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 "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 {"output.vol"};
  int xMin {0};
  int yMin {0};
  int zMin {0};
  int xMax;
  int yMax;
  int zMax;
  
  app.description("Crops a 3D vol image from domain coordinates.\n Basic usage: \n \t volCrop --input <volFileName> --o <volOutputFileName> (both files can be independently in vol, pgm3D, p3d format)\nExample:\n volCrop --xMin 50 --yMin 50 --zMin 10 --xMax 150 --yMax 150 --zMax 50 -i ${DGtal}/examples/samples/lobster.vol -o croppedLobster.vol \n");
  
  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("--xMin",xMin, "x coordinate of lower point.", true);
  app.add_option("--yMin",yMin, "y coordinate of lower point.", true);
  app.add_option("--zMin",zMin, "z coordinate of lower point.", true);
 
  app.add_option("--xMax",xMax, "x coordinate of upper point.")
   ->required();
  app.add_option("--yMax",yMax, "y coordinate of upper point.")
   ->required();
  app.add_option("--zMax",zMax, "z coordinate of upper point.")
   ->required();
  
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  // END parse command line using CLI ----------------------------------------------
  
  Z3i::Point ptLow( xMin, yMin, zMin);
  Z3i::Point ptMax(xMax , yMax, zMax);
  
  trace.beginBlock("Loading file");
  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  MyImageC;
  MyImageC  imageC = VolReader< MyImageC >::importVol ( inputFileName );
  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;
}