#include <mitkLabeledImageToSurfaceFilter.h>

Inheritance diagram for mitk::LabeledImageToSurfaceFilter:

Collaboration diagram for mitk::LabeledImageToSurfaceFilter:

Public Types
typedef LabeledImageToSurfaceFilter	Self
typedef ImageToSurfaceFilter	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
typedef int	LabelType
typedef std::map< LabelType, unsigned long >	LabelMapType
typedef std::map< unsigned int, LabelType >	IdxToLabelMapType
Public Member Functions
virtual const char *	GetClassName () const
virtual void	SetGenerateAllLabels (bool _arg)
virtual bool	GetGenerateAllLabels ()
virtual void	GenerateAllLabelsOn ()
virtual void	GenerateAllLabelsOff ()
virtual void	SetLabel (LabelType _arg)
virtual LabelType	GetLabel ()
virtual void	SetBackgroundLabel (LabelType _arg)
virtual LabelType	GetBackgroundLabel ()
virtual void	SetGaussianStandardDeviation (double _arg)
virtual double	GetGaussianStandardDeviation ()
LabelType	GetLabelForNthOutput (const unsigned int &i)
mitk::ScalarType	GetVolumeForNthOutput (const unsigned int &i)
mitk::ScalarType	GetVolumeForLabel (const LabelType &label)
Static Public Member Functions
static Pointer	New ()
Protected Member Functions
virtual void	GenerateData ()
virtual void	GenerateOutputInformation ()
virtual void	CreateSurface (int time, vtkImageData vtkimage, mitk::Surface surface, LabelType label)
virtual LabelMapType	GetAvailableLabels ()
	LabeledImageToSurfaceFilter ()
virtual	~LabeledImageToSurfaceFilter ()
Protected Attributes
double	m_GaussianStandardDeviation
bool	m_GenerateAllLabels
LabelType	m_Label
LabelType	m_BackgroundLabel
LabelMapType	m_AvailableLabels
IdxToLabelMapType	m_IdxToLabels

Detailed Description

Calculates surfaces for labeled images. If you have a labeled image containing 5 different labeled regions plus the background, this class creates 5 surface representations from the regions. Each surface is assigned to one output of the filter. You can figure out, which label corresponds to which output using the GetLabelForNthOutput() method. If you want to calculate a surface representation only for one specific label, you may call GenerateAllLabelsOff() and set the desired label by SetLabel(label).

Definition at line 40 of file mitkLabeledImageToSurfaceFilter.h.

Member Typedef Documentation

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

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 44 of file mitkLabeledImageToSurfaceFilter.h.

typedef std::map<unsigned int, LabelType> mitk::LabeledImageToSurfaceFilter::IdxToLabelMapType

Definition at line 52 of file mitkLabeledImageToSurfaceFilter.h.

typedef std::map<LabelType, unsigned long> mitk::LabeledImageToSurfaceFilter::LabelMapType

Definition at line 50 of file mitkLabeledImageToSurfaceFilter.h.

typedef int mitk::LabeledImageToSurfaceFilter::LabelType

Definition at line 46 of file mitkLabeledImageToSurfaceFilter.h.

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

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 44 of file mitkLabeledImageToSurfaceFilter.h.

typedef LabeledImageToSurfaceFilter mitk::LabeledImageToSurfaceFilter::Self

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 44 of file mitkLabeledImageToSurfaceFilter.h.

typedef ImageToSurfaceFilter mitk::LabeledImageToSurfaceFilter::Superclass

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 44 of file mitkLabeledImageToSurfaceFilter.h.

Constructor & Destructor Documentation

mitk::LabeledImageToSurfaceFilter::LabeledImageToSurfaceFilter ( ) [protected]

Definition at line 38 of file mitkLabeledImageToSurfaceFilter.cpp.

                                                             :
m_GaussianStandardDeviation(1.5),
m_GenerateAllLabels(true),
m_Label(1),
m_BackgroundLabel(0)
{
}

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

Definition at line 46 of file mitkLabeledImageToSurfaceFilter.cpp.

{
}

Member Function Documentation

void mitk::LabeledImageToSurfaceFilter::CreateSurface	(	int	time,
		vtkImageData *	vtkimage,
		mitk::Surface *	surface,
		LabelType	label
	)		`[protected, virtual]`

Definition at line 169 of file mitkLabeledImageToSurfaceFilter.cpp.

References matrix(), and mitk::Surface::SetVtkPolyData().

{
  vtkImageChangeInformation *indexCoordinatesImageFilter = vtkImageChangeInformation::New();
  indexCoordinatesImageFilter->SetInput(vtkimage);
  indexCoordinatesImageFilter->SetOutputOrigin(0.0,0.0,0.0);

    vtkImageThreshold* threshold = vtkImageThreshold::New();
    threshold->SetInput( indexCoordinatesImageFilter->GetOutput() );
    //indexCoordinatesImageFilter->Delete();
    threshold->SetInValue( 100 );
    threshold->SetOutValue( 0 );
    threshold->ThresholdBetween( label, label ); 
    threshold->SetOutputScalarTypeToUnsignedChar();
    threshold->ReleaseDataFlagOn();

    vtkImageGaussianSmooth *gaussian = vtkImageGaussianSmooth::New();
    gaussian->SetInput( threshold->GetOutput() ); 
    //threshold->Delete();
    gaussian->SetDimensionality( 3  );
    gaussian->SetRadiusFactor( 0.49 );
    gaussian->SetStandardDeviation( GetGaussianStandardDeviation() );
    gaussian->ReleaseDataFlagOn();
    gaussian->UpdateInformation();
    gaussian->Update();

  //MarchingCube -->create Surface
  vtkMarchingCubes *skinExtractor = vtkMarchingCubes::New();
  skinExtractor->ReleaseDataFlagOn();
  skinExtractor->SetInput(gaussian->GetOutput());//RC++
  indexCoordinatesImageFilter->Delete();
  skinExtractor->SetValue(0, 50);

  vtkPolyData *polydata;
  polydata = skinExtractor->GetOutput();
  polydata->Register(NULL);//RC++
  skinExtractor->Delete();

  if (m_Smooth)
  {
    vtkSmoothPolyDataFilter *smoother = vtkSmoothPolyDataFilter::New();
    //read poly1 (poly1 can be the original polygon, or the decimated polygon)
    smoother->SetInput(polydata);//RC++
    smoother->SetNumberOfIterations( m_SmoothIteration );
    smoother->SetRelaxationFactor( m_SmoothRelaxation );
    smoother->SetFeatureAngle( 60 );
    smoother->FeatureEdgeSmoothingOff();
    smoother->BoundarySmoothingOff();
    smoother->SetConvergence( 0 );

    polydata->Delete();//RC--
    polydata = smoother->GetOutput();
    polydata->Register(NULL);//RC++
    smoother->Delete();
  }

//
//#if (VTK_MAJOR_VERSION >= 5)
//  if (m_Decimate == Decimate )
//  {
//    MITK_ERROR << "vtkDecimate not available for VTK 5.0 and above.";
//    MITK_ERROR << " Using vtkDecimatePro instead." << std::endl;
//    m_Decimate = DecimatePro;
//  }
//#endif

  //decimate = to reduce number of polygons
  if(m_Decimate==DecimatePro)
  {
    vtkDecimatePro *decimate = vtkDecimatePro::New();
    decimate->SplittingOff();
    decimate->SetErrorIsAbsolute(5);
    decimate->SetFeatureAngle(30);
    decimate->PreserveTopologyOn();
    decimate->BoundaryVertexDeletionOff();
    decimate->SetDegree(10); //std-value is 25!

    decimate->SetInput(polydata);//RC++
    decimate->SetTargetReduction(m_TargetReduction);
    decimate->SetMaximumError(0.002);

    polydata->Delete();//RC--
    polydata = decimate->GetOutput();
    polydata->Register(NULL);//RC++
    decimate->Delete();
  }
#if (VTK_MAJOR_VERSION < 5)
  else if (m_Decimate==Decimate)
  {
    vtkDecimate *decimate = vtkDecimate::New();
    decimate->SetInput( polydata );
    decimate->PreserveTopologyOn();
    decimate->BoundaryVertexDeletionOff();
    decimate->SetTargetReduction( m_TargetReduction );
    polydata->Delete();//RC--
    polydata = decimate->GetOutput();
    polydata->Register(NULL);//RC++
    decimate->Delete();
  }
#endif

  polydata->Update();

  polydata->SetSource(NULL);

  if(polydata->GetNumberOfPoints() > 0)
  {
    mitk::Vector3D spacing = GetInput()->GetGeometry(time)->GetSpacing();

    vtkPoints * points = polydata->GetPoints();
    vtkMatrix4x4 *vtkmatrix = vtkMatrix4x4::New();
    GetInput()->GetGeometry(time)->GetVtkTransform()->GetMatrix(vtkmatrix);
    double (*matrix)[4] = vtkmatrix->Element;

    unsigned int i,j;
    for(i=0;i<3;++i)
      for(j=0;j<3;++j)
        matrix[i][j]/=spacing[j];

    unsigned int n = points->GetNumberOfPoints();
    vtkFloatingPointType point[3];

    for (i = 0; i < n; i++)
    {
      points->GetPoint(i, point);
      mitkVtkLinearTransformPoint(matrix,point,point);
      points->SetPoint(i, point);
    }
    vtkmatrix->Delete();
  }

  surface->SetVtkPolyData(polydata, time);
  polydata->UnRegister(NULL);

  gaussian->Delete();
  threshold->Delete();
}

virtual void mitk::LabeledImageToSurfaceFilter::GenerateAllLabelsOff ( ) [virtual]

virtual void mitk::LabeledImageToSurfaceFilter::GenerateAllLabelsOn ( ) [virtual]

void mitk::LabeledImageToSurfaceFilter::GenerateData ( ) [protected, virtual]

For each image time slice a surface will be created. This method is called by Update().

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 125 of file mitkLabeledImageToSurfaceFilter.cpp.

References mitk::SlicedData::GetRequestedRegion(), mitk::Image::GetVtkImageData(), and QuadProgPP::t().

{
  mitk::Image* image =  ( mitk::Image* )GetInput();
  if ( image == NULL )
  {
    itkWarningMacro("Image is NULL");
    return;
  }
    
  mitk::Image::RegionType outputRegion = image->GetRequestedRegion();

  m_IdxToLabels.clear();
  
  if ( this->GetNumberOfOutputs() == 0 )
    return;
  
  //
  // traverse the known labels and create surfaces for them.
  //
  unsigned int currentOutputIndex = 0;
  for ( LabelMapType::iterator it = m_AvailableLabels.begin() ; it != m_AvailableLabels.end() ; ++it )
  {
    if ( it->first == m_BackgroundLabel )
      continue;
    if ( ( it->second == 0 ) && m_GenerateAllLabels )
      continue;
    
    assert ( currentOutputIndex < this->GetNumberOfOutputs() );
    mitk::Surface::Pointer surface = this->GetOutput( currentOutputIndex );
    assert( surface.IsNotNull() );
    
    int tstart=outputRegion.GetIndex(3);
    int tmax=tstart+outputRegion.GetSize(3); //GetSize()==1 - will aber 0 haben, wenn nicht zeitaufgeloet
    int t;
    for( t=tstart; t < tmax; ++t)
    {
      vtkImageData *vtkimagedata =  image->GetVtkImageData( t );
      CreateSurface( t,vtkimagedata,surface.GetPointer(), it->first );
    }
    m_IdxToLabels[ currentOutputIndex ] = it->first;
    currentOutputIndex++;
  }
}

void mitk::LabeledImageToSurfaceFilter::GenerateOutputInformation ( void ) [protected, virtual]

Initializes the output information ( i.e. the geometry information ) of the output of the filter

Reimplemented from mitk::ImageToSurfaceFilter.

Definition at line 50 of file mitkLabeledImageToSurfaceFilter.cpp.

References mitk::Surface::Expand(), mitk::BaseData::GetTimeSlicedGeometry(), and mitk::TimeSlicedGeometry::GetTimeSteps().

{
  Superclass::GenerateOutputInformation();
  //
  // check which labels are available in the image
  //
  m_AvailableLabels = this->GetAvailableLabels();
  m_IdxToLabels.clear();
  
  //
  // if we don't want to generate surfaces for all labels
  // we have to remove all labels except m_Label and m_BackgroundLabel 
  // from the list of available labels
  //
  if ( ! m_GenerateAllLabels )
  {
    LabelMapType tmp;
    LabelMapType::iterator it;
    it = m_AvailableLabels.find( m_Label );
    if ( it != m_AvailableLabels.end() )
      tmp[m_Label] = it->second;
    else
      tmp[m_Label] = 0;
    
    it = m_AvailableLabels.find( m_BackgroundLabel );
    if ( it != m_AvailableLabels.end() )
      tmp[m_BackgroundLabel] = it->second;
    else
      tmp[m_BackgroundLabel] = 0;
    
    m_AvailableLabels = tmp;
  }
  
  //
  // check for the number of labels: if the whole image is filled, no
  // background is available and thus the numberOfOutpus is equal to the 
  // number of available labels in the image (which is a special case). 
  // If we have background voxels, the number of outputs is one less than
  // then number of available labels.
  //
  unsigned int numberOfOutputs = 0;
  if ( m_AvailableLabels.find( m_BackgroundLabel ) == m_AvailableLabels.end() )
    numberOfOutputs = m_AvailableLabels.size();
  else
    numberOfOutputs = m_AvailableLabels.size() - 1;
  if ( numberOfOutputs == 0 )
  {
    itkWarningMacro("Number of outputs == 0");
  }

  //
  // determine the number of time steps of the input image
  //
  mitk::Image* image =  ( mitk::Image* )GetInput();
  unsigned int numberOfTimeSteps = image->GetTimeSlicedGeometry()->GetTimeSteps();
    
  //
  // set the number of outputs to the number of labels used.
  // initialize the output surfaces accordingly (incl. time steps)
  //
  this->SetNumberOfOutputs( numberOfOutputs );
  this->SetNumberOfRequiredOutputs( numberOfOutputs );
  for ( unsigned int i = 0 ; i < numberOfOutputs; ++i )
  {
    if ( ! this->GetOutput( i ) )
    {
      mitk::Surface::Pointer output = static_cast<mitk::Surface*>( this->MakeOutput(0).GetPointer() );
      assert ( output.IsNotNull() );
      output->Expand( numberOfTimeSteps ); 
      this->SetNthOutput( i, output.GetPointer() );
    }
  }
}

mitk::LabeledImageToSurfaceFilter::LabelMapType mitk::LabeledImageToSurfaceFilter::GetAvailableLabels ( ) [protected, virtual]

Definition at line 334 of file mitkLabeledImageToSurfaceFilter.cpp.

References AccessFixedDimensionByItk_1, and GetAvailableLabelsInternal().

{
  mitk::Image::Pointer image =  ( mitk::Image* )GetInput();
  LabelMapType availableLabels;
  AccessFixedDimensionByItk_1( image, GetAvailableLabelsInternal, 3, availableLabels );
  return availableLabels;
}

virtual LabelType mitk::LabeledImageToSurfaceFilter::GetBackgroundLabel ( ) [virtual]

Returns the label of the background. No surface will be generated for this label!

Returns:: the label of the background, by default 0

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

Reimplemented from mitk::ImageToSurfaceFilter.

virtual double mitk::LabeledImageToSurfaceFilter::GetGaussianStandardDeviation ( ) [virtual]

Returns the standard deviation of the Gaussian filter which will be used when filter is enabled.

virtual bool mitk::LabeledImageToSurfaceFilter::GetGenerateAllLabels ( ) [virtual]

Returns:: if all labels or only a specific label should be extracted.

virtual LabelType mitk::LabeledImageToSurfaceFilter::GetLabel ( ) [virtual]

Returns the label you want to extract. This method only has an effect, if GenerateAllLabels() is set to false

Returns:: _arg the label to extract, by default 1

mitk::LabeledImageToSurfaceFilter::LabelType mitk::LabeledImageToSurfaceFilter::GetLabelForNthOutput ( const unsigned int & i )

Lets you retrieve the label which was used for generating the Nth output of this filter. If GenerateAllLabels() is set to false, this filter only knows about the label provided via SetLabel(). All other labels in the image are not known.

Parameters:

i	the index of the Nth output.

Returns:: the label used for calculating the Nth output of the filter. If i is out of range, itk::NumericLimits<LabelType>::max() is returned.

Definition at line 349 of file mitkLabeledImageToSurfaceFilter.cpp.

References QuadProgPP::max().

{
  IdxToLabelMapType::iterator it = m_IdxToLabels.find( idx );
  if ( it != m_IdxToLabels.end() )
  {
    return it->second;
  }
  else
  {
    itkWarningMacro( "Unknown index encountered: " << idx << ". There are " << this->GetNumberOfOutputs() << " outputs available." );
    return itk::NumericTraits<LabelType>::max();
  }
}

mitk::ScalarType mitk::LabeledImageToSurfaceFilter::GetVolumeForLabel ( const LabelType & label )

Lets you retrieve the volume in milliliters of the region with the given label. If GenerateAllLabels is set to false, you may only call this method for the label provided using the SetLabel() method.

Parameters:

label the label of the region you want to get the volume of

Returns:: the volume of the region with the given label. If label is invalid, 0.0 is returned.

Definition at line 368 of file mitkLabeledImageToSurfaceFilter.cpp.

References mitk::Geometry3D::GetFloatSpacing(), and mitk::SlicedData::GetSlicedGeometry().

{
  // get the image spacing 
  mitk::Image* image =  ( mitk::Image* )GetInput();
  const float* spacing = image->GetSlicedGeometry()->GetFloatSpacing();
  
  // get the number of voxels encountered for the given label,
  // calculate the volume and return it.
  LabelMapType::iterator it = m_AvailableLabels.find( label );
  if ( it != m_AvailableLabels.end() )
  {
    return static_cast<float>(it->second) * ( spacing[0] * spacing[1] * spacing[2] / 1000.0f );
  }
  else
  {
    itkWarningMacro( "Unknown label encountered: " << label );
    return 0.0;
  }
}

mitk::ScalarType mitk::LabeledImageToSurfaceFilter::GetVolumeForNthOutput ( const unsigned int & i )

Lets you retrieve the volume in milliliters of the region used to generate the Nth output.

Parameters:

i	the index of the Nth output.

Returns:: the volume of the region used to generate the Nth output of the filter. If i is out of range, 0.0 is returned.

Definition at line 363 of file mitkLabeledImageToSurfaceFilter.cpp.

{
  return GetVolumeForLabel( GetLabelForNthOutput( i ) );
}

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

Reimplemented from mitk::ImageToSurfaceFilter.

Referenced by mitkLabeledImageToSurfaceFilterTest().

virtual void mitk::LabeledImageToSurfaceFilter::SetBackgroundLabel ( LabelType _arg ) [virtual]

Set the label of the background. No surface will be generated for this label!

Parameters:

_arg	the label of the background, by default 0

virtual void mitk::LabeledImageToSurfaceFilter::SetGaussianStandardDeviation ( double _arg ) [virtual]

Set standard deviation for Gaussian Filter.

Parameters:

_arg	by default 1.5

virtual void mitk::LabeledImageToSurfaceFilter::SetGenerateAllLabels ( bool _arg ) [virtual]

Set whether you want to extract all (true) or only a specific label (false)

Parameters:

_arg	true by default

virtual void mitk::LabeledImageToSurfaceFilter::SetLabel ( LabelType _arg ) [virtual]

Set the label you want to extract. This method only has an effect, if GenerateAllLabels() is set to false

Parameters:

_arg	the label to extract, by default 1

Member Data Documentation

LabelMapType mitk::LabeledImageToSurfaceFilter::m_AvailableLabels [protected]

Definition at line 145 of file mitkLabeledImageToSurfaceFilter.h.

LabelType mitk::LabeledImageToSurfaceFilter::m_BackgroundLabel [protected]

Definition at line 143 of file mitkLabeledImageToSurfaceFilter.h.

double mitk::LabeledImageToSurfaceFilter::m_GaussianStandardDeviation [protected]

Definition at line 137 of file mitkLabeledImageToSurfaceFilter.h.

bool mitk::LabeledImageToSurfaceFilter::m_GenerateAllLabels [protected]

Definition at line 139 of file mitkLabeledImageToSurfaceFilter.h.

IdxToLabelMapType mitk::LabeledImageToSurfaceFilter::m_IdxToLabels [protected]

Definition at line 147 of file mitkLabeledImageToSurfaceFilter.h.

LabelType mitk::LabeledImageToSurfaceFilter::m_Label [protected]

Definition at line 141 of file mitkLabeledImageToSurfaceFilter.h.

The documentation for this class was generated from the following files:

mitk::LabeledImageToSurfaceFilter Class Reference

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation