volFlip.cpp

 
#include <iostream>
#include <DGtal/base/Common.h>
#include <DGtal/helpers/StdDefs.h>
#include "DGtal/io/readers/GenericReader.h"
#include "DGtal/io/writers/GenericWriter.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 {"result.vol"};
  
  std::vector <unsigned int> vectImgPlane {0,1};
  unsigned int dimFlip {0};
  
  app.description("Flip 2D slice image of an 3D vol image (mirror transformation)\nBasic usage:\n \t volFlip --input <volFileName> --imagePlane 0 1 --flipDimension 0 --o <volOutputFileName> (vol, longvol, p3d format)\n Example:\n volFlip --imagePlane 0 1 --flipDimension 0 -i ${DGtal}/examples/samples/lobster.vol -o flippedXxyLobster.vol \n The resulting Z slice images (Z= cst) of flippedXxyLobster.p3d will appears flipped according the x axis. \n");
  app.add_option("-i,--input,1", inputFileName, "Input vol file." )
  ->required()
  ->check(CLI::ExistingFile);
  
  app.add_option("--imagePlane", vectImgPlane, "arg=  {0,1,2} x {0,1,2} defines the axis of the slice image which will be transformed (by default arg= 0 1  i.e. the slice image defined in the X,Y plane (Z=cst)", true)
   ->expected(2);
  app.add_option("--flipDimension",dimFlip,"specify which axis will be used to apply the flip.", true);
  app.add_option("-o,--output, 2",outputFileName, "Output filename.", true );
 
 
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  // END parse command line using CLI ----------------------------------------------
 
  
  unsigned int dimFirstImg = vectImgPlane.at(0);
  unsigned int dimSecondImg = vectImgPlane.at(1);
  
  unsigned int normalImgDim = (dimFirstImg!=2 && dimSecondImg!=2)? 2 :( (dimFirstImg!=1 && dimSecondImg!=1)? 1:  0    );  
    
    
  trace.beginBlock("Loading file");
  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  Image3D;
  Image3D  imageSRC =  GenericReader<Image3D>::import ( inputFileName );
  trace.endBlock();
  Image3D  imageRes(imageSRC.domain());
  for(int i=0; i <= imageSRC.domain().upperBound()[normalImgDim]; i++){
    Point startPoint(0,0, 0);
    startPoint[normalImgDim]=i;
    for( Domain::ConstSubRange::ConstIterator 
           it = imageSRC.domain().subRange(dimFirstImg, dimSecondImg, 
                                           startPoint).begin(),
           itend =  imageSRC.domain().subRange(dimFirstImg, dimSecondImg, startPoint).end();
         it != itend; ++it){
      Point pt = *it;
      pt[dimFlip]= imageSRC.domain().upperBound()[dimFlip] - pt[dimFlip] ;
      imageRes.setValue(*it, imageSRC(pt)); 
    }
  }
 
  trace.beginBlock("Exporting...");
  bool res =  VolWriter<Image3D>::exportVol(outputFileName, imageRes);
  trace.endBlock();
  if (res) return 0; else return 1;
}