mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-06-04 00:50:42 +02:00
2 - Jf rawdataprocess fmt (#725)
* 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 requested changes to helper functions * fix const& --------- Co-authored-by: vhinger182 <hinger_v@hv_home_lt1.localdomain> Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>
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commit
72c992bc74
@ -406,9 +406,9 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
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np = 0;
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//int pn;
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// std::cout << dataSize << std::endl;
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if (ff >= 0)
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// fnum = ff;
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//std::cout << dataSize << std::endl;
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//if (ff >= 0) {
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// fnum = ff; }
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if (filebin.is_open()) {
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if (filebin.read(data, dataSize)) {
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@ -417,7 +417,10 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
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np = getPacketNumber(data);
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return data;
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}
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}
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std::cout << "#";
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} else {
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std::cout << "File not open" << std::endl;
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}
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return NULL;
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};
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@ -41,12 +41,37 @@
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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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std::cout << "pos1 " << pos1 << " pos2 " << pos2 << " size " << filepath.length() << std::endl;
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return filepath.substr( pos1+1, pos2-pos1-1 );
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}
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//Create file name string according to slsDetectorPackage format
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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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// 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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else if (fsuffix.length()!=0)
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return 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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}
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int main(int argc, char *argv[]) {
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if (argc < 5) {
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std::cout
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<< "Usage is " << argv[0]
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<< "indir outdir fname(with formatting, no extension) fextension "
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<< "indir outdir fprefix(excluding slsDetector standard suffixes and extension) fextension "
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"[runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
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"[nframes] [xmin xmax ymin ymax] [gainmap]"
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<< std::endl;
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@ -75,11 +100,11 @@ int main(int argc, char *argv[]) {
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int ff, np;
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// cout << " data size is " << dsize;
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ifstream filebin;
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char *indir = argv[1];
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char *outdir = argv[2];
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char *fformat = argv[3];
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char *fext = argv[4];
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//ifstream filebin;
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std::string indir(argv[1]);
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std::string outdir(argv[2]);
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std::string fprefix(argv[3]);
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std::string fext(argv[4]);
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int runmin = 0;
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// cout << "argc is " << argc << endl;
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@ -93,9 +118,9 @@ int main(int argc, char *argv[]) {
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runmax = atoi(argv[6]);
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}
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char *pedfile = NULL;
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std::string pedfilename{};
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if (argc >= 8) {
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pedfile = argv[7];
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pedfilename = argv[7];
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}
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double thr = 0;
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double thr1 = 1;
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@ -109,12 +134,7 @@ int main(int argc, char *argv[]) {
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if (argc >= 10) {
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nframes = atoi(argv[9]);
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}
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char ffname[10000];
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char fname[10000];
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char imgfname[10000];
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char cfname[10000];
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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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@ -137,36 +157,38 @@ int main(int argc, char *argv[]) {
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uint16_t yymax = 0;
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#ifndef ALDO
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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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{ //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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sprintf(ffname, "%s/%s.%s", indir, fformat, fext);
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sprintf(fname, (const char *)ffname, runmin);
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std::cout << "Reading header of file " << fname << " to check for ROI "
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<< std::endl;
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filebin.open((const char *)(fname), ios::in | ios::binary);
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if (filebin.is_open()) {
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} receiverRoi_compact;
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receiverRoi_compact croi;
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std::string fsuffix{};
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auto filename = createFileName( indir, fprefix, fsuffix, fext, runmin );
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std::cout << "Reading header of file " << filename << " to check for ROI "
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<< std::endl;
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ifstream firstfile(filename, 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 (filebin.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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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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filebin.close();
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} else
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std::cout << "Could not open " << fname << " for reading " << std::endl;
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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 " << filename << " 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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@ -213,14 +235,13 @@ int main(int argc, char *argv[]) {
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std::time_t end_time;
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FILE *of = NULL;
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std::cout << "input directory is " << indir << std::endl;
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std::cout << "output directory is " << outdir << std::endl;
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std::cout << "input file is " << fformat << std::endl;
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std::cout << "input file prefix is " << fprefix << std::endl;
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std::cout << "runmin is " << runmin << std::endl;
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std::cout << "runmax is " << runmax << std::endl;
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if (pedfile)
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std::cout << "pedestal file is " << pedfile << 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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@ -256,8 +277,6 @@ int main(int argc, char *argv[]) {
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char *buff;
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// multiThreadedAnalogDetector *mt=new
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// multiThreadedAnalogDetector(filter,nthreads,fifosize);
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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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@ -285,84 +304,75 @@ int main(int argc, char *argv[]) {
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int ifr = 0;
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char froot[1000];
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double *ped = new double[nx * ny]; //, *ped1;
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if (pedfilename.length()!=0) {
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int pos, pos1;
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std::string froot = getRootString(pedfilename);
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if (pedfile) {
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std::cout << "PEDESTAL " << std::endl;
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if (string(pedfile).find(".dat") != std::string::npos) {
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pos1 = string(pedfile).rfind("/");
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strcpy(froot, pedfile + pos1);
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pos = string(froot).find(".dat");
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froot[pos] = '\0';
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}
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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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std::cout << "PEDESTAL " << std::endl;
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// sprintf(imgfname, "%s/pedestals.tiff", outdir);
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mt->setFrameMode(ePedestal);
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if (string(pedfile).find(".tif") == std::string::npos) {
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sprintf(fname, "%s", pedfile);
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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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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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mt->setFrameMode(ePedestal);
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// sprintf(fn,fformat,irun);
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filebin.open((const char *)(fname), ios::in | ios::binary);
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// //open file
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if (filebin.is_open()) {
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std::cout << "bbbb" << std::ctime(&end_time) << std::endl;
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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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ff = -1;
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while (decoder->readNextFrame(filebin, 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); // << 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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// cout << ifr << " " << ff << " " << np << 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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filebin.close();
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while (mt->isBusy()) {
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;
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}
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sprintf(imgfname, "%s/%s_ped.tiff", outdir, froot);
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mt->writePedestal(imgfname);
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sprintf(imgfname, "%s/%s_rms.tiff", outdir, froot);
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mt->writePedestalRMS(imgfname);
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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::cout << "Could not open pedestal file " << fname
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<< " for reading " << std::endl;
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} else {
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float *pp = ReadFromTiff(pedfile, 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);
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std::cout << "Pedestal set from tiff file " << pedfile
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<< std::endl;
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} else {
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std::cout << "Could not open pedestal tiff file " << pedfile
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<< " for reading " << std::endl;
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}
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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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@ -373,27 +383,26 @@ int main(int argc, char *argv[]) {
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mt->setFrameMode(eFrame);
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FILE *of = NULL;
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for (int irun = runmin; irun <= runmax; irun++) {
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std::cout << "DATA ";
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// sprintf(fn,fformat,irun);
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sprintf(ffname, "%s/%s.%s", indir, fformat, fext);
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sprintf(fname, (const char *)ffname, irun);
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sprintf(ffname, "%s/%s.tiff", outdir, fformat);
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sprintf(imgfname, (const char *)ffname, irun);
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sprintf(ffname, "%s/%s.clust", outdir, fformat);
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sprintf(cfname, (const char *)ffname, irun);
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std::string fsuffix{};
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auto fname = createFileName( indir, fprefix, fsuffix, fext, irun );
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auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun );
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auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun );
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std::cout << fname << " ";
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std::cout << imgfname << std::endl;
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std::time(&end_time);
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std::cout << std::ctime(&end_time) << std::endl;
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// cout << fname << " " << outfname << " " << imgfname << endl;
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filebin.open((const char *)(fname), ios::in | ios::binary);
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// std::cout << fname << " " << outfname << " " << imgfname << std::endl;
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ifstream filebin(fname, ios::in | ios::binary);
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// //open file
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ifile = 0;
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if (filebin.is_open()) {
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if (thr <= 0 && cf != 0) { // cluster finder
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if (of == NULL) {
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of = fopen(cfname, "w");
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of = fopen(cfname.c_str(), "w");
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if (of) {
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mt->setFilePointer(of);
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std::cout << "file pointer set " << std::endl;
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@ -414,7 +423,7 @@ int main(int argc, char *argv[]) {
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if ((ifr + 1) % 100 == 0) {
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std::cout << " ****"
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<< decoder->getValue(buff, 20, 20); // << endl;
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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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@ -426,16 +435,14 @@ int main(int argc, char *argv[]) {
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std::cout << " " << ifr << " " << ff << std::endl;
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if (nframes > 0) {
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if (ifr % nframes == 0) {
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sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat,
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ifile);
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sprintf(imgfname, (const char *)ffname, irun);
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mt->writeImage(imgfname, thr1);
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imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
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mt->writeImage(imgfname.c_str(), thr1);
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mt->clearImage();
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ifile++;
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}
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}
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// } else
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// cout << ifr << " " << ff << " " << np << endl;
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//std::cout << ifr << " " << ff << " " << np << std::endl;
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ff = -1;
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}
|
||||
std::cout << "--" << std::endl;
|
||||
@ -444,16 +451,11 @@ int main(int argc, char *argv[]) {
|
||||
;
|
||||
}
|
||||
if (nframes >= 0) {
|
||||
if (nframes > 0) {
|
||||
sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat, ifile);
|
||||
sprintf(imgfname, (const char *)ffname, irun);
|
||||
} else {
|
||||
sprintf(ffname, "%s/%s.tiff", outdir, fformat);
|
||||
sprintf(imgfname, (const char *)ffname, irun);
|
||||
}
|
||||
if (nframes > 0)
|
||||
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
|
||||
std::cout << "Writing tiff to " << imgfname << " " << thr1
|
||||
<< std::endl;
|
||||
mt->writeImage(imgfname, thr1);
|
||||
mt->writeImage(imgfname.c_str(), thr1);
|
||||
mt->clearImage();
|
||||
if (of) {
|
||||
fclose(of);
|
||||
@ -468,10 +470,9 @@ int main(int argc, char *argv[]) {
|
||||
<< std::endl;
|
||||
}
|
||||
if (nframes < 0) {
|
||||
sprintf(ffname, "%s/%s.tiff", outdir, fformat);
|
||||
strcpy(imgfname, ffname);
|
||||
auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", -1, 0, 0, -1 );
|
||||
std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
|
||||
mt->writeImage(imgfname, thr1);
|
||||
mt->writeImage(imgfname.c_str(), thr1);
|
||||
}
|
||||
|
||||
return 0;
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user