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slsDetectorPackage/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxt.cpp
vhinger182 2b93ef4565 minor
2023-10-06 11:55:20 +02:00

531 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>
#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>
#include <nlohmann/json.hpp>
using json = nlohmann::json;
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 < 11) {
std::cout
<< "Usage is " << argv[0]
<< " filestxt outdir [json master] [pedfile (raw or tiff)] [xmin xmax ymin ymax] "
"[threshold] [nframes] [optional: bool read rxroi from data file header]"
"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 jsonmastername(argv[3]);
const std::string pedfilename(argv[4]);
double thr = 0;
double thr1 = 1;
thr = atof(argv[9]);
int nframes = 0;
nframes = atoi(argv[10]);
bool readrxroifromdatafile = false;
if (argc > 11)
readrxroifromdatafile = atoi(argv[11]);
//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;
// Receiver ROI
uint16_t rxroi_xmin = 0;
uint16_t rxroi_xmax = 0;
uint16_t rxroi_ymin = 0;
uint16_t rxroi_ymax = 0;
{ //protective scope so ifstream gets destroyed properly
std::ifstream masterfile(jsonmastername); //, ios::in | ios::binary);
if (masterfile.is_open()) {
json j;
masterfile >> j;
rxroi_xmin = j["Receiver Roi"]["xmin"];
rxroi_xmax = j["Receiver Roi"]["xmax"];
rxroi_ymin = j["Receiver Roi"]["ymin"];
rxroi_ymax = j["Receiver Roi"]["ymax"];
masterfile.close();
std::cout << "Read rxROI [" << rxroi_xmin << ", " << rxroi_xmax << ", "
<< rxroi_ymin << ", " << rxroi_ymax << "]" << std::endl;
} else
std::cout << "Could not open master file " << jsonmastername << 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;
#ifndef ALDO
if (readrxroifromdatafile)
{ //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;
std::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;
rxroi_xmin = croi.xmin;
rxroi_xmax = croi.xmax;
rxroi_ymin = croi.ymin;
rxroi_ymax = 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(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
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;
//Cluster finder ROI
int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
xmin = atoi(argv[5]);
xmax = atoi(argv[6]);
ymin = atoi(argv[7]);
ymax = atoi(argv[8]);
std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
<< std::endl;
/* old
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;
std::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;
}
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