diff --git a/slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h b/slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h index 494335607..eb45538c1 100644 --- a/slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h +++ b/slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h @@ -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 { 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 { 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 { 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 { 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 { 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 { ix = int ((ipx-x0)/multiplicator); for ( int m=0; m { } + 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 (y0ymax) std::cout << "Error ymax - normal for G3 since ROI only 64 row" << std::endl; + if (x0xmax) 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 { 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( /*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 { } } - cout << "sizeofheader = "<= 0) fnum = ff; if (filebin.is_open()) { if (filebin.read(data, dataSize)) { + std::cout << "*"; ff = getFrameNumber(data); np = getPacketNumber(data); return data; diff --git a/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp b/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp index 6aadba3b6..56d40a986 100644 --- a/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp +++ b/slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp @@ -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); }