Révision 28 src/lsm_cells.cpp
| lsm_cells.cpp (revision 28) | ||
|---|---|---|
| 161 | 161 |
int bg_evolution=abs(new_backsegm-backsegm); |
| 162 | 162 |
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| 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)) |
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| 165 | 164 |
if((it>10) and (bg_evolution<=evolution_min) ) |
| 166 | 165 |
{
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| 167 | 166 |
it_stop+=1; |
| 168 | 167 |
if(it_stop>3) |
| 169 |
{contour_evolve=false;
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| 170 |
cout<<"stopit "<<endl;} |
|
| 168 |
{contour_evolve=false;}
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| 171 | 169 |
} |
| 172 | 170 |
else |
| 173 | 171 |
{
|
| ... | ... | |
| 177 | 175 |
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| 178 | 176 |
it+=1; |
| 179 | 177 |
backsegm=new_backsegm; |
| 180 |
//cout<<"backsegm= "<<backsegm<<endl; |
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| 181 | 178 |
} |
| 182 |
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// cimg_forXYZ(psi,x,y,z) |
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| 184 |
// {
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// if(psi(x,y,z)>=0){psi(x,y,z)=4;}
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// else{psi(x,y,z)=-4;}
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// } |
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| 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};
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| 287 | 276 |
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| 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()); |
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mkdir="mkdir -p "+outputdir+"/evolution"; |
|
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syst=system(mkdir.c_str()); |
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| 422 |
if(system(mkdir.c_str())); |
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| 436 | 423 |
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string filename_cut=outputdir+"/evolution/"+filename;
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filename_cut.erase(filename_cut.size()-4);
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string filename_txt=outputdir+"/"+filename;
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| 425 |
filename_txt.erase(filename_txt.size()-4);
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| 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";
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| 436 |
string txt_name=filename_txt+".txt";
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| 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 |
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| 478 |
int cut=img._depth/2; |
|
| 479 |
cut = 82; |
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| 480 |
cout <<"cut z= "<<cut<<endl; |
|
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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()); |
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| 484 | 464 |
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| 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 |
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| 514 | 493 |
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| 515 |
CImg<float> gout=g; |
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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 |
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| 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;
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| 544 | 518 |
} |
| 545 | 519 |
} |
| 546 | 520 |
wat.assign(); |
| 547 | 521 |
|
| 548 |
//reconstruct image of eroded cell |
|
| 522 |
//reconstruct image of eroded cells
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| 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 |
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| 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; |
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| 564 | 535 |
cout<<"Evolving cells..... "<<endl; |
| 536 |
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| 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;
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|
| 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 |
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|
| 554 |
if(system(zip.c_str())); |
|
| 586 | 555 |
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| 587 |
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|
| 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 |
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| 593 |
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|
| 559 |
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| 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;
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|
| 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;
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| 564 |
cout<<"-edge detection : "<<time2<<"s"<<endl;
|
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| 565 |
file<<"total time : "<<time<<"s"<<" (~"<<time/60<<" mn ~"<<time/60/60<<" h)"<<endl;
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| 566 |
file<<"-initialization with erosion : "<<time1<<"s"<<endl;
|
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| 567 |
file<<"-edge detection : "<<time2<<"s"<<endl;
|
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| 602 | 568 |
file.close(); |
| 603 | 569 |
|
| 604 | 570 |
return 0; |
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