volCrop.cpp

#include <iostream>
#include <DGtal/base/Common.h>
#include <DGtal/io/readers/VolReader.h>
#include <DGtal/io/writers/VolWriter.h>
#include <DGtal/helpers/StdDefs.h>
#include <DGtal/images/ImageContainerBySTLVector.h>
#include <DGtal/images/ConstImageAdapter.h>
#include <boost/program_options/options_description.hpp>
#include <boost/program_options/parsers.hpp>
#include <boost/program_options/variables_map.hpp>


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

namespace po = boost::program_options;



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 ----------------------------------------------
  po::options_description general_opt ( "Allowed options are: " );
  general_opt.add_options()
    ( "help,h", "display this message." )
    ( "input,i", po::value<std::string>(), "Input vol file." )
    ( "xMin", po::value<unsigned int>()->default_value(0), "x coordinate of lower point." )
    ( "yMin", po::value<unsigned int >()->default_value(0), "y coordinate of lower point." )
    ( "zMin", po::value<unsigned int >()->default_value(0), "z coordinate of lower point." )
    ( "xMax", po::value<unsigned int >(), "x coordinate of upper point." )
    ( "yMax", po::value<unsigned int>(), "y coordinate of upper point." )
    ( "zMax", po::value<unsigned int>(), "z coordinate of upper point." )
    ( "output,o", po::value<string>()->default_value("output.vol"),"Output filename." );
  bool parseOK=true;
  
  po::variables_map vm;
  
  
  try{
    po::store ( po::parse_command_line ( argc, argv, general_opt ), vm );
  }catch(const std::exception& ex){
    parseOK=false;
    trace.info()<< "Error checking program options: "<< ex.what()<< endl;
  }
  po::notify ( vm );
  if (!parseOK || vm.count ( "help" ) || !vm.count("input"))
    {
      trace.info() << " Crops a 3D vol image from domain coordinates."<<std::endl
                   << std::endl << "Basic usage: "<<std::endl
                   << "\t volCrop --input <volFileName> --o <volOutputFileName> (both files can be independently in vol, pgm3D, p3d format)"<<std::endl
                   << general_opt << "\n";
      std::cout << "Example:\n"
                << "volCrop --xMin 50 --yMin 50 --zMin 10 --xMax 150 --yMax 150 --zMax 50 -i ${DGtal}/examples/samples/lobster.vol -o croppedLobster.vol \n";
      return 0;
    }


  //Parse options
  if ( ! ( vm.count ( "input" ) ) ) missingParam ( "--input" );
  if ( ! ( vm.count ( "xMax" ) ) ) missingParam ( "--xMax" );
  if ( ! ( vm.count ( "yMax" ) ) ) missingParam ( "--yMax" );
  if ( ! ( vm.count ( "zMax" ) ) ) missingParam ( "--zMax" );

  std::string filename = vm["input"].as<std::string>();
  if ( ! ( vm.count ( "output" ) ) ) missingParam ( "--output" );
  std::string outputFileName = vm["output"].as<std::string>();

  Z3i::Point ptLow( vm["xMin"].as<unsigned int>(), vm["yMin"].as<unsigned int>(),vm["zMin"].as<unsigned int>());
  Z3i::Point ptMax( vm["xMax"].as<unsigned int>(), vm["yMax"].as<unsigned int>(),vm["zMax"].as<unsigned int>());
    
  trace.beginBlock("Loading file");
  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  MyImageC;
  MyImageC  imageC = VolReader< MyImageC >::importVol ( filename );
  functors::Identity df;  
  
  typedef ConstImageAdapter<MyImageC, Domain, functors::Identity, MyImageC::Value, functors::Identity > ConstImageAdapterForSubImage;
  Domain subDomain(ptLow, ptMax);
  ConstImageAdapterForSubImage subImage(imageC, subDomain, df, df);
  trace.endBlock();

  trace.beginBlock("Exporting...");
  bool res =  VolWriter< ConstImageAdapterForSubImage>::exportVol(outputFileName, subImage);
  trace.endBlock();
  if (res) return 0; else return 1;
}