EL_API_VECTO::ParamFile::ParamFile
(
const ElSTDNS string & aName,
bool Inferieur ,
int Threshold
) :
ParamFonc
(
Pt2d2complex(Tiff_Im(aName.c_str()).sz()),
Inferieur,
GetThresh(aName,Threshold)
),
_TiffNameFile (aName)
{
}
//This function binarizes the nuclei in an image and colors connected components
void computebin(cv::Mat src, cv::Mat BinImPad, cv::Mat BinIm ){
//Get Image Dimensions
int thresh = GetThresh(src);
int nthreads, tid;
#pragma omp parallel private(tid,nthreads)
{
tid = omp_get_thread_num();
nthreads = omp_get_num_threads();
int start, end;
start = tid*(rows/nthreads);
end = (tid+1)*(rows/nthreads);
if( tid == (nthreads-1) ) end = rows;
for( int j=start; j<rows; ++j )
for( int i=0; i<cols; ++i )
if( src.at<unsigned char>(i,j) > thresh ){
BinIm.at<unsigned char>(i,j) = 0;
BIP((i+1),(j+1)) = 0;
}
else{
BinIm.at<unsigned char>(i,j) = 255;
BIP((i+1),(j+1)) = UCHAR_MAX;
}
}
//Set the borders of the padded image
for( int i=0; i<(cols+2); ++i ){
BIP(i,0) = 0;
BIP(i,(rows+1)) = 0;
}
for( int i=1; i<(rows+2); ++i ){
BIP(0,i) = 0;
BIP((cols+1),i) = 0;
}
if(write_files){
std::string out_str1 = "binary_" + file_open;
cv::imwrite(out_str1.c_str(),BinIm);
}
std::cout<<"The threshold is: "<<thresh<<std::endl;
}
