From e6dcc71c8c8ebc767bf4ea7105e572e5e7d24546 Mon Sep 17 00:00:00 2001
From: Kasper Marstal <kaspermarstal@gmail.com>
Date: Fri, 11 Dec 2015 17:34:44 +0100
Subject: [PATCH] WIP: CorrespondingPointsEuclideanDistanceMetric ElastixFilter
test
---
.../Elastix/include/elxElastixFilter.h | 16 +--
.../Elastix/include/elxElastixFilter.hxx | 15 +--
Testing/Unit/elxElastixFilterTest.cxx | 119 ++++++++++++------
3 files changed, 99 insertions(+), 51 deletions(-)
diff --git a/Modules/Components/Elastix/include/elxElastixFilter.h b/Modules/Components/Elastix/include/elxElastixFilter.h
index 3fe121b9..5da1b96d 100644
--- a/Modules/Components/Elastix/include/elxElastixFilter.h
+++ b/Modules/Components/Elastix/include/elxElastixFilter.h
@@ -52,13 +52,13 @@ public:
void SetParameterObject( ParameterObjectPointer parameterObject );
ParameterObjectConstPointer GetTransformParameters( void ) const;
- itkSetMacro( FixedPointSetFileName, std::string );
- itkGetConstMacro( FixedPointSetFileName, std::string );
- void DeleteFixedPointSet( void ) { this->SetFixedPointSetFileName( std::string() ); };
+ itkSetMacro( FixedMeshFileName, std::string );
+ itkGetConstMacro( FixedMeshFileName, std::string );
+ void DeleteFixedMesh( void ) { this->SetFixedMeshFileName( std::string() ); };
- itkSetMacro( MovingPointSetFileName, std::string );
- itkGetConstMacro( MovingPointSetFileName, std::string );
- void DeleteMovingPointSet( void ) { this->SetMovingPointSetFileName( std::string() ); };
+ itkSetMacro( MovingMeshFileName, std::string );
+ itkGetConstMacro( MovingMeshFileName, std::string );
+ void DeleteMovingMesh( void ) { this->SetMovingMeshFileName( std::string() ); };
itkSetMacro( LogToConsole, bool );
itkGetConstMacro( LogToConsole, bool );
@@ -82,8 +82,8 @@ private:
DataObjectContainerPointer m_FixedMaskContainer;
DataObjectContainerPointer m_MovingMaskContainer;
- std::string m_FixedPointSetFileName;
- std::string m_MovingPointSetFileName;
+ std::string m_FixedMeshFileName;
+ std::string m_MovingMeshFileName;
bool m_LogToConsole;
std::string m_LogToFile;
diff --git a/Modules/Components/Elastix/include/elxElastixFilter.hxx b/Modules/Components/Elastix/include/elxElastixFilter.hxx
index b2d92006..a9614a8b 100644
--- a/Modules/Components/Elastix/include/elxElastixFilter.hxx
+++ b/Modules/Components/Elastix/include/elxElastixFilter.hxx
@@ -17,8 +17,8 @@ ElastixFilter< TFixedImage, TMovingImage >
this->m_FixedImageContainer = DataObjectContainerType::New();
this->m_MovingImageContainer = DataObjectContainerType::New();
- this->m_FixedPointSetFileName = std::string();
- this->m_MovingPointSetFileName = std::string();
+ this->m_FixedMeshFileName = std::string();
+ this->m_MovingMeshFileName = std::string();
}
template< typename TFixedImage, typename TMovingImage >
@@ -58,15 +58,16 @@ ElastixFilter< TFixedImage, TMovingImage >
ArgumentMapType argumentMap;
argumentMap.insert( ArgumentMapEntryType( "-out", std::string( "output_path_not_set" ) ) );
- // Set point sets
- if( !this->m_FixedPointSetFileName.empty() )
+ // Fixed mesh (optional)
+ if( !this->m_FixedMeshFileName.empty() )
{
- argumentMap.insert( ArgumentMapEntryType( "-fp", std::string( this->m_FixedPointSetFileName ) ) );
+ argumentMap.insert( ArgumentMapEntryType( "-fp", std::string( this->m_FixedMeshFileName ) ) );
}
- if( !this->m_MovingPointSetFileName.empty() )
+ // Moving mesh (optional)
+ if( !this->m_MovingMeshFileName.empty() )
{
- argumentMap.insert( ArgumentMapEntryType( "-mp", std::string( this->m_MovingPointSetFileName ) ) );
+ argumentMap.insert( ArgumentMapEntryType( "-mp", std::string( this->m_MovingMeshFileName ) ) );
}
// Setup xout
diff --git a/Testing/Unit/elxElastixFilterTest.cxx b/Testing/Unit/elxElastixFilterTest.cxx
index a94d63c3..c0d71833 100644
--- a/Testing/Unit/elxElastixFilterTest.cxx
+++ b/Testing/Unit/elxElastixFilterTest.cxx
@@ -1,6 +1,8 @@
#include "elxElastixFilter.h"
#include "elxParameterObject.h"
+#include "itkMesh.h"
+#include "itkMeshFileReader.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
@@ -15,43 +17,54 @@ protected:
typedef DataManager DataManagerType;
- typedef itk::Image< float, 2u > ImageType;
+ // Mesh typedef
+ typedef itk::Mesh< float, 2u > MeshType;
+ typedef itk::MeshFileReader< MeshType > MeshReaderType;
+
+ // Image typedefs
+ typedef itk::Image< float, 2u > ImageType;
+ typedef itk::ImageFileReader< ImageType > ImageReaderType;
+ typedef itk::ImageFileWriter< ImageType > ImageWriterType;
+
+ // Parameter typedefs
+ typedef ParameterObject::ParameterValuesType ParameterValuesType;
+ typedef ParameterObject::ParameterMapType ParameterMapType;
+
+ // Elastix typedefs
+ typedef ElastixFilter< ImageType, ImageType > ElastixFilterType;
+ typedef ElastixFilterType::DataObjectContainerType DataObjectContainerType;
+ typedef ElastixFilterType::DataObjectContainerPointer DataObjectContainerPointer;
+
+ // Variables used by multiple tests
ImageType::Pointer fixedImage;
ImageType::Pointer movingImage;
ImageType::Pointer resultImage;
- typedef itk::ImageFileReader< ImageType > ImageReaderType;
- typedef itk::ImageFileWriter< ImageType > ImageWriterType;
+ std::string fixedMeshFileName;
+ std::string movingMeshFileName;
- typedef ParameterObject::ParameterValuesType ParameterValuesType;
- typedef ParameterObject::ParameterMapType ParameterMapType;
ParameterObject::Pointer parameterObject;
- ParameterObject::ConstPointer TransformParameterObject;
-
- typedef ElastixFilter< ImageType, ImageType > ElastixFilterType;
- typedef ElastixFilterType::DataObjectContainerType DataObjectContainerType;
- typedef ElastixFilterType::DataObjectContainerPointer DataObjectContainerPointer;
-
+ ParameterObject::Pointer correspondingPointsParameterObject;
+ 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: All calls to update here should not be needed but should be propagated to reader by ElastixFilter
- // TODO: Only call update on writer
- reader->Update();
+ // Input images
+ ImageReaderType::Pointer fixedImageReader = ImageReaderType::New();
+ fixedImageReader->SetFileName( dataManager->GetInputFile( "cthead1-Float.mha" ) );
+ fixedImage = fixedImageReader->GetOutput();
+ fixedImageReader->Update();
- reader->SetFileName( dataManager->GetInputFile( "cthead1-Float.mha" ) );
- movingImage = reader->GetOutput();
+ ImageReaderType::Pointer movingImageReader = ImageReaderType::New();
+ movingImageReader->SetFileName( dataManager->GetInputFile( "cthead1-Float.mha" ) );
+ movingImage = movingImageReader->GetOutput();
+ movingImageReader->Update();
- // TODO: Only call update on writer
- reader->Update();
-
- // ParameterMap
+ // Nonrigid ParameterMap
ParameterMapType parameterMap = ParameterMapType();
// Images
@@ -93,8 +106,18 @@ protected:
parameterMap[ "Metric" ] = ParameterValuesType( 1, "AdvancedMattesMutualInformation" );
parameterMap[ "MaximumNumberOfIterations" ] = ParameterValuesType( 1, "128" );
+ ParameterMapType nonRigidParameterMap = parameterMap;
parameterObject = ParameterObject::New();
- parameterObject->SetParameterMap( parameterMap );
+ parameterObject->SetParameterMap( nonRigidParameterMap );
+
+ ParameterMapType correspondingPointsParameterMap = parameterMap;
+
+ // TODO: WHY DOES THIS SEGFAULT?
+ //correspondingPointsParameterMap[ "Metric" ][ 1 ] = "CorrespondingPointsEuclideanDistanceMetric";
+ //correspondingPointsParameterObject->SetParameterMap( correspondingPointsParameterMap );
+
+ fixedMeshFileName = dataManager->GetInputFile( "bioid_0000.vtk" );
+ movingMeshFileName = dataManager->GetInputFile( "bioid_0001.vtk" );
}
};
@@ -107,16 +130,16 @@ TEST_F( ElastixFilterTest, PairwiseRegistration )
{
ElastixFilterType::Pointer elastixFilter = ElastixFilterType::New();
- elastixFilter->LogToConsoleOn();
- elastixFilter->SetFixedImage( fixedImage );
- elastixFilter->SetMovingImage( movingImage );
- elastixFilter->SetParameterObject( parameterObject );
+ EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImage ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImage ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
// TODO: This update should not be needed
- elastixFilter->Update();
+ EXPECT_NO_THROW( elastixFilter->Update() );
EXPECT_NO_THROW( resultImage = elastixFilter->GetOutput() );
- EXPECT_NO_THROW( TransformParameterObject = elastixFilter->GetTransformParameters() );
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
ImageWriterType::Pointer writer = ImageWriterType::New();
writer->SetFileName( "ElastixResultImage.nii" );
@@ -138,21 +161,45 @@ TEST_F( ElastixFilterTest, MultiPairwiseRegistration )
movingImages->CreateElementAt( 0 ) = static_cast< itk::DataObject* >( movingImage );
movingImages->CreateElementAt( 1 ) = static_cast< itk::DataObject* >( movingImage );
- elastixFilter->LogToConsoleOn();
- elastixFilter->SetFixedImage( fixedImages );
- elastixFilter->SetMovingImage( movingImages );
- elastixFilter->SetParameterObject( parameterObject );
+ EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImages ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImages ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
+
+ // TODO: This update should not be needed
+ EXPECT_NO_THROW( elastixFilter->Update() );
+
+ EXPECT_NO_THROW( resultImage = elastixFilter->GetOutput() );
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
+
+ ImageWriterType::Pointer writer = ImageWriterType::New();
+ writer->SetFileName( "ElastixResultImage.nii" );
+ writer->SetInput( elastixFilter->GetOutput() );
+ EXPECT_NO_THROW( writer->Update() );
+}
+
+TEST_F( ElastixFilterTest, PointSetRegistration )
+{
+ ElastixFilterType::Pointer elastixFilter = ElastixFilterType::New();
+
+ EXPECT_NO_THROW( elastixFilter->LogToConsoleOn() );
+ EXPECT_NO_THROW( elastixFilter->SetFixedImage( fixedImage ) );
+ EXPECT_NO_THROW( elastixFilter->SetFixedMeshFileName( fixedMeshFileName ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingImage( movingImage ) );
+ EXPECT_NO_THROW( elastixFilter->SetMovingMeshFileName( movingMeshFileName ) );
+ EXPECT_NO_THROW( elastixFilter->SetParameterObject( parameterObject ) );
// TODO: This update should not be needed
- elastixFilter->Update();
+ EXPECT_NO_THROW( elastixFilter->Update() );
EXPECT_NO_THROW( resultImage = elastixFilter->GetOutput() );
- EXPECT_NO_THROW( TransformParameterObject = elastixFilter->GetTransformParameters() );
+ EXPECT_NO_THROW( transformParameterObject = elastixFilter->GetTransformParameters() );
ImageWriterType::Pointer writer = ImageWriterType::New();
writer->SetFileName( "ElastixResultImage.nii" );
writer->SetInput( elastixFilter->GetOutput() );
EXPECT_NO_THROW( writer->Update() );
+
}
// TODO: Write test with point sets
--
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