mitkGIFLocalIntensity.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 <mitkGIFLocalIntensity.h>

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

// ITK
#include <itkImageRegionIteratorWithIndex.h>
#include <itkNeighborhoodIterator.h>
#include <itkLocalIntensityFilter.h>

// STL
#include <limits>

struct GIFLocalIntensityParameter
{
  double range;
  std::string prefix;
};


template<typename TPixel, unsigned int VImageDimension>
static void
CalculateIntensityPeak(itk::Image<TPixel, VImageDimension>* itkImage, mitk::Image::Pointer mask, mitk::GIFLocalIntensity::FeatureListType & featureList, GIFLocalIntensityParameter params)
{
  typedef itk::Image<TPixel, VImageDimension> ImageType;
  typedef itk::Image<unsigned short, VImageDimension> MaskType;

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

  double range = params.range;

  typename itk::LocalIntensityFilter<ImageType>::Pointer filter = itk::LocalIntensityFilter<ImageType>::New();
  filter->SetInput(itkImage);
  filter->SetMask(itkMask);
  filter->SetRange(range);
  filter->Update();

  featureList.push_back(std::make_pair(params.prefix + "2. Local Intensity Peak", filter->GetLocalPeak()));
  featureList.push_back(std::make_pair(params.prefix + "2. Global Intensity Peak", filter->GetGlobalPeak()));
}


mitk::GIFLocalIntensity::GIFLocalIntensity() :
m_Range(6.2)
{
  SetLongName("local-intensity");
  SetShortName("loci");
  SetFeatureClassName("Local Intensity");
}

mitk::GIFLocalIntensity::FeatureListType mitk::GIFLocalIntensity::CalculateFeatures(const Image::Pointer & image, const Image::Pointer &mask)
{
  FeatureListType featureList;
  if (image->GetDimension() < 3)
  {
    return featureList;
  }
  GIFLocalIntensityParameter params;
  params.range = GetRange();
  params.prefix = FeatureDescriptionPrefix();
  AccessByItk_3(image, CalculateIntensityPeak, mask, featureList, params);
  return featureList;
}

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


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

  parser.addArgument(GetLongName(), name, mitkCommandLineParser::Bool, "Use Local Intensity", "calculates local intensity based features", us::Any());
  parser.addArgument(name + "::range", name+"::range", mitkCommandLineParser::Float, "Range for the local intensity", "Give the range that should be used for the local intensity in mm", us::Any());
}

void
mitk::GIFLocalIntensity::CalculateFeaturesUsingParameters(const Image::Pointer & feature, const Image::Pointer &mask, const Image::Pointer &, FeatureListType &featureList)
{
  std::string name = GetOptionPrefix();
  auto parsedArgs = GetParameter();
  if (parsedArgs.count(GetLongName()))
  {
    if (parsedArgs.count(name + "::range"))
    {
      double range = us::any_cast<float>(parsedArgs[name + "::range"]);
      this->SetRange(range);
    }
    MITK_INFO << "Start calculating local intensity features ....";
    auto localResults = this->CalculateFeatures(feature, mask);
    featureList.insert(featureList.end(), localResults.begin(), localResults.end());
    MITK_INFO << "Finished calculating local intensity features....";
  }
}

std::string mitk::GIFLocalIntensity::GetCurrentFeatureEncoding()
{
  std::ostringstream  ss;
  ss << m_Range;
  std::string strRange = ss.str();
  return "Range-" + ss.str();
}