mitkVolumeCalculator.cpp

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

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

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

#include "mitkVolumeCalculator.h"
#include "mitkImageAccessByItk.h"
#include <itkImageRegionConstIterator.h>

#include "mitkImageStatisticsHolder.h"

template <typename TPixel, unsigned int VImageDimension>
void mitk::VolumeCalculator::InternalCompute(const itk::Image<TPixel, VImageDimension> *itkImage)
{
  itk::ImageRegionConstIterator<itk::Image<TPixel, VImageDimension>> imageIt(itkImage,
                                                                             itkImage->GetLargestPossibleRegion());
  unsigned long int count = 0;

  for (imageIt.GoToBegin(); !imageIt.IsAtEnd(); ++imageIt)
  {
    if ((int)(imageIt.Get()) >= m_Threshold)
    {
      count++;
    }
  }
  if (itkImage->GetLargestPossibleRegion().GetImageDimension() == 3)
  {
    m_Volume = count / 1000.0 * itkImage->GetSpacing()[0] * itkImage->GetSpacing()[1] * itkImage->GetSpacing()[2];
  }
  else if (itkImage->GetLargestPossibleRegion().GetImageDimension() == 2)
  {
    m_Volume = count / 100.0 * itkImage->GetSpacing()[0] * itkImage->GetSpacing()[1];
  }
  m_VoxelCount = count;
}

mitk::VolumeCalculator::VolumeCalculator() : m_Image(nullptr), m_Threshold(0), m_Volume(0)
{
  m_TimeSelector = ImageTimeSelector::New();
}

mitk::VolumeCalculator::~VolumeCalculator()
{
}

std::vector<float> mitk::VolumeCalculator::GetVolumes()
{
  return m_Volumes;
}

void mitk::VolumeCalculator::ComputeVolume()
{
  const_cast<Image *>(m_Image.GetPointer())->SetRequestedRegionToLargestPossibleRegion();
  if (m_Image->GetDimension() == 4)
  {
    m_TimeSelector->SetInput(m_Image);
    m_Volumes.resize(m_Image->GetDimension(3));
    for (unsigned int timeStep = 0; timeStep < m_Image->GetDimension(3); ++timeStep)
    {
      m_TimeSelector->SetTimeNr(timeStep);
      m_TimeSelector->Update();
      AccessFixedDimensionByItk(m_TimeSelector->GetOutput(), InternalCompute, 3);
      m_Volumes[timeStep] = m_Volume;
    }
  }
  else if (m_Image->GetDimension() == 3)
  {
    const_cast<Image *>(m_Image.GetPointer())->Update();
    AccessFixedDimensionByItk(m_Image, InternalCompute, 3);
  }
  else if (m_Image->GetDimension() == 2)
  {
    const_cast<Image *>(m_Image.GetPointer())->Update();
    AccessFixedDimensionByItk(m_Image, InternalCompute, 2);
  }
}

void mitk::VolumeCalculator::ComputeVolumeFromImageStatistics()
{
  unsigned int dim = m_Image->GetDimension();

  if (dim == 4)
  {
    m_Volumes.resize(m_Image->GetDimension(3), 0);
    Vector3D spacing = m_Image->GetSlicedGeometry()->GetSpacing();

    for (unsigned int t = 0; t < m_Image->GetDimension(3); ++t)
    {
      m_Volumes[t] =
        m_Image->GetStatistics()->GetCountOfMaxValuedVoxels(t) / 1000.0 * spacing[0] * spacing[1] * spacing[2];
    }
  }
  else if (dim == 3)
  {
    Vector3D spacing = m_Image->GetSlicedGeometry()->GetSpacing();
    m_Volume = m_Image->GetStatistics()->GetCountOfMaxValuedVoxels() / 1000.0 * spacing[0] * spacing[1] * spacing[2];
  }
  else if (dim == 2)
  {
    Vector3D spacing = m_Image->GetGeometry()->GetSpacing();
    m_Volume = m_Image->GetStatistics()->GetCountOfMaxValuedVoxels() / 100.0 * spacing[0] * spacing[1];
  }
  else
    itkExceptionMacro(<< "Wrong image dimension...");
}

float mitk::VolumeCalculator::ComputeVolume(Vector3D spacing, unsigned int voxelCount)
{
  return (voxelCount / 1000.0 * spacing[0] * spacing[1] * spacing[2]);
}