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slsDetectorPackage/slsDetectorCalibration/jungfrauExecutables/jungfrauPhotonCounter.cpp
Erik Frojdh c554bbb2d3 formatted slsDetectorCalibration
2022-01-24 11:26:56 +01:00

448 lines
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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 "moench03CommonMode.h"
#include "moench03GhostSummation.h"
#include "singlePhotonDetector.h"
//#include "interpolatingDetector.h"
#include <fstream>
#include <map>
#include <stdio.h>
#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_t 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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