vol2slice.cpp

#include <iostream>
#include "DGtal/base/Common.h"
#include "DGtal/helpers/StdDefs.h"
#include <boost/format.hpp>

#include "DGtal/io/readers/GenericReader.h"
#include "DGtal/io/writers/GenericWriter.h"
#include "DGtal/images/ConstImageAdapter.h"
#include "DGtal/kernel/BasicPointFunctors.h"

#include "CLI11.hpp"

using namespace std;
using namespace DGtal;



int main( int argc, char** argv )
{
  typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3D;
  typedef ImageContainerBySTLVector < Z2i::Domain, unsigned char > Image2D;
  typedef DGtal::ConstImageAdapter<Image3D, Image2D::Domain, DGtal::functors::Projector< DGtal::Z3i::Space>,
                                   Image3D::Value,  DGtal::functors::Identity >  SliceImageAdapter;

  CLI::App app;


  std::string inputFileName;
  std::string outputFileName = "result.pgm";
  DGtal::int64_t rescaleInputMin {0};
  DGtal::int64_t rescaleInputMax {255};
  int userStartSlice {0};
  int userEndSlice;
  unsigned int sliceOrientation {2};
  

  app.description("Convert a volumetric file (.vol, .longvol, .pgm3d) into a set of 2D slice  images. \n Typical use: to extract all slices defined in Y plane (y=cst): \n vol2slice  image3d.vol slice.pgm -s 1  \n");

  app.add_option("-i,--input,1", inputFileName, "vol file (.vol, .longvol .p3d, .pgm3d and if WITH_ITK is selected: dicom, dcm, mha, mhd). 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 ,"base_name.extension:  extracted 2D slice volumetric files (will result n files base_name_xxx.extension)", true);
  app.add_option("--setFirstSlice,-f", userStartSlice, "Set the first slice index to be extracted.", true)
    -> check(CLI::Number);
  app.add_option("--setLastSlice,-l", userEndSlice, "Set the last slice index to be extracted (by default set to maximal value according to the given volume).")
    -> check(CLI::Number);
  app.add_option("--sliceOrientation,-s", sliceOrientation, "specify the slice orientation for which the slice are defined (by default =2 (Z direction))", true)
    -> check(CLI::IsMember({0, 1, 2}));
  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);
  
  std::string outputExt = outputFileName.substr(outputFileName.find_last_of(".")+1);
  std::string outputBasename = outputFileName.substr(0, outputFileName.find_last_of("."));
     

  trace.info()<< "Importing volume file base name:  " << outputBasename << " extension: " << outputExt << " ..." ;
  typedef DGtal::functors::Rescaling<DGtal::int64_t ,unsigned char > RescalFCT;
  Image3D input3dImage =  GenericReader< Image3D >::importWithValueFunctor( inputFileName,RescalFCT(rescaleInputMin,
                                                                                                    rescaleInputMax,
                                                                                                    0, 255) );
  
  trace.info()<< "[done]" << endl;
  
  unsigned int startSlice=0;
  unsigned int endSlice=input3dImage.domain().upperBound()[sliceOrientation];

  if(userStartSlice !=0){
    startSlice = userStartSlice;
  }
  if(userEndSlice != 0){
    endSlice = userEndSlice;
  }

  //Processing each slice
#pragma omp parallel for schedule(dynamic)
   for( unsigned int i=startSlice; i <= endSlice; i++){
    trace.info() << "Exporting slice image "<< i ;
    DGtal::functors::Projector<DGtal::Z2i::Space>  invFunctor; invFunctor.initRemoveOneDim(sliceOrientation);
    DGtal::Z2i::Domain domain2D(invFunctor(input3dImage.domain().lowerBound()),
                                invFunctor(input3dImage.domain().upperBound()));
    DGtal::functors::Projector<DGtal::Z3i::Space> aSliceFunctor(i); aSliceFunctor.initAddOneDim(sliceOrientation);
    const DGtal::functors::Identity identityFunctor{};
    SliceImageAdapter sliceImage( input3dImage, domain2D, aSliceFunctor, identityFunctor );
    stringstream outName; outName << outputBasename << "_" <<  boost::format("%|05|")% i <<"."<< outputExt ;
    trace.info() << ": "<< outName.str() ;
    GenericWriter<SliceImageAdapter>::exportFile(outName.str(), sliceImage);
    trace.info() << " [done]"<< endl;
  }


  return 0;
}