32 #include "DGtal/base/Common.h" 33 #include "DGtal/helpers/StdDefs.h" 34 #include "DGtal/base/BasicFunctors.h" 35 #include "DGtal/images/ImageContainerBySTLVector.h" 36 #include "DGtal/io/writers/GenericWriter.h" 37 #include "DGtal/io/readers/ITKReader.h" 39 #include <boost/program_options/options_description.hpp> 40 #include <boost/program_options/parsers.hpp> 41 #include <boost/program_options/variables_map.hpp> 44 using namespace DGtal;
72 namespace po = boost::program_options;
75 int main(
int argc,
char** argv )
77 typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3D;
81 po::options_description general_opt(
"Allowed options are ");
82 general_opt.add_options()
83 (
"help,h",
"display this message")
84 (
"input,i", po::value<std::string>(),
"Any file format in the ITK library (mhd, mha, ...) " )
85 (
"output,o", po::value<std::string>(),
"volumetric file (.vol, .pgm3d) " )
86 (
"inputMin", po::value<int>()->default_value(-1000),
"set minimum density threshold on Hounsfield scale")
87 (
"inputMax", po::value<int>()->default_value(3000),
"set maximum density threshold on Hounsfield scale");
94 po::store(po::parse_command_line(argc, argv, general_opt), vm);
95 }
catch(
const std::exception& ex){
97 trace.info()<<
"Error checking program options: "<< ex.what()<< endl;
100 if( !parseOK || vm.count(
"help")||argc<=1)
102 std::cout <<
"Usage: " << argv[0] <<
" [input] [output]\n" 103 <<
"Converts itk file into a volumetric file (.vol, .pgm3d). " 104 << general_opt <<
"\n";
105 std::cout <<
"Example:\n" 106 <<
"itk2vol -i image.mhd --dicomMin -500 --dicomMax -100 -o sample.vol \n";
110 if(! vm.count(
"input") ||! vm.count(
"output"))
112 trace.error() <<
" Input and output filename are needed to be defined" << endl;
117 string inputFilename = vm[
"input"].as<std::string>();
118 string outputFilename = vm[
"output"].as<std::string>();
119 int inputMin = vm[
"inputMin"].as<
int>();
120 int inputMax = vm[
"inputMax"].as<
int>();
121 typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;
123 trace.info() <<
"Reading input input file " << inputFilename ;
124 Image3D inputImage = ITKReader< Image3D, RescalFCT >::importITK(inputFilename,
127 trace.info() <<
" [done] " << std::endl ;
128 trace.info() <<
" converting into vol file... " ;
129 inputImage >> outputFilename;
130 trace.info() <<
" [done] " << std::endl ;