Calculates some gray value statistics for segmentations. More...

#include <mitkCalculateGrayValueStatisticsTool.h>

Inheritance diagram for mitk::CalculateGrayValueStatisticsTool:

Collaboration diagram for mitk::CalculateGrayValueStatisticsTool:

Public Types
typedef CalculateGrayValueStatisticsTool	Self
typedef SegmentationsProcessingTool	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
typedef itk::Statistics::Histogram < double >	HistogramType
typedef HistogramType::MeasurementType	HistogramMeasurementType
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 std::string	GetReport () const
HistogramType::ConstPointer	GetHistogram ()
Static Public Member Functions
static Pointer	New ()
Public Attributes
Message	StatisticsCompleted
HistogramType::Pointer	m_ITKHistogram
Protected Member Functions
	CalculateGrayValueStatisticsTool ()
virtual	~CalculateGrayValueStatisticsTool ()
virtual void	StartProcessingAllData ()
	Subclasses should override this method.
virtual bool	ProcessOneWorkingData (DataNode *node)
	Subclasses should override this method.
virtual void	FinishProcessingAllData ()
	Subclasses should override this method.
virtual std::string	GetErrorMessage ()
	Describes the error (if one occurred during processing).
template<typename TPixel , unsigned int VImageDimension>
void	CalculateMinMax (itk::Image< TPixel, VImageDimension > referenceImage, Image segmentation, TPixel &minimum, TPixel &maximum)
template<typename TPixel , unsigned int VImageDimension>
void	ITKHistogramming (itk::Image< TPixel, VImageDimension > referenceImage, Image segmentation, std::stringstream &report)
Protected Attributes
std::stringstream	m_CompleteReport

Detailed Description

Calculates some gray value statistics for segmentations.

See also:: mitk::Tool; QmitkInteractiveSegmentation

Last contributor: $Author$

Definition at line 40 of file mitkCalculateGrayValueStatisticsTool.h.

Member Typedef Documentation

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

Reimplemented from mitk::SegmentationsProcessingTool.

Definition at line 46 of file mitkCalculateGrayValueStatisticsTool.h.

typedef HistogramType::MeasurementType mitk::CalculateGrayValueStatisticsTool::HistogramMeasurementType

Definition at line 63 of file mitkCalculateGrayValueStatisticsTool.h.

typedef itk::Statistics::Histogram<double> mitk::CalculateGrayValueStatisticsTool::HistogramType

Definition at line 58 of file mitkCalculateGrayValueStatisticsTool.h.

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

Reimplemented from mitk::SegmentationsProcessingTool.

Definition at line 46 of file mitkCalculateGrayValueStatisticsTool.h.

typedef CalculateGrayValueStatisticsTool mitk::CalculateGrayValueStatisticsTool::Self

Reimplemented from mitk::SegmentationsProcessingTool.

Definition at line 46 of file mitkCalculateGrayValueStatisticsTool.h.

typedef SegmentationsProcessingTool mitk::CalculateGrayValueStatisticsTool::Superclass

Reimplemented from mitk::SegmentationsProcessingTool.

Definition at line 46 of file mitkCalculateGrayValueStatisticsTool.h.

Constructor & Destructor Documentation

mitk::CalculateGrayValueStatisticsTool::CalculateGrayValueStatisticsTool ( ) [protected]

Definition at line 36 of file mitkCalculateGrayValueStatisticsTool.cpp.

{
}

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

Definition at line 40 of file mitkCalculateGrayValueStatisticsTool.cpp.

{
}

Member Function Documentation

template<typename TPixel , unsigned int VImageDimension>

void mitk::CalculateGrayValueStatisticsTool::CalculateMinMax	(	itk::Image< TPixel, VImageDimension > *	referenceImage,
		Image *	segmentation,
		TPixel &	minimum,
		TPixel &	maximum
	)		`[protected]`

Calculates the minimum and maximum of the pixelvalues. They have to be known to initialize the histogram.

Definition at line 142 of file mitkCalculateGrayValueStatisticsTool.cpp.

References mitk::CastToItkImage(), QuadProgPP::max(), min, and ROUND_P.

{
  typedef itk::Image<TPixel, VImageDimension> ImageType;
  typedef itk::Image<Tool::DefaultSegmentationDataType, VImageDimension> SegmentationType;

  typename SegmentationType::Pointer segmentationItk;
  CastToItkImage(segmentation, segmentationItk);

  typename SegmentationType::RegionType segmentationRegion =
      segmentationItk->GetLargestPossibleRegion();

  segmentationRegion.Crop(referenceImage->GetLargestPossibleRegion());

  itk::ImageRegionConstIteratorWithIndex<SegmentationType> segmentationIterator(segmentationItk,
      segmentationRegion);
  itk::ImageRegionConstIteratorWithIndex<ImageType> referenceIterator(referenceImage,
      segmentationRegion);

  segmentationIterator.GoToBegin();
  referenceIterator.GoToBegin();

  minimum = std::numeric_limits<TPixel>::max();
  maximum = std::numeric_limits<TPixel>::min();

  while (!segmentationIterator.IsAtEnd())
  {
    itk::Point<float, 3> pt;
    segmentationItk->TransformIndexToPhysicalPoint(segmentationIterator.GetIndex(), pt);

    typename ImageType::IndexType ind;
    itk::ContinuousIndex<float, 3> contInd;
    if (referenceImage->TransformPhysicalPointToContinuousIndex(pt, contInd))
    {
      for (unsigned int i = 0; i < 3; ++i)
        ind[i] = ROUND_P(contInd[i]);

      referenceIterator.SetIndex(ind);

      if (segmentationIterator.Get() > 0)
      {

        if (referenceIterator.Get() < minimum)
          minimum = referenceIterator.Get();
        if (referenceIterator.Get() > maximum)
          maximum = referenceIterator.Get();
      }
    }

    ++segmentationIterator;
  }

}

void mitk::CalculateGrayValueStatisticsTool::FinishProcessingAllData ( ) [protected, virtual]

Subclasses should override this method.

See also:: ProcessAllObjects

Reimplemented from mitk::SegmentationsProcessingTool.

Definition at line 130 of file mitkCalculateGrayValueStatisticsTool.cpp.

References mitk::SegmentationsProcessingTool::FinishProcessingAllData().

{
  SegmentationsProcessingTool::FinishProcessingAllData();

  // show/send results
  StatisticsCompleted.Send();
  //MITK_INFO << m_CompleteReport.str() << std::endl;
}

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

Reimplemented from mitk::SegmentationsProcessingTool.

std::string mitk::CalculateGrayValueStatisticsTool::GetErrorMessage ( ) [protected, virtual]

Describes the error (if one occurred during processing).

Reimplemented from mitk::SegmentationsProcessingTool.

Definition at line 54 of file mitkCalculateGrayValueStatisticsTool.cpp.

{
  return "No statistics generated for these segmentations:";
}

mitk::CalculateGrayValueStatisticsTool::HistogramType::ConstPointer mitk::CalculateGrayValueStatisticsTool::GetHistogram ( )

Definition at line 330 of file mitkCalculateGrayValueStatisticsTool.cpp.

{
  return m_ITKHistogram.GetPointer();
}

const char * mitk::CalculateGrayValueStatisticsTool::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 49 of file mitkCalculateGrayValueStatisticsTool.cpp.

{
  return "Statistics";
}

std::string mitk::CalculateGrayValueStatisticsTool::GetReport ( ) const [virtual]

Definition at line 325 of file mitkCalculateGrayValueStatisticsTool.cpp.

{
  return m_CompleteReport.str();
}

const char ** mitk::CalculateGrayValueStatisticsTool::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 44 of file mitkCalculateGrayValueStatisticsTool.cpp.

{
  return mitkCalculateGrayValueStatisticsTool_xpm;
}

template<typename TPixel , unsigned int VImageDimension>

void mitk::CalculateGrayValueStatisticsTool::ITKHistogramming	(	itk::Image< TPixel, VImageDimension > *	referenceImage,
		Image *	segmentation,
		std::stringstream &	report
	)		`[protected]`

initializes and fills the histogram
calculates mean, sd and quantiles

Definition at line 198 of file mitkCalculateGrayValueStatisticsTool.cpp.

References mitk::CastToItkImage(), QuadProgPP::max(), QuadProgPP::mean(), min, ROUND_P, and QuadProgPP::sqrt().

{
  typedef itk::Image<TPixel, VImageDimension> ImageType;
  typedef itk::Image<Tool::DefaultSegmentationDataType, VImageDimension> SegmentationType;

  typename SegmentationType::Pointer segmentationItk;
  CastToItkImage( segmentation, segmentationItk );

  // generate histogram
  typename SegmentationType::RegionType segmentationRegion = segmentationItk->GetLargestPossibleRegion();

  segmentationRegion.Crop( referenceImage->GetLargestPossibleRegion() );

  itk::ImageRegionConstIteratorWithIndex< SegmentationType > segmentationIterator( segmentationItk, segmentationRegion);
  itk::ImageRegionConstIteratorWithIndex< ImageType >        referenceIterator( referenceImage, segmentationRegion);

  segmentationIterator.GoToBegin();
  referenceIterator.GoToBegin();

  m_ITKHistogram = HistogramType::New();

  TPixel minimum = std::numeric_limits<TPixel>::max();
  TPixel maximum = std::numeric_limits<TPixel>::min();
    
  CalculateMinMax(referenceImage, segmentation, minimum, maximum);

  //initialize the histogram to the range of the cropped region
  HistogramType::SizeType size;
#if defined(ITK_USE_REVIEW_STATISTICS)
  typedef typename HistogramType::SizeType::ValueType HSizeValueType;
#else
  typedef typename HistogramType::SizeType::SizeValueType HSizeValueType;
#endif
  size.Fill(static_cast<HSizeValueType> (maximum - minimum + 1));
  HistogramType::MeasurementVectorType lowerBound;
  HistogramType::MeasurementVectorType upperBound;
  lowerBound[0] = minimum;
  upperBound[0] = maximum;
  m_ITKHistogram->Initialize(size, lowerBound, upperBound);

  double mean(0.0);
  double sd(0.0);
  double voxelCount(0.0);

  //iterate through the cropped region add the values to the histogram
  while (!segmentationIterator.IsAtEnd())
  {
    itk::Point< float, 3 > pt;
    segmentationItk->TransformIndexToPhysicalPoint( segmentationIterator.GetIndex(), pt );

    typename ImageType::IndexType ind;
    itk::ContinuousIndex<float, 3> contInd;
    if (referenceImage->TransformPhysicalPointToContinuousIndex(pt, contInd))
    {
      for (unsigned int i = 0; i < 3; ++i) ind[i] = ROUND_P(contInd[i]);

      referenceIterator.SetIndex( ind );

      if ( segmentationIterator.Get() > 0 )
      {
        HistogramType::MeasurementVectorType currentMeasurementVector;

        currentMeasurementVector[0]
            = static_cast<HistogramType::MeasurementType> (referenceIterator.Get());
        m_ITKHistogram->IncreaseFrequency(currentMeasurementVector, 1);

        mean = (mean * (static_cast<double> (voxelCount) / static_cast<double> (voxelCount + 1))) // 3 points:   old center * 2/3 + currentPoint * 1/3;
            + static_cast<double> (referenceIterator.Get()) / static_cast<double> (voxelCount + 1);

        voxelCount += 1.0;
      }
    }

    ++segmentationIterator;
  }

  // second pass for SD
  segmentationIterator.GoToBegin();
  referenceIterator.GoToBegin();
  while ( !segmentationIterator.IsAtEnd() )
  {
    itk::Point< float, 3 > pt;
    segmentationItk->TransformIndexToPhysicalPoint( segmentationIterator.GetIndex(), pt );

    typename ImageType::IndexType ind;
    itk::ContinuousIndex<float, 3> contInd;
    if (referenceImage->TransformPhysicalPointToContinuousIndex(pt, contInd))
    {
      for (unsigned int i = 0; i < 3; ++i) ind[i] = ROUND_P(contInd[i]);

      referenceIterator.SetIndex( ind );

      if ( segmentationIterator.Get() > 0 )
      {
        sd += ((static_cast<double>(referenceIterator.Get() ) - mean)*(static_cast<double>(referenceIterator.Get() ) - mean));
      }
    }

    ++segmentationIterator;
  }

  sd /= static_cast<double>(voxelCount - 1);
  sd = sqrt( sd );

  // generate quantiles
  TPixel histogramQuantileValues[5];
  histogramQuantileValues[0] = m_ITKHistogram->Quantile(0, 0.05);
  histogramQuantileValues[1] = m_ITKHistogram->Quantile(0, 0.25);
  histogramQuantileValues[2] = m_ITKHistogram->Quantile(0, 0.50);
  histogramQuantileValues[3] = m_ITKHistogram->Quantile(0, 0.75);
  histogramQuantileValues[4] = m_ITKHistogram->Quantile(0, 0.95);

  // report histogram values
report     << "         Minimum:" << minimum
           << "\n  5% quantile: " << histogramQuantileValues[0]
           << "\n 25% quantile: " << histogramQuantileValues[1]
           << "\n 50% quantile: " << histogramQuantileValues[2]
           << "\n 75% quantile: " << histogramQuantileValues[3]
           << "\n 95% quantile: " << histogramQuantileValues[4]
           << "\n      Maximum: " << maximum
           << "\n         Mean: " << mean
           << "\n           SD: " << sd
           << "\n";
}

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

bool mitk::CalculateGrayValueStatisticsTool::ProcessOneWorkingData ( DataNode * node ) [protected, virtual]

Subclasses should override this method.

See also:: ProcessAllObjects

Reimplemented from mitk::SegmentationsProcessingTool.

Definition at line 65 of file mitkCalculateGrayValueStatisticsTool.cpp.

References AccessFixedDimensionByItk_2, mitk::ProgressBar::AddStepsToDo(), mitk::StatusBar::DisplayText(), mitk::DataNode::GetData(), mitk::StatusBar::GetInstance(), mitk::ProgressBar::GetInstance(), mitk::DataNode::GetName(), mitk::ImageTimeSelector::New(), and mitk::ProgressBar::Progress().

{
  if (node)
  {
    Image::Pointer image = dynamic_cast<Image*>( node->GetData() );
    if (image.IsNull()) return false;

    DataNode* referencenode = m_ToolManager->GetReferenceData(0);
    if (!referencenode) return false;

    try
    {
      ProgressBar::GetInstance()->AddStepsToDo(1);

      // add to report
      std::string nodename("structure");
      node->GetName(nodename);

      std::string message = "Calculating statistics for ";
      message += nodename;

      StatusBar::GetInstance()->DisplayText(message.c_str());

      Image::Pointer refImage = dynamic_cast<Image*>( referencenode->GetData() );
      Image::Pointer image = dynamic_cast<Image*>( node->GetData() );

      m_CompleteReport << "======== Gray value analysis of " << nodename << " ========\n";

      if (image.IsNotNull() && refImage.IsNotNull() )
      {
        for (unsigned int timeStep = 0; timeStep < image->GetTimeSteps(); ++timeStep)
        {
          ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
          timeSelector->SetInput( refImage );
          timeSelector->SetTimeNr( timeStep );
          timeSelector->UpdateLargestPossibleRegion();
          Image::Pointer refImage3D = timeSelector->GetOutput();

          ImageTimeSelector::Pointer timeSelector2 = ImageTimeSelector::New();
          timeSelector2->SetInput( image );
          timeSelector2->SetTimeNr( timeStep );
          timeSelector2->UpdateLargestPossibleRegion();
          Image::Pointer image3D = timeSelector2->GetOutput();

          if (image3D.IsNotNull() && refImage3D.IsNotNull() )
          {
            m_CompleteReport << "=== " << nodename << ", time step " << timeStep << " ===\n";
            AccessFixedDimensionByItk_2( refImage3D, ITKHistogramming, 3, image3D, m_CompleteReport );
          }
        }
      }

      m_CompleteReport << "======== End of analysis for " << nodename << " ===========\n\n\n";

      ProgressBar::GetInstance()->Progress();
    }
    catch(...)
    {
      return false;
    }
  }

  return true;
}

void mitk::CalculateGrayValueStatisticsTool::StartProcessingAllData ( ) [protected, virtual]

Subclasses should override this method.

See also:: ProcessAllObjects

Reimplemented from mitk::SegmentationsProcessingTool.

Definition at line 59 of file mitkCalculateGrayValueStatisticsTool.cpp.

{
  // clear/prepare report
  m_CompleteReport.str("");
}

Member Data Documentation

std::stringstream mitk::CalculateGrayValueStatisticsTool::m_CompleteReport [protected]

Definition at line 91 of file mitkCalculateGrayValueStatisticsTool.h.

HistogramType::Pointer mitk::CalculateGrayValueStatisticsTool::m_ITKHistogram

Definition at line 59 of file mitkCalculateGrayValueStatisticsTool.h.

Message mitk::CalculateGrayValueStatisticsTool::StatisticsCompleted

Definition at line 44 of file mitkCalculateGrayValueStatisticsTool.h.

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

mitk::CalculateGrayValueStatisticsTool Class Reference [Classes related to InteractiveSegmentation]

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

mitk::CalculateGrayValueStatisticsTool Class Reference
[Classes related to InteractiveSegmentation]