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Read rx_ROI from json master

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This commit is contained in:
hinger_v
2023-08-03 18:25:43 +02:00
parent 558c2de85c
commit f90a9b7520
5 changed files with 367 additions and 143 deletions
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195
slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
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@ -41,6 +41,9 @@
#include <ctime>
#include <fmt/core.h>
#include <nlohmann/json.hpp>
using json = nlohmann::json;
std::string getRootString( const std::string& filepath ) {
size_t pos1 = filepath.find_last_of("/");
@ -61,20 +64,24 @@ std::string getRootString( const std::string& filepath ) {
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 ) {
if (outfilecounter >= 0)
return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}_f{:05d}.{:s}", dir, fprefix, mindex, findex, aindex, outfilecounter, fext);
else if (fsuffix.length()!=0)
return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
else if (fsuffix.length()!=0) {
if (fsuffix == "master")
return fmt::format("{:s}/{:s}_master_{:d}.{:s}", dir, fprefix, aindex, fext);
else
return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
}
else
return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}.{:s}", dir, fprefix, mindex, findex, aindex, fext);
}
int main(int argc, char *argv[]) {
if (argc < 5) {
if (argc < 6) {
std::cout
<< "Usage is " << argv[0]
<< "indir outdir fprefix(excluding slsDetector standard suffixes and extension) fextension "
"[runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
"[nframes] [xmin xmax ymin ymax] [gainmap]"
<< "indir outdir [fprefix(excluding slsDetector standard suffixes and extension)] [fextension] "
"[fmin] [fmax] [runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
"[nframes] [xmin xmax ymin ymax] [optional: bool read rxroi from data file header] [gainmap]"
<< std::endl;
std::cout
<< "threshold <0 means analog; threshold=0 means cluster finder; "
@ -106,36 +113,71 @@ int main(int argc, char *argv[]) {
std::string outdir(argv[2]);
std::string fprefix(argv[3]);
std::string fext(argv[4]);
int fmin = 0;
if (argc >= 6)
fmin = atoi(argv[5]);
int fmax = fmin;
if (argc >= 7)
fmax = atoi(argv[6]);
int runmin = 0;
// cout << "argc is " << argc << endl;
if (argc >= 6) {
runmin = atoi(argv[5]);
if (argc >= 8) {
runmin = atoi(argv[7]);
}
int runmax = runmin;
if (argc >= 7) {
runmax = atoi(argv[6]);
if (argc >= 9) {
runmax = atoi(argv[8]);
}
std::string pedfilename{};
if (argc >= 8) {
pedfilename = argv[7];
if (argc >= 10) {
pedfilename = argv[9];
}
double thr = 0;
double thr1 = 1;
if (argc >= 9) {
thr = atof(argv[8]);
if (argc >= 11) {
thr = atof(argv[10]);
}
int nframes = 0;
if (argc >= 10) {
nframes = atoi(argv[9]);
if (argc >= 12) {
nframes = atoi(argv[11]);
}
bool readrxroifromdatafile = false;
if (argc >= 17)
readrxroifromdatafile = atoi(argv[16]);
// Receiver ROI
uint16_t rxroi_xmin = 0;
uint16_t rxroi_xmax = 0;
uint16_t rxroi_ymin = 0;
uint16_t rxroi_ymax = 0;
{ //protective scope so ifstream gets destroyed properly
auto jsonmastername = createFileName( indir, fprefix, "master", "json", runmin );
std::cout << "json master file " << jsonmastername << std::endl;
std::ifstream masterfile(jsonmastername); //, ios::in | ios::binary);
if (masterfile.is_open()) {
json j;
masterfile >> j;
rxroi_xmin = j["Receiver Roi"]["xmin"];
rxroi_xmax = j["Receiver Roi"]["xmax"];
rxroi_ymin = j["Receiver Roi"]["ymin"];
rxroi_ymax = j["Receiver Roi"]["ymax"];
masterfile.close();
std::cout << "Read Receiver ROI [" << rxroi_xmin << ", " << rxroi_xmax << ", "
<< rxroi_ymin << ", " << rxroi_ymax << "] from json master file" << std::endl;
} else
std::cout << "Could not open master file " << jsonmastername << std::endl;
}
// Define decoders...
#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 && \
!defined JFSTRXCHIP6
@ -151,49 +193,45 @@ int main(int argc, char *argv[]) {
#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 fsuffix{};
auto filename = createFileName( indir, fprefix, fsuffix, fext, runmin );
std::cout << "Reading header of file " << filename << " to check for ROI "
<< std::endl;
ifstream firstfile(filename, 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 " << filename << " for reading " << std::endl;
} //end of protective scope
if (readrxroifromdatafile)
{ //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
using header = sls::defs::sls_receiver_header;
// check if there is a roi in the header
typedef struct {
uint16_t xmin;
uint16_t xmax;
uint16_t ymin;
uint16_t ymax;
} receiverRoi_compact;
receiverRoi_compact croi;
std::string fsuffix{};
auto filename = createFileName( indir, fprefix, fsuffix, fext, runmin );
std::cout << "Reading header of file " << filename << " to check for ROI "
<< std::endl;
ifstream firstfile(filename, ios::in | ios::binary);
if (firstfile.is_open()) {
header hbuffer;
std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
if (firstfile.read((char *)&hbuffer, sizeof(header))) {
memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
<< croi.ymin << ", " << croi.ymax << "]" << std::endl;
rxroi_xmin = croi.xmin;
rxroi_xmax = croi.xmax;
rxroi_ymin = croi.ymin;
rxroi_ymax = croi.ymax;
} else
std::cout << "reading error" << std::endl;
firstfile.close();
} else
std::cout << "Could not open " << filename << " for reading " << std::endl;
} //end of protective scope
#endif
jungfrauLGADStrixelsData *decoder =
new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
new jungfrauLGADStrixelsData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
int nx = 1024 / 3, ny = 512 * 5;
#endif
#ifdef JFSTRXCHIP1
@ -218,19 +256,20 @@ int main(int argc, char *argv[]) {
decoder->getDetectorSize(nx, ny);
std::cout << "Detector size is " << nx << " " << ny << std::endl;
//Cluster finder ROI
int xmin = 0, xmax = nx, ymin = 0, ymax = ny;
if (argc >= 14) {
xmin = atoi(argv[10]);
xmax = atoi(argv[11]);
ymin = atoi(argv[12]);
ymax = atoi(argv[13]);
if (argc >= 16) {
xmin = atoi(argv[12]);
xmax = atoi(argv[13]);
ymin = atoi(argv[14]);
ymax = atoi(argv[15]);
}
std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
<< std::endl;
char *gainfname = NULL;
if (argc > 14) {
gainfname = argv[14];
if (argc > 17) {
gainfname = argv[17];
std::cout << "Gain map file name is: " << gainfname << std::endl;
}
@ -239,6 +278,8 @@ int main(int argc, char *argv[]) {
std::cout << "input directory is " << indir << std::endl;
std::cout << "output directory is " << outdir << std::endl;
std::cout << "input file prefix is " << fprefix << std::endl;
std::cout << "fmin is " << fmin << std::endl;
std::cout << "fmax is " << fmax << std::endl;
std::cout << "runmin is " << runmin << std::endl;
std::cout << "runmax is " << runmax << std::endl;
if (pedfilename.length()!=0)
@ -380,26 +421,27 @@ int main(int argc, char *argv[]) {
}
ifr = 0;
int ifile = 0;
int ioutfile = 0;
mt->setFrameMode(eFrame);
FILE *of = NULL;
for (int irun = runmin; irun <= runmax; irun++) {
for (int irun = runmin; irun <= runmax; ++irun) {
for (int ifile = fmin; ifile <= fmax; ++ifile) {
std::cout << "DATA ";
std::string fsuffix{};
auto fname = createFileName( indir, fprefix, fsuffix, fext, irun );
auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun );
auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun );
auto fname = createFileName( indir, fprefix, fsuffix, fext, irun, 0, ifile );
auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, ifile );
auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun, 0, ifile );
std::cout << fname << " ";
std::cout << imgfname << std::endl;
std::time(&end_time);
std::cout << std::ctime(&end_time) << std::endl;
// std::cout << fname << " " << outfname << " " << imgfname << std::endl;
ifstream filebin(fname, ios::in | ios::binary);
std::ifstream filebin(fname, ios::in | ios::binary);
// //open file
ifile = 0;
ioutfile = 0;
if (filebin.is_open()) {
if (thr <= 0 && cf != 0) { // cluster finder
if (of == NULL) {
@ -436,10 +478,10 @@ int main(int argc, char *argv[]) {
std::cout << " " << ifr << " " << ff << std::endl;
if (nframes > 0) {
if (ifr % nframes == 0) {
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ioutfile );
mt->writeImage(imgfname.c_str(), thr1);
mt->clearImage();
ifile++;
ioutfile++;
}
}
// } else
@ -453,7 +495,7 @@ int main(int argc, char *argv[]) {
}
if (nframes >= 0) {
if (nframes > 0)
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ioutfile );
std::cout << "Writing tiff to " << imgfname << " " << thr1
<< std::endl;
mt->writeImage(imgfname.c_str(), thr1);
@ -469,9 +511,10 @@ int main(int argc, char *argv[]) {
} else
std::cout << "Could not open " << fname << " for reading "
<< std::endl;
}
}
if (nframes < 0) {
auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", -1, 0, 0, -1 );
auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", runmin, 0, fmin, -1 );
std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
mt->writeImage(imgfname.c_str(), thr1);
}