void setUp()
{
// reference files
m_InputDwi = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(GetTestDataFilePath("DiffusionImaging/Fiberfox/StickBall_RELAX.dwi"))->GetData());
// parameter setup
m_Parameters = FiberfoxParameters<short>();
m_Parameters.m_SignalGen.m_ImageRegion = m_InputDwi->GetVectorImage()->GetLargestPossibleRegion();
m_Parameters.m_SignalGen.m_ImageSpacing = m_InputDwi->GetVectorImage()->GetSpacing();
m_Parameters.m_SignalGen.m_ImageOrigin = m_InputDwi->GetVectorImage()->GetOrigin();
m_Parameters.m_SignalGen.m_ImageDirection = m_InputDwi->GetVectorImage()->GetDirection();
m_Parameters.m_SignalGen.m_Bvalue = m_InputDwi->GetReferenceBValue();
m_Parameters.m_SignalGen.SetGradienDirections(m_InputDwi->GetDirections());
}
void StartSimulation(FiberfoxParameters<double> parameters, FiberBundleX::Pointer fiberBundle, mitk::DiffusionImage<short>::Pointer refImage, string message)
{
itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
tractsToDwiFilter->SetUseConstantRandSeed(true);
tractsToDwiFilter->SetParameters(parameters);
tractsToDwiFilter->SetFiberBundle(fiberBundle);
tractsToDwiFilter->Update();
mitk::DiffusionImage<short>::Pointer testImage = mitk::DiffusionImage<short>::New();
testImage->SetVectorImage( tractsToDwiFilter->GetOutput() );
testImage->SetReferenceBValue(parameters.m_SignalGen.m_Bvalue);
testImage->SetDirections(parameters.m_SignalGen.GetGradientDirections());
testImage->InitializeFromVectorImage();
if (refImage.IsNotNull())
{
bool cond = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage());
if (!cond)
{
MITK_INFO << "Saving test and rference image to " << mitk::IOUtil::GetTempPath();
mitk::IOUtil::SaveBaseData(testImage, mitk::IOUtil::GetTempPath()+"testImage.dwi");
mitk::IOUtil::SaveBaseData(refImage, mitk::IOUtil::GetTempPath()+"refImage.dwi");
}
MITK_TEST_CONDITION_REQUIRED(cond, message);
}
}
void StartSimulation(string testFileName)
{
mitk::DiffusionImage<short>::Pointer refImage = NULL;
if (!testFileName.empty())
CPPUNIT_ASSERT(refImage = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(testFileName)->GetData()));
itk::AddArtifactsToDwiImageFilter< short >::Pointer artifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New();
artifactsToDwiFilter->SetUseConstantRandSeed(true);
artifactsToDwiFilter->SetInput(m_InputDwi->GetVectorImage());
artifactsToDwiFilter->SetParameters(m_Parameters);
CPPUNIT_ASSERT_NO_THROW(artifactsToDwiFilter->Update());
mitk::DiffusionImage<short>::Pointer testImage = mitk::DiffusionImage<short>::New();
testImage->SetVectorImage( artifactsToDwiFilter->GetOutput() );
testImage->SetReferenceBValue( m_Parameters.m_SignalGen.m_Bvalue);
testImage->SetDirections( m_Parameters.m_SignalGen.GetGradientDirections());
testImage->InitializeFromVectorImage();
if (refImage.IsNotNull())
{
if (!CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()))
mitk::IOUtil::SaveBaseData(testImage, mitk::IOUtil::GetTempPath()+"testImage.dwi");
CPPUNIT_ASSERT_MESSAGE(testFileName, CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()));
}
}
void StartSimulation(string testFileName)
{
mitk::DiffusionImage<short>::Pointer refImage = NULL;
if (!testFileName.empty())
CPPUNIT_ASSERT(refImage = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(testFileName)->GetData()));
itk::AddArtifactsToDwiImageFilter< short >::Pointer artifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New();
artifactsToDwiFilter->SetUseConstantRandSeed(true);
artifactsToDwiFilter->SetInput(m_InputDwi->GetVectorImage());
artifactsToDwiFilter->SetParameters(m_Parameters);
CPPUNIT_ASSERT_NO_THROW(artifactsToDwiFilter->Update());
mitk::DiffusionImage<short>::Pointer testImage = mitk::DiffusionImage<short>::New();
testImage->SetVectorImage( artifactsToDwiFilter->GetOutput() );
testImage->SetB_Value(m_Parameters.m_Bvalue);
testImage->SetDirections(m_Parameters.GetGradientDirections());
testImage->InitializeFromVectorImage();
if (refImage.IsNotNull())
{
bool ok = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage());
if (!ok)
{
mitk::IOUtil::SaveBaseData(testImage, "/tmp/test2.dwi");
mitk::IOUtil::SaveBaseData(refImage, "/tmp/ref2.dwi");
}
CPPUNIT_ASSERT_MESSAGE(testFileName, ok);
}
else
{
mitk::IOUtil::SaveBaseData(testImage, "/local/distortions2.dwi");
}
}
void QmitkPreprocessingView::CallMultishellToSingleShellFilter(itk::DWIVoxelFunctor * functor, mitk::DiffusionImage<DiffusionPixelType>::Pointer ImPtr, QString imageName)
{
typedef itk::RadialMultishellToSingleshellImageFilter<DiffusionPixelType, DiffusionPixelType> FilterType;
// filter input parameter
const mitk::DiffusionImage<DiffusionPixelType>::BValueMap
&originalShellMap = ImPtr->GetBValueMap();
const mitk::DiffusionImage<DiffusionPixelType>::ImageType
*vectorImage = ImPtr->GetVectorImage();
const mitk::DiffusionImage<DiffusionPixelType>::GradientDirectionContainerType::Pointer
gradientContainer = ImPtr->GetDirections();
const unsigned int
&bValue = ImPtr->GetReferenceBValue();
mitk::DataNode::Pointer imageNode = 0;
// filter call
FilterType::Pointer filter = FilterType::New();
filter->SetInput(vectorImage);
filter->SetOriginalGradientDirections(gradientContainer);
filter->SetOriginalBValueMap(originalShellMap);
filter->SetOriginalBValue(bValue);
filter->SetFunctor(functor);
filter->Update();
// create new DWI image
mitk::DiffusionImage<DiffusionPixelType>::Pointer outImage = mitk::DiffusionImage<DiffusionPixelType>::New();
outImage->SetVectorImage( filter->GetOutput() );
outImage->SetReferenceBValue( m_Controls->m_targetBValueSpinBox->value() );
outImage->SetDirections( filter->GetTargetGradientDirections() );
outImage->InitializeFromVectorImage();
imageNode = mitk::DataNode::New();
imageNode->SetData( outImage );
imageNode->SetName(imageName.toStdString().c_str());
GetDefaultDataStorage()->Add(imageNode);
if(m_Controls->m_OutputRMSErrorImage->isChecked()){
// create new Error image
FilterType::ErrorImageType::Pointer errImage = filter->GetErrorImage();
mitk::Image::Pointer mitkErrImage = mitk::Image::New();
mitkErrImage->InitializeByItk<FilterType::ErrorImageType>(errImage);
mitkErrImage->SetVolume(errImage->GetBufferPointer());
imageNode = mitk::DataNode::New();
imageNode->SetData( mitkErrImage );
imageNode->SetName((imageName+"_Error").toStdString().c_str());
GetDefaultDataStorage()->Add(imageNode);
}
}