selxRegistrationItkv4Test.cxx

/*=========================================================================
 *
 *  Copyright Leiden University Medical Center, Erasmus University Medical 
 *  Center and contributors
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *        http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

#include "selxSuperElastixFilter.h"

#include "TransformComponent1.h"
#include "MetricComponent1.h"
#include "GDOptimizer3rdPartyComponent.h"
#include "GDOptimizer4thPartyComponent.h"
#include "SSDMetric3rdPartyComponent.h"
#include "SSDMetric4thPartyComponent.h"

#include "selxItkSmoothingRecursiveGaussianImageFilterComponent.h"
#include "selxDisplacementFieldItkImageFilterSink.h"
#include "selxItkImageSource.h"
#include "selxItkImageSink.h"

#include "selxItkImageRegistrationMethodv4Component.h"
#include "selxItkANTSNeighborhoodCorrelationImageToImageMetricv4.h"
#include "selxItkMeanSquaresImageToImageMetricv4.h"
#include "selxItkGradientDescentOptimizerv4.h"
#include "selxItkAffineTransform.h"
#include "selxItkGaussianExponentialDiffeomorphicTransform.h"
#include "selxItkTransformDisplacementFilter.h"
#include "selxItkResampleFilter.h"
#include "selxItkImageSourceFixed.h"
#include "selxItkImageSourceMoving.h"

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkMeshFileReader.h"
#include "itkMeshFileWriter.h" 

#include "DefaultComponents.h"

#include "selxDataManager.h"
#include "gtest/gtest.h"

namespace selx {

class RegistrationItkv4Test : public ::testing::Test {
public:
  typedef Blueprint::Pointer                BlueprintPointerType;
  typedef Blueprint::ConstPointer           BlueprintConstPointerType;
  typedef Blueprint::ParameterMapType       ParameterMapType;
  typedef Blueprint::ParameterValueType     ParameterValueType;
  typedef DataManager DataManagerType;
  
     /** register all example components */
  typedef TypeList < TransformComponent1,
    MetricComponent1,
    GDOptimizer3rdPartyComponent,
    GDOptimizer4thPartyComponent,
    SSDMetric3rdPartyComponent,
    SSDMetric4thPartyComponent,
    DisplacementFieldItkImageFilterSinkComponent<3, double>,
    DisplacementFieldItkImageFilterSinkComponent<2, float>,
    ItkImageSinkComponent<3, double>,
    ItkImageSinkComponent<2, float>,
    ItkImageSourceFixedComponent<2, float>,
    ItkImageSourceMovingComponent<2, float>,
    ItkImageSourceFixedComponent<3, double>,
    ItkImageSourceMovingComponent<3, double>,
    ItkSmoothingRecursiveGaussianImageFilterComponent<3, double>,
    ItkSmoothingRecursiveGaussianImageFilterComponent<2, double>,
    ItkSmoothingRecursiveGaussianImageFilterComponent<3, float>,
    ItkSmoothingRecursiveGaussianImageFilterComponent<2, float>,
    ItkImageRegistrationMethodv4Component<3, double>,
    ItkImageRegistrationMethodv4Component<2, float>,
    ItkANTSNeighborhoodCorrelationImageToImageMetricv4Component<3, double>,
    ItkMeanSquaresImageToImageMetricv4Component<3, double>,
    ItkANTSNeighborhoodCorrelationImageToImageMetricv4Component<2, float>,
    ItkMeanSquaresImageToImageMetricv4Component < 2, float >,
    ItkGradientDescentOptimizerv4Component<double>,
    ItkAffineTransformComponent<double,3>,
    ItkGaussianExponentialDiffeomorphicTransformComponent<double, 3>,
    ItkTransformDisplacementFilterComponent<2, float, double >,
    ItkTransformDisplacementFilterComponent<3, double, double >,
    ItkResampleFilterComponent<2, float, double >,
    ItkResampleFilterComponent<3, double, double >> RegisterComponents;
	
  typedef SuperElastixFilter<RegisterComponents>          SuperElastixFilterType;

  typedef itk::Image<float, 2> Image2DType;
  typedef itk::ImageFileReader<Image2DType> ImageReader2DType;
  typedef itk::ImageFileWriter<Image2DType> ImageWriter2DType;

  typedef itk::Image<double, 3> Image3DType;
  typedef itk::ImageFileReader<Image3DType> ImageReader3DType;
  typedef itk::ImageFileWriter<Image3DType> ImageWriter3DType;

  typedef itk::Image<itk::Vector<double,3>, 3> DisplacementImage3DType;
  typedef itk::ImageFileWriter<DisplacementImage3DType> DisplacementImageWriter3DType;

  virtual void SetUp() {
 

  }

  virtual void TearDown() {
    itk::ObjectFactoryBase::UnRegisterAllFactories();
  }

  BlueprintPointerType blueprint;
  

};

// These test are disabled, since may not want to check each component with this much boilerplate code. 
// We should consider moving functional tests outside the unit tests
// Anyway, the Blueprint configuration needs to be updated
TEST_F(RegistrationItkv4Test, DISABLED_3DImagesOnly) 
{
  /** make example blueprint configuration */
  blueprint = Blueprint::New();

  ParameterMapType component0Parameters;
  component0Parameters["NameOfClass"] = { "ItkImageRegistrationMethodv4Component" };
  component0Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("RegistrationMethod", component0Parameters);

  ParameterMapType component1Parameters;
  component1Parameters["NameOfClass"] = { "ItkImageSourceFixedComponent" };
  component1Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("FixedImageSource", component1Parameters);

  ParameterMapType component2Parameters;
  component2Parameters["NameOfClass"] = { "ItkImageSourceMovingComponent" };
  component2Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("MovingImageSource", component2Parameters);

  ParameterMapType component3Parameters;
  component3Parameters["NameOfClass"] = { "ItkImageSinkComponent" };
  component3Parameters["Dimensionality"] = { "3" }; // should be derived from the outputs
  blueprint->AddComponent("ResultImageSink", component3Parameters);


  ParameterMapType connection1Parameters;
  connection1Parameters["NameOfInterface"] = { "itkImageFixedInterface" };
  blueprint->AddConnection("FixedImageSource", "RegistrationMethod", connection1Parameters);

  ParameterMapType connection2Parameters;
  connection2Parameters["NameOfInterface"] = { "itkImageMovingInterface" };
  blueprint->AddConnection("MovingImageSource", "RegistrationMethod", connection2Parameters);

  ParameterMapType connection3Parameters;
  connection3Parameters["NameOfInterface"] = { "itkImageInterface" };
  blueprint->AddConnection("RegistrationMethod", "ResultImageSink", connection3Parameters);

  // Instantiate SuperElastix
  SuperElastixFilterType::Pointer superElastixFilter;
  EXPECT_NO_THROW(superElastixFilter = SuperElastixFilterType::New());

  // Data manager provides the paths to the input and output data for unit tests
  DataManagerType::Pointer dataManager = DataManagerType::New();

  // Set up the readers and writers
  ImageReader3DType::Pointer fixedImageReader = ImageReader3DType::New();
  fixedImageReader->SetFileName(dataManager->GetInputFile("sphereA3d.mhd"));

  ImageReader3DType::Pointer movingImageReader = ImageReader3DType::New();
  movingImageReader->SetFileName(dataManager->GetInputFile("sphereB3d.mhd"));

  ImageWriter3DType::Pointer resultImageWriter = ImageWriter3DType::New();
  resultImageWriter->SetFileName(dataManager->GetOutputFile("RegistrationItkv4Test_ImagesOnly.mhd"));

  // Connect SuperElastix in an itk pipeline
  superElastixFilter->SetInput("FixedImageSource", fixedImageReader->GetOutput());
  superElastixFilter->SetInput("MovingImageSource", movingImageReader->GetOutput());
  resultImageWriter->SetInput(superElastixFilter->GetOutput<Image3DType>("ResultImageSink"));

  EXPECT_NO_THROW(superElastixFilter->SetBlueprint(blueprint));

  //Optional Update call
  //superElastixFilter->Update();

  // Update call on the writers triggers SuperElastix to configure and execute
  EXPECT_NO_THROW(resultImageWriter->Update());
    
}

// These test are disabled, since may not want to check each component with this much boilerplate code. 
// We should consider moving functional tests outside the unit tests
// Anyway, the Blueprint configuration needs to be updated
TEST_F(RegistrationItkv4Test, DISABLED_3DANTSCCMetric)
{
  /** make example blueprint configuration */
  blueprint = Blueprint::New();

  ParameterMapType component0Parameters;
  component0Parameters["NameOfClass"] = { "ItkImageRegistrationMethodv4Component" };
  component0Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("RegistrationMethod", component0Parameters);

  ParameterMapType component1Parameters;
  component1Parameters["NameOfClass"] = { "ItkImageSourceFixedComponent" };
  component1Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("FixedImageSource", component1Parameters);

  ParameterMapType component2Parameters;
  component2Parameters["NameOfClass"] = { "ItkImageSourceMovingComponent" };
  component2Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("MovingImageSource", component2Parameters);

  ParameterMapType component3Parameters;
  component3Parameters["NameOfClass"] = { "ItkImageSinkComponent" };
  component3Parameters["Dimensionality"] = { "3" }; // should be derived from the outputs
  blueprint->AddComponent("ResultImageSink", component3Parameters);

  ParameterMapType component4Parameters;
  component4Parameters["NameOfClass"] = { "ItkANTSNeighborhoodCorrelationImageToImageMetricv4Component" };
  component4Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("Metric", component4Parameters);

  ParameterMapType component5Parameters;
  component5Parameters["NameOfClass"] = { "ItkGradientDescentOptimizerv4Component" };
  component5Parameters["NumberOfIterations"] = { "1" };
  blueprint->AddComponent("Optimizer", component5Parameters);

  ParameterMapType connection1Parameters;
  connection1Parameters["NameOfInterface"] = { "itkImageFixedInterface" };
  blueprint->AddConnection("FixedImageSource", "RegistrationMethod", connection1Parameters);

  ParameterMapType connection2Parameters;
  connection2Parameters["NameOfInterface"] = { "itkImageMovingInterface" };
  blueprint->AddConnection("MovingImageSource", "RegistrationMethod", connection2Parameters);

  ParameterMapType connection3Parameters;
  connection3Parameters["NameOfInterface"] = { "itkImageInterface" };
  blueprint->AddConnection("RegistrationMethod", "ResultImageSink", connection3Parameters);
  
  ParameterMapType connection4Parameters;
  connection4Parameters["NameOfInterface"] = { "itkMetricv4Interface" };
  blueprint->AddConnection("Metric", "RegistrationMethod", connection4Parameters);

  ParameterMapType connection5Parameters;
  connection5Parameters["NameOfInterface"] = { "itkOptimizerv4Interface" };
  blueprint->AddConnection("Optimizer", "RegistrationMethod", connection5Parameters);


  // Instantiate SuperElastix
  SuperElastixFilterType::Pointer superElastixFilter;
  EXPECT_NO_THROW(superElastixFilter = SuperElastixFilterType::New());

  // Data manager provides the paths to the input and output data for unit tests
  DataManagerType::Pointer dataManager = DataManagerType::New();

  // Set up the readers and writers
  ImageReader3DType::Pointer fixedImageReader = ImageReader3DType::New();
  fixedImageReader->SetFileName(dataManager->GetInputFile("sphereA3d.mhd"));

  ImageReader3DType::Pointer movingImageReader = ImageReader3DType::New();
  movingImageReader->SetFileName(dataManager->GetInputFile("sphereB3d.mhd"));

  ImageWriter3DType::Pointer resultImageWriter = ImageWriter3DType::New();
  resultImageWriter->SetFileName(dataManager->GetOutputFile("RegistrationItkv4Test_WithANTSCCMetric.mhd"));

  // Connect SuperElastix in an itk pipeline
  superElastixFilter->SetInput("FixedImageSource", fixedImageReader->GetOutput());
  superElastixFilter->SetInput("MovingImageSource", movingImageReader->GetOutput());
  resultImageWriter->SetInput(superElastixFilter->GetOutput<Image3DType>("ResultImageSink"));

  EXPECT_NO_THROW(superElastixFilter->SetBlueprint(blueprint));

  //Optional Update call
  //superElastixFilter->Update();

  // Update call on the writers triggers SuperElastix to configure and execute
  EXPECT_NO_THROW(resultImageWriter->Update());
}

// These test are disabled, since may not want to check each component with this much boilerplate code. 
// We should consider moving functional tests outside the unit tests
// Anyway, the Blueprint configuration needs to be updated
TEST_F(RegistrationItkv4Test, DISABLED_3DMeanSquaresMetric)
{
  /** make example blueprint configuration */
  blueprint = Blueprint::New();

  ParameterMapType component0Parameters;
  component0Parameters["NameOfClass"] = { "ItkImageRegistrationMethodv4Component" };
  component0Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("RegistrationMethod", component0Parameters);

  ParameterMapType component1Parameters;
  component1Parameters["NameOfClass"] = { "ItkImageSourceFixedComponent" };
  component1Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("FixedImageSource", component1Parameters);

  ParameterMapType component2Parameters;
  component2Parameters["NameOfClass"] = { "ItkImageSourceMovingComponent" };
  component2Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("MovingImageSource", component2Parameters);

  ParameterMapType component3Parameters;
  component3Parameters["NameOfClass"] = { "ItkImageSinkComponent" };
  component3Parameters["Dimensionality"] = { "3" }; // should be derived from the outputs
  blueprint->AddComponent("ResultImageSink", component3Parameters);

  ParameterMapType component4Parameters;
  component4Parameters["NameOfClass"] = { "ItkMeanSquaresImageToImageMetricv4Component" };
  component4Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("Metric", component4Parameters);

  ParameterMapType component5Parameters;
  component5Parameters["NameOfClass"] = { "ItkGradientDescentOptimizerv4Component" };
  component5Parameters["NumberOfIterations"] = { "1" };
  blueprint->AddComponent("Optimizer", component5Parameters);

  ParameterMapType connection1Parameters;
  connection1Parameters["NameOfInterface"] = { "itkImageFixedInterface" };
  blueprint->AddConnection("FixedImageSource", "RegistrationMethod", connection1Parameters);

  ParameterMapType connection2Parameters;
  connection2Parameters["NameOfInterface"] = { "itkImageMovingInterface" };
  blueprint->AddConnection("MovingImageSource", "RegistrationMethod", connection2Parameters);

  ParameterMapType connection3Parameters;
  connection3Parameters["NameOfInterface"] = { "itkImageInterface" };
  blueprint->AddConnection("RegistrationMethod", "ResultImageSink", connection3Parameters);

  ParameterMapType connection4Parameters;
  connection4Parameters["NameOfInterface"] = { "itkMetricv4Interface" };
  blueprint->AddConnection("Metric", "RegistrationMethod", connection4Parameters);

  ParameterMapType connection5Parameters;
  connection5Parameters["NameOfInterface"] = { "itkOptimizerv4Interface" };
  blueprint->AddConnection("Optimizer", "RegistrationMethod", connection5Parameters);

  // Instantiate SuperElastix
  SuperElastixFilterType::Pointer superElastixFilter;
  EXPECT_NO_THROW(superElastixFilter = SuperElastixFilterType::New());

  // Data manager provides the paths to the input and output data for unit tests
  DataManagerType::Pointer dataManager = DataManagerType::New();

  // Set up the readers and writers
  ImageReader3DType::Pointer fixedImageReader = ImageReader3DType::New();
  fixedImageReader->SetFileName(dataManager->GetInputFile("sphereA3d.mhd"));

  ImageReader3DType::Pointer movingImageReader = ImageReader3DType::New();
  movingImageReader->SetFileName(dataManager->GetInputFile("sphereB3d.mhd"));

  ImageWriter3DType::Pointer resultImageWriter = ImageWriter3DType::New();
  resultImageWriter->SetFileName(dataManager->GetOutputFile("RegistrationItkv4Test_WithMeanSquaresMetric.mhd"));

  // Connect SuperElastix in an itk pipeline
  superElastixFilter->SetInput("FixedImageSource", fixedImageReader->GetOutput());
  superElastixFilter->SetInput("MovingImageSource", movingImageReader->GetOutput());
  resultImageWriter->SetInput(superElastixFilter->GetOutput<Image3DType>("ResultImageSink"));

  EXPECT_NO_THROW(superElastixFilter->SetBlueprint(blueprint));

  //Optional Update call
  //superElastixFilter->Update();

  // Update call on the writers triggers SuperElastix to configure and execute
  EXPECT_NO_THROW(resultImageWriter->Update());

}

TEST_F(RegistrationItkv4Test, FullyConfigured3d)
{
  /** make example blueprint configuration */
  blueprint = Blueprint::New();

  ParameterMapType component0Parameters;
  component0Parameters["NameOfClass"] = { "ItkImageRegistrationMethodv4Component" };
  component0Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("RegistrationMethod", component0Parameters);

  ParameterMapType component1Parameters;
  component1Parameters["NameOfClass"] = { "ItkImageSourceFixedComponent" };
  component1Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("FixedImageSource", component1Parameters);

  ParameterMapType component2Parameters;
  component2Parameters["NameOfClass"] = { "ItkImageSourceMovingComponent" };
  component2Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("MovingImageSource", component2Parameters);

  ParameterMapType component3Parameters;
  component3Parameters["NameOfClass"] = { "ItkImageSinkComponent" };
  component3Parameters["Dimensionality"] = { "3" }; // should be derived from the outputs
  blueprint->AddComponent("ResultImageSink", component3Parameters);

  ParameterMapType component4Parameters;
  component4Parameters["NameOfClass"] = { "DisplacementFieldItkImageFilterSinkComponent" };
  component4Parameters["Dimensionality"] = { "3" }; // should be derived from the outputs
  blueprint->AddComponent("ResultDisplacementFieldSink", component4Parameters);

  ParameterMapType component5Parameters;
  component5Parameters["NameOfClass"] = { "ItkANTSNeighborhoodCorrelationImageToImageMetricv4Component" };
  component5Parameters["Dimensionality"] = { "3" }; // should be derived from the inputs
  blueprint->AddComponent("Metric", component5Parameters);

  ParameterMapType component6Parameters;
  component6Parameters["NameOfClass"] = { "ItkTransformDisplacementFilterComponent" };
  component6Parameters["Dimensionality"] = { "3" }; // should be derived from the outputs
  blueprint->AddComponent("TransformDisplacementFilter", component6Parameters);

  ParameterMapType component7Parameters;
  component7Parameters["NameOfClass"] = { "ItkGradientDescentOptimizerv4Component" };
  component7Parameters["NumberOfIterations"] = { "1" };
  blueprint->AddComponent("Optimizer", component7Parameters);


  blueprint->AddComponent("ResampleFilter", { { "NameOfClass",    { "ItkResampleFilterComponent" } },
                                              { "Dimensionality", { "3" } } });
                                            
  blueprint->AddComponent("Transform",      { { "NameOfClass",    { "ItkGaussianExponentialDiffeomorphicTransformComponent" } },
                                              { "Dimensionality", { "3" } } });

  ParameterMapType connection1Parameters;
  connection1Parameters["NameOfInterface"] = { "itkImageFixedInterface" };
  blueprint->AddConnection("FixedImageSource", "RegistrationMethod", connection1Parameters);

  ParameterMapType connection2Parameters;
  connection2Parameters["NameOfInterface"] = { "itkImageMovingInterface" };
  blueprint->AddConnection("MovingImageSource", "RegistrationMethod", connection2Parameters);

  ParameterMapType connection3Parameters;
  connection3Parameters["NameOfInterface"] = { "itkImageInterface" };
  blueprint->AddConnection("ResampleFilter", "ResultImageSink", connection3Parameters);

  ParameterMapType connection4Parameters;
  connection4Parameters["NameOfInterface"] = { "DisplacementFieldItkImageSourceInterface" };
  blueprint->AddConnection("TransformDisplacementFilter", "ResultDisplacementFieldSink", connection4Parameters);

  ParameterMapType connection5Parameters;
  connection5Parameters["NameOfInterface"] = { "itkMetricv4Interface" };
  blueprint->AddConnection("Metric", "RegistrationMethod", connection5Parameters);
  
  blueprint->AddConnection("FixedImageSource", "Transform", { {} });
  blueprint->AddConnection("Transform", "RegistrationMethod", { {} }); 
  blueprint->AddConnection("Optimizer", "RegistrationMethod", { {} });
  blueprint->AddConnection("RegistrationMethod", "TransformDisplacementFilter", { {} });
  blueprint->AddConnection("FixedImageSource", "TransformDisplacementFilter", { {} });
  blueprint->AddConnection("RegistrationMethod", "ResampleFilter", { {} });
  blueprint->AddConnection("FixedImageSource", "ResampleFilter", { {} });
  blueprint->AddConnection("MovingImageSource", "ResampleFilter", { {} });

  // Instantiate SuperElastix
  SuperElastixFilterType::Pointer superElastixFilter;
  EXPECT_NO_THROW(superElastixFilter = SuperElastixFilterType::New());

  // Data manager provides the paths to the input and output data for unit tests
  DataManagerType::Pointer dataManager = DataManagerType::New();

  // Set up the readers and writers
  ImageReader3DType::Pointer fixedImageReader = ImageReader3DType::New();
  fixedImageReader->SetFileName(dataManager->GetInputFile("sphereA3d.mhd"));

  ImageReader3DType::Pointer movingImageReader = ImageReader3DType::New();
  movingImageReader->SetFileName(dataManager->GetInputFile("sphereB3d.mhd"));

  ImageWriter3DType::Pointer resultImageWriter = ImageWriter3DType::New();
  resultImageWriter->SetFileName(dataManager->GetOutputFile("RegistrationItkv4Test_DisplacementField_image.mhd"));

  DisplacementImageWriter3DType::Pointer resultDisplacementWriter = DisplacementImageWriter3DType::New();
  resultDisplacementWriter->SetFileName(dataManager->GetOutputFile("RegistrationItkv4Test_DisplacementField_displacement.mhd"));


  // Connect SuperElastix in an itk pipeline
  superElastixFilter->SetInput("FixedImageSource", fixedImageReader->GetOutput());
  superElastixFilter->SetInput("MovingImageSource", movingImageReader->GetOutput());
  resultImageWriter->SetInput(superElastixFilter->GetOutput<Image3DType>("ResultImageSink"));
  resultDisplacementWriter->SetInput(superElastixFilter->GetOutput<DisplacementImage3DType>("ResultDisplacementFieldSink"));

  EXPECT_NO_THROW(superElastixFilter->SetBlueprint(blueprint));

  //Optional Update call
  //superElastixFilter->Update();

  // Update call on the writers triggers SuperElastix to configure and execute
  EXPECT_NO_THROW(resultImageWriter->Update());
  EXPECT_NO_THROW(resultDisplacementWriter->Update());

  blueprint->WriteBlueprint(dataManager->GetOutputFile("RegistrationItkv4Test_DisplacementField_network.dot"));

}
} // namespace selx