itk2vol.cpp

#include <iostream>
#include <fstream>
#include "DGtal/base/Common.h"
#include "DGtal/helpers/StdDefs.h"
#include "DGtal/base/BasicFunctors.h"
#include "DGtal/images/ImageContainerBySTLVector.h"
#include "DGtal/io/writers/GenericWriter.h"
#include "DGtal/io/readers/ITKReader.h"

#include "CLI11.hpp"

using namespace std;
using namespace DGtal;

typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3DChar;


template<typename TImage, typename TImageMask>
void
applyMaskImage( TImage &imageInput,  const  TImageMask &maskImage,
                typename TImageMask::Value valRemove)
{
  for(const auto &p : imageInput.domain())
  {
    if (maskImage(p) == valRemove)
    {
      imageInput.setValue(p,0);
    }
  }
  
}

template<typename TImage, typename TRescale>
void
exportImageUCHAR(TImage img, const std::string resName, TRescale rScale)
{
  Image3DChar res ( img.domain() );
  
  for (const auto p: img.domain() ) {
    res.setValue(p, rScale(img(p)));
  }
  DGtal::GenericWriter<Image3DChar, 3, unsigned char>::exportFile(resName, res);
}



int main( int argc, char** argv )
{
  typedef ImageContainerBySTLVector < Z3i::Domain,  double > Image3D_D;
  typedef ImageContainerBySTLVector < Z3i::Domain,  int > Image3D_I;


   // parse command line using CLI ----------------------------------------------
   CLI::App app;
   std::string inputFileName;
   std::string outputFileName {"result.vol"};
   DGtal::int64_t inputMin {-1000};
   DGtal::int64_t inputMax  {3000};
   int  maskRemoveLabel {0};  
   string inputMask {""};
   string inputType {""};
   
   app.description("Converts itk file into a volumetric file (.vol, .pgm3d). \n Example:\n itk2vol  image.mhd sample.vol --inputMin -500 --inputMax -100 \n");
   app.add_option("-i,--input,1", inputFileName, "Any file format in the ITK library (mhd, mha, ...)." )
    ->required()
    ->check(CLI::ExistingFile);
   app.add_option("-o,--output,2", outputFileName, "volumetric file (.vol, .pgm3d).");
   app.add_option("-m,--maskImage", inputMask, "Use a mask image to remove image part (where mask is 0). The default mask value can be changed using mask default value.");
   app.add_option("-r,--maskRemoveLabel", maskRemoveLabel,"Change the label value that defines the part of input image to be removed by the option --maskImage." );
   app.add_option("--inputMin", inputMin, "set minimum density threshold on Hounsfield scale.");
   app.add_option("--inputMax", inputMax, "set maximum density threshold on Hounsfield scale.");
   app.add_option("-t,--inputType", inputType, "to specify the input image type (int or double).")
     -> check(CLI::IsMember({"int", "double"}));
   
   app.get_formatter()->column_width(40);
   CLI11_PARSE(app, argc, argv);
   // END parse command line using CLI ----------------------------------------------

   
  if (inputType == "double") {
      typedef DGtal::functors::Rescaling<double ,unsigned char > RescalFCT;
      trace.info() << "Reading input file (of type double)" << inputFileName ;
      Image3D_D inputImage = ITKReader< Image3D_D  >::importITK(inputFileName, true);
      trace.info() << " [done] " << std::endl ; 
      trace.info() << " converting into vol file... " ; 
      if ( inputMask != "")
      {
        Image3D_I maskImage = ITKReader< Image3D_I  >::importITK(inputMask);
        applyMaskImage(inputImage, maskImage, maskRemoveLabel);
      }
      RescalFCT rescaleCustom(inputMin, inputMax, 0, 255);
      exportImageUCHAR(inputImage,outputFileName, rescaleCustom );
  }else {
     typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;
      trace.info() << "Reading input file (of type int) " << inputFileName ;
      Image3D_I inputImage = ITKReader< Image3D_I  >::importITK(inputFileName, true);
      trace.info() << " [done] " << std::endl ; 
      trace.info() << " converting into vol file... " ; 
      RescalFCT rescaleCustom(inputMin, inputMax, 0, 255);
      exportImageUCHAR(inputImage,outputFileName, rescaleCustom );

      }
  trace.info() << " [done] " << std::endl ;   
  return EXIT_SUCCESS;  
}