Révision 28

lsm3D_compile.sh (revision 28)
1 1 
#! /bin/bash
2 2 

  		





  3
  3
  
    
bin_directory='../bin'


  		





  4
  
  
    
compiling_options=' -O2 -L/usr/X11R6/lib -lm -lpthread -lX11 '


  		





  
  4
  
    
compiling_options=' -O2 -lm -lpthread -lX11 '


  		





  5
  5
  
    

  		





  6
  6
  
    
cd src


  		





  7
  7
  
    
echo '------------------------------------'


  		












  

    
      src/lsm_cells.cpp	(revision 28)
    
  






  161
  161
  
    
      int bg_evolution=abs(new_backsegm-backsegm);


  		





  162
  162
  
    
	


  		





  163
  163
  
    
      // * if the evolution is less then evolution_min 3 consecutive times


  		





  164
  
  
    
      //if((it>10) and (bg_evolution<=evolution_min) and (bg_evolution>=evolution_max))


  		





  165
  164
  
    
      if((it>10) and (bg_evolution<=evolution_min) )


  		





  166
  165
  
    
	{


  		





  167
  166
  
    
	  it_stop+=1;


  		





  168
  167
  
    
	  if(it_stop>3)


  		





  169
  
  
    
	    {contour_evolve=false;


  		





  170
  
  
    
		cout<<"stopit "<<endl;}


  		





  
  168
  
    
	    {contour_evolve=false;}


  		





  171
  169
  
    
	}


  		





  172
  170
  
    
      else


  		





  173
  171
  
    
	{


  		





  ......




  177
  175
  
    

  		





  178
  176
  
    
      it+=1;


  		





  179
  177
  
    
      backsegm=new_backsegm;


  		





  180
  
  
    
      //cout<<"backsegm= "<<backsegm<<endl;     


  		





  181
  178
  
    
    }


  		





  182
  
  
    

  		





  183
  
  
    
//  cimg_forXYZ(psi,x,y,z)


  		





  184
  
  
    
//    {


  		





  185
  
  
    
//      if(psi(x,y,z)>=0){psi(x,y,z)=4;}


  		





  186
  
  
    
//      else{psi(x,y,z)=-4;}


  		





  187
  
  
    
//    }


  		





  188
  
  
    

  		





  189
  179
  
    
  return psi;


  		





  190
  180
  
    
}


  		





  191
  181
  
    

  		





  ......




  283
  273
  
    
  //Original image


  		





  284
  274
  
    
  CImg<char> description;


  		





  285
  275
  
    
  float tailleVoxel[3] = {0}; // resolution initialisation


  		





  286
  
  
    
  //float tailleVoxel[3] = {0.195177,0.195177,0.195177};


  		





  287
  276
  
    
  


  		





  288
  277
  
    
  bool gzipped=false;


  		





  289
  278
  
    
  


  		





  ......




  430
  419
  
    
  string outputdir=filename;


  		





  431
  420
  
    
  outputdir.erase(filename.size()-4);


  		





  432
  421
  
    
  string mkdir="mkdir -p "+outputdir;


  		





  433
  
  
    
  int syst=system(mkdir.c_str()); 


  		





  434
  
  
    
  mkdir="mkdir -p "+outputdir+"/evolution";


  		





  435
  
  
    
  syst=system(mkdir.c_str());


  		





  
  422
  
    
  if(system(mkdir.c_str())); 


  		





  436
  423
  
    

  		





  437
  
  
    
  string filename_cut=outputdir+"/evolution/"+filename;


  		





  438
  
  
    
  filename_cut.erase(filename_cut.size()-4);


  		





  
  424
  
    
  string filename_txt=outputdir+"/"+filename;


  		





  
  425
  
    
  filename_txt.erase(filename_txt.size()-4);


  		





  439
  426
  
    
  filename=outputdir+"/"+filename;


  		





  440
  427
  
    
  string wat_eroded_name=filename;


  		





  441
  428
  
    
  wat_eroded_name.insert(filename.size()-4,"_eroded");


  		





  ......




  446
  433
  
    

  		





  447
  434
  
    
  //txt files 


  		





  448
  435
  
    
  ofstream file;


  		





  449
  
  
    
  string txt_name=filename_cut+".txt";


  		





  
  436
  
    
  string txt_name=filename_txt+".txt";


  		





  450
  437
  
    
  file.open(txt_name.c_str());


  		





  451
  438
  
    
  file<<argv[0]<<endl;


  		





  452
  439
  
    
  time_t t;


  		





  ......




  474
  461
  
    
  file<<"timestep_max : "<<timestep_max <<endl;


  		





  475
  462
  
    

  		





  476
  463
  
    
  //-----------------------------------------Image Pre-processing


  		





  477
  
  
    
  //define cut


  		





  478
  
  
    
  int cut=img._depth/2;


  		





  479
  
  
    
  cut = 82;


  		





  480
  
  
    
  cout <<"cut z= "<<cut<<endl;


  		





  481
  
  
    
  file <<"\ncut z= "<<cut<<endl;


  		





  482
  
  
    
  CImg<float> imgCut=img.get_crop(0,0,cut,0,img._width,img._height,cut,0);


  		





  483
  
  
    
  imgCut.save((filename_cut+".png").c_str());


  		





  484
  464
  
    

  		





  485
  465
  
    
  //smooth image


  		





  486
  466
  
    
  file<<"smooth : "<<smooth<<endl;


  		





  ......




  510
  490
  
    
  CImgList<float> gg=gradient(g);


  		





  511
  491
  
    
  CImg<float> h=g;


  		





  512
  492
  
    
  img.assign();


  		





  513
  
  
    

  		





  514
  493
  
    
  


  		





  515
  
  
    
  CImg<float> gout=g;


  		





  516
  
  
    
  gout.crop(0,0,cut,0,g._width,g._height,cut,0);


  		





  517
  
  
    
  gout.normalize(0,255).save((filename_cut+"_edge_indicator.png").c_str());


  		





  518
  
  
    
  gout.assign();


  		





  519
  
  
    
  


  		





  520
  494
  
    
  //initialize psi for every cell


  		





  521
  495
  
    
  int maxcells=wat.max()+1; //indice maximum  


  		





  522
  496
  
    
  vector<int> list=index(wat,maxcells);


  		





  ......




  540
  514
  
    
      min_list[i][0]=xmin;


  		





  541
  515
  
    
      min_list[i][1]=ymin;


  		





  542
  516
  
    
      min_list[i][2]=zmin;


  		





  543
  
  
    
      cout <<"cell "<<ind<<endl;


  		





  
  517
  
    
      cout <<"cell "<<ind<<" initialised."<<endl;


  		





  544
  518
  
    
    }


  		





  545
  519
  
    
  }


  		





  546
  520
  
    
  wat.assign();


  		





  547
  521
  
    

  		





  548
  
  
    
  //reconstruct image of eroded cell


  		





  
  522
  
    
  //reconstruct image of eroded cells


  		





  549
  523
  
    
  CImg<unsigned short> wat_eroded=reconstruct(background,psi_list,min_list,nbcells,list);


  		





  
  524
  
    
  cout <<"saving file "<<wat_eroded_name<<"..."<<endl;


  		





  550
  525
  
    
  wat_eroded.save_inr(wat_eroded_name.c_str(),tailleVoxel);


  		





  551
  526
  
    
  string zip="gzip -f "+wat_eroded_name;


  		





  552
  
  
    
  syst=system(zip.c_str());


  		





  553
  
  
    
  wat_eroded.crop(0,0,cut,0,wat_eroded._width,wat_eroded._height,cut,0);


  		





  554
  
  
    
  wat_eroded.normalize(0,255).save((filename_cut+"_eroded.png").c_str());


  		





  555
  
  
    
  wat_eroded.assign();


  		





  
  527
  
    
  if(system(zip.c_str()));


  		





  
  528
  
    
  cout <<"Eroded watershed segmentation saved in file:"<<wat_eroded_name<<endl;


  		





  556
  529
  
    

  		





  557
  530
  
    
  //Segmented inital = background segmentation


  		





  558
  531
  
    
  CImg<unsigned char> segmented=background;


  		





  559
  532
  
    

  		





  560
  533
  
    
  double end1=omp_get_wtime();


  		





  561
  534
  
    
  double time1=double(end1-begin);


  		





  562
  
  
    
  cout<<"initialization with erosion : "<<time1<<endl;


  		





  563
  
  
    
  file<<"\ninitialization with erosion : "<<time1<<endl;


  		





  564
  535
  
    
  cout<<"Evolving cells..... "<<endl;


  		





  
  536
  
    
  


  		





  565
  537
  
    
  //---------------------------------------------------------Edge detection


  		





  566
  538
  
    
  //evolve each cell one by one, attract to maximal gradient


  		





  567
  539
  
    
#pragma omp parallel shared(psi_list,min_list,g,gg,h,lam,mu,alf,beta,epsilon,dt,list)


  		





  ......




  570
  542
  
    
  for(int i=0;i<nbcells;i++) 


  		





  571
  543
  
    
    {


  		





  572
  544
  
    
      psi_list[i]=lsm_segment2(psi_list[i],g,gg,h,lam,mu,alf,beta,epsilon,dt,min_list[i]);


  		





  573
  
  
    
      cout <<"cell evolution "<<list[i]<<endl;


  		





  
  545
  
    
      cout <<"cell "<<list[i]<<" evolved."<<endl;


  		





  574
  546
  
    
    }


  		





  575
  547
  
    
  }


  		





  576
  548
  
    

  		





  ......




  579
  551
  
    
  CImg<unsigned short> edge=reconstruct_overlap(background,psi_list,min_list,nbcells,free,list);


  		





  580
  552
  
    
  edge.save_inr(edge_detection_name.c_str(),tailleVoxel);


  		





  581
  553
  
    
  zip="gzip -f "+edge_detection_name;


  		





  582
  
  
    
  syst=system(zip.c_str());


  		





  583
  
  
    
  edge.crop(0,0,cut,0,edge._width,edge._height,cut,0);


  		





  584
  
  
    
  edge.normalize(0,255).save((filename_cut+"_evoEdge.png").c_str());


  		





  585
  
  
    
  


  		





  
  554
  
    
  if(system(zip.c_str()));


  		





  586
  555
  
    

  		





  587
  
  
    

  		





  
  556
  
    
// time measurements


  		





  588
  557
  
    
  double end2=omp_get_wtime();


  		





  589
  558
  
    
  double time2=double(end2-begin);


  		





  590
  
  
    
  cout<<"edge detection : "<<time2<<endl;


  		





  591
  
  
    
  file<<"edge detection : "<<time2<<endl;


  		





  592
  
  
    

  		





  593
  
  
    

  		





  
  559
  
    
  


  		





  594
  560
  
    
  double end=omp_get_wtime();


  		





  595
  561
  
    
  double time=double(end-begin);


  		





  596
  
  
    
  cout<<"total time : "<<time<<" (~"<<time/60<<" mn  ~"<<time/60/60<<" h)"<<endl;


  		





  597
  
  
    
  cout<<"initialization with erosion : "<<time1<<endl;


  		





  598
  
  
    
  cout<<"edge detection : "<<time2<<endl;


  		





  599
  
  
    
  file<<"total time : "<<time<<" (~"<<time/60<<" mn  ~"<<time/60/60<<" h)"<<endl;


  		





  600
  
  
    
  file<<"initialization with erosion : "<<time1<<endl;


  		





  601
  
  
    
  file<<"edge detection : "<<time2<<endl;


  		





  
  562
  
    
  cout<<"total time : "<<time<<"s"<<" (~"<<time/60<<" mn  ~"<<time/60/60<<" h)"<<endl;


  		





  
  563
  
    
  cout<<"-initialization with erosion : "<<time1<<"s"<<endl;


  		





  
  564
  
    
  cout<<"-edge detection : "<<time2<<"s"<<endl;


  		





  
  565
  
    
  file<<"total time : "<<time<<"s"<<" (~"<<time/60<<" mn  ~"<<time/60/60<<" h)"<<endl;


  		





  
  566
  
    
  file<<"-initialization with erosion : "<<time1<<"s"<<endl;


  		





  
  567
  
    
  file<<"-edge detection : "<<time2<<"s"<<endl;


  		





  602
  568
  
    
  file.close();


  		





  603
  569
  
    

  		





  604
  570
  
    
  return 0;


  		












  

    
      src/lsm_contour.cpp	(revision 28)
    
  






  116
  116
  
    
  outputdir.erase(filename.size()-4);


  		





  117
  117
  
    
  string mkdir="mkdir -p "+outputdir;


  		





  118
  118
  
    
  systout=system(mkdir.c_str()); 


  		





  119
  
  
    
  mkdir="mkdir -p "+outputdir+"/evolution";


  		





  120
  
  
    
  systout=system(mkdir.c_str());


  		





  121
  119
  
    

  		





  122
  
  
    
  string filename_cut=outputdir+"/evolution/"+filename;


  		





  123
  
  
    
  filename_cut.erase(filename_cut.size()-4);


  		





  
  120
  
    
  string filename_txt=outputdir+"/"+filename;


  		





  
  121
  
    
  filename_txt.erase(filename_txt.size()-4);


  		





  124
  122
  
    
  filename=outputdir+"/"+filename;


  		





  125
  123
  
    
  string result_name=filename;


  		





  126
  124
  
    

  		





  127
  125
  
    
  //txt files 


  		





  128
  126
  
    
  ofstream file;


  		





  129
  
  
    
  string txt_name=filename_cut+".txt";


  		





  
  127
  
    
  string txt_name=filename_txt+".txt";


  		





  130
  128
  
    
  file.open(txt_name.c_str());


  		





  131
  129
  
    
  file<<argv[0]<<endl;


  		





  132
  130
  
    
  time_t t;


  		





  ......




  150
  148
  
    
  file<<"perDown : "<<perDown<<endl;


  		





  151
  149
  
    

  		





  152
  150
  
    
  ofstream bg_file;


  		





  153
  
  
    
  string bg_name=filename_cut+"_BGgrowth.txt";


  		





  
  151
  
    
  string bg_name=filename_txt+"_BGgrowth.txt";


  		





  154
  152
  
    
  bg_file.open(bg_name.c_str());


  		





  155
  153
  
    
  bg_file<<"it\tbg_growth"<<endl;


  		





  156
  154
  
    

  		





  ......




  158
  156
  
    
  //add slices


  		





  159
  157
  
    
  img=add_side_slices(img,3);


  		





  160
  158
  
    

  		





  161
  
  
    
  //define and save cut


  		





  162
  
  
    
  int cut=img._depth/2;


  		





  163
  
  
    
  cout <<"cut z= "<<cut<<endl;


  		





  164
  
  
    
  file <<"\ncut z= "<<cut<<endl;


  		





  165
  
  
    
  CImg<float> imgCut=img.get_crop(0,0,cut,0,img._width,img._height,cut,0);


  		





  166
  
  
    
  imgCut.save((filename_cut+".png").c_str());


  		





  167
  
  
    

  		





  168
  159
  
    
  //smooth image


  		





  169
  160
  
    
  file<<"smooth : "<<smooth<<endl;


  		





  170
  161
  
    
  img.blur(smooth);


  		





  ......




  231
  222
  
    
	  it_stop=0;


  		





  232
  223
  
    
	}


  		





  233
  224
  
    

  		





  234
  
  
    
      //Graphics to follow evolution


  		





  235
  
  
    
      if((it%50==0)or(contour_evolves==false)or(it==timestep_max-1))


  		





  236
  
  
    
	{


  		





  237
  
  
    
	  ostringstream oss;


  		





  238
  
  
    
	  oss << it;


  		





  239
  
  
    
	  string iterstring="";


  		





  240
  
  
    
	  if(it<10) {iterstring="00"+oss.str();}


  		





  241
  
  
    
	  else if (it<100) {iterstring="0"+oss.str();}


  		





  242
  
  
    
	  else {iterstring=oss.str();}


  		





  243
  
  
    
	  cout<<"-----------------------------------"<<endl;


  		





  244
  
  
    
	  cout<<" *** time step for graphics : "<<iterstring<<endl;


  		





  245
  
  
    
	  //Save cut


  		





  246
  
  
    
	  CImg<float>segCut=segmented.get_crop(0,0,cut,0,img._width,img._height,cut,0);


  		





  247
  
  
    
	  string temp_name=filename_cut+"it"+iterstring+".png";


  		





  248
  
  
    
	  segCut.normalize(0,255).save(temp_name.c_str());


  		





  249
  
  
    
	}


  		





  
  225
  
    
    //Save result


  		





  250
  226
  
    
      if((((it%50)==0)and(it!=0))or(contour_evolves==false)or(it==timestep_max-1))


  		





  251
  
  
    
	{


  		





  252
  
  
    
	  //Save result


  		





  
  227
  
    
	{	  


  		





  253
  228
  
    
	  CImg<unsigned char>segSave=remove_side_slices(segmented,3);


  		





  254
  229
  
    
	  segSave.save_inr(result_name.c_str(),tailleVoxel);


  		





  255
  230
  
    
	  segSave.assign();


  		












Formats disponibles :
  Unified diff