HDF52vol.cpp

#include <iostream>
#include <DGtal/base/Common.h>
#include <DGtal/io/readers/HDF5Reader.h>
#include <DGtal/io/writers/VolWriter.h>
#include <DGtal/helpers/StdDefs.h>
#include <DGtal/images/Image.h>
#include <DGtal/images/ImageContainerBySTLVector.h>

#include "CLI11.hpp"


using namespace std;
using namespace DGtal;
using namespace Z3i;


void missingParam ( std::string param )
{
  trace.error() <<" Parameter: "<<param<<" is required..";
  trace.info() <<std::endl;
  exit ( 1 );
}


int main(int argc, char**argv)
{

// parse command line using CLI ----------------------------------------------
   CLI::App app;
   std::string inputFileName;
   std::string outputFileName {"result.vol"};

   app.description("Convert a 3D 8-bit HDF5 file to vol.");
   app.add_option("-i,--input,1", inputFileName, "Input HDF5 file." )
    ->required()
    ->check(CLI::ExistingFile);
   app.add_option("-o,--output,2", outputFileName, "Output vol filename.", true );

   app.get_formatter()->column_width(40);
   CLI11_PARSE(app, argc, argv);
   // END parse command line using CLI ----------------------------------------------
   
  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  MyImageC;

  MyImageC imageC = HDF5Reader< MyImageC >::importHDF5_3D( inputFileName, "/UInt8Array3D" );
  bool res = VolWriter< MyImageC>::exportVol(outputFileName, imageC);

  if (res)
    return EXIT_SUCCESS;
  else 
    {
      trace.error()<< "Error while exporting the volume."<<std::endl;
      return EXIT_FAILURE;
    }
}