void QmitkTensorReconstructionView::ItkTensorReconstruction(mitk::DataStorage::SetOfObjects::Pointer inImages)
{
try
{
itk::TimeProbe clock;
int nrFiles = inImages->size();
if (!nrFiles) return;
QString status;
mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles);
mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() );
mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() );
std::vector<mitk::DataNode::Pointer> nodes;
while ( itemiter != itemiterend ) // for all items
{
mitk::DiffusionImage<DiffusionPixelType>* vols =
static_cast<mitk::DiffusionImage<DiffusionPixelType>*>(
(*itemiter)->GetData());
std::string nodename;
(*itemiter)->GetStringProperty("name", nodename);
++itemiter;
// TENSOR RECONSTRUCTION
clock.Start();
MITK_DEBUG << "Tensor reconstruction ";
mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Tensor reconstruction for %s", nodename.c_str()).toAscii());
typedef itk::DiffusionTensor3DReconstructionImageFilter<
DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType;
TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter =
TensorReconstructionImageFilterType::New();
tensorReconstructionFilter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() );
tensorReconstructionFilter->SetBValue(vols->GetB_Value());
tensorReconstructionFilter->SetThreshold( m_Controls->m_TensorReconstructionThreshold->value() );
tensorReconstructionFilter->Update();
clock.Stop();
MITK_DEBUG << "took " << clock.GetMeanTime() << "s.";
// TENSORS TO DATATREE
mitk::TensorImage::Pointer image = mitk::TensorImage::New();
typedef itk::Image<itk::DiffusionTensor3D<TTensorPixelType>, 3> TensorImageType;
TensorImageType::Pointer tensorImage;
tensorImage = tensorReconstructionFilter->GetOutput();
// Check the tensor for negative eigenvalues
if(m_Controls->m_CheckNegativeEigenvalues->isChecked())
{
typedef itk::ImageRegionIterator<TensorImageType> TensorImageIteratorType;
TensorImageIteratorType tensorIt(tensorImage, tensorImage->GetRequestedRegion());
tensorIt.GoToBegin();
while(!tensorIt.IsAtEnd())
{
typedef itk::DiffusionTensor3D<TTensorPixelType> TensorType;
//typedef itk::Tensor<TTensorPixelType, 3> TensorType2;
TensorType tensor = tensorIt.Get();
TensorType::EigenValuesArrayType ev;
tensor.ComputeEigenValues(ev);
for(unsigned int i=0; i<ev.Size(); i++)
{
if(ev[i] < 0.0)
{
tensor.Fill(0.0);
tensorIt.Set(tensor);
break;
}
}
++tensorIt;
}
}
tensorImage->SetDirection( vols->GetVectorImage()->GetDirection() );
image->InitializeByItk( tensorImage.GetPointer() );
image->SetVolume( tensorReconstructionFilter->GetOutput()->GetBufferPointer() );
mitk::DataNode::Pointer node=mitk::DataNode::New();
node->SetData( image );
QString newname;
newname = newname.append(nodename.c_str());
newname = newname.append("_dti");
SetDefaultNodeProperties(node, newname.toStdString());
nodes.push_back(node);
mitk::ProgressBar::GetInstance()->Progress();
}
std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt)
GetDefaultDataStorage()->Add(*nodeIt);
mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii());
m_MultiWidget->RequestUpdate();
}
catch (itk::ExceptionObject &ex)
{
MITK_INFO << ex ;
QMessageBox::information(0, "Reconstruction not possible:", ex.GetDescription());
return;
}
}
/**
* Convert files from one ending to the other
*/
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", mitkCommandLineParser::InputFile, "Input file", "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false);
parser.addArgument("outFile", "o", mitkCommandLineParser::OutputFile, "Output file", "output file", us::Any(), false);
parser.addArgument("b0Threshold", "t", mitkCommandLineParser::Int, "b0 threshold", "baseline image intensity threshold", 0, true);
parser.setCategory("Signal Modelling");
parser.setTitle("Tensor Reconstruction");
parser.setDescription("");
parser.setContributor("MIC");
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
std::string inFileName = us::any_cast<std::string>(parsedArgs["input"]);
std::string outfilename = us::any_cast<std::string>(parsedArgs["outFile"]);
outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
outfilename += ".dti";
int threshold = 0;
if (parsedArgs.count("b0Threshold"))
threshold = us::any_cast<int>(parsedArgs["b0Threshold"]);
try
{
mitk::Image::Pointer dwi = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(inFileName)[0].GetPointer());
mitk::DiffusionPropertyHelper::ImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::ImageType::New();
mitk::CastToItkImage(dwi, itkVectorImagePointer);
typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType;
TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
filter->SetGradientImage( mitk::DiffusionPropertyHelper::GetGradientContainer(dwi), itkVectorImagePointer );
filter->SetBValue( mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi ));
filter->SetThreshold(threshold);
filter->Update();
// Save tensor image
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
io->SetFileType( itk::ImageIOBase::Binary );
io->UseCompressionOn();
itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::Pointer writer = itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::New();
writer->SetInput(filter->GetOutput());
writer->SetFileName(outfilename);
writer->SetImageIO(io);
writer->UseCompressionOn();
writer->Update();
}
catch ( itk::ExceptionObject &err)
{
std::cout << "Exception: " << err;
}
catch ( std::exception err)
{
std::cout << "Exception: " << err.what();
}
catch ( ... )
{
std::cout << "Exception!";
}
return EXIT_SUCCESS;
}
int mitkImageReconstructionTest(int argc, char* argv[])
{
MITK_TEST_BEGIN("mitkImageReconstructionTest");
MITK_TEST_CONDITION_REQUIRED(argc>1,"check for input data")
try
{
mitk::DiffusionImage<short>::Pointer dwi = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[1])->GetData());
{
MITK_INFO << "Tensor reconstruction " << argv[2];
mitk::TensorImage::Pointer tensorImage = dynamic_cast<mitk::TensorImage*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData());
typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType;
TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->Update();
mitk::TensorImage::Pointer testImage = mitk::TensorImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, tensorImage, 0.0001, true), "tensor reconstruction test.");
}
{
MITK_INFO << "Numerical Q-ball reconstruction " << argv[3];
mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData());
typedef itk::DiffusionQballReconstructionImageFilter<short, short, float, QBALL_ODFSIZE> QballReconstructionImageFilterType;
QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
filter->Update();
mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Numerical Q-ball reconstruction test.");
}
{
MITK_INFO << "Standard Q-ball reconstruction " << argv[4];
mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData());
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetLambda(0.006);
filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
filter->Update();
mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Standard Q-ball reconstruction test.");
}
{
MITK_INFO << "CSA Q-ball reconstruction " << argv[5];
mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData());
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetLambda(0.006);
filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
filter->Update();
mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "CSA Q-ball reconstruction test.");
}
{
MITK_INFO << "ADC profile reconstruction " << argv[6];
mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData());
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetLambda(0.006);
filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY);
filter->Update();
mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "ADC profile reconstruction test.");
}
{
MITK_INFO << "Raw signal modeling " << argv[7];
mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData());
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() );
filter->SetBValue(dwi->GetB_Value());
filter->SetLambda(0.006);
filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL);
filter->Update();
mitk::QBallImage::Pointer testImage = mitk::QBallImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Raw signal modeling test.");
}
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
MITK_TEST_END();
}
int mitkImageReconstructionTest(int argc, char* argv[])
{
MITK_TEST_BEGIN("mitkImageReconstructionTest");
MITK_TEST_CONDITION_REQUIRED(argc>1,"check for input data")
try
{
mitk::Image::Pointer dwi = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(argv[1])[0].GetPointer());
itk::VectorImage<short,3>::Pointer itkVectorImagePointer = itk::VectorImage<short,3>::New();
mitk::CastToItkImage(dwi, itkVectorImagePointer);
float b_value = mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi );
mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradients = mitk::DiffusionPropertyHelper::GetGradientContainer(dwi);
{
MITK_INFO << "Tensor reconstruction " << argv[2];
mitk::TensorImage::Pointer tensorImage = dynamic_cast<mitk::TensorImage*>(mitk::IOUtil::Load(argv[2])[0].GetPointer());
typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType;
TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
filter->SetBValue( b_value );
filter->SetGradientImage( gradients, itkVectorImagePointer );
filter->Update();
mitk::TensorImage::Pointer testImage = mitk::TensorImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *tensorImage, 0.0001, true), "tensor reconstruction test.");
}
{
MITK_INFO << "Numerical Q-ball reconstruction " << argv[3];
mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[3])[0].GetPointer());
typedef itk::DiffusionQballReconstructionImageFilter<short, short, float, ODF_SAMPLING_SIZE> QballReconstructionImageFilterType;
QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New();
filter->SetBValue( b_value );
filter->SetGradientImage( gradients, itkVectorImagePointer );
filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
filter->Update();
mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "Numerical Q-ball reconstruction test.");
}
{
MITK_INFO << "Standard Q-ball reconstruction " << argv[4];
mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[4])[0].GetPointer());
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetBValue( b_value );
filter->SetGradientImage( gradients, itkVectorImagePointer );
filter->SetLambda(0.006);
filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
filter->Update();
mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "Standard Q-ball reconstruction test.");
}
{
MITK_INFO << "CSA Q-ball reconstruction " << argv[5];
mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[5])[0].GetPointer());
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetBValue( b_value );
filter->SetGradientImage( gradients, itkVectorImagePointer );
filter->SetLambda(0.006);
filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
filter->Update();
mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "CSA Q-ball reconstruction test.");
}
{
MITK_INFO << "ADC profile reconstruction " << argv[6];
mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[6])[0].GetPointer());
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetBValue( b_value );
filter->SetGradientImage( gradients, itkVectorImagePointer );
filter->SetLambda(0.006);
filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY);
filter->Update();
mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "ADC profile reconstruction test.");
}
{
MITK_INFO << "Raw signal modeling " << argv[7];
mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[7])[0].GetPointer());
typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetBValue( b_value );
filter->SetGradientImage( gradients, itkVectorImagePointer );
filter->SetLambda(0.006);
filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL);
filter->Update();
mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
testImage->InitializeByItk( filter->GetOutput() );
testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "Raw signal modeling test.");
}
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
MITK_TEST_END();
}
