volReSample.cpp

 
#include <iostream>
#include "DGtal/base/Common.h"
#include "DGtal/helpers/StdDefs.h"
 
#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 DGtal::functors::BasicDomainSubSampler< HyperRectDomain<SpaceND<3, int> >,  
                                                  DGtal::int32_t, double >   ReSampler; 
  typedef DGtal::ConstImageAdapter<Image3D, Image3D::Domain, ReSampler,
                                   Image3D::Value,  DGtal::functors::Identity >  SamplerImageAdapter;
 
 
  
  // parse command line using CLI ----------------------------------------------
  CLI::App app;
  std::string inputFileName;
  std::string outputFileName {"result.vol"};
  std::vector<double> aGridSizeReSample;
  
  app.description("Re sample a 3D volumetric image (.vol, .longvol, .pgm3d)  with a given grid size. \n Example:\n to re sample an image with scale x,y,z  = 0.98, 0.98, 5.0,  you can do:\n volResSample -i image3d.vol -g 1 1 2  -o imageReSampled.vol \n " 
      "Note that if DGtal is compiled with the  option WITH_ITK set to ON, you can export the image in format ITK format and integrating image spacing.");
  app.add_option("-i,--input,1", inputFileName, "input volumetric file (.vol, .longvol, .pgm3d)." )
  ->required()
  ->check(CLI::ExistingFile);
  app.add_option("-o,--output,2", outputFileName, "the new volumetric file (.vol, .longvol, .pgm3d).", true );
  app.add_option("-g,--gridSize", aGridSizeReSample, "size_x size_y size_z : the grid size of the re sampling ")
   ->expected(3);
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  // END parse command line using CLI ----------------------------------------------
 
  
  trace.info()<< "Importing volume file :  " << inputFileName<< " ... " ;
  Image3D input3dImage = GenericReader<Image3D>::import(inputFileName);
  trace.info()<< "[done]" << endl;
  
  PointVector<3,int> shiftVector3D(0 ,0, 0);      
  DGtal::functors::BasicDomainSubSampler< HyperRectDomain<SpaceND<3, int> >,  
                                          DGtal::int32_t, double > reSampler(input3dImage.domain(),
                                                                             aGridSizeReSample,    shiftVector3D);
  const functors::Identity aFunctor{};
  SamplerImageAdapter sampledImage ( input3dImage, reSampler.getSubSampledDomain(), reSampler, aFunctor );
#ifdef WITH_ITK
    const std::string ext = outputFileName.substr( outputFileName.find_last_of(".") + 1 );
    if (std::find(ITK_IO_IMAGE_EXT.begin(),
                  ITK_IO_IMAGE_EXT.end(), ext) != ITK_IO_IMAGE_EXT.end() )
    {
        ITKWriter<SamplerImageAdapter>::exportITK(outputFileName, sampledImage,
                                                  Z3i::RealPoint(aGridSizeReSample[0],
                                                                 aGridSizeReSample[1],
                                                                 aGridSizeReSample[2]));
    }
    else
    {
        GenericWriter<SamplerImageAdapter>::exportFile(outputFileName, sampledImage);
    }
 
#else
  GenericWriter<SamplerImageAdapter>::exportFile(outputFileName, sampledImage);
#endif
  
  return 0;
}