vol2vox.cpp

 
#include <iostream>
#include <DGtal/base/Common.h>
#include <DGtal/io/readers/VolReader.h>
#include <DGtal/helpers/StdDefs.h>
#include <DGtal/images/Image.h>
#include <DGtal/images/ImageContainerBySTLVector.h>
 
#include "CLI11.hpp"
 
 
using namespace std;
using namespace DGtal;
using namespace Z3i;
 
 
void missingParam ( const std::string &param )
{
  trace.error() <<" Parameter: "<<param<<" is required..";
  trace.info() <<std::endl;
  exit ( 1 );
}
 
template <typename Word>
static
std::ostream& write_word( std::ostream& outs, Word value )
{
  for (unsigned size = sizeof( Word ); size; --size, value >>= 8)
    outs.put( static_cast <char> (value & 0xFF) );
  return outs;
}
 
 
int main(int argc, char**argv)
{
  
 
  
   // parse command line using CLI ----------------------------------------------
   CLI::App app;
   std::string inputFileName;
   std::string outputFileName{"result.vox"};
  app.description("Convert a vol (up to [0,126]^3) to a vox.\n The current exporter does not support custom colormaps, only the voxel values are exported \n Example: vol2vox  -i ${DGtal}/examples/samples/Al.100.vol -o Al.100.vox");
  app.add_option("-i,--input,1", inputFileName, "Input vol file.")
    ->required()
    ->check(CLI::ExistingFile);
  app.add_option("-o,--output,2", outputFileName, "Output filename.", true);
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
 
  
  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char>  MyImageC;
  trace.beginBlock("Loading..");
  MyImageC  imageL = VolReader< MyImageC >::importVol ( inputFileName );
  trace.endBlock();
 
   if ( (imageL.domain().upperBound() - imageL.domain().lowerBound()).max() > 126 )
   {
     trace.error() << "Vol file too large (width > 126)."<<std::endl;
     trace.info() << std::endl;
     exit(2);
   }
 
   trace.beginBlock("Exporting...");
   ofstream myfile;
   myfile.open (outputFileName, ios::out | ios::binary);
 
   DGtal::uint32_t cpt=0;
   for(auto it = imageL.range().begin(), itend = imageL.range().end();
       it!=itend; ++it)
     if (*it != 0)
       cpt++;
 
   Point size = imageL.domain().upperBound() - imageL.domain().lowerBound();
 
   /*
    * VOX file format:
    *
    4b VOX' '
    4b version (150)
 
    4b MAIN (chunckid)
    4b size chucnk content (n)
    4b size chunck children (m)
 
    4b SIZE (chunckid)
    4b chunck content
    4b chunck children
    4bx3  x,y,z
 
    4b VOXEL (chunckid)
    4b chunck content
    4b chunck children
    4b number of voxels
    1b x 4 (x,y,z,idcol)  x numVoxels
 
    */
 
   trace.info()<<size<<std::endl;
 
   //HEADER
   myfile <<'V'<<'O'<<'X'<<' ';
   //  version 150
   write_word(myfile, (DGtal::uint32_t)150);
 
   //Chunck MAIN
   myfile <<'M'<<'A'<<'I'<<'N';
   write_word(myfile,DGtal::uint32_t(0)); //size content
   write_word(myfile,DGtal::uint32_t( (4+4+4 + 12 ) + ((4+ 4 + 4) + (4+ cpt*4)))); //size children
 
   //Chunck SIZE
   myfile <<'S'<<'I'<<'Z'<<'E';
   write_word(myfile,DGtal::uint32_t(12)); //3x4
   write_word(myfile,DGtal::uint32_t(0));  //0 children
   write_word(myfile,DGtal::uint32_t(size[0]+1));
   write_word(myfile,DGtal::uint32_t(size[1]+1));
   write_word(myfile,DGtal::uint32_t(size[2]+1));
 
   //Chunck VOXEL
   myfile << 'X'<<'Y'<<'Z'<<'I';
   write_word(myfile, (DGtal::uint32_t)(4+cpt*4));  // 4 + numvoxel * 4
   write_word(myfile,DGtal::uint32_t(0));  //0 children
   write_word(myfile, DGtal::uint32_t(cpt)); //numvoxels
 
   trace.info() << "Number of voxels= "<<cpt<<std::endl;
 
   //Data
   for(auto it = imageL.domain().begin(), itend = imageL.domain().end();
       it!=itend; ++it)
     if (imageL(*it) != 0)
     {
       Point p = (*it) - imageL.domain().lowerBound();
       myfile.put((DGtal::uint8_t)p[0]);
       myfile.put( (DGtal::uint8_t)p[1]);
       myfile.put( (DGtal::uint8_t)p[2]);
       myfile.put(imageL(*it));
     }
 
   myfile.close();
   trace.endBlock();
 
  return 0;
}