointer dti = duplicator->GetModifiableOutput();
-    dti->DisconnectPipeline();
+    typename TensorImageType::Pointer dti = duplicator->GetOutput();
 
     // If we are to apply intersubject variability, we calculate random
     // projection.

Examples/CreateTiledMosaic.cxx

@@ -950,7 +950,7 @@ int CreateMosaic( itk::ants::CommandLineParser *parser )
           duplicator->SetInputImage( outputRgbSlice2 );
           duplicator->Update();
 
-          compositeRgbSlice = duplicator->GetModifiableOutput();
+          compositeRgbSlice = duplicator->GetOutput();
           }
         compositeAlpha = currentAlpha;
         }

Examples/ImageMath_Templates.hxx

@@ -7869,7 +7869,12 @@ int PropagateLabelsThroughMask(int argc, char *argv[])
   std::string lname = tempname + std::string("_label") + extension;
   WriteImage<ImageType>(fastimage, kname.c_str() );
   WriteImage<ImageType>(outlabimage, outname.c_str() );
-  WriteImage<LabelImageType>(fastMarching->GetLabelImage(), lname.c_str() );
+
+// this nonsense fixes a type error
+  typedef itk::CastImageFilter<LabelImageType, LabelImageType>                 CastFilterType;
+  typename CastFilterType::Pointer castRegions = CastFilterType::New();
+  castRegions->SetInput( fastMarching->GetLabelImage() );
+  WriteImage<LabelImageType>( castRegions->GetOutput(), lname.c_str() );
   return 0;
 }
 
@@ -8141,7 +8146,13 @@ int itkPropagateLabelsThroughMask(int argc, char *argv[])
   std::string lname = tempname + std::string("_label") + extension;
   WriteImage<ImageType>(fastimage, kname.c_str() );
   WriteImage<ImageType>(outlabimage, outname.c_str() );
-  WriteImage<LabelImageType>(fastMarching->GetLabelImage(), lname.c_str() );
+
+  // this nonsense fixes a type error
+  typedef itk::CastImageFilter<LabelImageType, LabelImageType>                 CastFilterType;
+  typename CastFilterType::Pointer castRegions = CastFilterType::New();
+  castRegions->SetInput( fastMarching->GetLabelImage() );
+  WriteImage<LabelImageType>( castRegions->GetOutput(), lname.c_str() );
+
   return 0;
 }
 
@@ -8701,7 +8712,7 @@ int PoissonDiffusion( int argc, char *argv[])
   duplicator->SetInputImage( reader->GetOutput() );
   duplicator->Update();
 
-  typename ImageType::Pointer output = duplicator->GetModifiableOutput();
+  typename ImageType::Pointer output = duplicator->GetOutput();
   output->DisconnectPipeline();
 
   typedef itk::ImageFileReader<LabelImageType> LabelReaderType;
@@ -12750,7 +12761,7 @@ int InPaint(int argc, char *argv[])
   typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
   duplicator->SetInputImage( image1 );
   duplicator->Update();
-  typename ImageType::Pointer varimage = duplicator->GetModifiableOutput();
+  typename ImageType::Pointer varimage = duplicator->GetOutput();
   for ( unsigned int i = 0; i < sigma; i++ )
     {
     typedef itk::ConvolutionImageFilter< ImageType, ImageType > FilterType;
@@ -12991,7 +13002,7 @@ int Check3TissueLabeling( int argc, char *argv[] )
     duplicator->SetInputImage( labelImage );
     duplicator->Update();
 
-    typename LabelImageType::Pointer permutedLabelImage = duplicator->GetModifiableOutput();
+    typename LabelImageType::Pointer permutedLabelImage = duplicator->GetOutput();
 
     itk::ImageRegionIterator<LabelImageType> ItP( permutedLabelImage, permutedLabelImage->GetRequestedRegion() );
     for( ItP.GoToBegin(); !ItP.IsAtEnd(); ++ItP )
@@ -13065,7 +13076,7 @@ int Check3TissueLabeling( int argc, char *argv[] )
         duplicator->SetInputImage( labelImage );
         duplicator->Update();
 
-        typename LabelImageType::Pointer permutedLabelImage = duplicator->GetModifiableOutput();
+        typename LabelImageType::Pointer permutedLabelImage = duplicator->GetOutput();
 
         itk::ImageRegionIteratorWithIndex<LabelImageType> ItP( permutedLabelImage,
                                                                permutedLabelImage->GetRequestedRegion() );

Examples/LabelClustersUniquely.cxx

@@ -181,6 +181,11 @@ int LabelClustersUniquely( std::vector<std::string> args, std::ostream* /*out_st
       return LabelUniquely<3>(argc, argv + 1);
       }
       break;
+    case 4:
+      {
+      return LabelUniquely<4>(argc, argv + 1);
+      }
+      break;
     default:
       std::cout << "Unsupported dimension" << std::endl;
       return EXIT_FAILURE;

Examples/LabelGeometryMeasures.cxx

@@ -148,13 +148,13 @@ int LabelGeometryMeasures( int argc, char * argv[] )
       }
 
     std::vector<std::string>   rowHeaders;
-    std::ostringstream convert;// stream used for the conversion
     for( allLabelsIt = allLabels.begin(); allLabelsIt != allLabels.end(); allLabelsIt++ )
       {
       if( *allLabelsIt == 0 )
         {
         continue;
         }
+      std::ostringstream convert;// stream used for the conversion
       convert << *allLabelsIt;   // insert the textual representation of 'Number' in the characters in the stream
       rowHeaders.push_back( convert.str() ); // set 'Result' to the contents of the stream
       }

Examples/SmoothDisplacementField.cxx

@@ -59,7 +59,7 @@ int SmoothDisplacementField( int argc, char *argv[] )
     duplicator->SetInputImage( field );
     duplicator->Update();
 
-    smoothField = duplicator->GetModifiableOutput();
+    smoothField = duplicator->GetOutput();
 
     itk::TimeProbe timer;
     timer.Start();

Examples/antsAI.cxx

@@ -764,13 +764,15 @@ int antsAI( itk::ants::CommandLineParser *parser )
   itk::ants::CommandLineParser::OptionType::Pointer translationSearchGridOption = parser->GetOption( "translation-search-grid" );
   if( translationSearchGridOption && translationSearchGridOption->GetNumberOfFunctions() )
     {
-    translationSearchGrid = parser->ConvertVector<RealType>( translationSearchGridOption->GetFunction( 0 )->GetParameter( 0 ) );
+
+    translationSearchStepSize = parser->Convert<RealType>( translationSearchGridOption->GetFunction( 0 )->GetParameter( 0 ) );
+
     if( translationSearchGridOption->GetFunction( 0 )->GetNumberOfParameters() > 1 )
       {
-      translationSearchStepSize = parser->Convert<RealType>( translationSearchGridOption->GetFunction( 0 )->GetParameter( 1 ) );
+      translationSearchGrid = parser->ConvertVector<RealType>( translationSearchGridOption->GetFunction( 0 )->GetParameter( 1 ) );
       }
     }
-  
+
   itk::ants::CommandLineParser::OptionType::Pointer transformOption = parser->GetOption( "transform" );
   if( transformOption && transformOption->GetNumberOfFunctions() )
     {
@@ -1179,8 +1181,16 @@ int antsAI( itk::ants::CommandLineParser *parser )
 
     typedef typename itk::Statistics::MersenneTwisterRandomVariateGenerator RandomizerType;
     typename RandomizerType::Pointer randomizer = RandomizerType::New();
-    randomizer->SetSeed( 1234 );
 
+    char* antsRandomSeed = getenv( "ANTS_RANDOM_SEED" );
+    if ( antsRandomSeed != NULL )
+      {
+      randomizer->SetSeed( atoi( antsRandomSeed ) );
+      }
+    else
+      {
+      randomizer->SetSeed( 1234 );
+      }
     unsigned long index = 0;
 
     switch( samplingStrategy )
@@ -1295,7 +1305,7 @@ int antsAI( itk::ants::CommandLineParser *parser )
   multiStartOptimizer->SetMetric( imageMetric );
 
   unsigned int trialCounter = 0;
-  
+
   typename MultiStartOptimizerType::ParametersListType parametersList = multiStartOptimizer->GetParametersList();
   for( RealType angle1 = ( vnl_math::pi * -arcFraction ); angle1 <= ( vnl_math::pi * arcFraction + 0.000001 ); angle1 += searchFactor )
     {
@@ -1310,14 +1320,14 @@ int antsAI( itk::ants::CommandLineParser *parser )
           typename AffineTransformType::OutputVectorType searchTranslation;
           searchTranslation[0] = translation1;
           searchTranslation[1] = translation2;
-            
+
           affineSearchTransform->SetIdentity();
           affineSearchTransform->SetCenter( initialTransform->GetCenter() );
           affineSearchTransform->SetMatrix( initialTransform->GetMatrix() );
           affineSearchTransform->SetOffset( initialTransform->GetOffset() );
           affineSearchTransform->Translate( searchTranslation , 1 );
           affineSearchTransform->Rotate2D( angle1, 1 );
-          
+
           if( strcmp( transform.c_str(), "affine" ) == 0 )
             {
             affineSearchTransform->Scale( bestScale );
@@ -1329,7 +1339,7 @@ int antsAI( itk::ants::CommandLineParser *parser )
             rigidSearchTransform->SetCenter( initialTransform->GetCenter() );
             rigidSearchTransform->SetMatrix( affineSearchTransform->GetMatrix() );
             rigidSearchTransform->SetOffset( initialTransform->GetOffset() );
-            
+
             parametersList.push_back( rigidSearchTransform->GetParameters() );
             }
           else if( strcmp( transform.c_str(), "similarity" ) == 0 )
@@ -1339,9 +1349,9 @@ int antsAI( itk::ants::CommandLineParser *parser )
             similaritySearchTransform->SetMatrix( affineSearchTransform->GetMatrix() );
             similaritySearchTransform->SetOffset( initialTransform->GetOffset() );
             similaritySearchTransform->SetScale( bestScale );
-            
+
             similaritySearchTransform->SetScale( bestScale );
-            
+
             parametersList.push_back( similaritySearchTransform->GetParameters() );
             }
           trialCounter++;
@@ -1367,7 +1377,7 @@ int antsAI( itk::ants::CommandLineParser *parser )
                 searchTranslation[0] = translation1;
                 searchTranslation[1] = translation2;
                 searchTranslation[2] = translation3;
-                
+
                 affineSearchTransform->SetIdentity();
                 affineSearchTransform->SetCenter( initialTransform->GetCenter() );
                 affineSearchTransform->SetOffset( initialTransform->GetOffset() );
@@ -1376,7 +1386,7 @@ int antsAI( itk::ants::CommandLineParser *parser )
                 affineSearchTransform->Rotate3D( axis1, angle1, 1 );
                 affineSearchTransform->Rotate3D( axis2, angle2, 1 );
                 affineSearchTransform->Rotate3D( axis1, angle3, 1 );
-                
+
                 if( strcmp( transform.c_str(), "affine" ) == 0 )
                   {
                   affineSearchTransform->Scale( bestScale );
@@ -1398,7 +1408,7 @@ int antsAI( itk::ants::CommandLineParser *parser )
                   similaritySearchTransform->SetOffset( initialTransform->GetOffset() );
                   similaritySearchTransform->SetMatrix( affineSearchTransform->GetMatrix() );
                   similaritySearchTransform->SetScale( bestScale );
-                
+
                   parametersList.push_back( similaritySearchTransform->GetParameters() );
                   }
                 }
@@ -1409,17 +1419,17 @@ int antsAI( itk::ants::CommandLineParser *parser )
         }
       }
     }
-  
+
   if( verbose )
     {
     std::cout << "Starting optimizer with " << trialCounter << " starting points" << std::endl;
     }
-  
+
   multiStartOptimizer->SetParametersList( parametersList );
   multiStartOptimizer->SetLocalOptimizer( localOptimizer );
   multiStartOptimizer->StartOptimization();
 
-    
+
   /////////////////////////////////////////////////////////////////
   //
   //         Write the output after convergence
@@ -1572,7 +1582,7 @@ void InitializeCommandLineOptions( itk::ants::CommandLineParser *parser )
   option->SetDescription( description );
   parser->AddOption( option );
   }
- 
+
   {
   std::string description =
     std::string( "Number of iterations." );

Examples/antsDisplacementAndVelocityFieldRegistrationCommandIterationUpdate.h

@@ -269,8 +269,8 @@ class antsDisplacementAndVelocityFieldRegistrationCommandIterationUpdate : publi
                                                          GetInverseDisplacementField() );
       FixedInverseDisplacementDuplicator->Update();
 
-      myFixedToMiddleTransform->SetDisplacementField( FixedDisplacementDuplicator->GetModifiableOutput() );
-      myFixedToMiddleTransform->SetInverseDisplacementField( FixedInverseDisplacementDuplicator->GetModifiableOutput() );
+      myFixedToMiddleTransform->SetDisplacementField( FixedDisplacementDuplicator->GetOutput() );
+      myFixedToMiddleTransform->SetInverseDisplacementField( FixedInverseDisplacementDuplicator->GetOutput() );
 
       // copy MovingToMiddleTransform
       typename DisplacementFieldDuplicatorType::Pointer MovingDisplacementDuplicator =
@@ -288,8 +288,8 @@ class antsDisplacementAndVelocityFieldRegistrationCommandIterationUpdate : publi
                                                           GetInverseDisplacementField() );
       MovingInverseDisplacementDuplicator->Update();
 
-      myMovingToMiddleTransform->SetDisplacementField( MovingDisplacementDuplicator->GetModifiableOutput() );
-      myMovingToMiddleTransform->SetInverseDisplacementField( MovingInverseDisplacementDuplicator->GetModifiableOutput() );
+      myMovingToMiddleTransform->SetDisplacementField( MovingDisplacementDuplicator->GetOutput() );
+      myMovingToMiddleTransform->SetInverseDisplacementField( MovingInverseDisplacementDuplicator->GetOutput() );
 
       // Based on SyN Registration implementation, fixed composite and moving composite transforms are generated to
       // compute the metric value at each iteration.
@@ -413,8 +413,8 @@ class antsDisplacementAndVelocityFieldRegistrationCommandIterationUpdate : publi
     disInverseDuplicator->Update();
 
     typename DisplacementFieldTransformType::Pointer outputTransformReadyToUse = DisplacementFieldTransformType::New();
-    outputTransformReadyToUse->SetDisplacementField( disDuplicator->GetModifiableOutput() );
-    outputTransformReadyToUse->SetInverseDisplacementField( disInverseDuplicator->GetModifiableOutput() );
+    outputTransformReadyToUse->SetDisplacementField( disDuplicator->GetOutput() );
+    outputTransformReadyToUse->SetInverseDisplacementField( disInverseDuplicator->GetOutput() );
 
     // Now add this updated transform to the composite transform including the initial trnasform
     typedef typename TFilter::InitialTransformType InitialTransformType;