void QmitkQBallReconstructionView::NumericalQBallReconstruction
(mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization)
{
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;
// QBALL RECONSTRUCTION
clock.Start();
MBI_INFO << "QBall reconstruction ";
mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
"QBall reconstruction for %s", nodename.c_str()).toAscii());
typedef itk::DiffusionQballReconstructionImageFilter
<DiffusionPixelType, DiffusionPixelType, TTensorPixelType, QBALL_ODFSIZE>
QballReconstructionImageFilterType;
QballReconstructionImageFilterType::Pointer filter =
QballReconstructionImageFilterType::New();
filter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() );
filter->SetNumberOfThreads( m_Controls->m_QBallReconstructionNumberThreadsSpinbox->value() );
filter->SetBValue(vols->GetB_Value());
filter->SetThreshold( m_Controls->m_QBallReconstructionThreasholdEdit->text().toFloat() );
switch(normalization)
{
case 0:
{
filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
break;
}
case 1:
{
filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO_B_VALUE);
break;
}
case 2:
{
filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO);
break;
}
case 3:
{
filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_NONE);
break;
}
default:
{
filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
}
}
filter->Update();
clock.Stop();
MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ;
// ODFs TO DATATREE
mitk::QBallImage::Pointer image = mitk::QBallImage::New();
image->InitializeByItk( filter->GetOutput() );
//image->SetImportVolume( filter->GetOutput()->GetBufferPointer(), 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory );
image->SetVolume( filter->GetOutput()->GetBufferPointer() );
mitk::DataNode::Pointer node=mitk::DataNode::New();
node->SetData( image );
QString newname;
newname = newname.append(nodename.c_str());
newname = newname.append("_QN%1").arg(normalization);
SetDefaultNodeProperties(node, newname.toStdString());
nodes.push_back(node);
// B-Zero TO DATATREE
if(m_Controls->m_OutputB0Image->isChecked())
{
mitk::Image::Pointer image4 = mitk::Image::New();
image4->InitializeByItk( filter->GetBZeroImage().GetPointer() );
image4->SetVolume( filter->GetBZeroImage()->GetBufferPointer() );
mitk::DataNode::Pointer node4=mitk::DataNode::New();
node4->SetData( image4 );
node4->SetProperty( "name", mitk::StringProperty::New(
QString(nodename.c_str()).append("_b0").toStdString()) );
nodes.push_back(node4);
}
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)
{
MBI_INFO << ex ;
return ;
}
}
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();
}
