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#include "antsUtilities.h"
#include "antsAllocImage.h"
#include <algorithm>
#include "ReadWriteData.h"
#include <cstdio>
#include "itkBoundingBox.h"
#include "itkImage.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkPointSet.h"
#include "itkScalarImageToRunLengthFeaturesFilter.h"
#include "itkDenseFrequencyContainer2.h"
namespace ants
{
template <unsigned int ImageDimension>
int
TextureRunLengthFeatures(int argc, char * argv[])
{
using PixelType = float;
using RealType = float;
using ImageType = itk::Image<PixelType, ImageDimension>;
using RealImageType = itk::Image<RealType, ImageDimension>;
typename ImageType::Pointer inputImage = ImageType::New();
ReadImage<ImageType>(inputImage, argv[2]);
using HistogramFrequencyContainerType = itk::Statistics::DenseFrequencyContainer2;
using RunLengthFilterType =
itk::Statistics::ScalarImageToRunLengthFeaturesFilter<RealImageType, HistogramFrequencyContainerType>;
typename RunLengthFilterType::Pointer runLengthFilter = RunLengthFilterType::New();
runLengthFilter->SetInput(inputImage);
typename ImageType::Pointer mask = nullptr;
PixelType label = itk::NumericTraits<PixelType>::OneValue();
if (argc > 4)
{
ReadImage<ImageType>(mask, argv[4]);
runLengthFilter->SetMaskImage(mask);
if (argc > 5)
{
label = static_cast<PixelType>(std::stoi(argv[5]));
}
runLengthFilter->SetInsidePixelValue(label);
}
unsigned int numberOfBins = 256;
if (argc > 3)
{
numberOfBins = static_cast<PixelType>(std::stoi(argv[3]));
}
runLengthFilter->SetNumberOfBinsPerAxis(numberOfBins);
itk::ImageRegionIteratorWithIndex<ImageType> ItI(inputImage, inputImage->GetLargestPossibleRegion());
PixelType maxValue = itk::NumericTraits<PixelType>::NonpositiveMin();
PixelType minValue = itk::NumericTraits<PixelType>::max();
using BoundingBoxType = itk::BoundingBox<unsigned long, ImageDimension, RealType>;
typename BoundingBoxType::Pointer bbox = BoundingBoxType::New();
typename BoundingBoxType::PointsContainerPointer points = BoundingBoxType::PointsContainer::New();
itk::Point<RealType, ImageDimension> point;
unsigned int idx = 0;
for (ItI.GoToBegin(); !ItI.IsAtEnd(); ++ItI)
{
if (!mask || (itk::Math::FloatAlmostEqual(mask->GetPixel(ItI.GetIndex()), label)))
{
if (ItI.Get() < minValue)
{
minValue = ItI.Get();
}
else if (ItI.Get() > maxValue)
{
maxValue = ItI.Get();
}
inputImage->TransformIndexToPhysicalPoint(ItI.GetIndex(), point);
points->InsertElement(idx++, point);
}
}
bbox->SetPoints(points);
bbox->ComputeBoundingBox();
typename BoundingBoxType::PointType pointMin = bbox->GetMinimum();
typename BoundingBoxType::PointType pointMax = bbox->GetMaximum();
runLengthFilter->SetPixelValueMinMax(minValue, maxValue);
runLengthFilter->SetDistanceValueMinMax(0, pointMin.EuclideanDistanceTo(pointMax));
runLengthFilter->SetNumberOfBinsPerAxis(numberOfBins);
runLengthFilter->FastCalculationsOff();
runLengthFilter->Update();
typename RunLengthFilterType::FeatureValueVectorPointer means = runLengthFilter->GetFeatureMeans();
const typename RunLengthFilterType::FeatureNameVector * names = runLengthFilter->GetRequestedFeatures();
typename RunLengthFilterType::FeatureValueVector::ConstIterator mIt = means->Begin();
typename RunLengthFilterType::FeatureNameVector::ConstIterator nIt = names->Begin();
while (mIt != means->End())
{
// std::cout << nIt.Value() << ": " << mIt.Value() << std::endl;
std::cout << mIt.Value() << " ";
++mIt;
++nIt;
}
std::cout << std::endl;
return EXIT_SUCCESS;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
TextureRunLengthFeatures(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
{
// put the arguments coming in as 'args' into standard (argc,argv) format;
// 'args' doesn't have the command name as first, argument, so add it manually;
// 'args' may have adjacent arguments concatenated into one argument,
// which the parser should handle
args.insert(args.begin(), "TextureRunLengthFeatures");
int argc = args.size();
char ** argv = new char *[args.size() + 1];
for (unsigned int i = 0; i < args.size(); ++i)
{
// allocate space for the string plus a null character
argv[i] = new char[args[i].length() + 1];
std::strncpy(argv[i], args[i].c_str(), args[i].length());
// place the null character in the end
argv[i][args[i].length()] = '\0';
}
argv[argc] = nullptr;
// class to automatically cleanup argv upon destruction
class Cleanup_argv
{
public:
Cleanup_argv(char ** argv_, int argc_plus_one_)
: argv(argv_)
, argc_plus_one(argc_plus_one_)
{}
~Cleanup_argv()
{
for (unsigned int i = 0; i < argc_plus_one; ++i)
{
delete[] argv[i];
}
delete[] argv;
}
private:
char ** argv;
unsigned int argc_plus_one;
};
Cleanup_argv cleanup_argv(argv, argc + 1);
if (argc < 3)
{
std::cout << "Usage: " << argv[0] << " imageDimension inputImage "
<< "[numberOfBinsPerAxis=256] [maskImage] [maskLabel=1]" << std::endl;
std::cout << "Features: ShortRunEmphasis,LongRunEmphasis,GreyLevelNonuniformity,";
std::cout << "RunLengthNonuniformity,LowGreyLevelRunEmphasis,HighGreyLevelRunEmphasis,";
std::cout << "ShortRunLowGreyLevelEmphasis,ShortRunHighGreyLevelEmphasis,";
std::cout << "LongRunLowGreyLevelEmphasis,LongRunHighGreyLevelEmphasis" << std::endl;
exit(1);
}
switch (std::stoi(argv[1]))
{
case 2:
TextureRunLengthFeatures<2>(argc, argv);
break;
case 3:
TextureRunLengthFeatures<3>(argc, argv);
break;
default:
std::cerr << "Unsupported dimension" << std::endl;
exit(EXIT_FAILURE);
}
return EXIT_SUCCESS;
}
} // namespace ants
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