/usr/include/gofigure2/itkBinaryMaskImageToGoFigureMeshAttributes.txx

/*=========================================================================
 Authors: The GoFigure Dev. Team.
 at Megason Lab, Systems biology, Harvard Medical school, 2009-11

 Copyright (c) 2009-11, President and Fellows of Harvard College.
 All rights reserved.

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 nor the names of its contributors may be used to endorse or promote
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#ifndef __itkBinaryMaskImageToGoFigureMeshAttributes_txx
#define __itkBinaryMaskImageToGoFigureMeshAttributes_txx

namespace itk
{
template< class TInput, class TMask >
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::BinaryMaskImageToGoFigureMeshAttributes()
{
  m_IntensityComputation = true;
  m_Mean = 0;
  m_Sum = 0;
  m_Size = 0;
  m_PhysicalSize = 0;
}

template< class TInput, class TMask >
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::
~BinaryMaskImageToGoFigureMeshAttributes()
{
}

template< class TInput, class TMask >
void
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::SetIntensityBasedComputation(const bool & iComputation)
{
  m_IntensityComputation = iComputation;
}

template< class TInput, class TMask >
void
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::SetImage(ImageType *iInput)
{
  m_InputImage = iInput;
}

template< class TInput, class TMask >
void
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::SetMaskImage(MaskImageType *iMask)
{
  m_MaskImage = iMask;
}

template< class TInput, class TMask >
void
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::Update()
{
  GenerateData();
}

template< class TInput, class TMask >
unsigned int
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::GetSize()
{
  return m_Size;
}

template< class TInput, class TMask >
double
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::GetPhysicalSize()
{
  return m_PhysicalSize;
}

template< class TInput, class TMask >
double BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::GetMeanIntensity()
{
  return m_Mean;
}

template< class TInput, class TMask >
double BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::GetSumIntensity()
{
  return m_Sum;
}

template< class TInput, class TMask >
void
BinaryMaskImageToGoFigureMeshAttributes< TInput, TMask >::GenerateData()
{
  // shape stuff
  ShapeConverterPointer shapeConverter = ShapeConverterType::New();

  shapeConverter->SetInput(m_MaskImage);
  shapeConverter->SetBackgroundValue(0);
  shapeConverter->SetComputePerimeter(false);
  try
    {
    shapeConverter->Update();
    }
  catch(itk::ExceptionObject & e)
    {
    std::cerr << "Exception Caught: " << e << std::endl;
    std::cerr << "shapeConverter->Update()" << std::endl;
    return;
    }

  ShapeLabelMapPointer shapeLabelMap = shapeConverter->GetOutput();
  LabelType maxLabel = NumericTraits< LabelType >::max();

  if ( shapeLabelMap->HasLabel(maxLabel) )
    {
    const ShapeLabelObjectType *shapeObject = shapeLabelMap->GetLabelObject(maxLabel);

    // Number of voxels;
    m_Size = shapeObject->Size();

    // Volume or area in um^3
    m_PhysicalSize = shapeObject->GetPhysicalSize();
    }
  else
    {
    // Number of voxels;
    m_Size = 0;

    // Volume or area in um^3
    m_PhysicalSize = 0;
    }

  if ( m_IntensityComputation )
    {
    // stat stuff
    StatConverterPointer statConverter = StatConverterType::New();
    statConverter->SetInput(m_MaskImage);
    statConverter->SetFeatureImage(m_InputImage);
    statConverter->SetBackgroundValue(0);
    statConverter->SetComputePerimeter(false);
    try
      {
      statConverter->Update();
      }
    catch(itk::ExceptionObject & e)
      {
      std::cerr << "Exception Caught: " << e << std::endl;
      std::cerr << "statConverter->Update()" << std::endl;
      return;
      }

    StatLabelMapPointer statLabelMap = statConverter->GetOutput();

    if ( statLabelMap->HasLabel(maxLabel) )
      {
      const StatLabelObjectType *statObject = statLabelMap->GetLabelObject(maxLabel);

      m_Mean = statObject->GetMean();
      m_Sum = statObject->GetSum();
      }
    else
      {
      m_Mean = 0;
      m_Sum = 0;
      }
    }
}

}

#endif
libgofigure-dev 0.9.0-3+b1 / usr / include / gofigure2 / itkBinaryMaskImageToGoFigureMeshAttributes.txx
