dicom2vol.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/DicomReader.h"
 
 
#include "CLI11.hpp"
 
 
using namespace std;
using namespace DGtal;
 
 
int main( int argc, char** argv )
{
  typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3D;
  
   // parse command line using CLI ----------------------------------------------
   CLI::App app;
   std::string inputFileName;
   std::string outputFileName {"result.raw"};
   DGtal::int64_t dicomMin {-1000};
   DGtal::int64_t dicomMax {3000};
 
   app.description("Convert dicom file into a volumetric file (.vol, .longvol .pgm3d).\n Example:\n dicom2vol  ${DGtal}/tests/samples/dicomSample/1629.dcm sample.vol --dicomMin 0 --dicomMax 300.");
   app.add_option("-i,--input,1", inputFileName, "dicom image  (.dcm)." )
    ->required()
    ->check(CLI::ExistingFile);
   app.add_option("-o,--output,2", outputFileName, "volumetric file (.vol, .longvol .pgm3d, .raw)", true);
   app.add_option("--dicomMin",dicomMin,"set minimum density threshold on Hounsfield scale" );
   app.add_option("--dicomMax",dicomMax,"set maximum density threshold on Hounsfield scale" );
 
   app.get_formatter()->column_width(40);
   CLI11_PARSE(app, argc, argv);
   // END parse command line using CLI ----------------------------------------------
   
   typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;
  
   trace.info() << "Reading input dicom file " << inputFileName ; 
  Image3D inputImage = DicomReader< Image3D,  RescalFCT  >::importDicom(inputFileName, 
                                                                        RescalFCT(dicomMin,dicomMax, 0, 255) );
  trace.info() << " [done] " << std::endl ; 
  trace.info() << " converting into vol file... " ; 
  inputImage >> outputFileName; 
  trace.info() << " [done] " << std::endl ;   
 
  return EXIT_SUCCESS;
}