diff --git a/CMake/elxModules.cmake b/CMake/elxModules.cmake
index 5cc11cd58dd02129e7b9591c53a2f7221917bc4e..c3ea62004d852b823a794e25498d2548cd8df42f 100644
--- a/CMake/elxModules.cmake
+++ b/CMake/elxModules.cmake
@@ -16,7 +16,7 @@ macro( _elxmodule_enable MODULE_NAME )
_elxmodule_check_name( ${MODULE_NAME} )
if( NOT ${MODULE_NAME}_ENABLED )
- set( USE_${MODULE_NAME} ON )
+ set( ${MODULE_NAME}_ENABLED ON )
include( ${${MODULE_NAME}_FILE} )
@@ -29,6 +29,10 @@ macro( _elxmodule_enable MODULE_NAME )
list( APPEND SUPERELASTIX_LIBRARIES ${${MODULE_NAME}_LIBRARIES} )
endif()
+ if( ${MODULE_NAME}_TESTS )
+ list( APPEND SUPERELASTIX_TESTS ${${MODULE_NAME}_TESTS} )
+ endif()
+
# TODO: Add support for indicating dependencies between modules and recursive enabling of these dependencies
endif()
@@ -39,8 +43,9 @@ macro( _elxmodule_disable MODULE_NAME )
endmacro()
macro( _elxmodules_initialize )
- set( SUPERELASTIX_LIBRARIES )
set( SUPERELASTIX_MODULES )
+ set( SUPERELASTIX_LIBRARIES )
+ set( SUPERELASTIX_TESTS )
file( GLOB_RECURSE MODULE_FILES RELATIVE "${CMAKE_SOURCE_DIR}"
"${CMAKE_SOURCE_DIR}/Modules/*/Module*.cmake"
@@ -64,7 +69,7 @@ macro( _elxmodules_initialize )
set( ${MODULE_NAME}_LIBRARY_DIRS )
set( ${MODULE_NAME}_LIBRARIES )
- list(APPEND SUPERELASTIX_MODULES ${MODULE_NAME} )
+ list( APPEND SUPERELASTIX_MODULES ${MODULE_NAME} )
endforeach()
endmacro()
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5166656282880a9012c86bf9235fa7effefc3504..b3f6a08a5a13c8e8931ba9ebfef71a9f75730376 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -63,16 +63,6 @@ include("${CMAKE_CURRENT_SOURCE_DIR}/CMake/elxRequiredITKModules.cmake")
find_package( Boost REQUIRED )
include_directories( ${Boost_INCLUDE_DIRS} )
-# ---------------------------------------------------------------------
-# OpenMP Library
-# Required for ElastixComponent
-# gcc needs the appropriate flags to support OpenMP
-find_package(OpenMP)
-if (OPENMP_FOUND)
- set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
- set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-endif()
-
# ---------------------------------------------------------------------
# Build SuperElastix
diff --git a/Modules/Components/Elastix/ModuleElastix.cmake b/Modules/Components/Elastix/ModuleElastix.cmake
index 4d54550cce7922242e43706778cd745a47d29829..6fc59d6eae1e615162c042bcae519415ea0dc72d 100644
--- a/Modules/Components/Elastix/ModuleElastix.cmake
+++ b/Modules/Components/Elastix/ModuleElastix.cmake
@@ -1,28 +1,35 @@
# Module that exposes old elastix as an ITK filter
set( MODULE ModuleElastix )
-if( NOT EXISTS ${ELASTIX_USE_FILE} )
- set( ELASTIX_USE_FILE )
- message( FATAL_ERROR "${MODULE} could not find ELASTIX_USE_FILE. Use the SuperBuild or manually point the ELASTIX_USE_FILE CMake variable to the UseElastix.cmake file in the root of your elastix build tree." )
-endif()
-
-include( ${ELASTIX_USE_FILE} )
-
-# If OpenMP is supported by this machine, elastix will be compiled with
+# If OpenMP is supported, elastix will have beeen compiled with
# OpenMP flags, and we need to add them here as well
find_package( OpenMP )
-if (OPENMP_FOUND)
+if( OPENMP_FOUND )
set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}" )
set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}" )
endif()
+# Find UseElastix.cmake
+if( NOT EXISTS ${ELASTIX_USE_FILE} )
+ set( ELASTIX_USE_FILE ${ELASTIX_DIR}/UseElastix.cmake )
+endif()
+
+if( NOT EXISTS ${ELASTIX_USE_FILE} )
+ set( ELASTIX_DIR "" CACHE PATH "Path to elastix build folder" )
+ message(FATAL_ERROR "Could not find UseElastix.cmake. Point ELASTIX_DIR to folder containing UseElastix.cmake or use SuperBuild.")
+endif()
+
# Export include files
-set( ${MODULE}_INCLUDE_DIRS
- ${${MODULE}_SOURCE_DIR}/include
-)
+include( ${ELASTIX_USE_FILE} )
# Export libraries
set( ${MODULE}_LIBRARIES
elastix
transformix
)
+
+# Export tests
+set( ${MODULE}_TESTS
+ elxElastixFilterTest.cxx
+ elxTransformixFilterTest.cxx
+)
diff --git a/Modules/Components/Elastix/include/elxElastixFilter.h b/Modules/Components/Elastix/include/elxElastixFilter.h
deleted file mode 100644
index 5283a74c4f6f30542c0fa34250f82a01b07298a7..0000000000000000000000000000000000000000
--- a/Modules/Components/Elastix/include/elxElastixFilter.h
+++ /dev/null
@@ -1,156 +0,0 @@
-#ifndef ElastixFilter_h
-#define ElastixFilter_h
-
-// ITK
-#include "itkImageSource.h"
-
-// Elastix
-#include "elxElastixMain.h"
-
-// SuperElastix
-#include "elxMacro.h"
-#include "elxParameterObject.h"
-
-/**
- * Elastix registration library exposed as an ITK filter.
- *
- * We have to do some additional bookeeping on input images so that they can
- * be split into separate containers fixed and moving images at a later stage.
- * This is because ITK filters uses a single input container to drive the
- * pipeline while elastix use seperate containers for fixed and moving images.
- *
- */
-
-namespace selx {
-
-template< typename TFixedImage,
- typename TMovingImage >
-class ElastixFilter : public itk::ImageSource< TFixedImage >
-{
-public:
-
- elxNewMacro( ElastixFilter, itk::ImageSource );
-
- typedef elastix::ElastixMain ElastixMainType;
- typedef ElastixMainType::Pointer ElastixMainPointer;
- typedef std::vector< ElastixMainPointer > ElastixMainVectorType;
- typedef ElastixMainType::ObjectPointer ElastixMainObjectPointer;
-
- typedef ElastixMainType::FlatDirectionCosinesType FlatDirectionCosinesType;
-
- typedef ElastixMainType::ArgumentMapType ArgumentMapType;
- typedef ArgumentMapType::value_type ArgumentMapEntryType;
-
- typedef itk::ProcessObject::DataObjectIdentifierType DataObjectIdentifierType;
- typedef itk::ProcessObject::DataObjectPointerArraySizeType DataObjectPointerArraySizeType;
- typedef itk::ProcessObject::NameArray InputNameArrayType;
-
- typedef ElastixMainType::DataObjectContainerType DataObjectContainerType;
- typedef ElastixMainType::DataObjectContainerPointer DataObjectContainerPointer;
- typedef DataObjectContainerType::Iterator DataObjectContainerIterator;
-
- typedef ParameterObject::ParameterMapListType ParameterMapListType;
- typedef ParameterObject::ParameterMapType ParameterMapType;
- typedef ParameterObject::ParameterVectorType ParameterVectorType;
- typedef ParameterObject::Pointer ParameterObjectPointer;
- typedef ParameterObject::ConstPointer ParameterObjectConstPointer;
-
- typedef typename TFixedImage::Pointer FixedImagePointer;
- typedef typename TMovingImage::Pointer MovingImagePointer;
-
- void SetFixedImage( FixedImagePointer fixedImage );
- void SetFixedImage( DataObjectContainerPointer fixedImages );
- void AddFixedImage( FixedImagePointer fixedImage );
-
- void SetMovingImage( MovingImagePointer movingImages );
- void SetMovingImage( DataObjectContainerPointer movingImage );
- void AddMovingImage( MovingImagePointer movingImage );
-
- void SetFixedMask( FixedImagePointer fixedMask );
- void SetMovingMask( MovingImagePointer movingMask );
-
- void SetParameterObject( ParameterObjectPointer parameterObject );
- ParameterObjectPointer GetTransformParameters( void );
-
- itkSetMacro( FixedMeshFileName, std::string );
- itkGetConstMacro( FixedMeshFileName, std::string );
- void RemoveFixedMeshFileName( void ) { this->SetFixedMeshFileName( std::string() ); };
-
- itkSetMacro( MovingMeshFileName, std::string );
- itkGetConstMacro( MovingMeshFileName, std::string );
- void RemoveMovingMeshFileName( void ) { this->SetMovingMeshFileName( std::string() ); };
-
- itkSetMacro( OutputDirectory, std::string );
- itkGetConstMacro( OutputDirectory, std::string );
- void RemoveOutputDirectory() { this->m_OutputDirectory = std::string(); };
-
- void SetLogFileName( std::string logFileName )
- {
- this->m_LogFileName = logFileName;
- this->LogToFileOn();
- this->Modified();
- }
-
- itkGetConstMacro( LogFileName, std::string );
-
- void RemoveLogFileName( void ) {
- this->m_LogFileName = std::string();
- this->LogToFileOff();
- };
-
- itkSetMacro( LogToConsole, bool );
- itkGetConstMacro( LogToConsole, bool );
- itkBooleanMacro( LogToConsole );
-
- itkSetMacro( LogToFile, bool );
- itkGetConstMacro( LogToFile, bool );
- itkBooleanMacro( LogToFile );
-
- // TODO: Superclass GetOutput() does not trigger an Update() as it should
- TFixedImage* GetOutput()
- {
- this->Update();
- return static_cast< TFixedImage* >( itk::ProcessObject::GetPrimaryOutput() );
- }
-
-protected:
-
- void GenerateData( void ) ITK_OVERRIDE;
-
-private:
-
- ElastixFilter();
-
- void AddInputAutoIncrementName( DataObjectIdentifierType key, itk::DataObject* input );
-
- bool IsFixedImage( DataObjectIdentifierType key );
- bool IsMovingImage( DataObjectIdentifierType key );
-
- void RemoveFixedImages( void );
- void RemoveMovingImages( void );
-
- // TODO: When set to true, ReleaseDataFlag should also touch these containers
- DataObjectContainerPointer m_FixedImageContainer;
- DataObjectContainerPointer m_MovingImageContainer;
- DataObjectContainerPointer m_FixedMaskContainer;
- DataObjectContainerPointer m_MovingMaskContainer;
-
- std::string m_FixedMeshFileName;
- std::string m_MovingMeshFileName;
-
- std::string m_OutputDirectory;
- std::string m_LogFileName;
-
- bool m_LogToConsole;
- bool m_LogToFile;
-
-
-};
-
-} // namespace selx
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "elxElastixFilter.hxx"
-#endif
-
-#endif // ElastixFilter_h
\ No newline at end of file
diff --git a/Modules/Components/Elastix/include/elxElastixFilter.hxx b/Modules/Components/Elastix/include/elxElastixFilter.hxx
deleted file mode 100644
index c49adeab48bc9d148fa43abcaf45f023951b5af7..0000000000000000000000000000000000000000
--- a/Modules/Components/Elastix/include/elxElastixFilter.hxx
+++ /dev/null
@@ -1,428 +0,0 @@
-#ifndef ElastixFilter_hxx
-#define ElastixFilter_hxx
-
-namespace selx {
-
-template< typename TFixedImage, typename TMovingImage >
-ElastixFilter< TFixedImage, TMovingImage >
-::ElastixFilter( void )
-{
- this->AddRequiredInputName( "FixedImage" );
- this->AddRequiredInputName( "MovingImage" );
- this->AddRequiredInputName( "ParameterObject");
-
- this->SetPrimaryInputName( "FixedImage" );
- this->SetPrimaryOutputName( "ResultImage" );
-
- this->m_FixedImageContainer = DataObjectContainerType::New();
- this->m_MovingImageContainer = DataObjectContainerType::New();
-
- this->m_FixedMeshFileName = std::string();
- this->m_MovingMeshFileName = std::string();
-
- this->m_OutputDirectory = std::string();
- this->m_LogFileName = std::string();
-
- this->LogToConsoleOff();
- this->LogToFileOff();
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::GenerateData( void )
-{
- // Initialize variables here so they don't go out of scope between iterations of the main loop
- ElastixMainObjectPointer transform = 0;
- DataObjectContainerPointer fixedImageContainer = DataObjectContainerType::New();
- DataObjectContainerPointer movingImageContainer = DataObjectContainerType::New();
- DataObjectContainerPointer fixedMaskContainer = 0;
- DataObjectContainerPointer movingMaskContainer = 0;
- DataObjectContainerPointer resultImageContainer = 0;
- ParameterMapListType TransformParameterMapList;
- FlatDirectionCosinesType fixedImageOriginalDirection;
-
- // Split input images into two seperate fixed and moving image containers
- InputNameArrayType inputNames = this->GetInputNames();
- for( unsigned int i = 0; i < inputNames.size(); ++i )
- {
- if( this->IsFixedImage( inputNames[ i ] ) )
- {
- fixedImageContainer->push_back( this->GetInput( inputNames[ i ] ) );
- }
-
- if( this->IsMovingImage( inputNames[ i ] ) )
- {
- movingImageContainer->push_back( this->GetInput( inputNames[ i ] ) );
- }
- }
-
- // Fixed mask (optional)
- if( this->HasInput( "FixedMask" ) )
- {
- fixedMaskContainer = DataObjectContainerType::New();
- fixedMaskContainer->CreateElementAt( 0 ) = this->GetInput( "FixedMask" );
- }
-
- // Moving mask (optional)
- if( this->HasInput( "MovingMask" ) )
- {
- movingMaskContainer = DataObjectContainerType::New();
- movingMaskContainer->CreateElementAt( 0 ) = this->GetInput( "MovingMask" );
- }
-
- ArgumentMapType argumentMap;
- if( this->GetOutputDirectory().empty() ) {
- // There must be an "-out", this is checked later in the code
- argumentMap.insert( ArgumentMapEntryType( "-out", "output_path_not_set" ) );
- }
- else
- {
- argumentMap.insert( ArgumentMapEntryType( "-out", this->GetOutputDirectory() ) );
- }
-
- // Fixed mesh (optional)
- if( !this->m_FixedMeshFileName.empty() )
- {
- argumentMap.insert( ArgumentMapEntryType( "-fp", std::string( this->m_FixedMeshFileName ) ) );
- }
-
- // Moving mesh (optional)
- if( !this->m_MovingMeshFileName.empty() )
- {
- argumentMap.insert( ArgumentMapEntryType( "-mp", std::string( this->m_MovingMeshFileName ) ) );
- }
-
- // Setup xout
- std::string logFileName;
- if( this->GetLogToFile() )
- {
- if( this->GetOutputDirectory().empty() )
- {
- itkExceptionMacro( "LogToFileOn() requires an output directory to be specified. Use SetOutputDirectory().")
- }
-
- if( !itksys::SystemTools::FileExists( this->GetOutputDirectory() ) )
- {
- itkExceptionMacro( "Output directory \"" << this->GetOutputDirectory() << "\" does not exist." )
- }
-
- if( this->GetOutputDirectory().back() != '/' || this->GetOutputDirectory().back() != '\\' )
- {
- this->SetOutputDirectory( this->GetOutputDirectory() + "/" );
- }
-
- if( this->GetLogFileName().empty() )
- {
- logFileName = this->GetOutputDirectory() + "transformix.log";
- }
- else
- {
- logFileName = this->GetOutputDirectory() + this->GetLogFileName();
- }
- }
-
- if( elx::xoutSetup( logFileName.c_str(), this->GetLogToFile(), this->GetLogToConsole() ) )
- {
- itkExceptionMacro( "ERROR while setting up xout" );
- }
-
- // Get ParameterMap
- ParameterObjectConstPointer parameterObject = static_cast< const ParameterObject* >( this->GetInput( "ParameterObject" ) );
- ParameterMapListType parameterMapList = parameterObject->GetParameterMapList();
-
- // Run the (possibly multiple) registration(s)
- for( unsigned int i = 0; i < parameterMapList.size(); ++i )
- {
- // Create another instance of ElastixMain
- ElastixMainPointer elastix = ElastixMainType::New();
-
- // Set the current elastix-level
- elastix->SetElastixLevel( i );
- elastix->SetTotalNumberOfElastixLevels( parameterMapList.size() );
-
- // Set stuff we get from a previous registration
- elastix->SetInitialTransform( transform );
- elastix->SetFixedImageContainer( fixedImageContainer );
- elastix->SetMovingImageContainer( movingImageContainer );
- elastix->SetFixedMaskContainer( fixedMaskContainer );
- elastix->SetMovingMaskContainer( movingMaskContainer );
- elastix->SetResultImageContainer( resultImageContainer );
- elastix->SetOriginalFixedImageDirectionFlat( fixedImageOriginalDirection );
-
- // Start registration
- unsigned int isError = 0;
- try
- {
- unsigned int isError = elastix->Run( argumentMap, parameterMapList[ i ] );
- }
- catch( itk::ExceptionObject &e )
- {
- itkExceptionMacro( << "Errors occurred during registration: " << e.what() );
- }
-
- if( isError == -2 )
- {
- itkExceptionMacro( << "Errors occurred during registration: Output directory does not exist." );
- }
-
- if( isError != 0 )
- {
- itkExceptionMacro( << "Uncought errors occurred during registration." );
- }
-
- // Get the transform, the fixedImage and the movingImage
- // in order to put it in the next registration
- transform = elastix->GetFinalTransform();
- fixedImageContainer = elastix->GetFixedImageContainer();
- movingImageContainer = elastix->GetMovingImageContainer();
- fixedMaskContainer = elastix->GetFixedMaskContainer();
- movingMaskContainer = elastix->GetMovingMaskContainer();
- resultImageContainer = elastix->GetResultImageContainer();
- fixedImageOriginalDirection = elastix->GetOriginalFixedImageDirectionFlat();
-
- TransformParameterMapList.push_back( elastix->GetTransformParametersMap() );
-
- // Set initial transform to an index number instead of a parameter filename
- if( i > 0 )
- {
- std::stringstream index;
- index << ( i - 1 );
- TransformParameterMapList[ i ][ "InitialTransformParametersFileName" ][ 0 ] = index.str();
- }
- } // End loop over registrations
-
- // Save result image
- if( resultImageContainer.IsNotNull() && resultImageContainer->Size() > 0 )
- {
- this->GraftOutput( "ResultImage", resultImageContainer->ElementAt( 0 ) );
- }
-
- // Save parameter map
- ParameterObject::Pointer TransformParameters = ParameterObject::New();
- TransformParameters->SetParameterMapList( TransformParameterMapList );
- this->SetOutput( "TransformParameterObject", static_cast< itk::DataObject* >( TransformParameters ) );
-
- // Close the modules
- ElastixMainType::UnloadComponents();
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetParameterObject( ParameterObjectPointer parameterObject )
-{
- this->SetInput( "ParameterObject", static_cast< itk::DataObject* >( parameterObject ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-typename selx::ElastixFilter< TFixedImage, TMovingImage >::ParameterObjectPointer
-ElastixFilter< TFixedImage, TMovingImage >
-::GetTransformParameters( void )
-{
- // Make sure the transform parameters are up to date
- this->Update();
-
- return static_cast< ParameterObject* >( itk::ProcessObject::GetOutput( "TransformParameterObject" ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetFixedImage( FixedImagePointer fixedImage )
-{
- // Free references to fixed images that has already been set
- this->RemoveFixedImages();
-
- this->SetInput( "FixedImage", static_cast< itk::DataObject* >( fixedImage ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetFixedImage( DataObjectContainerPointer fixedImages )
-{
- if( fixedImages->Size() == 0 )
- {
- itkExceptionMacro( "Cannot set fixed images from empty container.")
- }
-
- // Free references to fixed images that has already been set
- this->RemoveFixedImages();
-
- // The first image will be used as the "FixedImage" required input.
- // The rest of the images will be appended to the input container
- // suffixed with _1, _2, etc. This allows us to read out only the
- // fixed images for elastix fixed image container at a later stage
- DataObjectContainerIterator fixedImageIterator = fixedImages->Begin();
- this->SetInput( "FixedImage", fixedImageIterator->Value() );
- ++fixedImageIterator;
-
- while( fixedImageIterator != fixedImages->End() )
- {
- this->AddInputAutoIncrementName( "FixedImage", fixedImageIterator->Value() );
- ++fixedImageIterator;
- }
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::AddFixedImage( FixedImagePointer fixedImage )
-{
- if( !this->HasInput( "FixedImage") )
- {
- this->SetFixedImage( fixedImage );
- }
- else
- {
- this->AddInputAutoIncrementName( "FixedImage", static_cast< itk::DataObject* >( fixedImage ) );
- }
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetMovingImage( MovingImagePointer movingImage )
-{
- // Free references to moving images that has already been set
- this->RemoveMovingImages();
-
- this->SetInput( "MovingImage", static_cast< itk::DataObject* >( movingImage ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetMovingImage( DataObjectContainerPointer movingImages )
-{
- if( movingImages->Size() == 0 )
- {
- itkExceptionMacro( "Cannot set moving images from empty container.")
- }
-
- // Free references to fixed images that has already been set
- this->RemoveMovingImages();
-
- // The first image will be used as the "MovingImage" required input.
- // The rest of the images will be appended to the input container
- // suffixed with _1, _2, etc. This allows us to read out only the
- // moving images for elastix moving image container at a later stage
- DataObjectContainerIterator movingImageIterator = movingImages->Begin();
- this->SetInput( "MovingImage", movingImageIterator->Value() );
- ++movingImageIterator;
-
- while( movingImageIterator != movingImages->End() )
- {
- this->AddInputAutoIncrementName( "MovingImage", static_cast< itk::DataObject* >( movingImageIterator->Value() ) );
- ++movingImageIterator;
- }
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::AddMovingImage( MovingImagePointer movingImage )
-{
- if( !this->HasInput( "MovingImage") )
- {
- this->SetMovingImage( movingImage );
- }
- else
- {
- this->AddInputAutoIncrementName( "MovingImage", static_cast< itk::DataObject* >( movingImage ) );
- }
-}
-
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetFixedMask( FixedImagePointer fixedMask )
-{
- this->SetInput( "FixedMask", static_cast< itk::DataObject* >( fixedMask ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetMovingMask( MovingImagePointer movingMask )
-{
- this->SetInput( "MovingMask", static_cast< itk::DataObject* >( movingMask ) );
-}
-
-/*
- * Adds a named input to the first null position in the input list
- * Expands the list memory if necessary
- */
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::AddInputAutoIncrementName( DataObjectIdentifierType key, itk::DataObject* input )
-{
- for ( unsigned idx = 0; idx < this->GetNumberOfIndexedInputs(); ++idx )
- {
- if ( !this->GetInput( idx ) )
- {
- key += this->MakeNameFromInputIndex( idx );
- this->SetInput( key, input );
- return;
- }
- }
-
- key += this->MakeNameFromInputIndex( this->GetNumberOfIndexedInputs() );
- this->SetInput( key, input );
- return;
-}
-
-template< typename TFixedImage, typename TMovingImage >
-bool
-ElastixFilter< TFixedImage, TMovingImage >
-::IsFixedImage( DataObjectIdentifierType key )
-{
- return std::strncmp( "FixedImage", key.c_str(), 10 ) == 0;
-}
-
-template< typename TFixedImage, typename TMovingImage >
-bool
-ElastixFilter< TFixedImage, TMovingImage >
-::IsMovingImage( DataObjectIdentifierType key )
-{
- return std::strncmp( "MovingImage", key.c_str(), 11 ) == 0;
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::RemoveFixedImages( void )
-{
- // Free references to fixed images that has already been set
- InputNameArrayType inputNames = this->GetInputNames();
- for( unsigned int i = 0; i < inputNames.size(); ++i )
- {
- if ( this->IsFixedImage( inputNames[ i ] ) )
- {
- this->RemoveInput( inputNames[ i ] );
- }
- }
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::RemoveMovingImages( void )
-{
- // Free references to fixed images that has already been set
- InputNameArrayType inputNames = this->GetInputNames();
- for( unsigned int i = 0; i < inputNames.size(); ++i )
- {
- if ( this->IsMovingImage( inputNames[ i ] ) )
- {
- this->RemoveInput( inputNames[ i ] );
- }
- }
-}
-
-} // namespace selx
-
-#endif // ElastixFilter_hxx
\ No newline at end of file
diff --git a/Modules/Components/Elastix/include/elxTransformixFilter.h b/Modules/Components/Elastix/include/elxTransformixFilter.h
deleted file mode 100644
index 563cd62bb7ea8ebef973cdcf9e6c1dd049ec058f..0000000000000000000000000000000000000000
--- a/Modules/Components/Elastix/include/elxTransformixFilter.h
+++ /dev/null
@@ -1,115 +0,0 @@
-#ifndef TransformixFilter_h
-#define TransformixFilter_h
-
-// ITK
-#include "itkImageSource.h"
-
-// Transformix
-#include "elxTransformixMain.h"
-
-// SuperElastix
-#include "elxMacro.h"
-#include "elxParameterObject.h"
-
-namespace selx {
-
-template< typename TInputImage >
-class TransformixFilter : public itk::ImageSource< TInputImage >
-{
-public:
-
- elxNewMacro( TransformixFilter, itk::ImageSource );
-
- typedef elastix::TransformixMain TransformixMainType;
- typedef TransformixMainType::Pointer TransformixMainPointer;
- typedef TransformixMainType::ArgumentMapType ArgumentMapType;
- typedef ArgumentMapType::value_type ArgumentMapEntryType;
-
- typedef itk::ProcessObject::DataObjectIdentifierType DataObjectIdentifierType;
- typedef TransformixMainType::DataObjectContainerType DataObjectContainerType;
- typedef TransformixMainType::DataObjectContainerPointer DataObjectContainerPointer;
-
- typedef ParameterObject::ParameterMapListType ParameterMapListType;
- typedef ParameterObject::ParameterMapType ParameterMapType;
- typedef ParameterObject::ParameterVectorType ParameterVectorType;
- typedef typename ParameterObject::Pointer ParameterObjectPointer;
- typedef typename ParameterObject::ConstPointer ParameterObjectConstPointer;
-
- typedef typename TInputImage::Pointer InputImagePointer;
-
- void SetInputImage( InputImagePointer inputImage );
-
- void SetTransformParameterObject( ParameterObjectPointer parameterObject );
- ParameterObjectPointer GetTransformParameters( void );
-
- itkSetMacro( ComputeSpatialJacobian, bool );
- itkGetConstMacro( ComputeSpatialJacobian, bool );
- itkBooleanMacro( ComputeSpatialJacobian );
-
- itkSetMacro( ComputeDeterminantOfSpatialJacobian, bool );
- itkGetConstMacro( ComputeDeterminantOfSpatialJacobian, bool );
- itkBooleanMacro( ComputeDeterminantOfSpatialJacobian );
-
- itkSetMacro( ComputeDeformationField, bool );
- itkGetConstMacro( ComputeDeformationField, bool );
- itkBooleanMacro( ComputeDeformationField );
-
- itkSetMacro( PointSetFileName, std::string );
- itkGetConstMacro( PointSetFileName, std::string );
- void RemovePointSetFileName() { this->m_PointSetFileName = std::string(); };
-
- itkSetMacro( OutputDirectory, std::string );
- itkGetConstMacro( OutputDirectory, std::string );
- void RemoveOutputDirectory() { this->m_OutputDirectory = std::string(); };
-
- void SetLogFileName( std::string logFileName )
- {
- this->m_LogFileName = logFileName;
- this->LogToFileOn();
- this->Modified();
- }
-
- itkGetConstMacro( LogFileName, std::string );
-
- void RemoveLogFileName( void ) {
- this->m_LogFileName = std::string();
- this->LogToFileOff();
- };
-
- itkSetMacro( LogToConsole, bool );
- itkGetConstMacro( LogToConsole, bool );
- itkBooleanMacro( LogToConsole );
-
- itkSetMacro( LogToFile, bool );
- itkGetConstMacro( LogToFile, bool );
- itkBooleanMacro( LogToFile );
-
-protected:
-
- void GenerateData( void ) ITK_OVERRIDE;
-
-private:
-
- TransformixFilter();
-
- bool m_ComputeSpatialJacobian;
- bool m_ComputeDeterminantOfSpatialJacobian;
- bool m_ComputeDeformationField;
- std::string m_PointSetFileName;
-
- std::string m_OutputDirectory;
- std::string m_LogFileName;
-
- bool m_LogToConsole;
- bool m_LogToFile;
-
-
-};
-
-} // namespace selx
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "elxTransformixFilter.hxx"
-#endif
-
-#endif // TransformixFilter_h
\ No newline at end of file
diff --git a/Modules/Components/Elastix/include/elxTransformixFilter.hxx b/Modules/Components/Elastix/include/elxTransformixFilter.hxx
deleted file mode 100644
index eb47dd85600340b822723d7930e0b15f657bd2e6..0000000000000000000000000000000000000000
--- a/Modules/Components/Elastix/include/elxTransformixFilter.hxx
+++ /dev/null
@@ -1,206 +0,0 @@
-#ifndef TransformixFilter_hxx
-#define TransformixFilter_hxx
-
-namespace selx {
-
-template< typename TInputImage >
-TransformixFilter< TInputImage >
-::TransformixFilter( void )
-{
- this->AddRequiredInputName( "TransformParameterObject");
-
- this->SetPrimaryInputName( "InputImage" );
- this->SetPrimaryOutputName( "ResultImage" );
-
- this->ComputeSpatialJacobianOff();
- this->ComputeDeterminantOfSpatialJacobianOff();
- this->ComputeDeformationFieldOff();
- this->m_PointSetFileName = std::string();
-
- this->m_OutputDirectory = std::string();
- this->m_LogFileName = std::string();
-
- this->LogToConsoleOff();
- this->LogToFileOff();
-}
-
-template< typename TInputImage >
-void
-TransformixFilter< TInputImage >
-::GenerateData( void )
-{
- // Assert that at least one output has been requested
- if( !this->HasInput( "InputImage" ) &&
- !this->GetComputeSpatialJacobian() &&
- !this->GetComputeDeterminantOfSpatialJacobian() &&
- !this->GetComputeDeformationField() &&
- this->GetPointSetFileName().empty() )
- {
- itkExceptionMacro( << "Expected at least one of SetInputImage(), ComputeSpatialJacobianOn(), "
- << "ComputeDeterminantOfSpatialJacobianOn(), SetPointSetFileName() or " );
- }
-
- // Check if an output directory is needed
- // TODO: Change behaviour upstream to have transformix save all output to its resultImageContainer
- if( ( this->GetComputeSpatialJacobian() ||
- this->GetComputeDeterminantOfSpatialJacobian() ||
- this->GetComputeDeformationField() ||
- !this->GetPointSetFileName().empty() ||
- this->GetLogToFile() ) &&
- ( this->GetOutputDirectory().empty() ) )
- {
- itkExceptionMacro( << "The requested outputs require an output directory to be specified."
- << "Use SetOutputDirectory()." )
- }
-
- if( ( this->GetComputeSpatialJacobian() ||
- this->GetComputeDeterminantOfSpatialJacobian() ||
- this->GetComputeDeformationField() ||
- !this->GetPointSetFileName().empty() ||
- this->GetLogToFile() ) &&
- !itksys::SystemTools::FileExists( this->GetOutputDirectory() ) )
- {
- itkExceptionMacro( "Output directory \"" << this->GetOutputDirectory() << "\" does not exist." )
- }
-
- // Transformix uses "-def" for path to point sets AND as flag for writing deformatin field
- // TODO: Change behaviour upstream: Split into seperate arguments
- if( this->GetComputeDeformationField() && !this->GetPointSetFileName().empty() )
- {
- itkExceptionMacro( << "For backwards compatibility, only one of ComputeDeformationFieldOn() or SetPointSetFileName() can be "
- << "active at any one time." )
- }
-
- // Setup argument map which transformix uses internally ito figure out what needs to be done
- ArgumentMapType argumentMap;
- if( this->GetOutputDirectory().empty() ) {
- // There must be an "-out", this is checked later in the code
- argumentMap.insert( ArgumentMapEntryType( "-out", "output_path_not_set" ) );
- }
- else
- {
- argumentMap.insert( ArgumentMapEntryType( "-out", this->GetOutputDirectory() ) );
- }
-
- if( this->GetComputeSpatialJacobian() )
- {
- argumentMap.insert( ArgumentMapEntryType( "-jacmat", "all" ) );
- }
-
- if( this->GetComputeDeterminantOfSpatialJacobian() )
- {
- argumentMap.insert( ArgumentMapEntryType( "-jac", "all" ) );
- }
-
- if( this->GetComputeDeformationField() )
- {
- argumentMap.insert( ArgumentMapEntryType( "-def" , "all" ) );
- }
-
- if( !this->GetPointSetFileName().empty() )
- {
- argumentMap.insert( ArgumentMapEntryType( "-def", this->GetPointSetFileName() ) );
- }
-
- // Setup xout
- std::string logFileName;
- if( this->GetLogToFile() )
- {
- if( this->GetOutputDirectory().empty() )
- {
- itkExceptionMacro( "LogToFileOn() requires an output directory to be specified. Use SetOutputDirectory().")
- }
-
- if( this->GetOutputDirectory().back() != '/' || this->GetOutputDirectory().back() != '\\' )
- {
- this->SetOutputDirectory( this->GetOutputDirectory() + "/" );
- }
-
- if( this->GetLogFileName().empty() )
- {
- logFileName = this->GetOutputDirectory() + "transformix.log";
- }
- else
- {
- logFileName = this->GetOutputDirectory() + this->GetLogFileName();
- }
- }
-
- if( elx::xoutSetup( logFileName.c_str(), this->GetLogToFile(), this->GetLogToConsole() ) )
- {
- itkExceptionMacro( "ERROR while setting up xout" );
- }
-
- // Instantiate transformix
- TransformixMainPointer transformix = TransformixMainType::New();
-
- // Setup image containers
- DataObjectContainerPointer inputImageContainer = 0;
- DataObjectContainerPointer resultImageContainer = 0;
-
- if( this->HasInput( "InputImage" ) ) {
- DataObjectContainerPointer inputImageContainer = DataObjectContainerType::New();
- inputImageContainer->CreateElementAt( 0 ) = this->GetInput("InputImage");
- transformix->SetInputImageContainer( inputImageContainer );
- transformix->SetResultImageContainer( resultImageContainer );
- }
-
- // Get ParameterMap
- ParameterObjectConstPointer transformParameterObject = static_cast< const ParameterObject* >( this->GetInput( "TransformParameterObject" ) );
- ParameterMapListType transformParameterMapList = transformParameterObject->GetParameterMapList();
-
- // Run transformix
- unsigned int isError = 0;
- try
- {
- isError = transformix->Run( argumentMap, transformParameterMapList );
- }
- catch( itk::ExceptionObject &e )
- {
- itkExceptionMacro( << "Errors occured during registration: " << e.what() );
- }
-
- if( isError != 0 )
- {
- itkExceptionMacro( << "Uncought errors occured during registration." );
- }
-
- // Save result image
- resultImageContainer = transformix->GetResultImageContainer();
- if( resultImageContainer.IsNotNull() && resultImageContainer->Size() > 0 )
- {
- std::cout << "Setting result image: " << resultImageContainer->ElementAt( 0 ) << std::endl;
- this->GraftOutput( "ResultImage", resultImageContainer->ElementAt( 0 ) );
- }
-
- // Clean up
- TransformixMainType::UnloadComponents();
-}
-
-template< typename TInputImage >
-void
-TransformixFilter< TInputImage >
-::SetInputImage( InputImagePointer inputImage )
-{
- this->SetInput( "InputImage", static_cast< itk::DataObject* >( inputImage ) );
-}
-
-template< typename TInputImage >
-void
-TransformixFilter< TInputImage >
-::SetTransformParameterObject( ParameterObjectPointer parameterObject )
-{
- this->SetInput( "TransformParameterObject", static_cast< itk::DataObject* >( parameterObject ) );
-}
-
-template< typename TInputImage >
-typename selx::TransformixFilter< TInputImage >::ParameterObjectPointer
-TransformixFilter< TInputImage >
-::GetTransformParameters( void )
-{
- return static_cast< ParameterObject* >( this->GetInput( "TransformParameterObject" ) );
-}
-
-} // namespace selx
-
-#endif // TransformixFilter_hxx
\ No newline at end of file
diff --git a/Modules/Core/ModuleCore.cmake b/Modules/Core/ModuleCore.cmake
index e2d6c9d582c0696e561d67440480705e20e673f9..f88315ebceaab6c18f8a919098e7e95d5b7b2952 100644
--- a/Modules/Core/ModuleCore.cmake
+++ b/Modules/Core/ModuleCore.cmake
@@ -12,13 +12,19 @@ file(GLOB ${MODULE}_HEADER_FILES "${${MODULE}_SOURCE_DIR}/*/include/*.*")
#@Kasper: file GLOB is generally disencouraged for source files (missing files are not detected and CMake doesn't know if the project has to be updated when due to a checkout extra source files are in the tree), but since this I think is not really an issue for header files...
#I read: CMake will figure out that they're headers; it won't try to build them. http://stackoverflow.com/questions/8316104/specify-how-cmake-creates-visual-studio-project
-
-
# Export libraries
set( ${MODULE}_LIBRARIES
${MODULE}
)
+# Export tests
+set( ${MODULE}_TESTS
+ elxBlueprintTest.cxx
+ elxComponentFactoryTest.cxx
+ elxComponentInterfaceTest.cxx
+ elxOverlordTest.cxx
+)
+
# Module source files
set( ${MODULE}_SOURCE_FILES
${${MODULE}_SOURCE_DIR}/Blueprints/src/elxBlueprint.cxx
@@ -28,7 +34,5 @@ set( ${MODULE}_SOURCE_FILES
)
# Compile library
-
add_library( ${MODULE} STATIC "${${MODULE}_SOURCE_FILES}" ${${MODULE}_HEADER_FILES} )
-
target_link_libraries( ${MODULE} ${ELASTIX_LIBRARIES} )
diff --git a/Modules/Core/ParameterObject/include/elxParameterObject.h b/Modules/Core/ParameterObject/include/elxParameterObject.h
deleted file mode 100644
index 9cb838f17127694bfdf312f8f9412578e57c40a8..0000000000000000000000000000000000000000
--- a/Modules/Core/ParameterObject/include/elxParameterObject.h
+++ /dev/null
@@ -1,54 +0,0 @@
-#ifndef ParameterObject_h
-#define ParameterObject_h
-
-#include "itkObjectFactory.h"
-#include "itkDataObject.h"
-
-#include "elxMacro.h"
-
-namespace selx {
-
-class ParameterObject : public itk::DataObject
-{
-public:
-
- elxNewMacro( ParameterObject, itk::DataObject );
-
- typedef std::string ParameterKeyType;
- typedef std::string ParameterValueType;
- typedef std::vector< ParameterKeyType > ParameterVectorType;
- typedef std::map< ParameterKeyType, ParameterVectorType > ParameterMapType;
- typedef std::vector< ParameterMapType > ParameterMapListType;
-
- void SetParameterMap( ParameterMapType parameterMap )
- {
- ParameterMapListType parameterMapList;
- parameterMapList.push_back( parameterMap );
- this->SetParameterMapList( parameterMapList );
- }
-
- void SetParameterMapList( ParameterMapListType parameterMapList )
- {
- this->m_ParameterMapList = parameterMapList;
- };
-
- ParameterMapListType& GetParameterMapList( void )
- {
- this->Modified();
- return this->m_ParameterMapList;
- };
-
- const ParameterMapListType& GetParameterMapList( void ) const
- {
- return this->m_ParameterMapList;
- };
-
-private:
-
- ParameterMapListType m_ParameterMapList;
-
-};
-
-} // namespace elx
-
-#endif // #define ParameterMap_h
\ No newline at end of file
diff --git a/SuperBuild/CMakeLists.txt b/SuperBuild/CMakeLists.txt
index 097964a8c4670be97270b4a53c00ffb1ed30f7b9..ce4016f2f4d46fd5a84eb46ec016fe54e159da0e 100644
--- a/SuperBuild/CMakeLists.txt
+++ b/SuperBuild/CMakeLists.txt
@@ -59,10 +59,6 @@ endif()
# ---------------------------------------------------------------------
# Build Old Elastix
-set( ELASTIX_VERSION_MAJOR "4" )
-set( ELASTIX_VERSION_MINOR "8" )
-set( ELASTIX_VERSION_STRING "${ELASTIX_VERSION_MAJOR}.${ELASTIX_VERSION_MINOR}" )
-
mark_as_advanced( SUPERELASTIX_BUILD_ELASTIX )
option( SUPERELASTIX_BUILD_ELASTIX "Build support for Elastix ${ELASTIX_VERSION_STRING}." ON )
if( SUPERELASTIX_BUILD_ELASTIX )
@@ -70,10 +66,8 @@ if( SUPERELASTIX_BUILD_ELASTIX )
option( USE_SYSTEM_ELASTIX "Use an installed version of Elastix." OFF )
if( USE_SYSTEM_ELASTIX )
if( NOT EXISTS ${ELASTIX_USE_FILE} )
- # Expose CMake variable to user
- set( ELASTIX_USE_FILE )
- # Stop the build
- message( FATAL_ERROR "Please point ELASTIX_USE_FILE to your systems UseElastix.cmake file." )
+ set( ELASTIX_USE_FILE "NOT_FOUND" CACHE PATH "Absolute path to UseElastix.cmake in the root of the elastix build tree." )
+ message( FATAL_ERROR "Could not find the ELASTIX_USE_FILE (${ELASTIX_USE_FILE}). Use the SuperBuild or manually point the ELASTIX_USE_FILE CMake variable to the UseElastix.cmake file in the root of your elastix build tree." )
endif()
else()
include( ExternalElastix )
diff --git a/SuperBuild/ExternalElastix.cmake b/SuperBuild/ExternalElastix.cmake
index 8a922598183686109bb27a7e9b283e18fb369d56..a9cbc55d080e780de9e17cfdee164d9b98587ba9 100644
--- a/SuperBuild/ExternalElastix.cmake
+++ b/SuperBuild/ExternalElastix.cmake
@@ -1,11 +1,11 @@
set( proj Elastix )
-set( ELASTIX_REPOSITORY https://github.com/mstaring/elastix.git )
-set( ELASTIX_TAG c35842cd0152d8fd2894e7c6706d2dd8396f0fed )
+set( ELASTIX_REPOSITORY https://svn.bigr.nl/elastix/trunkpublic/ )
+set( ELASTIX_REVISION 5186 )
ExternalProject_Add( ${proj}
- GIT_REPOSITORY ${ELASTIX_REPOSITORY}
- GIT_TAG ${ELASTIX_TAG}
+ SVN_REPOSITORY ${ELASTIX_REPOSITORY}
+ SVN_REVISION -r ${ELASTIX_REVISION}
UPDATE_COMMAND ""
SOURCE_DIR ${proj}
BINARY_DIR ${proj}-build
diff --git a/Testing/Unit/CMakeLists.txt b/Testing/Unit/CMakeLists.txt
index 93f35c58d08c650d6f90eb5f873d6cd501f35d8b..274f50751c3ee268fbd9b8e3cdc17afd160b043d 100644
--- a/Testing/Unit/CMakeLists.txt
+++ b/Testing/Unit/CMakeLists.txt
@@ -1,18 +1,9 @@
# ---------------------------------------------------------------------
-# To add a test to the build system, append it to the list below.
+# To add a test to the build system, append it to the module's list of
+# tests in the module's CMake file (e.g. "Modules/Core/ModuleCore.cmake").
# Any GoogleTests in these files are automatically added to CTest and
# the elastix dashboard.
-set( ElastixUnitTestFilenames
- elxBlueprintTest.cxx
- elxElastixFilterTest.cxx
- elxTransformixFilterTest.cxx
- elxComponentFactoryTest.cxx
- elxComponentInterfaceTest.cxx
- elxOverlordTest.cxx
- elxitkImageFilterTest.cxx
-)
-
# ---------------------------------------------------------------------
# Options
if( SUPERELASTIX_BUILD_LONG_TESTS )
@@ -37,6 +28,7 @@ endif()
# ---------------------------------------------------------------------
# Build test data manager
+
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/elxDataDirectories.h.in
${CMAKE_CURRENT_BINARY_DIR}/elxDataDirectories.h
@@ -52,13 +44,13 @@ list( APPEND TEST_LIBRARIES
# ---------------------------------------------------------------------
# Build tests
-message( STATUS "ITK_LIBRARIES: ${ITK_LIBRARIES}" )
-foreach( ElastixUnitTestFilename ${ElastixUnitTestFilenames} )
+
+foreach( SuperElastixUnitTestFilename ${SUPERELASTIX_TESTS} )
# Build tests executables
- string( REPLACE ".cxx" "" ElastixUnitTest ${ElastixUnitTestFilename} )
- add_executable( ${ElastixUnitTest} ${ElastixUnitTestFilename} )
- target_link_libraries( "${ElastixUnitTest}" ${SUPERELASTIX_LIBRARIES} ${ITK_LIBRARIES} ${TEST_LIBRARIES} )
+ string( REPLACE ".cxx" "" SuperElastixUnitTest ${SuperElastixUnitTestFilename} )
+ add_executable( ${SuperElastixUnitTest} ${SuperElastixUnitTestFilename} )
+ target_link_libraries( "${SuperElastixUnitTest}" ${SUPERELASTIX_LIBRARIES} ${ITK_LIBRARIES} ${TEST_LIBRARIES} )
# Add GoogleTest to CTest
- GTEST_ADD_TESTS( ${ElastixUnitTest} "--gtest_output=xml:${CMAKE_BINARY_DIR}/Testing/Unit/${ElastixUnitTest}.xml" ${ElastixUnitTestFilename} )
+ GTEST_ADD_TESTS( ${SuperElastixUnitTest} "--gtest_output=xml:${CMAKE_BINARY_DIR}/Testing/Unit/${SuperElastixUnitTest}.xml" ${SuperElastixUnitTestFilename} )
endforeach()
diff --git a/Testing/Unit/elxElastixFilterTest.cxx b/Testing/Unit/elxElastixFilterTest.cxx
index 50ab660e6cb6b9c8066f48950460032ba6a331d2..9c510eaa966b5516ea7bc470ce63d5eb08f1c44e 100644
--- a/Testing/Unit/elxElastixFilterTest.cxx
+++ b/Testing/Unit/elxElastixFilterTest.cxx
@@ -7,77 +7,17 @@
#include "elxDataManager.h"
#include "gtest/gtest.h"
-// TODO:
-// - In the following examples, why do we need to call update on both reader and elastixFilter
-// before using the writer? Should the call to update on the writer not be propagated upstream?
-// (See http://itk.org/Wiki/ITK/Examples/Segmentation/OtsuThresholdImageFilter which defeats the whole
-// purpose of having a pipeline, no?)
-// - Compare result images against baseline
-// - SetUp() runs before every test. Does GoogleTest have a function that is called once before tests are run?
+// TODO: Check that desired results are actually obtained, e.g. by comparing result
+// images against a baseline. Right now we only check that no errors are thrown.
-
-using namespace selx;
+using namespace elastix;
class ElastixFilterTest : public ::testing::Test
{
protected:
typedef DataManager DataManagerType;
-
- // Parameter typedefs
- typedef ParameterObject::ParameterVectorType ParameterVectorType;
- typedef ParameterObject::ParameterMapType ParameterMapType;
-
- ParameterMapType parameterMap;
- ParameterObject::Pointer nonRigidParameterObject;
- ParameterObject::Pointer nonRigidParameterObject3D;
- ParameterObject::Pointer groupwiseParameterObject;
- ParameterObject::ConstPointer transformParameterObject;
-
- virtual void SetUp()
- {
- // Nonrigid ParameterMap
- parameterMap = ParameterMapType();
-
- // Images
- parameterMap[ "FixedInternalImagePixelType" ] = ParameterVectorType( 1, "float" );
- parameterMap[ "FixedImageDimension" ] = ParameterVectorType( 1, "2" );
- parameterMap[ "MovingInternalImagePixelType" ] = ParameterVectorType( 1, "float" );
- parameterMap[ "MovingImageDimension" ] = ParameterVectorType( 1, "2" );
- parameterMap[ "ResultImagePixelType" ] = ParameterVectorType( 1, "float" );
-
- // Common components
- parameterMap[ "FixedImagePyramid" ] = ParameterVectorType( 1, "FixedSmoothingImagePyramid" );
- parameterMap[ "MovingImagePyramid" ] = ParameterVectorType( 1, "MovingSmoothingImagePyramid" );
- parameterMap[ "Interpolator"] = ParameterVectorType( 1, "LinearInterpolator");
- parameterMap[ "Optimizer" ] = ParameterVectorType( 1, "AdaptiveStochasticGradientDescent" );
- parameterMap[ "Resampler"] = ParameterVectorType( 1, "DefaultResampler" );
- parameterMap[ "ResampleInterpolator"] = ParameterVectorType( 1, "FinalLinearInterpolator" );
- parameterMap[ "FinalBSplineInterpolationOrder" ] = ParameterVectorType( 1, "2" );
- parameterMap[ "NumberOfResolutions" ] = ParameterVectorType( 1, "2" );
-
- // Image Sampler
- parameterMap[ "ImageSampler" ] = ParameterVectorType( 1, "RandomCoordinate" );
- parameterMap[ "NumberOfSpatialSamples"] = ParameterVectorType( 1, "2048" );
- parameterMap[ "CheckNumberOfSamples" ] = ParameterVectorType( 1, "true" );
- parameterMap[ "MaximumNumberOfSamplingAttempts" ] = ParameterVectorType( 1, "8" );
- parameterMap[ "NewSamplesEveryIteration" ] = ParameterVectorType( 1, "true");
-
- // Optimizer
- parameterMap[ "NumberOfSamplesForExactGradient" ] = ParameterVectorType( 1, "4096" );
- parameterMap[ "DefaultPixelValue" ] = ParameterVectorType( 1, "0" );
- parameterMap[ "AutomaticParameterEstimation" ] = ParameterVectorType( 1, "true" );
-
- // Output
- parameterMap[ "WriteResultImage" ] = ParameterVectorType( 1, "true" );
- parameterMap[ "ResultImageFormat" ] = ParameterVectorType( 1, "nii" );
-
- // Registration
- parameterMap[ "Registration" ] = ParameterVectorType( 1, "MultiResolutionRegistration" );
- parameterMap[ "Transform" ] = ParameterVectorType( 1, "EulerTransform" );
- parameterMap[ "Metric" ] = ParameterVectorType( 1, "AdvancedMattesMutualInformation" );
- parameterMap[ "MaximumNumberOfIterations" ] = ParameterVectorType( 1, "128" );
- }
+ typedef ParameterObject::ParameterValueVectorType ParameterValueVectorType;
};
TEST_F( ElastixFilterTest, Instantiation )
@@ -87,7 +27,8 @@ TEST_F( ElastixFilterTest, Instantiation )
EXPECT_NO_THROW( ElastixFilterType::Pointer elastixFilter = ElastixFilterType::New() );
}
-TEST_F( ElastixFilterTest, UpdateOnGetOutputEuler2D )
+
+TEST_F( ElastixFilterTest, DefaultParameterObject2D )
{
typedef itk::Image< float, 2 > ImageType;
typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
@@ -98,22 +39,44 @@ TEST_F( ElastixFilterTest, UpdateOnGetOutputEuler2D )
ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader->Update();
ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
- movingImageReader->Update();
- ParameterObject::Pointer eulerTransformParameterObject;
- EXPECT_NO_THROW( eulerTransformParameterObject = ParameterObject::New() );
- EXPECT_NO_THROW( eulerTransformParameterObject->SetParameterMap( parameterMap ) );
+ ElastixFilterType::Pointer elastixFilter;
+
+ EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
+ EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->Update() );
+}
+
+TEST_F( ElastixFilterTest, UpdateOnGetOutputEuler2D )
+{
+ ParameterObject::Pointer parameterObject;
+ EXPECT_NO_THROW( parameterObject = ParameterObject::New() );
+ EXPECT_NO_THROW( parameterObject->SetParameterMap( "rigid" ) );
+
+ typedef itk::Image< float, 2 > ImageType;
+ typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
+ typedef itk::ImageFileWriter< ImageType > ImageFileWriterType;
+ typedef ElastixFilter< ImageType, ImageType > ElastixFilterType;
+
+ DataManagerType::Pointer dataManager = DataManagerType::New();
+
+ ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
+ fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
+
+ ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
+ movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
ElastixFilterType::Pointer elastixFilter;
EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( eulerTransformParameterObject ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
// We try to write the image because simply calling GetOutput() will not result in an
// error (a pointer is still passed even if elastix has not run, although the pointee is empty)
@@ -125,6 +88,10 @@ TEST_F( ElastixFilterTest, UpdateOnGetOutputEuler2D )
TEST_F( ElastixFilterTest, UpdateOnGetTransformParametersEuler2D )
{
+ ParameterObject::Pointer parameterObject;
+ EXPECT_NO_THROW( parameterObject = ParameterObject::New() );
+ EXPECT_NO_THROW( parameterObject->SetParameterMap( "rigid" ) );
+
typedef itk::Image< float, 2 > ImageType;
typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
typedef itk::ImageFileWriter< ImageType > ImageFileWriterType;
@@ -134,15 +101,9 @@ TEST_F( ElastixFilterTest, UpdateOnGetTransformParametersEuler2D )
ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader->Update();
ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
- movingImageReader->Update();
-
- ParameterObject::Pointer eulerTransformParameterObject;
- EXPECT_NO_THROW( eulerTransformParameterObject = ParameterObject::New() );
- EXPECT_NO_THROW( eulerTransformParameterObject->SetParameterMap( parameterMap ) );
ElastixFilterType::Pointer elastixFilter;
ParameterObject::Pointer transformParameters;
@@ -151,13 +112,26 @@ TEST_F( ElastixFilterTest, UpdateOnGetTransformParametersEuler2D )
EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( eulerTransformParameterObject ) );
- EXPECT_NO_THROW( transformParameters = elastixFilter->GetTransformParameters() );
- EXPECT_TRUE( transformParameters->GetParameterMapList()[ 0 ].size() > 0 );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
+ EXPECT_NO_THROW( transformParameters = elastixFilter->GetTransformParameterObject() );
+ EXPECT_TRUE( transformParameters->GetParameterMap()[ 0 ].size() > 0 );
}
-TEST_F( ElastixFilterTest, AffineWithMultipleFixedAndMovingImages2D )
+TEST_F( ElastixFilterTest, AffineWithDataObjectContainerInterface2D )
{
+ // TODO: Internal logic to automatically broadcast metric, sampler,
+ // interpolator and pyramids to match the number of metrics. Can do
+ // it in such a way that we are guaranteed to not mess up user settings?
+ ParameterObject::Pointer parameterObject;
+ EXPECT_NO_THROW( parameterObject = ParameterObject::New() );
+ EXPECT_NO_THROW( parameterObject->SetParameterMap( "affine" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Registration" ] = ParameterValueVectorType( 1, "MultiMetricMultiResolutionRegistration" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Metric" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "Metric" ][ 0 ] ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "ImageSampler" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "ImageSampler" ][ 0 ] ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Interpolator" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "Interpolator" ][ 0 ] ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "FixedImagePyramid" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "FixedImagePyramid" ][ 0 ] ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "MovingImagePyramid" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "MovingImagePyramid" ][ 0 ] ) );
+
typedef itk::Image< float, 2 > ImageType;
typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
typedef itk::ImageFileWriter< ImageType > ImageFileWriterType;
@@ -169,35 +143,35 @@ TEST_F( ElastixFilterTest, AffineWithMultipleFixedAndMovingImages2D )
ImageFileReaderType::Pointer fixedImageReader0 = ImageFileReaderType::New();
fixedImageReader0->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader0->Update();
ImageFileReaderType::Pointer fixedImageReader1 = ImageFileReaderType::New();
fixedImageReader1->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader1->Update();
ImageFileReaderType::Pointer movingImageReader0 = ImageFileReaderType::New();
movingImageReader0->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17S12.png" ) );
- movingImageReader0->Update();
ImageFileReaderType::Pointer movingImageReader1 = ImageFileReaderType::New();
movingImageReader1->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17S12.png" ) );
- movingImageReader1->Update();
-
- ParameterMapType affineTransformParameterMap = parameterMap;
- affineTransformParameterMap[ "Transform" ] = ParameterVectorType( 1, "AffineTransform" );
- ParameterObject::Pointer affineTransformParameterObject;
- EXPECT_NO_THROW( affineTransformParameterObject = ParameterObject::New() );
- EXPECT_NO_THROW( affineTransformParameterObject->SetParameterMap( affineTransformParameterMap ) );
+ // We fill the first pair of fixed and moving images with zeros to be able
+ // to inspect if the subsequent pair is able to drive the registration
+ ImageType::Pointer fixedImage0 = fixedImageReader0->GetOutput();
+ fixedImage0->Update();
+ fixedImage0->DisconnectPipeline();
+ fixedImage0->FillBuffer( 0.0 );
+ ImageType::Pointer movingImage0 = movingImageReader0->GetOutput();
+ movingImage0->Update();
+ movingImage0->DisconnectPipeline();
+ movingImage0->FillBuffer( 0.0 );
DataObjectContainerPointer fixedImages;
EXPECT_NO_THROW( fixedImages = DataObjectContainerType::New() );
- EXPECT_NO_THROW( fixedImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( fixedImageReader0->GetOutput() ) );
+ EXPECT_NO_THROW( fixedImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( fixedImage0 ) );
EXPECT_NO_THROW( fixedImages->CreateElementAt( 1 ) = static_cast< itk::DataObject* >( fixedImageReader1->GetOutput() ) );
DataObjectContainerPointer movingImages;
EXPECT_NO_THROW( movingImages = DataObjectContainerType::New() );
- EXPECT_NO_THROW( movingImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( movingImageReader0->GetOutput() ) );
+ EXPECT_NO_THROW( movingImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( movingImage0 ) );
EXPECT_NO_THROW( movingImages->CreateElementAt( 1 ) = static_cast< itk::DataObject* >( movingImageReader1->GetOutput() ) );
ElastixFilterType::Pointer elastixFilter;
@@ -205,21 +179,92 @@ TEST_F( ElastixFilterTest, AffineWithMultipleFixedAndMovingImages2D )
EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImages ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImages ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( affineTransformParameterObject ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
- // TODO: This update should not be needed (see description above)
- EXPECT_NO_THROW( elastixFilter->Update() );
+ ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
+ EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "AffineWithDataObjectContainerInterface2D.nii" ) ) );
+ EXPECT_NO_THROW( writer->SetInput( elastixFilter->GetOutput() ) );
+ EXPECT_NO_THROW( writer->Update() );
+
+ ParameterObject::Pointer transformParameterObject;
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameterObject() );
+}
+
+TEST_F( ElastixFilterTest, AffineWithAddImagesInterface2D )
+{
+ // TODO: Internal logic to automatically broadcast metric, sampler,
+ // interpolator and pyramids to match the number of metrics. Can do
+ // it in such a way that we are guaranteed to not mess up user settings?
+ ParameterObject::Pointer parameterObject;
+ EXPECT_NO_THROW( parameterObject = ParameterObject::New() );
+ EXPECT_NO_THROW( parameterObject->SetParameterMap( "affine" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Registration" ] = ParameterValueVectorType( 1, "MultiMetricMultiResolutionRegistration" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Metric" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "Metric" ][ 0 ] ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "ImageSampler" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "ImageSampler" ][ 0 ] ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Interpolator" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "Interpolator" ][ 0 ] ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "FixedImagePyramid" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "FixedImagePyramid" ][ 0 ] ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "MovingImagePyramid" ] = ParameterValueVectorType( 2, parameterObject->GetParameterMap( 0 )[ "MovingImagePyramid" ][ 0 ] ) );
+
+ typedef itk::Image< float, 2 > ImageType;
+ typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
+ typedef itk::ImageFileWriter< ImageType > ImageFileWriterType;
+ typedef ElastixFilter< ImageType, ImageType > ElastixFilterType;
+ typedef ElastixFilterType::DataObjectContainerType DataObjectContainerType;
+ typedef ElastixFilterType::DataObjectContainerPointer DataObjectContainerPointer;
+
+ DataManagerType::Pointer dataManager = DataManagerType::New();
+
+ ImageFileReaderType::Pointer fixedImageReader0 = ImageFileReaderType::New();
+ fixedImageReader0->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
+
+ ImageFileReaderType::Pointer fixedImageReader1 = ImageFileReaderType::New();
+ fixedImageReader1->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
+
+ ImageFileReaderType::Pointer movingImageReader0 = ImageFileReaderType::New();
+ movingImageReader0->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17S12.png" ) );
+
+ ImageFileReaderType::Pointer movingImageReader1 = ImageFileReaderType::New();
+ movingImageReader1->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17S12.png" ) );
+
+ // We fill the first pair of fixed and moving images with zeros to be able
+ // to inspect that the subsequent pair is really driving the registration
+ ImageType::Pointer fixedImage0 = fixedImageReader0->GetOutput();
+ fixedImage0->Update();
+ fixedImage0->DisconnectPipeline();
+ fixedImage0->FillBuffer( 0.0 );
+ ImageType::Pointer movingImage0 = movingImageReader0->GetOutput();
+ movingImage0->Update();
+ movingImage0->DisconnectPipeline();
+ movingImage0->FillBuffer( 0.0 );
+
+ ElastixFilterType::Pointer elastixFilter;
+ EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
+ EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( elastixFilter->AddFixedImage( fixedImage0 ) );
+ EXPECT_NO_THROW( elastixFilter->AddFixedImage( fixedImageReader1->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->AddMovingImage( movingImage0 ) );
+ EXPECT_NO_THROW( elastixFilter->AddMovingImage( movingImageReader1->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
- EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "AffineWithMultipleFixedAndMovingImages2DResultImage.nii" ) ) );
+ EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "AffineWithAddImagesInterface2D.nii" ) ) );
EXPECT_NO_THROW( writer->SetInput( elastixFilter->GetOutput() ) );
EXPECT_NO_THROW( writer->Update() );
- EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
+ ParameterObject::Pointer transformParameterObject;
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameterObject() );
}
TEST_F( ElastixFilterTest, TranslationWithPointSets2D )
{
+ ParameterObject::Pointer parameterObject;
+ EXPECT_NO_THROW( parameterObject = ParameterObject::New() );
+ EXPECT_NO_THROW( parameterObject->SetParameterMap( "translation" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Registration" ] = ParameterValueVectorType( 1, "MultiMetricMultiResolutionRegistration" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Transform" ] = ParameterValueVectorType( 1, "TranslationTransform" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Metric" ].push_back( "CorrespondingPointsEuclideanDistanceMetric" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "Metric0Weight"] = ParameterValueVectorType( 1, "0.0" ) );
+
typedef itk::Image< float, 2 > ImageType;
typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
typedef itk::ImageFileWriter< ImageType > ImageFileWriterType;
@@ -228,56 +273,42 @@ TEST_F( ElastixFilterTest, TranslationWithPointSets2D )
DataManagerType::Pointer dataManager = DataManagerType::New();
// We generate the point sets manually
- std::ofstream fixedMeshFile;
- fixedMeshFile.open( dataManager->GetInputFile( "FixedMesh.pts" ));
- fixedMeshFile << "point\n";
- fixedMeshFile << "1\n";
- fixedMeshFile << "128.0 128.0\n";
- fixedMeshFile.close();
-
- std::ofstream movingMeshFile;
- movingMeshFile.open( dataManager->GetInputFile( "MovingMesh.pts" ));
- movingMeshFile << "point\n";
- movingMeshFile << "1\n";
- movingMeshFile << "115.0 111.0\n";
- movingMeshFile.close();
+ std::ofstream fixedPointSetFile;
+ fixedPointSetFile.open( dataManager->GetInputFile( "FixedPointSet.pts" ) );
+ fixedPointSetFile << "point\n";
+ fixedPointSetFile << "1\n";
+ fixedPointSetFile << "128.0 128.0\n";
+ fixedPointSetFile.close();
+
+ std::ofstream movingPointSetFile;
+ movingPointSetFile.open( dataManager->GetInputFile( "MovingPointSet.pts" ) );
+ movingPointSetFile << "point\n";
+ movingPointSetFile << "1\n";
+ movingPointSetFile << "115.0 111.0\n";
+ movingPointSetFile.close();
ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader->Update();
ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceShifted13x17y.png" ) );
- movingImageReader->Update();
-
- ParameterMapType correspondingPointsParameterMap = parameterMap;
- correspondingPointsParameterMap[ "Registration" ] = ParameterVectorType( 1, "MultiMetricMultiResolutionRegistration" );
- correspondingPointsParameterMap[ "Transform" ] = ParameterVectorType( 1, "TranslationTransform" );
- correspondingPointsParameterMap[ "Metric" ].push_back( "CorrespondingPointsEuclideanDistanceMetric" );
- correspondingPointsParameterMap[ "Metric0Weight"] = ParameterVectorType( 1, "0.0" );
-
- ParameterObject::Pointer correspondingPointsParameterObject;
- EXPECT_NO_THROW( correspondingPointsParameterObject = ParameterObject::New() );
- EXPECT_NO_THROW( correspondingPointsParameterObject->SetParameterMap( correspondingPointsParameterMap ) );
ElastixFilterType::Pointer elastixFilter;
EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetFixedMeshFileName( dataManager->GetInputFile( "FixedMesh.pts" ) ) );
+ EXPECT_NO_THROW( elastixFilter->SetFixedPointSetFileName( dataManager->GetInputFile( "FixedPointSet.pts" ) ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetMovingMeshFileName( dataManager->GetInputFile( "MovingMesh.pts" ) ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( correspondingPointsParameterObject ) );
-
- // TODO: This update should not be needed (see description above)
- EXPECT_NO_THROW( elastixFilter->Update() );
+ EXPECT_NO_THROW( elastixFilter->SetMovingPointSetFileName( dataManager->GetInputFile( "MovingPointSet.pts" ) ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
EXPECT_NO_THROW( writer->SetFileName( "TranslationWithPointSets2DResultImage.nii" ) );
EXPECT_NO_THROW( writer->SetInput( elastixFilter->GetOutput() ) );
EXPECT_NO_THROW( writer->Update() );
- EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
+ ParameterObject::Pointer transformParameterObject;
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameterObject() );
}
TEST_F( ElastixFilterTest, BSplineWithFixedMask2D )
@@ -291,20 +322,12 @@ TEST_F( ElastixFilterTest, BSplineWithFixedMask2D )
ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader->Update();
ImageFileReaderType::Pointer fixedMaskReader = ImageFileReaderType::New();
fixedMaskReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20Mask.png" ) );
- fixedMaskReader->Update();
ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
- movingImageReader->Update();
-
- ParameterMapType nonRigidParameterMap = parameterMap;
- nonRigidParameterMap[ "Transform" ] = ParameterVectorType( 1, "BSplineTransform" );
- ParameterObject::Pointer nonRigidParameterObject = ParameterObject::New();
- nonRigidParameterObject->SetParameterMap( nonRigidParameterMap );
ElastixFilterType::Pointer elastixFilter;
EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
@@ -312,23 +335,25 @@ TEST_F( ElastixFilterTest, BSplineWithFixedMask2D )
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
EXPECT_NO_THROW( elastixFilter->SetFixedMask( fixedMaskReader->GetOutput() ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( nonRigidParameterObject ) );
-
- // TODO: This update should not be needed (see description above)
- EXPECT_NO_THROW( elastixFilter->Update() );
ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "BSplineWithFixedMask2DResultImage.nii" ) ) );
EXPECT_NO_THROW( writer->SetInput( elastixFilter->GetOutput() ) );
EXPECT_NO_THROW( writer->Update() );
- EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
+ ParameterObject::Pointer transformParameterObject;
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameterObject() );
}
#ifdef SUPERELASTIX_BUILD_LONG_TESTS
TEST_F( ElastixFilterTest, BSpline3D )
{
+ ParameterObject::Pointer parameterObject;
+ EXPECT_NO_THROW( parameterObject = ParameterObject::New() );
+ EXPECT_NO_THROW( parameterObject->SetParameterMap( "nonrigid" ) );
+ EXPECT_NO_THROW( parameterObject->GetParameterMap( 0 )[ "MaximumNumberOfIterations" ] = ParameterValueVectorType( 1, "8" ) );
+
typedef itk::Image< float, 3 > ImageType;
typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
typedef itk::ImageFileWriter< ImageType > ImageFileWriterType;
@@ -338,92 +363,64 @@ TEST_F( ElastixFilterTest, BSpline3D )
ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
fixedImageReader->SetFileName( dataManager->GetInputFile( "OAS1_0001_MR1_mpr-1_anon.nrrd" ) );
- fixedImageReader->Update();
ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
movingImageReader->SetFileName( dataManager->GetInputFile( "OAS1_0002_MR1_mpr-1_anon.nrrd" ) );
- movingImageReader->Update();
-
- ParameterMapType nonRigidParameterMap3D = parameterMap;
- nonRigidParameterMap3D[ "FixedInternalImagePixelType" ] = ParameterVectorType( 1, "float" );
- nonRigidParameterMap3D[ "FixedImageDimension" ] = ParameterVectorType( 1, "3" );
- nonRigidParameterMap3D[ "MovingInternalImagePixelType" ] = ParameterVectorType( 1, "float" );
- nonRigidParameterMap3D[ "MovingImageDimension" ] = ParameterVectorType( 1, "3" );
- nonRigidParameterMap3D[ "ResultImagePixelType" ] = ParameterVectorType( 1, "float" );
- nonRigidParameterMap3D[ "Transform" ] = ParameterVectorType( 1, "BSplineTransform" );
- nonRigidParameterMap3D[ "MaximumNumberOfIterations" ] = ParameterVectorType( 1, "8" );
-
- ParameterObject::Pointer nonRigidParameterObject3D;
- EXPECT_NO_THROW( nonRigidParameterObject3D = ParameterObject::New() );
- EXPECT_NO_THROW( nonRigidParameterObject3D->SetParameterMap( nonRigidParameterMap3D ) );
ElastixFilterType::Pointer elastixFilter;
EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( nonRigidParameterObject3D ) );
-
- // TODO: This update should not be needed (see description above)
- EXPECT_NO_THROW( elastixFilter->Update() );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "BSpline3DResultImage.nii" ) ) );
EXPECT_NO_THROW( writer->SetInput( elastixFilter->GetOutput() ) );
EXPECT_NO_THROW( writer->Update() );
- EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
+ ParameterObject::Pointer transformParameterObject;
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameterObject() );
}
-// TODO: Find out why this segfaults
-//TEST_F( ElastixFilterTest, BSpline4D )
-//{
-// typedef itk::Image< float, 4 > ImageType;
-// typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
-// typedef itk::ImageFileWriter< ImageType > ImageFileWriterType;
-// typedef ElastixFilter< ImageType, ImageType > ElastixFilterType;
-//
-// DataManagerType::Pointer dataManager = DataManagerType::New();
-//
-// ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
-// fixedImageReader->SetFileName( dataManager->GetInputFile( "4D.nii.gz" ) );
-// fixedImageReader->Update();
-//
-// ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
-// movingImageReader->SetFileName( dataManager->GetInputFile( "4D.nii.gz" ) );
-// movingImageReader->Update();
-//
-// ParameterMapType groupwiseParameterMap = parameterMap;
-// groupwiseParameterMap[ "FixedInternalImagePixelType" ] = ParameterVectorType( 1, "float" );
-// groupwiseParameterMap[ "FixedImageDimension" ] = ParameterVectorType( 1, "4" );
-// groupwiseParameterMap[ "MovingInternalImagePixelType" ] = ParameterVectorType( 1, "float" );
-// groupwiseParameterMap[ "MovingImageDimension" ] = ParameterVectorType( 1, "4" );
-// groupwiseParameterMap[ "ResultImagePixelType" ] = ParameterVectorType( 1, "float" );
-// groupwiseParameterMap[ "Transform" ] = ParameterVectorType( 1, "BSplineStackTransform" );
-// groupwiseParameterMap[ "Metric" ] = ParameterVectorType( 1, "VarianceOverLastDimensionMetric" );
-// groupwiseParameterMap[ "MaximumNumberOfIterations" ] = ParameterVectorType( 1, "512" );
-// groupwiseParameterMap[ "Interpolator"] = ParameterVectorType( 1, "ReducedDimensionBSplineInterpolator" );
-// groupwiseParameterMap[ "ResampleInterpolator" ] = ParameterVectorType( 1, "FinalReducedDimensionBSplineInterpolator" );
-// groupwiseParameterMap[ "MaximumNumberOfIterations" ] = ParameterVectorType( 1, "8" );
-// ParameterObject::Pointer groupwiseParameterObject = ParameterObject::New();
-// groupwiseParameterObject->SetParameterMap( nonRigidParameterMap );
-//
-// ElastixFilterType::Pointer elastixFilter;
-// EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
-// EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
-// EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
-// EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
-// EXPECT_NO_THROW( elastixFilter->SetParameterObject( groupwiseParameterObject ) );
-//
-// // TODO: This update should not be needed (see description above)
-// EXPECT_NO_THROW( elastixFilter->Update() );
-//
-// ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
-// writer->SetFileName( dataManager->GetOutputFile( "BSpline4DResultImage.nii" ) );
-// writer->SetInput( elastixFilter->GetOutput() );
-// EXPECT_NO_THROW( writer->Update() );
-//
-// EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
-//}
+#include "itkCastImageFilter.h"
+TEST_F( ElastixFilterTest, BSpline4D )
+{
+ ParameterObject::Pointer parameterObject = ParameterObject::New();
+ parameterObject->SetParameterMap( "groupwise" );
+ parameterObject->GetParameterMap( 0 )[ "MaximumNumberOfIterations" ] = ParameterValueVectorType( 1, "4" );
+
+ typedef itk::Image< float, 4 > FloatImageType;
+ typedef itk::ImageFileReader< FloatImageType > ImageFileReaderType;
+
+ DataManagerType::Pointer dataManager = DataManagerType::New();
+
+ ImageFileReaderType::Pointer imageReader = ImageFileReaderType::New();
+ imageReader->SetFileName( dataManager->GetInputFile( "4D.nii.gz" ) );
+
+ // Elastix is not compiled with the combination of float and dim = 4 by default
+ typedef itk::Image< short, 4 > ShortImageType;
+ typedef itk::CastImageFilter< FloatImageType, ShortImageType > CastImageFilterType;
+ typedef itk::ImageFileWriter< ShortImageType > ImageFileWriterType;
+ typedef ElastixFilter< ShortImageType, ShortImageType > ElastixFilterType;
+
+ CastImageFilterType::Pointer castImageFilter = CastImageFilterType::New();
+ castImageFilter->SetInput( imageReader->GetOutput() );
+
+ ElastixFilterType::Pointer elastixFilter;
+ EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
+ EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( castImageFilter->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( castImageFilter->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
+
+ ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
+ EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "BSpline4DResultImage.nii" ) ) );
+ EXPECT_NO_THROW( writer->SetInput( elastixFilter->GetOutput() ) );
+ EXPECT_NO_THROW( writer->Update() );
+
+ ParameterObject::Pointer transformParameterObject;
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameterObject() );
+}
#endif // SUPERELASTIX_BUILD_LONG_TESTS
diff --git a/Testing/Unit/elxTransformixFilterTest.cxx b/Testing/Unit/elxTransformixFilterTest.cxx
index 3579796124c25d050a47ad7e6e385cbfe744d2e8..bb08242d778dd473c36bb7dd1039f9dbd40f0a92 100644
--- a/Testing/Unit/elxTransformixFilterTest.cxx
+++ b/Testing/Unit/elxTransformixFilterTest.cxx
@@ -8,7 +8,7 @@
#include "elxDataManager.h"
#include "gtest/gtest.h"
-using namespace selx;
+using namespace elastix;
class TransformixFilterTest : public ::testing::Test
{
@@ -16,8 +16,8 @@ protected:
typedef DataManager DataManagerType;
- typedef ParameterObject::ParameterVectorType ParameterVectorType;
- typedef ParameterObject::ParameterMapType ParameterMapType;
+ typedef ParameterObject::ParameterValueVectorType ParameterValueVectorType;
+ typedef ParameterObject::ParameterMapType ParameterMapType;
typedef itk::Image< float, 2 > ImageType;
typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
@@ -26,64 +26,6 @@ protected:
typedef TransformixFilter< ImageType > TransformixFilterType;
ElastixFilterType::Pointer elastixFilter;
- ParameterObject::Pointer eulerTransformParameterObject;
-
- virtual void SetUp()
- {
- // Nonrigid ParameterMap
- ParameterMapType parameterMap = ParameterMapType();
-
- // Images
- parameterMap[ "FixedInternalImagePixelType" ] = ParameterVectorType( 1, "float" );
- parameterMap[ "FixedImageDimension" ] = ParameterVectorType( 1, "2" );
- parameterMap[ "MovingInternalImagePixelType" ] = ParameterVectorType( 1, "float" );
- parameterMap[ "MovingImageDimension" ] = ParameterVectorType( 1, "2" );
- parameterMap[ "ResultImagePixelType" ] = ParameterVectorType( 1, "float" );
-
- // Common components
- parameterMap[ "FixedImagePyramid" ] = ParameterVectorType( 1, "FixedSmoothingImagePyramid" );
- parameterMap[ "MovingImagePyramid" ] = ParameterVectorType( 1, "MovingSmoothingImagePyramid" );
- parameterMap[ "Interpolator"] = ParameterVectorType( 1, "LinearInterpolator");
- parameterMap[ "Optimizer" ] = ParameterVectorType( 1, "AdaptiveStochasticGradientDescent" );
- parameterMap[ "Resampler"] = ParameterVectorType( 1, "DefaultResampler" );
- parameterMap[ "ResampleInterpolator"] = ParameterVectorType( 1, "FinalLinearInterpolator" );
- parameterMap[ "FinalBSplineInterpolationOrder" ] = ParameterVectorType( 1, "2" );
- parameterMap[ "NumberOfResolutions" ] = ParameterVectorType( 1, "2" );
-
- // Image Sampler
- parameterMap[ "ImageSampler" ] = ParameterVectorType( 1, "RandomCoordinate" );
- parameterMap[ "NumberOfSpatialSamples"] = ParameterVectorType( 1, "2048" );
- parameterMap[ "CheckNumberOfSamples" ] = ParameterVectorType( 1, "true" );
- parameterMap[ "MaximumNumberOfSamplingAttempts" ] = ParameterVectorType( 1, "8" );
- parameterMap[ "NewSamplesEveryIteration" ] = ParameterVectorType( 1, "true");
-
- // Optimizer
- parameterMap[ "NumberOfSamplesForExactGradient" ] = ParameterVectorType( 1, "4096" );
- parameterMap[ "DefaultPixelValue" ] = ParameterVectorType( 1, "0" );
- parameterMap[ "AutomaticParameterEstimation" ] = ParameterVectorType( 1, "true" );
-
- // Output
- parameterMap[ "WriteResultImage" ] = ParameterVectorType( 1, "true" );
- parameterMap[ "ResultImageFormat" ] = ParameterVectorType( 1, "nii" );
-
- // Registration
- parameterMap[ "Registration" ] = ParameterVectorType( 1, "MultiResolutionRegistration" );
- parameterMap[ "Transform" ] = ParameterVectorType( 1, "EulerTransform" );
- parameterMap[ "Metric" ] = ParameterVectorType( 1, "AdvancedMattesMutualInformation" );
- parameterMap[ "MaximumNumberOfIterations" ] = ParameterVectorType( 1, "128" );
-
- eulerTransformParameterObject = ParameterObject::New();
- eulerTransformParameterObject->SetParameterMap( parameterMap );
-
- // We generate the point sets manually
- DataManagerType::Pointer dataManager = DataManagerType::New();
- std::ofstream inputMeshFile;
- inputMeshFile.open( dataManager->GetInputFile( "InputMesh.pts" ));
- inputMeshFile << "point\n";
- inputMeshFile << "1\n";
- inputMeshFile << "115.0 111.0\n";
- inputMeshFile.close();
- }
};
TEST_F( TransformixFilterTest, Instantiation )
@@ -99,31 +41,29 @@ TEST_F( TransformixFilterTest, Euler2D )
ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader->Update();
ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
- movingImageReader->Update();
ElastixFilterType::Pointer elastixFilter;
EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( eulerTransformParameterObject ) );
+ elastixFilter->LogToConsoleOn();
TransformixFilterType::Pointer transformixFilter;
EXPECT_NO_THROW( transformixFilter = TransformixFilterType::New() );
EXPECT_NO_THROW( transformixFilter->SetInputImage( movingImageReader->GetOutput() ) );
EXPECT_NO_THROW( transformixFilter->SetOutputDirectory( dataManager->GetOutputDirectory() ) );
- EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameters() ) );
+ EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameterObject() ) );
EXPECT_NO_THROW( transformixFilter->LogToConsoleOn() );
EXPECT_NO_THROW( transformixFilter->LogToFileOn() );
EXPECT_NO_THROW( transformixFilter->Update() );
ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
- writer->SetFileName( dataManager->GetOutputFile( "Euler2DTransformixResultImage.nii" ) );
- writer->SetInput( transformixFilter->GetOutput() );
- writer->Update();
+ EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "Euler2DTransformixResultImage.nii" ) ) );
+ EXPECT_NO_THROW( writer->SetInput( transformixFilter->GetOutput() ) );
+ EXPECT_NO_THROW( writer->Update() );
}
@@ -133,67 +73,163 @@ TEST_F( TransformixFilterTest, UpdateOnGetOutput )
ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader->Update();
ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
- movingImageReader->Update();
ElastixFilterType::Pointer elastixFilter;
EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( eulerTransformParameterObject ) );
TransformixFilterType::Pointer transformixFilter;
EXPECT_NO_THROW( transformixFilter = TransformixFilterType::New() );
EXPECT_NO_THROW( transformixFilter->SetInputImage( movingImageReader->GetOutput() ) );
EXPECT_NO_THROW( transformixFilter->SetOutputDirectory( dataManager->GetOutputDirectory() ) );
- EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameters() ) );
+ EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameterObject() ) );
EXPECT_NO_THROW( transformixFilter->LogToConsoleOn() );
EXPECT_NO_THROW( transformixFilter->LogToFileOn() );
ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
- writer->SetFileName( dataManager->GetOutputFile( "Euler2DTransformixResultImage.nii" ) );
- writer->SetInput( transformixFilter->GetOutput() );
- writer->Update();
+ EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "Euler2DTransformixResultImage.nii" ) ) );
+ EXPECT_NO_THROW( writer->SetInput( transformixFilter->GetOutput() ) );
+ EXPECT_NO_THROW( writer->Update() );
}
-TEST_F( TransformixFilterTest, UpdateOnGetTransformParameters )
+TEST_F( TransformixFilterTest, UpdateOnGetTransformParameterObject )
{
DataManagerType::Pointer dataManager = DataManagerType::New();
ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
- fixedImageReader->Update();
ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
- movingImageReader->Update();
ElastixFilterType::Pointer elastixFilter;
EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
- EXPECT_NO_THROW( elastixFilter->SetParameterObject( eulerTransformParameterObject ) );
TransformixFilterType::Pointer transformixFilter;
EXPECT_NO_THROW( transformixFilter = TransformixFilterType::New() );
EXPECT_NO_THROW( transformixFilter->SetInputImage( movingImageReader->GetOutput() ) );
EXPECT_NO_THROW( transformixFilter->SetOutputDirectory( dataManager->GetOutputDirectory() ) );
- EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameters() ) );
+ EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameterObject() ) );
EXPECT_NO_THROW( transformixFilter->LogToConsoleOn() );
EXPECT_NO_THROW( transformixFilter->LogToFileOn() );
- EXPECT_NO_THROW( ParameterObject::Pointer transformParameters = transformixFilter->GetTransformParameters() );
+ EXPECT_NO_THROW( ParameterObject::Pointer transformParameters = transformixFilter->GetTransformParameterObject() );
ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
- writer->SetFileName( dataManager->GetOutputFile( "Euler2DTransformixResultImage.nii" ) );
- writer->SetInput( transformixFilter->GetOutput() );
- writer->Update();
+ EXPECT_NO_THROW( writer->SetFileName( dataManager->GetOutputFile( "Euler2DTransformixResultImage.nii" ) ) );
+ EXPECT_NO_THROW( writer->SetInput( transformixFilter->GetOutput() ) );
+ EXPECT_NO_THROW( writer->Update() );
}
-// TODO: Write tests for
-// EXPECT_NO_THROW( transformixFilter->ComputeSpatialJacobianOn() );
-// EXPECT_NO_THROW( transformixFilter->ComputeDeterminantOfSpatialJacobianOn() );
-// EXPECT_NO_THROW( transformixFilter->ComputeDeformationFieldOn() );
-// EXPECT_NO_THROW( transformixFilter->SetPointSetFileName( dataManager->GetInputFile( "InputMesh.pts" ) ) );
+TEST_F( TransformixFilterTest, ComputeSpatialJacobian )
+{
+ DataManagerType::Pointer dataManager = DataManagerType::New();
+
+ ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
+ fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
+
+ ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
+ movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
+
+ ElastixFilterType::Pointer elastixFilter;
+ EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
+
+ TransformixFilterType::Pointer transformixFilter;
+ EXPECT_NO_THROW( transformixFilter = TransformixFilterType::New() );
+ EXPECT_NO_THROW( transformixFilter->SetOutputDirectory( dataManager->GetOutputDirectory() ) );
+ EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameterObject() ) );
+ EXPECT_NO_THROW( transformixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( transformixFilter->LogToFileOn() );
+ EXPECT_NO_THROW( transformixFilter->ComputeSpatialJacobianOn() );
+ transformixFilter->Update();
+}
+
+TEST_F( TransformixFilterTest, ComputeDeterminantOfSpatialJacobian )
+{
+ DataManagerType::Pointer dataManager = DataManagerType::New();
+
+ ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
+ fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
+
+ ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
+ movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
+
+ ElastixFilterType::Pointer elastixFilter;
+ EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
+
+ TransformixFilterType::Pointer transformixFilter;
+ EXPECT_NO_THROW( transformixFilter = TransformixFilterType::New() );
+ EXPECT_NO_THROW( transformixFilter->SetOutputDirectory( dataManager->GetOutputDirectory() ) );
+ EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameterObject() ) );
+ EXPECT_NO_THROW( transformixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( transformixFilter->LogToFileOn() );
+ EXPECT_NO_THROW( transformixFilter->ComputeDeterminantOfSpatialJacobianOn() );
+ EXPECT_NO_THROW( transformixFilter->Update() );
+}
+
+TEST_F( TransformixFilterTest, ComputeDeformationField )
+{
+ DataManagerType::Pointer dataManager = DataManagerType::New();
+
+ ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
+ fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
+
+ ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
+ movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
+
+ ElastixFilterType::Pointer elastixFilter;
+ EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
+
+ TransformixFilterType::Pointer transformixFilter;
+ EXPECT_NO_THROW( transformixFilter = TransformixFilterType::New() );
+ EXPECT_NO_THROW( transformixFilter->SetOutputDirectory( dataManager->GetOutputDirectory() ) );
+ EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameterObject() ) );
+ EXPECT_NO_THROW( transformixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( transformixFilter->LogToFileOn() );
+ EXPECT_NO_THROW( transformixFilter->ComputeDeformationFieldOn() );
+ EXPECT_NO_THROW( transformixFilter->Update() );
+}
+
+TEST_F( TransformixFilterTest, TransformPointSet )
+{
+ DataManagerType::Pointer dataManager = DataManagerType::New();
+
+ ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
+ fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
+
+ ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
+ movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
+
+ // We generate point set manually
+ std::ofstream fixedMeshFile;
+ fixedMeshFile.open( dataManager->GetInputFile( "InputPoints.pts" ));
+ fixedMeshFile << "point\n";
+ fixedMeshFile << "1\n";
+ fixedMeshFile << "128.0 128.0\n";
+ fixedMeshFile.close();
+
+ ElastixFilterType::Pointer elastixFilter;
+ EXPECT_NO_THROW( elastixFilter = ElastixFilterType::New() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImageReader->GetOutput() ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImageReader->GetOutput() ) );
+
+ TransformixFilterType::Pointer transformixFilter;
+ EXPECT_NO_THROW( transformixFilter = TransformixFilterType::New() );
+ EXPECT_NO_THROW( transformixFilter->SetOutputDirectory( dataManager->GetOutputDirectory() ) );
+ EXPECT_NO_THROW( transformixFilter->SetTransformParameterObject( elastixFilter->GetTransformParameterObject() ) );
+ EXPECT_NO_THROW( transformixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( transformixFilter->LogToFileOn() );
+ EXPECT_NO_THROW( transformixFilter->SetInputPointSetFileName( dataManager->GetInputFile( "InputPoints.pts" ) ) );
+ EXPECT_NO_THROW( transformixFilter->Update() );
+}
\ No newline at end of file