volShapeMetrics.cpp

 
#include <iostream>
#include <DGtal/base/Common.h>
#include <DGtal/io/readers/GenericReader.h>
#include <DGtal/io/writers/GenericWriter.h>
#include <DGtal/helpers/StdDefs.h>
#include <DGtal/images/Image.h>
#include <DGtal/images/ImageContainerBySTLVector.h>
#include <DGtal/images/imagesSetsUtils/SetFromImage.h>
#include <DGtal/geometry/volumes/distance/DistanceTransformation.h>
#include <DGtal/math/Statistic.h>
 
#include "CLI11.hpp"
 
#include <limits>
 
using namespace std;
using namespace DGtal;
using namespace Z3i;
 
 
typedef ImageContainerBySTLVector < Z3i::Domain,  int > Image3D;
typedef ImageContainerBySTLVector < Z2i::Domain,  int > Image2D;
 
 
bool 
isDiff(const Image3D &imageA, int aMin, int aMax, const Image3D &imageB, 
       int bMin, int bMax, const Point &pt){
  bool isRefOn = (imageA(pt)<= aMax) && (imageA(pt) >= aMin);
  bool isCompOn = (imageB(pt)<= bMax) && (imageB(pt) >= bMin);
  return ((!isRefOn && isCompOn) || (isRefOn && !isCompOn));
}
 
 
 
void
getStatsFromDistanceMap(Statistic<double> & stats, const Image3D &imageA, int aMin, int aMax,
                        const Image3D & imageB,  int bMin, int bMax, 
                        bool statOnFalsePositiveOnly=false, Point *ptMax=0){
 
  // Get the digital set from ref image by computing the surface (use -1 and +1 since the interval of append function are open)
  Z3i::DigitalSet set3dRef (imageA.domain()); 
  SetFromImage<Z3i::DigitalSet>::append<Image3D>(set3dRef, imageA, aMin-1,aMax);  
  typedef functors::NotPointPredicate<Z3i::DigitalSet> NegPredicate;
  
 
  // Applying the distance transform on the digital surface of the set: 
  typedef  DistanceTransformation<Z3i::Space, NegPredicate, Z3i::L2Metric> DTL2;
  const NegPredicate aPredicate( set3dRef );
  DTL2 dtL2( imageA.domain(), aPredicate, Z3i::l2Metric );
 
  // Get the set of point of imageB: (use -1 and +1 since the interval of append function are open)
  Z3i::DigitalSet set3dComp (imageB.domain()); 
  SetFromImage<Z3i::DigitalSet>::append<Image3D>(set3dComp, imageB, bMin-1, bMax);
 
  unsigned int nbAdded=0;
  double maxDist=0;
  //Applying stats from the set to be compared (from imageB)
  for(Z3i::DigitalSet::ConstIterator it= set3dComp.begin();  it!= set3dComp.end(); ++it){
    if((!statOnFalsePositiveOnly) || (isDiff(imageA, aMin, aMax, imageB, bMin, bMax, *it))){
      DTL2::Value distance = dtL2(*it);   
      stats.addValue(distance);
      nbAdded++;
      if(maxDist<distance){
        maxDist=distance;
        if(ptMax!=0){
          (*ptMax)[0]=(*it)[0]; 
          (*ptMax)[1]=(*it)[1];
          (*ptMax)[2]=(*it)[2];
        }
      }
    }
  }
  
  if(nbAdded==0)
    trace.error() << "No point added to statistics, will failed..." << endl;
}
 
 
void
getVoxelsStats(const Image3D &imageA,  int aMin, int aMax, const Image3D &imageB, 
               int bMin, int bMax, bool exportStatVoxels,  std::vector<Point> &vectPtBinA,  
               std::vector<Point> &vectPtCompBinCompA,  std::vector<Point> &vectPtBnotInA, 
               std::vector<Point> &vectPtnotBInA, bool precisionRecallFMean ){
  int numBinA = 0; // true positif with A as ref shape.
  int numCompBinCompA = 0; // true neg with A as ref shape.
  int numBnotInA = 0; // false pos with A as ref shape
  int numNotBinA = 0; // false neg with A as ref shape
  int numTotalInA = 0; // total pos in reference shape
  int numTotalInB = 0; // total pos in compared shape
  int numTotalinCompA = 0; //total in complement A 
  int numTotalinCompB = 0; //total in complement B
 
  for(Image3D::Domain::ConstIterator it = imageA.domain().begin(); it!=imageA.domain().end(); it++){
    // voxels in A
    if(imageA(*it) <= aMax && imageA(*it) >= aMin){
      numTotalInA++;
      //voxels in B 
      if(imageB(*it) <= bMax && imageB(*it) >= bMin){
        numTotalInB++;
        numBinA++;
        if(exportStatVoxels) vectPtBinA.push_back(*it);
      }else{
        numTotalinCompB++;
        numNotBinA++;
        if(exportStatVoxels) vectPtnotBInA.push_back(*it);
      }
      // voxels outside A
    }else{
      numTotalinCompA++;
      // voxels in B
      if(imageB(*it) <= bMax && imageB(*it) >= bMin){
        numBnotInA++;
        numTotalInB++;
        if(exportStatVoxels) vectPtBnotInA.push_back(*it);
      }else{
        numTotalinCompB++;
        numCompBinCompA++;
        if(exportStatVoxels) vectPtCompBinCompA.push_back(*it);
      }      
    }
  }
 
  std::cout << numBinA << " " << numCompBinCompA << " " << numBnotInA 
            << " " << numNotBinA  << " " << numTotalInA << " " 
            << numTotalInB << " " << numTotalinCompA << " " << numTotalinCompB;
  if(precisionRecallFMean){
    double precision = (double)numBinA/(numBinA + numBnotInA);
    double recall = (double)numBinA/(numBinA+numNotBinA);
    double fmean = (2.0*precision*recall)/(precision+recall);
    std::cout << " " << precision<<  " " << recall << " " << fmean ; 
  }
}
 
 
// total ref: True Positive, True Negative, False Positive, False Negative
void
getVoxelsStats(const Image3D &imageA,  int aMin, int aMax, const Image3D &imageB, 
               int bMin, int bMax, bool precisionRecallFMean ){
  std::vector<Point> v1, v2, v3, v4;
  return getVoxelsStats(imageA, aMin, aMax, imageB, bMin, bMax, false, v1, v2, v3, v4, precisionRecallFMean);
}
 
 
 
 
 
void 
exportSetofPoints(string filename, std::vector<Point> aVectPoint){
  std::ofstream ofs;
  ofs.open(filename.c_str(), std::ofstream::out );
  ofs<< "# Set of 3d points with format: x y z" << std::endl;
  for (unsigned int i =0; i< aVectPoint.size(); i++){
    ofs << aVectPoint.at(i)[0] << " " << aVectPoint.at(i)[1] << " "<< aVectPoint.at(i)[2] << std::endl;
  }
  ofs.close();
}
 
 
 
int main(int argc, char**argv)
{
 
  
  // parse command line ----------------------------------------------
  // A = ref
  // B= comp
  // parse command line using CLI ----------------------------------------------
  CLI::App app;
  std::string volAFilename;
  std::string volBFilename;
 
  int aMin {0};
  int aMax {128} ;
  int bMin {0};
  int bMax {128};
  bool noDistanceComparisons {false};
  bool distancesFromBnotInAOnly {false};
  bool displayTFstats {false};
  bool exportSDP {false};
  
  app.description("Apply shape measures for comparing two volumetric images A and B (shape defined from thresholds).\n It can compute: \n  - voxel count from voxel partition (number of voxel from (B-A), (A-B) ...): usefull to determine classical statistics like false positive related stats.\n - euclidean distance between two volumetric images A and B\n Basic usage: \t volShapeMetrics --volA <volAFilename> --volB <volBFilename>\nTypical use :\n  volShapeMetrics -a imageA.vol --aMin 128 --aMax 255 -b imageB.vol --bMin 128 --bMax 255 --distancesFromBnotInAOnly \n");
  
  
  
  app.add_option("-a,--volA,1", volAFilename, "Input filename of volume A (vol format, and other pgm3d can also be used)." )
  ->required()
  ->check(CLI::ExistingFile);
  
  app.add_option("-b,--volB,2", volBFilename, "Input filename of volume B (vol format, and other pgm3d can also be used).")
  ->required()
  ->check(CLI::ExistingFile);
  app.add_option("--aMin",aMin, "min threshold for a voxel to be considered as belonging to the object of volume A. (default 0)",true);
  app.add_option("--aMax",aMax, "max threshold for a voxel to be considered as belonging to the object of volume A. (default 128)",true);
 
  app.add_option("--bMin",bMin, "min threshold for a voxel to be considered as belonging to the object of volume B. (default 0)",true);
  app.add_option("--bMax",bMax, "max threshold for a voxel to be considered as belonging to the object of volume B. (default 128)",true);
 
  app.add_flag("--noDistanceComparisons", noDistanceComparisons, "to avoid to apply distance map computation if the distance comparaison are not needed.");
 
  app.add_flag("--distancesFromBnotInAOnly",distancesFromBnotInAOnly, "apply distance map measures only for voxels of B which are not in A (else the measure are given from all distances of the object B).");
  
  app.add_flag("--displayTFstats", displayTFstats, "Change the comparison diplay by using the  true/false/positive/negative notation and considering the shape A as reference. It also display precision/recall/f-mean statistics.");
  app.add_flag("--exportSDP", exportSDP, "Export voxels belonging to each categorie (voxels of ( B in A) , (NOT in B and NOT in A),   (B and NOT in A) and (Voxels of NOT in B and in A)).");
  
  
  app.get_formatter()->column_width(40);
  CLI11_PARSE(app, argc, argv);
  // END parse command line using CLI ----------------------------------------------
 
  
  Image3D imageA = GenericReader<Image3D>::import(volAFilename);
  Image3D imageB = GenericReader<Image3D>::import(volBFilename);
 
  std::cout << "# Shape comparisons (generated with volShapeMetrics) given with the reference shape A: "<< volAFilename
            << " (defined with threshold min: " << aMin << " and max: " << aMax << " )"<< endl
            << "# and with the compared shape B: "<< volBFilename << "  (defined with threshold min: " << bMin << " and max: " << bMax << " )"<< endl;
  if(displayTFstats){
    std::cout << "# #True_Positive #TrueNegative #FalsePositive #FalseNegative  #TotalinA #TotalInB #TotalComplementOfRef #TotalComplementOfComp Precision Recall F-Mean  ";
  }else{
    std::cout << "# #(Voxels of B in A) #(Voxels of NOT in B and NOT in A) #(Voxels of B and NOT in A)  #(Voxels of NOT in B and in A) #(Voxels in A) #(Voxels in B) #(Voxels not in A) #(Voxels not in B) ";
  }
  
  if(!noDistanceComparisons){
    std::cout << " Max(MinDistance(shape B to shape A) Mean(MinDistance(shape B to shape A) Variance(MinDistance(shape B to shape A)) "
              << " Mediane(MinDistance(shape B to shape A)  Farthest point of B to A ";
    if(distancesFromBnotInAOnly){
      std::cout << "*** for parts of B which are not in A only ***" ;
    }
  }
  std::cout << std::endl; 
 
  if(exportSDP){
    std::vector<Point> voxelsBinA, voxelsNotInBNotInA, voxelsBNotInA, voxelsNotInBInA; 
    if(displayTFstats){
      getVoxelsStats(imageA, aMin, aMax,  imageB,  bMin, bMax, true, voxelsBinA, voxelsNotInBNotInA, voxelsBNotInA, voxelsNotInBInA, true);    
      exportSetofPoints("truePos.sdp",  voxelsBinA);
      exportSetofPoints("trueNeg.sdp",  voxelsNotInBNotInA);
      exportSetofPoints("falsePos.sdp", voxelsBNotInA);
      exportSetofPoints("falseNeg.sdp", voxelsNotInBInA);
    }else{
      std::vector<Point> voxelsBinA, voxelsNotInBNotInA, voxelsBNotInA, voxelsNotInBInA; 
      getVoxelsStats(imageA, aMin, aMax,  imageB,  bMin, bMax, true, voxelsBinA, voxelsNotInBNotInA, voxelsBNotInA, voxelsNotInBInA, false);    
      exportSetofPoints("inBinA.sdp",  voxelsBinA);
      exportSetofPoints("notinBnotinA.sdp",  voxelsNotInBNotInA);
      exportSetofPoints("inBnotinA.sdp", voxelsBNotInA);
      exportSetofPoints("notinBinA.sdp", voxelsNotInBInA);
    }
  }else{
    getVoxelsStats(imageA, aMin, aMax,  imageB,  bMin, bMax, displayTFstats);
  }
  
  if(!noDistanceComparisons){
    trace.info() << "Computing Distance Map stats ...";
    Statistic<double> statDistances(true); 
    Point ptMax;
    getStatsFromDistanceMap(statDistances, imageA, aMin, aMax, imageB, bMin, bMax, false, &ptMax );
    std::cout << " " << statDistances.max() << " " << statDistances.mean()  << " " << statDistances.variance()  << "  "<< statDistances.median() << " " << ptMax[0] << " " << ptMax[1] << " " << ptMax[2] << std::endl; 
 
    trace.info() << " [done] " << std::endl;
  }    
   
   return 1;
}