raw2HDF5.cpp

 
#include <iostream>
#include <DGtal/base/Common.h>
#include <DGtal/io/readers/RawReader.h>
#include <DGtal/io/writers/HDF5Writer.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.hdf5"};
  unsigned int x, y, z;
   
  app.description("Converts a 3D 8-bit raw file to HDF5.\n Basic usage \n \traw2HDF5 -x 128 -y 128 -z 128 --input <RawFileName> --output <HDF5OutputFileName>");
   
  app.add_option("-i,--input,1", inputFileName, "Input raw file." )
    ->required()
    ->check(CLI::ExistingFile);
   app.add_option("-o,--output,2",outputFileName,"Output hdf5 filename.", true);
   app.add_option("--x,-x", x, "x extent." )
   ->required();
   app.add_option("--y,-y", y, "y extent." )
     ->required();
   app.add_option("--z,-z", z, "z extent." )
     ->required(); 
   
  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 = RawReader< MyImageC >::importRaw8 ( inputFileName, Z3i::Vector(x,y,z) );
  bool res =  HDF5Writer< MyImageC>::exportHDF5_3D(outputFileName, imageC, "/UInt8Array3D");
 
 
  if (res)
     return EXIT_SUCCESS;
  else 
    {
      trace.error()<< "Error while exporting the volume."<<std::endl;
      return EXIT_FAILURE;
    }
 
}