mitkGIFGreyLevelRunLength.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 <mitkGIFGreyLevelRunLength.h>

// MITK
#include <mitkITKImageImport.h>
#include <mitkImageCast.h>
#include <mitkImageAccessByItk.h>

// ITK
#include <itkEnhancedScalarImageToRunLengthFeaturesFilter.h>

// STL
#include <sstream>

template<typename TPixel, unsigned int VImageDimension>
void
  CalculateGrayLevelRunLengthFeatures(itk::Image<TPixel, VImageDimension>* itkImage, mitk::Image::Pointer mask, mitk::GIFGreyLevelRunLength::FeatureListType & featureList, mitk::GIFGreyLevelRunLength::ParameterStruct params)
{
  typedef itk::Image<TPixel, VImageDimension> ImageType;
  typedef itk::Image<TPixel, VImageDimension> MaskType;
  typedef itk::Statistics::EnhancedScalarImageToRunLengthFeaturesFilter<ImageType> FilterType;
  typedef typename FilterType::RunLengthFeaturesFilterType TextureFilterType;

  typename MaskType::Pointer maskImage = MaskType::New();
  mitk::CastToItkImage(mask, maskImage);

  typename FilterType::Pointer filter = FilterType::New();
  typename FilterType::Pointer filter2 = FilterType::New();

  typename FilterType::OffsetVector::Pointer newOffset = FilterType::OffsetVector::New();
  auto oldOffsets = filter->GetOffsets();
  auto oldOffsetsIterator = oldOffsets->Begin();
  while (oldOffsetsIterator != oldOffsets->End())
  {
    bool continueOuterLoop = false;
    typename FilterType::OffsetType offset = oldOffsetsIterator->Value();
    for (unsigned int i = 0; i < VImageDimension; ++i)
    {
      if (params.m_Direction == i + 2 && offset[i] != 0)
      {
        continueOuterLoop = true;
      }
    }
    if (params.m_Direction == 1)
    {
      offset[0] = 0;
      offset[1] = 0;
      offset[2] = 1;
      newOffset->push_back(offset);
      break;
    }

    oldOffsetsIterator++;
    if (continueOuterLoop)
      continue;
    newOffset->push_back(offset);
  }
  filter->SetOffsets(newOffset);
  filter2->SetOffsets(newOffset);


  // All features are required
  typename FilterType::FeatureNameVectorPointer requestedFeatures = FilterType::FeatureNameVector::New();
  requestedFeatures->push_back(TextureFilterType::ShortRunEmphasis);
  requestedFeatures->push_back(TextureFilterType::LongRunEmphasis);
  requestedFeatures->push_back(TextureFilterType::GreyLevelNonuniformity);
  requestedFeatures->push_back(TextureFilterType::GreyLevelNonuniformityNormalized);
  requestedFeatures->push_back(TextureFilterType::RunLengthNonuniformity);
  requestedFeatures->push_back(TextureFilterType::RunLengthNonuniformityNormalized);
  requestedFeatures->push_back(TextureFilterType::LowGreyLevelRunEmphasis);
  requestedFeatures->push_back(TextureFilterType::HighGreyLevelRunEmphasis);
  requestedFeatures->push_back(TextureFilterType::ShortRunLowGreyLevelEmphasis);
  requestedFeatures->push_back(TextureFilterType::ShortRunHighGreyLevelEmphasis);
  requestedFeatures->push_back(TextureFilterType::LongRunLowGreyLevelEmphasis);
  requestedFeatures->push_back(TextureFilterType::LongRunHighGreyLevelEmphasis);
  requestedFeatures->push_back(TextureFilterType::RunPercentage);
  requestedFeatures->push_back(TextureFilterType::NumberOfRuns);
  requestedFeatures->push_back(TextureFilterType::GreyLevelVariance);
  requestedFeatures->push_back(TextureFilterType::RunLengthVariance);
  requestedFeatures->push_back(TextureFilterType::RunEntropy);

  filter->SetInput(itkImage);
  filter->SetMaskImage(maskImage);
  filter->SetRequestedFeatures(requestedFeatures);
  filter2->SetInput(itkImage);
  filter2->SetMaskImage(maskImage);
  filter2->SetRequestedFeatures(requestedFeatures);
  int numberOfBins = params.Bins;
  if (numberOfBins < 2)
    numberOfBins = 256;

  double minRange = params.MinimumIntensity;
  double maxRange = params.MaximumIntensity;

  filter->SetPixelValueMinMax(minRange, maxRange);
  filter->SetNumberOfBinsPerAxis(numberOfBins);
  filter2->SetPixelValueMinMax(minRange, maxRange);
  filter2->SetNumberOfBinsPerAxis(numberOfBins);

  filter->SetDistanceValueMinMax(0, numberOfBins);
  filter2->SetDistanceValueMinMax(0, numberOfBins);

  filter2->CombinedFeatureCalculationOn();

  filter->Update();
  filter2->Update();

  auto featureMeans = filter->GetFeatureMeans ();
  auto featureStd = filter->GetFeatureStandardDeviations();
  auto featureCombined = filter2->GetFeatureMeans();

  for (std::size_t i = 0; i < featureMeans->size(); ++i)
  {
    switch (i)
    {
    case TextureFilterType::ShortRunEmphasis :
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run emphasis Means",featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run emphasis Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run emphasis Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::LongRunEmphasis :
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run emphasis Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run emphasis Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run emphasis Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::GreyLevelNonuniformity :
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level nonuniformity Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level nonuniformity Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level nonuniformity Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::GreyLevelNonuniformityNormalized :
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level nonuniformity normalized Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level nonuniformity normalized Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level nonuniformity normalized Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::RunLengthNonuniformity :
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length nonuniformity Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length nonuniformity Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length nonuniformity Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::RunLengthNonuniformityNormalized :
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length nonuniformity normalized Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length nonuniformity normalized Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length nonuniformity normalized Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::LowGreyLevelRunEmphasis :
      featureList.push_back(std::make_pair(params.featurePrefix + "Low grey level run emphasis Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Low grey level run emphasis Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Low grey level run emphasis Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::HighGreyLevelRunEmphasis :
      featureList.push_back(std::make_pair(params.featurePrefix + "High grey level run emphasis Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "High grey level run emphasis Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "High grey level run emphasis Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::ShortRunLowGreyLevelEmphasis :
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run low grey level emphasis Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run low grey level emphasis  Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run low grey level emphasis  Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::ShortRunHighGreyLevelEmphasis :
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run high grey level emphasis Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run high grey level emphasis Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Short run high grey level emphasis Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::LongRunLowGreyLevelEmphasis :
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run low grey level emphasis Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run low grey level emphasis Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run low grey level emphasis Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::LongRunHighGreyLevelEmphasis :
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run high grey level emphasis Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run high grey level emphasis Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Long run high grey level emphasis Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::RunPercentage :
      featureList.push_back(std::make_pair(params.featurePrefix + "Run percentage Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run percentage Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run percentage Comb.", featureCombined->ElementAt(i) / newOffset->size()));
      break;
    case TextureFilterType::NumberOfRuns :
      featureList.push_back(std::make_pair(params.featurePrefix + "Number of runs Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Number of runs Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Number of runs Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::GreyLevelVariance :
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level variance Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level variance Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Grey level variance Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::RunLengthVariance :
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length variance Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length variance Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length variance Comb.", featureCombined->ElementAt(i)));
      break;
    case TextureFilterType::RunEntropy :
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length entropy Means", featureMeans->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length entropy Std.", featureStd->ElementAt(i)));
      featureList.push_back(std::make_pair(params.featurePrefix + "Run length entropy Comb.", featureCombined->ElementAt(i)));
      break;
    default:
      break;
    }
  }
}

mitk::GIFGreyLevelRunLength::GIFGreyLevelRunLength()
{
  SetShortName("rl");
  SetLongName("run-length");
  SetFeatureClassName("Run Length");
}

mitk::GIFGreyLevelRunLength::FeatureListType mitk::GIFGreyLevelRunLength::CalculateFeatures(const Image::Pointer & image, const Image::Pointer &mask)
{
  InitializeQuantifier(image, mask);
  FeatureListType featureList;

  ParameterStruct params;

  params.m_Direction = GetDirection();

  params.MinimumIntensity = GetQuantifier()->GetMinimum();
  params.MaximumIntensity = GetQuantifier()->GetMaximum();
  params.Bins = GetQuantifier()->GetBins();
  params.featurePrefix = FeatureDescriptionPrefix();

  MITK_INFO << params.MinimumIntensity;
  MITK_INFO << params.MaximumIntensity;
  MITK_INFO << params.m_Direction;
  MITK_INFO << params.Bins;

  AccessByItk_3(image, CalculateGrayLevelRunLengthFeatures, mask, featureList,params);

  return featureList;
}

mitk::GIFGreyLevelRunLength::FeatureNameListType mitk::GIFGreyLevelRunLength::GetFeatureNames()
{
  FeatureNameListType featureList;
  return featureList;
}


void mitk::GIFGreyLevelRunLength::AddArguments(mitkCommandLineParser &parser)
{
  std::string name = GetOptionPrefix();

  parser.addArgument(GetLongName(), name, mitkCommandLineParser::Bool, "Use Run-Length", "Calculates Run-Length based features", us::Any());
  AddQuantifierArguments(parser);
}

void
mitk::GIFGreyLevelRunLength::CalculateFeaturesUsingParameters(const Image::Pointer & feature, const Image::Pointer &, const Image::Pointer &maskNoNAN, FeatureListType &featureList)
{
  auto parsedArgs = GetParameter();
  std::string name = GetOptionPrefix();

  if (parsedArgs.count(GetLongName()))
  {
    InitializeQuantifierFromParameters(feature, maskNoNAN);

    MITK_INFO << "Start calculating Run-length";
    auto localResults = this->CalculateFeatures(feature, maskNoNAN);
    featureList.insert(featureList.end(), localResults.begin(), localResults.end());
    MITK_INFO << "Finished calculating Run-length";
  }

}

std::string mitk::GIFGreyLevelRunLength::GetCurrentFeatureEncoding()
{
  return QuantifierParameterString();
}