vol2sdp.cpp

#include <iostream>
#include <fstream>
#include "DGtal/base/Common.h"
#include "DGtal/helpers/StdDefs.h"
#include "DGtal/images/ImageContainerBySTLVector.h"
#include "DGtal/io/readers/GenericReader.h"

#include "CLI11.hpp"


using namespace std;
using namespace DGtal;



int main( int argc, char** argv )
{
  CLI::App app;
  std::string inputFilename;
  std::string outputFilename {"result.sdp"};
  bool exportImageValues {false};
  int thresholdMin {128};
  int thresholdMax {255};  
  DGtal::int64_t rescaleInputMin {0};
  DGtal::int64_t rescaleInputMax {255};
  typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3D;
  
  // parse command line using CLI ----------------------------------------------
  app.description("Convert volumetric  file into a digital set of points from a given threshold.\n vol2sdp -i ${DGtal}/examples/samples/lobster.vol -o volumeList.sdp");
  app.add_option("-i,--input,1", inputFilename,  "vol file (.vol, .longvol .p3d, .pgm3d and if WITH_ITK is selected: dicom, dcm, mha, mhd) or sdp (sequence of discrete points). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255." )
    ->required()
    ->check(CLI::ExistingFile);
  app.add_option("--output,-o,2", outputFilename, "sequence of discrete point file (.sdp)", true);
  app.add_flag("--exportImageValues,-e",exportImageValues, "option to export also the image value of the voxel in a fourth field.");
  app.add_option("--thresholdMin,-m", thresholdMin, "threshold min (excluded) to define binary shape.", true);
  app.add_option("--thresholdMax,-M", thresholdMax, "threshold max (included) to define binary shape.", true);
  app.add_option("--rescaleInputMin", rescaleInputMin, "min value used to rescale the input intensity (to avoid basic cast into 8  bits image).", true);
  app.add_option("--rescaleInputMax", rescaleInputMax, "max value used to rescale the input intensity (to avoid basic cast into 8  bits image).", true);

  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  // END parse command line using CLI ----------------------------------------------

  typedef DGtal::functors::Rescaling<DGtal::int64_t ,unsigned char > RescalFCT;
  Image3D inputImage =  GenericReader< Image3D >::importWithValueFunctor( inputFilename,
                                                                          RescalFCT(rescaleInputMin,
                                                                                    rescaleInputMax,
                                                                                    0, 255) );
  trace.info() << " [done] " << std::endl ; 
  std::ofstream outStream;
  outStream.open(outputFilename.c_str());

  trace.info() << "Processing image to output file " << outputFilename ; 
  //Processing all points
  outStream << "# sdp file generate by vol2sdp with source vol:" << inputFilename
            << " and threshold min: " <<  thresholdMin << " max:" << thresholdMax << std::endl;
  outStream << "# format: x y z ";
  if(exportImageValues){
    outStream << " image_value";
  }
  outStream << std::endl;
  
  for(Image3D::Domain::ConstIterator it=inputImage.domain().begin(); it != inputImage.domain().end(); ++it){
    if(inputImage(*it) >= thresholdMin && inputImage(*it) <= thresholdMax ){
      outStream << (*it)[0] << " " << (*it)[1] << " " << (*it)[2];
      if(exportImageValues){
        outStream << " " << (unsigned int) inputImage(*it);
      }
      
      outStream << std::endl;
    }
  }
  outStream.close();
  trace.info() << " [done] " << std::endl ;   
  return EXIT_SUCCESS;
}