LabelImageType::Pointer getYousefSegmented(InputImageType::Pointer im_input,std::list<Seed> &seed_list,char *filename)
{
// copy the image into a unsigned char *
char configfile[1024];
strcpy(configfile,filename);
printf("Entering YousefSeg\n");
InputImageType::SizeType size = im_input->GetLargestPossibleRegion().GetSize();
unsigned char * in_Image;
in_Image = (unsigned char*) malloc( size[0]*size[1]*(size[2]+1)*sizeof(unsigned char));
if(in_Image == NULL)
{
printf("Couldn't allocate memory\n");
}
memset(in_Image,0,size[0]*size[1]*(size[2]+1)*sizeof(unsigned char));
ConstIteratorType pix_buf(im_input,im_input->GetLargestPossibleRegion());
int ind = 0;
for ( pix_buf.GoToBegin(); !pix_buf.IsAtEnd(); ++pix_buf, ++ind )
in_Image[ind]=(pix_buf.Get());
printf("Copied input data\n");
yousef_nucleus_seg *NucleusSeg = new yousef_nucleus_seg();
NucleusSeg->readParametersFromFile(configfile);
NucleusSeg->setDataImage(in_Image,size[0],size[1],size[2]+1,"null");
unsigned short * output_img;
// int *bounds_img;
NucleusSeg->runBinarization();
output_img = NucleusSeg->getBinImage();
// getITKImage(output_img);
// getProcessedBinaryImage(
NucleusSeg->runSeedDetection();
std::vector<Seed> seeds = NucleusSeg->getSeeds();
printf("In yousef_seg Seed size = %d\n", (int)seeds.size());
std::vector<Seed>::iterator iter = seeds.begin();
for(;iter!=seeds.end();iter++)
{
seed_list.push_back(*iter);
}
NucleusSeg->runClustering();
printf("Finished Clustering\n");
if(NucleusSeg->isSegmentationFinEnabled())
{
NucleusSeg->runAlphaExpansion3D();
output_img=NucleusSeg->getSegImage();
}
else
{
output_img=NucleusSeg->getClustImage();
}
// bounds_img = NucleusSeg->getBoundsImage();
printf("Finished segmentation\n");
LabelImageType::Pointer label = LabelImageType::New();
label->SetRegions(im_input->GetLargestPossibleRegion());
label->Allocate();
LabelIteratorType liter(label,label->GetLargestPossibleRegion());
ind = 0;
for(liter.GoToBegin();!liter.IsAtEnd();++liter,++ind)
{
liter.Set(output_img[ind]);
}
delete NucleusSeg;
free(in_Image);
return label;
}
