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Generalize HDF5 reader for 3- or 4-dimensional datasets

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This commit is contained in:
hinger_v
2025-02-03 17:28:33 +01:00
parent 25854f7736
commit 71ca4e9f0f
4 changed files with 438 additions and 261 deletions
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69
slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxtH5.cpp
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@ -30,6 +30,11 @@
using json = nlohmann::json;
*/
/*Dataset paths according to different beamlines*/
std::string const data_datasetname_furka("/data/JF18T01V01/data");
std::string const index_datasetname_furka("/data/JF18T01V01/frame_index");
std::string const data_datasetname_xfelSCS("/INSTRUMENT/SCS_HRIXS_JUNGF/DET/JNGFR01:daqOutput/data/adc");
std::string const index_datasetname_xfelSCS("/INSTRUMENT/SCS_HRIXS_JUNGF/DET/JNGFR01:daqOutput/data/frameNumber");
std::string getRootString( std::string const& filepath ) {
size_t pos1;
@ -64,9 +69,11 @@ int main(int argc, char *argv[]) {
if (argc < 4) {
std::cout
<< "Usage is " << argv[0]
<< " filestxt outdir [pedfile (h5)] optional: [bool validate h5 rank] "
"[xmin xmax ymin ymax] [threshold] [nframes] "
"NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS! "
<< " filestxt outdir [pedfile (h5)] "
" optional: [int dataset path; 0 means Furka, 1 means XFEL; overwrites default given in HDF5File.h] "
" [bool validate h5 rank] "
" [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; "
@ -91,18 +98,35 @@ int main(int argc, char *argv[]) {
std::string const outdir(argv[2]);
std::string const pedfilename(argv[3]);
std::string datasetpath{};
std::string frameindexpath{};
if (argc > 4) {
switch (atoi(argv[4])) {
case 0:
datasetpath = data_datasetname_furka;
frameindexpath = index_datasetname_furka;
break;
case 1:
datasetpath = data_datasetname_xfelSCS;
frameindexpath = index_datasetname_xfelSCS;
break;
default:
break;
}
}
bool validate_rank=true;
if (argc > 4)
validate_rank = atoi(argv[4]);
if (argc > 5)
validate_rank = atoi(argv[5]);
double thr = 0;
double thr1 = 1;
if (argc > 8)
thr = atof(argv[8]);
if (argc > 9)
thr = atof(argv[9]);
int nframes = 0;
if (argc > 9)
nframes = atoi(argv[9]);
if (argc > 10)
nframes = atoi(argv[10]);
//Get vector of filenames from input txt-file
std::vector<std::string> filenames{};
@ -142,11 +166,11 @@ int main(int argc, char *argv[]) {
//Cluster finder ROI
int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
if (argc > 8) {
xmin = atoi(argv[5]);
xmax = atoi(argv[6]);
ymin = atoi(argv[7]);
ymax = atoi(argv[8]);
if (argc > 9) {
xmin = atoi(argv[6]);
xmax = atoi(argv[7]);
ymin = atoi(argv[8]);
ymax = atoi(argv[9]);
}
std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
<< std::endl;
@ -214,7 +238,7 @@ int main(int argc, char *argv[]) {
int ifr = 0; //frame counter of while loop
int framenumber = -1; //framenumber as read from file (detector)
int iframe = 0; //frame counter internal to HDF5File::ReadImage (provided for sanity check/debugging)
std::vector<hsize_t> h5offset(1,0); //frame counter internal to HDF5File::ReadImage (provided for sanity check/debugging)
if (pedfilename.length()>1) {
@ -232,13 +256,15 @@ int main(int argc, char *argv[]) {
//HDF5File pedefile;
auto pedefile = std::make_unique<HDF5File>();
pedefile->SetFrameIndexPath(frameindexpath);
pedefile->SetFrameIndexPath(datasetpath);
// //open file
if ( pedefile->OpenResources(fname.c_str(),validate_rank) ) {
std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
framenumber = -1;
while ( decoder->readNextFrame(*pedefile, framenumber, iframe, buff) ) {
while ( decoder->readNextFrame(*pedefile, framenumber, h5offset, buff) ) {
if ((ifr + 1) % 100 == 0) {
std::cout
@ -250,7 +276,7 @@ int main(int argc, char *argv[]) {
mt->popFree(buff);
++ifr;
if (ifr % 100 == 0) {
std::cout << " ****" << ifr << " " << framenumber << " " << iframe
std::cout << " ****" << ifr << " " << framenumber << " " << h5offset[0]
<< std::endl;
} // else
@ -316,6 +342,8 @@ int main(int argc, char *argv[]) {
//HDF5File fileh5;
auto fileh5 = std::make_unique<HDF5File>();
fileh5->SetFrameIndexPath(frameindexpath);
fileh5->SetImageDataPath(datasetpath);
// //open file
ioutfile = 0;
if ( fileh5->OpenResources(filenames[ifile].c_str(), validate_rank) ) {
@ -344,10 +372,10 @@ int main(int argc, char *argv[]) {
// //while read frame
framenumber = -1;
iframe = 0;
h5offset[0] = 0;
ifr = 0;
//std::cout << "Here! " << framenumber << " ";
while ( decoder->readNextFrame(*fileh5, framenumber, iframe, buff) ) {
while ( decoder->readNextFrame(*fileh5, framenumber, h5offset, buff) ) {
//std::cout << "Here! " << framenumber << " ";
// //push
if ((ifr + 1) % 1000 == 0) {
@ -364,7 +392,8 @@ int main(int argc, char *argv[]) {
++ifr;
if (ifr % 1000 == 0)
std::cout << " " << ifr << " " << framenumber << std::endl;
std::cout << " " << ifr << " " << framenumber << " " << h5offset[0]
<< std::endl;
if (nframes > 0) {
if (ifr % nframes == 0) {
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ioutfile );