SmoothImage.cxx

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

  Program:   Advanced Normalization Tools

  Copyright (c) ConsortiumOfANTS. All rights reserved.
  See accompanying COPYING.txt or
 https://github.com/stnava/ANTs/blob/master/ANTSCopyright.txt 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.

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

#include "antsUtilities.h"
#include <algorithm>

#include "itkMedianImageFilter.h"
#include "itkSmoothingRecursiveGaussianImageFilter.h"
#include "ReadWriteData.h"

namespace ants
{
template <unsigned int ImageDimension>
int
SmoothImage(int argc, char * argv[])
{
  using PixelType = float;
  using ImageType = itk::Image<PixelType, ImageDimension>;

  std::vector<float> sigmaVector = ConvertVector<float>(argv[3]);

  typename ImageType::Pointer image1 = nullptr;
  typename ImageType::Pointer varimage = nullptr;
  ReadImage<ImageType>(image1, argv[2]);

  using rgf = itk::SmoothingRecursiveGaussianImageFilter<ImageType, ImageType>;
  using medf = itk::MedianImageFilter<ImageType, ImageType>;
  typename rgf::Pointer        filter = rgf::New();
  typename medf::Pointer       filter2 = medf::New();
  typename rgf::SigmaArrayType sigmaArray;
  auto &                       spacing = image1->GetSpacing();
  // If true, sigma is in spacing units (usually mm), not voxels
  // The recursive filter wants a sigma in mm so we convert if given voxels
  bool sigmaInSpacingUnits = false;
  if (argc > 5)
  {
    sigmaInSpacingUnits = std::stoi(argv[5]);
  }
  bool usemedian = false;
  if (argc > 6)
  {
    usemedian = std::stoi(argv[6]);
  }

  if (!usemedian)
  {
    if ((sigmaVector.size() == ImageDimension) || (sigmaVector.size() == 1))
    {

      for (unsigned int d = 0; d < ImageDimension; d++)
      {
        if (sigmaVector.size() == 1)
        {
          if (sigmaInSpacingUnits)
          {
            sigmaArray[d] = sigmaVector[0];
          }
          else
          {
            sigmaArray[d] = sigmaVector[0] * static_cast<float>(spacing[d]);
          }
        }
        else if (sigmaInSpacingUnits)
        {
          sigmaArray[d] = sigmaVector[d];
        }
        else
        {
          sigmaArray[d] = sigmaVector[d] * static_cast<float>(spacing[d]);
        }
      }
      filter->SetSigmaArray(sigmaArray);
    }
    else
    {
      std::cerr << "Incorrect sigma vector size.  Must either be of size 1 or ImageDimension." << std::endl;
    }
    filter->SetInput(image1);
    filter->Update();
    varimage = filter->GetOutput();
  }
  else
  {
    typename ImageType::SizeType rad;
    if (sigmaVector.size() == 1)
    {
      rad.Fill(static_cast<unsigned long>(sigmaVector[0]));
    }
    else if (sigmaVector.size() == ImageDimension)
    {
      for (unsigned int d = 0; d < ImageDimension; d++)
      {
        rad[d] = sigmaVector[d];
      }
    }
    else
    {
      std::cerr << "Incorrect sigma vector size.  Must either be of size 1 or ImageDimension." << std::endl;
    }
    filter2->SetRadius(rad);
    filter2->SetInput(image1);
    filter2->Update();
    varimage = filter2->GetOutput();
  }
  ANTs::WriteImage<ImageType>(varimage, argv[4]);
  return EXIT_SUCCESS;
}

// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
SmoothImage(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(), "SmoothImage");

  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);

  // antscout->set_stream( out_stream );

  if (argc < 4)
  {
    std::cout << "Usage:  " << std::endl;
    std::cout
      << argv[0]
      << " ImageDimension image.ext smoothingsigma outimage.ext {sigma-is-in-spacing-units-(0)/1} {medianfilter-(0)/1}"
      << std::endl;
    std::cout << " If using median filter, sigma is the radius of filtering, in voxels " << std::endl;
    std::cout << " A separate sigma can be specified for each dimension, e.g., 1.5x1x2 " << std::endl;
    if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
    {
      return EXIT_SUCCESS;
    }
    return EXIT_FAILURE;
  }

  switch (std::stoi(argv[1]))
  {
    case 2:
    {
      return SmoothImage<2>(argc, argv);
    }
    break;
    case 3:
    {
      return SmoothImage<3>(argc, argv);
    }
    break;
    case 4:
    {
      return SmoothImage<4>(argc, argv);
    }
    break;
    default:
      std::cout << "Unsupported dimension" << std::endl;
      return EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}
} // namespace ants