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almost compiles, error: undefined reference to vtable for jungfrauLGADStrixelsDataQuadH5

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This commit is contained in:
hinger_v 2024-08-26 18:50:56 +02:00
parent 543b311c06
commit 69fb5876cb
4 changed files with 93 additions and 81 deletions
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19
slsDetectorCalibration/dataStructures/HDF5File.cpp
View File

@ -231,8 +231,17 @@ void HDF5File::CloseResources () {
//if (memspace >= 0) H5Sclose(memspace); // VH: I am getting memory leaks after recompilation
}
int HDF5File::ReadImage (uint16_t** image, int& iFrame) {
/*
* Function takes uint16_t* argument to make explicit that the caller has to handle memory allocation and deallocation.
* This is legacy caused by the structure with which the slsDetectorCalibration cluster finder is written.
* Best practice for modern C++ would be to rewrite using smart pointers.
*/
int HDF5File::ReadImage (uint16_t* image, int& iFrame) {
/*
* Originially, this function took uint16_t** but this may lead to memory management issues since image gets redirected
* to point to current_image, which is owned by HDF5File.
* (Usually, this would be good practice and classic C-style.)
*/
// no images in this frame
if (frame_index_list[frame_offset[Z]] == 0) {
@ -252,7 +261,7 @@ int HDF5File::ReadImage (uint16_t** image, int& iFrame) {
hid_t memspace = H5Screate_simple (RANK, frame_size, NULL);
// create hyperslab
// If I understand correctly, this puts dataspace such that we read the correct frame
// This aligns dataspace such that we read the correct frame
if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, frame_offset, NULL, frame_size, NULL) < 0 ) {
cprintf (RED,"Could not create hyperslab for frame count %llu\n", frame_offset[Z]);
CloseResources ();
@ -260,12 +269,12 @@ int HDF5File::ReadImage (uint16_t** image, int& iFrame) {
}
// read dataset into current_image
if (H5Dread(dataset, H5T_STD_U16LE, memspace, dataspace, H5P_DEFAULT, current_image) < 0 ) {
if (H5Dread(dataset, H5T_STD_U16LE, memspace, dataspace, H5P_DEFAULT, image /*was 'current_image'*/) < 0 ) {
cprintf (RED,"Could not read dataset for frame count %llu\n", frame_offset[Z]);
CloseResources ();
return -99;
}
*image = current_image;
//*image = current_image; //if uint16_t** is passed, HDF5File owns the resource image points to, which is potentially dangerous
// return frame number and then increment frame count number
unsigned int retval = frame_index_list[frame_offset[Z]];

2
slsDetectorCalibration/dataStructures/HDF5File.h
View File

@ -71,7 +71,7 @@ public:
* Read an image into current_image
* @returns frame number read,
*/
int ReadImage (uint16_t** image, int& iFrame);
int ReadImage (uint16_t* image, int& iFrame);
/**
* Print current image in memory

108
slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsDataQuadH5.h
View File

@ -248,6 +248,11 @@ class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
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!
char* readNextFrame( std::ifstream &filebin );
int getFrameNumber(char *buff); //Provided via public method readNextFrame
int getPacketNumber(char *buff); //Not provided
public:
using header = sls::defs::sls_receiver_header;
@ -315,77 +320,64 @@ class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
uint16_t val = getChannel(data, ix, iy) & 0x3fff;
return val;
};
};
/**
Returns the frame number for the given dataset. Purely virtual func.
\param buff pointer to the dataset
\returns frame number
*/
/*
int getFrameNumber(char *buff) {
#ifdef ALDO // VH
return ((jf_header *)buff)->bunchNumber; // VH
#endif // VH
return ((header *)buff)->detHeader.frameNumber;
};
*/
/**
Returns the packet number for the given dataset. purely virtual func
\param buff pointer to the dataset
\returns packet number number
*/
/*
int getPacketNumber(char *buff) {
#ifdef ALDO // VH
// uint32_t fakePacketNumber = 1000;
// return fakePacketNumber; //VH //TODO: Keep in mind in case of bugs!
// //This is definitely bad!
return 1000;
#endif // VH
return ((header *)buff)->detHeader.packetNumber;
};
*/
char* readNextFrame(const HDF5File& hfile) {
char* readNextFrame( HDF5File& hfile ) {
int fn = 0, iframe = 0;
return readNextFrame(hfile, fn, iframe);
};
char* readNextFrame(const HDF5File& hfile, int& fn) {
char* readNextFrame( HDF5File& hfile, int& fn ) {
int iframe = 0;
return readNextFrame(hfile, fn, iframe);
};
char *readNextFrame(const HDF5File& hfile, int& fn, int& iframe) {
char *data = new char[dataSize];
char *d = readNextFrame(hfile, fn, iframe, data);
if (d == NULL) {
delete[] data;
data = NULL;
}
return data;
};
char* readNextFrame( HDF5File& hfile, int& fn, int& iframe ) {
//framenumber: Framenumber as written in the file (defined by the time of detector power on)
//iframe: Counter how often ReadImage has been called, ReadImage return value
char* readNextFrame(const HDF5File& hfile, int& framenumber, int& iframe, char* data) {
if (iframe>=0) {
std::cout << "*";
iframe = hfile.ReadImage( data, framenumber )
return data;
// Ensure dataSize is a valid size for allocation
if (dataSize <= 0) {
// Handle error case appropriately, e.g., log an error message
return nullptr;
}
std::cout << "#";
return NULL;
char* data = new char[dataSize];
char* readResult = readNextFrame(hfile, fn, iframe, 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!
*/
char* readNextFrame( HDF5File& hfile, int& framenumber, int& iframe, char* data ) {
if (iframe >= 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)
iframe = hfile.ReadImage( data_ptr, framenumber );
return data; // return reinterpret_cast<char*>(data_ptr); // Equivalent
}
std::cout << "#";
return nullptr;
};
/* 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
*/

45
slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxtH5.cpp
View File

@ -113,7 +113,7 @@ int main(int argc, char *argv[]) {
double *gainmap = NULL;
// float *gm;
int ff, np;
//int ff, np;
// cout << " data size is " << dsize;
const std::string txtfilename(argv[1]);
@ -375,7 +375,9 @@ int main(int argc, char *argv[]) {
// cout << "mt " << endl;
int ifr = 0;
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)
if (pedfilename.length()>1) {
@ -391,13 +393,16 @@ int main(int argc, char *argv[]) {
mt->setFrameMode(ePedestal);
std::ifstream pedefile(fname, ios::in | ios::binary);
//std::ifstream pedefile(fname, ios::in | ios::binary);
HDF5File pedefile;
// //open file
if (pedefile.is_open()) {
if ( pedefile.OpenResources(fname.c_str(),1) ) {
std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
ff = -1;
while (decoder->readNextFrame(pedefile, ff, np, buff)) {
framenumber = -1;
while ( decoder->readNextFrame(pedefile, framenumber, iframe, buff) ) {
// if (np == 40) {
if ((ifr + 1) % 100 == 0) {
std::cout
@ -407,17 +412,18 @@ int main(int argc, char *argv[]) {
mt->pushData(buff);
mt->nextThread();
mt->popFree(buff);
ifr++;
++ifr;
if (ifr % 100 == 0) {
std::cout << " ****" << ifr << " " << ff << " " << np
std::cout << " ****" << ifr << " " << framenumber << " " << iframe
<< std::endl;
} // else
//std::cout << ifr << " " << ff << " " << np << std::endl;
if (ifr >= 1000)
break;
ff = -1;
framenumber = -1;
}
pedefile.close();
//pedefile.close();
pedefile.CloseResources();
while (mt->isBusy()) {
;
}
@ -471,10 +477,11 @@ int main(int argc, char *argv[]) {
std::time(&end_time);
std::cout << std::ctime(&end_time) << std::endl;
std::ifstream filebin(filenames[ifile], ios::in | ios::binary);
//std::ifstream filebin(filenames[ifile], ios::in | ios::binary);
HDF5File fileh5;
// //open file
ioutfile = 0;
if (filebin.is_open()) {
if ( fileh5.OpenResources(filenames[ifile].c_str(), 1) ) {
if (thr <= 0 && cf != 0) { // cluster finder
if (of == NULL) {
of = fopen(cfname.c_str(), "w");
@ -490,9 +497,12 @@ int main(int argc, char *argv[]) {
}
}
// //while read frame
ff = -1;
framenumber = -1;
iframe = 0;
ifr = 0;
while (decoder->readNextFrame(filebin, ff, np, buff)) {
while ( decoder->readNextFrame(fileh5, framenumber, iframe, buff) ) {
// if (np == 40) {
// //push
@ -507,7 +517,7 @@ int main(int argc, char *argv[]) {
ifr++;
if (ifr % 100 == 0)
std::cout << " " << ifr << " " << ff << std::endl;
std::cout << " " << ifr << " " << framenumber << std::endl;
if (nframes > 0) {
if (ifr % nframes == 0) {
imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", ioutfile );
@ -518,10 +528,11 @@ int main(int argc, char *argv[]) {
}
// } else
//std::cout << ifr << " " << ff << " " << np << std::endl;
ff = -1;
framenumber = -1;
}
std::cout << "aa --" << std::endl;
filebin.close();
//filebin.close();
fileh5.CloseResources();
std::cout << "bb --" << std::endl;
while (mt->isBusy()) {
;