Polish data structure

This commit is contained in:
hinger_v 2025-04-30 11:01:24 +02:00
parent 3e2d34bec7
commit 01d3dc7115
2 changed files with 239 additions and 235 deletions

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@ -9,9 +9,9 @@
#endif
#include "slsDetectorData.h"
//This needs to be linked correctly
#include "HDF5File.h" //this includes hdf5.h and hdf5_hl.h
// This needs to be linked correctly
#include "HDF5File.cpp"
#include "HDF5File.h" //this includes hdf5.h and hdf5_hl.h
// #define VERSION_V2
/**
@ -32,42 +32,40 @@
@li version is the version number of this structure format
*/
//#include <algorithm>
// #include <algorithm>
#include <numeric>
#include <tuple>
namespace strixelQuad {
constexpr int nc_rawimg = 1024; // for full images //256;
constexpr int nc_quad = 512;
constexpr int nr_rawimg = 512;
constexpr int nr_chip = 256;
constexpr int gr = 9;
constexpr int nc_rawimg = 1024; // for full images //256;
constexpr int nc_quad = 512;
constexpr int nr_rawimg = 512;
constexpr int nr_chip = 256;
constexpr int gr = 9;
//shift due to extra pixels
constexpr int shift_x = 2; //left
constexpr int nc_strixel = ( nc_quad - shift_x - 2*gr ) / 3; //164
constexpr int nr_strixel = ( nr_chip - 1 - gr ) * 3; //one half (-1 because double sided pixel) //738
constexpr int nr_center = 12; //double sided pixels to be skipped
// shift due to extra pixels
constexpr int shift_x = 2; // left
// boundaries in ASIC coordinates (pixels at both bounds are included)
constexpr int xstart = 256 + gr; // 265
constexpr int xend = 255 + nc_quad - gr; // 758
constexpr int bottom_ystart = gr; // 9
constexpr int bottom_yend = nr_chip - 2; // 254
constexpr int top_ystart = nr_chip + 1; // 257
constexpr int top_yend = nr_chip*2 - gr - 1; // 502
constexpr int nc_strixel = (nc_quad - shift_x - 2 * gr) / 3; // 164
constexpr int nr_strixel =
(nr_chip - 1 - gr) * 3; // one half (-1 because double sided pixel) //738
constexpr int nr_center = 12; // double sided pixels to be skipped
// x shift because of 2-pixel strixels on one side
constexpr int shift = 2;
// boundaries in ASIC coordinates (pixels at both bounds are included)
constexpr int xstart = 256 + gr; // 265
constexpr int xend = 255 + nc_quad - gr; // 758
constexpr int bottom_ystart = gr; // 9
constexpr int bottom_yend = nr_chip - 2; // 254
constexpr int top_ystart = nr_chip + 1; // 257
constexpr int top_yend = nr_chip * 2 - gr - 1; // 502
// x shift because of 2-pixel strixels on one side
constexpr int shift = 2;
} // namespace strixelQuad
//to account for module rotation
enum rotation {
NORMAL = 0,
INVERSE = 1
};
// to account for module rotation
enum rotation { NORMAL = 0, INVERSE = 1 };
const int rota = NORMAL;
@ -85,232 +83,230 @@ class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
int iframe;
int x0, y0, x1, y1, shifty;
struct {
uint16_t xmin;
uint16_t xmax;
uint16_t ymin;
uint16_t ymax;
int nc;
uint16_t xmin;
uint16_t xmax;
uint16_t ymin;
uint16_t ymax;
int nc;
} globalROI;
//to account for the inverted routing of the two different quad halfs
enum location {
BOTTOM = 0,
TOP = 1
};
// to account for the inverted routing of the two different quad halfs
enum location { BOTTOM = 0, TOP = 1 };
int multiplicator = 3;
std::vector<int> mods{ 0, 1, 2 };
std::vector<int> mods{0, 1, 2};
void reverseVector( std::vector<int>& v ) {
std::reverse( v.begin(), v.end() );
std::cout << "mods reversed ";
for ( auto i : v )
std::cout << i << " ";
std::cout << '\n';
void reverseVector(std::vector<int> &v) {
std::reverse(v.begin(), v.end());
std::cout << "mods reversed ";
for (auto i : v)
std::cout << i << " ";
std::cout << '\n';
}
void setMappingShifts( const int rot, const int half ) {
void setMappingShifts(const int rot, const int half) {
x0 = xstart;
x1 = xend;
x0 = xstart;
x1 = xend;
if (rot==NORMAL) {
x0 += shift;
} else {
x1-=shift;
reverseVector(mods);
}
if (half==BOTTOM) {
y0 = bottom_ystart;
y1 = bottom_yend;
shifty = 0;
} else {
y0 = top_ystart;
y1 = top_yend;
reverseVector(mods);
shifty = nr_strixel + nr_center; //double-sided pixels in the center have to be jumped
}
if (rot == NORMAL) {
x0 += shift;
} else {
x1 -= shift;
reverseVector(mods);
}
if (half == BOTTOM) {
y0 = bottom_ystart;
y1 = bottom_yend;
shifty = 0;
} else {
y0 = top_ystart;
y1 = top_yend;
reverseVector(mods);
shifty = nr_strixel + nr_center; // double-sided pixels in the
// center have to be jumped
}
}
void remap( int xmin=0, int xmax=0, int ymin=0, int ymax=0 ) {
void remap(int xmin = 0, int xmax = 0, int ymin = 0, int ymax = 0) {
int ix, iy = 0;
// remapping loop
int ix, iy = 0;
// remapping loop
for (int ipy = y0; ipy <= y1; ++ipy) {
for (int ipx = x0; ipx <= x1; ++ipx) {
ix = int((ipx - x0) / multiplicator);
for (int m = 0; m < multiplicator; ++m) {
if ((ipx - x0) % multiplicator == m)
iy = (ipy - y0) * multiplicator + mods[m] + shifty;
}
ix = int((ipx - x0) / multiplicator);
for (int m = 0; m < multiplicator; ++m) {
if ((ipx - x0) % multiplicator == m)
iy = (ipy - y0) * multiplicator + mods[m] + shifty;
}
// if (iy< 40) cout << iy << " " << ix <<endl;
if (xmin < xmax && ymin < ymax) {
if ( ipx>=xmin && ipx<=xmax && ipy>=ymin && ipy <=ymax )
dataMap[iy][ix] =
(globalROI.nc * (ipy - globalROI.ymin) + (ipx - globalROI.xmin)) * 2;
} else {
dataMap[iy][ix] = (nc_rawimg * ipy + ipx) * 2;
}
// if (iy< 40) cout << iy << " " << ix <<endl;
if (xmin < xmax && ymin < ymax) { // if ROI
if (ipx >= xmin && ipx <= xmax && ipy >= ymin &&
ipy <= ymax)
dataMap[iy][ix] =
(globalROI.nc * (ipy - globalROI.ymin) +
(ipx - globalROI.xmin)) *
2;
} else { // if full Quad
dataMap[iy][ix] = (nc_rawimg * ipy + ipx) * 2;
}
}
}
}
void remapQuad(const int rot) {
setMappingShifts( rot, BOTTOM );
remap();
setMappingShifts( rot, TOP );
remap();
setMappingShifts(rot, BOTTOM);
remap();
setMappingShifts(rot, TOP);
remap();
}
std::tuple< uint16_t, uint16_t, uint16_t, uint16_t > adjustROItoLimits(uint16_t xmin,
uint16_t xmax,
uint16_t ymin,
uint16_t ymax,
uint16_t lim_roi_xmin,
uint16_t lim_roi_xmax,
uint16_t lim_roi_ymin,
uint16_t lim_roi_ymax) {
uint16_t xmin_roi, xmax_roi, ymin_roi, ymax_roi;
if ( xmin < lim_roi_xmin)
xmin_roi = lim_roi_xmin;
else
xmin_roi = xmin;
if ( xmax > lim_roi_xmax )
xmax_roi = lim_roi_xmax;
else
xmax_roi = xmax;
if ( ymin < lim_roi_ymin )
ymin_roi = lim_roi_ymin;
else
ymin_roi = ymin;
if ( ymax > lim_roi_ymax )
ymax_roi = lim_roi_ymax;
else
ymax_roi = ymax;
return std::make_tuple(xmin_roi, xmax_roi, ymin_roi, ymax_roi);
std::tuple<uint16_t, uint16_t, uint16_t, uint16_t>
adjustROItoLimits(uint16_t xmin, uint16_t xmax, uint16_t ymin,
uint16_t ymax, uint16_t lim_roi_xmin,
uint16_t lim_roi_xmax, uint16_t lim_roi_ymin,
uint16_t lim_roi_ymax) {
uint16_t xmin_roi, xmax_roi, ymin_roi, ymax_roi;
if (xmin < lim_roi_xmin)
xmin_roi = lim_roi_xmin;
else
xmin_roi = xmin;
if (xmax > lim_roi_xmax)
xmax_roi = lim_roi_xmax;
else
xmax_roi = xmax;
if (ymin < lim_roi_ymin)
ymin_roi = lim_roi_ymin;
else
ymin_roi = ymin;
if (ymax > lim_roi_ymax)
ymax_roi = lim_roi_ymax;
else
ymax_roi = ymax;
return std::make_tuple(xmin_roi, xmax_roi, ymin_roi, ymax_roi);
}
std::vector < std::tuple< int, uint16_t, uint16_t, uint16_t, uint16_t > > mapSubROIs(uint16_t xmin,
uint16_t xmax,
uint16_t ymin,
uint16_t ymax) {
bool bottom = false;
bool top = false;
// The strixel Quad has a mirrored symmetry from the center axis
// So we need to distinguish between bottom and top half for remapping
std::vector<std::tuple<int, uint16_t, uint16_t, uint16_t, uint16_t>>
mapSubROIs(uint16_t xmin, uint16_t xmax, uint16_t ymin, uint16_t ymax) {
bool bottom = false;
bool top = false;
for ( int x=xmin; x!=xmax+1; ++x ) {
for ( int y=ymin; y!=ymax; ++y ) {
if ( xstart<=x && x<=xend && bottom_ystart<=y && y<=bottom_yend )
bottom = true;
if ( xstart<=x && x<=xend && top_ystart<=y && y<=top_yend )
top = true;
}
}
for (int x = xmin; x != xmax + 1; ++x) {
for (int y = ymin; y != ymax; ++y) {
if (xstart <= x && x <= xend && bottom_ystart <= y &&
y <= bottom_yend)
bottom = true;
if (xstart <= x && x <= xend && top_ystart <= y &&
y <= top_yend)
top = true;
}
}
uint16_t xmin_roi{}, xmax_roi{}, ymin_roi{}, ymax_roi{};
std::vector < std::tuple< int, uint16_t, uint16_t, uint16_t, uint16_t > > rois{};
uint16_t xmin_roi{}, xmax_roi{}, ymin_roi{}, ymax_roi{};
std::vector<std::tuple<int, uint16_t, uint16_t, uint16_t, uint16_t>>
rois{};
if (bottom) {
std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
adjustROItoLimits( xmin, xmax, ymin, ymax,
xstart, xend, bottom_ystart, bottom_yend );
rois.push_back( std::make_tuple( BOTTOM, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
}
if (top) {
std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
adjustROItoLimits( xmin, xmax, ymin, ymax,
xstart, xend, top_ystart, top_yend );
rois.push_back( std::make_tuple( TOP, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
}
if (bottom) {
std::tie(xmin_roi, xmax_roi, ymin_roi, ymax_roi) =
adjustROItoLimits(xmin, xmax, ymin, ymax, xstart, xend,
bottom_ystart, bottom_yend);
rois.push_back(std::make_tuple(BOTTOM, xmin_roi, xmax_roi, ymin_roi,
ymax_roi));
}
if (top) {
std::tie(xmin_roi, xmax_roi, ymin_roi, ymax_roi) =
adjustROItoLimits(xmin, xmax, ymin, ymax, xstart, xend,
top_ystart, top_yend);
rois.push_back(
std::make_tuple(TOP, xmin_roi, xmax_roi, ymin_roi, ymax_roi));
}
return rois;
return rois;
}
void remapROI(std::tuple< int, uint16_t, uint16_t, uint16_t, uint16_t > roi, const int rot ) {
void remapROI(std::tuple<int, uint16_t, uint16_t, uint16_t, uint16_t> roi,
const int rot) {
int half, xmin, xmax, ymin, ymax;
std::tie( half, xmin, xmax, ymin, ymax ) = roi;
setMappingShifts(rot, half);
int half, xmin, xmax, ymin, ymax;
std::tie(half, xmin, xmax, ymin, ymax) = roi;
std::cout << "remapping roi: "
<< ", x0: " << x0 << ", x1: " << x1 << ", y0: " << y0
<< ", y1: " << y1 << std::endl;
std::cout << "Adjusted roi: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]" << std::endl;
setMappingShifts(rot, half);
remap( xmin, xmax, ymin, ymax );
std::cout << "remapping roi: "
<< ", x0: " << x0 << ", x1: " << x1 << ", y0: " << y0
<< ", y1: " << y1 << std::endl;
std::cout << "Adjusted roi: [" << xmin << ", " << xmax << ", " << ymin
<< ", " << ymax << "]" << std::endl;
remap(xmin, xmax, ymin, ymax);
}
//The following functions are pure virtual in the base class. But I don't want them to be accessible here!
//Implement the functions as private (to satisfy the linker)
//int getFrameNumber(char* buff){return 0;} //This is actually needed because the cluster finder writes the framenumber
int getPacketNumber(char* buff){return 0;} //Not provided
// The following functions are pure virtual in the base class. But I don't
// want them to be accessible here! Implement the functions as private (to
// satisfy the linker) int getFrameNumber(char* buff){return 0;} //This is
// actually needed because the cluster finder writes the framenumber
int getPacketNumber(char *buff) { return 0; } // Not provided
//Mark overwritten functions as override final
char* readNextFrame( std::ifstream &filebin ) override final {return nullptr;}
// Mark overwritten functions as override final
char *readNextFrame(std::ifstream &filebin) override final {
return nullptr;
}
public:
using header = sls::defs::sls_receiver_header;
jungfrauLGADStrixelsDataQuadH5(uint16_t xmin = 0, uint16_t xmax = 0,
uint16_t ymin = 0, uint16_t ymax = 0)
uint16_t ymin = 0, uint16_t ymax = 0)
: slsDetectorData<uint16_t>(
//nc_strixel,
//nr_strixel * 2 + nr_center,
//nc_strixel * ( nr_strixel * 2 + nr_center ) * 2
512/2,
1024*2,
512 * 1024 * 2 ) {
// nc_strixel,
// nr_strixel * 2 + nr_center,
// nc_strixel * ( nr_strixel * 2 + nr_center ) * 2
512 / 2, 1024 * 2, 512 * 1024 * 2) {
std::cout << "Jungfrau strixels quad with full module data "
<< std::endl;
// Fill all strixels with dummy values
//for (int ix = 0; ix != nc_strixel; ++ix) {
// for (int ix = 0; ix != nc_strixel; ++ix) {
// for (int iy = 0; iy != nr_strixel * 2 + nr_center; ++iy) {
for (int ix = 0; ix != 512/2; ++ix) {
for (int iy = 0; iy != 1024*2; ++iy) {
dataMap[iy][ix] = sizeof(header); //maybe another value is safer
for (int ix = 0; ix != 512 / 2; ++ix) {
for (int iy = 0; iy != 1024 * 2; ++iy) {
// Set everything to dummy value
dataMap[iy][ix] = sizeof(header);
}
}
globalROI.xmin = xmin;
globalROI.xmax = xmax;
globalROI.ymin = ymin;
globalROI.ymax = ymax;
globalROI.xmin = xmin;
globalROI.xmax = xmax;
globalROI.ymin = ymin;
globalROI.ymax = ymax;
//std::cout << "sizeofheader = " << sizeof(header) << std::endl;
// std::cout << "sizeofheader = " << sizeof(header) << std::endl;
std::cout << "Jungfrau strixels quad with full module data "
<< std::endl;
if (xmin < xmax && ymin < ymax) {
// get ROI raw image number of columns
globalROI.nc = xmax - xmin + 1;
std::cout << "nc_roi = " << globalROI.nc << std::endl;
dataSize =
(xmax - xmin + 1) * (ymax - ymin + 1) * 2;
std::cout << "datasize " << dataSize << std::endl;
// get ROI raw image number of columns
globalROI.nc = xmax - xmin + 1;
std::cout << "nc_roi = " << globalROI.nc << std::endl;
auto rois = mapSubROIs(xmin, xmax, ymin, ymax);
//function to fill vector of rois from globalROI
dataSize = (xmax - xmin + 1) * (ymax - ymin + 1) * 2;
std::cout << "datasize " << dataSize << std::endl;
for ( auto roi : rois )
remapROI(roi, rota);
auto rois = mapSubROIs(xmin, xmax, ymin, ymax);
// function to fill vector of rois from globalROI
for (auto roi : rois)
remapROI(roi, rota);
} else {
remapQuad( rota );
remapQuad(rota);
}
iframe = 0;
@ -325,78 +321,86 @@ class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
required as double
*/
virtual double getValue(char* data, int ix, int iy = 0) {
virtual double getValue(char *data, int ix, int iy = 0) {
uint16_t val = getChannel(data, ix, iy) & 0x3fff;
return val;
};
};
char* readNextFrame( HDF5File& hfile ) {
char *readNextFrame(HDF5File &hfile) {
int fn = 0;
std::vector<hsize_t> h5offset(1);
return readNextFrame(hfile, fn, h5offset);
};
char* readNextFrame( HDF5File& hfile, int& fn ) {
char *readNextFrame(HDF5File &hfile, int &fn) {
std::vector<hsize_t> h5offset(1);
return readNextFrame(hfile, fn, h5offset);
};
char* readNextFrame( HDF5File& hfile, int& fn, std::vector<hsize_t>& h5offset ) {
char *readNextFrame(HDF5File &hfile, int &fn,
std::vector<hsize_t> &h5offset) {
// Ensure dataSize is a valid size for allocation
if (dataSize <= 0) {
// Handle error case appropriately, e.g., log an error message
return nullptr;
}
// Ensure dataSize is a valid size for allocation
if (dataSize <= 0) {
// Handle error case appropriately, e.g., log an error message
return nullptr;
}
char* data = new char[dataSize];
char* readResult = readNextFrame(hfile, fn, h5offset, data);
// Check if reading failed
if (readResult == nullptr) {
delete[] data; // Free allocated memory
data = nullptr; // Set to nullptr to avoid dangling pointer
}
return data; //returning data is equivalent to returning reinterpret_cast<char*>(data_ptr) as they both point to the same memory
char *data = new char[dataSize];
char *readResult = readNextFrame(hfile, fn, h5offset, data);
// Check if reading failed
if (readResult == nullptr) {
delete[] data; // Free allocated memory
data = nullptr; // Set to nullptr to avoid dangling pointer
}
return data; // returning data is equivalent to returning
// reinterpret_cast<char*>(data_ptr) as they both point to
// the same memory
};
/*
* This is the most recent function. This is used in the cluster finder!
* The overloads are legacy!
* Note that caller has to allocate and deallocate memory for data!
* \param hfile object of type HDF5File (reader class)
* \param framenumber frame number as read from the HDF5 file
* \param h5offset vector defining offset parameters for HDF5 hyperslab selection (dimensions Z and S), incremented automatially
* \param data pointer to image buffer (converted to hold uint16_t by definition of HDF5File)
* \param h5offset vector defining offset parameters for HDF5 hyperslab
* selection (dimensions Z and S), incremented automatially
* \param data pointer to image buffer (converted to hold uint16_t by
* definition of HDF5File)
*/
char* readNextFrame( HDF5File& hfile, int& framenumber, std::vector<hsize_t>& h5offset, char* data ) {
char *readNextFrame(HDF5File &hfile, int &framenumber,
std::vector<hsize_t> &h5offset, char *data) {
if (framenumber >= 0) {
if (h5offset[0] % 10 == 0)
std::cout << "*";
if (framenumber >= 0) {
if (h5offset[0] % 10 == 0)
std::cout << "*";
//Storing the reinterpret_cast in the variable data_ptr ensures that I can pass it to a function that expects at uint16_t*
uint16_t* data_ptr = reinterpret_cast<uint16_t*>(data); //now data_ptr points where data points (thus modifies the same memory)
// Storing the reinterpret_cast in the variable data_ptr ensures
// that I can pass it to a function that expects at uint16_t*
uint16_t *data_ptr = reinterpret_cast<uint16_t *>(
data); // now data_ptr points where data points (thus modifies
// the same memory)
framenumber = hfile.ReadImage( data_ptr, h5offset );
iframe = h5offset[0]; //iframe is a class member!
return data; // return reinterpret_cast<char*>(data_ptr); // Equivalent
}
framenumber = hfile.ReadImage(data_ptr, h5offset);
iframe = h5offset[0]; // iframe is a class member!
return data; // return reinterpret_cast<char*>(data_ptr); //
// Equivalent
}
std::cout << "#";
return nullptr;
std::cout << "#";
return nullptr;
};
int getFrameNumber(char* buff){return iframe;} //Provided via public method readNextFrame
//It is debatable if one might not instead want to provide the "real" frame number as read from the file here
//For now, this is the frame offset counter (that always has to start at 0 for each new file)
int getFrameNumber(char *buff) {
return iframe;
} // Provided via public method readNextFrame
// It is debatable if one might not instead want to provide the "real" frame
// number as read from the file here For now, this is the frame offset
// counter (that always has to start at 0 for each new file)
/* Loops over a memory slot until a complete frame is found (i.e. all */
/* packets 0 to nPackets, same frame number). purely virtual func \param
@ -414,7 +418,7 @@ class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
/* found */
/* *\/ */
virtual char* findNextFrame(char* data, int& ndata, int dsize) {
virtual char *findNextFrame(char *data, int &ndata, int dsize) {
if (dsize < dataSize)
ndata = dsize;
else

View File

@ -221,7 +221,7 @@ int main(int argc, char *argv[]) {
auto firstfileh5 = std::make_unique<HDF5File>();
firstfileh5->SetFrameIndexPath(frameindexpath);
firstfileh5->SetImageDataPath(datasetpath);
std::cout << "Debug: Attempting to open file " << filenames[0].c_str() << std::endl;
//std::cout << "Debug: Attempting to open file " << filenames[0].c_str() << std::endl;
if ( firstfileh5->OpenResources(filenames[0].c_str(), validate_rank) ) {
// Validate number of threads