Révision 24 src/lsm_cells.cpp
| lsm_cells.cpp (revision 24) | ||
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Parallel standard version |
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To compile : |
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g++ -o lsm_cells_20160610.exe lsm_cells_20160610.cpp -O2 -L/usr/X11R6/lib -lm -lpthread -lX11 -fopenmp
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g++ -o lsm_cells lsm_cells.cpp -O2 -L/usr/X11R6/lib -lm -lpthread -lX11 -fopenmp
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Need CImg.h and lsm_lib.h |
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To execute : |
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./lsm_cells.exe img img_wat img_contour erosion
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./lsm_cells img img_wat img_contour erosion |
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image in .inr or .inr.gz, save in .inr.gz |
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img : grayscale image of cells (unsigned char) |
| ... | ... | |
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//Stop criteria |
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int bg_evolution=abs(new_backsegm-backsegm); |
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/* |
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if((it>20)and(bg_evolution<evolution_min)) |
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{contour_evolve=false;}
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*/ |
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//New stop criteria |
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if((it>10) and (bg_evolution<=evolution_min) and (bg_evolution>=evolution_max)) |
| ... | ... | |
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if(argc<5) |
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{
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cout<<"!! wrong number of arguments ("<<argc<<")"<<endl;
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cout<<"how to execute : ./lsm_cells.exe img img_wat img_contour erosion [a b smooth lsm_type]"<<endl;
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cout<<"Usage : lsm_cells img img_wat img_contour erosion [a b smooth lsm_type]"<<endl;
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cout<<"----------------- "<<endl; |
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cout<<"img : grayscale image of cells, (.inr or .inr.gz)"<<endl; |
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cout<<"img_wat : image of seeds, (.inr or .inr.gz)"<<endl; |
| ... | ... | |
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cout<<" if negative, the object retracts"<<endl; |
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cout<<" if positive, the object inflates"<<endl; |
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cout<<"b : curvature term (float) --> 0 or 1 (the default is 0)"<<endl; |
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cout<<"gamma : scale parameter (float>0) --> 0.5 or 1 (the default is 0)"<<endl;
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cout<<"gamma : scale parameter (float>0) --> 0.5 or 1 (the default is 1)"<<endl;
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cout<<"smooth : gaussian blur to apply to the image (int) --> 0 or 1 (the default is 0)"<<endl; |
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cout<<"lsm_type : image, gradient or hessien based evolution --> 'i', 'g' or 'h' (the default is g)"<<endl; |
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return 0; |
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//---------------------------------------------------------------Parameters |
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//model parameters |
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//int alfabis=100; |
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//float betabis=0; |
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int c0=-4; |
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int erosion=atoi(argv[4]); |
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//------------------------------------Names and directories |
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//new name with arguments |
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//string ar=argv[4]; |
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//string insert="_cellLSM-d"+ar; |
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filename.insert(filename.size()-4,insert); |
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//create directories and update names |
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CImgList<float> gg=gradient(g); |
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CImg<float> h=g; |
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img.assign(); |
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// save edge indicator |
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string edge_indicator_name = "edge_indicator.inr"; |
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g.save_inr(edge_indicator_name.c_str(),tailleVoxel); |
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string zip="gzip -f "+edge_indicator_name; |
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syst=system(zip.c_str()); |
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//g.crop(0,0,cut,0,g._width,g._height,cut,0); |
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//g.normalize(0,255).save((filename_cut+"_edge_indicator.png").c_str()); |
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// warning !!! once normalised, one cannot do computations with it |
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CImg<float> gout=g; |
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gout.crop(0,0,cut,0,g._width,g._height,cut,0); |
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gout.normalize(0,255).save((filename_cut+"_edge_indicator.png").c_str()); |
| ... | ... | |
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//reconstruct image of eroded cell |
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CImg<unsigned short> wat_eroded=reconstruct(background,psi_list,min_list,nbcells,list); |
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wat_eroded.save_inr(wat_eroded_name.c_str(),tailleVoxel); |
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zip="gzip -f "+wat_eroded_name; |
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string zip="gzip -f "+wat_eroded_name;
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syst=system(zip.c_str()); |
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wat_eroded.crop(0,0,cut,0,wat_eroded._width,wat_eroded._height,cut,0); |
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wat_eroded.normalize(0,255).save((filename_cut+"_eroded.png").c_str()); |
| ... | ... | |
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file<<"edge detection : "<<time2<<endl; |
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/* |
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//--------------------------------------------------------Edge evolution |
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//evolve every cell to fill the gaps |
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lam=0; |
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alf=alfabis; |
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beta=betabis; |
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bool contour_evolve=true; |
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float backsegm=free.sum(); |
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int it=0; |
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int it_stop=0; |
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while((it<timestep_max)and(contour_evolve==true)) |
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{
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//each cell evolve one time step |
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#pragma omp parallel shared(psi_list,min_list,g,gg,h,lam,mu,alf,beta,epsilon,dt,free) |
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{
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#pragma omp for schedule(dynamic) |
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for(int i=0;i<nbcells;i++) |
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{
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psi_list[i]=evolution_AK2_contour_interact(psi_list[i],g,gg,h,lam,mu,alf,beta,epsilon,dt,free,min_list[i]); |
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} |
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} |
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//reconstruct image of edge detection, overlap=not segmented |
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edge=reconstruct_overlap(background,psi_list,min_list,nbcells,free,list); |
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//bg evolution |
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float newsegm=free.sum(); |
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float bg_evolution=newsegm-backsegm; |
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backsegm=newsegm; |
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//stop criteria |
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//double stop_criteria=size-newsegm; |
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if((it>40)and(abs(bg_evolution)<1)) |
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{
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contour_evolve=false; |
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} |
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//save |
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if(((it%100==0)and(it!=0))or(contour_evolve==false)or(it==timestep_max-1)) |
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{
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edge.save_inr(edge_evolve_name.c_str(),tailleVoxel); |
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zip="gzip -f "+edge_evolve_name; |
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syst=system(zip.c_str()); |
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CImg<unsigned short> edgeCrop=edge.get_crop(0,0,cut,0,edge._width,edge._height,cut,0); |
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edgeCrop.normalize(0,255).save((filename_cut+"_final.png").c_str()); |
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} |
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cout<<"it "<<it<<" evo "<<bg_evolution<<endl; |
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it+=1; |
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} |
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*/ |
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double end=omp_get_wtime(); |
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double time=double(end-begin); |
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cout<<"total time : "<<time<<" (~"<<time/60<<" mn ~"<<time/60/60<<" h)"<<endl; |
Formats disponibles : Unified diff