volSegment.cpp

 
#include <iostream>
#include <fstream>
 
#include "DGtal/base/Common.h"
#include "DGtal/helpers/StdDefs.h"
#include "DGtal/topology/helpers/Surfaces.h"
 
#include "DGtal/images/ImageContainerBySTLVector.h"
#include "DGtal/io/readers/GenericReader.h"
#include "DGtal/io/writers/GenericWriter.h"
 
#include "DGtal/images/IntervalForegroundPredicate.h"
#include <DGtal/topology/SetOfSurfels.h>
#include "DGtal/topology/DigitalSurface.h"
#include "DGtal/topology/helpers/Surfaces.h"
 
#include "CLI11.hpp"
 
 
using namespace std;
using namespace DGtal;
 
 
typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3D;
typedef ImageContainerBySTLVector < Z3i::Domain, DGtal::uint64_t > Image3DI;
 
typedef Z3i::KSpace::SurfelSet SurfelSet;
typedef SetOfSurfels< Z3i::KSpace, SurfelSet > MySetOfSurfels;
 
 
std::vector<unsigned int> getHistoFromImage(const Image3D &image){
  const Image3D::Domain &imgDom = image.domain();
  std::vector<unsigned int> vectHisto(UCHAR_MAX);
  for(Image3D::Domain::ConstIterator it=imgDom.begin(); it!= imgDom.end(); ++it){
    vectHisto[image(*it)]++;
  }
  return vectHisto;
}
 
 
unsigned int 
getOtsuThreshold(const Image3D &image){
  std::vector<unsigned int> histo = getHistoFromImage(image);
  unsigned int imageSize = image.domain().size();
  unsigned int sumA = 0;
  unsigned int sumB = imageSize;
  unsigned int muA=0;
  unsigned int muB=0;
  unsigned int sumMuAll= 0;
  for( unsigned int t=0; t< histo.size();t++){
    sumMuAll+=histo[t]*t;
  }
  
  unsigned int thresholdRes=0;
  double valMax=0.0;
  for( unsigned int t=0; t< histo.size(); t++){
    sumA+=histo[t];
    if(sumA==0)
      continue; 
    sumB=imageSize-sumA;
    if(sumB==0){
      break;
    }
    
    muA+=histo[t]*t;
    muB=sumMuAll-muA;
    double muAr=muA/(double)sumA;
    double muBr=muB/(double)sumB;
    double sigma=  (double)sumA*(double)sumB*(muAr-muBr)*(muAr-muBr);
    if(valMax<=sigma){
      valMax=sigma;
      thresholdRes=t;
    }
  }
  return thresholdRes;
}
 
 
template<typename TImageOutput>
void
applySegmentation(TImageOutput &imageResuSegmentation,  const Image3D &inputImage, CLI::Option *labelOpt, int maxTh, int minTh) {
  functors::IntervalForegroundPredicate<Image3D> simplePredicate ( inputImage, minTh, maxTh );
  SurfelAdjacency< Z3i::KSpace::dimension > SAdj ( true );
  Z3i::KSpace K;
  bool space_ok = K.init( inputImage.domain().lowerBound(), inputImage.domain().upperBound(), false );
  if(!space_ok){
    trace.error() << "problem initializing 3d space" << endl;
  }
  
  std::vector< std::vector<Z3i::SCell > > vectConnectedSCell;
  Surfaces<Z3i::KSpace>::extractAllConnectedSCell(vectConnectedSCell,K, SAdj, simplePredicate, false);
  trace.progressBar(0, vectConnectedSCell.size());
  for(unsigned int i = 0; i<vectConnectedSCell.size(); i++)
  {
    trace.progressBar(i, vectConnectedSCell.size());
    MySetOfSurfels  aSet(K, SAdj);
    Z3i::Point lowerPoint, upperPoint;
    Z3i::Point p1;
    Z3i::Point p2;
    for(std::vector<Z3i::SCell>::const_iterator it= vectConnectedSCell.at(i).begin(); it != vectConnectedSCell.at(i).end(); ++it)
    {
      aSet.surfelSet().insert(aSet.surfelSet().begin(),  *it);
      unsigned int orth_dir = K.sOrthDir( *it );
      p1 =  K.sCoords( K.sIncident( *it, orth_dir, true ) );
      p2 =  K.sCoords( K.sIncident( *it, orth_dir, false ) );
      if(p1[0] < lowerPoint[0]) lowerPoint[0]= p1[0];
      if(p1[1] < lowerPoint[1]) lowerPoint[1]= p1[1];
      if(p1[2] < lowerPoint[2]) lowerPoint[2]= p1[2];
      
      if(p1[0] > upperPoint[0]) upperPoint[0]= p1[0];
      if(p1[1] > upperPoint[1]) upperPoint[1]= p1[1];
      if(p1[2] > upperPoint[2]) upperPoint[2]= p1[2];
      
      if(p2[0] < lowerPoint[0]) lowerPoint[0]= p2[0];
      if(p2[1] < lowerPoint[1]) lowerPoint[1]= p2[1];
      if(p2[2] < lowerPoint[2]) lowerPoint[2]= p2[2];
      
      if(p2[0] > upperPoint[0]) upperPoint[0]= p2[0];
      if(p2[1] > upperPoint[1]) upperPoint[1]= p2[1];
      if(p2[2] > upperPoint[2]) upperPoint[2]= p2[2];
      
    }
    
    Z3i::KSpace kRestr ;
    kRestr.init( lowerPoint, upperPoint, false );
    if(simplePredicate(p2)){
      DGtal::Surfaces<Z3i::KSpace>::uFillInterior( kRestr,  aSet.surfelPredicate(),
                                                  imageResuSegmentation,
                                                  i, false, false);
    }else if (labelOpt->count() > 0){
      DGtal::Surfaces<Z3i::KSpace>::uFillExterior( kRestr,  aSet.surfelPredicate(),
                                                  imageResuSegmentation,
                                                  i+1, false, false);
    }
  }
  trace.progressBar(vectConnectedSCell.size(), vectConnectedSCell.size());
  trace.info() << std::endl;
}
 
 
 
 
 
int main( int argc, char** argv )
{
  
  // parse command line using CLI ----------------------------------------------
  CLI::App app;
  std::string inputFileName;
  std::string outputFileName {"result.vol"};
  bool labelBackground {false};
  int minTh {0};
  int maxTh {255};
  bool outputTypeInt {false};
 
  app.description("Segment volumetric file from a simple threshold which can be set automatically from the otsu estimation.\n The segmentation result is given by an integer label given in the resulting image. Example:\n volSegment ${DGtal}/examples/samples/lobster.vol segmentation.vol \n");
  app.add_option("-i,--input,1", inputFileName, "volumetric input file (.vol, .pgm, .pgm3d, .longvol)." )
  ->required()
  ->check(CLI::ExistingFile);
  app.add_option("-o,--output,2", outputFileName, "volumetric output file (.vol, .pgm, .pgm3d, .longvol)", true);
 
  app.add_flag("--outputTypeUInt", outputTypeInt, "to specify the output image type (unsigned int) instead using the default unsigned char. If this flag is selected you have to check the output file format type (longvol, or an ITK image type if the DGtal WITH_ITK option is selected).");
 
  auto labelOpt = app.add_flag("--labelBackground",labelBackground, "option to define a label to regions associated to object background.");
  app.add_option("-m,--thresholdMin",minTh, "min threshold (if not given the max threshold is computed with Otsu algorithm).", true );
  auto maxThOpt = app.add_option("-M,--thresholdMax", maxTh, "max threshold", true );
 
  
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  // END parse command line using CLI ----------------------------------------------
 
  trace.info() << "Reading input file " << inputFileName ;
  Image3D inputImage = DGtal::GenericReader<Image3D>::import(inputFileName);
  trace.info() << " [done] " << std::endl ;
  
  std::ofstream outStream;
  outStream.open(outputFileName.c_str());
  if(maxThOpt->count()==0){
    maxTh = getOtsuThreshold(inputImage);
    trace.info() << "maximal threshold value not specified, using Otsu value: "  << maxTh << std::endl;
  }
  trace.info() << "Processing image to output file " << outputFileName << std::endl;
 
  
  if (outputTypeInt)
  {
    Image3DI imageResuSegmentation(inputImage.domain());
    applySegmentation(imageResuSegmentation, inputImage, labelOpt, maxTh, minTh);
    GenericWriter<Image3DI>::exportFile(outputFileName, imageResuSegmentation);
    
  }else{
    Image3D imageResuSegmentation(inputImage.domain());
    applySegmentation(imageResuSegmentation, inputImage, labelOpt, maxTh, minTh);
    GenericWriter<Image3D>::exportFile(outputFileName, imageResuSegmentation);
  }
  return 0;
}