Merge branch 'develop' into ELASTIX-44-Unite-Interface-framework-with-Factory-framework

Testing/Unit/Data/Input/BrainProtonDensitySliceShifted13x17y.png.md5

+d3568c0d5c44afedb78305f620c0a79b

Testing/Unit/Data/Input/OAS1_0001_MR1_mpr-1_anon.nrrd.md5

+034e616e71ade1535cba4a77180ad79d
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Testing/Unit/Data/Input/OAS1_0002_MR1_mpr-1_anon.nrrd.md5

+49129770e7152ea5d203a519ac17be43
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Testing/Unit/Data/Input/cthead1-Float.mha.md5

-25de5707b18c0c684fd5fa30351bf787
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Testing/Unit/elxTransformixFilterTest.cxx

+#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() );
+}