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slsDetectorPackage/slsDetectorCalibration/moenchExecutables/moenchRawDataProcess.cpp
Dhanya Thattil 97f0c1fe46
8.0.1.rc (#891) 
* forward declare zmq_msg_t and moved include

* removed zmq as dependency for slsdet (#870)

* Fixed path when building as submodule

* new moench data structure for offline processing

* meonch raw data and zmq process files updated to 7.0.3 version

* implemented config file for Zmq file

* raw data and zmq work with config file, but only with one file/interface

* zmq config change

* added config examples for zmq and rawdata

* update release notes, release versions

---------

Co-authored-by: Erik Frojdh <erik.frojdh@gmail.com>
Co-authored-by: froejdh_e <erik.frojdh@psi.ch>
Co-authored-by: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Co-authored-by: anberga <34126852+anberga@users.noreply.github.com>
2024-01-16 15:31:25 +01:00

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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
#undef CORR
#define C_GHOST 0 //0.0004
#define CM_ROWS 20
#define RAWDATA
#ifndef MOENCH04
#ifndef RECT
#include "moench03v2Data.h"
#endif
#endif
#ifdef RECT
#include "moench03T1ReceiverDataNewRect.h"
#endif
#ifdef MOENCH04
#include "moench04CtbZmq10GbData.h"
#endif
#include "multiThreadedCountingDetector.h"
#include "moench03CommonMode.h"
#include "moench03GhostSummation.h"
#include "singlePhotonDetector.h"
#include <fstream>
#include <map>
#include <stdio.h>
#include <sys/stat.h>
#include <ctime>
using namespace std;
int main(int argc, char *argv[]) {
std::map<std::string, std::string> args = {
{"numfiles","1"},
{"nthreads","5"},
{"fifosize","5000"},
{"nsigma","5"},
{"gainfile","none"},
{"detectorMode","counting"},
{"threshold","0"},
{"pedestalfile","none"},
{"nframes","0"},
{"xMin","0"},
{"xMax","400"},
{"yMin","0"},
{"yMax","400"},
{"eMin","0"},
{"eMax","16000"},
{"outdir","./"},
{"indir","./"},
{"flist","none"},
{"fformat","none"},
{"runmin","0"},
{"runmax","-1"},
{"readnrows","400"}
};
//float *gm;
int ff, np;
// cout << " data size is " << dsize;
ifstream filebin;
if (argc < 4) {
std::string name, value,sline;
int ic=0;
ifstream flist;
flist.open (argv[1], std::ifstream::in);
if (flist.is_open()) {
cout << "Using config file " <<argv[1] << endl;
while (std::getline(flist,sline)){
if (sline.at(0)!='#') {
ic=sline.find(' ');
name = sline.substr(0,ic);
value = sline.substr(ic+1,sline.size()-ic);
args[name]=value;
}
}
flist.close();
} else {
cout << "Usage is " << argv[0]
<< "indir outdir fname(no extension) [runmin] [runmax] [pedfile (raw or tiff)] [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 EXIT_FAILURE;
}
} else {
args["indir"]=argv[1];
args["outdir"]=argv[1];
args["fformat"]=argv[3];
if (argc >= 5) {
args["runmin"] = argv[4];
}
args["runmax"] = args["runmin"];
if (argc >= 6) {
args["runmax"] = argv[5];
}
if (argc >= 7) {
args["pedestalfile"] = argv[6];
}
if (argc >= 8) {
args["threshold"] = argv[7];
}
if (argc >= 9) {
args["nframes"] = argv[8];
}
if (argc >= 13) {
args["xMin"] = argv[9];
args["xMax"] = argv[10];
args["yMin"] = argv[11];
args["yMax"] = argv[12];
}
if (argc > 13) {
args["gainfile"] = argv[13];
}
if (atof(args["threshold"].c_str())<0) {
args["detectorMode"]="analog";
}
}
for (auto const& x : args)
{
std::cout << x.first // string (key)
<< ':'
<< x.second // string's value
<< std::endl;
}
string indir=args["indir"];
string outdir = args["outdir"];
string fformat= args["fformat"];
int runmin = atoi(args["runmin"].c_str());
int runmax = atoi(args["runmin"].c_str());
string pedfile =args["pedestalfile"];
double thr = atof(args["threshold"].c_str());
double thr1 = 1;
int nframes = atoi(args["nframes"].c_str());
int xmin = atoi(args["xMin"].c_str()), xmax = atoi(args["xMax"].c_str()), ymin = atoi(args["yMin"].c_str()), ymax = atoi(args["yMax"].c_str());
string gainfname=args["gainfile"];
int fifosize = atoi(args["fifosize"].c_str());
int nthreads = atoi(args["nthreads"].c_str());
int nsigma = atoi(args["nsigma"].c_str());
int nrows = atoi(args["readnrows"].c_str());
float eMin = atof(args["eMin"].c_str());
float eMax = atof(args["eMax"].c_str());
int csize = 3;
int nped = 1000;
int cf = 0;
int numberOfPackets=nrows/8;
#ifdef RECT
cout << "Should be rectangular but now it will crash! No data structure defined!" << endl;
#endif
#ifndef MOENCH04
moench03v2Data *decoder = new moench03v2Data(100);
cout << "MOENCH03!" << endl;
#endif
#ifdef MOENCH04
#ifndef MOENCH04_DGS
moench04CtbZmq10GbData *decoder = new moench04CtbZmq10GbData(5000,0);
cout << "MOENCH04!" << endl;
#endif
#ifdef MOENCH04_DGS
moench04CtbZmq10GbData *decoder = new moench04CtbZmq10GbData(5000,5000);
cout << "MOENCH04 DGS!" << endl;
numberOfPackets=45;
#endif
#endif
int nx , ny;
decoder->getDetectorSize(nx, ny);
//Read detector size from decoder
char ffname[10000];
char fname[10000];
char imgfname[10000];
char cfname[10000];
std::time_t end_time;
FILE *of = NULL;
uint32_t nnx, nny;
moench03CommonMode *cm = nullptr;
moench03GhostSummation *gs = nullptr;
double *gainmap = nullptr;
#ifdef CORR
int ncol_cm = CM_ROWS;
double xt_ghost = C_GHOST;
std::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.c_str()))
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();
if (thr > 0) {
cout << "threshold is " << thr << endl;
filter->setThreshold(thr);
cf = 0;
} else
cf = 1;
filter->setROI(xmin, xmax, ymin, ymax);
filter->setEnergyRange(eMin, eMax);
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);
if (args["detectorMode"]=="counting") {
mt->setDetectorMode(ePhotonCounting);
if (thr > 0) {
cf = 0;
}
} else {
mt->setDetectorMode(eAnalog);
cf = 0;
}
// #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;
char froot[1000];
double *ped=new double[nx * ny];//, *ped1;
int pos,pos1;
//return 0;
if (pedfile.find(".raw") != std::string::npos) {
pos1=pedfile.rfind("/");
strcpy(froot,pedfile.substr(pos1).c_str());
pos=string(froot).find(".raw");
froot[pos]='\0';
}
cout << "PEDESTAL " << endl;
if (pedfile.find(".tif") == std::string::npos) {
sprintf(fname, "%s", pedfile.c_str());
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 == numberOfPackets) {
mt->pushData(buff);
mt->nextThread();
mt->popFree(buff);
ifr++;
if (ifr % 100 == 0)
cout << ifr << " " << ff << " " << np << endl;
// break;
} else {
cout << ifr << " " << ff << " " << np << endl;
break;
}
ff = -1;
}
filebin.close();
while (mt->isBusy()) {
;
}
sprintf(imgfname, "%s/%s_ped.tiff", outdir.c_str(),froot);
mt->writePedestal(imgfname);
sprintf(imgfname, "%s/%s_var.tiff", outdir.c_str(),froot);
mt->writePedestalRMS(imgfname);
} else
cout << "Could not open pedestal file " << fname
<< " for reading " << endl;
} else {
float *pp = ReadFromTiff(pedfile.c_str(), nny, nnx);
if (pp && (int)nnx == nx && (int)nny == ny) {
for (int i = 0; i < nx * ny; i++) {
ped[i] = pp[i];
}
delete[] pp;
mt->setPedestal(ped);
cout << "Pedestal set from tiff file " << pedfile << endl;
} else {
cout << "Could not open pedestal tiff file " << pedfile
<< " for reading " << endl;
}
}
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
ifr = 0;
int ifile = 0;
mt->setFrameMode(eFrame);
//t filelist=0;
ifstream flist;
flist.open (args["flist"].c_str(), std::ifstream::in);
if (flist.is_open()) {
cout << "Using file list" << endl;
runmin=0;
runmax=0;
while (flist.getline(ffname,10000)){
cout << ffname << endl;
runmax++;
}
runmax--;
flist.close();
cout << "Found " << runmax << " files " << endl;
flist.open (fformat, std::ifstream::in);
}
for (int irun = runmin; irun <= runmax; irun++) {
cout << "DATA ";
// sprintf(fn,fformat,irun);
// sprintf(ffname, "%s/%s.raw", indir, fformat);
// sprintf(fname, (const char*)ffname, irun);
// sprintf(ffname, "%s/%s.tiff", outdir, fformat);
// sprintf(imgfname, (const char*)ffname, irun);
// sprintf(ffname, "%s/%s.clust", outdir, fformat);
// sprintf(cfname, (const char*)ffname, irun);
if (flist.is_open()) {
flist.getline(ffname,10000);
cout << "file list " << ffname << endl;
} else {
//sprintf(ffname,(const char*)fformat,irun);
sprintf(ffname,args["fformat"].c_str(),irun);
cout << "loop " << ffname << endl;
}
cout << "ffname "<< ffname << endl;
sprintf(fname, "%s/%s.raw",indir.c_str(),ffname);
sprintf(imgfname, "%s/%s.tiff",outdir.c_str(),ffname);
sprintf(cfname, "%s/%s.clust",outdir.c_str(),ffname);
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 (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 == numberOfPackets) {
// //push
mt->pushData(buff);
// // //pop
mt->nextThread();
mt->popFree(buff);
ifr++;
if (ifr % 100 == 0)
cout << ifr << " " << ff << " " << np << endl;
//break;
if (nframes > 0) {
if (ifr % nframes == 0) {
// sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat,
// ifile);
// sprintf(imgfname, (const char*)ffname, irun);
sprintf(imgfname, "%s/%s_f%05d.tiff",outdir.c_str(),ffname,ifile);
while (mt->isBusy())
;
mt->writeImage(imgfname, thr1);
mt->clearImage();
ifile++;
}
}
} else {
cout << "bp " << ifr << " " << ff << " " << np << endl;
//break;
}
ff = -1;
}
cout << "--" << endl;
filebin.close();
while (mt->isBusy()) {
;
}
if (nframes >= 0) {
if (nframes > 0) {
sprintf(imgfname, "%s/%s_f%05d.tiff",outdir.c_str(),ffname,ifile);
// sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat, ifile);
//sprintf(imgfname, (const char*)ffname, irun);
} else {
sprintf(imgfname, "%s/%s.tiff",outdir.c_str(),ffname);
// sprintf(ffname, "%s/%s.tiff", outdir, fformat);
// sprintf(imgfname, (const char*)ffname, irun);
}
cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
while (mt->isBusy())
;
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);
sprintf(imgfname, "%s/%s_tot.tiff",outdir.c_str(),ffname);
cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
while (mt->isBusy())
;
mt->writeImage(imgfname, thr1);
}
if (flist.is_open()) {
flist.close();
}
return 0;
}
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