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Implement automatic strixel mapping according to rx_roi (#710)

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Co-authored-by: Erik Fröjdh <erik.frojdh@gmail.com>
This commit is contained in:
hinger_v 2023-03-31 17:14:35 +02:00 committed by GitHub
parent 37e7471dc4
commit b442b17415
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 231 additions and 119 deletions
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135
slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h
View File

@ -49,7 +49,32 @@ namespace strixelSingleChip {
constexpr int nc_strixel = 2*gr + 1 + g1_ncols; //group 1 is the "longest" group in x and has one extra square pixel
constexpr int nr_strixel = 2*gr + g1_nrows + g2_nrows + g3_nrows;
//chip and group boundaries in ASIC coordinates (pixels at both bounds are included in the group)
//y does NOT take into account the shifts for M408!
constexpr int c1g1_xstart = 256 + gr + 1; //266
constexpr int c1g2_xstart = 256 + gr + 3; //268
constexpr int c1g3_xstart = 256 + gr + 2; //267
constexpr int c1_xend = 255 + 256 - gr; //502
constexpr int c1g1_ystart = gr; // 9
constexpr int c1g1_yend = 63; // 63
constexpr int c1g2_ystart = c1g1_yend + 1; // 64
constexpr int c1g2_yend = c1g1_yend + 64; //127
constexpr int c1g3_ystart = c1g2_yend + 1; //128
constexpr int c1g3_yend = c1g2_yend + 2*64 - gr; //246
constexpr int c6_xstart = 256 + 256 + gr; //521
constexpr int c6g1_xend = 255 + 2*256 - gr - 1; //757
constexpr int c6g2_xend = 256 + 2*256 - gr - 3; //755
constexpr int c6g3_xend = 256 + 2*256 - gr - 2; //756
constexpr int c6g3_ystart = 256 + gr; //265
constexpr int c6g3_yend = 255 + 2*64; //383
constexpr int c6g2_ystart = c6g3_yend + 1; //384
constexpr int c6g2_yend = c6g3_yend + 64; //447
constexpr int c6g1_ystart = c6g2_yend + 1; //448
constexpr int c6g1_yend = c6g2_yend + 64 - gr; //502
//y shift due to faulty bonding (relevant for M408)
constexpr int bond_shift_y = 0; //CHANGE IF YOU CHANGE MODULE!
}
@ -69,12 +94,10 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
int mchip;
int chip_x0;
int chip_y0;
int x0, y0, x1, y1, shifty;
void remapGroup( const int group ) {
int ix, iy=0;
int x0, y0, x1, y1, shifty;
int getMultiplicator( const int group ) {
int multiplicator;
int shiftx;
switch (group) {
default:
case 1:
@ -87,16 +110,20 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
multiplicator = 4;
break;
}
return multiplicator;
}
if ( mchip == 1 ) {
void setMappingShifts( const int group ) {
if ( mchip == 1 ) {
chip_x0=256;
chip_y0=1; //because of bump bonding issues(+1 row) on M408
chip_y0=bond_shift_y; //because of bump bonding issues(+1 row) on M408
switch (group) {
default:
case 1:
x0 = 10+chip_x0; //9 gr + 1 sq pixel
x0 = 10+chip_x0; //9 gr + 1 sq pixel
x1 = 246+chip_x0;
y0 = 9+chip_y0;
y1 = 64+chip_y0;
@ -114,7 +141,7 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
x1 = 247+chip_x0;
y0 = 128+chip_y0;
y1 = 247+chip_y0;
shifty = g2_nrows+g1_nrows;
shifty = g2_nrows+g1_nrows;
break;
}
}
@ -122,7 +149,7 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
if ( mchip == 6 ) {
chip_x0=512;
chip_y0=255; //should be 256 but is 255 because of bump bonding issues (+1 row) on M408
chip_y0=256-bond_shift_y; //should be 256 but is 255 because of bump bonding issues (+1 row) on M408
switch (group) {
default:
@ -157,6 +184,15 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
break;
}
}
}
void remapGroup( const int group ) {
int multiplicator = getMultiplicator(group);
int shiftx;
int ix, iy=0;
setMappingShifts(group);
//remapping loop
for ( int ipy=y0; ipy<=y1;ipy++) {
@ -165,8 +201,6 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
ix = int ((ipx-x0)/multiplicator);
for ( int m=0; m<multiplicator;m++ ) {
if ( (ipx-x0)%multiplicator==m ) iy=(ipy-y0)*multiplicator +m + shifty;
}
// if (iy< 40) cout << iy << " " << ix <<endl;
@ -177,6 +211,48 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
}
void remapROI( uint16_t xmin, uint16_t xmax, uint16_t ymin, uint16_t ymax ) {
//determine group and chip selected by ROI
int group;
if ( ymax <= c1g1_yend+bond_shift_y ) { group = 1; mchip = 1; }
else if ( ymax <= c1g2_yend+bond_shift_y ) { group = 2; mchip = 1; }
else if ( ymax <= c1g3_yend+bond_shift_y ) { group = 3; mchip = 1; }
else if ( ymax <= c6g3_yend-bond_shift_y ) { group = 3; mchip = 6; }
else if ( ymax <= c6g2_yend-bond_shift_y ) { group = 2; mchip = 6; }
else if ( ymax <= c6g1_yend-bond_shift_y ) { group = 1; mchip = 6; }
int multiplicator = getMultiplicator(group);
setMappingShifts(group);
std::cout << "group: " << group << ", m: " << multiplicator << ", x0: " << x0 << ", x1: " << x1 << ", y0: " << y0 << ", y1: " << y1 << std::endl;
//get ROI raw image number of columns
int nc_roi = xmax - xmin + 1;
std::cout << "nc_roi = " << nc_roi << std::endl;
//make sure loop bounds are correct
if (y0<ymin) std::cout << "Error ymin" << std::endl;
if (y1>ymax) std::cout << "Error ymax - normal for G3 since ROI only 64 row" << std::endl;
if (x0<xmin) std::cout << "Error xmin" << std::endl;
if (x1>xmax) std::cout << "Error xmax" << std::endl;
//remapping loop
int ix, iy=0;
for ( int ipy=y0; ipy<=y1; ++ipy) {
for ( int ipx=x0; ipx<=x1; ++ipx ) {
ix = int ((ipx-x0-xmin)/multiplicator);
for ( int m=0; m<multiplicator;m++ ) {
if ( (ipx-x0-xmin)%multiplicator==m ) iy=(ipy-y0-ymin)*multiplicator +m + shifty;
}
// if (iy< 40) cout << iy << " " << ix <<endl;
dataMap[iy][ix] = sizeof(header) + (nc_roi * (ipy-ymin) + (ipx-xmin)) * 2;
groupmap[iy][ix]=group-1;
}
}
}
public:
int groupmap[512*5][1024/3];
@ -184,14 +260,13 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
using header = sls::defs::sls_receiver_header;
jungfrauLGADStrixelsData()
jungfrauLGADStrixelsData( uint16_t xmin=0, uint16_t xmax=0, uint16_t ymin=0, uint16_t ymax=0 )
: slsDetectorData<uint16_t>( /*nc_strixel*/g1_ncols, /*nr_strixel*/ 2*g1_nrows+2*g2_nrows+2*g3_nrows,
g1_ncols* (2*g1_nrows+2*g2_nrows+2*g3_nrows) * 2 + sizeof(header) ) {
std::cout << "Jungfrau strixels 2X single chip with full module data " << std::endl;
//Fill all strixels with dummy values
for (int ix = 0; ix != g1_ncols; ++ix) {
for (int iy = 0; iy != 2*g1_nrows+2*g2_nrows+2*g3_nrows; ++iy) {
@ -200,20 +275,27 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
}
}
cout << "sizeofheader = "<<sizeof(header)<<endl;
std::cout << "Jungfrau strixels 2X single chip with full module data " << std::endl;
std::cout << "sizeofheader = "<<sizeof(header)<<std::endl;
std::cout << "Jungfrau strixels 2X single chip with full module data " << std::endl;
mchip = 1;
remapGroup(1);
if (xmin<xmax && ymin<ymax) {
remapGroup(2);
remapGroup(3);
dataSize=(xmax-xmin+1)*(ymax-ymin+1)*2 + sizeof(header);
std::cout << "datasize " << dataSize << std::endl;
remapROI( xmin, xmax, ymin, ymax );
} else {
mchip = 6;
remapGroup(1);
remapGroup(2);
remapGroup(3);
mchip = 1;
remapGroup(1);
remapGroup(2);
remapGroup(3);
mchip = 6;
remapGroup(1);
remapGroup(2);
remapGroup(3);
}
iframe = 0;
std::cout << "data struct created" << std::endl;
@ -298,12 +380,13 @@ std::cout << "Jungfrau strixels 2X single chip with full module data " << std::e
np = 0;
int pn;
// cout << dataSize << endl;
//std::cout << dataSize << std::endl;
if (ff >= 0)
fnum = ff;
if (filebin.is_open()) {
if (filebin.read(data, dataSize)) {
std::cout << "*";
ff = getFrameNumber(data);
np = getPacketNumber(data);
return data;

215
slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
View File

@ -20,7 +20,7 @@
#endif
#ifdef JFSTRX
#include "jungfrauLGADStrixelsData.h"
#include "jungfrauLGADStrixelsData_new.h"
#endif
#if defined JFSTRXCHIP1 || defined JFSTRXCHIP6
#include "jungfrauLGADStrixelsDataSingleChip.h"
@ -64,55 +64,6 @@ int main(int argc, char *argv[]) {
int cf = 0;
#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;
jungfrauLGADStrixelsData *decoder = new jungfrauLGADStrixelsData();
int nx = 1024/5, 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);
cout << "Detector size is " << nx << " " << ny << endl;
double *gainmap = NULL;
//float *gm;
@ -154,6 +105,83 @@ int main(int argc, char *argv[]) {
nframes = atoi(argv[9]);
}
char ffname[10000];
char fname[10000];
char imgfname[10000];
char cfname[10000];
//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
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;
sprintf(ffname, "%s/%s.%s", indir, fformat, fext);
sprintf(fname, (const char*)ffname, runmin);
std::cout << "Reading header of file " << fname << " to check for ROI " << std::endl;
filebin.open((const char *)(fname), ios::in | ios::binary);
if (filebin.is_open()) {
header hbuffer;
std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
if ( filebin.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;
} else
std::cout << "reading error" << std::endl;
filebin.close();
} else
std::cout << "Could not open " << fname << " for reading " << std::endl;
#endif
jungfrauLGADStrixelsData *decoder = new jungfrauLGADStrixelsData( croi.xmin, croi.xmax, croi.ymin, croi.ymax );
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;
int xmin = 0, xmax = nx, ymin = 0, ymax = ny;
if (argc >= 14) {
xmin = atoi(argv[10]);
@ -161,43 +189,42 @@ int main(int argc, char *argv[]) {
ymin = atoi(argv[12]);
ymax = atoi(argv[13]);
}
std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " " << std::endl;
char *gainfname = NULL;
if (argc > 14) {
gainfname = argv[14];
cout << "Gain map file name is: " << gainfname << endl;
std::cout << "Gain map file name is: " << gainfname << std::endl;
}
char ffname[10000];
char fname[10000];
char imgfname[10000];
char cfname[10000];
std::time_t end_time;
FILE *of = NULL;
cout << "input directory is " << indir << endl;
cout << "output directory is " << outdir << endl;
cout << "input file is " << fformat << endl;
cout << "runmin is " << runmin << endl;
cout << "runmax is " << runmax << endl;
std::cout << "input directory is " << indir << std::endl;
std::cout << "output directory is " << outdir << std::endl;
std::cout << "input file is " << fformat << std::endl;
std::cout << "runmin is " << runmin << std::endl;
std::cout << "runmax is " << runmax << std::endl;
if (pedfile)
cout << "pedestal file is " << pedfile << endl;
std::cout << "pedestal file is " << pedfile << std::endl;
if (thr > 0)
cout << "threshold is " << thr << endl;
cout << "Nframes is " << nframes << endl;
std::cout << "threshold is " << thr << std::endl;
std::cout << "Nframes is " << nframes << std::endl;
//std::cout << "HHHEEEEEEEEEEEEEEEEEEEEEEERE!!!!!" << 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))
cout << "using gain map " << gainfname << endl;
std::cout << "using gain map " << gainfname << std::endl;
else
cout << "Could not open gain map " << gainfname << endl;
std::cout << "Could not open gain map " << gainfname << std::endl;
} else
thr = 0.15 * thr;
filter->newDataSet();
@ -213,7 +240,7 @@ int main(int argc, char *argv[]) {
filter->setROI(xmin, xmax, ymin, ymax);
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
std::cout << std::ctime(&end_time) << std::endl;
char *buff;
@ -225,7 +252,7 @@ int main(int argc, char *argv[]) {
#ifndef ANALOG
mt->setDetectorMode(ePhotonCounting);
cout << "Counting!" << endl;
std::cout << "Counting!" << std::endl;
if (thr > 0) {
cf = 0;
}
@ -233,7 +260,7 @@ int main(int argc, char *argv[]) {
//{
#ifdef ANALOG
mt->setDetectorMode(eAnalog);
cout << "Analog!" << endl;
std::cout << "Analog!" << std::endl;
cf = 0;
// thr1=thr;
#endif
@ -265,27 +292,29 @@ int main(int argc, char *argv[]) {
if (string(pedfile).find(".tif") == std::string::npos) {
sprintf(fname, "%s", pedfile);
cout << fname << endl;
std::cout << fname << std::endl;
std::time(&end_time);
//cout << "aaa" << std::ctime(&end_time) << endl;
std::cout << "aaa" << std::ctime(&end_time) << std::endl;
mt->setFrameMode(ePedestal);
// sprintf(fn,fformat,irun);
filebin.open((const char *)(fname), ios::in | ios::binary);
// //open file
if (filebin.is_open()) {
std::cout << "bbbb" << std::ctime(&end_time) << std::endl;
ff = -1;
while (decoder->readNextFrame(filebin, ff, np, buff)) {
// if (np == 40) {
if ((ifr+1) % 100 == 0) {
cout << " ****" << decoder->getValue(buff,20,20);// << endl;
std::cout << " ****" << decoder->getValue(buff,20,20);// << endl;
}
mt->pushData(buff);
mt->nextThread();
mt->popFree(buff);
ifr++;
if (ifr % 100 == 0) {
cout << " ****" << ifr << " " << ff << " " << np << endl;
std::cout << " ****" << ifr << " " << ff << " " << np << std::endl;
} //else
//cout << ifr << " " << ff << " " << np << endl;
if (ifr>=1000)
@ -303,8 +332,8 @@ int main(int argc, char *argv[]) {
mt->writePedestalRMS(imgfname);
} else
cout << "Could not open pedestal file " << fname
<< " for reading " << endl;
std::cout << "Could not open pedestal file " << fname
<< " for reading " << std::endl;
} else {
float *pp = ReadFromTiff(pedfile, nny, nnx);
if (pp && (int)nnx == nx && (int)nny == ny) {
@ -313,14 +342,14 @@ int main(int argc, char *argv[]) {
}
delete[] pp;
mt->setPedestal(ped);
cout << "Pedestal set from tiff file " << pedfile << endl;
std::cout << "Pedestal set from tiff file " << pedfile << std::endl;
} else {
cout << "Could not open pedestal tiff file " << pedfile
<< " for reading " << endl;
std::cout << "Could not open pedestal tiff file " << pedfile
<< " for reading " << std::endl;
}
}
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
std::cout << std::ctime(&end_time) << std::endl;
}
ifr = 0;
@ -329,7 +358,7 @@ int main(int argc, char *argv[]) {
mt->setFrameMode(eFrame);
for (int irun = runmin; irun <= runmax; irun++) {
cout << "DATA ";
std::cout << "DATA ";
// sprintf(fn,fformat,irun);
sprintf(ffname, "%s/%s.%s", indir, fformat, fext);
sprintf(fname, (const char*)ffname, irun);
@ -337,10 +366,10 @@ int main(int argc, char *argv[]) {
sprintf(imgfname, (const char*)ffname, irun);
sprintf(ffname, "%s/%s.clust", outdir, fformat);
sprintf(cfname, (const char*)ffname, irun);
cout << fname << " ";
cout << imgfname << endl;
std::cout << fname << " ";
std::cout << imgfname << std::endl;
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
std::cout << std::ctime(&end_time) << std::endl;
// cout << fname << " " << outfname << " " << imgfname << endl;
filebin.open((const char *)(fname), ios::in | ios::binary);
// //open file
@ -351,10 +380,10 @@ int main(int argc, char *argv[]) {
of = fopen(cfname, "w");
if (of) {
mt->setFilePointer(of);
cout << "file pointer set " << endl;
std::cout << "file pointer set " << std::endl;
} else {
cout << "Could not open " << cfname << " for writing "
<< endl;
std::cout << "Could not open " << cfname << " for writing "
<< std::endl;
mt->setFilePointer(NULL);
return 1;
}
@ -368,7 +397,7 @@ int main(int argc, char *argv[]) {
// //push
if ((ifr+1) % 100 == 0) {
cout << " ****" << decoder->getValue(buff,20,20);// << endl;
std::cout << " ****" << decoder->getValue(buff,20,20);// << endl;
}
mt->pushData(buff);
// // //pop
@ -377,7 +406,7 @@ int main(int argc, char *argv[]) {
ifr++;
if (ifr % 100 == 0)
cout << " " << ifr << " " << ff << endl;
std::cout << " " << ifr << " " << ff << std::endl;
if (nframes > 0) {
if (ifr % nframes == 0) {
sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat,
@ -392,7 +421,7 @@ int main(int argc, char *argv[]) {
// cout << ifr << " " << ff << " " << np << endl;
ff = -1;
}
cout << "--" << endl;
std::cout << "--" << std::endl;
filebin.close();
while (mt->isBusy()) {
;
@ -405,7 +434,7 @@ int main(int argc, char *argv[]) {
sprintf(ffname, "%s/%s.tiff", outdir, fformat);
sprintf(imgfname, (const char*)ffname, irun);
}
cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
mt->writeImage(imgfname, thr1);
mt->clearImage();
if (of) {
@ -415,14 +444,14 @@ int main(int argc, char *argv[]) {
}
}
std::time(&end_time);
cout << std::ctime(&end_time) << endl;
std::cout << std::ctime(&end_time) << std::endl;
} else
cout << "Could not open " << fname << " for reading " << endl;
std::cout << "Could not open " << fname << " for reading " << std::endl;
}
if (nframes < 0) {
sprintf(ffname, "%s/%s.tiff", outdir, fformat);
strcpy(imgfname, ffname);
cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
mt->writeImage(imgfname, thr1);
}