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https://github.com/slsdetectorgroup/slsDetectorPackage.git
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458 lines
15 KiB
C++
458 lines
15 KiB
C++
// SPDX-License-Identifier: LGPL-3.0-or-other
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// Copyright (C) 2021 Contributors to the SLS Detector Package
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// #include "sls/ansi.h"
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//#include <iostream>
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#undef CORR
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#define C_GHOST 0.0004
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#define CM_ROWS 50
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#define RAWDATA
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#include "jungfrauLGADStrixelsDataQuadH5.h"
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#include "multiThreadedCountingDetector.h"
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#include "singlePhotonDetector.h"
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#include <fstream>
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#include <map>
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#include <memory>
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#include <stdio.h>
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#include <sys/stat.h>
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#include <ctime>
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#include <fmt/core.h>
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/*
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#include <nlohmann/json.hpp>
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using json = nlohmann::json;
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*/
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/*Dataset paths according to different beamlines*/
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std::string const data_datasetname_furka("/data/JF18T01V01/data");
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std::string const index_datasetname_furka("/data/JF18T01V01/frame_index");
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std::string const data_datasetname_xfelSCS("/INSTRUMENT/SCS_HRIXS_JUNGF/DET/JNGFR01:daqOutput/data/adc");
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std::string const index_datasetname_xfelSCS("/INSTRUMENT/SCS_HRIXS_JUNGF/DET/JNGFR01:daqOutput/data/frameNumber");
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std::string getRootString( std::string const& filepath ) {
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size_t pos1;
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if (filepath.find("/") == std::string::npos )
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pos1 = 0;
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else
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pos1 = filepath.find_last_of("/")+1;
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size_t pos2 = filepath.find_last_of(".");
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//std::cout << "pos1 " << pos1 << " pos2 " << pos2 << " size " << filepath.length() << std::endl;
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return filepath.substr( pos1, pos2-pos1 );
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}
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//Create file name string
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// dir: directory
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// fprefix: fileprefix (without extension)
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// fsuffix: filesuffix (for output files, e.g. "ped")
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// fext: file extension (e.g. "raw")
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std::string createFileName( std::string const& dir, std::string const& fprefix="run",
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std::string const& fsuffix="", std::string const& fext="raw", int const outfilecounter=-1 ) {
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std::string return_string;
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if (outfilecounter >= 0)
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return_string = fmt::format("{:s}/{:s}_{:s}_f{:05d}", dir, fprefix, fsuffix, outfilecounter);
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else if (fsuffix.length()!=0)
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return_string = fmt::format("{:s}/{:s}_{:s}", dir, fprefix, fsuffix);
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else
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return_string = fmt::format("{:s}/{:s}", dir, fprefix);
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if (fext.length()!=0)
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return_string += "." + fext;
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return return_string;
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}
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//NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
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int main(int argc, char *argv[]) {
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if (argc < 4) {
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std::cout
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<< "Usage is " << argv[0]
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<< " filestxt outdir [pedfile (h5)] "
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" optional: [int dataset path; 0 means Furka, 1 means XFEL; overwrites default given in HDF5File.h] "
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" [bool validate h5 rank] "
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" [xmin xmax ymin ymax] [threshold] [nframes] "
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" NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS! "
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<< std::endl;
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std::cout
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<< "threshold <0 means analog; threshold=0 means cluster finder; "
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"threshold>0 means photon counting"
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<< std::endl;
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std::cout
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<< "nframes <0 means sum everything; nframes=0 means one file per "
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"run; nframes>0 means one file every nframes"
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<< std::endl;
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return 1;
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}
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int const fifosize = 100; //1000;
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int const nthreads = 10;
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int const csize = 3; // 3
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int const nsigma = 5;
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int const nped = 10000;
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int cf = 0;
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std::string const txtfilename(argv[1]);
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std::string const outdir(argv[2]);
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std::string const pedfilename(argv[3]);
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std::string datasetpath{};
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std::string frameindexpath{};
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if (argc > 4) {
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switch (atoi(argv[4])) {
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case 0:
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datasetpath = data_datasetname_furka;
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frameindexpath = index_datasetname_furka;
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break;
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case 1:
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datasetpath = data_datasetname_xfelSCS;
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frameindexpath = index_datasetname_xfelSCS;
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break;
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default:
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break;
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}
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}
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bool validate_rank=true;
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if (argc > 5)
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validate_rank = atoi(argv[5]);
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double thr = 0;
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double thr1 = 1;
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if (argc > 9)
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thr = atof(argv[9]);
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int nframes = 0;
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if (argc > 10)
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nframes = atoi(argv[10]);
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//Get vector of filenames from input txt-file
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std::vector<std::string> filenames{};
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//filenames.reserve(512);
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{ //Safety scope for ifstream
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ifstream inputs( txtfilename, std::ios::in );
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if (inputs.is_open()) {
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std::cout << "Reading imput filenames from txt-file ..." << std::endl;
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std::string line{};
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while (!inputs.eof()) {
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std::getline(inputs, line);
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if(line.find(".h5") != std::string::npos) {
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filenames.emplace_back(line);
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std::cout << line << std::endl; //" line.max_size() " << line.max_size() << " filenames.capacity() " << filenames.capacity() << '\n';
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}
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}
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inputs.close();
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std::cout << "---- Reached end of txt-file. ----" << std::endl;
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} else
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std::cout << "Could not open " << txtfilename << std::endl;
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if (filenames.size()>0) {
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std::cout << filenames.size() << " filenames found in " << txtfilename << std::endl;
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std::cout << "The files will be processed in the same order as found in the txt-file." << std::endl;
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} else {
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std::cout << "No files found in txt-file!" << std::endl;
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return 1;
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}
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}
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std::cout << "###############" << std::endl;
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// Define decoder
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std::cout << "Jungfrau strixel quad h5" << std::endl;
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jungfrauLGADStrixelsDataQuadH5* decoder = new jungfrauLGADStrixelsDataQuadH5();
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//auto decoder = std::make_unique<jungfrauLGADStrixelsDataQuadH5>();
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int nx = 1024 / 3, ny = 512 * 3;
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//Cluster finder ROI
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int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
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if (argc > 9) {
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xmin = atoi(argv[6]);
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xmax = atoi(argv[7]);
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ymin = atoi(argv[8]);
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ymax = atoi(argv[9]);
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}
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std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
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<< std::endl;
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decoder->getDetectorSize(nx, ny);
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std::cout << "Detector size is " << nx << " " << ny << std::endl;
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std::time_t end_time;
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std::cout << "output directory is " << outdir << std::endl;
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if (pedfilename.length()!=0)
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std::cout << "pedestal file is " << pedfilename << std::endl;
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if (thr > 0)
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std::cout << "threshold is " << thr << std::endl;
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std::cout << "Nframes is " << nframes << std::endl;
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uint32_t nnx, nny;
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singlePhotonDetector* filter =
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new singlePhotonDetector(decoder, 3, nsigma, 1, NULL, nped, 200, -1, -1, NULL, NULL);
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//auto filter = std::make_unique<singlePhotonDetector>(decoder.get(), 3, nsigma, 1, nullptr, nped, 200, -1, -1, nullptr, nullptr);
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thr = 0.15 * thr;
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//filter->newDataSet(); //This only initializes the dataset for the first thread (the other threads are created via cloning)
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// int dsize = decoder->getDataSize();
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if (thr > 0) {
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std::cout << "threshold is " << thr << std::endl;
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filter->setThreshold(thr);
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cf = 0;
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} else
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cf = 1;
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filter->setROI(xmin, xmax, ymin, ymax);
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std::time(&end_time);
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std::cout << std::ctime(&end_time) << std::endl;
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char* buff;
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multiThreadedCountingDetector* mt =
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new multiThreadedCountingDetector(filter, nthreads, fifosize);
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//auto mt = std::make_unique<multiThreadedCountingDetector>(filter.get(), nthreads, fifosize);
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mt->setClusterSize(csize, csize);
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mt->newDataSet(); //Initialize new dataset for each thread
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#ifndef ANALOG
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mt->setDetectorMode(ePhotonCounting);
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std::cout << "Counting!" << std::endl;
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if (thr > 0) {
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cf = 0;
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}
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#endif
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//{
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#ifdef ANALOG
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mt->setDetectorMode(eAnalog);
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std::cout << "Analog!" << std::endl;
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cf = 0;
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// thr1=thr;
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#endif
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// }
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mt->StartThreads();
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mt->popFree(buff);
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int ifr = 0; //frame counter of while loop
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int framenumber = 0; //framenumber as read from file (detector)
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std::vector<hsize_t> h5offset(1,0); //frame counter internal to HDF5File::ReadImage (provided for sanity check/debugging)
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if (pedfilename.length()>1) {
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std::cout << "PEDESTAL " << std::endl;
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if (pedfilename.find(".tif") == std::string::npos) { //not a tiff file
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std::string const fname(pedfilename);
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std::cout << fname << std::endl;
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std::time(&end_time);
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std::cout << "aaa " << std::ctime(&end_time) << std::endl;
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mt->setFrameMode(ePedestal);
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//HDF5File pedefile;
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auto pedefile = std::make_unique<HDF5File>();
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pedefile->SetFrameIndexPath(frameindexpath);
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pedefile->SetImageDataPath(datasetpath);
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// //open file
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if ( pedefile->OpenResources(fname.c_str(),validate_rank) ) {
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std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
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framenumber = 0;
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while ( decoder->readNextFrame(*pedefile, framenumber, h5offset, buff) ) {
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if ((ifr + 1) % 100 == 0) {
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std::cout
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<< " ****"
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<< decoder->getValue(buff, 20, 20); // << std::endl;
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}
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mt->pushData(buff);
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mt->nextThread();
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mt->popFree(buff);
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++ifr;
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if (ifr % 100 == 0) {
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std::cout << " ****" << ifr << " " << framenumber << " " << h5offset[0]
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<< std::endl;
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} // else
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if (ifr >= 1000)
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break;
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//framenumber = 0;
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}
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pedefile->CloseResources();
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while (mt->isBusy()) {
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;
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}
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std::cout << "Writing pedestal to " << getRootString(pedfilename) << "_ped.tiff" << std::endl;
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auto imgfname = createFileName( outdir, getRootString(pedfilename), "ped", "");
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mt->writePedestal(imgfname.c_str());
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std::cout << "Writing pedestal rms to " << getRootString(pedfilename) << "_rms.tiff" << std::endl;
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imgfname = createFileName( outdir, getRootString(pedfilename), "rms", "");
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mt->writePedestalRMS(imgfname.c_str());
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} else
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std::cout << "Could not open pedestal file " << fname
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<< " for reading " << std::endl;
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} else { //is a tiff file
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std::vector<double> ped(nx * ny);
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float* pp = ReadFromTiff(pedfilename.c_str(), nny, nnx);
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if (pp && (int)nnx == nx && (int)nny == ny) {
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for (int i = 0; i < nx * ny; i++) {
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ped[i] = pp[i];
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}
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delete[] pp;
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mt->setPedestal(ped.data());
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std::cout << "Pedestal set from tiff file " << pedfilename
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<< std::endl;
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} else {
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std::cout << "Could not open pedestal tiff file " << pedfilename
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<< " for reading " << std::endl;
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}
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}
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std::time(&end_time);
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std::cout << std::ctime(&end_time) << std::endl;
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}
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ifr = 0;
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int ioutfile = 0;
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mt->setFrameMode(eFrame);
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FILE* of = nullptr;
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//NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
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for (unsigned int ifile = 0; ifile != filenames.size(); ++ifile) {
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std::cout << "DATA " << filenames[ifile] << " " << std::endl;
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auto imgfname( createFileName( outdir, getRootString(filenames[ifile]), "", "" ) );
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std::string const cfname( createFileName( outdir, getRootString(filenames[ifile]), "", "clust" ) );
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std::time(&end_time);
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std::cout << std::ctime(&end_time) << std::endl;
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//HDF5File fileh5;
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auto fileh5 = std::make_unique<HDF5File>();
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fileh5->SetFrameIndexPath(frameindexpath);
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fileh5->SetImageDataPath(datasetpath);
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// //open file
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ioutfile = 0;
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if ( fileh5->OpenResources(filenames[ifile].c_str(), validate_rank) ) {
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if (thr <= 0 && cf != 0) { // cluster finder
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if (of == nullptr) {
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of = fopen(cfname.c_str(), "w");
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if (of) {
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if (mt) {
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mt->setFilePointer(of);
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std::cout << "file pointer set " << std::endl;
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} else {
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std::cerr << "Error: mt is null." << std::endl;
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return 1;
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}
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//mt->setFilePointer(of);
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//std::cout << "file pointer set " << std::endl;
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//std::cout << "Here! " << framenumber << " ";
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} else {
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std::cout << "Could not open " << cfname
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<< " for writing " << std::endl;
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mt->setFilePointer(nullptr);
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return 1;
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}
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}
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}
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// //while read frame
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framenumber = 0;
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h5offset[0] = 0;
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ifr = 0;
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//std::cout << "Here! " << framenumber << " ";
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while ( decoder->readNextFrame(*fileh5, framenumber, h5offset, buff) ) {
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//std::cout << "Here! " << framenumber << " ";
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// //push
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if ((ifr + 1) % 1000 == 0) {
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std::cout << " ****"
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<< decoder->getValue(buff, 20, 20); // << std::endl;
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}
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mt->pushData(buff);
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// // //pop
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mt->nextThread();
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mt->popFree(buff); /* In the last execution of the loop,
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* this leaves buff outside of the Fifo!
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* Free explicitely at the end! */
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++ifr;
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if (ifr % 1000 == 0)
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std::cout << " " << ifr << " " << framenumber << " " << h5offset[0]
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<< std::endl;
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if (nframes > 0) {
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if (ifr % nframes == 0) {
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imgfname = createFileName( outdir, getRootString(filenames[ifile]), "", "", ioutfile );
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mt->writeImage(imgfname.c_str(), thr1);
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mt->clearImage();
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++ioutfile;
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}
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}
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//framenumber = 0;
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}
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//std::cout << "aa --" << std::endl;
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fileh5->CloseResources();
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//std::cout << "bb --" << std::endl;
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while (mt->isBusy()) {
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;
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}
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//std::cout << "cc --" << std::endl;
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if (nframes >= 0) {
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if (nframes > 0)
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imgfname = createFileName( outdir, getRootString(filenames[ifile]), "", "", ioutfile );
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std::cout << "Writing tiff to " << imgfname << " " << thr1 << ".tiff"
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<< std::endl;
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mt->writeImage(imgfname.c_str(), thr1);
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mt->clearImage();
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if (of) {
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fclose(of);
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of = nullptr;
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mt->setFilePointer(nullptr);
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}
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}
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std::time(&end_time);
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std::cout << std::ctime(&end_time) << std::endl;
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} else
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std::cout << "Could not open " << filenames[ifile] << " for reading "
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<< std::endl;
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}
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if (nframes < 0) {
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//std::string fprefix( getRootString(filenames[0]) ); //Possibly, non-ideal name choice for file
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auto imgfname( createFileName( outdir, getRootString(filenames[0]), "sum", "" ) );
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std::cout << "Writing tiff to " << imgfname << " " << thr1 << ".tiff" << std::endl;
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mt->writeImage(imgfname.c_str(), thr1);
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}
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//std::cout << "Calling delete..." << std::endl;
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/* Info: Previously, 'delete mt' caused crash
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(double calls of StopThread() in both destructors of
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multiThreadedAnalogDetector and threadedAnalogDetector)
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Now fixed! */
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delete mt; // triggers cleanup of all threads and singlePhotonDetector instances (delete filter is obsolete)
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delete decoder;
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free(buff); // Free explicitly as it gets popped out of the Fifo at termination of while(readNextFrame)
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return 0;
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}
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