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;
}
}
bool itkDataTensorImageReaderBase::read (const QString &path)
{
if (this->io.IsNull())
return false;
this->readInformation ( path );
qDebug() << "Read with: " << this->identifier();
if (medAbstractData *medData = dynamic_cast<medAbstractData*>(this->data()) ) {
if (medData->identifier()=="itkDataTensorImageDouble3") {
if (this->io->GetNumberOfComponents()==6) {
typedef itk::Tensor<double, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<double, 6> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for( unsigned int j=0; j<6; j++) {
tensor[j] = vec[j];
}
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else if (this->io->GetNumberOfComponents()==9) {
typedef itk::Tensor<double, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<double, 9> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
tensor.SetComponent (i, j, vec[i*3+j]);
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else {
qDebug() << "Unsupported number of components";
return false;
}
}
else if (medData->identifier()=="itkDataTensorImageFloat3") {
if (this->io->GetNumberOfComponents()==6) {
typedef itk::Tensor<float, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<float, 6> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for( unsigned int j=0; j<6; j++) {
tensor[j] = vec[j];
}
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else if (this->io->GetNumberOfComponents()==9) {
typedef itk::Tensor<float, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<float, 9> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
tensor.SetComponent (i, j, vec[i*3+j]);
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else {
qDebug() << "Unsupported number of components";
return false;
}
}
else {
qDebug() << "Unsupported data type";
return false;
}
}
else {
qDebug() << "No data set or could not create one";
return false;
}
return true;
}