volBoundary2obj.cpp

#include <iostream>
#include <set>
#include "CLI11.hpp"

#include "DGtal/base/Common.h"
#include "DGtal/base/BasicFunctors.h"
#include "DGtal/kernel/SpaceND.h"
#include "DGtal/kernel/domains/HyperRectDomain.h"
#include "DGtal/images/ImageSelector.h"
#include "DGtal/images/IntervalForegroundPredicate.h"
#include "DGtal/topology/KhalimskySpaceND.h"
#include "DGtal/topology/DigitalSurface.h"
#include "DGtal/topology/SetOfSurfels.h"
#include "DGtal/io/boards/Board3D.h"
#include "DGtal/io/readers/PointListReader.h"
#include "DGtal/io/readers/GenericReader.h"
#ifdef WITH_ITK
#include "DGtal/io/readers/DicomReader.h"
#endif
#include "DGtal/io/Color.h"
#include "DGtal/io/colormaps/GradientColorMap.h"

#include "DGtal/helpers/StdDefs.h"
#include "DGtal/helpers/Shortcuts.h"
#include "DGtal/helpers/ShortcutsGeometry.h"

using namespace std;
using namespace DGtal;



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

  CLI::App app;
  
  
  // Using standard 3D digital space.
  typedef Shortcuts<Z3i::KSpace> SH3;
  typedef ShortcutsGeometry<Z3i::KSpace> SHG3;
  auto params = SH3::defaultParameters() | SHG3::defaultParameters();
  
  int thresholdMin {128};
  int thresholdMax {255};  
  string inputFilename;
  DGtal::int64_t rescaleInputMin {0};
  DGtal::int64_t rescaleInputMax {255};
  std::vector<unsigned int > vectCol=  {230, 230, 230, 255};
  bool triangulatedSurface {false};
  std::string outputFilename = "result.obj";
 
  app.description("Export the boundary of a volume file to OBJ format. By default the resulting mesh is defined from the surfels of the surface elements, a triangulated (dual)");
  
  app.add_option("-i,--input,1", inputFilename, "vol file (.vol, .longvol .p3d, .pgm3d and if WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255." )
    ->required()
    ->check(CLI::ExistingFile);
  app.add_option("--output,-o,2",outputFilename ,"output file (.obj or .off).");
  app.add_option("--thresholdMin,-m", thresholdMin, "threshold min (excluded) to define binary shape.", true);
  app.add_option("--thresholdMax,-M", thresholdMax, "threshold max (included) to define binary shape.", true);
  app.add_option("--rescaleInputMin", rescaleInputMin, "min value used to rescale the input intensity (to avoid basic cast into 8  bits image).", true);
  app.add_option("--rescaleInputMax", rescaleInputMax, "max value used to rescale the input intensity (to avoid basic cast into 8  bits image).", true);
  app.add_option("--customDiffuse,-c", vectCol, "set the R, G, B, A components of the diffuse colors of the mesh faces.", true)
    ->expected(4);
  app.add_flag("--triangulatedSurface,-t", triangulatedSurface, "save the dual triangulated surface instead instead the default digital surface.");
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  


  typedef DGtal::functors::Rescaling<DGtal::int64_t ,unsigned char > RescalFCT;
  RescalFCT f (rescaleInputMin, rescaleInputMax,0, 255);

  trace.beginBlock( "Loading file.." );
  SH3::GrayScaleImage image =
  GenericReader< SH3::GrayScaleImage >::importWithValueFunctor(inputFilename, f );
  
  auto gimage = CountedPtr<SH3::GrayScaleImage>( new SH3::GrayScaleImage( image ) );
  auto bimage = SH3::makeBinaryImage(gimage,params( "thresholdMin", thresholdMin )
                                                  ( "thresholdMax", thresholdMax ) );
  
  
  trace.info() << "Image loaded: "<<gimage<< std::endl;
  trace.endBlock();
  params( "faceSubdivision", "Centroid" )( "surfelAdjacency", 1);
  auto K         = SH3::getKSpace( bimage);

  SH3::Color cD (vectCol[0], vectCol[1], vectCol[2], vectCol[3]);
  
  
  auto surface = SH3::makeDigitalSurface( bimage, K );
  const std::string extension = outputFilename.substr( outputFilename.find_last_of(".") + 1 );  
  if (extension != "obj" && extension != "off")
  {
    trace.warning() << "File extension not recognized, saving by default in objg format"<< std::endl;
  }
  if (triangulatedSurface)
  {
    auto tr = SH3::makeTriangulatedSurface(surface);
    bool ok = true;
    if (extension!="off")
    {
      ok  = SH3::saveOBJ( tr, SH3::RealVectors(), SH3::Colors(), outputFilename, Color( 32, 32, 32 ), cD );
    }
    else 
    {
      ok  = SH3::saveOFF( tr, outputFilename, cD);
    }
    return ok ? EXIT_SUCCESS : EXIT_FAILURE ;
  }
  else
  {
    bool ok = true;
    if (extension!="off")
    {
      ok  = SH3::saveOBJ( surface, SH3::RealVectors(), SH3::Colors(), outputFilename, Color( 32, 32, 32 ), cD);
    } else
    {
      ok  = SH3::saveOFF( surface, outputFilename, cD);
    }
    return  ok ? EXIT_SUCCESS : EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}