freImageSampleCharacteristicsCalculator.txx

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/*=========================================================================

  Program:   F.R.E.E. - flexible registration evaluation engine
  Version:   v.1.0.0
  Date:      $Date: 2006/09/01 12:00:00 $
  Module:    $RCSfile: freImageSampleCharacteristicsCalculator.txx,v $
  Language:  C++



  Copyright (c) 2007 Ralf o Floca (Department of Medical Informatics,
  Institute for Medical Biometry and Informatics, University of Heidelberg,
  Germany). All rights reserved.
  See FREECopyright.txt or http://www.mi.med.uni-hd.de/free/copyright.htm
  for details.

     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#ifndef _freImageSampleCharacteristicsCalculator_txx
#define _freImageSampleCharacteristicsCalculator_txx

#include "freImageSampleCharacteristicsCalculator.h"

#include "itkNumericTraits.h"
#include "itkScalarImageToListAdaptor.h"
#include "itkCovarianceCalculator.h"
#include "itkMeanCalculator.h"
#include "itkSubsample.h"
#include "itkStatisticsAlgorithm.h"
#include "itkScalarToArrayCastImageFilter.h"

namespace FREE
{

template <class TImage>
void
ImageSampleCharacteristicsCalculator<TImage>::
Compute()
{
        if (m_smpImage.IsNull()) return;

        typedef itk::Statistics::ScalarImageToListAdaptor< ImageType > SampleType;
        typename SampleType::Pointer sample = SampleType::New();
        sample->SetImage( m_smpImage );

        // Calculate mean and variance
        typedef itk::Statistics::CovarianceCalculator< SampleType > CovarianceAlgorithmType;

        typename CovarianceAlgorithmType::Pointer covarianceAlgorithm = CovarianceAlgorithmType::New();
        covarianceAlgorithm->SetInputSample( sample );
        covarianceAlgorithm->SetMean( 0 );
        covarianceAlgorithm->Update();

        m_Mean = covarianceAlgorithm->GetMean()->GetElement(0);
        const typename CovarianceAlgorithmType::OutputType* matrix = covarianceAlgorithm->GetOutput();

        m_Variance = (*matrix)(0,0);

        // Calculate median
        typedef itk::Statistics::Subsample< SampleType > SubsampleType;
        typename SubsampleType::Pointer subsample = SubsampleType::New();
        subsample->SetSample( sample );
        subsample->InitializeWithAllInstances();
        m_Median = itk::Statistics::QuickSelect< SubsampleType >( subsample, 0, 0, subsample->Size(), subsample->Size()/2 );
};

template <class TImage>
void
ImageSampleCharacteristicsCalculator<TImage>::
ComputeMean()
{
        typedef itk::Statistics::ImageToListAdaptor< ImageType > SampleType;
        typedef itk::Statistics::MeanCalculator< SampleType > MeanAlgorithmType;

        if (m_smpImage.IsNull()) return;

        typename SampleType::Pointer sample = SampleType::New();
        sample->SetImage(m_smpImage);

        typename MeanAlgorithmType::Pointer meanAlgorithm = MeanAlgorithmType::New();
        meanAlgorithm->SetInputSample( sample );
        meanAlgorithm->Update();

        m_Mean = meanAlgorithm->GetOutput();
};

template <class TImage>
void
ImageSampleCharacteristicsCalculator<TImage>::
ComputeVariance(const ResultType& mean)
{
        if (m_smpImage.IsNull()) return;

        typedef itk::Statistics::ScalarImageToListAdaptor< ImageType > SampleType;
        typename SampleType::Pointer sample = SampleType::New();
        sample->SetImage( m_smpImage );

        // Calculate mean and variance
        typedef itk::Statistics::CovarianceCalculator< SampleType > CovarianceAlgorithmType;

        typename CovarianceAlgorithmType::Pointer covarianceAlgorithm = CovarianceAlgorithmType::New();
        covarianceAlgorithm->SetInputSample( sample );
        covarianceAlgorithm->SetMean( 0 );
        covarianceAlgorithm->Update();

        const typename CovarianceAlgorithmType::OutputType* matrix = covarianceAlgorithm->GetOutput();
        m_Variance = (*matrix)(0,0);
};

template <class TImage>
void
ImageSampleCharacteristicsCalculator<TImage>::
ComputeMedian()
{
        typedef itk::FixedArray< ResultType, 1 > MeasurementVectorType;
        typedef itk::Image< MeasurementVectorType, 2 > ArrayImageType;
        typedef itk::ScalarToArrayCastImageFilter< ImageType, ArrayImageType > CasterType;

        if (m_smpImage.IsNull()) return;

        typename CasterType::Pointer caster = CasterType::New();
        caster->SetInput( m_smpImage );
        caster->Update();

        typedef itk::Statistics::ImageToListAdaptor< ArrayImageType > SampleType;
        typename SampleType::Pointer sample = SampleType::New();
        sample->SetImage( caster->GetOutput() );

        // Calculate median
        typedef itk::Statistics::Subsample< SampleType > SubsampleType;
        typename SubsampleType::Pointer subsample = SubsampleType::New();
        subsample->SetSample( sample );
        subsample->InitializeWithAllInstances();
        m_Median = itk::Statistics::QuickSelect< SubsampleType >( subsample, 0, 0, subsample->Size(), subsample->Size()/2 );
};

template <class TImage>
typename ImageSampleCharacteristicsCalculator<TImage>::ResultType
ImageSampleCharacteristicsCalculator<TImage>::
GetMean() const
{
        return m_Mean;
};

template <class TImage>
typename ImageSampleCharacteristicsCalculator<TImage>::ResultType
ImageSampleCharacteristicsCalculator<TImage>::
GetVariance() const
{
        return m_Variance;
};

template <class TImage>
typename ImageSampleCharacteristicsCalculator<TImage>::ValueType
ImageSampleCharacteristicsCalculator<TImage>::
GetMedian() const
{
        return m_Median;
};

template <class TImage>
typename ImageSampleCharacteristicsCalculator<TImage>::ValueType
ImageSampleCharacteristicsCalculator<TImage>::
GetNativeMean() const
{
        return m_Mean;
};

template <class TImage>
typename ImageSampleCharacteristicsCalculator<TImage>::ValueType
ImageSampleCharacteristicsCalculator<TImage>::
GetNativeVariance() const
{
        return m_Variance;
};

template <class TImage>
void
ImageSampleCharacteristicsCalculator<TImage>::
SetImage(const ImageType* pField)
{
  m_smpImage = pField;
};

template <class TImage>
ImageSampleCharacteristicsCalculator<TImage>::
ImageSampleCharacteristicsCalculator()
{
  m_Mean = itk::NumericTraits< ResultType >::Zero;
  m_Variance = itk::NumericTraits< ResultType >::Zero;
  m_Median = itk::NumericTraits< ValueType >::Zero;
};

} // namespace free

#endif

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