libgofigure-dev 0.9.0-3+b1 / usr / include / gofigure2 / itkCellFeatureGenerator.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 __itkCellFeatureGenerator_txx
#define __itkCellFeatureGenerator_txx

#include "itkCellFeatureGenerator.h"

namespace itk
{
//  Software Guide : BeginCodeSnippet
template< class TFeatureImage, class TInputImage, class TSegmentImage >
CellFeatureGenerator< TFeatureImage, TInputImage, TSegmentImage >
::CellFeatureGenerator()
{
  m_NucleiSigma = 0.2;
  m_MembraneSigma = 0.2;
  m_LargestCellRadius = 4.0;
  m_DistanceMapWeight = 1.0;
  m_NucleiGradientWeight = 0.0;
  m_MembraneWeight = 0.0;

  m_ForegroundMap = NULL;
  m_DistanceMap = NULL;
  m_Gradient = NULL;

  this->Superclass::SetNumberOfRequiredInputs (2);
  this->Superclass::SetNumberOfRequiredOutputs (1);
  this->Superclass::SetNthOutput ( 0, TInputImage::New() );
}

template< class TFeatureImage, class TInputImage, class TSegmentImage >
void
CellFeatureGenerator< TFeatureImage, TInputImage, TSegmentImage >
::DistanceMap()
{
  MaurerPointer m_Maurer = MaurerType::New();

  m_Maurer->SetInput (m_ForegroundMap);
  m_Maurer->SetSquaredDistance (0);
  m_Maurer->SetUseImageSpacing (1);
  m_Maurer->SetInsideIsPositive (0);
  m_Maurer->Update();

  AbsFilterPointer m_absFilter = AbsFilterType::New();
  m_absFilter->SetInput ( m_Maurer->GetOutput() );
  m_absFilter->Update();

  ThreshFilterPointer m_thresh = ThreshFilterType::New();
  m_thresh->SetInput ( m_absFilter->GetOutput() );
  m_thresh->ThresholdAbove (m_LargestCellRadius);
  m_thresh->SetOutsideValue (m_LargestCellRadius);
  m_thresh->Update();

  m_DistanceMap = m_thresh->GetOutput();
}

template< class TFeatureImage, class TInputImage, class TSegmentImage >
void
CellFeatureGenerator< TFeatureImage, TInputImage, TSegmentImage >
::Gradient()
{
  // Compute the gradient magnitude
  GradientFilterPointer m_gradientMagnitude = GradientFilterType::New();

  m_gradientMagnitude->SetInput ( this->GetInput (0) );
  m_gradientMagnitude->SetSigma (m_NucleiSigma);
  m_gradientMagnitude->Update();

  IteratorType distIt( m_DistanceMap, m_DistanceMap->GetLargestPossibleRegion() );

  IteratorType gradientIt( m_gradientMagnitude->GetOutput(),
                           m_gradientMagnitude->GetOutput()->GetLargestPossibleRegion() );

  double alpha = -1, beta = 0;
  float  k1 = 0, k2 = 0;
  int    n1 = 0, n2 = 0;
  for ( distIt.GoToBegin(), gradientIt.GoToBegin(); !distIt.IsAtEnd(); ++distIt,
        ++gradientIt )
    {
    if ( distIt.Get() < m_LargestCellRadius / 4 )
      {
      k1 += gradientIt.Get();
      ++n1;
      }
    else
      {
      k2 += gradientIt.Get();
      ++n2;
      }
    }

  if ( ( n1 > 0 ) && ( n2 > 0 ) )
    {
    k1 /= static_cast< float >(n1);
    k2 /= static_cast< float >(n2);
    alpha = ( k2 - k1 ) / 2;
    beta = ( k2 + k1 ) / 2;
    }
//   std::cout << k1 << ' ' << k2 << std::endl;
//   std::cout << "Estimating Alpha and Beta complete..." << std::endl;
//   std::cout << alpha << ' ' << beta << std::endl;

  SigmoidFilterPointer m_sigmoid = SigmoidFilterType::New();
  m_sigmoid->SetInput ( m_gradientMagnitude->GetOutput() );
  m_sigmoid->SetOutputMinimum (0.0);
  m_sigmoid->SetOutputMaximum (1);
  m_sigmoid->SetAlpha (alpha);
  m_sigmoid->SetBeta (beta);
  m_sigmoid->Update();

  m_Gradient = m_sigmoid->GetOutput();
}

template< class TFeatureImage, class TInputImage, class TSegmentImage >
void
CellFeatureGenerator< TFeatureImage, TInputImage, TSegmentImage >::GenerateData()
{
  ImagePointer outputImg = ImageType::New();

  outputImg->SetRegions ( this->GetInput(0)->GetLargestPossibleRegion() );
  outputImg->SetSpacing ( this->GetInput(0)->GetSpacing() );
  outputImg->SetOrigin ( this->GetInput(0)->GetOrigin() );
  outputImg->Allocate();
  outputImg->FillBuffer (0);

  if ( m_DistanceMapWeight > 0 )
    {
    DistanceMap();
    }
  m_ForegroundMap = 0;

  if ( m_NucleiGradientWeight > 0 )
    {
    Gradient();
    m_Gradient->SetSpacing ( m_DistanceMap->GetSpacing() );
    }
  else
    {
    m_Gradient = outputImg;
    }

  FeatureMinMaxCalculatorPointer minMax1 = FeatureMinMaxCalculatorType::New();
  minMax1->SetImage( this->GetInput(1) );
  minMax1->ComputeMaximum();
  double mmax = static_cast< double >( minMax1->GetMaximum() );

  MinMaxCalculatorPointer minMax2 = MinMaxCalculatorType::New();
  minMax2->SetImage(m_DistanceMap);
  minMax2->ComputeMaximum();
  double dmax = static_cast< double >( minMax2->GetMaximum() );

  double weight = m_DistanceMapWeight + m_NucleiGradientWeight + m_MembraneWeight;

  IteratorType It( outputImg,
                   outputImg->GetLargestPossibleRegion() );

  IteratorType dIt( m_DistanceMap,
                    m_DistanceMap->GetLargestPossibleRegion() );

  IteratorType gIt( m_Gradient,
                    m_Gradient->GetLargestPossibleRegion() );

  ConstIteratorType mIt( this->GetInput(1),
                         this->GetInput(1)->GetLargestPossibleRegion() );

  double dterm, gterm, mterm;

  mIt.GoToBegin();
  gIt.GoToBegin();
  dIt.GoToBegin();
  It.GoToBegin();
  while ( !mIt.IsAtEnd() )
    {
    dterm = ( dIt.Get() / dmax ) * m_DistanceMapWeight;
    gterm = gIt.Get() * m_NucleiGradientWeight;
    mterm = ( 1 - mIt.Get() / mmax ) * m_MembraneWeight;

    It.Set ( static_cast< ImagePixelType >(
               ( dterm + gterm + mterm ) / weight) );

    ++mIt;
    ++gIt;
    ++dIt;
    ++It;
    }

  this->GraftOutput (outputImg);
}

template< class TFeatureImage, class TInputImage, class TSegmentImage >
void
CellFeatureGenerator< TFeatureImage, TInputImage, TSegmentImage >::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf (os, indent);
  os << indent << "Class Name:              " << this->GetNameOfClass()
     << std::endl;
  os << indent << "Nuclei Sigma:              " << this->GetNucleiSigma() << std::endl;
  os << indent << "Membrane Sigma:       " << this->GetMembraneSigma()
     << std::endl;
  os << indent << "Largest Cell Radius:     " << this->GetLargestCellRadius()
     << std::endl;
  os << indent << "DistanceMapWeight:       " << this->GetDistanceMapWeight()
     << std::endl;
  os << indent << "NucleiGradientWeight: " << this->GetNucleiGradientWeight()
     << std::endl;
  os << indent << "MembraneWeight:         " << this->GetMembraneWeight()
     << std::endl;
}

} /* end namespace itk */

#endif