libgofigure-dev 0.9.0-3+b1 / usr / include / gofigure2 / itkCellForegroundExtraction.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.
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#ifndef __itkCellForegroundExtraction_txx
#define __itkCellForegroundExtraction_txx

#include "itkCellForegroundExtraction.h"

namespace itk
{
template< class TFeatureImage, class TInputImage, class TSegmentImage >
CellForegroundExtraction< TFeatureImage, TInputImage, TSegmentImage >
::CellForegroundExtraction() : m_SigmaForm (2.0),
  m_ThresholdCellmin (10), m_ThresholdCellmax (30),  m_ThresholdMembrane (0),
  m_ThresholdForm (0.15), m_LargestCellRadius (4.0)
{
  m_Sampling = 0;
  this->Superclass::SetNumberOfRequiredInputs (2);
  this->Superclass::SetNumberOfRequiredOutputs (1);

  this->Superclass::SetNthOutput ( 0, TSegmentImage::New() );
}

template< class TFeatureImage, class TInputImage, class TSegmentImage >
typename CellForegroundExtraction< TFeatureImage, TInputImage, TSegmentImage >::FeatureImagePointer
CellForegroundExtraction< TFeatureImage, TInputImage, TSegmentImage >
::ResampleInput
  (FeatureImageConstPointer input, FeatureImageSpacingType spacing,
  FeatureImageSizeType size, FeatureImagePointType origin)
{
  // create the resample filter, transform and interpolator
  TransformPointer transform = TransformType::New();

  transform->SetIdentity();

  InterpolatorFeaturePointer interp = InterpolatorFeatureType::New();

  ResampleFeatureFilterPointer m_resamp = ResampleFeatureFilterType::New();
  m_resamp->SetTransform (transform);
  m_resamp->SetInterpolator (interp);
  m_resamp->SetInput (input);
  m_resamp->SetSize (size);
  m_resamp->SetOutputOrigin (origin);
  m_resamp->SetOutputSpacing (spacing);
  m_resamp->SetDefaultPixelValue (0);
  m_resamp->Update();

  return ( m_resamp->GetOutput() );
}

template< class TFeatureImage, class TInputImage, class TSegmentImage >
typename CellForegroundExtraction< TFeatureImage, TInputImage, TSegmentImage >::ImagePointer
CellForegroundExtraction< TFeatureImage, TInputImage, TSegmentImage >
::Resample
  (ImagePointer input, FeatureImageSpacingType spacing,
  FeatureImageSizeType size, FeatureImagePointType origin)
{
  // create the resample filter, transform and interpolator
  TransformPointer transform = TransformType::New();

  transform->SetIdentity();

  InterpolatorPointer interp = InterpolatorType::New();

  ResampleFilterPointer m_resamp = ResampleFilterType::New();
  m_resamp->SetTransform (transform);
  m_resamp->SetInterpolator (interp);
  m_resamp->SetInput (input);
  m_resamp->SetSize (size);
  m_resamp->SetOutputOrigin (origin);
  m_resamp->SetOutputSpacing (spacing);
  m_resamp->SetDefaultPixelValue (0);
  m_resamp->Update();

  return ( m_resamp->GetOutput() );
}

template< class TFeatureImage, class TInputImage, class TSegmentImage >
void
CellForegroundExtraction< TFeatureImage, TInputImage, TSegmentImage >::GenerateData()
{
  FeatureImageConstPointer cellImg = this->GetInput();
  FeatureImageSpacingType  spacing = cellImg->GetSpacing();
  FeatureImageSizeType     size = cellImg->GetLargestPossibleRegion().GetSize();
  FeatureImagePointType    origin = cellImg->GetOrigin();

  FeatureImageSpacingType subSpacing;
  FeatureImageSizeType    subSize;

  float t;

  for ( unsigned int i = 0; i < ImageDimension; i++ )
    {
    if ( m_Sampling )
      {
      t = m_Sampling[i];
      }
    else
      {
      t = 1.0;
      }
    subSpacing[i] = spacing[i] * t;
    subSize[i]    = static_cast< ImageSizeValueType >(size[i] / t);
    }

    {
    ImagePointer gaussCorrImg;
      {
      FeatureImagePointer rawSubsampledImage = ResampleInput (
          cellImg, subSpacing, subSize, origin);

      GaussProfileFilterPointer gaussCorr = GaussProfileFilterType::New();
      gaussCorr->SetInput(rawSubsampledImage);
      gaussCorr->SetSigmaForm(m_SigmaForm);
      gaussCorr->SetNumberOfThreads( this->GetNumberOfThreads() );
      try
        {
        gaussCorr->Update();
        }
      catch (itk::ExceptionObject e)
        {
        std::cerr << "Error: " << e << std::endl;
        }

      gaussCorrImg = Resample (gaussCorr->GetOutput(), spacing, size, origin);
      }

    RescaleFilterPointer m_rescale = RescaleFilterType::New();
    m_rescale->SetInput (gaussCorrImg);
    m_rescale->SetOutputMinimum (0);
    m_rescale->SetOutputMaximum (1);
    m_rescale->Update();

    gauss = m_rescale->GetOutput();
    gauss->DisconnectPipeline();
    }

  FeatureImageConstPointer membraneImg = this->GetInput(1);

  SegmentImagePointer fg = SegmentImageType::New();
  fg->SetRegions( cellImg->GetLargestPossibleRegion() );
  fg->CopyInformation(cellImg);
  fg->Allocate();
  fg->FillBuffer(0);

  // We reuse the space allocated in cellImg to now represent the foreground
  // Fuzzy thresholding operation
  SegmentIteratorType oIt( fg, fg->GetLargestPossibleRegion() );

  IteratorType GaussIt( gauss, gauss->GetLargestPossibleRegion() );

  FeatureConstIteratorType mIt( membraneImg, membraneImg->GetLargestPossibleRegion() );

  FeatureConstIteratorType It( cellImg, cellImg->GetLargestPossibleRegion() );

  oIt.GoToBegin();
  It.GoToBegin();
  GaussIt.GoToBegin();
  mIt.GoToBegin();
  while ( !It.IsAtEnd() )
    {
    if ( ( It.Get()  > m_ThresholdCellmax )
         && ( mIt.Get() < m_ThresholdMembrane ) )
      {
      oIt.Set (1);
      }
    else if ( ( It.Get()      > m_ThresholdCellmin )
              && ( GaussIt.Get() > m_ThresholdForm )
              && ( mIt.Get() < m_ThresholdMembrane ) )
      {
      oIt.Set (1);
      }
    else
      {
      oIt.Set (0);
      }
    ++oIt;
    ++It;
    ++GaussIt;
    ++mIt;
    }

  this->GraftOutput (fg);
}

template< class TFeatureImage, class TInputImage, class TSegmentImage >
void
CellForegroundExtraction< TFeatureImage, TInputImage, TSegmentImage >::PrintSelf(std::ostream & os,
                                                                                 Indent indent) const
{
  Superclass::PrintSelf (os, indent);
  os << indent << "Class Name:        " << GetNameOfClass() << std::endl;
  os << indent << "SigmaForm:         " << GetSigmaForm() << std::endl;
  os << indent << "ThresholdCellmin:  " << GetThresholdCellmin() << std::endl;
  os << indent << "ThresholdCellmax:  " << GetThresholdCellmax() << std::endl;
  os << indent << "ThresholdMembrane: " << GetThresholdMembrane()
     << std::endl;
  os << indent << "ThresholdForm:     " << GetThresholdForm() << std::endl;
  os << indent << "Largest cell radius: " << GetLargestCellRadius()
     << std::endl;
  os << indent << "Sampling factors:  ";
  for ( unsigned int i = 0; i < ImageDimension; i++ )
    {
    std::cout << ( this->m_Sampling )[i] << ' ';
    }
  std::cout << std::endl;
}

} /* end namespace itk */

#endif