Calculates the segmented volumes for binary images. More...

#include <mitkBinaryThresholdTool.h>

Inheritance diagram for mitk::BinaryThresholdTool:

Collaboration diagram for mitk::BinaryThresholdTool:

Public Types
typedef BinaryThresholdTool	Self
typedef AutoSegmentationTool	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
Public Member Functions
virtual const char *	GetClassName () const
virtual const char **	GetXPM () const
	Returns an icon in the XPM format.
virtual const char *	GetName () const
	Returns the name of this tool. Make it short!
virtual void	Activated ()
	Called when the tool gets activated (registered to mitk::GlobalInteraction).
virtual void	Deactivated ()
	Called when the tool gets deactivated (unregistered from mitk::GlobalInteraction).
virtual void	SetThresholdValue (int value)
virtual void	AcceptCurrentThresholdValue (const std::string &organName, const Color &color)
virtual void	CancelThresholding ()
Static Public Member Functions
static Pointer	New ()
Public Attributes
Message2< int, int >	IntervalBordersChanged
Message1< int >	ThresholdingValueChanged
Protected Member Functions
	BinaryThresholdTool ()
virtual	~BinaryThresholdTool ()
void	SetupPreviewNodeFor (DataNode *nodeForThresholding)
void	CreateNewSegmentationFromThreshold (DataNode *node, const std::string &organType, const Color &color)
void	OnRoiDataChanged ()
template<typename TPixel , unsigned int VImageDimension>
void	ITKThresholding (itk::Image< TPixel, VImageDimension > originalImage, mitk::Image segmentation, unsigned int timeStep)
Protected Attributes
DataNode::Pointer	m_ThresholdFeedbackNode
DataNode::Pointer	m_OriginalImageNode
DataNode::Pointer	m_NodeForThresholding
int	m_SensibleMinimumThresholdValue
int	m_SensibleMaximumThresholdValue
int	m_CurrentThresholdValue

Detailed Description

Calculates the segmented volumes for binary images.

See also:: mitk::Tool; QmitkInteractiveSegmentation

Last contributor: $Author$

Definition at line 40 of file mitkBinaryThresholdTool.h.

Member Typedef Documentation

typedef itk::SmartPointer<const Self> mitk::BinaryThresholdTool::ConstPointer

Reimplemented from mitk::AutoSegmentationTool.

Definition at line 47 of file mitkBinaryThresholdTool.h.

typedef itk::SmartPointer<Self> mitk::BinaryThresholdTool::Pointer

Reimplemented from mitk::AutoSegmentationTool.

Definition at line 47 of file mitkBinaryThresholdTool.h.

typedef BinaryThresholdTool mitk::BinaryThresholdTool::Self

Reimplemented from mitk::AutoSegmentationTool.

Definition at line 47 of file mitkBinaryThresholdTool.h.

typedef AutoSegmentationTool mitk::BinaryThresholdTool::Superclass

Reimplemented from mitk::AutoSegmentationTool.

Definition at line 47 of file mitkBinaryThresholdTool.h.

Constructor & Destructor Documentation

mitk::BinaryThresholdTool::BinaryThresholdTool ( ) [protected]

Definition at line 44 of file mitkBinaryThresholdTool.cpp.

References mitk::CoreObjectFactory::GetInstance(), m_ThresholdFeedbackNode, mitk::FloatProperty::New(), mitk::StringProperty::New(), mitk::LevelWindowProperty::New(), mitk::IntProperty::New(), mitk::BoolProperty::New(), mitk::ColorProperty::New(), New(), and mitk::Tool::SupportRoiOn().

:m_SensibleMinimumThresholdValue(-100),
 m_SensibleMaximumThresholdValue(+100),
 m_CurrentThresholdValue(1)
{
  this->SupportRoiOn();

  m_ThresholdFeedbackNode = DataNode::New();
  mitk::CoreObjectFactory::GetInstance()->SetDefaultProperties( m_ThresholdFeedbackNode );

  m_ThresholdFeedbackNode->SetProperty( "color", ColorProperty::New(1.0, 0.0, 0.0) );
  m_ThresholdFeedbackNode->SetProperty( "texture interpolation", BoolProperty::New(false) );
  m_ThresholdFeedbackNode->SetProperty( "layer", IntProperty::New( 100 ) );
  m_ThresholdFeedbackNode->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow(100, 1) ) );
  m_ThresholdFeedbackNode->SetProperty( "name", StringProperty::New("Thresholding feedback") );
  m_ThresholdFeedbackNode->SetProperty( "opacity", FloatProperty::New(0.3) );
  m_ThresholdFeedbackNode->SetProperty( "helper object", BoolProperty::New(true) );
}

mitk::BinaryThresholdTool::~BinaryThresholdTool ( ) [protected, virtual]

Definition at line 63 of file mitkBinaryThresholdTool.cpp.

{
}

Member Function Documentation

void mitk::BinaryThresholdTool::AcceptCurrentThresholdValue	(	const std::string &	organName,
		const Color &	color
	)		`[virtual]`

Definition at line 123 of file mitkBinaryThresholdTool.cpp.

References mitk::RenderingManager::GetInstance(), and mitk::RenderingManager::RequestUpdateAll().

{

  CreateNewSegmentationFromThreshold(m_NodeForThresholding, organName, color );

  RenderingManager::GetInstance()->RequestUpdateAll();
  m_ToolManager->ActivateTool(-1);
}

void mitk::BinaryThresholdTool::Activated ( ) [virtual]

Called when the tool gets activated (registered to mitk::GlobalInteraction).

Derived tools should call their parents implementation.

Reimplemented from mitk::Tool.

Definition at line 77 of file mitkBinaryThresholdTool.cpp.

References OnRoiDataChanged().

{
  m_ToolManager->RoiDataChanged += mitk::MessageDelegate<mitk::BinaryThresholdTool>(this, &mitk::BinaryThresholdTool::OnRoiDataChanged);
  m_OriginalImageNode = m_ToolManager->GetReferenceData(0);
  m_NodeForThresholding = m_OriginalImageNode;

  if ( m_NodeForThresholding.IsNotNull() )
  {
    SetupPreviewNodeFor( m_NodeForThresholding );
  }
  else
  {
    m_ToolManager->ActivateTool(-1);
  }
}

void mitk::BinaryThresholdTool::CancelThresholding ( ) [virtual]

Definition at line 132 of file mitkBinaryThresholdTool.cpp.

{
  m_ToolManager->ActivateTool(-1);
}

void mitk::BinaryThresholdTool::CreateNewSegmentationFromThreshold	(	DataNode *	node,
		const std::string &	organType,
		const Color &	color
	)		`[protected]`

Definition at line 178 of file mitkBinaryThresholdTool.cpp.

References AccessFixedDimensionByItk_2, mitk::Tool::CreateEmptySegmentationNode(), mitk::Tool::ErrorMessage, and mitk::ImageTimeSelector::New().

{
  if (node)
  {
    Image::Pointer image = dynamic_cast<Image*>( m_NodeForThresholding->GetData() );
    if (image.IsNotNull())
    {
      // create a new image of the same dimensions and smallest possible pixel type
      DataNode::Pointer emptySegmentation = Tool::CreateEmptySegmentationNode( image, organName, color );

      if (emptySegmentation)
      {
        // actually perform a thresholding and ask for an organ type
        for (unsigned int timeStep = 0; timeStep < image->GetTimeSteps(); ++timeStep)
        {
          try
          {
            ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
            timeSelector->SetInput( image );
            timeSelector->SetTimeNr( timeStep );
            timeSelector->UpdateLargestPossibleRegion();
            Image::Pointer image3D = timeSelector->GetOutput();

            AccessFixedDimensionByItk_2( image3D, ITKThresholding, 3, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
          }
          catch(...)
          {
            Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation.");
          }
        }

        if (DataStorage* storage = m_ToolManager->GetDataStorage())
        {
          storage->Add( emptySegmentation, m_OriginalImageNode ); // add as a child, because the segmentation "derives" from the original
        }

        m_ToolManager->SetWorkingData( emptySegmentation );
      }
    }
  }
}

void mitk::BinaryThresholdTool::Deactivated ( ) [virtual]

Called when the tool gets deactivated (unregistered from mitk::GlobalInteraction).

Derived tools should call their parents implementation.

Reimplemented from mitk::Tool.

Definition at line 93 of file mitkBinaryThresholdTool.cpp.

References mitk::RenderingManager::GetInstance(), OnRoiDataChanged(), and mitk::RenderingManager::RequestUpdateAll().

{
  m_ToolManager->RoiDataChanged -= mitk::MessageDelegate<mitk::BinaryThresholdTool>(this, &mitk::BinaryThresholdTool::OnRoiDataChanged);
  m_NodeForThresholding = NULL;
  m_OriginalImageNode = NULL;
  try
  {
    if (DataStorage* storage = m_ToolManager->GetDataStorage())
    {
      storage->Remove( m_ThresholdFeedbackNode );
      RenderingManager::GetInstance()->RequestUpdateAll();
    }
  }
  catch(...)
  {
    // don't care
  }
  m_ThresholdFeedbackNode->SetData(NULL);
}

virtual const char* mitk::BinaryThresholdTool::GetClassName ( ) const [virtual]

Reimplemented from mitk::AutoSegmentationTool.

const char * mitk::BinaryThresholdTool::GetName ( ) const [virtual]

Returns the name of this tool. Make it short!

This name has to fit into some kind of button in most applications, so take some time to think of a good name!

Implements mitk::Tool.

Definition at line 72 of file mitkBinaryThresholdTool.cpp.

{
  return "Thresholding";
}

const char ** mitk::BinaryThresholdTool::GetXPM ( ) const [virtual]

Returns an icon in the XPM format.

This icon has to fit into some kind of button in most applications, so make it smaller than 25x25 pixels.

XPM is e.g. supported by The Gimp. But if you open any XPM file in your text editor, you will see that you could also "draw" it with an editor.

Implements mitk::Tool.

Definition at line 67 of file mitkBinaryThresholdTool.cpp.

{
  return mitkBinaryThresholdTool_xpm;
}

template<typename TPixel , unsigned int VImageDimension>

void mitk::BinaryThresholdTool::ITKThresholding	(	itk::Image< TPixel, VImageDimension > *	originalImage,
		mitk::Image *	segmentation,
		unsigned int	timeStep
	)		`[protected]`

Definition at line 221 of file mitkBinaryThresholdTool.cpp.

References mitk::CastToItkImage(), and mitk::ImageTimeSelector::New().

{
  ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
  timeSelector->SetInput( segmentation );
  timeSelector->SetTimeNr( timeStep );
  timeSelector->UpdateLargestPossibleRegion();
  Image::Pointer segmentation3D = timeSelector->GetOutput();

  typedef itk::Image< Tool::DefaultSegmentationDataType, 3> SegmentationType; // this is sure for new segmentations
  SegmentationType::Pointer itkSegmentation;
  CastToItkImage( segmentation3D, itkSegmentation );

  // iterate over original and segmentation
  typedef itk::ImageRegionConstIterator< itk::Image<TPixel, VImageDimension> >     InputIteratorType;
  typedef itk::ImageRegionIterator< SegmentationType >     SegmentationIteratorType;

  InputIteratorType inputIterator( originalImage, originalImage->GetLargestPossibleRegion() );
  SegmentationIteratorType outputIterator( itkSegmentation, itkSegmentation->GetLargestPossibleRegion() );

  inputIterator.GoToBegin();
  outputIterator.GoToBegin();

  while (!outputIterator.IsAtEnd())
  {
    if ( (signed)inputIterator.Get() >= m_CurrentThresholdValue )
    {
      outputIterator.Set( 1 );
    }
    else
    {
      outputIterator.Set( 0 );
    }

    ++inputIterator;
    ++outputIterator;
  }
}

static Pointer mitk::BinaryThresholdTool::New ( ) [static]

Referenced by BinaryThresholdTool().

void mitk::BinaryThresholdTool::OnRoiDataChanged ( ) [protected]

Definition at line 259 of file mitkBinaryThresholdTool.cpp.

References mitk::CastToItkImage(), mitk::CastToMitkImage(), mitk::DataNode::GetData(), mitk::BoundingObjectToSegmentationFilter::New(), mitk::Image::New(), and mitk::DataNode::New().

Referenced by Activated(), and Deactivated().

{
  typedef itk::Image<int, 3> ItkImageType;
  typedef itk::Image<unsigned char, 3> ItkMaskType;
  typedef itk::MaskImageFilter<ItkImageType, ItkMaskType, ItkImageType> MaskFilterType;
  mitk::DataNode* node = m_ToolManager->GetRoiData(0);
  if (node == NULL)
  {
    this->SetupPreviewNodeFor(m_OriginalImageNode);
    m_NodeForThresholding = m_OriginalImageNode;
    return;
  }

  mitk::DataNode::Pointer new_node = mitk::DataNode::New();
  mitk::Image* image = dynamic_cast<mitk::Image*> (m_OriginalImageNode->GetData());
  mitk::Image::Pointer new_image = mitk::Image::New();

  mitk::Image::Pointer roi;
  mitk::BoundingObject* boundingObject = dynamic_cast<mitk::BoundingObject*> (node->GetData());

  if (boundingObject)
  {
    mitk::BoundingObjectToSegmentationFilter::Pointer filter = mitk::BoundingObjectToSegmentationFilter::New();
    filter->SetBoundingObject( boundingObject);
    filter->SetInput(image);
    filter->Update();
    roi = filter->GetOutput();
  }
  else
    roi =  dynamic_cast<mitk::Image*> (node->GetData());

  if (roi)
  {
    MaskFilterType::Pointer filter = MaskFilterType::New();
    ItkMaskType::Pointer itkRoi = ItkMaskType::New();
    ItkImageType::Pointer itkImage = ItkImageType::New();
    mitk::CastToItkImage(image, itkImage);
    mitk::CastToItkImage(roi, itkRoi);
    filter->SetInput1(itkImage);
    filter->SetInput2(itkRoi);
    filter->SetOutsideValue(-32765);
    filter->Update();
    mitk::CastToMitkImage(filter->GetOutput(),new_image);
  }
  new_node->SetData(new_image);

  this->SetupPreviewNodeFor(new_node);
  m_NodeForThresholding = new_node;
}

void mitk::BinaryThresholdTool::SetThresholdValue ( int value ) [virtual]

Definition at line 113 of file mitkBinaryThresholdTool.cpp.

References mitk::RenderingManager::GetInstance(), mitk::LevelWindowProperty::New(), and mitk::RenderingManager::RequestUpdateAll().

{
  if (m_ThresholdFeedbackNode.IsNotNull())
  {
    m_CurrentThresholdValue = value;
    m_ThresholdFeedbackNode->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow(m_CurrentThresholdValue, 1) ) );
    RenderingManager::GetInstance()->RequestUpdateAll();
  }
}

void mitk::BinaryThresholdTool::SetupPreviewNodeFor ( DataNode * nodeForThresholding ) [protected]

Definition at line 137 of file mitkBinaryThresholdTool.cpp.

References mitk::DataNode::GetData(), and mitk::DataNode::GetIntProperty().

{
  if (nodeForThresholding)
  {
    Image::Pointer image = dynamic_cast<Image*>( nodeForThresholding->GetData() );
    Image::Pointer originalImage = dynamic_cast<Image*> (m_OriginalImageNode->GetData());
    if (image.IsNotNull())
    {
      // initialize and a new node with the same image as our reference image
      // use the level window property of this image copy to display the result of a thresholding operation
      m_ThresholdFeedbackNode->SetData( image );
      int layer(50);
      nodeForThresholding->GetIntProperty("layer", layer);
      m_ThresholdFeedbackNode->SetIntProperty("layer", layer+1);

      if (DataStorage* storage = m_ToolManager->GetDataStorage())
      {
        if (storage->Exists(m_ThresholdFeedbackNode))
          storage->Remove(m_ThresholdFeedbackNode);
        storage->Add( m_ThresholdFeedbackNode, nodeForThresholding );
      }

      m_SensibleMinimumThresholdValue = static_cast<int>( originalImage->GetScalarValueMin() );
      m_SensibleMaximumThresholdValue = static_cast<int>( originalImage->GetScalarValueMax() );

      LevelWindowProperty::Pointer lwp = dynamic_cast<LevelWindowProperty*>( m_ThresholdFeedbackNode->GetProperty( "levelwindow" ));
      if (lwp)
      {
        m_CurrentThresholdValue = static_cast<int>( lwp->GetLevelWindow().GetLevel() );
      }
      else
      {
        m_CurrentThresholdValue = (m_SensibleMaximumThresholdValue + m_SensibleMinimumThresholdValue)/2;
      }

      IntervalBordersChanged.Send(m_SensibleMinimumThresholdValue, m_SensibleMaximumThresholdValue);
      ThresholdingValueChanged.Send(m_CurrentThresholdValue);
    }
  }
}