#include <QmitkPreprocessingView.h>

Inheritance diagram for QmitkPreprocessingView:

Collaboration diagram for QmitkPreprocessingView:

Public Member Functions
	QmitkPreprocessingView ()
virtual	~QmitkPreprocessingView ()
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.preprocessing"
static const int	nrconvkernels
Protected Slots
void	AverageGradients ()
void	DoAverageGradients (mitk::DataStorage::SetOfObjects::Pointer inImages)
void	ExtractB0 ()
void	DoExtractB0 (mitk::DataStorage::SetOfObjects::Pointer inImages)
void	BrainMask ()
void	DoBrainMask (mitk::DataStorage::SetOfObjects::Pointer inImages)
Protected Member Functions
void	SetDefaultNodeProperties (mitk::DataNode::Pointer node, std::string name)
Protected Attributes
Ui::QmitkPreprocessingViewControls *	m_Controls
QmitkStdMultiWidget *	m_MultiWidget
berry::ISelectionListener::Pointer	m_SelListener
berry::IStructuredSelection::ConstPointer	m_CurrentSelection
Friends
struct	PrpSelListener

Detailed Description

QmitkPreprocessingView.

Document your class here.

See also:: QmitkFunctionality

Definition at line 47 of file QmitkPreprocessingView.h.

Constructor & Destructor Documentation

QmitkPreprocessingView::QmitkPreprocessingView ( )

Definition at line 131 of file QmitkPreprocessingView.cpp.

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

QmitkPreprocessingView::~QmitkPreprocessingView ( ) [virtual]

Definition at line 138 of file QmitkPreprocessingView.cpp.

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

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

Member Function Documentation

void QmitkPreprocessingView::Activated ( ) [virtual]

Called when the functionality is activated.

Reimplemented from QmitkFunctionality.

Definition at line 182 of file QmitkPreprocessingView.cpp.

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

{
  QmitkFunctionality::Activated();

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

void QmitkPreprocessingView::AverageGradients ( ) [protected, slot]

Definition at line 272 of file QmitkPreprocessingView.cpp.

References berry::SmartPointer< TObjectType >::Cast(), DoAverageGradients(), 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("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0)
        {
          set->InsertElement(at++, node);
        }
      }
    }

    DoAverageGradients(set);

  }

}

void QmitkPreprocessingView::BrainMask ( ) [protected, slot]

Definition at line 325 of file QmitkPreprocessingView.cpp.

References berry::SmartPointer< TObjectType >::Cast(), DoBrainMask(), 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("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0)
        {
          set->InsertElement(at++, node);
        }
      }
    }

    DoBrainMask(set);

  }

}

void QmitkPreprocessingView::CreateConnections ( ) [virtual]

Creation of the connections of main and control widget.

Definition at line 171 of file QmitkPreprocessingView.cpp.

References AverageGradients(), BrainMask(), ExtractB0(), Ui_QmitkPreprocessingViewControls::m_ButtonAverageGradients, Ui_QmitkPreprocessingViewControls::m_ButtonBrainMask, Ui_QmitkPreprocessingViewControls::m_ButtonExtractB0, and m_Controls.

Referenced by CreateQtPartControl().

{
  if ( m_Controls )
  {
    connect( (QObject*)(m_Controls->m_ButtonAverageGradients), SIGNAL(clicked()), this, SLOT(AverageGradients()) );
    connect( (QObject*)(m_Controls->m_ButtonExtractB0), SIGNAL(clicked()), this, SLOT(ExtractB0()) );
    connect( (QObject*)(m_Controls->m_ButtonBrainMask), SIGNAL(clicked()), this, SLOT(BrainMask()) );

  }
}

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

Implements berry::QtViewPart.

Definition at line 143 of file QmitkPreprocessingView.cpp.

References berry::SmartPointer< TObjectType >::Cast(), CreateConnections(), berry::WorkbenchPart::GetSite(), m_Controls, m_CurrentSelection, m_SelListener, PrpSelListener, and Ui_QmitkPreprocessingViewControls::setupUi().

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

  m_SelListener = berry::ISelectionListener::Pointer(new PrpSelListener(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<PrpSelListener>()->DoSelectionChanged(sel);
}

void QmitkPreprocessingView::Deactivated ( ) [virtual]

Only called when IsExclusiveFunctionality() returns true.

See also:: IsExclusiveFunctionality()

Reimplemented from QmitkFunctionality.

Definition at line 192 of file QmitkPreprocessingView.cpp.

{
  QmitkFunctionality::Deactivated();
}

void QmitkPreprocessingView::DoAverageGradients ( mitk::DataStorage::SetOfObjects::Pointer inImages ) [protected, slot]

Definition at line 303 of file QmitkPreprocessingView.cpp.

References mitk::DiffusionImage< TPixelType >::AverageRedundantGradients().

Referenced by AverageGradients().

{
  int nrFiles = inImages->size();
  if (!nrFiles) return;

  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());

    vols->AverageRedundantGradients(m_Controls->m_Blur->value());

    ++itemiter;
  }
}

void QmitkPreprocessingView::DoBrainMask ( mitk::DataStorage::SetOfObjects::Pointer inImages ) [protected, slot]

Definition at line 356 of file QmitkPreprocessingView.cpp.

References mitk::DiffusionImage< TPixelType >::GetDirections(), mitk::DiffusionImage< TPixelType >::GetVectorImage(), mitk::StringProperty::New(), mitk::DataNode::New(), and mitk::Image::New().

Referenced by BrainMask().

{
  int nrFiles = inImages->size();
  if (!nrFiles) return;

  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);

    // Extract image using found index
    typedef itk::B0ImageExtractionImageFilter<short, short> FilterType;
    FilterType::Pointer filter = FilterType::New();
    filter->SetInput(vols->GetVectorImage());
    filter->SetDirections(vols->GetDirections());

    typedef itk::CastImageFilter<itk::Image<short,3>, itk::Image<unsigned short,3> > CastFilterType;
    CastFilterType::Pointer castfilter = CastFilterType::New();
    castfilter->SetInput(filter->GetOutput());
    
    typedef itk::BrainMaskExtractionImageFilter<unsigned char> MaskFilterType;
    MaskFilterType::Pointer maskfilter = MaskFilterType::New();
    maskfilter->SetInput(castfilter->GetOutput());
    maskfilter->Update();

    mitk::Image::Pointer mitkImage = mitk::Image::New();
    mitkImage->InitializeByItk( maskfilter->GetOutput() );
    mitkImage->SetVolume( maskfilter->GetOutput()->GetBufferPointer() );
    mitk::DataNode::Pointer node=mitk::DataNode::New();
    node->SetData( mitkImage );
    node->SetProperty( "name", mitk::StringProperty::New(nodename + "_Mask"));

    GetDefaultDataStorage()->Add(node);

    ++itemiter;
  }
}

void QmitkPreprocessingView::DoExtractB0 ( mitk::DataStorage::SetOfObjects::Pointer inImages ) [protected, slot]

Definition at line 228 of file QmitkPreprocessingView.cpp.

References mitk::StringProperty::New(), mitk::DataNode::New(), and mitk::Image::New().

Referenced by ExtractB0().

{
  typedef mitk::DiffusionImage<DiffusionPixelType>              DiffusionImageType;
  typedef DiffusionImageType::GradientDirectionContainerType    GradientContainerType;

  int nrFiles = inImages->size();
  if (!nrFiles) return;

  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
  {

    DiffusionImageType* vols = 
      static_cast<DiffusionImageType*>(
      (*itemiter)->GetData());

    std::string nodename;
    (*itemiter)->GetStringProperty("name", nodename);

    // Extract image using found index
    typedef itk::B0ImageExtractionImageFilter<short, short> FilterType;
    FilterType::Pointer filter = FilterType::New();
    filter->SetInput(vols->GetVectorImage());
    filter->SetDirections(vols->GetDirections());
    filter->Update();

    mitk::Image::Pointer mitkImage = mitk::Image::New();
    mitkImage->InitializeByItk( filter->GetOutput() );
    mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
    mitk::DataNode::Pointer node=mitk::DataNode::New();
    node->SetData( mitkImage );
    node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0"));

    GetDefaultDataStorage()->Add(node);

    ++itemiter;
  }


}

void QmitkPreprocessingView::ExtractB0 ( ) [protected, slot]

Definition at line 198 of file QmitkPreprocessingView.cpp.

References berry::SmartPointer< TObjectType >::Cast(), DoExtractB0(), 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("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0)
        {
          set->InsertElement(at++, node);
        }
      }
    }

    DoExtractB0(set);

  }
}