main.cpp
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#include <CImg.h>
#include <stdlib.h>
#include <iostream>
#include <map>
#include <string>
#include <fstream>
#include <time.h>
#define pow2(X) ((X)*(X))
using namespace cimg_library;
int main(unsigned int argc, char **argv) {
unsigned int exitCode(0);
try{
//=====get commandline parameters ====
cimg_usage("Create background mask for scanned images");
cimg_help("Usage: setBGmask [OPTIONS] IMAGEFILE \nReport bugs to <jap441@psu.edu>.\n");
//set parameters
double glimax = cimg_option("-txg",600,"Max intensity for green leaves");
double glimin = cimg_option("-tmg",150,"Min intensity for green leaves");
double glrgmax = cimg_option("-trg", 1.0,"Max red/green ratio for green leaves");
double plimax = cimg_option("-txp",600,"Max intensity for purple leaves");
double plimin = cimg_option("-tmp",200,"Min intensity for purple leaves");
double plgbmax = cimg_option("-tgbp",1.1,"Max green/blue ratio for purple leaves");
double resimin = cimg_option("-tri",360,"Min intensity for residue");
double resrmin = cimg_option("-trr",155,"Min red for residue");
double soilimax = cimg_option("-tsi",360,"Max intensity for soil");
double soilrmax = cimg_option("-tsr",155,"Max red for soil");
double bline = cimg_option("-bl",2,"Percentage range for border-line pixels ");
//unsigned int denoise = cimg_option("-nbg",7,"Noise reduction size in pixels (large values maybe slow)");
bool show = cimg_option("-s",false,"Show image");
bool header = cimg_option("-header",true,"Include header in textfile");
bool textfile = cimg_option("-tf",false,"Data to textfile");
//create file names for output masks
// the "X" is added onto the filenames of the masks so they can easily be deleted later w/o deleting the images or evaluation images
std::string filename(argv[argc-1]);
if (filename=="-h" || filename=="--help") filename="";
std::string ext=cimg_option("-ext",".jpg","Output extension");
std::string leafsfilename(filename.substr(0,filename.size()-4)+"_lfsX"+ext);
std::string residuefilename(filename.substr(0,filename.size()-4)+"_resX"+ext);
std::string soilfilename(filename.substr(0,filename.size()-4)+"_soilX"+ext);
std::string blfilename(filename.substr(0,filename.size()-4)+"_xblX"+ext);
std::string evaluationfilename(filename.substr(0,filename.size()-4)+"_eval"+ext);
std::string textfilename(filename.substr(0,filename.size()-4)+"dat.txt");
bool verbose = cimg_option("-v",false,"Be verbose");
bool sverbose = cimg_option("-V",false,"Be super verbose");
if(sverbose) verbose=true;
//instantiate image
if(filename=="") return 0;
if(verbose) std::cout<<"Processing image "<<filename<<"\n";
CImg<unsigned char> image(filename.c_str());
//===========Create Leaf Mask==================
//includes both green and purple colored leaves
//purple leaves would not be found if the threshold were made very small
if(sverbose) std::cout<<"Creating leaf mask\n";
CImg<unsigned char> glmask,blmask;
glmask.assign(image.dimx(),image.dimy(),1,1,0); // create the glmask image
blmask.assign(image.dimx(),image.dimy(),1,1,0); // create the blmask image - borderline pixels
unsigned int blcount(0); // borderline pixel counter
unsigned int glcount(0); // leaf pixel counter
unsigned int intensity(0);
double glibl((glimax-glimin)*(bline/100)); // green leaf intensity borderline ((max-min)*%)
double plibl((plimax-plimin)*(bline/100)); // purple leaf intensity borderline ((max-min)*%)
double glrgbl(glrgmax*bline/100); //green leaf red:green borderline
double plgbbl(plgbmax*bline/100); //purple leaf green:blue borderline
double redgreenratio(0),greenblueratio(0);
cimg_forXY(image,x,y) {
intensity=image(x,y,0)+image(x,y,1)+image(x,y,2);
// (x,y,0) refers to the red channel, (x,y,1) to the green, and (x,y,2) to the blue
redgreenratio=(double)image(x,y,0)/((double)image(x,y,1)+0.1);
greenblueratio=(double)image(x,y,1)/((double)image(x,y,2)+0.1);
if((intensity<glimax && intensity>glimin && redgreenratio<glrgmax)||
(intensity<plimax && intensity>plimin && greenblueratio<plgbmax) ){
glmask(x,y,0)=255;
++glcount; // >>> count glmask pixels
}
// count borderline pixels for green leaves
if((intensity<glimax+glibl && intensity>glimin-glibl && redgreenratio<glrgmax+glrgbl
&& redgreenratio>glrgmax-glrgbl) || //r:g border for green leaves
(redgreenratio<glrgmax-glrgbl && //r:g right, test max and min bands
((intensity>glimax-glibl && intensity<glimax+glibl) || //max band
(intensity>glimin-glibl && intensity<glimin+glibl))) ){ //min band
blmask(x,y,0)=255;
++blcount; // count borderline pixels for green leaves
}
// count borderline pixels for purple leaves
if((intensity<plimax+plibl && intensity>plimin-plibl && greenblueratio<plgbmax+plgbbl
&& greenblueratio>plgbmax-plgbbl) || //g:b border for purple leaves
(greenblueratio<plgbmax-plgbbl && //g:b right, test max and min bands
((intensity>plimax-plibl && intensity<plimax+plibl) || //max band
(intensity>plimin-plibl && intensity<plimin+plibl))) ){ //min band
blmask(x,y,0)=255;
++blcount; // count borderline pixels for purple leaves
}
};
//============Create Residue Mask=====================
CImg<unsigned char> resmask;
if(sverbose) std::cout<<"Creating residue mask\n";
resmask.assign(image.dimx(),image.dimy(),1,1,0);
unsigned int rescount(0);
double resrbl(resrmin*bline/100); // residue red borderline
double resibl(resimin*bline/100); // residue intensity borderline
cimg_forXY(image,x,y) {
if (glmask(x,y,0)!=255){
intensity=image(x,y,0)+image(x,y,1)+image(x,y,2);
if(intensity>resimin && image(x,y,0)>resrmin) {//intensity rule true & red rule true
resmask(x,y,0)=255;
++rescount; //increment residue counter
};
// count borderline pixels
if ((image(x,y,0)>resrmin-resrbl && image(x,y,0)<resrmin+resrbl && intensity>resimin-resibl) || // red borderline
(intensity>resimin-resibl && intensity<resimin+resibl && image(x,y,0)>resrmin+resrbl)){ // intensity borderline
blmask(x,y,0)=255;
++blcount; } //count borderline pixels
};
};
//===========Create Soil Mask====================
//everything that is not leaves, ambiguous or residue
CImg<unsigned char> soilmask;
if(sverbose) std::cout<<"Creating soil mask\n";
soilmask.assign(image.dimx(),image.dimy(),1,1,0);
unsigned int slcount(0); // soil pixel counter
double soilrbl(soilrmax*bline/100); // soil red borderline
double soilibl(soilimax*bline/100); // soil intensity borderline
cimg_forXY(image,x,y) {
if (glmask(x,y,0)!=255 && resmask(x,y,0)!=255){
intensity=image(x,y,0)+image(x,y,1)+image(x,y,2);
if(intensity<soilimax && image(x,y,0)<soilrmax) {//intensity rule true & red rule true
soilmask(x,y,0)=255;
++slcount; //increment residue counter
};
// >>> count pixels near boundary
if ((image(x,y,0)>soilrmax-soilrbl && image(x,y,0)<soilrmax+soilrbl && intensity<soilimax+soilibl) || // red borderline
(intensity>soilimax-soilibl && intensity<soilimax+soilibl && image(x,y,0)<soilrmax-soilibl)){ // intensity borderline
blmask(x,y,0)=255;
++blcount; } //count borderline pixels
};
};
//===========Create Ambiguous Mask====================
//everything that is not leaves, residue, or soil
CImg<unsigned char> ambmask;
if(sverbose) std::cout<<"Creating ambiguous mask\n";
ambmask.assign(image.dimx(),image.dimy(),1,1,0);
unsigned int ambcount(0);
cimg_forXY(image,x,y) {
if (glmask(x,y,0)!=255 && resmask(x,y,0)!=255 && soilmask(x,y,0)!=255){
ambmask(x,y,0)=255;
++ambcount; //increment ambiguous counter
};
};
double totpix((double)glcount + (double)rescount + (double)slcount + (double)ambcount);
double check(image.dimx()*image.dimy());
if(totpix!=check) std::cerr<<"Total number of classified pixels is different from total number of pixels in image. Classified="<<totpix<<" Image=" <<check<<std::endl;
if(verbose)std::cout<<"Leaves = "<<(double)glcount/totpix<<" *100%\n";
if(verbose)std::cout<<"Residue = "<<(double)rescount/totpix<<" *100%\n";
if(verbose)std::cout<<"Soil = "<<(double)slcount/totpix<<" *100%\n";
if(verbose)std::cout<<"Ambiguous residue or soil = "<<(double)ambcount/totpix<<" *100%\n";
if(verbose)std::cout<<"Borderline pixels = "<<(double)blcount/totpix<<" *100%\n";
//===========Create Evaluation Image===============
CImg<unsigned char> imageCopy;
imageCopy.assign(image);
cimg_forXY(imageCopy,x,y) {
if (glmask(x,y,0)==255){
imageCopy(x,y,0)/=2; // divide red and blue by 2
//imageCopy(x,y,1)=255;
imageCopy(x,y,2)/=2;
};
if(resmask(x,y,0)==255){
imageCopy(x,y,0)/=2;
imageCopy(x,y,1)/=2; //divide red and green by 2
//imageCopy(x,y,2)=255;
};
if(ambmask(x,y,0)==255){
imageCopy(x,y,0)=200;
imageCopy(x,y,1)=150;
imageCopy(x,y,2)=0;
};
if(soilmask(x,y,0)==255){
//imageCopy(x,y,0)*=2;
imageCopy(x,y,1)/=2;
imageCopy(x,y,2)/=2;
};
};
//===============Output============================
//textfile output
if(textfile){
std::ofstream textfile;
textfile.open(textfilename.c_str());
char del('\t');
//time
time_t rawtime;
time ( &rawtime );
struct tm * timeinfo(localtime ( &rawtime ));
char date [80];
strftime (date,80,"%x",timeinfo);
//header
if(header) textfile << "Filename" << del << "Date" << del << "%Leaves" << del << "%Residue" << del << "%Soil" << del << "%Ambiguous" << del << "%Borderline" << del << "ClassifiedPixels" << del << "TotalPixels" << std::endl;
textfile << filename.substr(0,filename.size()-4) << del << date << del << (double)glcount/totpix << del << (double)rescount/totpix << del << (double)slcount/totpix << del << (double)ambcount/totpix << del << (double)blcount/totpix << del << totpix << del << check << std::endl;
};
//image output
if(show){
//open displays showing images
CImgDisplay main_disp(image,"Original"),
mask_disp(glmask,"Leafs mask"),
rmask_disp(resmask,"Residue mask"),
smask_disp(soilmask,"Soil mask"),
nmask_disp(imageCopy,"Evaluation mask");
while (!main_disp.is_closed) main_disp.wait();
}else{
//write mask images to file
glmask.save(leafsfilename.c_str());
resmask.save(residuefilename.c_str());
soilmask.save(soilfilename.c_str());
blmask.save(blfilename.c_str());
imageCopy.save(evaluationfilename.c_str());
};
//============catch errors=========================
} catch (std::exception& error){
std::cout << error.what() ;
exitCode=1;
};
return exitCode;
}
