From 17a138cbcc4595033e73e63d05c70546d7362834 Mon Sep 17 00:00:00 2001
From: Kasper Marstal <kaspermarstal@gmail.com>
Date: Tue, 5 Jan 2016 20:00:27 +0100
Subject: [PATCH] ENH: Move ElastixFilter and TransformixFilter upstream
---
.../Components/Elastix/ModuleElastix.cmake | 22 +-
.../Elastix/include/elxElastixFilter.h | 251 --------
.../Elastix/include/elxElastixFilter.hxx | 542 ------------------
.../Elastix/include/elxTransformixFilter.h | 125 ----
.../Elastix/include/elxTransformixFilter.hxx | 220 -------
Modules/Core/ModuleCore.cmake | 7 +-
.../include/elxParameterObject.h | 63 --
.../src/elxParameterObject.cxx | 274 ---------
8 files changed, 13 insertions(+), 1491 deletions(-)
delete mode 100644 Modules/Components/Elastix/include/elxElastixFilter.h
delete mode 100644 Modules/Components/Elastix/include/elxElastixFilter.hxx
delete mode 100644 Modules/Components/Elastix/include/elxTransformixFilter.h
delete mode 100644 Modules/Components/Elastix/include/elxTransformixFilter.hxx
delete mode 100644 Modules/Core/ParameterObject/include/elxParameterObject.h
delete mode 100644 Modules/Core/ParameterObject/src/elxParameterObject.cxx
diff --git a/Modules/Components/Elastix/ModuleElastix.cmake b/Modules/Components/Elastix/ModuleElastix.cmake
index 72927257..4a999b93 100644
--- a/Modules/Components/Elastix/ModuleElastix.cmake
+++ b/Modules/Components/Elastix/ModuleElastix.cmake
@@ -1,13 +1,6 @@
# 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( ${ELASTIX_USE_FILE} )
-
# If OpenMP is supported, elastix will have beeen compiled with
# OpenMP flags, and we need to add them here as well
find_package( OpenMP )
@@ -16,13 +9,22 @@ if( OPENMP_FOUND )
set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}" )
endif()
+if( NOT EXISTS ${ELASTIX_USE_FILE} )
+ option( ELASTIX_USE_FILE "NOT_FOUND" )
+ message( FATAL_ERROR "${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 local elastix build tree." )
+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 61a263c0..00000000
--- a/Modules/Components/Elastix/include/elxElastixFilter.h
+++ /dev/null
@@ -1,251 +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.
- */
-
-namespace selx {
-
-// PixelType traits for writing types as strings to parameter files
-template < typename T >
-struct TypeName
-{
- static const char* ToString()
- {
- itkGenericExceptionMacro( "Pixel type \"" << typeid(T).name() << "\" not supported by elastix." )
- }
-};
-
-template <>
-struct TypeName< char >
-{
- static const char* ToString()
- {
- return "char";
- }
-};
-
-template <>
-struct TypeName< unsigned char >
-{
- static const char* ToString()
- {
- return "unsigned char";
- }
-};
-
-template <>
-struct TypeName< short >
-{
- static const char* ToString()
- {
- return "short";
- }
-};
-
-template <>
-struct TypeName< unsigned short >
-{
- static const char* ToString()
- {
- return "unsigned short";
- }
-};
-
-template <>
-struct TypeName< int >
-{
- static const char* ToString()
- {
- return "int";
- }
-};
-
-template <>
-struct TypeName< unsigned int >
-{
- static const char* ToString()
- {
- return "unsigned int";
- }
-};
-
-template <>
-struct TypeName< long >
-{
- static const char* ToString()
- {
- return "long";
- }
-};
-
-template <>
-struct TypeName< unsigned long >
-{
- static const char* ToString()
- {
- return "unsigned long";
- }
-};
-
-template <>
-struct TypeName< float >
-{
- static const char* ToString()
- {
- return "float";
- }
-};
-
-template <>
-struct TypeName< double >
-{
- static const char* ToString()
- {
- return "double";
- }
-};
-
-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::ParameterMapVectorType ParameterMapVectorType;
- typedef ParameterObject::ParameterMapType ParameterMapType;
- typedef ParameterObject::ParameterValueVectorType ParameterValueVectorType;
- typedef ParameterObject::Pointer ParameterObjectPointer;
- typedef ParameterObject::ConstPointer ParameterObjectConstPointer;
-
- typedef typename TFixedImage::Pointer FixedImagePointer;
- typedef typename TMovingImage::Pointer MovingImagePointer;
-
- itkStaticConstMacro( FixedImageDimension, unsigned int, TFixedImage::ImageDimension );
- itkStaticConstMacro( MovingImageDimension, unsigned int, TMovingImage::ImageDimension );
-
- void SetFixedImage( FixedImagePointer fixedImage );
- void SetFixedImage( DataObjectContainerPointer fixedImages );
- void AddFixedImage( FixedImagePointer fixedImage );
-
- void SetMovingImage( MovingImagePointer movingImages );
- void SetMovingImage( DataObjectContainerPointer movingImages );
- void AddMovingImage( MovingImagePointer movingImage );
-
- void SetFixedMask( FixedImagePointer fixedMask );
- void SetFixedMask( DataObjectContainerPointer fixedMasks );
- void AddFixedMask( FixedImagePointer fixedMask );
- void RemoveFixedMask( void );
-
- void SetMovingMask( MovingImagePointer movingMask );
- void SetMovingMask( DataObjectContainerPointer movingMasks );
- void AddMovingMask( MovingImagePointer movingMask );
- void RemoveMovingMask( void );
-
- 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 );
-
- FixedImagePointer GetOutput( void );
-
-protected:
-
- void GenerateData( void ) ITK_OVERRIDE;
-
-private:
-
- ElastixFilter();
-
- void AddInputAutoIncrementName( DataObjectIdentifierType key, itk::DataObject* input );
-
- bool IsInputType( DataObjectIdentifierType inputType, DataObjectIdentifierType inputName );
- void RemoveInputType( DataObjectIdentifierType inputName );
-
- // 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 01132cab..00000000
--- a/Modules/Components/Elastix/include/elxElastixFilter.hxx
+++ /dev/null
@@ -1,542 +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();
-
- ParameterObjectPointer defaultParameterObject = ParameterObject::New();
- defaultParameterObject->AddParameterMap( "rigid" );
- defaultParameterObject->AddParameterMap( "affine" );
- defaultParameterObject->AddParameterMap( "nonrigid" );
- this->SetParameterObject( defaultParameterObject );
-}
-
-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;
- ParameterMapVectorType TransformParameterMapVector;
- FlatDirectionCosinesType fixedImageOriginalDirection;
-
- if( this->HasInput( "FixedMask" ) )
- {
- fixedMaskContainer = DataObjectContainerType::New();
- }
-
- if( this->HasInput( "MovingMask" ) )
- {
- movingMaskContainer = DataObjectContainerType::New();
- }
-
- // Split inputs into separate containers
- InputNameArrayType inputNames = this->GetInputNames();
- for( unsigned int i = 0; i < inputNames.size(); ++i )
- {
- if( this->IsInputType( "FixedImage", inputNames[ i ] ) )
- {
- fixedImageContainer->push_back( this->GetInput( inputNames[ i ] ) );
- continue;
- }
-
- if( this->IsInputType( "MovingImage", inputNames[ i ] ) )
- {
- movingImageContainer->push_back( this->GetInput( inputNames[ i ] ) );
- continue;
- }
-
- if( this->IsInputType( "FixedMask", inputNames[ i ] ) )
- {
- fixedMaskContainer->push_back( this->GetInput( inputNames[ i ] ) );
- continue;
- }
-
- if( this->IsInputType( "Movingmask", inputNames[ i ] ) )
- {
- movingMaskContainer->push_back( this->GetInput( inputNames[ i ] ) );
- }
- }
-
- ArgumentMapType argumentMap;
- if( this->GetOutputDirectory().empty() ) {
- if( this->GetLogToFile() )
- {
- itkExceptionMacro( "LogToFileOn() requires an output directory to be specified. Use SetOutputDirectory().")
- }
-
- // There must be an "-out", this is checked later in the code
- argumentMap.insert( ArgumentMapEntryType( "-out", "output_path_not_set" ) );
- }
- else
- {
- 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() + "/" );
- }
-
- 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->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" ) );
- ParameterMapVectorType parameterMapVector = parameterObject->GetParameterMap();
-
- if( parameterMapVector.size() == 0 )
- {
- itkExceptionMacro( "Parameter object contains an empty parameter map list." );
- }
-
- // Elastix must always write result image to guarantee that the ITK pipeline is in a consistent state
- parameterMapVector[ parameterMapVector.size()-1 ][ "WriteResultImage" ] = ParameterValueVectorType( 1, "true" );
-
- // Run the (possibly multiple) registration(s)
- for( unsigned int i = 0; i < parameterMapVector.size(); ++i )
- {
- // Elastix reads type information from parameter files. We set this information automatically and overwrite
- // user settings in case they are incorrect (elastix will segfault or throw exception when casting)
- parameterMapVector[ i ][ "FixedInternalImagePixelType" ] = ParameterValueVectorType( 1, TypeName< typename TFixedImage::PixelType >::ToString() );
- parameterMapVector[ i ][ "FixedImageDimension" ] = ParameterValueVectorType( 1, std::to_string( FixedImageDimension ) );
- parameterMapVector[ i ][ "MovingInternalImagePixelType" ] = ParameterValueVectorType( 1, TypeName< typename TMovingImage::PixelType >::ToString() );
- parameterMapVector[ i ][ "MovingImageDimension" ] = ParameterValueVectorType( 1, std::to_string( MovingImageDimension ) );
- parameterMapVector[ i ][ "ResultImagePixelType" ] = ParameterValueVectorType( 1, TypeName< typename TFixedImage::PixelType >::ToString() );
-
- // Create another instance of ElastixMain
- ElastixMainPointer elastix = ElastixMainType::New();
-
- // Set the current elastix-level
- elastix->SetElastixLevel( i );
- elastix->SetTotalNumberOfElastixLevels( parameterMapVector.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, parameterMapVector[ i ] );
- }
- catch( itk::ExceptionObject &e )
- {
- itkExceptionMacro( << "Errors occurred during registration: " << e.what() );
- }
-
- 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();
-
- TransformParameterMapVector.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 );
- TransformParameterMapVector[ 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 TransformParameterObject = ParameterObject::New();
- TransformParameterObject->SetParameterMap( TransformParameterMapVector );
- this->SetOutput( "TransformParameterObject", static_cast< itk::DataObject* >( TransformParameterObject ) );
-
- // Close the modules
- ElastixMainType::UnloadComponents();
-}
-
-template< typename TFixedImage, typename TMovingImage >
-typename ElastixFilter< TFixedImage, TMovingImage >::FixedImagePointer
-ElastixFilter< TFixedImage, TMovingImage >
-::GetOutput( void )
-{
- // TODO: This update should not be needed upstream is not updated without it
- this->Update();
-
- return static_cast< TFixedImage* >( itk::ProcessObject::GetPrimaryOutput() );
-}
-
-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->RemoveInputType( "FixedImage" );
-
- 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->RemoveInputType( "FixedImage" );
-
- // The ITK filter requires a "FixedImage" named input. The first image
- // will be named "FixedImage" while the rest of the images will
- // be appended to the input container suffixed with _1, _2, etc.
- // The common prefix 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->RemoveInputType( "MovingImage" );
-
- 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->RemoveInputType( "MovingImage" );
-
- // The ITK filter requires a "MovingImage" named input. The first image
- // will be named "MovingImage" while the rest of the images will
- // be appended to the input container suffixed with _1, _2, etc.
- // The common prefix 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 )
-{
- // Free references to fixed masks that has already been set
- this->RemoveInputType( "FixedMask" );
-
- this->SetInput( "FixedMask", static_cast< itk::DataObject* >( fixedMask ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetFixedMask( DataObjectContainerPointer fixedMasks )
-{
- if( fixedMasks->Size() == 0 )
- {
- itkExceptionMacro( "Cannot set fixed masks from empty container.")
- }
-
- // Free references to fixed images that has already been set
- this->RemoveInputType( "FixedMask" );
-
- // The first mask will be named "FixedMask" so that HasInput( "FixedMask" )
- // can be used to check if masks are used. The rest of the images will
- // be appended to the input container suffixed with _1, _2, etc.
- // The common prefix allows us to read out only the fixed masks
- // for elastix fixed mask container at a later stage
- DataObjectContainerIterator fixedMaskIterator = fixedMasks->Begin();
- this->SetInput( "FixedMask", fixedMaskIterator->Value() );
- ++fixedMaskIterator;
-
- while( fixedMaskIterator != fixedMasks->End() )
- {
- this->AddInputAutoIncrementName( "FixedMask", fixedMaskIterator->Value() );
- ++fixedMaskIterator;
- }
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::AddFixedMask( FixedImagePointer fixedMask )
-{
- this->AddInputAutoIncrementName( "FixedMask", static_cast< itk::DataObject* >( fixedMask ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::RemoveFixedMask( void )
-{
- this->RemoveInputType( "FixedMask" );
- this->m_FixedMaskContainer = 0;
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetMovingMask( MovingImagePointer movingMask )
-{
- // Free references to moving masks that has already been set
- this->RemoveInputType( "MovingMask" );
-
- this->SetInput( "MovingMask", static_cast< itk::DataObject* >( movingMask ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::SetMovingMask( DataObjectContainerPointer movingMasks )
-{
- if( movingMasks->Size() == 0 )
- {
- itkExceptionMacro( "Cannot set moving images from empty container.")
- }
-
- // Free references to moving masks that has already been set
- this->RemoveInputType( "MovingMask" );
-
- // The first mask will be named "MovingMask" so that HasInput( "MovingMask" )
- // can be used to check if masks are used. The rest of the images will
- // be appended to the input container suffixed with _1, _2, etc.
- // The common prefix allows us to read out only the moving mask
- // for elastix moving mask container at a later stage
- DataObjectContainerIterator movingMaskIterator = movingMasks->Begin();
- this->SetInput( "MovingMask", movingMaskIterator->Value() );
- ++movingMaskIterator;
-
- while( movingMaskIterator != movingMasks->End() )
- {
- this->AddInputAutoIncrementName( "MovingMask", movingMaskIterator->Value() );
- ++movingMaskIterator;
- }
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::AddMovingMask( MovingImagePointer movingMask )
-{
- this->AddInputAutoIncrementName( "MovingMask", static_cast< itk::DataObject* >( movingMask ) );
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::RemoveMovingMask( void )
-{
- this->RemoveInputType( "MovingMask" );
- this->m_MovingMaskContainer = 0;
-}
-
-/*
- * Adds a named input to the first null position in the input list
- * and expands the list memory if necessary
- */
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::AddInputAutoIncrementName( DataObjectIdentifierType inputName, itk::DataObject* input )
-{
- for ( unsigned idx = 0; idx < this->GetNumberOfIndexedInputs(); ++idx )
- {
- if ( !this->GetInput( idx ) )
- {
- // Append number to name (e.g. '_2' to inputName for idx = 2)
- inputName += this->MakeNameFromInputIndex( idx );
- this->SetInput( inputName, input );
- return;
- }
- }
-
- inputName += this->MakeNameFromInputIndex( this->GetNumberOfIndexedInputs() );
- this->SetInput( inputName, input );
- return;
-}
-
-template< typename TFixedImage, typename TMovingImage >
-bool
-ElastixFilter< TFixedImage, TMovingImage >
-::IsInputType( DataObjectIdentifierType inputType, DataObjectIdentifierType inputName )
-{
- return std::strncmp( inputType.c_str(), inputName.c_str(), inputType.size() ) == 0;
-}
-
-template< typename TFixedImage, typename TMovingImage >
-void
-ElastixFilter< TFixedImage, TMovingImage >
-::RemoveInputType( DataObjectIdentifierType inputType )
-{
- // Free references to inputType images that has already been set
- InputNameArrayType inputNames = this->GetInputNames();
- for( unsigned int i = 0; i < inputNames.size(); ++i )
- {
- if( this->IsInputType( inputType, 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 320e037b..00000000
--- a/Modules/Components/Elastix/include/elxTransformixFilter.h
+++ /dev/null
@@ -1,125 +0,0 @@
-#ifndef TransformixFilter_h
-#define TransformixFilter_h
-
-// ITK
-#include "itkImageSource.h"
-
-// Transformix
-#include "elxTransformixMain.h"
-
-// SuperElastix
-#include "elxMacro.h"
-#include "elxParameterObject.h"
-
-/**
- * Transformix library exposed as an ITK filter.
- *
- * Make sure the compiler can also see itkElastixFilter.h
- * for the TypeName trait structs (usually not a problem if
- * the files are placed in the same include directory).
- */
-
-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::ParameterMapVectorType ParameterMapVectorType;
- typedef ParameterObject::ParameterMapType ParameterMapType;
- typedef ParameterObject::ParameterValueVectorType ParameterValueVectorType;
- typedef typename ParameterObject::Pointer ParameterObjectPointer;
- typedef typename ParameterObject::ConstPointer ParameterObjectConstPointer;
-
- typedef typename TInputImage::Pointer InputImagePointer;
-
- itkStaticConstMacro( InputImageDimension, unsigned int, TInputImage::ImageDimension );
-
- 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 ef350fab..00000000
--- a/Modules/Components/Elastix/include/elxTransformixFilter.hxx
+++ /dev/null
@@ -1,220 +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() or SetPointSetFileName() or "
- << "to be set.");
- }
-
- // Check if an output directory is needed
- // TODO: Change behaviour upstream to have transformix save all outputs as data objects
- 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() ) {
- if( this->GetLogToFile() )
- {
- itkExceptionMacro( "LogToFileOn() requires an output directory to be specified. Use SetOutputDirectory().")
- }
-
- // There must be an "-out", this is checked later in the code
- argumentMap.insert( ArgumentMapEntryType( "-out", "output_path_not_set" ) );
- }
- else
- {
- 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() + "/" );
- }
-
- 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->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" ) );
- ParameterMapVectorType transformParameterMapVector = transformParameterObject->GetParameterMap();
-
- for( unsigned int i = 0; i < transformParameterMapVector.size(); ++i )
- {
- // Transformix reads type information from parameter files. We set this information automatically and overwrite
- // user settings in case they are incorrect (elastix will segfault or throw exception when casting)
- transformParameterMapVector[ i ][ "MovingInternalImagePixelType" ] = ParameterValueVectorType( 1, TypeName< typename TInputImage::PixelType >::ToString() );
- transformParameterMapVector[ i ][ "MovingImageDimension" ] = ParameterValueVectorType( 1, std::to_string( InputImageDimension ) );
- transformParameterMapVector[ i ][ "ResultImagePixelType" ] = ParameterValueVectorType( 1, TypeName< typename TInputImage::PixelType >::ToString() );
- }
-
- // Run transformix
- unsigned int isError = 0;
- try
- {
- isError = transformix->Run( argumentMap, transformParameterMapVector );
- }
- 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 )
- {
- 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 ff83b08c..c5db8845 100644
--- a/Modules/Core/ModuleCore.cmake
+++ b/Modules/Core/ModuleCore.cmake
@@ -13,8 +13,6 @@ 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}
@@ -23,7 +21,6 @@ set( ${MODULE}_LIBRARIES
# Module source files
set( ${MODULE}_SOURCE_FILES
${${MODULE}_SOURCE_DIR}/Blueprints/src/elxBlueprint.cxx
- ${${MODULE}_SOURCE_DIR}/ParameterObject/src/elxParameterObject.cxx
${${MODULE}_SOURCE_DIR}/ComponentInterface/src/ComponentBase.cxx
${${MODULE}_SOURCE_DIR}/ExampleComponents/src/Example3rdPartyCode.cxx
${${MODULE}_SOURCE_DIR}/ExampleComponents/src/Example4thPartyCode.cxx
@@ -38,7 +35,5 @@ set( ${MODULE}_SOURCE_FILES
)
# Compile library
-
-add_library( ${MODULE} STATIC "${${MODULE}_SOURCE_FILES}" ${${MODULE}_HEADER_FILES})
-
+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 71816b06..00000000
--- a/Modules/Core/ParameterObject/include/elxParameterObject.h
+++ /dev/null
@@ -1,63 +0,0 @@
-#ifndef ParameterObject_h
-#define ParameterObject_h
-
-// ITK
-#include "itkObjectFactory.h"
-#include "itkDataObject.h"
-
-// elastix
-#include "elxMacro.h"
-#include "itkParameterFileParser.h"
-
-namespace selx {
-
-class ParameterObject : public itk::DataObject
-{
-public:
-
- elxNewMacro( ParameterObject, itk::DataObject );
-
- typedef std::string ParameterKeyType;
- typedef std::string ParameterValueType;
- typedef std::vector< ParameterValueType > ParameterValueVectorType;
- typedef std::map< ParameterKeyType, ParameterValueVectorType > ParameterMapType;
- typedef ParameterMapType::iterator ParameterMapIterator;
- typedef ParameterMapType::const_iterator ParameterMapConstIterator;
- typedef std::vector< ParameterMapType > ParameterMapVectorType;
- typedef std::string ParameterFileNameType;
- typedef std::vector< ParameterFileNameType > ParameterFileNameVectorType;
- typedef ParameterFileNameVectorType::iterator ParameterFileNameVectorIterator;
- typedef ParameterFileNameVectorType::const_iterator ParameterFileNameVectorConstIterator;
-
- typedef itk::ParameterFileParser ParameterFileParserType;
- typedef ParameterFileParserType::Pointer ParameterFileParserPointer;
-
- void SetParameterMap( const ParameterMapType parameterMap );
- void SetParameterMap( const ParameterMapVectorType parameterMapVector );
- void AddParameterMap( const ParameterMapType parameterMap );
-
- ParameterMapType& GetParameterMap( unsigned int index );
- ParameterMapVectorType& GetParameterMap( void );
- const ParameterMapVectorType& GetParameterMap( void ) const;
-
- void ReadParameterFile( const ParameterFileNameType parameterFileName );
- void ReadParameterFile( const ParameterFileNameVectorType parameterFileNameVector );
- void AddParameterFile( const ParameterFileNameType parameterFileName );
-
- void WriteParameterFile( const ParameterFileNameType parameterFileName );
- void WriteParameterFile( const ParameterFileNameVectorType parameterFileNameVector );
-
- // Default parameter maps
- void SetParameterMap( const std::string transformName, const unsigned int numberOfResolutions = 3u, const double finalGridSpacingInPhysicalUnits = 10.0 );
- void AddParameterMap( const std::string transformName, const unsigned int numberOfResolutions = 3u, const double finalGridSpacingInPhysicalUnits = 10.0 );
- ParameterMapType GetParameterMap( const std::string transformName, const unsigned int numberOfResolutions = 3u, const double finalGridSpacingInPhysicalUnits = 10.0 );
-
-private:
-
- ParameterMapVectorType m_ParameterMapVector;
-
-};
-
-} // namespace elx
-
-#endif // #define ParameterMap_h
\ No newline at end of file
diff --git a/Modules/Core/ParameterObject/src/elxParameterObject.cxx b/Modules/Core/ParameterObject/src/elxParameterObject.cxx
deleted file mode 100644
index 36b393ce..00000000
--- a/Modules/Core/ParameterObject/src/elxParameterObject.cxx
+++ /dev/null
@@ -1,274 +0,0 @@
-#ifndef ParameterObject_cxx
-#define ParameterObject_cxx
-
-// ITK
-#include "itkFileTools.h"
-
-// elastix
-#include "elxParameterObject.h"
-
-namespace selx {
-
-void
-ParameterObject
-::SetParameterMap( const ParameterMapType parameterMap )
-{
- ParameterMapVectorType parameterMapVector;
- parameterMapVector.push_back( parameterMap );
- this->SetParameterMap( parameterMapVector );
-}
-
-void
-ParameterObject
-::SetParameterMap( const ParameterMapVectorType parameterMapVector )
-{
- this->m_ParameterMapVector = parameterMapVector;
-}
-
-void
-ParameterObject
-::AddParameterMap( const ParameterMapType parameterMap )
-{
- this->m_ParameterMapVector.push_back( parameterMap );
-}
-
-ParameterObject::ParameterMapType&
-ParameterObject
-::GetParameterMap( unsigned int index )
-{
- this->Modified();
- return this->m_ParameterMapVector[ index ];
-}
-
-ParameterObject::ParameterMapVectorType&
-ParameterObject
-::GetParameterMap( void )
-{
- this->Modified();
- return this->m_ParameterMapVector;
-}
-
-const ParameterObject::ParameterMapVectorType&
-ParameterObject
-::GetParameterMap( void ) const
-{
- return this->m_ParameterMapVector;
-}
-
-void
-ParameterObject
-::ReadParameterFile( const ParameterFileNameType parameterFileName )
-{
- ParameterFileParserPointer parameterFileParser = ParameterFileParserType::New();
- parameterFileParser->SetParameterFileName( parameterFileName );
- parameterFileParser->ReadParameterFile();
- this->m_ParameterMapVector = ParameterMapVectorType( 1, parameterFileParser->GetParameterMap() );
-}
-
-void
-ParameterObject
-::ReadParameterFile( const ParameterFileNameVectorType parameterFileNameVector )
-{
- if( parameterFileNameVector.size() == 0 )
- {
- itkExceptionMacro( "Parameter filename container is empty." );
- }
-
- this->m_ParameterMapVector.clear();
-
- for( unsigned int i = 0; i < parameterFileNameVector.size(); ++i )
- {
- if( !itksys::SystemTools::FileExists( parameterFileNameVector[ i ] ) )
- {
- itkExceptionMacro( "Parameter file \"" << parameterFileNameVector[ i ] << "\" does not exist." )
- }
-
- this->AddParameterFile( parameterFileNameVector[ i ] );
- }
-}
-
-void
-ParameterObject
-::AddParameterFile( const ParameterFileNameType parameterFileName )
-{
- ParameterFileParserPointer parameterFileParser = ParameterFileParserType::New();
- parameterFileParser->SetParameterFileName( parameterFileName );
- parameterFileParser->ReadParameterFile();
- this->m_ParameterMapVector.push_back( parameterFileParser->GetParameterMap() );
-}
-
-void
-ParameterObject
-::WriteParameterFile( const ParameterFileNameType parameterFileName )
-{
- if( this->m_ParameterMapVector.size() != 1 )
- {
- itkExceptionMacro( "ParameterObject contains multiple parameter files. Please provide a vector of filenames." );
- }
-
- this->WriteParameterFile( ParameterFileNameVectorType( 1, parameterFileName ) );
-}
-
-void
-ParameterObject
-::WriteParameterFile( const ParameterFileNameVectorType parameterFileNameVector )
-{
- for( unsigned int i = 0; i < parameterFileNameVector.size(); ++i )
- {
- ParameterFileNameType fileName = parameterFileNameVector[ i ];
- std::ofstream parameterFile;
- parameterFile << std::fixed;
- parameterFile.open( fileName.c_str(), std::ofstream::out );
- ParameterMapConstIterator parameterMapIterator = this->m_ParameterMapVector[ i ].begin();
- ParameterMapConstIterator parameterMapIteratorEnd = this->m_ParameterMapVector[ i ].end();
- while( parameterMapIterator != parameterMapIteratorEnd )
- {
- parameterFile << "(" << parameterMapIterator->first;
-
- ParameterValueVectorType parameterMapValueVector = parameterMapIterator->second;
- for( unsigned int i = 0; i < parameterMapValueVector.size(); ++i )
- {
- std::stringstream stream( parameterMapValueVector[ i ] );
- float number;
- stream >> number;
- if( stream.fail() || stream.bad() ) {
- parameterFile << " \"" << parameterMapValueVector[ i ] << "\"";
- }
- else
- {
- parameterFile << " " << number;
- }
- }
-
- parameterFile << ")" << std::endl;
- parameterMapIterator++;
- }
-
- parameterFile.close();
- }
-}
-
-void
-ParameterObject
-::SetParameterMap( const std::string transformName, const unsigned int numberOfResolutions, const double finalGridSpacingInPhysicalUnits )
-{
- this->m_ParameterMapVector = ParameterMapVectorType( 1, this->GetParameterMap( transformName, numberOfResolutions, finalGridSpacingInPhysicalUnits ) );
-}
-
-void
-ParameterObject
-::AddParameterMap( const std::string transformName, const unsigned int numberOfResolutions, const double finalGridSpacingInPhysicalUnits )
-{
- this->m_ParameterMapVector.push_back( this->GetParameterMap( transformName, numberOfResolutions, finalGridSpacingInPhysicalUnits ) );
-}
-
-ParameterObject::ParameterMapType
-ParameterObject
-::GetParameterMap( const std::string transformName, const unsigned int numberOfResolutions, const double finalGridSpacingInPhysicalUnits )
-{
-
- // Parameters that depend on size and number of resolutions
- ParameterMapType parameterMap = ParameterMapType();
-
- // Common Components
- parameterMap[ "FixedImagePyramid" ] = ParameterValueVectorType( 1, "FixedSmoothingImagePyramid" );
- parameterMap[ "MovingImagePyramid" ] = ParameterValueVectorType( 1, "MovingSmoothingImagePyramid" );
- parameterMap[ "Interpolator"] = ParameterValueVectorType( 1, "LinearInterpolator");
- parameterMap[ "Optimizer" ] = ParameterValueVectorType( 1, "AdaptiveStochasticGradientDescent" );
- parameterMap[ "Resampler"] = ParameterValueVectorType( 1, "DefaultResampler" );
- parameterMap[ "ResampleInterpolator"] = ParameterValueVectorType( 1, "FinalBSplineInterpolator" );
- parameterMap[ "FinalBSplineInterpolationOrder" ] = ParameterValueVectorType( 1, "3" );
-
- std::ostringstream numberOfResolutionsToString;
- numberOfResolutionsToString << numberOfResolutions;
- parameterMap[ "NumberOfResolutions" ] = ParameterValueVectorType( 1, numberOfResolutionsToString.str() );
-
- // Image Sampler
- parameterMap[ "ImageSampler" ] = ParameterValueVectorType( 1, "RandomCoordinate" );
- parameterMap[ "NumberOfSpatialSamples"] = ParameterValueVectorType( 1, "2048" );
- parameterMap[ "CheckNumberOfSamples" ] = ParameterValueVectorType( 1, "true" );
- parameterMap[ "MaximumNumberOfSamplingAttempts" ] = ParameterValueVectorType( 1, "8" );
- parameterMap[ "NewSamplesEveryIteration" ] = ParameterValueVectorType( 1, "true");
-
- // Optimizer
- parameterMap[ "NumberOfSamplesForExactGradient" ] = ParameterValueVectorType( 1, "4096" );
- parameterMap[ "DefaultPixelValue" ] = ParameterValueVectorType( 1, "0" );
- parameterMap[ "AutomaticParameterEstimation" ] = ParameterValueVectorType( 1, "true" );
-
- // Output
- parameterMap[ "WriteResultImage" ] = ParameterValueVectorType( 1, "true" );
- parameterMap[ "ResultImageFormat" ] = ParameterValueVectorType( 1, "nii" );
-
- // transformNames
- if( transformName == "translation" )
- {
- parameterMap[ "Registration" ] = ParameterValueVectorType( 1, "MultiResolutionRegistration" );
- parameterMap[ "transform" ] = ParameterValueVectorType( 1, "TranslationTransform" );
- parameterMap[ "Metric" ] = ParameterValueVectorType( 1, "AdvancedMattesMutualInformation" );
- parameterMap[ "MaximumNumberOfIterations" ] = ParameterValueVectorType( 1, "128" );
- parameterMap[ "Interpolator"] = ParameterValueVectorType( 1, "LinearInterpolator");
- }
- else if( transformName == "rigid" )
- {
- parameterMap[ "Registration" ] = ParameterValueVectorType( 1, "MultiResolutionRegistration" );
- parameterMap[ "Transform" ] = ParameterValueVectorType( 1, "EulerTransform" );
- parameterMap[ "Metric" ] = ParameterValueVectorType( 1, "AdvancedMattesMutualInformation" );
- parameterMap[ "MaximumNumberOfIterations" ] = ParameterValueVectorType( 1, "128" );
- parameterMap[ "AutomaticTransformInitialization" ] = ParameterValueVectorType( 1, "true" );
- parameterMap[ "AutomaticTransformInitializationMethod" ] = ParameterValueVectorType( 1, "CenterOfGravity" );
- }
- else if( transformName == "affine" )
- {
- parameterMap[ "Registration" ] = ParameterValueVectorType( 1, "MultiResolutionRegistration" );
- parameterMap[ "Transform" ] = ParameterValueVectorType( 1, "AffineTransform" );
- parameterMap[ "Metric" ] = ParameterValueVectorType( 1, "AdvancedMattesMutualInformation" );
- parameterMap[ "MaximumNumberOfIterations" ] = ParameterValueVectorType( 1, "256" );
- }
- else if( transformName == "nonrigid" )
- {
- parameterMap[ "Registration" ] = ParameterValueVectorType( 1, "MultiMetricMultiResolutionRegistration" );
- parameterMap[ "Transform" ] = ParameterValueVectorType( 1, "BSplineTransform" );
- parameterMap[ "Metric" ] = ParameterValueVectorType( 1, "AdvancedMattesMutualInformation" );
- parameterMap[ "Metric" ] .push_back( "TransformBendingEnergyPenalty" );
- parameterMap[ "Metric0Weight" ] = ParameterValueVectorType( 1, "0.0001" );
- parameterMap[ "Metric1Weight" ] = ParameterValueVectorType( 1, "0.9999" );
- parameterMap[ "MaximumNumberOfIterations" ] = ParameterValueVectorType( 1, "512" );
- }
- else if( transformName == "groupwise" )
- {
- parameterMap[ "Registration" ] = ParameterValueVectorType( 1, "MultiResolutionRegistration" );
- parameterMap[ "Transform" ] = ParameterValueVectorType( 1, "BSplineStackTransform" );
- parameterMap[ "Metric" ] = ParameterValueVectorType( 1, "VarianceOverLastDimensionMetric" );
- parameterMap[ "MaximumNumberOfIterations" ] = ParameterValueVectorType( 1, "512" );
- parameterMap[ "Interpolator"] = ParameterValueVectorType( 1, "ReducedDimensionBSplineInterpolator" );
- parameterMap[ "ResampleInterpolator" ] = ParameterValueVectorType( 1, "FinalReducedDimensionBSplineInterpolator" );
- }
- else
- {
- itkExceptionMacro( "No default parameter map \"" << transformName << "\"." );
- }
-
- // B-spline transformNames settings
- if( transformName == "nonrigid" || transformName == "groupwise" )
- {
- ParameterValueVectorType gridSpacingSchedule = ParameterValueVectorType();
- for( unsigned int resolution = 0; resolution < numberOfResolutions; ++resolution )
- {
- std::ostringstream resolutionPowerToString;
- resolutionPowerToString << pow( 2, resolution );
- gridSpacingSchedule.insert( gridSpacingSchedule.begin(), resolutionPowerToString.str() );
- }
-
- parameterMap[ "GridSpacingSchedule" ] = gridSpacingSchedule;
-
- std::ostringstream finalGridSpacingInPhysicalUnitsToString;
- finalGridSpacingInPhysicalUnitsToString << finalGridSpacingInPhysicalUnits;
- parameterMap[ "FinalGridSpacingInPhysicalUnits" ] = ParameterValueVectorType( 1, finalGridSpacingInPhysicalUnitsToString.str() );
- }
-
- return parameterMap;
-}
-
-} // namespace selx
-
-#endif // ParameterObject_cxx
--
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