#include <QmitkTensorReconstructionView.h>

Inheritance diagram for QmitkTensorReconstructionView:

Collaboration diagram for QmitkTensorReconstructionView:

Public Member Functions
	QmitkTensorReconstructionView ()
virtual	~QmitkTensorReconstructionView ()
virtual void	CreateQtPartControl (QWidget *parent)
virtual void	CreateConnections ()
	Creation of the connections of main and control widget.
virtual void	Activated ()
	Called when the functionality is activated.
virtual void	Deactivated ()
virtual void	StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget)
virtual void	StdMultiWidgetNotAvailable ()
Static Public Attributes
static const std::string	VIEW_ID = "org.mitk.views.tensorreconstruction"
static const int	nrconvkernels
Protected Slots
void	TensorsToDWI ()
void	DoTensorsToDWI (mitk::DataStorage::SetOfObjects::Pointer inImages)
void	TeemCheckboxClicked ()
void	Advanced1CheckboxClicked ()
void	Advanced2CheckboxClicked ()
void	ManualThresholdClicked ()
void	MethodChoosen (int method)
void	Reconstruct (int method)
void	TeemReconstruction ()
void	ItkReconstruction ()
void	ItkTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages)
void	TeemTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages)
Protected Member Functions
template<int ndirs>
std::vector< itk::Vector < double, 3 > >	MakeGradientList ()
template<int L>
void	TemplatedAnalyticalTensorReconstruction (mitk::DiffusionImage< DiffusionPixelType > vols, float lambda, std::string nodename, std::vector< mitk::DataNode::Pointer > nodes, int normalization)
void	SetDefaultNodeProperties (mitk::DataNode::Pointer node, std::string name)
Protected Attributes
Ui::QmitkTensorReconstructionViewControls *	m_Controls
QmitkStdMultiWidget *	m_MultiWidget
berry::ISelectionListener::Pointer	m_SelListener
berry::IStructuredSelection::ConstPointer	m_CurrentSelection
Friends
struct	TrSelListener

Detailed Description

QmitkTensorReconstructionView.

Document your class here.

See also:: QmitkFunctionality

Definition at line 47 of file QmitkTensorReconstructionView.h.

Constructor & Destructor Documentation

QmitkTensorReconstructionView::QmitkTensorReconstructionView ( )

Definition at line 136 of file QmitkTensorReconstructionView.cpp.

: QmitkFunctionality(),
m_Controls(NULL),
m_MultiWidget(NULL)
{
}

QmitkTensorReconstructionView::~QmitkTensorReconstructionView ( ) [virtual]

Definition at line 143 of file QmitkTensorReconstructionView.cpp.

References berry::WorkbenchPart::GetSite(), and m_SelListener.

{
  this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener);
}

Member Function Documentation

void QmitkTensorReconstructionView::Activated ( ) [virtual]

Called when the functionality is activated.

Reimplemented from QmitkFunctionality.

Definition at line 256 of file QmitkTensorReconstructionView.cpp.

{
  QmitkFunctionality::Activated();
}

void QmitkTensorReconstructionView::Advanced1CheckboxClicked ( ) [protected, slot]

Definition at line 234 of file QmitkTensorReconstructionView.cpp.

References Ui_QmitkTensorReconstructionViewControls::frame, and m_Controls.

Referenced by CreateConnections(), and CreateQtPartControl().

{
  bool check = m_Controls->
    m_Advanced1->isChecked();

  m_Controls->frame->setVisible(check);
}

void QmitkTensorReconstructionView::Advanced2CheckboxClicked ( ) [protected, slot]

Definition at line 242 of file QmitkTensorReconstructionView.cpp.

References Ui_QmitkTensorReconstructionViewControls::frame_2, and m_Controls.

Referenced by CreateConnections(), and CreateQtPartControl().

{
  bool check = m_Controls->
    m_Advanced2->isChecked();

  m_Controls->frame_2->setVisible(check);
}

void QmitkTensorReconstructionView::CreateConnections ( ) [virtual]

Creation of the connections of main and control widget.

Definition at line 213 of file QmitkTensorReconstructionView.cpp.

Referenced by CreateQtPartControl().

{
  if ( m_Controls )
  {
    connect( (QObject*)(m_Controls->m_TeemToggle), SIGNAL(clicked()), this, SLOT(TeemCheckboxClicked()) );
    connect( (QObject*)(m_Controls->m_ItkReconstruction), SIGNAL(clicked()), this, SLOT(ItkReconstruction()) );
    connect( (QObject*)(m_Controls->m_TeemReconstruction), SIGNAL(clicked()), this, SLOT(TeemReconstruction()) );
    connect( (QObject*)(m_Controls->m_TensorEstimationTeemEstimationMethodCombo), SIGNAL(currentIndexChanged(int)), this, SLOT(MethodChoosen(int)) );
    connect( (QObject*)(m_Controls->m_Advanced1), SIGNAL(clicked()), this, SLOT(Advanced1CheckboxClicked()) );
    connect( (QObject*)(m_Controls->m_Advanced2), SIGNAL(clicked()), this, SLOT(Advanced2CheckboxClicked()) );
    connect( (QObject*)(m_Controls->m_TensorEstimationManualThreashold), SIGNAL(clicked()), this, SLOT(ManualThresholdClicked()) );
    connect( (QObject*)(m_Controls->m_TensorsToDWIButton), SIGNAL(clicked()), this, SLOT(TensorsToDWI()) );
  }
}

void QmitkTensorReconstructionView::CreateQtPartControl ( QWidget * parent ) [virtual]

Implements berry::QtViewPart.

Definition at line 148 of file QmitkTensorReconstructionView.cpp.

{
  if (!m_Controls)
  {
    // create GUI widgets
    m_Controls = new Ui::QmitkTensorReconstructionViewControls;
    m_Controls->setupUi(parent);
    this->CreateConnections();

    m_Controls->m_TensorReconstructionNumberThreadsSpinbox->setValue(8);

    QStringList items;
    items << "LLS (Linear Least Squares)"
      << "MLE (Maximum Likelihood)"
      << "NLS (Nonlinear Least Squares)"
      << "WLS (Weighted Least Squares)";
    m_Controls->m_TensorEstimationTeemEstimationMethodCombo->addItems(items);
    m_Controls->m_TensorEstimationTeemEstimationMethodCombo->setCurrentIndex(0);

    m_Controls->m_TensorEstimationManualThreashold->setChecked(false);
    m_Controls->m_TensorEstimationTeemSigmaEdit->setText("NaN");
    m_Controls->m_TensorEstimationTeemNumItsSpin->setValue(1);
    m_Controls->m_TensorEstimationTeemFuzzyEdit->setText("0.0");
    m_Controls->m_TensorEstimationTeemMinValEdit->setText("1.0");

    m_Controls->m_TensorEstimationTeemNumItsLabel_2->setEnabled(true);
    m_Controls->m_TensorEstimationTeemNumItsSpin->setEnabled(true);

    m_Controls->m_TensorsToDWIBValueEdit->setText("1000");

    Advanced1CheckboxClicked();
    Advanced2CheckboxClicked();
    TeemCheckboxClicked();

#ifndef DIFFUSION_IMAGING_EXTENDED
    m_Controls->m_TeemToggle->setVisible(false);
#endif

    // define data type for combobox
    //m_Controls->m_ImageSelector->SetDataStorage( this->GetDefaultDataStorage() );
    //m_Controls->m_ImageSelector->SetPredicate( mitk::NodePredicateDataType::New("DiffusionImage") );
  }

  m_SelListener = berry::ISelectionListener::Pointer(new TrSelListener(this));
  this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener);
  berry::ISelection::ConstPointer sel(
    this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager"));
  m_CurrentSelection = sel.Cast<const IStructuredSelection>();
  m_SelListener.Cast<TrSelListener>()->DoSelectionChanged(sel);
}

void QmitkTensorReconstructionView::Deactivated ( ) [virtual]

Only called when IsExclusiveFunctionality() returns true.

See also:: IsExclusiveFunctionality()

Reimplemented from QmitkFunctionality.

Definition at line 261 of file QmitkTensorReconstructionView.cpp.

{
  QmitkFunctionality::Deactivated();
}

void QmitkTensorReconstructionView::DoTensorsToDWI ( mitk::DataStorage::SetOfObjects::Pointer inImages ) [protected, slot]

Definition at line 600 of file QmitkTensorReconstructionView.cpp.

References mitk::StatusBar::GetInstance(), mitk::ProgressBar::GetInstance(), mitk::DiffusionImage< TPixelType >::InitializeFromVectorImage(), MBI_DEBUG, MBI_INFO, mitk::DataNode::New(), mitk::DiffusionImage< TPixelType >::New(), mitk::DiffusionImage< TPixelType >::SetB_Value(), mitk::DiffusionImageMapper< TPixelType >::SetDefaultProperties(), mitk::DiffusionImage< TPixelType >::SetDirections(), and mitk::DiffusionImage< TPixelType >::SetVectorImage().

Referenced by TensorsToDWI().

{
  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
    {

      std::string nodename;
      (*itemiter)->GetStringProperty("name", nodename);
      
      mitk::TensorImage* vol = 
        static_cast<mitk::TensorImage*>((*itemiter)->GetData());
      
      ++itemiter;

      typedef float                                       TTensorPixelType;
      typedef itk::DiffusionTensor3D< TTensorPixelType >  TensorPixelType;
      typedef itk::Image< TensorPixelType, 3 >            TensorImageType;

      
      TensorImageType::Pointer itkvol = TensorImageType::New();
      mitk::CastToItkImage<TensorImageType>(vol, itkvol);

      typedef itk::TensorImageToDiffusionImageFilter< 
        TTensorPixelType, DiffusionPixelType > FilterType;

      FilterType::GradientListType gradientList;

      switch(m_Controls->m_TensorsToDWINumDirsSelect->currentIndex())
      {
      case 0:
        gradientList = MakeGradientList<12>();
        break;
      case 1:
        gradientList = MakeGradientList<42>();
        break;
      case 2:
        gradientList = MakeGradientList<92>();
        break;
      case 3:
        gradientList = MakeGradientList<162>();
        break;
      case 4:
        gradientList = MakeGradientList<252>();
        break;
      case 5:
        gradientList = MakeGradientList<362>();
        break;
      case 6:
        gradientList = MakeGradientList<492>();
        break;
      case 7:
        gradientList = MakeGradientList<642>();
        break;
      case 8:
        gradientList = MakeGradientList<812>();
        break;
      case 9:
        gradientList = MakeGradientList<1002>();
        break;
      default:
        gradientList = MakeGradientList<92>();

      }

      double bVal = m_Controls->m_TensorsToDWIBValueEdit->text().toDouble();

      // DWI ESTIMATION
      clock.Start();
      MBI_INFO << "DWI Estimation ";
      mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
        "DWI Estimation for %s", nodename.c_str()).toAscii());
      FilterType::Pointer filter = FilterType::New();
      filter->SetInput( itkvol );
      filter->SetBValue(bVal);  
      filter->SetGradientList(gradientList);  
      filter->SetNumberOfThreads(1);
      filter->Update();
      clock.Stop();
      MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";

      itk::Vector<double,3> v;
      v[0] = 0; v[1] = 0; v[2] = 0;
      gradientList.push_back(v);

      // TENSORS TO DATATREE
      mitk::DiffusionImage<DiffusionPixelType>::Pointer image = mitk::DiffusionImage<DiffusionPixelType>::New();
      image->SetVectorImage( filter->GetOutput() );
      image->SetB_Value(bVal);
      image->SetDirections(gradientList);
      image->InitializeFromVectorImage();
      mitk::DataNode::Pointer node=mitk::DataNode::New();
      node->SetData( image );

      mitk::DiffusionImageMapper<short>::SetDefaultProperties(node);

      QString newname;
      newname = newname.append(nodename.c_str());
      newname = newname.append("_dwi");
      node->SetName(newname.toAscii());

      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)
  {
    MBI_INFO << ex ;
    return ;
  }
}

void QmitkTensorReconstructionView::ItkReconstruction ( ) [protected, slot]

Definition at line 272 of file QmitkTensorReconstructionView.cpp.

References Reconstruct().

Referenced by CreateConnections().

{
  Reconstruct(0);
}

void QmitkTensorReconstructionView::ItkTensorReconstruction ( mitk::DataStorage::SetOfObjects::Pointer inImages ) [protected, slot]

Definition at line 319 of file QmitkTensorReconstructionView.cpp.

References mitk::DiffusionImage< TPixelType >::GetB_Value(), mitk::DiffusionImage< TPixelType >::GetDirections(), mitk::StatusBar::GetInstance(), mitk::ProgressBar::GetInstance(), mitk::DiffusionImage< TPixelType >::GetVectorImage(), MBI_DEBUG, MBI_INFO, mitk::DataNode::New(), and mitk::TensorImage::New().

Referenced by Reconstruct().

{
  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();
      MBI_INFO << "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->SetNumberOfThreads( m_Controls->m_TensorReconstructionNumberThreadsSpinbox->value() );
      tensorReconstructionFilter->SetBValue(vols->GetB_Value());  
      tensorReconstructionFilter->SetThreshold( m_Controls->m_TensorReconstructionThreasholdEdit->text().toFloat() );
      tensorReconstructionFilter->Update();
      clock.Stop();
      MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";

      // TENSORS TO DATATREE
      mitk::TensorImage::Pointer image = mitk::TensorImage::New();
      image->InitializeByItk( tensorReconstructionFilter->GetOutput() );
      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)
  {
    MBI_INFO << ex ;
    return ;
  }
}

template<int ndirs>

std::vector< itk::Vector< double, 3 > > QmitkTensorReconstructionView::MakeGradientList ( ) [protected]

Definition at line 584 of file QmitkTensorReconstructionView.cpp.

{
  std::vector<itk::Vector<double,3> > retval;
  vnl_matrix_fixed<double, 3, ndirs>* U =
    itk::PointShell<ndirs, vnl_matrix_fixed<double, 3, ndirs> >::DistributePointShell();

  for(int i=0; i<ndirs;i++) 
  {
    itk::Vector<double,3> v;
    v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i);
    retval.push_back(v);
  }
  return retval;
}

void QmitkTensorReconstructionView::ManualThresholdClicked ( ) [protected, slot]

Definition at line 250 of file QmitkTensorReconstructionView.cpp.

References m_Controls, Ui_QmitkTensorReconstructionViewControls::m_TensorEstimationManualThreashold, and Ui_QmitkTensorReconstructionViewControls::m_TensorReconstructionThreasholdEdit_2.

Referenced by CreateConnections().

{
  m_Controls->m_TensorReconstructionThreasholdEdit_2->setEnabled(
    m_Controls->m_TensorEstimationManualThreashold->isChecked());
}

void QmitkTensorReconstructionView::MethodChoosen ( int method ) [protected, slot]

Definition at line 266 of file QmitkTensorReconstructionView.cpp.

References m_Controls, Ui_QmitkTensorReconstructionViewControls::m_TensorEstimationTeemNumItsLabel_2, and Ui_QmitkTensorReconstructionViewControls::m_TensorEstimationTeemNumItsSpin.

Referenced by CreateConnections().

{
  m_Controls->m_TensorEstimationTeemNumItsLabel_2->setEnabled(method==3);
  m_Controls->m_TensorEstimationTeemNumItsSpin->setEnabled(method==3);
}

void QmitkTensorReconstructionView::Reconstruct ( int method ) [protected, slot]

Definition at line 282 of file QmitkTensorReconstructionView.cpp.

References berry::SmartPointer< TObjectType >::Cast(), ItkTensorReconstruction(), m_CurrentSelection, and TeemTensorReconstruction().

Referenced by ItkReconstruction(), and TeemReconstruction().

{
  if (m_CurrentSelection)
  {
    mitk::DataStorage::SetOfObjects::Pointer set =
      mitk::DataStorage::SetOfObjects::New();

    int at = 0;
    for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); 
      i != m_CurrentSelection->End(); 
      ++i)
    {

      if (mitk::DataNodeObject::Pointer nodeObj = i->Cast<mitk::DataNodeObject>())
      {
        mitk::DataNode::Pointer node = nodeObj->GetDataNode();
        if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0)
        {
          set->InsertElement(at++, node);
        }
      }
    }

    if(method == 0)
    {
      ItkTensorReconstruction(set);
    }

    if(method == 1)
    {
      TeemTensorReconstruction(set);
    }

  }
}

void QmitkTensorReconstructionView::SetDefaultNodeProperties	(	mitk::DataNode::Pointer	node,
		std::string	name
	)		`[protected]`

Definition at line 498 of file QmitkTensorReconstructionView.cpp.

References mitk::StringProperty::New(), mitk::BoolProperty::New(), mitk::OdfScaleByProperty::New(), mitk::OdfNormalizationMethodProperty::New(), mitk::FloatProperty::New(), and mitk::IntProperty::New().

{
  node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 500 ) );
  node->SetProperty( "Scaling", mitk::FloatProperty::New( 1.0 ) );
  node->SetProperty( "Normalization", mitk::OdfNormalizationMethodProperty::New());
  node->SetProperty( "ScaleBy", mitk::OdfScaleByProperty::New());
  node->SetProperty( "IndexParam1", mitk::FloatProperty::New(2));
  node->SetProperty( "IndexParam2", mitk::FloatProperty::New(1));
  node->SetProperty( "visible", mitk::BoolProperty::New( true ) );
  node->SetProperty( "VisibleOdfs", mitk::BoolProperty::New( false ) );
  node->SetProperty ("layer", mitk::IntProperty::New(100));
  node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) );
  //node->SetProperty( "opacity", mitk::FloatProperty::New(1.0f) );

  node->SetProperty( "name", mitk::StringProperty::New(name) );
}

void QmitkTensorReconstructionView::StdMultiWidgetAvailable ( QmitkStdMultiWidget & stdMultiWidget ) [virtual]

Called when a StdMultiWidget is available. Should not be used anymore, see GetActiveStdMultiWidget()

See also:: GetActiveStdMultiWidget()

Reimplemented from QmitkFunctionality.

Definition at line 199 of file QmitkTensorReconstructionView.cpp.

References berry::SmartPointer< TObjectType >::Cast(), berry::WorkbenchPart::GetSite(), m_CurrentSelection, m_MultiWidget, and m_SelListener.

{
  berry::ISelection::ConstPointer sel(
    this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager"));
  m_CurrentSelection = sel.Cast<const IStructuredSelection>();
  m_SelListener.Cast<TrSelListener>()->DoSelectionChanged(sel);
  m_MultiWidget = &stdMultiWidget;
}

void QmitkTensorReconstructionView::StdMultiWidgetNotAvailable ( ) [virtual]

Called when no StdMultiWidget is available anymore. Should not be used anymore, see GetActiveStdMultiWidget()

See also:: GetActiveStdMultiWidget()

Reimplemented from QmitkFunctionality.

Definition at line 208 of file QmitkTensorReconstructionView.cpp.

References m_MultiWidget.

{
  m_MultiWidget = NULL;
}

void QmitkTensorReconstructionView::TeemCheckboxClicked ( ) [protected, slot]

Definition at line 228 of file QmitkTensorReconstructionView.cpp.

References Ui_QmitkTensorReconstructionViewControls::groupBox_3, and m_Controls.

Referenced by CreateConnections(), and CreateQtPartControl().

{
  m_Controls->groupBox_3->setVisible(m_Controls->
    m_TeemToggle->isChecked());  
}

void QmitkTensorReconstructionView::TeemReconstruction ( ) [protected, slot]

Definition at line 277 of file QmitkTensorReconstructionView.cpp.

References Reconstruct().

Referenced by CreateConnections().

{
  Reconstruct(1);
}

void QmitkTensorReconstructionView::TeemTensorReconstruction ( mitk::DataStorage::SetOfObjects::Pointer inImages ) [protected, slot]

Definition at line 399 of file QmitkTensorReconstructionView.cpp.

References mitk::StatusBar::GetInstance(), mitk::ProgressBar::GetInstance(), MBI_DEBUG, MBI_INFO, mitk::DataNode::New(), mitk::TeemTensorEstimationMethodsLLS, mitk::TeemTensorEstimationMethodsMLE, mitk::TeemTensorEstimationMethodsNLS, and mitk::TeemTensorEstimationMethodsWLS.

Referenced by Reconstruct().

{
  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();
      MBI_INFO << "Teem Tensor reconstruction ";
      mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
        "Teem Tensor reconstruction for %s", nodename.c_str()).toAscii());
      typedef mitk::TeemDiffusionTensor3DReconstructionImageFilter< 
        DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType;
      TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = 
        TensorReconstructionImageFilterType::New();
      tensorReconstructionFilter->SetInput( vols );
      if(!m_Controls->m_TensorEstimationTeemSigmaEdit->text().contains(QString("NaN")))
        tensorReconstructionFilter->SetSigma( m_Controls->m_TensorEstimationTeemSigmaEdit->text().toFloat() );
      switch(m_Controls->m_TensorEstimationTeemEstimationMethodCombo->currentIndex())
      {
        //  items << "LLS (Linear Least Squares)"
        //<< "MLE (Maximum Likelihood)"
        //<< "NLS (Nonlinear Least Squares)"
        //<< "WLS (Weighted Least Squares)";
      case 0:
        tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS);
        break;
      case 1:
        tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsMLE);
        break;
      case 2:
        tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsNLS);
        break;
      case 3:
        tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsWLS);
        break;
      default:
        tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS);
      }
      tensorReconstructionFilter->SetNumIterations( m_Controls->m_TensorEstimationTeemNumItsSpin->value() );
      if(m_Controls->m_TensorEstimationManualThreashold->isChecked())
        tensorReconstructionFilter->SetConfidenceThreshold( m_Controls->m_TensorReconstructionThreasholdEdit_2->text().toDouble() );
      tensorReconstructionFilter->SetConfidenceFuzzyness( m_Controls->m_TensorEstimationTeemFuzzyEdit->text().toFloat() );
      tensorReconstructionFilter->SetMinPlausibleValue( m_Controls->m_TensorEstimationTeemMinValEdit->text().toDouble() );
      tensorReconstructionFilter->Update();
      clock.Stop();
      MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ;

      // TENSORS TO DATATREE
      mitk::DataNode::Pointer node2=mitk::DataNode::New();
      node2->SetData( tensorReconstructionFilter->GetOutputItk() );

      QString newname;
      newname = newname.append(nodename.c_str());
      newname = newname.append("_dtix");

      SetDefaultNodeProperties(node2, newname.toStdString());
      nodes.push_back(node2);

      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 ;
  }
}

template<int L>

void QmitkTensorReconstructionView::TemplatedAnalyticalTensorReconstruction	(	mitk::DiffusionImage< DiffusionPixelType > *	vols,
		float	lambda,
		std::string	nodename,
		std::vector< mitk::DataNode::Pointer > *	nodes,
		int	normalization
	)		`[protected]`

void QmitkTensorReconstructionView::TensorsToDWI ( ) [protected, slot]

Definition at line 556 of file QmitkTensorReconstructionView.cpp.

References berry::SmartPointer< TObjectType >::Cast(), DoTensorsToDWI(), and m_CurrentSelection.

Referenced by CreateConnections().

{
  if (m_CurrentSelection)
  {
    mitk::DataStorage::SetOfObjects::Pointer set =
      mitk::DataStorage::SetOfObjects::New();

    int at = 0;
    for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); 
      i != m_CurrentSelection->End(); 
      ++i)
    {

      if (mitk::DataNodeObject::Pointer nodeObj = i->Cast<mitk::DataNodeObject>())
      {
        mitk::DataNode::Pointer node = nodeObj->GetDataNode();
        if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0)
        {
          set->InsertElement(at++, node);
        }
      }
    }

    DoTensorsToDWI(set);
  }
}