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https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-04-26 16:20:03 +02:00
wip
This commit is contained in:
parent
5ad3205fe8
commit
0e7c643cf9
@ -13,151 +13,6 @@
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#include <libgen.h> //basename
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#include <libgen.h> //basename
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#include <string.h>
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#include <string.h>
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std::mutex HDF5File::hdf5Lib;
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HDF5File::HDF5File(int ind, uint32_t *maxf, int *nd, std::string *fname,
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std::string *fpath, uint64_t *findex, bool *owenable,
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int *dindex, int *nunits, uint64_t *nf, uint32_t *dr,
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uint32_t *portno, uint32_t nx, uint32_t ny, bool *smode)
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:
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File(ind, HDF5, maxf, nd, fname, fpath, findex, owenable, dindex, nunits,
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nf, dr, portno, smode),
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masterfd(nullptr), virtualfd(0), filefd(nullptr), dataspace(nullptr),
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dataset(nullptr), datatype(PredType::STD_U16LE), nPixelsX(nx),
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nPixelsY(ny), numFramesInFile(0), numFilesinAcquisition(0),
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dataspace_para(nullptr), extNumImages(0) {
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PrintMembers();
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dataset_para.clear();
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parameterNames.clear();
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parameterDataTypes.clear();
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parameterNames = std::vector<std::string>{
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"frame number",
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"exp length or sub exposure time",
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"packets caught",
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"bunch id",
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"timestamp",
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"mod id",
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"row",
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"column",
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"reserved",
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"debug",
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"round robin number",
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"detector type",
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"detector header version",
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"packets caught bit mask",
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};
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StrType strdatatype(PredType::C_S1, sizeof(bitset_storage));
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parameterDataTypes = std::vector<DataType>{
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PredType::STD_U64LE, PredType::STD_U32LE, PredType::STD_U32LE,
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PredType::STD_U64LE, PredType::STD_U64LE, PredType::STD_U16LE,
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PredType::STD_U16LE, PredType::STD_U16LE, PredType::STD_U16LE,
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PredType::STD_U32LE, PredType::STD_U16LE, PredType::STD_U8LE,
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PredType::STD_U8LE, strdatatype};
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}
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HDF5File::~HDF5File() { CloseAllFiles(); }
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void HDF5File::SetNumberofPixels(uint32_t nx, uint32_t ny) {
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nPixelsX = nx;
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nPixelsY = ny;
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}
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void HDF5File::CreateFile() {
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numFilesinAcquisition++;
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numFramesInFile = 0;
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// first time
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if (subFileIndex == 0u) {
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switch (*dynamicRange) {
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case 16:
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datatype = PredType::STD_U16LE;
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break;
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case 32:
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datatype = PredType::STD_U32LE;
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break;
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default:
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datatype = PredType::STD_U8LE;
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break;
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}
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}
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CreateDataFile();
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}
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void HDF5File::CloseAllFiles() {
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CloseCurrentDataFile();
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CloseMasterFile();
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}
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void HDF5File::CloseMasterFile() {
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if (master) {
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CloseFile(masterfd, true);
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// close virtual file
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// c code due to only c implementation of H5Pset_virtual available
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if (virtualfd != 0) {
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if (H5Fclose(virtualfd) < 0) {
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LOG(logERROR) << "Could not close virtual HDF5 handles";
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}
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virtualfd = 0;
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}
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}
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}
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void HDF5File::CloseCurrentDataFile() {
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CloseFile(filefd, false);
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for (unsigned int i = 0; i < dataset_para.size(); ++i)
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delete dataset_para[i];
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dataset_para.clear();
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if (dataspace_para) {
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delete dataspace_para;
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dataspace_para = nullptr;
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}
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if (dataset) {
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delete dataset;
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dataset = nullptr;
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}
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if (dataspace) {
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delete dataspace;
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dataspace = nullptr;
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}
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}
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void HDF5File::WriteToFile(char *buffer, int bufferSize,
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uint64_t currentFrameNumber,
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uint32_t numPacketsCaught) {
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// check if maxframesperfile = 0 for infinite
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if ((*maxFramesPerFile) && (numFramesInFile >= (*maxFramesPerFile))) {
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CloseCurrentFile();
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++subFileIndex;
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CreateFile();
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}
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numFramesInFile++;
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// extend dataset (when receiver start followed by many status starts
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// (jungfrau)))
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if (currentFrameNumber >= extNumImages) {
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ExtendDataset();
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}
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WriteDataFile(currentFrameNumber, buffer + sizeof(sls_receiver_header));
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WriteParameterDatasets(currentFrameNumber, (sls_receiver_header *)(buffer));
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}
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void HDF5File::CreateMasterFile(MasterAttributes *attr) {
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if (master) {
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virtualfd = 0;
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CreateMasterDataFile(attr);
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}
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}
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void HDF5File::StartofAcquisition() {
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numFilesinAcquisition = 0;
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numFramesInFile = 0;
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extNumImages = *numImages;
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}
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void HDF5File::EndofAcquisition(bool anyPacketsCaught,
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void HDF5File::EndofAcquisition(bool anyPacketsCaught,
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uint64_t numImagesCaught) {
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uint64_t numImagesCaught) {
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// not created before
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// not created before
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@ -190,313 +45,6 @@ void HDF5File::EndofAcquisition(bool anyPacketsCaught,
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numFilesinAcquisition = 0;
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numFilesinAcquisition = 0;
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}
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}
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void HDF5File::CloseFile(H5File *&fd, bool masterFile) {
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std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
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try {
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Exception::dontPrint(); // to handle errors
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if (fd) {
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fd->close();
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delete fd;
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fd = nullptr;
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}
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} catch (const Exception &error) {
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LOG(logERROR) << "Could not close " << (masterFile ? "master" : "data")
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<< " HDF5 handles of index " << index;
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error.printErrorStack();
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}
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}
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void HDF5File::WriteDataFile(uint64_t currentFrameNumber, char *buffer) {
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std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
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uint64_t nDimx =
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((*maxFramesPerFile == 0) ? currentFrameNumber
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: currentFrameNumber % (*maxFramesPerFile));
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uint32_t nDimy = nPixelsY;
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uint32_t nDimz = ((*dynamicRange == 4) ? (nPixelsX / 2) : nPixelsX);
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hsize_t count[3] = {1, nDimy, nDimz};
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hsize_t start[3] = {nDimx, 0, 0};
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hsize_t dims2[2] = {nDimy, nDimz};
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try {
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Exception::dontPrint(); // to handle errors
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dataspace->selectHyperslab(H5S_SELECT_SET, count, start);
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DataSpace memspace(2, dims2);
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dataset->write(buffer, datatype, memspace, *dataspace);
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memspace.close();
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} catch (const Exception &error) {
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LOG(logERROR) << "Could not write to file in object " << index;
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error.printErrorStack();
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throw sls::RuntimeError("Could not write to file in object " +
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std::to_string(index));
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}
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}
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void HDF5File::WriteParameterDatasets(uint64_t currentFrameNumber,
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sls_receiver_header *rheader) {
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std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
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uint64_t fnum =
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((*maxFramesPerFile == 0) ? currentFrameNumber
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: currentFrameNumber % (*maxFramesPerFile));
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sls_detector_header header = rheader->detHeader;
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hsize_t count[1] = {1};
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hsize_t start[1] = {fnum};
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int i = 0;
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try {
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Exception::dontPrint(); // to handle errors
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dataspace_para->selectHyperslab(H5S_SELECT_SET, count, start);
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DataSpace memspace(H5S_SCALAR);
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dataset_para[0]->write(&header.frameNumber, parameterDataTypes[0],
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memspace, *dataspace_para);
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i = 1;
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dataset_para[1]->write(&header.expLength, parameterDataTypes[1],
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memspace, *dataspace_para);
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i = 2;
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dataset_para[2]->write(&header.packetNumber, parameterDataTypes[2],
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memspace, *dataspace_para);
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i = 3;
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dataset_para[3]->write(&header.bunchId, parameterDataTypes[3], memspace,
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*dataspace_para);
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i = 4;
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dataset_para[4]->write(&header.timestamp, parameterDataTypes[4],
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memspace, *dataspace_para);
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i = 5;
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dataset_para[5]->write(&header.modId, parameterDataTypes[5], memspace,
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*dataspace_para);
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i = 6;
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dataset_para[6]->write(&header.row, parameterDataTypes[6], memspace,
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*dataspace_para);
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i = 7;
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dataset_para[7]->write(&header.column, parameterDataTypes[7], memspace,
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*dataspace_para);
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i = 8;
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dataset_para[8]->write(&header.reserved, parameterDataTypes[8],
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memspace, *dataspace_para);
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i = 9;
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dataset_para[9]->write(&header.debug, parameterDataTypes[9], memspace,
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*dataspace_para);
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i = 10;
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dataset_para[10]->write(&header.roundRNumber, parameterDataTypes[10],
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memspace, *dataspace_para);
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i = 11;
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dataset_para[11]->write(&header.detType, parameterDataTypes[11],
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memspace, *dataspace_para);
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i = 12;
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dataset_para[12]->write(&header.version, parameterDataTypes[12],
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memspace, *dataspace_para);
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i = 13;
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// contiguous bitset
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if (sizeof(sls_bitset) == sizeof(bitset_storage)) {
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dataset_para[13]->write((char *)&(rheader->packetsMask),
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parameterDataTypes[13], memspace,
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*dataspace_para);
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}
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// not contiguous bitset
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else {
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// get contiguous representation of bit mask
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bitset_storage storage;
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memset(storage, 0, sizeof(bitset_storage));
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sls_bitset bits = rheader->packetsMask;
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for (int i = 0; i < MAX_NUM_PACKETS; ++i)
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storage[i >> 3] |= (bits[i] << (i & 7));
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// write bitmask
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dataset_para[13]->write((char *)storage, parameterDataTypes[13],
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memspace, *dataspace_para);
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}
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i = 14;
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} catch (const Exception &error) {
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error.printErrorStack();
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throw sls::RuntimeError(
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"Could not write parameters (index:" + std::to_string(i) +
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") to file in object " + std::to_string(index));
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}
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}
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void HDF5File::ExtendDataset() {
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std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
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try {
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Exception::dontPrint(); // to handle errors
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hsize_t dims[3];
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dataspace->getSimpleExtentDims(dims);
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dims[0] += *numImages;
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dataset->extend(dims);
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delete dataspace;
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dataspace = nullptr;
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dataspace = new DataSpace(dataset->getSpace());
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hsize_t dims_para[1] = {dims[0]};
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for (unsigned int i = 0; i < dataset_para.size(); ++i)
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dataset_para[i]->extend(dims_para);
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delete dataspace_para;
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dataspace_para = nullptr;
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dataspace_para = new DataSpace(dataset_para[0]->getSpace());
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} catch (const Exception &error) {
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error.printErrorStack();
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throw sls::RuntimeError("Could not extend dataset in object " +
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std::to_string(index));
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}
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if (!(*silentMode)) {
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LOG(logINFO) << index << " Extending HDF5 dataset by " << extNumImages
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<< ", Total x Dimension: " << (extNumImages + *numImages);
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}
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extNumImages += *numImages;
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}
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void HDF5File::CreateDataFile() {
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std::ostringstream os;
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os << *filePath << "/" << *fileNamePrefix << "_d"
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<< (*detIndex * (*numUnitsPerDetector) + index) << "_f" << subFileIndex
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<< '_' << *fileIndex << ".h5";
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currentFileName = os.str();
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std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
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uint64_t framestosave =
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((*maxFramesPerFile == 0) ? *numImages : // infinite images
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(((extNumImages - subFileIndex) > (*maxFramesPerFile))
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? // save up to maximum at a time
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(*maxFramesPerFile)
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: (extNumImages - subFileIndex)));
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uint64_t nDimx = framestosave;
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uint32_t nDimy = nPixelsY;
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uint32_t nDimz = ((*dynamicRange == 4) ? (nPixelsX / 2) : nPixelsX);
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try {
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Exception::dontPrint(); // to handle errors
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// file
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FileAccPropList fapl;
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fapl.setFcloseDegree(H5F_CLOSE_STRONG);
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filefd = nullptr;
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if (!(*overWriteEnable))
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filefd = new H5File(currentFileName.c_str(), H5F_ACC_EXCL,
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FileCreatPropList::DEFAULT, fapl);
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else
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filefd = new H5File(currentFileName.c_str(), H5F_ACC_TRUNC,
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FileCreatPropList::DEFAULT, fapl);
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// attributes - version
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double dValue = HDF5_WRITER_VERSION;
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DataSpace dataspace_attr = DataSpace(H5S_SCALAR);
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Attribute attribute = filefd->createAttribute(
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"version", PredType::NATIVE_DOUBLE, dataspace_attr);
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attribute.write(PredType::NATIVE_DOUBLE, &dValue);
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// dataspace
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hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
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hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
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dataspace = nullptr;
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dataspace = new DataSpace(3, srcdims, srcdimsmax);
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// dataset name
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std::ostringstream osfn;
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osfn << "/data";
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if (*numImages > 1)
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osfn << "_f" << std::setfill('0') << std::setw(12) << subFileIndex;
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std::string dsetname = osfn.str();
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|
|
||||||
// dataset
|
|
||||||
// fill value
|
|
||||||
DSetCreatPropList plist;
|
|
||||||
int fill_value = -1;
|
|
||||||
plist.setFillValue(datatype, &fill_value);
|
|
||||||
// always create chunked dataset as unlimited is only
|
|
||||||
// supported with chunked layout
|
|
||||||
hsize_t chunk_dims[3] = {MAX_CHUNKED_IMAGES, nDimy, nDimz};
|
|
||||||
plist.setChunk(3, chunk_dims);
|
|
||||||
dataset = nullptr;
|
|
||||||
dataset = new DataSet(filefd->createDataSet(dsetname.c_str(), datatype,
|
|
||||||
*dataspace, plist));
|
|
||||||
|
|
||||||
// create parameter datasets
|
|
||||||
hsize_t dims[1] = {nDimx};
|
|
||||||
hsize_t dimsmax[1] = {H5S_UNLIMITED};
|
|
||||||
dataspace_para = nullptr;
|
|
||||||
dataspace_para = new DataSpace(1, dims, dimsmax);
|
|
||||||
|
|
||||||
// always create chunked dataset as unlimited is only
|
|
||||||
// supported with chunked layout
|
|
||||||
DSetCreatPropList paralist;
|
|
||||||
hsize_t chunkpara_dims[3] = {MAX_CHUNKED_IMAGES};
|
|
||||||
paralist.setChunk(1, chunkpara_dims);
|
|
||||||
|
|
||||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
|
||||||
DataSet *ds = new DataSet(filefd->createDataSet(
|
|
||||||
parameterNames[i].c_str(), parameterDataTypes[i],
|
|
||||||
*dataspace_para, paralist));
|
|
||||||
dataset_para.push_back(ds);
|
|
||||||
}
|
|
||||||
} catch (const Exception &error) {
|
|
||||||
error.printErrorStack();
|
|
||||||
if (filefd) {
|
|
||||||
filefd->close();
|
|
||||||
}
|
|
||||||
throw sls::RuntimeError("Could not create HDF5 handles in object " +
|
|
||||||
index);
|
|
||||||
}
|
|
||||||
if (!(*silentMode)) {
|
|
||||||
LOG(logINFO) << *udpPortNumber
|
|
||||||
<< ": HDF5 File created: " << currentFileName;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CreateMasterDataFile(MasterAttributes *attr) {
|
|
||||||
|
|
||||||
std::ostringstream os;
|
|
||||||
os << *filePath << "/" << *fileNamePrefix << "_master"
|
|
||||||
<< "_" << *fileIndex << ".h5";
|
|
||||||
masterFileName = os.str();
|
|
||||||
|
|
||||||
if (!(*silentMode)) {
|
|
||||||
LOG(logINFO) << "Master File: " << masterFileName;
|
|
||||||
}
|
|
||||||
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
|
|
||||||
try {
|
|
||||||
Exception::dontPrint(); // to handle errors
|
|
||||||
|
|
||||||
FileAccPropList flist;
|
|
||||||
flist.setFcloseDegree(H5F_CLOSE_STRONG);
|
|
||||||
masterfd = nullptr;
|
|
||||||
if (!(*overWriteEnable))
|
|
||||||
masterfd = new H5File(masterFileName.c_str(), H5F_ACC_EXCL,
|
|
||||||
FileCreatPropList::DEFAULT, flist);
|
|
||||||
else
|
|
||||||
masterfd = new H5File(masterFileName.c_str(), H5F_ACC_TRUNC,
|
|
||||||
FileCreatPropList::DEFAULT, flist);
|
|
||||||
|
|
||||||
// Create a group in the file
|
|
||||||
Group group1(masterfd->createGroup("entry"));
|
|
||||||
Group group2(group1.createGroup("data"));
|
|
||||||
Group group3(group1.createGroup("instrument"));
|
|
||||||
Group group4(group3.createGroup("beam"));
|
|
||||||
Group group5(group3.createGroup("detector"));
|
|
||||||
Group group6(group1.createGroup("sample"));
|
|
||||||
|
|
||||||
attr->WriteMasterHDF5Attributes(masterfd, &group5);
|
|
||||||
masterfd->close();
|
|
||||||
|
|
||||||
} catch (const Exception &error) {
|
|
||||||
error.printErrorStack();
|
|
||||||
if (masterfd) {
|
|
||||||
masterfd->close();
|
|
||||||
}
|
|
||||||
throw sls::RuntimeError("Could not create master HDF5 handles");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CreateVirtualDataFile(uint32_t maxFramesPerFile, uint64_t numf) {
|
void HDF5File::CreateVirtualDataFile(uint32_t maxFramesPerFile, uint64_t numf) {
|
||||||
|
|
||||||
std::ostringstream osfn;
|
std::ostringstream osfn;
|
||||||
|
|||||||
Loading…
x
Reference in New Issue
Block a user