#include <QmitkTbssView.h>

Inheritance diagram for QmitkTbssView:

Collaboration diagram for QmitkTbssView:

Public Member Functions
	QmitkTbssView ()
virtual	~QmitkTbssView ()
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.tbss"
static const int	nrconvkernels
Protected Slots
void	OutputValues ()
void	OutputUnconnectedPointValues ()
Protected Member Functions
void	SetDefaultNodeProperties (mitk::DataNode::Pointer node, std::string name)
void	SkeletonSelected (mitk::DataNode::Pointer skeletonNode)
void	RoiSelected (mitk::DataNode::Pointer roiNode)
std::vector < RoiImageType::IndexType >	SortPoints (RoiImageType::Pointer roi)
bool	PointVisited (std::vector< RoiImageType::IndexType > points, RoiImageType::IndexType point)
RoiImageType::IndexType	FindNextPoint (std::vector< RoiImageType::IndexType > pointsVisited, RoiImageType::IndexType currentPoint, RoiImageType::Pointer roi, bool &ready)
Protected Attributes
Ui::QmitkTbssViewControls *	m_Controls
QmitkStdMultiWidget *	m_MultiWidget
berry::ISelectionListener::Pointer	m_SelListener
berry::IStructuredSelection::ConstPointer	m_CurrentSelection
bool	m_IsInitialized
mitk::DataNode::Pointer	m_SkeletonNode
mitk::DataNode::Pointer	m_RoiNode
Friends
struct	TbSelListener

Detailed Description

QmitkTensorReconstructionView.

Document your class here.

See also:: QmitkFunctionality

Definition at line 52 of file QmitkTbssView.h.

Constructor & Destructor Documentation

QmitkTbssView::QmitkTbssView ( )

Definition at line 183 of file QmitkTbssView.cpp.

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

QmitkTbssView::~QmitkTbssView ( ) [virtual]

Definition at line 190 of file QmitkTbssView.cpp.

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

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

Member Function Documentation

void QmitkTbssView::Activated ( ) [virtual]

Called when the functionality is activated.

Reimplemented from QmitkFunctionality.

Definition at line 238 of file QmitkTbssView.cpp.

{
  QmitkFunctionality::Activated();
}

void QmitkTbssView::CreateConnections ( ) [virtual]

Creation of the connections of main and control widget.

Definition at line 229 of file QmitkTbssView.cpp.

References m_Controls, OutputUnconnectedPointValues(), and OutputValues().

Referenced by CreateQtPartControl().

{
  if ( m_Controls )
  {
    connect( (QObject*)(m_Controls->m_OutputValues), SIGNAL(clicked()), this, SLOT(OutputValues()) );
    connect( (QObject*)(m_Controls->m_OutputPoints), SIGNAL(clicked()), this, SLOT(OutputUnconnectedPointValues()) );
  }
}

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

Implements berry::QtViewPart.

Definition at line 195 of file QmitkTbssView.cpp.

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

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

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

void QmitkTbssView::Deactivated ( ) [virtual]

Only called when IsExclusiveFunctionality() returns true.

See also:: IsExclusiveFunctionality()

Reimplemented from QmitkFunctionality.

Definition at line 243 of file QmitkTbssView.cpp.

{
  QmitkFunctionality::Deactivated();
}

RoiImageType::IndexType QmitkTbssView::FindNextPoint	(	std::vector< RoiImageType::IndexType >	pointsVisited,
		RoiImageType::IndexType	currentPoint,
		RoiImageType::Pointer	roi,
		bool &	ready
	)		`[protected]`

Definition at line 485 of file QmitkTbssView.cpp.

References PointVisited().

Referenced by SortPoints().

{  

  RoiImageType::IndexValueType dx[26] = {0, 0, 1, 1, 1, 0,-1,-1,-1,0,1,1, 1, 0,-1,-1,-1, 0, 1, 1, 1, 0,-1,-1,-1, 0};
  RoiImageType::IndexValueType dy[26] = {0, 1, 1, 0,-1,-1,-1, 0, 1,1,1,0,-1,-1,-1, 0, 1, 1, 1, 0,-1,-1,-1, 0, 1, 0};
  RoiImageType::IndexValueType dz[26] = {0, 0, 0, 0, 0, 0, 0, 0, 0,1,1,1, 1, 1, 1, 1, 1,-1,-1,-1,-1,-1,-1,-1,-1, 1};

  RoiImageType::IndexType newPoint;   

  for (int step=0; step<26; step++)
  {
    newPoint[0] = currentPoint[0] + dx[step];
    newPoint[1] = currentPoint[1] + dy[step];
    newPoint[2] = currentPoint[2] + dz[step];

    // Check if point is not yet visited
    if(!PointVisited(pointsVisited, newPoint))
    {
      if(roi->GetPixel(newPoint) == 1)
        return newPoint;
    }
  }

  // No points yet to be visited found so we are done searching
  ready = true;
  return currentPoint;

}

void QmitkTbssView::OutputUnconnectedPointValues ( ) [protected, slot]

Definition at line 262 of file QmitkTbssView.cpp.

References mitk::CastToItkImage(), m_SkeletonNode, and QuadProgPP::t().

Referenced by CreateConnections().

{
  if(m_SkeletonNode.IsNull())
  {
    return;
  }

  //read roi
  /*mitk::Image::Pointer image = dynamic_cast<mitk::Image*>( m_RoiNode->GetData() ); 
  RoiImageType::Pointer roi = RoiImageType::New();
  mitk::CastToItkImage(image, roi);*/
  
   //read the 4D skeleton
  mitk::Image::Pointer image2 = dynamic_cast<mitk::Image*>( m_SkeletonNode->GetData() ); 
  AllSkeletonType::Pointer skeleton = AllSkeletonType::New();  
  mitk::CastToItkImage(image2, skeleton);

 // RoiImageType::SizeType roiSize = roi->GetLargestPossibleRegion().GetSize();
  AllSkeletonType::SizeType skeletonSize = skeleton->GetLargestPossibleRegion().GetSize();



  AllSkeletonType::IndexType indices[3];
  indices[2][0] = 98; indices[2][1] = 126; indices[2][2] = 105;
  indices[3][0] = 101; indices[3][1] = 98; indices[3][2] = 104;
  indices[4][0] = 101; indices[4][1] = 76; indices[4][2] = 92;

  // output file
  std::string filename = "G://home//vanbrugg//spie2011//CingulumHealthy.csv";
  std::ofstream f;
  f.open(filename.c_str());

  for (int s=0; s<skeletonSize[3]; s++)
  {
    
    for(int t=0; t<3; t++)
    {
      indices[t][3] = s;     
      f << skeleton->GetPixel(indices[t]) << ",";
    }

    f << std::endl;
  }
  f.close();

  //for(int x=0; x<roiSize[0]; x++)
  //{
  //  for(int y=0; y<roiSize[1]; y++)
  //  {
  //    for(int z=0; z<roiSize[2]; z++)
  //    {
  //      RoiImageType::IndexType index;
  //      index[0] = x;
  //      index[1] = y;
  //      index[2] = z;
  //      if (roi->GetPixel(index) != 0)
  //      {
  //        // Output the values of this point for all subjects
  //        AllSkeletonType::IndexType skeletonIndex;
  //        skeletonIndex[0] = index[0];
  //        skeletonIndex[1] = index[1];
  //        skeletonIndex[2] = index[2];

  //       

  //        for(int t=0; t<skeletonSize[3]; t++)
  //        {
  //          if(index[0] == 90 && index[1] == 98 && index[2] == 95)
  //          {
  //            std::cout << "the empty voxel" << std::endl;
  //          }
  //          skeletonIndex[3] = t;
  //          std::cout << skeleton->GetPixel(skeletonIndex) << std::endl;
  //        }

  //        std::cout << " ";
  //      }
  //    }
  //  }
  //}

}

void QmitkTbssView::OutputValues ( ) [protected, slot]

Definition at line 345 of file QmitkTbssView.cpp.

References mitk::CastToItkImage(), m_RoiNode, m_SkeletonNode, and SortPoints().

Referenced by CreateConnections().

{

  if(m_SkeletonNode.IsNull() || m_RoiNode.IsNull())
  {
    return;
  }


  //read roi
  mitk::Image::Pointer image = dynamic_cast<mitk::Image*>( m_RoiNode->GetData() ); 
  RoiImageType::Pointer roi = RoiImageType::New();
  mitk::CastToItkImage(image, roi);

  //read the 4D skeleton
  mitk::Image::Pointer image2 = dynamic_cast<mitk::Image*>( m_SkeletonNode->GetData() ); 
  AllSkeletonType::Pointer skeleton = AllSkeletonType::New();  
  mitk::CastToItkImage(image2, skeleton);

  RoiImageType::SizeType roiSize = roi->GetLargestPossibleRegion().GetSize();
  AllSkeletonType::SizeType skeletonSize = skeleton->GetLargestPossibleRegion().GetSize();

  std::vector<RoiImageType::IndexType> indices = SortPoints(roi);


  //For every subject (4th axis of the 4D volume) output the tract of interest and write results to file
  std::string filename = "G://home//vanbrugg//spie2011//paraHipLeftHealthy.csv";
  std::ofstream f;
  f.open(filename.c_str());
  

  for (int s=0; s<skeletonSize[3]; s++)
  {
    std::vector<RoiImageType::IndexType>::iterator it = indices.begin();    
    while(it != indices.end())
    {
      RoiImageType::IndexType roiIndex = *it;
      AllSkeletonType::IndexType skeletonIndex;
      skeletonIndex[0] = roiIndex[0];
      skeletonIndex[1] = roiIndex[1];
      skeletonIndex[2] = roiIndex[2];
      skeletonIndex[3] = s;

      //std::cout << skeleton->GetPixel(skeletonIndex) << ",";

      f << skeleton->GetPixel(skeletonIndex) << ",";
     

      ++it;
    }
    f << std::endl;
  }

  f.close();

  //for(int x=0; x<roiSize[0]; x++)
  //{
  //  for(int y=0; y<roiSize[1]; y++)
  //  {
  //    for(int z=0; z<roiSize[2]; z++)
  //    {
  //      RoiImageType::IndexType index;
  //      index[0] = x;
  //      index[1] = y;
  //      index[2] = z;
  //      if (roi->GetPixel(index) != 0)
  //      {
  //        // Output the values of this point for all subjects
  //        AllSkeletonType::IndexType skeletonIndex;
  //        skeletonIndex[0] = index[0];
  //        skeletonIndex[1] = index[1];
  //        skeletonIndex[2] = index[2];

  //       

  //        for(int t=0; t<skeletonSize[3]; t++)
  //        {
  //          if(index[0] == 90 && index[1] == 98 && index[2] == 95)
  //          {
  //            std::cout << "the empty voxel" << std::endl;
  //          }
  //          skeletonIndex[3] = t;
  //          std::cout << skeleton->GetPixel(skeletonIndex) << std::endl;
  //        }

  //        std::cout << " ";
  //      }
  //    }
  //  }
  //}
  
   
  
}

bool QmitkTbssView::PointVisited	(	std::vector< RoiImageType::IndexType >	points,
		RoiImageType::IndexType	point
	)		`[protected]`

Definition at line 468 of file QmitkTbssView.cpp.

Referenced by FindNextPoint().

{
  bool ret = false;
  std::vector<RoiImageType::IndexType>::iterator it = points.begin();
  while(it != points.end())
  {
    RoiImageType::IndexType p = *it;
    if(p[0] == point[0] && p[1] == point[1] && p[2] == point[2])
    {
      ret = true;
    }
    ++it;
  }

  return ret;
}

void QmitkTbssView::RoiSelected ( mitk::DataNode::Pointer roiNode ) [protected]

Definition at line 255 of file QmitkTbssView.cpp.

References m_Controls, and m_RoiNode.

{
  m_RoiNode = roiNode; 
  m_RoiNode->SetVisibility(true);
  m_Controls->m_RoiNameLabel->setText(QString::fromStdString(m_RoiNode->GetName()));
}

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

void QmitkTbssView::SkeletonSelected ( mitk::DataNode::Pointer skeletonNode ) [protected]

Definition at line 248 of file QmitkTbssView.cpp.

References m_Controls, and m_SkeletonNode.

{
  m_SkeletonNode = skeletonNode; 
  m_SkeletonNode->SetVisibility(true);
  m_Controls->m_SkeletonNameLabel->setText(QString::fromStdString(m_SkeletonNode->GetName()));  
}

std::vector< RoiImageType::IndexType > QmitkTbssView::SortPoints ( RoiImageType::Pointer roi ) [protected]

Definition at line 440 of file QmitkTbssView.cpp.

References FindNextPoint().

Referenced by OutputValues().

{
  std::vector<RoiImageType::IndexType> indices;
  
  //set current point to be the start point. Hard coded for now, should be changed to function in general
  RoiImageType::IndexType currentPoint;
  //currentPoint[0] = 90; // For Corpus Callosum the constant index;
  //currentPoint[1] = 88;
  //currentPoint[2] = 82;

  //currentPoint[0] = 65; //standard for right parahippocampal white matter
  //currentPoint[1] = 108;
  //currentPoint[2] = 45;

  currentPoint[0] = 95; 
  currentPoint[1] = 166;
  currentPoint[2] = 78;

  bool ready = false;
  while(!ready)
  {
    indices.push_back(currentPoint);
    currentPoint = FindNextPoint(indices, currentPoint, roi, ready);
  }

  return indices;
}

void QmitkTbssView::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 215 of file QmitkTbssView.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<TbSelListener>()->DoSelectionChanged(sel);
  m_MultiWidget = &stdMultiWidget;
}