mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-04-20 02:40:03 +02:00
498 lines
14 KiB
C++
498 lines
14 KiB
C++
// SPDX-License-Identifier: LGPL-3.0-or-other
|
|
// Copyright (C) 2021 Contributors to the SLS Detector Package
|
|
// #include "sls/ansi.h"
|
|
#include <iostream>
|
|
#undef CORR
|
|
|
|
#define C_GHOST 0.0004
|
|
|
|
#define CM_ROWS 50
|
|
|
|
#define RAWDATA
|
|
|
|
#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 && \
|
|
!defined JFSTRXCHIP6
|
|
#ifndef MODULE
|
|
#include "jungfrauHighZSingleChipData.h"
|
|
#endif
|
|
#ifdef MODULE
|
|
#include "jungfrauModuleData.h"
|
|
#endif
|
|
#endif
|
|
|
|
#ifdef JFSTRX
|
|
#include "jungfrauLGADStrixelsData_new.h"
|
|
#endif
|
|
#if defined JFSTRXCHIP1 || defined JFSTRXCHIP6
|
|
#include "jungfrauLGADStrixelsDataSingleChip.h"
|
|
#endif
|
|
#ifdef JFSTRXOLD
|
|
#include "jungfrauStrixelsHalfModuleOldDesign.h"
|
|
#endif
|
|
|
|
#include "multiThreadedCountingDetector.h"
|
|
#include "singlePhotonDetector.h"
|
|
|
|
#include <fstream>
|
|
#include <map>
|
|
#include <stdio.h>
|
|
#include <sys/stat.h>
|
|
|
|
#include <ctime>
|
|
#include <fmt/core.h>
|
|
|
|
|
|
std::string getRootString( const std::string& filepath ) {
|
|
size_t pos1;
|
|
if (filepath.find("/") == std::string::npos )
|
|
pos1 = 0;
|
|
else
|
|
pos1 = filepath.find_last_of("/")+1;
|
|
size_t pos2 = filepath.find_last_of(".");
|
|
//std::cout << "pos1 " << pos1 << " pos2 " << pos2 << " size " << filepath.length() << std::endl;
|
|
return filepath.substr( pos1, pos2-pos1 );
|
|
}
|
|
|
|
//Create file name string
|
|
// dir: directory
|
|
// fprefix: fileprefix (without extension)
|
|
// fsuffix: filesuffix (for output files, e.g. "ped")
|
|
// fext: file extension (e.g. "raw")
|
|
std::string createFileName( const std::string& dir, const std::string& fprefix="run", const std::string& fsuffix="", const std::string& fext="raw", int outfilecounter=-1 ) {
|
|
if (outfilecounter >= 0)
|
|
return fmt::format("{:s}/{:s}_{:s}_f{:05d}.{:s}", dir, fprefix, fsuffix, outfilecounter, fext);
|
|
else if (fsuffix.length()!=0)
|
|
return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
|
|
else
|
|
return fmt::format("{:s}/{:s}.{:s}", dir, fprefix, fext);
|
|
}
|
|
|
|
|
|
//NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
|
|
int main(int argc, char *argv[]) {
|
|
|
|
if (argc < 10) {
|
|
std::cout
|
|
<< "Usage is " << argv[0]
|
|
<< " filestxt outdir [pedfile (raw or tiff)] [xmin xmax ymin ymax] "
|
|
"[threshold] [nframes] "
|
|
"NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS! "
|
|
<< std::endl;
|
|
std::cout
|
|
<< "threshold <0 means analog; threshold=0 means cluster finder; "
|
|
"threshold>0 means photon counting"
|
|
<< std::endl;
|
|
std::cout
|
|
<< "nframes <0 means sum everything; nframes=0 means one file per "
|
|
"run; nframes>0 means one file every nframes"
|
|
<< std::endl;
|
|
return 1;
|
|
}
|
|
|
|
int fifosize = 1000;
|
|
int nthreads = 10;
|
|
int csize = 3; // 3
|
|
int nsigma = 5;
|
|
int nped = 10000;
|
|
|
|
int cf = 0;
|
|
|
|
double *gainmap = NULL;
|
|
// float *gm;
|
|
|
|
int ff, np;
|
|
// cout << " data size is " << dsize;
|
|
|
|
const std::string txtfilename(argv[1]);
|
|
const std::string outdir(argv[2]);
|
|
const std::string pedfilename(argv[3]);
|
|
|
|
int xmin = atoi(argv[4]);
|
|
int xmax = atoi(argv[5]);
|
|
int ymin = atoi(argv[6]);
|
|
int ymax = atoi(argv[7]);
|
|
|
|
double thr = 0;
|
|
double thr1 = 1;
|
|
thr = atof(argv[8]);
|
|
|
|
int nframes = 0;
|
|
nframes = atoi(argv[9]);
|
|
|
|
//Get vector of filenames from input txt-file
|
|
std::vector<std::string> filenames{};
|
|
//filenames.reserve(512);
|
|
{ //Safety scope for ifstream
|
|
ifstream inputs( txtfilename, std::ios::in );
|
|
if (inputs.is_open()) {
|
|
std::cout << "Reading imput filenames from txt-file ..." << std::endl;
|
|
std::string line{};
|
|
while (!inputs.eof()) {
|
|
std::getline(inputs, line);
|
|
filenames.emplace_back(line);
|
|
std::cout << line << " line.max_size() " << line.max_size() << " filenames.capacity() " << filenames.capacity() << '\n';
|
|
}
|
|
inputs.close();
|
|
std::cout << "---- Reached end of txt-file. ----" << std::endl;
|
|
} else
|
|
std::cout << "Could not open " << txtfilename << std::endl;
|
|
if (filenames.size()>0) {
|
|
std::cout << filenames.size() << " filenames found in " << txtfilename << std::endl;
|
|
std::cout << "The files will be processed in the same order as found in the txt-file." << std::endl;
|
|
} else {
|
|
std::cout << "No files found in txt-file!" << std::endl;
|
|
return 1;
|
|
}
|
|
}
|
|
|
|
std::cout << "###############" << std::endl;
|
|
|
|
// Define decoders...
|
|
#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 && \
|
|
!defined JFSTRXCHIP6
|
|
#ifndef MODULE
|
|
jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
|
|
int nx = 256, ny = 256;
|
|
#endif
|
|
#ifdef MODULE
|
|
jungfrauModuleData *decoder = new jungfrauModuleData();
|
|
int nx = 1024, ny = 512;
|
|
#endif
|
|
#endif
|
|
|
|
#ifdef JFSTRX
|
|
cout << "Jungfrau strixel full module readout" << endl;
|
|
// ROI
|
|
uint16_t xxmin = 0;
|
|
uint16_t xxmax = 0;
|
|
uint16_t yymin = 0;
|
|
uint16_t yymax = 0;
|
|
|
|
#ifndef ALDO
|
|
{ //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
|
|
using header = sls::defs::sls_receiver_header;
|
|
// check if there is a roi in the header
|
|
typedef struct {
|
|
uint16_t xmin;
|
|
uint16_t xmax;
|
|
uint16_t ymin;
|
|
uint16_t ymax;
|
|
} receiverRoi_compact;
|
|
receiverRoi_compact croi;
|
|
//std::string filepath(argv[9]); //This is a problem if the input files have different ROIs!
|
|
std::cout << "Reading header of file " << filenames[0] << " to check for ROI "
|
|
<< std::endl;
|
|
ifstream firstfile(filenames[0], ios::in | ios::binary);
|
|
if (firstfile.is_open()) {
|
|
header hbuffer;
|
|
std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
|
|
if (firstfile.read((char *)&hbuffer, sizeof(header))) {
|
|
memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
|
|
std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
|
|
<< croi.ymin << ", " << croi.ymax << "]" << std::endl;
|
|
xxmin = croi.xmin;
|
|
xxmax = croi.xmax;
|
|
yymin = croi.ymin;
|
|
yymax = croi.ymax;
|
|
} else
|
|
std::cout << "reading error" << std::endl;
|
|
firstfile.close();
|
|
} else
|
|
std::cout << "Could not open " << filenames[0] << " for reading " << std::endl;
|
|
} //end of protective scope
|
|
#endif
|
|
|
|
jungfrauLGADStrixelsData *decoder =
|
|
new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
|
|
int nx = 1024 / 3, ny = 512 * 5;
|
|
#endif
|
|
#ifdef JFSTRXCHIP1
|
|
std::cout << "Jungfrau strixel LGAD single chip 1" << std::endl;
|
|
jungfrauLGADStrixelsDataSingleChip *decoder =
|
|
new jungfrauLGADStrixelsDataSingleChip(1);
|
|
int nx = 256 / 3, ny = 256 * 5;
|
|
#endif
|
|
#ifdef JFSTRXCHIP6
|
|
std::cout << "Jungfrau strixel LGAD single chip 6" << std::endl;
|
|
jungfrauLGADStrixelsDataSingleChip *decoder =
|
|
new jungfrauLGADStrixelsDataSingleChip(6);
|
|
int nx = 256 / 3, ny = 256 * 5;
|
|
#endif
|
|
#ifdef JFSTRXOLD
|
|
std::cout << "Jungfrau strixels old design" << std::endl;
|
|
jungfrauStrixelsHalfModuleOldDesign *decoder =
|
|
new jungfrauStrixelsHalfModuleOldDesign();
|
|
int nx = 1024 * 3, ny = 512 / 3;
|
|
#endif
|
|
|
|
decoder->getDetectorSize(nx, ny);
|
|
std::cout << "Detector size is " << nx << " " << ny << std::endl;
|
|
|
|
|
|
if ( xmin == xmax ) {
|
|
xmin = 0;
|
|
xmax = nx;
|
|
}
|
|
if ( ymin == ymax ) {
|
|
ymin = 0;
|
|
ymax = ny;
|
|
}
|
|
std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
|
|
<< std::endl;
|
|
|
|
/*
|
|
char *gainfname = NULL;
|
|
if (argc > 14) {
|
|
gainfname = argv[14];
|
|
std::cout << "Gain map file name is: " << gainfname << std::endl;
|
|
}
|
|
*/
|
|
|
|
std::time_t end_time;
|
|
|
|
std::cout << "output directory is " << outdir << std::endl;
|
|
if (pedfilename.length()!=0)
|
|
std::cout << "pedestal file is " << pedfilename << std::endl;
|
|
if (thr > 0)
|
|
std::cout << "threshold is " << thr << std::endl;
|
|
std::cout << "Nframes is " << nframes << std::endl;
|
|
|
|
uint32_t nnx, nny;
|
|
|
|
singlePhotonDetector *filter = new singlePhotonDetector(
|
|
decoder, 3, nsigma, 1, NULL, nped, 200, -1, -1, gainmap, NULL);
|
|
|
|
/*
|
|
if (gainfname) {
|
|
|
|
if (filter->readGainMap(gainfname))
|
|
std::cout << "using gain map " << gainfname << std::endl;
|
|
else
|
|
std::cout << "Could not open gain map " << gainfname << std::endl;
|
|
} else
|
|
*/
|
|
thr = 0.15 * thr;
|
|
filter->newDataSet();
|
|
// int dsize = decoder->getDataSize();
|
|
|
|
if (thr > 0) {
|
|
std::cout << "threshold is " << thr << std::endl;
|
|
filter->setThreshold(thr);
|
|
cf = 0;
|
|
|
|
} else
|
|
cf = 1;
|
|
|
|
filter->setROI(xmin, xmax, ymin, ymax);
|
|
std::time(&end_time);
|
|
std::cout << std::ctime(&end_time) << std::endl;
|
|
|
|
char *buff;
|
|
|
|
multiThreadedCountingDetector *mt =
|
|
new multiThreadedCountingDetector(filter, nthreads, fifosize);
|
|
mt->setClusterSize(csize, csize);
|
|
|
|
#ifndef ANALOG
|
|
mt->setDetectorMode(ePhotonCounting);
|
|
std::cout << "Counting!" << std::endl;
|
|
if (thr > 0) {
|
|
cf = 0;
|
|
}
|
|
#endif
|
|
//{
|
|
#ifdef ANALOG
|
|
mt->setDetectorMode(eAnalog);
|
|
std::cout << "Analog!" << std::endl;
|
|
cf = 0;
|
|
// thr1=thr;
|
|
#endif
|
|
// }
|
|
|
|
mt->StartThreads();
|
|
mt->popFree(buff);
|
|
|
|
// cout << "mt " << endl;
|
|
|
|
int ifr = 0;
|
|
|
|
if (pedfilename.length()>1) {
|
|
|
|
std::string froot = getRootString(pedfilename);
|
|
|
|
std::cout << "PEDESTAL " << std::endl;
|
|
|
|
if (pedfilename.find(".tif") == std::string::npos) {
|
|
const std::string fname(pedfilename);
|
|
std::cout << fname << std::endl;
|
|
std::time(&end_time);
|
|
std::cout << "aaa " << std::ctime(&end_time) << std::endl;
|
|
|
|
mt->setFrameMode(ePedestal);
|
|
|
|
std::ifstream pedefile(fname, ios::in | ios::binary);
|
|
// //open file
|
|
if (pedefile.is_open()) {
|
|
std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
|
|
|
|
ff = -1;
|
|
while (decoder->readNextFrame(pedefile, ff, np, buff)) {
|
|
// if (np == 40) {
|
|
if ((ifr + 1) % 100 == 0) {
|
|
std::cout
|
|
<< " ****"
|
|
<< decoder->getValue(buff, 20, 20); // << std::endl;
|
|
}
|
|
mt->pushData(buff);
|
|
mt->nextThread();
|
|
mt->popFree(buff);
|
|
ifr++;
|
|
if (ifr % 100 == 0) {
|
|
std::cout << " ****" << ifr << " " << ff << " " << np
|
|
<< std::endl;
|
|
} // else
|
|
//std::cout << ifr << " " << ff << " " << np << std::endl;
|
|
if (ifr >= 1000)
|
|
break;
|
|
ff = -1;
|
|
}
|
|
pedefile.close();
|
|
while (mt->isBusy()) {
|
|
;
|
|
}
|
|
|
|
std::cout << "froot " << froot << std::endl;
|
|
auto imgfname = createFileName( outdir, froot, "ped", "tiff");
|
|
mt->writePedestal(imgfname.c_str());
|
|
imgfname = createFileName( outdir, froot, "rms", "tiff");
|
|
mt->writePedestalRMS(imgfname.c_str());
|
|
|
|
} else
|
|
std::cout << "Could not open pedestal file " << fname
|
|
<< " for reading " << std::endl;
|
|
} else {
|
|
std::vector<double> ped(nx * ny);
|
|
float *pp = ReadFromTiff(pedfilename.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.data());
|
|
std::cout << "Pedestal set from tiff file " << pedfilename
|
|
<< std::endl;
|
|
} else {
|
|
std::cout << "Could not open pedestal tiff file " << pedfilename
|
|
<< " for reading " << std::endl;
|
|
}
|
|
}
|
|
std::time(&end_time);
|
|
std::cout << std::ctime(&end_time) << std::endl;
|
|
}
|
|
|
|
ifr = 0;
|
|
int ioutfile = 0;
|
|
|
|
mt->setFrameMode(eFrame);
|
|
|
|
FILE *of = NULL;
|
|
std::ifstream filebin{};
|
|
|
|
//NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
|
|
for (unsigned int ifile = 0; ifile != filenames.size(); ++ifile) {
|
|
std::cout << "DATA ";
|
|
std::string fsuffix{};
|
|
const std::string fprefix( getRootString(filenames[ifile]) );
|
|
std::string imgfname( createFileName( outdir, fprefix, fsuffix, "tiff" ) );
|
|
const std::string cfname( createFileName( outdir, fprefix, fsuffix, "clust" ) );
|
|
std::cout << filenames[ifile] << " ";
|
|
std::cout << imgfname << std::endl;
|
|
std::time(&end_time);
|
|
std::cout << std::ctime(&end_time) << std::endl;
|
|
|
|
ifstream filebin(filenames[ifile], ios::in | ios::binary);
|
|
// //open file
|
|
ioutfile = 0;
|
|
if (filebin.is_open()) {
|
|
if (thr <= 0 && cf != 0) { // cluster finder
|
|
if (of == NULL) {
|
|
of = fopen(cfname.c_str(), "w");
|
|
if (of) {
|
|
mt->setFilePointer(of);
|
|
std::cout << "file pointer set " << std::endl;
|
|
} else {
|
|
std::cout << "Could not open " << cfname
|
|
<< " for writing " << std::endl;
|
|
mt->setFilePointer(NULL);
|
|
return 1;
|
|
}
|
|
}
|
|
}
|
|
// //while read frame
|
|
ff = -1;
|
|
ifr = 0;
|
|
while (decoder->readNextFrame(filebin, ff, np, buff)) {
|
|
// if (np == 40) {
|
|
// //push
|
|
|
|
if ((ifr + 1) % 100 == 0) {
|
|
std::cout << " ****"
|
|
<< decoder->getValue(buff, 20, 20); // << std::endl;
|
|
}
|
|
mt->pushData(buff);
|
|
// // //pop
|
|
mt->nextThread();
|
|
mt->popFree(buff);
|
|
|
|
ifr++;
|
|
if (ifr % 100 == 0)
|
|
std::cout << " " << ifr << " " << ff << std::endl;
|
|
if (nframes > 0) {
|
|
if (ifr % nframes == 0) {
|
|
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ioutfile );
|
|
mt->writeImage(imgfname.c_str(), thr1);
|
|
mt->clearImage();
|
|
++ioutfile;
|
|
}
|
|
}
|
|
// } else
|
|
//std::cout << ifr << " " << ff << " " << np << std::endl;
|
|
ff = -1;
|
|
}
|
|
std::cout << "aa --" << std::endl;
|
|
filebin.close();
|
|
std::cout << "bb --" << std::endl;
|
|
while (mt->isBusy()) {
|
|
;
|
|
}
|
|
std::cout << "cc --" << std::endl;
|
|
if (nframes >= 0) {
|
|
if (nframes > 0)
|
|
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ioutfile );
|
|
std::cout << "Writing tiff to " << imgfname << " " << thr1
|
|
<< std::endl;
|
|
mt->writeImage(imgfname.c_str(), thr1);
|
|
mt->clearImage();
|
|
if (of) {
|
|
fclose(of);
|
|
of = NULL;
|
|
mt->setFilePointer(NULL);
|
|
}
|
|
}
|
|
std::time(&end_time);
|
|
std::cout << std::ctime(&end_time) << std::endl;
|
|
} else
|
|
std::cout << "Could not open " << filenames[ifile] << " for reading "
|
|
<< std::endl;
|
|
}
|
|
if (nframes < 0) {
|
|
//std::string fname(argv[10]);
|
|
std::string fprefix( getRootString(filenames[0]) ); //This might by a non-ideal name choice for that file
|
|
std::string imgfname( createFileName( outdir, fprefix, "sum", "tiff" ) );
|
|
std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
|
|
mt->writeImage(imgfname.c_str(), thr1);
|
|
}
|
|
|
|
return 0;
|
|
}
|