int main(int argc, char **argv)
{
if(argc <5)
{
std::cout<<"Usage: mixture_segment <MixtureLabelImageFileName> <OutputMixtureLabelImageFileName> <volume1> <volume2>\n";
return 0;
}
// read the parameters //
std::string ifName = argv[1];
std::string ofName = argv[2];
unsigned int volume1 = atoi(argv[3]); // minimum area1 of the large components
unsigned int volume2 = atoi(argv[4]); // minimum area2 of the small components ( heads of the cells )
printf("volume1: %d\t",volume1);
printf("volume2: %d\n",volume2);
// read input image:
LabelImageType::Pointer mixtureLabelImage = readImage<LabelImageType>(ifName.c_str());
LabelPixelType nr = mixtureLabelImage->GetLargestPossibleRegion().GetSize()[0];
LabelPixelType nc = mixtureLabelImage->GetLargestPossibleRegion().GetSize()[1];
LabelPixelType ns = mixtureLabelImage->GetLargestPossibleRegion().GetSize()[2];
LabelPixelType * mixtureLabelImagePtr = mixtureLabelImage->GetBufferPointer();
//generate label image
LabelImageType::SizeType size;
size[0] = nr;
size[1] = nc;
size[2] = ns;
LabelImageType::Pointer outputImage = GetITKImageOfSize<LabelImageType>(size);
LabelPixelType * outputImagePtr = outputImage->GetBufferPointer();
// parameters for 2D image
LabelImageType::SizeType sz2;
sz2[0] = nr;
sz2[1] = nc;
sz2[2] = 1;
unsigned int sz = nr*nc;
//bool FoundLabel = true;
omp_set_num_threads(1);
itk::MultiThreader::SetGlobalDefaultNumberOfThreads(1);
#pragma omp parallel for num_threads(80)
for(size_t t = 0; t<ns; ++t)
{
LabelImageType::Pointer output2DImage = GetITKImageOfSize<LabelImageType>(sz2);
LabelPixelType * output2DImagePtr = output2DImage->GetBufferPointer();
unsigned int i;
LabelImageType::Pointer binaryLabelImage = GetITKImageOfSize<LabelImageType>(sz2);
LabelPixelType * binaryLabelImagePtr = binaryLabelImage->GetBufferPointer();
size_t offset = t*((nr*nc));
// first mixture
for(i = 0; i < sz; ++i)
{
if(mixtureLabelImagePtr[i+offset]>0)
{
binaryLabelImagePtr[i] = 1;
//printf("set pixel to one\n");
}
else
{
binaryLabelImagePtr[i] = 0;
}
}
// well size is 90x90: if any of the connected components is larger than that it meas something went wrong with the segmnetation
// bool isEmpty = CleanImage(binaryLabelImage,6000);
bool isEmpty = false;
if(!isEmpty)
{
RemoveSmallComponents(binaryLabelImage, volume1);
// copy the clean image to the output
for(i = 0; i < sz; ++i)
{
if(binaryLabelImagePtr[i]>0)
{
output2DImagePtr[i] +=1;
//printf("added\n");
}
}
// second mixture
for(i = 0; i < sz; ++i)
{
if(mixtureLabelImagePtr[i+offset]>1)
{
binaryLabelImagePtr[i] = 1;
}
else
{
binaryLabelImagePtr[i] = 0;
}
}
RemoveSmallComponents(binaryLabelImage, volume2);
// copy the clean image to the output
for(i = 0; i < sz; ++i)
{
if(binaryLabelImagePtr[i]>0)
{
output2DImagePtr[i] +=1;
//printf("added2\n");
}
}
}// end of if statement
for(i=0 ; i<sz ; ++i)
outputImagePtr[i+offset] = output2DImagePtr[i];
} // end of time loop
writeImage<LabelImageType>(outputImage, ofName.c_str());
return 0;
}
