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https://github.com/slsdetectorgroup/slsDetectorPackage.git
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3 - Jf rawdataprocess wildcards (#723)
* Fix ROI mapping * Formatting * Minor edit * intial draft of cmake for jungfrau executables Makefile.rawdataprocess * added the cmake file * missed Makefile * added libfmt * Fix some compiler warnings * Fix some compiler warnings * Create filename usining fmt::format * Rewrite command line parsing with std::string and fmt::format * Fix file reading * Fix root string extraction * Fix ifstream file reading * Clean up comments * Add version of rawdataprocess with bash wildcards * Add version of rawdataprocess that reads inputs from txt-file, still buggy * fixing missing cstdint --------- Co-authored-by: vhinger182 <hinger_v@hv_home_lt1.localdomain> Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch> Co-authored-by: Erik Fröjdh <erik.frojdh@gmail.com>
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@ -2,6 +2,7 @@
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// Copyright (C) 2021 Contributors to the SLS Detector Package
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#ifndef JUNGFRAUMODULEDATA_H
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#define JUNGFRAUMODULEDATA_H
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#include <cstdint>
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#include "slsDetectorData.h"
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//#define VERSION_V2
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@ -2,6 +2,7 @@
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# Copyright (C) 2021 Contributors to the SLS Detector Package
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#module add CBFlib/0.9.5
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INCDIR=-I. -I../ -I../interpolations -I../interpolations/etaVEL -I../dataStructures -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../tiffio/include -I/afs/psi/project/sls_det_software/conda/envs/pyclang_fmt/include/
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LDFLAG= ../tiffio/src/tiffIO.cpp -L/afs/psi/project/sls_det_software/conda/envs/pyclang_fmt/lib/ -L/usr/lib64/ -lpthread -lm -lstdc++ -pthread -lrt -ltiff -O3 -std=c++11 -lfmt
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@ -41,6 +41,7 @@
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#include <ctime>
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#include <fmt/core.h>
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std::string getRootString( const std::string& filepath ) {
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size_t pos1 = filepath.find_last_of("/");
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size_t pos2 = filepath.find_last_of(".");
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@ -56,14 +57,16 @@ std::string getRootString( const std::string& filepath ) {
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// mindex: module index ("d0" in standard)
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// findex: file index for one acquisition ("f0")
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// aindex: acquisition index (i.e. "run number")
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std::string createFileName( const std::string& dir, const std::string& fprefix="run", const std::string& fsuffix="", const std::string& fext="raw", int aindex=0, int mindex=0, int findex=0, int outfilecounter=-1 ) {
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std::string filename{};
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if (outfilecounter >= 0)
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return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}_f{:05d}.{:s}", dir, fprefix, mindex, findex, aindex, outfilecounter, fext);
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filename = fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}_f{:05d}.{:s}", dir, fprefix, mindex, findex, aindex, outfilecounter, fext);
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else if (fsuffix.length()!=0)
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return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
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filename = fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
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else
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return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}.{:s}", dir, fprefix, mindex, findex, aindex, fext);
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filename = fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}.{:s}", dir, fprefix, mindex, findex, aindex, fext);
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return filename;
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}
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int main(int argc, char *argv[]) {
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@ -0,0 +1,467 @@
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// 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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#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 && \
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!defined JFSTRXCHIP6
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#ifndef MODULE
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#include "jungfrauHighZSingleChipData.h"
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#endif
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#ifdef MODULE
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#include "jungfrauModuleData.h"
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#endif
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#endif
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#ifdef JFSTRX
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#include "jungfrauLGADStrixelsData_new.h"
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#endif
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#if defined JFSTRXCHIP1 || defined JFSTRXCHIP6
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#include "jungfrauLGADStrixelsDataSingleChip.h"
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#endif
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#ifdef JFSTRXOLD
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#include "jungfrauStrixelsHalfModuleOldDesign.h"
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#endif
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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 <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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std::string getRootString( const std::string 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( const std::string dir, std::string fprefix="run", std::string fsuffix="", std::string fext="raw", int outfilecounter=-1 ) {
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std::string filename{};
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if (outfilecounter >= 0)
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filename = fmt::format("{:s}/{:s}_{:s}_f{:05d}.{:s}", dir, fprefix, fsuffix, outfilecounter, fext);
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else if (fsuffix.length()!=0)
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filename = fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
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else
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filename = fmt::format("{:s}/{:s}.{:s}", dir, fprefix, fext);
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return filename;
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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 < 10) {
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std::cout
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<< "Usage is " << argv[0]
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<< "outdir [pedfile (raw or tiff)] [xmin xmax ymin ymax] "
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"[threshold] [nframes] [full file path and names (with bash wildcards)] "
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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 fifosize = 1000;
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int nthreads = 10;
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int csize = 3; // 3
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int nsigma = 5;
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int nped = 10000;
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int cf = 0;
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double *gainmap = NULL;
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// float *gm;
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int ff, np;
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// cout << " data size is " << dsize;
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std::string outdir(argv[1]);
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std::string pedfilename(argv[2]);
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int xmin = atoi(argv[3]);
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int xmax = atoi(argv[4]);
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int ymin = atoi(argv[5]);
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int ymax = atoi(argv[6]);
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double thr = 0;
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double thr1 = 1;
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thr = atof(argv[7]);
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int nframes = 0;
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nframes = atoi(argv[8]);
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// Define decoders...
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#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 && \
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!defined JFSTRXCHIP6
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#ifndef MODULE
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jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
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int nx = 256, ny = 256;
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#endif
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#ifdef MODULE
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jungfrauModuleData *decoder = new jungfrauModuleData();
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int nx = 1024, ny = 512;
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#endif
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#endif
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#ifdef JFSTRX
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cout << "Jungfrau strixel full module readout" << endl;
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// ROI
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uint16_t xxmin = 0;
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uint16_t xxmax = 0;
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uint16_t yymin = 0;
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uint16_t yymax = 0;
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#ifndef ALDO
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{ //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
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using header = sls::defs::sls_receiver_header;
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// check if there is a roi in the header
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typedef struct {
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uint16_t xmin;
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uint16_t xmax;
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uint16_t ymin;
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uint16_t ymax;
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} receiverRoi_compact;
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receiverRoi_compact croi;
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std::string filepath(argv[9]); //This is a problem if the input files have different ROIs!
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std::cout << "Reading header of file " << filepath << " to check for ROI "
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<< std::endl;
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ifstream firstfile(filepath, ios::in | ios::binary);
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if (firstfile.is_open()) {
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header hbuffer;
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std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
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if (firstfile.read((char *)&hbuffer, sizeof(header))) {
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memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
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std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
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<< croi.ymin << ", " << croi.ymax << "]" << std::endl;
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xxmin = croi.xmin;
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xxmax = croi.xmax;
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yymin = croi.ymin;
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yymax = croi.ymax;
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} else
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std::cout << "reading error" << std::endl;
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firstfile.close();
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} else
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std::cout << "Could not open " << filepath << " for reading " << std::endl;
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} //end of protective scope
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#endif
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jungfrauLGADStrixelsData *decoder =
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new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
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int nx = 1024 / 3, ny = 512 * 5;
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#endif
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#ifdef JFSTRXCHIP1
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std::cout << "Jungfrau strixel LGAD single chip 1" << std::endl;
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jungfrauLGADStrixelsDataSingleChip *decoder =
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new jungfrauLGADStrixelsDataSingleChip(1);
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int nx = 256 / 3, ny = 256 * 5;
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#endif
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#ifdef JFSTRXCHIP6
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std::cout << "Jungfrau strixel LGAD single chip 6" << std::endl;
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jungfrauLGADStrixelsDataSingleChip *decoder =
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new jungfrauLGADStrixelsDataSingleChip(6);
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int nx = 256 / 3, ny = 256 * 5;
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#endif
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#ifdef JFSTRXOLD
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std::cout << "Jungfrau strixels old design" << std::endl;
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jungfrauStrixelsHalfModuleOldDesign *decoder =
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new jungfrauStrixelsHalfModuleOldDesign();
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int nx = 1024 * 3, ny = 512 / 3;
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#endif
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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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if ( xmin == xmax ) {
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xmin = 0;
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xmax = nx;
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}
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if ( ymin == ymax ) {
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ymin = 0;
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ymax = ny;
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}
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std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
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<< std::endl;
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/*
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char *gainfname = NULL;
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if (argc > 14) {
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gainfname = argv[14];
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std::cout << "Gain map file name is: " << gainfname << std::endl;
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}
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*/
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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 = new singlePhotonDetector(
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decoder, 3, nsigma, 1, NULL, nped, 200, -1, -1, gainmap, NULL);
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/*
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if (gainfname) {
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if (filter->readGainMap(gainfname))
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std::cout << "using gain map " << gainfname << std::endl;
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else
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std::cout << "Could not open gain map " << gainfname << std::endl;
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} else
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*/
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thr = 0.15 * thr;
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filter->newDataSet();
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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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mt->setClusterSize(csize, csize);
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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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// cout << "mt " << endl;
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int ifr = 0;
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if (pedfilename.length()>1) {
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std::string froot = getRootString(pedfilename);
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std::cout << "PEDESTAL " << std::endl;
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if (pedfilename.find(".tif") == std::string::npos) {
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std::string 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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ifstream pedefile(fname, ios::in | ios::binary);
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// //open file
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if (pedefile.is_open()) {
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std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
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ff = -1;
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while (decoder->readNextFrame(pedefile, ff, np, buff)) {
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// if (np == 40) {
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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 << " " << ff << " " << np
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<< std::endl;
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} // else
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//std::cout << ifr << " " << ff << " " << np << std::endl;
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if (ifr >= 1000)
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break;
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ff = -1;
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}
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pedefile.close();
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while (mt->isBusy()) {
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;
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}
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std::cout << "froot " << froot << std::endl;
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auto imgfname = createFileName( outdir, froot, "ped", "tiff");
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mt->writePedestal(imgfname.c_str());
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imgfname = createFileName( outdir, froot, "rms", "tiff");
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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 {
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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 ifile = 0;
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mt->setFrameMode(eFrame);
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FILE *of = NULL;
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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 (int iargc = 9; iargc != argc; ++iargc) {
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std::cout << "DATA ";
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std::string fname(argv[iargc]);
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std::string fsuffix{};
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std::string fprefix = getRootString(fname);
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std::string imgfname = createFileName( outdir, fprefix, fsuffix, "tiff" );
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std::string cfname = createFileName( outdir, fprefix, fsuffix, "clust" );
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std::cout << fname << " ";
|
||||
std::cout << imgfname << std::endl;
|
||||
std::time(&end_time);
|
||||
std::cout << std::ctime(&end_time) << std::endl;
|
||||
|
||||
ifstream filebin(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.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", ifile );
|
||||
mt->writeImage(imgfname.c_str(), thr1);
|
||||
mt->clearImage();
|
||||
ifile++;
|
||||
}
|
||||
}
|
||||
// } else
|
||||
//std::cout << ifr << " " << ff << " " << np << std::endl;
|
||||
ff = -1;
|
||||
}
|
||||
std::cout << "--" << std::endl;
|
||||
filebin.close();
|
||||
while (mt->isBusy()) {
|
||||
;
|
||||
}
|
||||
if (nframes >= 0) {
|
||||
if (nframes > 0)
|
||||
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ifile );
|
||||
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 " << fname << " for reading "
|
||||
<< std::endl;
|
||||
}
|
||||
if (nframes < 0) {
|
||||
std::string fname(argv[10]);
|
||||
auto fprefix = getRootString(fname); //This might by a non-ideal name choice for that file
|
||||
auto imgfname = createFileName( outdir, fprefix, "sum", "tiff" );
|
||||
std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
|
||||
mt->writeImage(imgfname.c_str(), thr1);
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
@ -0,0 +1,491 @@
|
||||
// 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, std::string fprefix="run", std::string fsuffix="", std::string fext="raw", int outfilecounter=-1 ) {
|
||||
std::string filename{};
|
||||
if (outfilecounter >= 0)
|
||||
filename = fmt::format("{:s}/{:s}_{:s}_f{:05d}.{:s}", dir, fprefix, fsuffix, outfilecounter, fext);
|
||||
else if (fsuffix.length()!=0)
|
||||
filename = fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
|
||||
else
|
||||
filename = fmt::format("{:s}/{:s}.{:s}", dir, fprefix, fext);
|
||||
return filename;
|
||||
}
|
||||
|
||||
|
||||
//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;
|
||||
|
||||
std::string txtfilename(argv[1]);
|
||||
std::string outdir(argv[2]);
|
||||
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{};
|
||||
{ //Safety scope for ifstream
|
||||
ifstream inputs( txtfilename, std::ios::in );
|
||||
if (inputs.is_open()) {
|
||||
std::cout << "Reading imput filenames from txt-file ..." << std::endl;
|
||||
while (!inputs.eof()) {
|
||||
std::string line{};
|
||||
std::getline(inputs, line);
|
||||
filenames.push_back(line);
|
||||
}
|
||||
std::cout << "---- Reached end of txt-file. ----" << 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;
|
||||
}
|
||||
} else
|
||||
std::cout << "Could not open " << txtfilename << 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) {
|
||||
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);
|
||||
|
||||
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;
|
||||
|
||||
//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 fname(argv[iargc]);
|
||||
std::string fsuffix{};
|
||||
std::string fprefix = getRootString(filenames[ifile]);
|
||||
std::string imgfname = createFileName( outdir, fprefix, fsuffix, "tiff" );
|
||||
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
|
||||
ifile = 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 << "--" << std::endl;
|
||||
filebin.close();
|
||||
while (mt->isBusy()) {
|
||||
;
|
||||
}
|
||||
if (nframes >= 0) {
|
||||
if (nframes > 0)
|
||||
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ifile );
|
||||
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]);
|
||||
auto fprefix = getRootString(filenames[0]); //This might by a non-ideal name choice for that file
|
||||
auto imgfname = createFileName( outdir, fprefix, "sum", "tiff" );
|
||||
std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
|
||||
mt->writeImage(imgfname.c_str(), thr1);
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
@ -4,6 +4,7 @@
|
||||
#include <array>
|
||||
#include <iostream>
|
||||
#include <string>
|
||||
#include <cstdint>
|
||||
|
||||
namespace sls {
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user