int mitkExtractSingleShellTest( int argc, char* argv[] )
{
MITK_TEST_BEGIN("mitkExtractSingleShellTest");
MITK_TEST_CONDITION_REQUIRED( argc > 3, "Specify input and output and the shell to be extracted");
/*
1. Get input data
*/
mitk::Image::Pointer dwimage = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load( argv[1] )[0].GetPointer());
mitk::GradientDirectionsProperty::Pointer gradientsProperty = static_cast<mitk::GradientDirectionsProperty *>( dwimage->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() );
MITK_TEST_CONDITION_REQUIRED( gradientsProperty.IsNotNull(), "Input is a dw-image");
unsigned int extract_value = 0;
std::istringstream input(argv[3]);
input >> extract_value;
typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter<DiffusionPixelType, DiffusionPixelType> FilterType;
typedef mitk::DiffusionPropertyHelper::BValueMapType BValueMap;
// GetShellSelection from GUI
BValueMap shellSelectionMap;
BValueMap originalShellMap = static_cast<mitk::BValueMapProperty*>(dwimage->GetProperty(mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() )->GetBValueMap();
std::vector<unsigned int> newNumGradientDirections;
shellSelectionMap[extract_value] = originalShellMap[extract_value];
newNumGradientDirections.push_back( originalShellMap[extract_value].size() ) ;
itk::VectorImage< short, 3 >::Pointer itkVectorImagePointer = itk::VectorImage< short, 3 >::New();
mitk::CastToItkImage(dwimage, itkVectorImagePointer);
itk::VectorImage< short, 3 > *vectorImage = itkVectorImagePointer.GetPointer();
mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientContainer = static_cast<mitk::GradientDirectionsProperty*>( dwimage->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer();
FilterType::Pointer filter = FilterType::New();
filter->SetInput(vectorImage);
filter->SetOriginalGradientDirections(gradientContainer);
filter->SetNumGradientDirections(newNumGradientDirections);
filter->SetOriginalBValueMap(originalShellMap);
filter->SetShellSelectionBValueMap(shellSelectionMap);
try
{
filter->Update();
}
catch( const itk::ExceptionObject& e)
{
MITK_TEST_FAILED_MSG( << "Failed due to ITK exception: " << e.what() );
}
mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() );
mitk::DiffusionPropertyHelper::CopyProperties(dwimage, outImage, true);
outImage->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( filter->GetGradientDirections() ) );
mitk::DiffusionPropertyHelper propertyHelper( outImage );
propertyHelper.InitializeImage();
/*
* 3. Write output data
**/
try
{
mitk::IOUtil::Save(outImage, argv[2]);
}
catch( const itk::ExceptionObject& e)
{
MITK_ERROR << "Catched exception: " << e.what();
mitkThrow() << "Failed with exception from subprocess!";
}
MITK_TEST_END();
}
