/ - Diff - lsm3d - Forge du Centre Blaise Pascal

Révision 24

     cd src
     echo '------------------------------------'
     echo 'compiling lsm_detect_contour...'
     g++ -o $bin_directory/lsm_detect_contour.exe lsm_detect_contour.cpp $compiling_options
     g++ -o $bin_directory/lsm_detect_contour lsm_detect_contour.cpp $compiling_options
     echo 'compiling lsm_cells...'
     g++ -o $bin_directory/lsm_cells.exe lsm_cells.cpp $compiling_options -lX11 -fopenmp
     g++ -o $bin_directory/lsm_cells lsm_cells.cpp $compiling_options -lX11 -fopenmp
     echo 'Done!'
     cd ..

     Stop criteria parameters in command lines
     To compile
      g++ -o lsm_detect_contour_full.exe lsm_detect_contour_full.cpp -O2 -L/usr/X11R6/lib -lm -lpthread -lX11 -l:libtiff.so.5
      g++ -o lsm_detect_contour lsm_detect_contour_full.cpp -O2 -L/usr/X11R6/lib -lm -lpthread -lX11 -l:libtiff.so.5
      Need CImg.h and lsm_lib.h
     To execute
-...
       if(argc!=9)
+        {
           cout<<"!! wrong number of arguments"<<endl;
           cout<<"Usage : ./xxxx.exe img t_up t_down a b smooth perUp perDown"<<endl;
           cout<<"Usage : lsm_detect_contour img t_up t_down a b smooth perUp perDown"<<endl;
           cout<<"Examples for parameter values:"<<endl;
           cout<<"------------------------------"<<endl;
           cout<<"img : grayscale image of cells, (.inr or .inr.gz)"<<endl;
           cout<<"Upper threshold : t_up = 20"<<endl;
           cout<<"Down threshold : t_down = 5"<<endl;
           cout<<"Area term : a = 0 (0.5, 1)"<<endl;

     Parallel standard version
     To compile :
      g++ -o lsm_cells_20160610.exe lsm_cells_20160610.cpp -O2 -L/usr/X11R6/lib -lm -lpthread -lX11 -fopenmp
      g++ -o lsm_cells lsm_cells.cpp -O2 -L/usr/X11R6/lib -lm -lpthread -lX11 -fopenmp
      Need CImg.h and lsm_lib.h
     To execute :
      ./lsm_cells.exe img img_wat img_contour erosion
      ./lsm_cells img img_wat img_contour erosion
      image in .inr or .inr.gz, save in .inr.gz
      img : grayscale image of cells (unsigned char)
-...
           //Stop criteria
           int bg_evolution=abs(new_backsegm-backsegm);
           /*
           if((it>20)and(bg_evolution<evolution_min))
     	{contour_evolve=false;}
     	*/
           //New stop criteria
           if((it>10) and (bg_evolution<=evolution_min) and (bg_evolution>=evolution_max))
-...
       if(argc<5)
+        {
         cout<<"!! wrong number of arguments ("<<argc<<")"<<endl;
         cout<<"how to execute : ./lsm_cells.exe img img_wat img_contour erosion [a b smooth lsm_type]"<<endl;
         cout<<"Usage : lsm_cells img img_wat img_contour erosion [a b smooth lsm_type]"<<endl;
         cout<<"----------------- "<<endl;
     	cout<<"img : grayscale image of cells, (.inr or .inr.gz)"<<endl;
     	cout<<"img_wat : image of seeds, (.inr or .inr.gz)"<<endl;
-...
     	cout<<"              if negative, the object retracts"<<endl;
     	cout<<"              if positive, the object inflates"<<endl;
     	cout<<"b : curvature term (float) --> 0 or 1 (the default is 0)"<<endl;
     	cout<<"gamma : scale parameter (float>0) --> 0.5 or 1 (the default is 0)"<<endl;
     	cout<<"gamma : scale parameter (float>0) --> 0.5 or 1 (the default is 1)"<<endl;
     	cout<<"smooth : gaussian blur to apply to the image (int) --> 0 or 1 (the default is 0)"<<endl;
         cout<<"lsm_type : image, gradient or hessien based evolution --> 'i', 'g' or 'h' (the default is g)"<<endl;
           return 0;
-...
       //---------------------------------------------------------------Parameters
       //model parameters
       //int alfabis=100;
       //float betabis=0;
       int c0=-4;
       int erosion=atoi(argv[4]);
-...
       //------------------------------------Names and directories
       //new name with arguments
       //string ar=argv[4];
       //string insert="_cellLSM-d"+ar;
       filename.insert(filename.size()-4,insert);
       //create directories and update names
-...
       CImgList<float> gg=gradient(g);
       CImg<float> h=g;
       img.assign();
       // save edge indicator
       string edge_indicator_name = "edge_indicator.inr";
       g.save_inr(edge_indicator_name.c_str(),tailleVoxel);
       string zip="gzip -f "+edge_indicator_name;
       syst=system(zip.c_str());
       //g.crop(0,0,cut,0,g._width,g._height,cut,0);
       //g.normalize(0,255).save((filename_cut+"_edge_indicator.png").c_str());
       // warning !!! once normalised, one cannot do computations with it
       CImg<float> gout=g;
       gout.crop(0,0,cut,0,g._width,g._height,cut,0);
       gout.normalize(0,255).save((filename_cut+"_edge_indicator.png").c_str());
-...
       //reconstruct image of eroded cell
       CImg<unsigned short> wat_eroded=reconstruct(background,psi_list,min_list,nbcells,list);
       wat_eroded.save_inr(wat_eroded_name.c_str(),tailleVoxel);
       zip="gzip -f "+wat_eroded_name;
       string zip="gzip -f "+wat_eroded_name;
       syst=system(zip.c_str());
       wat_eroded.crop(0,0,cut,0,wat_eroded._width,wat_eroded._height,cut,0);
       wat_eroded.normalize(0,255).save((filename_cut+"_eroded.png").c_str());
-...
       file<<"edge detection : "<<time2<<endl;
     /*
       //--------------------------------------------------------Edge evolution
       //evolve every cell to fill the gaps
       lam=0;
       alf=alfabis;
       beta=betabis;
       bool contour_evolve=true;
       float backsegm=free.sum();
       int it=0;
       int it_stop=0;
       while((it<timestep_max)and(contour_evolve==true))
+        {
           //each cell evolve one time step
     #pragma omp parallel shared(psi_list,min_list,g,gg,h,lam,mu,alf,beta,epsilon,dt,free)
+          {
     #pragma omp for schedule(dynamic)
     	for(int i=0;i<nbcells;i++)
+    	  {
     	  psi_list[i]=evolution_AK2_contour_interact(psi_list[i],g,gg,h,lam,mu,alf,beta,epsilon,dt,free,min_list[i]);
+    	  }
+          }
           //reconstruct image of edge detection, overlap=not segmented
           edge=reconstruct_overlap(background,psi_list,min_list,nbcells,free,list);
           //bg evolution
           float newsegm=free.sum();
           float bg_evolution=newsegm-backsegm;
           backsegm=newsegm;
           //stop criteria
           //double stop_criteria=size-newsegm;
           if((it>40)and(abs(bg_evolution)<1))
+    	{
     	    contour_evolve=false;
+    	}
           //save
           if(((it%100==0)and(it!=0))or(contour_evolve==false)or(it==timestep_max-1))
+    	{
     	  edge.save_inr(edge_evolve_name.c_str(),tailleVoxel);
     	  zip="gzip -f "+edge_evolve_name;
     	  syst=system(zip.c_str());
     	  CImg<unsigned short> edgeCrop=edge.get_crop(0,0,cut,0,edge._width,edge._height,cut,0);
     	  edgeCrop.normalize(0,255).save((filename_cut+"_final.png").c_str());
+    	}
           cout<<"it "<<it<<" evo "<<bg_evolution<<endl;
           it+=1;
+        }
     */
       double end=omp_get_wtime();
       double time=double(end-begin);
       cout<<"total time : "<<time<<" (~"<<time/60<<" mn  ~"<<time/60/60<<" h)"<<endl;

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Laboratoire RDP » Biophysics Team » lsm3d

Révision 24