volTrValues.cpp

#include <iostream>
#include <DGtal/base/Common.h>
#include <DGtal/io/readers/GenericReader.h>
#include <DGtal/io/writers/GenericWriter.h>
#include <DGtal/helpers/StdDefs.h>
#include <DGtal/images/ImageContainerBySTLVector.h>
#include <DGtal/images/ConstImageAdapter.h>

#include "CLI11.hpp"

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

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

  // parse command line ----------------------------------------------
  // parse command line using CLI ----------------------------------------------
  CLI::App app;
  std::string inputFileName;
  std::string outputFileName {"result.vol"};
  std::vector<unsigned int> inputVals;
  std::vector<unsigned int>  outputVals;

  app.description("Apply basic vol image transform from the input values to output values.\n Basic usage:\n \t volTrValues --input <volFileName> --o <volOutputFileName> -s 1 99 -r 100 200 \n\t => all voxel of values 1 (resp. 99) will be 100 (resp. 200) in the resulting image.");
  
  app.add_option("-i,--input,1", inputFileName, "Input vol file." )
  ->required()
  ->check(CLI::ExistingFile);
  
  app.add_option("--output,-o,2",outputFileName, "Output filename.", true);
  app.add_option("--inputVals,-s", inputVals, "specify the values which will be transformed with the output values (given with --outputVals).") ->required();
  app.add_option("--outputVals,-r", outputVals, "specify the values which will be transformed with the output values (given with --outputVals).") ->required();
  
 
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  // END parse command line using CLI ----------------------------------------------


  if(inputVals.size()!=outputVals.size()){
    trace.error()<< "Transformation not possible the two sets of input/output values should have the same size." << std::endl;
    exit(1);
  }
  
  trace.beginBlock("Loading file");
  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  MyImageC;
  MyImageC  image = GenericReader< MyImageC >::import( inputFileName );
  trace.endBlock();  
  unsigned int val;
  for(MyImageC::Domain::ConstIterator it = image.domain().begin(),
        itend = image.domain().end(); it != itend; ++it)
    {
      val = image(*it);
      for(unsigned int i = 0; i< inputVals.size(); i++){
        if(inputVals.at(i)==val){
          image.setValue( *it , outputVals.at(i));
        }
      }
    } 

  trace.beginBlock("Exporting...");
  bool res =  GenericWriter<MyImageC>::exportFile(outputFileName, image);
  trace.endBlock();

  if (res) return 0; else return 1;
}