3dVolBoundaryViewer.cpp

 
#include <iostream>
#include <sstream>
#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/viewers/PolyscopeViewer.h"
#include "DGtal/io/readers/PointListReader.h"
#include "DGtal/io/readers/GenericReader.h"
#ifdef DGTAL_WITH_ITK
#include "DGtal/io/readers/DicomReader.h"
#endif
#include "DGtal/io/Color.h"
#include "DGtal/io/colormaps/GradientColorMap.h"
 
#include "CLI11.hpp"
 
 
using namespace std;
using namespace DGtal;
 
 
int main( int argc, char** argv )
{
  typedef SpaceND<3,int> Space;
  typedef KhalimskySpaceND<3,int> KSpace;
  typedef HyperRectDomain<Space> Domain;
  typedef ImageSelector<Domain, unsigned char>::Type Image;
  typedef DigitalSetSelector< Domain, BIG_DS+HIGH_BEL_DS >::Type DigitalSet;
  typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency;
  
  // parse command line using CLI ----------------------------------------------
  CLI::App app;
  app.description("Display the boundary of a volume file by using PolyscopeViewer. The mode specifies if you wish to see surface elements (BDRY), the inner voxels (INNER) or the outer voxels (OUTER) that touch the boundary. \n \t Example: 3dVolBoundaryViewer  $DGtal/examples/samples/lobster.vol -m 60");
  std::string inputFileName;
  DGtal::int64_t rescaleInputMin {0};
  DGtal::int64_t rescaleInputMax {255};
  int dicomMin {-1000};
  int dicomMax {3000};
  int thresholdMin {0};
  int thresholdMax {255};
  std::string mode {"INNER"};
  
  app.add_option("-i,--input,1", inputFileName, "vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_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("--thresholdMin,-m", thresholdMin, "threshold min (excluded) to define binary shape.");
  app.add_option("--thresholdMax,-M", thresholdMax, "threshold max (included) to define binary shape.");
#ifdef DGTAL_WITH_ITK
  app.add_option("--dicomMin",dicomMin,"set minimum density threshold on Hounsfield scale" );
  app.add_option("--dicomMax",dicomMin,"set maximum density threshold on Hounsfield scale" );
#endif
  app.add_option("--mode", mode,"set mode for display: INNER: inner voxels, OUTER: outer voxels, BDRY: surfels" )
  -> check(CLI::IsMember({"INNER", "OUTER", "BDRY"}));
  
  
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  // END parse command line using CLI ----------------------------------------------
  
  
  string extension = inputFileName.substr(inputFileName.find_last_of(".") + 1);
  if(extension!="vol" && extension != "p3d" && extension != "pgm3D" && extension != "pgm3d" && extension != "sdp" && extension != "pgm"
#ifdef DGTAL_WITH_ITK
     && extension !="dcm"
#endif
     ){
    trace.info() << "File extension not recognized: "<< extension << std::endl;
    return 0;
  }
  
  if(extension=="vol" || extension=="pgm3d" || extension=="pgm3D"
#ifdef DGTAL_WITH_ITK
     || extension =="dcm"
#endif
     ){
    trace.beginBlock( "Loading image into memory." );
#ifdef DGTAL_WITH_ITK
    typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;
    Image image = extension == "dcm" ? DicomReader< Image,  RescalFCT  >::importDicom( inputFileName,
                                                                                      RescalFCT(dicomMin,
                                                                                                dicomMax,
                                                                                                0, 255) ) :
    GenericReader<Image>::import( inputFileName );
#else
    Image image = GenericReader<Image>::import (inputFileName );
#endif
    trace.info() << "Image loaded: "<<image<< std::endl;
    trace.endBlock();
    
    trace.beginBlock( "Construct the Khalimsky space from the image domain." );
    Domain domain = image.domain();
    KSpace ks;
    bool space_ok = ks.init( domain.lowerBound(), domain.upperBound(), true );
    if (!space_ok)
    {
      trace.error() << "Error in the Khamisky space construction."<<std::endl;
      return 2;
    }
    trace.endBlock();
    
    trace.beginBlock( "Wrapping a digital set around image. " );
    typedef functors::IntervalForegroundPredicate<Image> ThresholdedImage;
    ThresholdedImage thresholdedImage( image, thresholdMin, thresholdMax );
    trace.endBlock();
    
    trace.beginBlock( "Extracting boundary by scanning the space. " );
    typedef KSpace::SurfelSet SurfelSet;
    typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels;
    typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface;
    MySurfelAdjacency surfAdj( true ); // interior in all directions.
    MySetOfSurfels theSetOfSurfels( ks, surfAdj );
    Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(),
                                    ks, thresholdedImage,
                                    domain.lowerBound(),
                                    domain.upperBound() );
    MyDigitalSurface digSurf( theSetOfSurfels );
    trace.info() << "Digital surface has " << digSurf.size() << " surfels."
    << std::endl;
    trace.endBlock();
    
    trace.beginBlock( "Displaying everything. " );
    stringstream s;
    s << "3dVolBoundaryViewer - DGtalTools: ";
    string name = inputFileName.substr(inputFileName.find_last_of("/")+1,inputFileName.size()) ;
    s << " " <<  name ;
    polyscope::options::programName = s.str();
    polyscope::options::groundPlaneMode = polyscope::GroundPlaneMode::None;
    polyscope::view::setNavigateStyle(polyscope::NavigateStyle::Free);
 
    PolyscopeViewer<Space,KSpace> viewer(ks);
    viewer.allowReuseList = true;
    typedef MyDigitalSurface::ConstIterator ConstIterator;
    if ( mode == "BDRY" )
    {
      viewer.drawAsSimplified();
      for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
        viewer << ks.unsigns( *it );
    }else if ( mode == "INNER" )
      for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
        viewer << ks.sCoords( ks.sDirectIncident( *it, ks.sOrthDir( *it ) ) );
    else if ( mode == "OUTER" )
      for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
        viewer << ks.sCoords( ks.sIndirectIncident( *it, ks.sOrthDir( *it ) ) );
    else{
      trace.error() << "Warning display mode (" << mode << ") not implemented." << std::endl;
      trace.error() << "The display will be empty." << std::endl;
    }
    trace.endBlock();
    viewer.show();
  }
  return 0;
}