diff --git a/CMake/elxModules.cmake b/CMake/elxModules.cmake
index 894204aebbf5c5098a57bfd09d967c535fee639b..5cc11cd58dd02129e7b9591c53a2f7221917bc4e 100644
--- a/CMake/elxModules.cmake
+++ b/CMake/elxModules.cmake
@@ -35,7 +35,7 @@ macro( _elxmodule_enable MODULE_NAME )
endmacro()
macro( _elxmodule_disable MODULE_NAME )
- # TODO
+ # TODO: elxmodule_disable
endmacro()
macro( _elxmodules_initialize )
diff --git a/CMake/elxITKRequiredModules.cmake b/CMake/elxRequiredITKModules.cmake
similarity index 70%
rename from CMake/elxITKRequiredModules.cmake
rename to CMake/elxRequiredITKModules.cmake
index c9cce4a03c670dab607b646114c1f44a241e44d8..61e56e78903db275dbfc4be42cad8266853a7a62 100644
--- a/CMake/elxITKRequiredModules.cmake
+++ b/CMake/elxRequiredITKModules.cmake
@@ -1,8 +1,8 @@
-list( APPEND ElastixRequiredITKModules
+list( APPEND RequiredITKModules
ITKReview
)
-foreach( ITKModule ${ElastixRequiredITKModules} )
+foreach( ITKModule ${RequiredITKModules} )
if( NOT ${ITKModule}_LOADED )
message( FATAL_ERROR "Elastix requires that ITK is build with ${ITKModule}. Please rebuild ITK with Module_${ITKModule} set to ON." )
endif()
diff --git a/CMake/elxWinConfig.cmake b/CMake/elxWinConfig.cmake
deleted file mode 100644
index e0b1b38c129f9632c7c919475551c72a54c8bdf7..0000000000000000000000000000000000000000
--- a/CMake/elxWinConfig.cmake
+++ /dev/null
@@ -1,18 +0,0 @@
-# Visual Studio complains if paths are too long
-string( LENGTH "${CMAKE_CURRENT_SOURCE_DIR}" n )
-if( n GREATER 50 )
-message(
- FATAL_ERROR
- "Source code directory path length is too long for MSVC (${n} > 50)."
- "Please move the source code directory to a directory with a shorter path."
- )
-endif()
-
-string( LENGTH "${CMAKE_CURRENT_BINARY_DIR}" n )
-if( n GREATER 50 )
-message(
- FATAL_ERROR
- "Build directory path length is too long for MSVC (${n} > 50)."
- "Please move the build directory to a directory with a shorter path."
- )
-endif()
\ No newline at end of file
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9215420345da586c296658a2a617844fb37b2bd4..4f3daa923ad33969697cacfe13c932ea64c1fb53 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required( VERSION 2.8 )
+cmake_minimum_required( VERSION 3.0.2 )
# Explicitly add INCREMENTAL linking option to command lines.
# http://www.cmake.org/pipermail/cmake/2010-February/035174.html
@@ -17,9 +17,36 @@ set( CMAKE_RUNTIME_OUTPUT_DIRECTORY
# Include SuperElastix CMake scripts
list( APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/CMake" )
+# -----------------------------------------------------------------
+# Compiler-dependent settings
+# GCC
+if( ${CMAKE_CXX_COMPILER_ID} STREQUAL GNU )
+ add_definitions(
+ -DVCL_CAN_STATIC_CONST_INIT_FLOAT=0
+ -DVCL_CAN_STATIC_CONST_INIT_INT=0
+ )
+endif()
+
+# MSVC
if( ${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC )
- include( elxWinConfig )
+ string( LENGTH "${CMAKE_CURRENT_SOURCE_DIR}" n )
+ if( n GREATER 50 )
+ message(
+ FATAL_ERROR
+ "Source code directory path length is too long for MSVC (${n} > 50)."
+ "Please move the source code directory to a directory with a shorter path."
+ )
+ endif()
+
+ string( LENGTH "${CMAKE_CURRENT_BINARY_DIR}" n )
+ if( n GREATER 50 )
+ message(
+ FATAL_ERROR
+ "Build directory path length is too long for MSVC (${n} > 50)."
+ "Please move the build directory to a directory with a shorter path."
+ )
+ endif()
endif()
# ---------------------------------------------------------------------
@@ -30,11 +57,11 @@ endif()
find_package( ITK REQUIRED )
include( ${ITK_USE_FILE} )
-include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/elxITKRequiredModules.cmake" )
+include("${CMAKE_CURRENT_SOURCE_DIR}/CMake/elxRequiredITKModules.cmake")
# ---------------------------------------------------------------------
# Boost Graph Library
-find_package( Boost )
+find_package( Boost REQUIRED )
include_directories( ${Boost_INCLUDE_DIRS} )
# ---------------------------------------------------------------------
@@ -49,24 +76,20 @@ endif()
# ---------------------------------------------------------------------
# Build SuperElastix
+
# For now we just enable all modules
include( elxModules )
elxmodule_enable( ModuleCore )
elxmodule_enable( ModuleElastix )
+# TODO: Build tests depending on enabled modules
+
# ---------------------------------------------------------------------
# Testing
-# Testing requires CMake version 2.8.11 to download test data
-if( CMAKE_VERSION VERSION_LESS 2.8.11 )
- set( SUPERELASTIX_BUILD_TESTING_DEFAULT OFF )
- message( STATUS "ELASTIX_BUILD_TESTING is set to OFF because CMake version is less than 2.8.11" )
-else()
- set( SUPERELASTIX_BUILD_TESTING_DEFAULT ON )
-endif()
-
-option( SUPERELASTIX_BUILD_TESTING "Enable building tests." ${SUPERELASTIX_BUILD_TESTING_DEFAULT} )
+option( SUPERELASTIX_BUILD_TESTING "Enable building tests." ON )
if( ${SUPERELASTIX_BUILD_TESTING} )
+ option( SUPERELASTIX_BUILD_LONG_TESTS OFF )
enable_testing()
add_subdirectory( Testing )
endif()
diff --git a/Modules/Components/Elastix/ModuleElastix.cmake b/Modules/Components/Elastix/ModuleElastix.cmake
index 62e52cbe820ec5017440d40d59e32e9de35f8529..4d54550cce7922242e43706778cd745a47d29829 100644
--- a/Modules/Components/Elastix/ModuleElastix.cmake
+++ b/Modules/Components/Elastix/ModuleElastix.cmake
@@ -1,4 +1,4 @@
-# Module that exposes the old elastix as a component
+# Module that exposes old elastix as an ITK filter
set( MODULE ModuleElastix )
if( NOT EXISTS ${ELASTIX_USE_FILE} )
@@ -8,6 +8,14 @@ endif()
include( ${ELASTIX_USE_FILE} )
+# If OpenMP is supported by this machine, elastix will be compiled with
+# OpenMP flags, and we need to add them here as well
+find_package( OpenMP )
+if (OPENMP_FOUND)
+ set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}" )
+ set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}" )
+endif()
+
# Export include files
set( ${MODULE}_INCLUDE_DIRS
${${MODULE}_SOURCE_DIR}/include
diff --git a/Modules/Components/Elastix/include/elxElastixFilter.h b/Modules/Components/Elastix/include/elxElastixFilter.h
index 3ae5102b1b0e56e06e9c8bd75c45b76cec9c0cf2..c333e0d1d167de899a20bdcac3241f5a14a240b4 100644
--- a/Modules/Components/Elastix/include/elxElastixFilter.h
+++ b/Modules/Components/Elastix/include/elxElastixFilter.h
@@ -1,8 +1,7 @@
-#ifndef ElastixComponent_h
-#define ElastixComponent_h
+#ifndef ElastixFilter_h
+#define ElastixFilter_h
// ITK
-#include "itkProcessObject.h"
#include "itkImageSource.h"
// Elastix
@@ -15,9 +14,8 @@
namespace selx {
template< typename TFixedImage,
- typename TMovingImage,
- typename TOutputImage >
-class ElastixFilter : public itk::ImageSource< TOutputImage >
+ typename TMovingImage >
+class ElastixFilter : public itk::ImageSource< TFixedImage >
{
public:
@@ -37,8 +35,9 @@ public:
typedef ParameterObject::ParameterMapListType ParameterMapListType;
typedef ParameterObject::ParameterMapType ParameterMapType;
- typedef ParameterObject::ParameterValuesType ParameterValuesType;
+ typedef ParameterObject::ParameterVectorType ParameterVectorType;
typedef typename ParameterObject::Pointer ParameterObjectPointer;
+ typedef typename ParameterObject::ConstPointer ParameterObjectConstPointer;
typedef typename TFixedImage::Pointer FixedImagePointer;
typedef typename TMovingImage::Pointer MovingImagePointer;
@@ -47,18 +46,31 @@ public:
void SetFixedImage( DataObjectContainerPointer fixedImage );
void SetMovingImage( MovingImagePointer movingImage );
void SetMovingImage( DataObjectContainerPointer movingImage );
- void SetParameterObject( ParameterObjectPointer parameterObject );
void SetFixedMask( FixedImagePointer fixedMask );
void SetMovingMask( MovingImagePointer movingMask );
+ void SetParameterObject( ParameterObjectPointer parameterObject );
ParameterObjectPointer GetTransformParameters( void );
+ itkSetMacro( FixedMeshFileName, std::string );
+ itkGetConstMacro( FixedMeshFileName, std::string );
+ void DeleteFixedMeshFileName( void ) { this->SetFixedMeshFileName( std::string() ); };
+
+ itkSetMacro( MovingMeshFileName, std::string );
+ itkGetConstMacro( MovingMeshFileName, std::string );
+ void DeleteMovingMeshFileName( void ) { this->SetMovingMeshFileName( std::string() ); };
+
+ itkSetMacro( OutputDirectory, std::string );
+ itkGetConstMacro( OutputDirectory, std::string );
+ void DeleteOutputDirectory() { this->m_OutputDirectory = std::string(); };
+
itkSetMacro( LogToConsole, bool );
- itkGetMacro( LogToConsole, bool );
+ itkGetConstMacro( LogToConsole, bool );
itkBooleanMacro( LogToConsole );
- itkSetMacro( LogToFile, std::string );
- itkGetMacro( LogToFile, std::string );
+ itkSetMacro( LogToFile, bool );
+ itkGetConstMacro( LogToFile, bool );
+ itkBooleanMacro( LogToFile );
protected:
@@ -68,13 +80,18 @@ private:
ElastixFilter();
+ // TODO: When set to true, ReleaseDataFlag should also touch these input 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;
bool m_LogToConsole;
- std::string m_LogToFile;
+ bool m_LogToFile;
};
diff --git a/Modules/Components/Elastix/include/elxElastixFilter.hxx b/Modules/Components/Elastix/include/elxElastixFilter.hxx
index 1cacc6e9bac66f1b06d9ac37de4c46aca5142a51..a213d50c6cf86453f347c8d7aa2892a8bc74989e 100644
--- a/Modules/Components/Elastix/include/elxElastixFilter.hxx
+++ b/Modules/Components/Elastix/include/elxElastixFilter.hxx
@@ -1,10 +1,10 @@
-#ifndef ElastixComponent_hxx
-#define ElastixComponent_hxx
+#ifndef ElastixFilter_hxx
+#define ElastixFilter_hxx
namespace selx {
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
+ElastixFilter< TFixedImage, TMovingImage >
::ElastixFilter( void )
{
this->AddRequiredInputName( "FixedImage" );
@@ -16,60 +16,99 @@ ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
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->LogToConsoleOff();
+ this->LogToFileOff();
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
void
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+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 = this->m_FixedImageContainer;
DataObjectContainerPointer movingImageContainer = this->m_MovingImageContainer;
DataObjectContainerPointer fixedMaskContainer = 0;
DataObjectContainerPointer movingMaskContainer = 0;
DataObjectContainerPointer resultImageContainer = 0;
-
ParameterMapListType TransformParameterMapList;
+ FlatDirectionCosinesType fixedImageOriginalDirection;
// Fixed mask (optional)
if( this->HasInput( "FixedMask" ) )
{
- fixedMaskContainer = DataObjectContainerType::New();
+ fixedMaskContainer = DataObjectContainerType::New();
fixedMaskContainer->CreateElementAt( 0 ) = this->GetInput( "FixedMask" );
}
// Moving mask (optional)
if( this->HasInput( "MovingMask" ) )
{
- movingMaskContainer = DataObjectContainerType::New();
+ movingMaskContainer = DataObjectContainerType::New();
movingMaskContainer->CreateElementAt( 0 ) = this->GetInput( "MovingMask" );
}
- // Get ParameterMap
- ParameterObjectPointer parameterObject = static_cast< ParameterObject* >( this->GetInput( "ParameterObject" ) );
- ParameterMapListType parameterMapList = parameterObject->GetParameterMapList();
-
- // Emulate command line parameters. There must be an "-out", this is checked later in code
+ // There must be an "-out", this is checked later in the code
ArgumentMapType argumentMap;
- argumentMap.insert( ArgumentMapEntryType( std::string( "-out" ), std::string( "output_path_not_set" ) ) );
+ 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 ) ) );
+ }
- // Direction Cosines
- FlatDirectionCosinesType fixedImageOriginalDirection;
+ // Moving mesh (optional)
+ if( !this->m_MovingMeshFileName.empty() )
+ {
+ argumentMap.insert( ArgumentMapEntryType( "-mp", std::string( this->m_MovingMeshFileName ) ) );
+ }
// Setup xout
- if( elx::xoutSetup( this->GetLogToFile().c_str(), this->GetLogToFile() != std::string(), this->GetLogToConsole() ) )
+ std::string logFileName;
+ if( this->GetLogToFile() )
+ {
+ if( this->GetOutputDirectory().empty() )
+ {
+ itkExceptionMacro( "LogToFileOn() requires an output directory to be specified. Use SetOutputDirectory().")
+ }
+ logFileName = this->GetOutputDirectory() + "transformix.log";
+ }
+
+ if( elx::xoutSetup( logFileName.c_str(), this->GetLogToFile(), this->GetLogToConsole() ) )
{
- itkExceptionMacro( "ERROR while setting up xout." );
+ // TODO: The following exception thrown if two different filters are initialized by the same process
+ 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)
- unsigned int isError;
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 );
@@ -79,20 +118,26 @@ ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
elastix->SetResultImageContainer( resultImageContainer );
elastix->SetOriginalFixedImageDirectionFlat( fixedImageOriginalDirection );
- // Set the current elastix-level
- elastix->SetElastixLevel( i );
- elastix->SetTotalNumberOfElastixLevels( 1 );
-
- // ITK pipe-line mechanism need a result image
- parameterMapList[ i ][ "WriteResultImage"] = ParameterValuesType( 1, std::string( "true" ) );
-
// Start registration
- isError = elastix->Run( argumentMap, parameterMapList[ i ] );
+ 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." );
+ }
- // Assert success
if( isError != 0 )
{
- itkExceptionMacro( "Errors occured" );
+ std::cout << std::endl << isError << std::endl;
+ itkExceptionMacro( << "Uncought errors occurred during registration." );
}
// Get the transform, the fixedImage and the movingImage
@@ -125,30 +170,30 @@ ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
// Save parameter map
ParameterObject::Pointer TransformParameters = ParameterObject::New();
TransformParameters->SetParameterMapList( TransformParameterMapList );
- this->SetOutput( "TransformParametersObject", static_cast< itk::DataObject* >( TransformParameters ) );
+ this->SetOutput( "TransformParameterObject", static_cast< itk::DataObject* >( TransformParameters ) );
// Clean up
- transform = 0;
- fixedImageContainer = 0;
- movingImageContainer = 0;
- fixedMaskContainer = 0;
- movingMaskContainer = 0;
- resultImageContainer = 0;
+ transform = ITK_NULLPTR;
+ fixedImageContainer = ITK_NULLPTR;
+ movingImageContainer = ITK_NULLPTR;
+ fixedMaskContainer = ITK_NULLPTR;
+ movingMaskContainer = ITK_NULLPTR;
+ resultImageContainer = ITK_NULLPTR;
// Close the modules
ElastixMainType::UnloadComponents();
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
void
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+ElastixFilter< TFixedImage, TMovingImage >
::SetFixedImage( FixedImagePointer fixedImage )
{
+ // Free references to fixed images that has already been set
if( this->m_FixedImageContainer->Size() > 0 )
{
- // Free images that has already been given
- this->m_FixedImageContainer = 0;
+ this->m_FixedImageContainer = ITK_NULLPTR;
}
// Input for elastix
@@ -158,9 +203,9 @@ ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
this->SetInput( DataObjectIdentifierType( "FixedImage" ), this->m_FixedImageContainer->ElementAt( 0 ) );
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
void
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+ElastixFilter< TFixedImage, TMovingImage >
::SetFixedImage( DataObjectContainerPointer fixedImages )
{
// Input for elastix
@@ -170,68 +215,69 @@ ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
this->SetInput( DataObjectIdentifierType( "FixedImage" ), this->m_FixedImageContainer->ElementAt( 0 ) );
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
void
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+ElastixFilter< TFixedImage, TMovingImage >
::SetMovingImage( MovingImagePointer movingImage )
{
+ // Free references to moving images that has already been set
if( this->m_MovingImageContainer->Size() > 0 )
{
- // Free images that has already been given
- this->m_MovingImageContainer = 0;
+
+ this->m_MovingImageContainer = ITK_NULLPTR;
}
// Input for elastix
this->m_MovingImageContainer->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( movingImage ) ;
- // Primary input for ITK pipeline
+ // Input for ITK pipeline
this->SetInput( DataObjectIdentifierType( "MovingImage" ), this->m_MovingImageContainer->ElementAt( 0 ) );
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
void
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+ElastixFilter< TFixedImage, TMovingImage >
::SetMovingImage( DataObjectContainerPointer movingImages )
{
// Input for elastix
this->m_MovingImageContainer = movingImages;
- // Primary input for ITK pipeline
+ // Input for ITK pipeline
this->SetInput( DataObjectIdentifierType( "MovingImage" ), this->m_MovingImageContainer->ElementAt( 0 ) );
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
void
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+ElastixFilter< TFixedImage, TMovingImage >
::SetParameterObject( ParameterObjectPointer parameterObject )
{
this->SetInput( DataObjectIdentifierType( "ParameterObject" ), static_cast< itk::DataObject* >( parameterObject ) );
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
void
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+ElastixFilter< TFixedImage, TMovingImage >
::SetFixedMask( FixedImagePointer fixedMask )
{
this->SetInput( DataObjectIdentifierType( "FixedMask" ), static_cast< itk::DataObject* >( fixedMask ) );
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
void
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+ElastixFilter< TFixedImage, TMovingImage >
::SetMovingMask( MovingImagePointer movingMask )
{
this->SetInput( DataObjectIdentifierType( "MovingMask" ), static_cast< itk::DataObject* >( movingMask ) );
}
-template< typename TFixedImage, typename TMovingImage, typename TOutputImage >
-typename selx::ElastixFilter< TFixedImage, TMovingImage, TOutputImage >::ParameterObjectPointer
-ElastixFilter< TFixedImage, TMovingImage, TOutputImage >
+template< typename TFixedImage, typename TMovingImage >
+typename selx::ElastixFilter< TFixedImage, TMovingImage >::ParameterObjectPointer
+ElastixFilter< TFixedImage, TMovingImage >
::GetTransformParameters( void )
{
- return static_cast< ParameterObject* >( itk::ProcessObject::GetOutput( DataObjectIdentifierType( "TransformParametersObject" ) ) );
+ return static_cast< ParameterObject* >( itk::ProcessObject::GetOutput( DataObjectIdentifierType( "TransformParameterObject" ) ) );
}
} // namespace selx
-#endif // ElastixComponent_hxx
\ No newline at end of file
+#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
new file mode 100644
index 0000000000000000000000000000000000000000..a981680a92257b5d20103fc2771ad2d7239aaa69
--- /dev/null
+++ b/Modules/Components/Elastix/include/elxTransformixFilter.h
@@ -0,0 +1,99 @@
+#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 SetTransformParameters( 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 DeletePointSetFileName() { this->m_PointSetFileName = std::string(); };
+
+ itkSetMacro( OutputDirectory, std::string );
+ itkGetConstMacro( OutputDirectory, std::string );
+ void DeleteOutputDirectory() { this->m_OutputDirectory = std::string(); };
+
+ 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;
+ 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
new file mode 100644
index 0000000000000000000000000000000000000000..29136c2c0cf9af0696c0c8149dd9ece9c3d70616
--- /dev/null
+++ b/Modules/Components/Elastix/include/elxTransformixFilter.hxx
@@ -0,0 +1,177 @@
+#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->m_PointSetFileName = 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()." )
+ }
+
+ // 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( << "Only one of ComputeDeformationFieldOn() or SetPointSetFileName() can be "
+ << "active at any one time for backwards compatibility." )
+ }
+
+ // Setup arguments that transformix uses to 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().")
+ }
+ logFileName = this->GetOutputDirectory() + "transformix.log";
+ }
+
+ if( elx::xoutSetup( logFileName.c_str(), this->GetLogToFile(), this->GetLogToConsole() ) )
+ {
+ // TODO: The following exception is thrown if two different filters are initialized by the same process
+ itkExceptionMacro( "ERROR while setting up xout" );
+ }
+
+ TransformixMainPointer transformix = TransformixMainType::New();
+
+ // Setup image containers
+ DataObjectContainerPointer inputImageContainer = 0;
+ if( this->HasInput( "InputImage" ) ) {
+ std::cout << "Input image is set" << std::endl;
+ DataObjectContainerPointer inputImageContainer = DataObjectContainerType::New();
+ inputImageContainer->CreateElementAt(0) = this->GetInput("InputImage");
+ }
+ transformix->SetMovingImageContainer( inputImageContainer );
+
+ DataObjectContainerPointer resultImageContainer = 0;
+ 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 )
+ {
+ std::cout << std::endl << isError << std::endl;
+ itkExceptionMacro( << "Uncought errors occured during registration." );
+ }
+
+ // Save result image
+ resultImageContainer = transformix->GetResultImageContainer();
+ if( resultImageContainer.IsNotNull() && resultImageContainer->Size() > 0 )
+ {
+ this->SetOutput( "ResultImage", resultImageContainer->ElementAt( 0 ) );
+ }
+}
+
+template< typename TInputImage >
+void
+TransformixFilter< TInputImage >
+::SetInputImage( InputImagePointer inputImage )
+{
+ this->SetInput( DataObjectIdentifierType( "InputImage" ), static_cast< itk::DataObject* >( inputImage ) );
+}
+
+template< typename TInputImage >
+void
+TransformixFilter< TInputImage >
+::SetTransformParameters( ParameterObjectPointer parameterObject )
+{
+ this->SetInput( DataObjectIdentifierType( "TransformParameterObject" ), static_cast< itk::DataObject* >( parameterObject ) );
+}
+
+template< typename TInputImage >
+typename selx::TransformixFilter< TInputImage >::ParameterObjectPointer
+TransformixFilter< TInputImage >
+::GetTransformParameters( void )
+{
+ return static_cast< ParameterObject* >( itk::ProcessObject::GetInput( DataObjectIdentifierType( "TransformParameterObject" ) ) );
+}
+
+} // namespace selx
+
+#endif // TransformixFilter_hxx
\ No newline at end of file
diff --git a/Modules/Core/Common/include/elxMacro.h b/Modules/Core/Common/include/elxMacro.h
index 15f63f9ee33b2af82f4136af788092f07e9e3095..b2d2de1c8351e4d5bdb508b0437412f483497e19 100644
--- a/Modules/Core/Common/include/elxMacro.h
+++ b/Modules/Core/Common/include/elxMacro.h
@@ -1,5 +1,5 @@
-#ifndef __elxMacro_h
-#define __elxMacro_h
+#ifndef elxMacro_h
+#define elxMacro_h
/**
* Register class with the object factory and set RTTI (Run-Time Type
@@ -12,4 +12,4 @@
itkNewMacro( Self ); \
itkTypeMacro( Self, superClassName ); \
-#endif // __elxMacro_h
\ No newline at end of file
+#endif // elxMacro_h
\ No newline at end of file
diff --git a/Modules/Core/ParameterObject/include/elxParameterObject.h b/Modules/Core/ParameterObject/include/elxParameterObject.h
index 3bfbe1f49cbd15f614cd49c7daa0adb7e698701e..9cb838f17127694bfdf312f8f9412578e57c40a8 100644
--- a/Modules/Core/ParameterObject/include/elxParameterObject.h
+++ b/Modules/Core/ParameterObject/include/elxParameterObject.h
@@ -14,9 +14,11 @@ public:
elxNewMacro( ParameterObject, itk::DataObject );
- typedef std::vector< std::string > ParameterValuesType;
- typedef std::map< std::string, ParameterValuesType > ParameterMapType;
- typedef std::vector< ParameterMapType > ParameterMapListType;
+ 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 )
{
@@ -30,20 +32,16 @@ public:
this->m_ParameterMapList = parameterMapList;
};
- ParameterMapListType GetParameterMapList( void )
+ ParameterMapListType& GetParameterMapList( void )
{
+ this->Modified();
return this->m_ParameterMapList;
};
- // TODO:
- // itkSetMacro( ParameterMap, ParameterMapType )
- // itkGetMacro( ParameterMap, ParameterMapType )
-
- // friend ITKCommon_EXPORT std::ostream& operator<<( std::ostream& os, const ParameterObject& parameterObject )
- // {
- // os << parameterObject.m_ParameterMapList;
- // return os;
- // }
+ const ParameterMapListType& GetParameterMapList( void ) const
+ {
+ return this->m_ParameterMapList;
+ };
private:
diff --git a/SuperBuild/CMakeLists.txt b/SuperBuild/CMakeLists.txt
index 0b216a8174184a8c62d742f48b41f3cb0824b267..3b25ce094423203ccf017218f4033fec70ee2c87 100644
--- a/SuperBuild/CMakeLists.txt
+++ b/SuperBuild/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required( VERSION 2.8 )
+cmake_minimum_required( VERSION 3.0.2 )
# ---------------------------------------------------------------------
project( SuperElastixSuperBuild )
@@ -56,6 +56,28 @@ else()
include( ExternalITK )
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 SuperElastix support Elastix ${ELASTIX_VERSION_STRING}." ON )
+if( SUPERELASTIX_BUILD_ELASTIX )
+ 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." )
+ endif()
+ else()
+ include( ExternalElastix )
+ endif()
+endif()
+
# ---------------------------------------------------------------------
# Boost Graph Library
@@ -81,24 +103,6 @@ if ( SUPERELASTIX_BUILD_TESTING )
endif()
endif()
-# ---------------------------------------------------------------------
-# Build Elastix
-
-mark_as_advanced( SUPERELASTIX_BUILD_ELASTIX )
-option( SUPERELASTIX_BUILD_ELASTIX ON )
-if( SUPERELASTIX_BUILD_ELASTIX )
- 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." )
- endif()
- else()
- include( ExternalElastix )
- endif()
-endif()
-
# ---------------------------------------------------------------------
# Build SuperElastix
diff --git a/SuperBuild/ExternalElastix.cmake b/SuperBuild/ExternalElastix.cmake
index c1fe6b59df0d56977f82eead1b340b63d644d1ff..8a922598183686109bb27a7e9b283e18fb369d56 100644
--- a/SuperBuild/ExternalElastix.cmake
+++ b/SuperBuild/ExternalElastix.cmake
@@ -1,6 +1,6 @@
set( proj Elastix )
-set( ELASTIX_REPOSITORY git://github.com/mstaring/elastix.git )
+set( ELASTIX_REPOSITORY https://github.com/mstaring/elastix.git )
set( ELASTIX_TAG c35842cd0152d8fd2894e7c6706d2dd8396f0fed )
ExternalProject_Add( ${proj}
diff --git a/Testing/Unit/CMakeLists.txt b/Testing/Unit/CMakeLists.txt
index 6270de443aa16e688de9ea1d79e562e6ce98df6f..0e9d8951907de462a75b703d71b6cd1756cd6fef 100644
--- a/Testing/Unit/CMakeLists.txt
+++ b/Testing/Unit/CMakeLists.txt
@@ -6,10 +6,16 @@
set( ElastixUnitTestFilenames
elxBlueprintTest.cxx
elxElastixFilterTest.cxx
+ elxTransformixFilterTest.cxx
elxComponentFactoryTest.cxx
elxComponentInterfaceTest.cxx
)
+# ---------------------------------------------------------------------
+# Options
+if( SUPERELASTIX_BUILD_LONG_TESTS )
+ add_definitions( -DSUPERELASTIX_RUN_LONG_TESTS )
+endif()
# ---------------------------------------------------------------------
# Set data directories
@@ -44,6 +50,7 @@ list( APPEND TEST_LIBRARIES
# ---------------------------------------------------------------------
# Build tests
+message( STATUS "ITK_LIBRARIES: ${ITK_LIBRARIES}" )
foreach( ElastixUnitTestFilename ${ElastixUnitTestFilenames} )
# Build tests executables
string( REPLACE ".cxx" "" ElastixUnitTest ${ElastixUnitTestFilename} )
diff --git a/Testing/Unit/Data/Input/4D.nii.gz.md5 b/Testing/Unit/Data/Input/4D.nii.gz.md5
new file mode 100644
index 0000000000000000000000000000000000000000..6a3350182109aafc0de6a8976e5ccf192bd3b48b
--- /dev/null
+++ b/Testing/Unit/Data/Input/4D.nii.gz.md5
@@ -0,0 +1 @@
+58e10b6898a5d5271a890eecf25093c2
diff --git a/Testing/Unit/Data/Input/BrainProtonDensitySlice.png.md5 b/Testing/Unit/Data/Input/BrainProtonDensitySlice.png.md5
index 317f8a125578f6b03363ddc5c3ff4ce81209960e..274d1daaee9552f0b254c0e66d8e740c54d37aa7 100644
--- a/Testing/Unit/Data/Input/BrainProtonDensitySlice.png.md5
+++ b/Testing/Unit/Data/Input/BrainProtonDensitySlice.png.md5
@@ -1 +1 @@
-073df8eb397d1746d2343c78dd4bd964
\ No newline at end of file
+073df8eb397d1746d2343c78dd4bd964
diff --git a/Testing/Unit/Data/Input/BrainProtonDensitySliceBorder20.png.md5 b/Testing/Unit/Data/Input/BrainProtonDensitySliceBorder20.png.md5
new file mode 100644
index 0000000000000000000000000000000000000000..6302135e8a2fc9ca1e3abff8507d6765ea90ad40
--- /dev/null
+++ b/Testing/Unit/Data/Input/BrainProtonDensitySliceBorder20.png.md5
@@ -0,0 +1 @@
+9967b9c9bae3af9c3aac9676663ee05d
diff --git a/Testing/Unit/Data/Input/BrainProtonDensitySliceBorder20Mask.png.md5 b/Testing/Unit/Data/Input/BrainProtonDensitySliceBorder20Mask.png.md5
new file mode 100644
index 0000000000000000000000000000000000000000..3e5cf3a48eb5af617335075c95d615cbdab909b4
--- /dev/null
+++ b/Testing/Unit/Data/Input/BrainProtonDensitySliceBorder20Mask.png.md5
@@ -0,0 +1 @@
+646be5659d98e7cef40b63b3dff86726
diff --git a/Testing/Unit/Data/Input/BrainProtonDensitySliceR10X13Y17.png.md5 b/Testing/Unit/Data/Input/BrainProtonDensitySliceR10X13Y17.png.md5
index 93f3cd126feb7e33c9878ecf57b35692788d44e1..8058585db4a233381a44807b77344690a92a41f6 100644
--- a/Testing/Unit/Data/Input/BrainProtonDensitySliceR10X13Y17.png.md5
+++ b/Testing/Unit/Data/Input/BrainProtonDensitySliceR10X13Y17.png.md5
@@ -1 +1 @@
-610392a128986d934dfc0a1b0dc27e91
\ No newline at end of file
+610392a128986d934dfc0a1b0dc27e91
diff --git a/Testing/Unit/Data/Input/BrainProtonDensitySliceR10X13Y17S12.png.md5 b/Testing/Unit/Data/Input/BrainProtonDensitySliceR10X13Y17S12.png.md5
new file mode 100644
index 0000000000000000000000000000000000000000..42e5aa4981dbb5804312f4fa60344d470cd2f977
--- /dev/null
+++ b/Testing/Unit/Data/Input/BrainProtonDensitySliceR10X13Y17S12.png.md5
@@ -0,0 +1 @@
+eefa617b3220c1cea47bdc4672541b2d
diff --git a/Testing/Unit/Data/Input/BrainProtonDensitySliceShifted13x17y.png.md5 b/Testing/Unit/Data/Input/BrainProtonDensitySliceShifted13x17y.png.md5
new file mode 100644
index 0000000000000000000000000000000000000000..98dda290136268cbbe59b6847fc7262db576f320
--- /dev/null
+++ b/Testing/Unit/Data/Input/BrainProtonDensitySliceShifted13x17y.png.md5
@@ -0,0 +1 @@
+d3568c0d5c44afedb78305f620c0a79b
diff --git a/Testing/Unit/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd.md5 b/Testing/Unit/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd.md5
new file mode 100644
index 0000000000000000000000000000000000000000..52d8753b024de51c98f35a06c0b28e5d36ec314f
--- /dev/null
+++ b/Testing/Unit/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd.md5
@@ -0,0 +1 @@
+034e616e71ade1535cba4a77180ad79d
\ No newline at end of file
diff --git a/Testing/Unit/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd.md5 b/Testing/Unit/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd.md5
new file mode 100644
index 0000000000000000000000000000000000000000..151510adabe0f63adc8671662a149bf68cdf1eb1
--- /dev/null
+++ b/Testing/Unit/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd.md5
@@ -0,0 +1 @@
+49129770e7152ea5d203a519ac17be43
\ No newline at end of file
diff --git a/Testing/Unit/Data/Input/cthead1-Float.mha.md5 b/Testing/Unit/Data/Input/cthead1-Float.mha.md5
deleted file mode 100644
index 815300480e124b9a3eca98655a895642354483c2..0000000000000000000000000000000000000000
--- a/Testing/Unit/Data/Input/cthead1-Float.mha.md5
+++ /dev/null
@@ -1 +0,0 @@
-25de5707b18c0c684fd5fa30351bf787
\ No newline at end of file
diff --git a/Testing/Unit/elxElastixFilterTest.cxx b/Testing/Unit/elxElastixFilterTest.cxx
index 6dac45f0457d4ea648045eefedbf9c59e265a677..29fdc2e3cc79cc1f9957c44016a70faf382d7695 100644
--- a/Testing/Unit/elxElastixFilterTest.cxx
+++ b/Testing/Unit/elxElastixFilterTest.cxx
@@ -7,6 +7,15 @@
#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?
+
+
using namespace selx;
class ElastixFilterTest : public ::testing::Test
@@ -15,141 +24,368 @@ protected:
typedef DataManager DataManagerType;
- typedef itk::Image< float, 2u > ImageType;
- ImageType::Pointer fixedImage;
- ImageType::Pointer movingImage;
- ImageType::Pointer resultImage;
-
- typedef itk::ImageFileReader< ImageType > ImageReaderType;
- typedef itk::ImageFileWriter< ImageType > ImageWriterType;
-
- typedef ParameterObject::ParameterValuesType ParameterValuesType;
- typedef ParameterObject::ParameterMapType ParameterMapType;
- ParameterObject::Pointer parameterObject;
- ParameterObject::Pointer TransformParameterObject;
-
- typedef ElastixFilter< ImageType, ImageType, ImageType > ElastixFilterType;
- typedef ElastixFilterType::DataObjectContainerType DataObjectContainerType;
- typedef ElastixFilterType::DataObjectContainerPointer DataObjectContainerPointer;
+ // Parameter typedefs
+ typedef ParameterObject::ParameterVectorType ParameterVectorType;
+ typedef ParameterObject::ParameterMapType ParameterMapType;
+ ParameterMapType parameterMap;
+ ParameterObject::Pointer eulerTransformParameterObject;
+ ParameterObject::Pointer affineTransformParameterObject;
+ ParameterObject::Pointer correspondingPointsParameterObject;
+ ParameterObject::Pointer nonRigidParameterObject;
+ ParameterObject::Pointer nonRigidParameterObject3D;
+ ParameterObject::Pointer groupwiseParameterObject;
+ ParameterObject::ConstPointer transformParameterObject;
virtual void SetUp()
{
- DataManagerType::Pointer dataManager = DataManagerType::New();
-
- ImageReaderType::Pointer reader = ImageReaderType::New();
-
- reader->SetFileName( dataManager->GetInputFile( "cthead1-Float.mha" ) );
- fixedImage = reader->GetOutput();
-
- // TODO: Only call update on writer
- reader->Update();
-
- reader->SetFileName( dataManager->GetInputFile( "cthead1-Float.mha" ) );
- movingImage = reader->GetOutput();
-
- // TODO: Only call update on writer
- reader->Update();
-
- // ParameterMap
+ // Nonrigid ParameterMap
ParameterMapType parameterMap = ParameterMapType();
// Images
- parameterMap[ "FixedInternalImagePixelType" ] = ParameterValuesType( 1, "float" );
- parameterMap[ "FixedImageDimension" ] = ParameterValuesType( 1, "2" );
- parameterMap[ "MovingInternalImagePixelType" ] = ParameterValuesType( 1, "float" );
- parameterMap[ "MovingImageDimension" ] = ParameterValuesType( 1, "2" );
- parameterMap[ "ResultImagePixelType" ] = ParameterValuesType( 1, "float" );
+ 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" ] = ParameterValuesType( 1, "FixedSmoothingImagePyramid" );
- parameterMap[ "MovingImagePyramid" ] = ParameterValuesType( 1, "MovingSmoothingImagePyramid" );
- parameterMap[ "Interpolator"] = ParameterValuesType( 1, "LinearInterpolator");
- parameterMap[ "Optimizer" ] = ParameterValuesType( 1, "AdaptiveStochasticGradientDescent" );
- parameterMap[ "Resampler"] = ParameterValuesType( 1, "DefaultResampler" );
- parameterMap[ "ResampleInterpolator"] = ParameterValuesType( 1, "FinalLinearInterpolator" );
- parameterMap[ "FinalBSplineInterpolationOrder" ] = ParameterValuesType( 1, "2" );
- parameterMap[ "NumberOfResolutions" ] = ParameterValuesType( 1, "2" );
+ 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" ] = ParameterValuesType( 1, "RandomCoordinate" );
- parameterMap[ "NumberOfSpatialSamples"] = ParameterValuesType( 1, "2048" );
- parameterMap[ "CheckNumberOfSamples" ] = ParameterValuesType( 1, "true" );
- parameterMap[ "MaximumNumberOfSamplingAttempts" ] = ParameterValuesType( 1, "8" );
- parameterMap[ "NewSamplesEveryIteration" ] = ParameterValuesType( 1, "true");
+ 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" ] = ParameterValuesType( 1, "4096" );
- parameterMap[ "DefaultPixelValue" ] = ParameterValuesType( 1, "0" );
- parameterMap[ "AutomaticParameterEstimation" ] = ParameterValuesType( 1, "true" );
+ parameterMap[ "NumberOfSamplesForExactGradient" ] = ParameterVectorType( 1, "4096" );
+ parameterMap[ "DefaultPixelValue" ] = ParameterVectorType( 1, "0" );
+ parameterMap[ "AutomaticParameterEstimation" ] = ParameterVectorType( 1, "true" );
// Output
- parameterMap[ "WriteResultImage" ] = ParameterValuesType( 1, "false" );
- parameterMap[ "ResultImageFormat" ] = ParameterValuesType( 1, "nii" );
+ parameterMap[ "WriteResultImage" ] = ParameterVectorType( 1, "true" );
+ parameterMap[ "ResultImageFormat" ] = ParameterVectorType( 1, "nii" );
// Registration
- parameterMap[ "Registration" ] = ParameterValuesType( 1, "MultiResolutionRegistration" );
- parameterMap[ "Transform" ] = ParameterValuesType( 1, "EulerTransform" );
- parameterMap[ "Metric" ] = ParameterValuesType( 1, "AdvancedMattesMutualInformation" );
- parameterMap[ "MaximumNumberOfIterations" ] = ParameterValuesType( 1, "128" );
-
- parameterObject = ParameterObject::New();
- parameterObject->SetParameterMap( parameterMap );
+ 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 );
+
+ ParameterMapType affineTransformParameterMap = parameterMap;
+ affineTransformParameterMap[ "Transform" ] = ParameterVectorType( 1, "AffineTransform" );
+ affineTransformParameterObject = ParameterObject::New();
+ affineTransformParameterObject->SetParameterMap( affineTransformParameterMap );
+
+ ParameterMapType correspondingPointsParameterMap = parameterMap;
+ correspondingPointsParameterMap[ "Registration" ] = ParameterVectorType( 1, "MultiMetricMultiResolutionRegistration" );
+ correspondingPointsParameterMap[ "Transform" ] = ParameterVectorType( 1, "TranslationTransform" );
+ correspondingPointsParameterMap[ "Metric" ].push_back( "CorrespondingPointsEuclideanDistanceMetric" );
+ correspondingPointsParameterMap[ "Metric0Weight"] = ParameterVectorType( 1, "0.0" );
+ correspondingPointsParameterObject = ParameterObject::New();
+ correspondingPointsParameterObject->SetParameterMap( correspondingPointsParameterMap );
+
+ ParameterMapType nonRigidParameterMap = parameterMap;
+ nonRigidParameterMap[ "Transform" ] = ParameterVectorType( 1, "BSplineTransform" );
+ nonRigidParameterObject = ParameterObject::New();
+ nonRigidParameterObject->SetParameterMap( nonRigidParameterMap );
+
+ 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" );
+ nonRigidParameterObject3D = ParameterObject::New();
+ nonRigidParameterObject3D->SetParameterMap( nonRigidParameterMap3D );
+
+ 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" );
+ groupwiseParameterObject = ParameterObject::New();
+ groupwiseParameterObject->SetParameterMap( nonRigidParameterMap );
}
};
TEST_F( ElastixFilterTest, Instantiation )
{
+ typedef itk::Image< float, 2 > ImageType;
+ typedef ElastixFilter< ImageType, ImageType > ElastixFilterType;
EXPECT_NO_THROW( ElastixFilterType::Pointer elastixFilter = ElastixFilterType::New() );
}
-TEST_F( ElastixFilterTest, PairwiseRegistration )
+TEST_F( ElastixFilterTest, Euler2D )
{
- ElastixFilterType::Pointer elastixFilter = ElastixFilterType::New();
+ 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();
- elastixFilter->LogToConsoleOn();
- elastixFilter->SetFixedImage( fixedImage );
- elastixFilter->SetMovingImage( movingImage );
- elastixFilter->SetParameterObject( parameterObject );
+ ImageFileReaderType::Pointer fixedImageReader = ImageFileReaderType::New();
+ fixedImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceBorder20.png" ) );
+ fixedImageReader->Update();
- // TODO: This update should not be needed
- elastixFilter->Update();
+ ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
+ movingImageReader->SetFileName( dataManager->GetInputFile( "BrainProtonDensitySliceR10X13Y17.png" ) );
+ movingImageReader->Update();
- EXPECT_NO_THROW( resultImage = elastixFilter->GetOutput() );
- EXPECT_NO_THROW( TransformParameterObject = elastixFilter->GetTransformParameters() );
+ 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 ) );
- ImageWriterType::Pointer writer = ImageWriterType::New();
- writer->SetFileName( "ElastixResultImage.nii" );
+ // TODO: This update should not be needed (see description above)
+ EXPECT_NO_THROW( elastixFilter->Update() );
+
+ ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
+ writer->SetFileName( dataManager->GetOutputFile( "Euler2DResultImage.nii" ) );
writer->SetInput( elastixFilter->GetOutput() );
EXPECT_NO_THROW( writer->Update() );
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
}
-TEST_F( ElastixFilterTest, MultiPairwiseRegistration )
+TEST_F( ElastixFilterTest, AffineWithMultipleFixedAndMovingImages2D )
+ {
+ 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" ) );
+ 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();
+
+ DataObjectContainerPointer fixedImages = DataObjectContainerType::New();
+ fixedImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( fixedImageReader0->GetOutput() );
+ fixedImages->CreateElementAt( 1 ) = static_cast< itk::DataObject* >( fixedImageReader1->GetOutput() );
+
+ DataObjectContainerPointer movingImages = DataObjectContainerType::New();
+ movingImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( movingImageReader0->GetOutput() );
+ movingImages->CreateElementAt( 1 ) = static_cast< itk::DataObject* >( movingImageReader1->GetOutput() );
+
+ ElastixFilterType::Pointer elastixFilter = ElastixFilterType::New();
+ EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImages ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImages ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( affineTransformParameterObject ) );
+
+ // 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( "AffineWithMultipleFixedAndMovingImages2DResultImage.nii" ) ) );
+ EXPECT_NO_THROW( writer->SetInput( elastixFilter->GetOutput() ) );
+ EXPECT_NO_THROW( writer->Update() );
+
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
+ }
+
+TEST_F( ElastixFilterTest, TranslationWithPointSets2D )
{
+ 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();
+
+ // 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();
+
+ 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();
+
ElastixFilterType::Pointer 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->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() );
+
+ ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
+ writer->SetFileName( "TranslationWithPointSets2DResultImage.nii" );
+ writer->SetInput( elastixFilter->GetOutput() );
+ EXPECT_NO_THROW( writer->Update() );
- DataObjectContainerPointer fixedImages = DataObjectContainerType::New();
- fixedImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( fixedImage );
- fixedImages->CreateElementAt( 1 ) = static_cast< itk::DataObject* >( fixedImage );
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
+ }
- DataObjectContainerPointer movingImages = DataObjectContainerType::New();
- movingImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( movingImage );
- movingImages->CreateElementAt( 1 ) = static_cast< itk::DataObject* >( movingImage );
+TEST_F( ElastixFilterTest, BSplineWithFixedMask2D )
+{
+ 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" ) );
+ 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();
+
+ 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->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();
+ writer->SetFileName( dataManager->GetOutputFile( "BSplineWithFixedMask2DResultImage.nii" ) );
+ writer->SetInput( elastixFilter->GetOutput() );
+ EXPECT_NO_THROW( writer->Update() );
+
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
+}
+
+#ifdef SUPERELASTIX_RUN_LONG_TESTS
+
+TEST_F( ElastixFilterTest, BSpline3D )
+{
+ typedef itk::Image< float, 3 > 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( "OAS1_0001_MR1_mpr-1_anon.nrrd" ) );
+ fixedImageReader->Update();
- elastixFilter->LogToConsoleOn();
- elastixFilter->SetFixedImage( fixedImages );
- elastixFilter->SetMovingImage( movingImages );
- elastixFilter->SetParameterObject( parameterObject );
+ ImageFileReaderType::Pointer movingImageReader = ImageFileReaderType::New();
+ movingImageReader->SetFileName( dataManager->GetInputFile( "OAS1_0002_MR1_mpr-1_anon.nrrd" ) );
+ movingImageReader->Update();
- // TODO: This update should not be needed
- elastixFilter->Update();
+ 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 ) );
- EXPECT_NO_THROW( resultImage = elastixFilter->GetOutput() );
- EXPECT_NO_THROW( TransformParameterObject = elastixFilter->GetTransformParameters() );
+ // TODO: This update should not be needed (see description above)
+ EXPECT_NO_THROW( elastixFilter->Update() );
- ImageWriterType::Pointer writer = ImageWriterType::New();
- writer->SetFileName( "ElastixResultImage.nii" );
+ ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
+ writer->SetFileName( dataManager->GetOutputFile( "BSpline3DResultImage.nii" ) );
writer->SetInput( elastixFilter->GetOutput() );
EXPECT_NO_THROW( writer->Update() );
+
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
}
+
+// 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();
+//
+// 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() );
+//}
+
+#endif // SUPERELASTIX_RUN_LONG_TESTS
diff --git a/Testing/Unit/elxTransformixFilterTest.cxx b/Testing/Unit/elxTransformixFilterTest.cxx
new file mode 100644
index 0000000000000000000000000000000000000000..cfe47b1462947cca8ca15244220f158420c3b038
--- /dev/null
+++ b/Testing/Unit/elxTransformixFilterTest.cxx
@@ -0,0 +1,134 @@
+#include "elxElastixFilter.h"
+#include "elxTransformixFilter.h"
+#include "elxParameterObject.h"
+
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+
+#include "elxDataManager.h"
+#include "gtest/gtest.h"
+
+using namespace selx;
+
+class TransformixFilterTest : public ::testing::Test
+{
+protected:
+
+ typedef DataManager DataManagerType;
+
+ typedef ParameterObject::ParameterVectorType ParameterVectorType;
+ typedef ParameterObject::ParameterMapType ParameterMapType;
+
+ typedef itk::Image< float, 2 > ImageType;
+ typedef itk::ImageFileReader< ImageType > ImageFileReaderType;
+ typedef itk::ImageFileWriter< ImageType > ImageFileWriterType;
+ typedef ElastixFilter< ImageType, ImageType > ElastixFilterType;
+ 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 )
+{
+ typedef itk::Image< float, 2 > ImageType;
+ typedef ElastixFilter< ImageType, ImageType > ElastixFilterType;
+ EXPECT_NO_THROW( ElastixFilterType::Pointer elastixFilter = ElastixFilterType::New() );
+}
+
+TEST_F( TransformixFilterTest, Euler2D )
+{
+ 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 ) );
+
+ // TODO: This update should not be needed (see description in elxElastixFilterTest.cxx)
+ elastixFilter->Update();
+
+ TransformixFilterType::Pointer transformixFilter;
+ EXPECT_NO_THROW( transformixFilter = TransformixFilterType::New() );
+ EXPECT_NO_THROW( transformixFilter->SetInputImage( movingImageReader->GetOutput() ) );
+ EXPECT_NO_THROW( transformixFilter->SetTransformParameters( elastixFilter->GetTransformParameters() ) );
+ EXPECT_NO_THROW( transformixFilter->ComputeSpatialJacobianOn() );
+ EXPECT_NO_THROW( transformixFilter->ComputeDeterminantOfSpatialJacobianOn() );
+ EXPECT_NO_THROW( transformixFilter->ComputeDeformationFieldOn() );
+ // EXPECT_NO_THROW( transformixFilter->SetPointSetFileName( dataManager->GetInputFile( "InputMesh.pts" ) ) );
+ EXPECT_NO_THROW( transformixFilter->SetOutputDirectory( dataManager->GetOutputDirectory() ) );
+
+ transformixFilter->Update();
+
+ ImageFileWriterType::Pointer writer = ImageFileWriterType::New();
+ writer->SetFileName( dataManager->GetOutputFile( "Euler2DTransformixResultImage.nii" ) );
+ writer->SetInput( transformixFilter->GetOutput() );
+ writer->Update();
+ EXPECT_NO_THROW( writer->Update() );
+}