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slsDetectorPackage/slsDetectorCalibration/moenchExecutables/moenchPhotonCounter.cpp

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// SPDX-License-Identifier: LGPL-3.0-or-other
// Copyright (C) 2021 Contributors to the SLS Detector Package
//#include "sls/ansi.h"
#include <iostream>
#define CORR
#define C_GHOST 0.0004
#define CM_ROWS 50
//#define VERSION_V1
//#include "moench03T1ZmqData.h"
#ifdef NEWRECEIVER
#ifndef RECT
#include "moench03T1ReceiverDataNew.h"
#endif
#ifdef RECT
#include "moench03T1ReceiverDataNewRect.h"
#endif
#endif
#ifdef CSAXS_FP
#include "moench03T1ReceiverData.h"
#endif
#ifdef OLDDATA
#include "moench03Ctb10GbT1Data.h"
#endif
// #include "interpolatingDetector.h"
//#include "etaInterpolationPosXY.h"
// #include "linearInterpolation.h"
// #include "noInterpolation.h"
#include "multiThreadedCountingDetector.h"
//#include "multiThreadedAnalogDetector.h"
#include "singlePhotonDetector.h"
#include "moench03GhostSummation.h"
#include "moench03CommonMode.h"
//#include "interpolatingDetector.h"
#include <stdio.h>
#include <map>
#include <fstream>
#include <sys/stat.h>
#include <ctime>
using namespace std;
int main(int argc, char *argv[]) {
if (argc<4) {
cout << "Usage is " << argv[0] << "indir outdir fname [runmin] [runmax] [pedfile] [threshold] [nframes] [xmin xmax ymin ymax] [gainmap]" << endl;
cout << "threshold <0 means analog; threshold=0 means cluster finder; threshold>0 means photon counting" << endl;
cout << "nframes <0 means sum everything; nframes=0 means one file per run; nframes>0 means one file every nframes" << endl;
return 1;
}
int p=10000;
int fifosize=1000;
int nthreads=10;
int nsubpix=25;
int etabins=nsubpix*10;
double etamin=-1, etamax=2;
int csize=3;
int save=1;
int nsigma=5;
int nped=10000;
int ndark=100;
int ok;
int iprog=0;
int cf=0;
#ifdef NEWRECEIVER
#ifdef RECT
cout << "Should be rectangular!" <<endl;
#endif
moench03T1ReceiverDataNew *decoder=new moench03T1ReceiverDataNew();
cout << "RECEIVER DATA WITH ONE HEADER!"<<endl;
#endif
#ifdef CSAXS_FP
moench03T1ReceiverData *decoder=new moench03T1ReceiverData();
cout << "RECEIVER DATA WITH ALL HEADERS!"<<endl;
#endif
#ifdef OLDDATA
moench03Ctb10GbT1Data *decoder=new moench03Ctb10GbT1Data();
cout << "OLD RECEIVER DATA!"<<endl;
#endif
int nx=400, ny=400;
decoder->getDetectorSize(nx,ny);
int ncol_cm=CM_ROWS;
double xt_ghost=C_GHOST;
moench03CommonMode *cm=NULL;
moench03GhostSummation *gs;
double *gainmap=NULL;
float *gm;
int size = 327680;////atoi(argv[3]);
int* image;
//int* image =new int[327680/sizeof(int)];
int ff, np;
//cout << " data size is " << dsize;
ifstream filebin;
char *indir=argv[1];
char *outdir=argv[2];
char *fformat=argv[3];
int runmin=0;
// cout << "argc is " << argc << endl;
if (argc>=5) {
runmin=atoi(argv[4]);
}
int runmax=runmin;
if (argc>=6) {
runmax=atoi(argv[5]);
}
char *pedfile=NULL;
if (argc>=7) {
pedfile=argv[6];
}
double thr=0;
double thr1=1;
if (argc>=8) {
thr=atof(argv[7]);
}
int nframes=0;
if (argc>=9) {
nframes=atoi(argv[8]);
}
int xmin=0, xmax=nx, ymin=0, ymax=ny;
if (argc>=13) {
xmin=atoi(argv[9]);
xmax=atoi(argv[10]);
ymin=atoi(argv[11]);
ymax=atoi(argv[12]);
}
char *gainfname=NULL;
if (argc>13) {
gainfname=argv[13];
cout << "Gain map file name is: " << gainfname << endl;
}
char ffname[10000];
char fname[10000];
char imgfname[10000];
char cfname[10000];
char fn[10000];
std::time_t end_time;
FILE *of=NULL;
cout << "input directory is " << indir << endl;
cout << "output directory is " << outdir << endl;
cout << "input file is " << fformat << endl;
cout << "runmin is " << runmin << endl;
cout << "runmax is " << runmax << endl;
if (pedfile)
cout << "pedestal file is " << pedfile << endl;
if (thr>0)
cout << "threshold is " << thr << endl;
cout << "Nframes is " << nframes << endl;
uint32 nnx, nny;
double *gmap;
// if (gainfname) {
// gm=ReadFromTiff(gainfname, nny, nnx);
// if (gm && nnx==nx && nny==ny) {
// gmap=new double[nx*ny];
// for (int i=0; i<nx*ny; i++) {
// gmap[i]=gm[i];
// }
// delete gm;
// } else
// cout << "Could not open gain map " << gainfname << endl;
// }
#ifdef CORR
cout << "Applying common mode " << ncol_cm << endl;
cm=new moench03CommonMode(ncol_cm);
cout << "Applying ghost corrections " << xt_ghost << endl;
gs=new moench03GhostSummation(decoder, xt_ghost);
#endif
singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, cm, nped, 200, -1, -1, gainmap, gs);
if (gainfname) {
if (filter->readGainMap(gainfname))
cout << "using gain map " << gainfname << endl;
else
cout << "Could not open gain map " << gainfname << endl;
} else
thr=0.15*thr;
filter->newDataSet();
int dsize=decoder->getDataSize();
char data[dsize];
//#ifndef ANALOG
if (thr>0) {
cout << "threshold is " << thr << endl;
//#ifndef ANALOG
filter->setThreshold(thr);
//#endif
cf=0;
} else
cf=1;
//#endif
filter->setROI(xmin,xmax,ymin,ymax);
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
char* buff;
// multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
#ifndef ANALOG
mt->setDetectorMode(ePhotonCounting);
cout << "Counting!" << endl;
if (thr>0) {
cf=0;
}
#endif
//{
#ifdef ANALOG
mt->setDetectorMode(eAnalog);
cout << "Analog!" << endl;
cf=0;
//thr1=thr;
#endif
// }
mt->StartThreads();
mt->popFree(buff);
// cout << "mt " << endl;
int ifr=0;
double ped[nx*ny], *ped1;
if (pedfile) {
cout << "PEDESTAL " << endl;
sprintf(imgfname,"%s/pedestals.tiff",outdir);
if (string(pedfile).find(".tif")==std::string::npos){
sprintf(fname,"%s.raw",pedfile);
cout << fname << endl ;
std::time(&end_time);
cout << "aaa" << std::ctime(&end_time) << endl;
mt->setFrameMode(ePedestal);
// sprintf(fn,fformat,irun);
filebin.open((const char *)(fname), ios::in | ios::binary);
// //open file
if (filebin.is_open()){
ff=-1;
while (decoder->readNextFrame(filebin, ff, np,buff)) {
if (np==40) {
mt->pushData(buff);
mt->nextThread();
mt->popFree(buff);
ifr++;
if (ifr%100==0)
cout << ifr << " " << ff << " " << np << endl;
} else
cout << ifr << " " << ff << " " << np << endl;
ff=-1;
}
filebin.close();
while (mt->isBusy()) {;}
} else
cout << "Could not open pedestal file "<< fname << " for reading " << endl;
} else {
float *pp=ReadFromTiff(pedfile, nny, nnx);
if (pp && nnx==nx && nny==ny) {
for (int i=0; i<nx*ny; i++) {
ped[i]=pp[i];
}
delete [] pp;
mt->setPedestal(ped);
// ped1=mt->getPedestal();
// for (int i=0; i<nx*ny; i++) {
// cout << ped[i]<<"/"<<ped1[i] << " " ;
// }
cout << "Pedestal set from tiff file " << pedfile << endl;
} else {
cout << "Could not open pedestal tiff file "<< pedfile << " for reading " << endl;
}
}
mt->writePedestal(imgfname);
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
}
ifr=0;
int ifile=0;
mt->setFrameMode(eFrame);
for (int irun=runmin; irun<=runmax; irun++) {
cout << "DATA " ;
// sprintf(fn,fformat,irun);
sprintf(ffname,"%s/%s.raw",indir,fformat);
sprintf(fname,ffname,irun);
sprintf(ffname,"%s/%s.tiff",outdir,fformat);
sprintf(imgfname,ffname,irun);
sprintf(ffname,"%s/%s.clust",outdir,fformat);
sprintf(cfname,ffname,irun);
cout << fname << " " ;
cout << imgfname << endl;
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
// cout << fname << " " << outfname << " " << imgfname << endl;
filebin.open((const char *)(fname), ios::in | ios::binary);
// //open file
ifile=0;
if (filebin.is_open()){
if (thr<=0 && cf!=0) { //cluster finder
if (of==NULL) {
of=fopen(cfname,"w");
if (of) {
mt->setFilePointer(of);
cout << "file pointer set " << endl;
} else {
cout << "Could not open "<< cfname << " for writing " << endl;
mt->setFilePointer(NULL);
return 1;
}
}
}
// //while read frame
ff=-1;
ifr=0;
while (decoder->readNextFrame(filebin, ff, np,buff)) {
if (np==40) {
// cout << "*"<<ifr++<<"*"<<ff<< endl;
// cout << ff << " " << np << endl;
// //push
mt->pushData(buff);
// // //pop
mt->nextThread();
// // // cout << " " << (void*)buff;
mt->popFree(buff);
ifr++;
if (ifr%100==0) cout << ifr << " " << ff << endl;
if (nframes>0) {
if (ifr%nframes==0) {
//The name has an additional "_fXXXXX" at the end, where "XXXXX" is the initial frame number of the image (0,1000,2000...)
sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
sprintf(imgfname,ffname,irun);
//cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
mt->writeImage(imgfname, thr1);
mt->clearImage();
ifile++;
}
}
} else
cout << ifr << " " << ff << " " << np << endl;
ff=-1;
}
cout << "--" << endl;
filebin.close();
// //close file
// //join threads
while (mt->isBusy()) {;}
if (nframes>=0) {
if (nframes>0) {
sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
sprintf(imgfname,ffname,irun);
} else {
sprintf(ffname,"%s/%s.tiff",outdir,fformat);
sprintf(imgfname,ffname,irun);
}
cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
mt->writeImage(imgfname, thr1);
mt->clearImage();
if (of) {
fclose(of);
of=NULL;
mt->setFilePointer(NULL);
}
}
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
} else
cout << "Could not open "<< fname << " for reading " << endl;
}
if (nframes<0){
sprintf(ffname,"%s/%s.tiff",outdir,fformat);
strcpy(imgfname,ffname);
cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
mt->writeImage(imgfname, thr1);
}
return 0;
}
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