mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-06-20 08:38:00 +02:00
wip
This commit is contained in:
@ -1,173 +0,0 @@
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/************************************************
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* @file BinaryFile.cpp
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* @short sets/gets properties for the binary file,
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* creates/closes the file and writes data to it
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***********************************************/
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#include "BinaryFile.h"
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#include "Fifo.h"
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#include "MasterAttributes.h"
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#include "receiver_defs.h"
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#include <iomanip>
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#include <iostream>
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#include <string.h>
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FILE *BinaryFile::masterfd = nullptr;
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BinaryFile::BinaryFile(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, bool *smode)
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: File(ind, BINARY, maxf, nd, fname, fpath, findex, owenable, dindex,
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nunits, nf, dr, portno, smode) {
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#ifdef VERBOSE
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PrintMembers();
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#endif
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}
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BinaryFile::~BinaryFile() { CloseAllFiles(); }
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void BinaryFile::PrintMembers(TLogLevel level) {
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File::PrintMembers(level);
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LOG(logINFO) << "Max Frames Per File: " << *maxFramesPerFile;
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LOG(logINFO) << "Number of Frames in File: " << numFramesInFile;
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}
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void BinaryFile::CreateFile() {
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numFramesInFile = 0;
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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 << ".raw";
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currentFileName = os.str();
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if (!(*overWriteEnable)) {
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if (nullptr ==
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(filefd = fopen((const char *)currentFileName.c_str(), "wx"))) {
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filefd = nullptr;
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throw sls::RuntimeError("Could not create/overwrite file " +
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currentFileName);
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}
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} else if (nullptr ==
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(filefd = fopen((const char *)currentFileName.c_str(), "w"))) {
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filefd = nullptr;
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throw sls::RuntimeError("Could not create file " + currentFileName);
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}
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// setting to no file buffering
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setvbuf(filefd, nullptr, _IONBF, 0);
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if (!(*silentMode)) {
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LOG(logINFO) << "[" << *udpPortNumber
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<< "]: Binary File created: " << currentFileName;
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}
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}
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void BinaryFile::CloseAllFiles() {
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CloseCurrentDataFile();
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CloseMasterFile();
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}
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void BinaryFile::CloseMasterFile() {
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if (master) {
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if (masterfd)
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fclose(masterfd);
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masterfd = nullptr;
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}
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}
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void BinaryFile::CloseCurrentDataFile() {
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if (filefd)
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fclose(filefd);
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filefd = nullptr;
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}
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int BinaryFile::WriteData(char *buf, int bsize) {
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if (!filefd)
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return 0;
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return fwrite(buf, 1, bsize, filefd);
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}
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void BinaryFile::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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// write to file
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int ret = 0;
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// contiguous bitset
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if (sizeof(sls_bitset) == sizeof(bitset_storage)) {
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ret = WriteData(buffer, buffersize);
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}
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// not contiguous bitset
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else {
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// write detector header
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ret = WriteData(buffer, sizeof(sls_detector_header));
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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 = *(sls_bitset *)(buffer + sizeof(sls_detector_header));
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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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ret += WriteData((char *)storage, sizeof(bitset_storage));
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// write data
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ret += WriteData(buffer + sizeof(sls_detector_header),
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buffersize - sizeof(sls_receiver_header));
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}
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// if write error
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if (ret != buffersize) {
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throw sls::RuntimeError(std::to_string(index) +
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" : Write to file failed for image number " +
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std::to_string(currentFrameNumber));
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}
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}
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void BinaryFile::CreateMasterFile(MasterAttributes *attr) {
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if (master) {
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std::ostringstream os;
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os << *filePath << "/" << *fileNamePrefix << "_master"
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<< "_" << *fileIndex << ".raw";
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masterFileName = os.str();
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if (!(*silentMode)) {
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LOG(logINFO) << "Master File: " << masterFileName;
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}
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// create master file
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if (!(*overWriteEnable)) {
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if (nullptr == (masterfd = fopen(
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(const char *)masterFileName.c_str(), "wx"))) {
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masterfd = nullptr;
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throw sls::RuntimeError("Could not create binary master file "
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"(without overwrite enable) " +
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masterFileName);
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}
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} else if (nullptr ==
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(masterfd =
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fopen((const char *)masterFileName.c_str(), "w"))) {
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masterfd = nullptr;
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throw sls::RuntimeError("Could not create binary master file "
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"(with overwrite enable) " +
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masterFileName);
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}
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attr->WriteMasterBinaryAttributes(masterfd);
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if (masterfd)
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fclose(masterfd);
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masterfd = nullptr;
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}
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}
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void BinaryFile::StartofAcquisition() { numFramesInFile = 0; }
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@ -1,58 +0,0 @@
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#pragma once
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/************************************************
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* @file BinaryFile.h
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* @short sets/gets properties for the binary file,
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* creates/closes the file and writes data to it
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***********************************************/
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/**
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*@short sets/gets properties for the binary file, creates/closes the file and
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*writes data to it
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*/
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#include "File.h"
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#include <string>
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class BinaryFile : private virtual slsDetectorDefs, public File {
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public:
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/**
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* Constructor
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* creates the File Writer
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* @param ind self index
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* @param maxf pointer to max frames per file
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* @param nd pointer to number of detectors in each dimension
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* @param fname pointer to file name prefix
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* @param fpath pointer to file path
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* @param findex pointer to file index
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* @param owenable pointer to over write enable
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* @param dindex pointer to detector index
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* @param nunits pointer to number of theads/ units per detector
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* @param nf pointer to number of images in acquisition
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* @param dr pointer to dynamic range
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* @param portno pointer to udp port number for logging
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* @param smode pointer to silent mode
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*/
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BinaryFile(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, bool *smode);
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~BinaryFile();
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void PrintMembers(TLogLevel level = logDEBUG1) override;
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void CreateFile() override;
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void CreateMasterFile(MasterAttributes *attr) override;
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void StartofAcquisition() override;
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void CloseAllFiles() override;
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void CloseCurrentDataFile() override;
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void CloseMasterFile() override;
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void WriteToFile(char *buffer, int buffersize, uint64_t currentFrameNumber,
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uint32_t numPacketsCaught) override;
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private:
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int WriteData(char *buf, int bsize);
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FILE *filefd = nullptr;
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static FILE *masterfd;
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uint32_t numFramesInFile = 0;
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};
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@ -1,173 +0,0 @@
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/************************************************
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* @file BinaryFile.cpp
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* @short sets/gets properties for the binary file,
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* creates/closes the file and writes data to it
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***********************************************/
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#include "BinaryFile.h"
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#include "Fifo.h"
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#include "MasterAttributes.h"
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#include "receiver_defs.h"
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#include <iomanip>
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#include <iostream>
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#include <string.h>
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FILE *BinaryFile::masterfd = nullptr;
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BinaryFile::BinaryFile(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, bool *smode)
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: File(ind, BINARY, maxf, nd, fname, fpath, findex, owenable, dindex,
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nunits, nf, dr, portno, smode) {
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#ifdef VERBOSE
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PrintMembers();
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#endif
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}
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BinaryFile::~BinaryFile() { CloseAllFiles(); }
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void BinaryFile::PrintMembers(TLogLevel level) {
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File::PrintMembers(level);
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LOG(logINFO) << "Max Frames Per File: " << *maxFramesPerFile;
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LOG(logINFO) << "Number of Frames in File: " << numFramesInFile;
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}
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void BinaryFile::CreateFile() {
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numFramesInFile = 0;
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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 << ".raw";
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currentFileName = os.str();
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|
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if (!(*overWriteEnable)) {
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if (nullptr ==
|
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(filefd = fopen((const char *)currentFileName.c_str(), "wx"))) {
|
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filefd = nullptr;
|
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throw sls::RuntimeError("Could not create/overwrite file " +
|
|
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currentFileName);
|
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}
|
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} else if (nullptr ==
|
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(filefd = fopen((const char *)currentFileName.c_str(), "w"))) {
|
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filefd = nullptr;
|
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throw sls::RuntimeError("Could not create file " + currentFileName);
|
|
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}
|
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// setting to no file buffering
|
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setvbuf(filefd, nullptr, _IONBF, 0);
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|
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if (!(*silentMode)) {
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LOG(logINFO) << "[" << *udpPortNumber
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|
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<< "]: Binary File created: " << currentFileName;
|
|
||||||
}
|
|
||||||
}
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|
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void BinaryFile::CloseAllFiles() {
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CloseCurrentDataFile();
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|
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CloseMasterFile();
|
|
||||||
}
|
|
||||||
|
|
||||||
void BinaryFile::CloseMasterFile() {
|
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if (master) {
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|
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if (masterfd)
|
|
||||||
fclose(masterfd);
|
|
||||||
masterfd = nullptr;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void BinaryFile::CloseCurrentDataFile() {
|
|
||||||
if (filefd)
|
|
||||||
fclose(filefd);
|
|
||||||
filefd = nullptr;
|
|
||||||
}
|
|
||||||
|
|
||||||
int BinaryFile::WriteData(char *buf, int bsize) {
|
|
||||||
if (!filefd)
|
|
||||||
return 0;
|
|
||||||
return fwrite(buf, 1, bsize, filefd);
|
|
||||||
}
|
|
||||||
|
|
||||||
void BinaryFile::WriteToFile(char *buffer, int buffersize,
|
|
||||||
uint64_t currentFrameNumber,
|
|
||||||
uint32_t numPacketsCaught) {
|
|
||||||
// check if maxframesperfile = 0 for infinite
|
|
||||||
if ((*maxFramesPerFile) && (numFramesInFile >= (*maxFramesPerFile))) {
|
|
||||||
CloseCurrentFile();
|
|
||||||
++subFileIndex;
|
|
||||||
CreateFile();
|
|
||||||
}
|
|
||||||
numFramesInFile++;
|
|
||||||
|
|
||||||
// write to file
|
|
||||||
int ret = 0;
|
|
||||||
|
|
||||||
// contiguous bitset
|
|
||||||
if (sizeof(sls_bitset) == sizeof(bitset_storage)) {
|
|
||||||
ret = WriteData(buffer, buffersize);
|
|
||||||
}
|
|
||||||
|
|
||||||
// not contiguous bitset
|
|
||||||
else {
|
|
||||||
// write detector header
|
|
||||||
ret = WriteData(buffer, sizeof(sls_detector_header));
|
|
||||||
|
|
||||||
// get contiguous representation of bit mask
|
|
||||||
bitset_storage storage;
|
|
||||||
memset(storage, 0, sizeof(bitset_storage));
|
|
||||||
sls_bitset bits = *(sls_bitset *)(buffer + sizeof(sls_detector_header));
|
|
||||||
for (int i = 0; i < MAX_NUM_PACKETS; ++i)
|
|
||||||
storage[i >> 3] |= (bits[i] << (i & 7));
|
|
||||||
// write bitmask
|
|
||||||
ret += WriteData((char *)storage, sizeof(bitset_storage));
|
|
||||||
|
|
||||||
// write data
|
|
||||||
ret += WriteData(buffer + sizeof(sls_detector_header),
|
|
||||||
buffersize - sizeof(sls_receiver_header));
|
|
||||||
}
|
|
||||||
|
|
||||||
// if write error
|
|
||||||
if (ret != buffersize) {
|
|
||||||
throw sls::RuntimeError(std::to_string(index) +
|
|
||||||
" : Write to file failed for image number " +
|
|
||||||
std::to_string(currentFrameNumber));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void BinaryFile::CreateMasterFile(MasterAttributes *attr) {
|
|
||||||
if (master) {
|
|
||||||
std::ostringstream os;
|
|
||||||
os << *filePath << "/" << *fileNamePrefix << "_master"
|
|
||||||
<< "_" << *fileIndex << ".raw";
|
|
||||||
masterFileName = os.str();
|
|
||||||
if (!(*silentMode)) {
|
|
||||||
LOG(logINFO) << "Master File: " << masterFileName;
|
|
||||||
}
|
|
||||||
|
|
||||||
// create master file
|
|
||||||
if (!(*overWriteEnable)) {
|
|
||||||
if (nullptr == (masterfd = fopen(
|
|
||||||
(const char *)masterFileName.c_str(), "wx"))) {
|
|
||||||
masterfd = nullptr;
|
|
||||||
throw sls::RuntimeError("Could not create binary master file "
|
|
||||||
"(without overwrite enable) " +
|
|
||||||
masterFileName);
|
|
||||||
}
|
|
||||||
} else if (nullptr ==
|
|
||||||
(masterfd =
|
|
||||||
fopen((const char *)masterFileName.c_str(), "w"))) {
|
|
||||||
masterfd = nullptr;
|
|
||||||
throw sls::RuntimeError("Could not create binary master file "
|
|
||||||
"(with overwrite enable) " +
|
|
||||||
masterFileName);
|
|
||||||
}
|
|
||||||
|
|
||||||
attr->WriteMasterBinaryAttributes(masterfd);
|
|
||||||
if (masterfd)
|
|
||||||
fclose(masterfd);
|
|
||||||
masterfd = nullptr;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void BinaryFile::StartofAcquisition() { numFramesInFile = 0; }
|
|
||||||
@ -1,58 +0,0 @@
|
|||||||
#pragma once
|
|
||||||
/************************************************
|
|
||||||
* @file BinaryFile.h
|
|
||||||
* @short sets/gets properties for the binary file,
|
|
||||||
* creates/closes the file and writes data to it
|
|
||||||
***********************************************/
|
|
||||||
/**
|
|
||||||
*@short sets/gets properties for the binary file, creates/closes the file and
|
|
||||||
*writes data to it
|
|
||||||
*/
|
|
||||||
|
|
||||||
#include "File.h"
|
|
||||||
|
|
||||||
#include <string>
|
|
||||||
|
|
||||||
class BinaryFile : private virtual slsDetectorDefs, public File {
|
|
||||||
|
|
||||||
public:
|
|
||||||
/**
|
|
||||||
* Constructor
|
|
||||||
* creates the File Writer
|
|
||||||
* @param ind self index
|
|
||||||
* @param maxf pointer to max frames per file
|
|
||||||
* @param nd pointer to number of detectors in each dimension
|
|
||||||
* @param fname pointer to file name prefix
|
|
||||||
* @param fpath pointer to file path
|
|
||||||
* @param findex pointer to file index
|
|
||||||
* @param owenable pointer to over write enable
|
|
||||||
* @param dindex pointer to detector index
|
|
||||||
* @param nunits pointer to number of theads/ units per detector
|
|
||||||
* @param nf pointer to number of images in acquisition
|
|
||||||
* @param dr pointer to dynamic range
|
|
||||||
* @param portno pointer to udp port number for logging
|
|
||||||
* @param smode pointer to silent mode
|
|
||||||
*/
|
|
||||||
BinaryFile(int ind, uint32_t *maxf, int *nd, std::string *fname,
|
|
||||||
std::string *fpath, uint64_t *findex, bool *owenable,
|
|
||||||
int *dindex, int *nunits, uint64_t *nf, uint32_t *dr,
|
|
||||||
uint32_t *portno, bool *smode);
|
|
||||||
~BinaryFile();
|
|
||||||
|
|
||||||
void PrintMembers(TLogLevel level = logDEBUG1) override;
|
|
||||||
void CreateFile() override;
|
|
||||||
void CreateMasterFile(MasterAttributes *attr) override;
|
|
||||||
void StartofAcquisition() override;
|
|
||||||
void CloseAllFiles() override;
|
|
||||||
void CloseCurrentDataFile() override;
|
|
||||||
void CloseMasterFile() override;
|
|
||||||
void WriteToFile(char *buffer, int buffersize, uint64_t currentFrameNumber,
|
|
||||||
uint32_t numPacketsCaught) override;
|
|
||||||
|
|
||||||
private:
|
|
||||||
int WriteData(char *buf, int bsize);
|
|
||||||
|
|
||||||
FILE *filefd = nullptr;
|
|
||||||
static FILE *masterfd;
|
|
||||||
uint32_t numFramesInFile = 0;
|
|
||||||
};
|
|
||||||
@ -1,515 +0,0 @@
|
|||||||
/************************************************
|
|
||||||
* @file DataProcessor.cpp
|
|
||||||
* @short creates data processor thread that
|
|
||||||
* pulls pointers to memory addresses from fifos
|
|
||||||
* and processes data stored in them & writes them to file
|
|
||||||
***********************************************/
|
|
||||||
|
|
||||||
#include "DataProcessor.h"
|
|
||||||
#include "BinaryFile.h"
|
|
||||||
#include "Fifo.h"
|
|
||||||
#include "GeneralData.h"
|
|
||||||
#include "MasterAttributes.h"
|
|
||||||
#ifdef HDF5C
|
|
||||||
#include "HDF5File.h"
|
|
||||||
#endif
|
|
||||||
#include "DataStreamer.h"
|
|
||||||
#include "sls/sls_detector_exceptions.h"
|
|
||||||
|
|
||||||
#include <cerrno>
|
|
||||||
#include <cstring>
|
|
||||||
#include <iostream>
|
|
||||||
|
|
||||||
const std::string DataProcessor::TypeName = "DataProcessor";
|
|
||||||
|
|
||||||
DataProcessor::DataProcessor(int ind, detectorType dtype, Fifo *f, bool act,
|
|
||||||
bool depaden, bool *dsEnable, uint32_t *freq,
|
|
||||||
uint32_t *timer, uint32_t *sfnum, bool *fp,
|
|
||||||
bool *sm, std::vector<int> *cdl, int *cdo,
|
|
||||||
int *cad)
|
|
||||||
: ThreadObject(ind, TypeName), fifo(f), myDetectorType(dtype),
|
|
||||||
dataStreamEnable(dsEnable), activated(act),
|
|
||||||
deactivatedPaddingEnable(depaden), streamingFrequency(freq),
|
|
||||||
streamingTimerInMs(timer), streamingStartFnum(sfnum), silentMode(sm),
|
|
||||||
framePadding(fp), ctbDbitList(cdl), ctbDbitOffset(cdo),
|
|
||||||
ctbAnalogDataBytes(cad), firstStreamerFrame(false) {
|
|
||||||
LOG(logDEBUG) << "DataProcessor " << ind << " created";
|
|
||||||
memset((void *)&timerBegin, 0, sizeof(timespec));
|
|
||||||
}
|
|
||||||
|
|
||||||
DataProcessor::~DataProcessor() {
|
|
||||||
delete file;
|
|
||||||
delete masterFile;
|
|
||||||
delete virtualFile;
|
|
||||||
}
|
|
||||||
|
|
||||||
/** getters */
|
|
||||||
|
|
||||||
bool DataProcessor::GetStartedFlag() { return startedFlag; }
|
|
||||||
|
|
||||||
uint64_t DataProcessor::GetNumFramesCaught() { return numFramesCaught; }
|
|
||||||
|
|
||||||
uint64_t DataProcessor::GetCurrentFrameIndex() { return currentFrameIndex; }
|
|
||||||
|
|
||||||
uint64_t DataProcessor::GetProcessedIndex() {
|
|
||||||
return currentFrameIndex - firstIndex;
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::SetFifo(Fifo *f) { fifo = f; }
|
|
||||||
|
|
||||||
void DataProcessor::ResetParametersforNewAcquisition() {
|
|
||||||
StopRunning();
|
|
||||||
startedFlag = false;
|
|
||||||
numFramesCaught = 0;
|
|
||||||
firstIndex = 0;
|
|
||||||
currentFrameIndex = 0;
|
|
||||||
firstStreamerFrame = true;
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::RecordFirstIndex(uint64_t fnum) {
|
|
||||||
// listen to this fnum, later +1
|
|
||||||
currentFrameIndex = fnum;
|
|
||||||
|
|
||||||
startedFlag = true;
|
|
||||||
firstIndex = fnum;
|
|
||||||
|
|
||||||
LOG(logDEBUG1) << index << " First Index:" << firstIndex;
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::SetGeneralData(GeneralData *g) {
|
|
||||||
generalData = g;
|
|
||||||
if (file != nullptr) {
|
|
||||||
if (file->GetFileType() == HDF5) {
|
|
||||||
file->SetNumberofPixels(generalData->nPixelsX,
|
|
||||||
generalData->nPixelsY);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
if (masterFile != nullptr) {
|
|
||||||
if (masterFile->GetFileType() == HDF5) {
|
|
||||||
masterFile->SetNumberofPixels(generalData->nPixelsX,
|
|
||||||
generalData->nPixelsY);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
if (virtualFile != nullptr) {
|
|
||||||
if (virtualFile->GetFileType() == HDF5) {
|
|
||||||
virtualFile->SetNumberofPixels(generalData->nPixelsX,
|
|
||||||
generalData->nPixelsY);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::SetupFileWriter(fileFormat ftype, bool fwe, int act,
|
|
||||||
int depaden, int *nd, uint32_t *maxf,
|
|
||||||
std::string *fname, std::string *fpath,
|
|
||||||
uint64_t *findex, bool *owenable,
|
|
||||||
int *dindex, int *nunits, uint64_t *nf,
|
|
||||||
uint32_t *dr, uint32_t *portno,
|
|
||||||
GeneralData *g) {
|
|
||||||
activated = act;
|
|
||||||
deactivatedPaddingEnable = depaden;
|
|
||||||
if (g != nullptr)
|
|
||||||
generalData = g;
|
|
||||||
|
|
||||||
// close existing file objects
|
|
||||||
if (file != nullptr) {
|
|
||||||
delete file;
|
|
||||||
file = nullptr;
|
|
||||||
}
|
|
||||||
if (masterFile != nullptr) {
|
|
||||||
delete masterFile;
|
|
||||||
masterFile = nullptr;
|
|
||||||
}
|
|
||||||
if (virtualFile != nullptr) {
|
|
||||||
delete virtualFile;
|
|
||||||
virtualFile = nullptr;
|
|
||||||
}
|
|
||||||
// skip data file writing for deactivated non padded parts
|
|
||||||
bool skipDataFileWriting = false;
|
|
||||||
if (myDetectorType == EIGER && !activated && !deactivatedPaddingEnable) {
|
|
||||||
skipDataFileWriting = true;
|
|
||||||
}
|
|
||||||
|
|
||||||
// create file objects
|
|
||||||
if (fwe) {
|
|
||||||
switch (fileFormatType) {
|
|
||||||
#ifdef HDF5C
|
|
||||||
case HDF5:
|
|
||||||
// data file
|
|
||||||
if (!skipDataFileWriting) {
|
|
||||||
file = new HDF5File(index, maxf, nd, fname, fpath, findex,
|
|
||||||
owenable, dindex, nunits, nf, dr, portno,
|
|
||||||
generalData->nPixelsX,
|
|
||||||
generalData->nPixelsY, silentMode);
|
|
||||||
}
|
|
||||||
// master file
|
|
||||||
if ((index == 0) && (*dindex == 0)) {
|
|
||||||
masterFile = new HDF5File(index, maxf, nd, fname, fpath, findex,
|
|
||||||
owenable, dindex, nunits, nf, dr,
|
|
||||||
portno, generalData->nPixelsX,
|
|
||||||
generalData->nPixelsY, silentMode);
|
|
||||||
virtualFile = new HDF5File(index, maxf, nd, fname, fpath,
|
|
||||||
findex, owenable, dindex, nunits, nf,
|
|
||||||
dr, portno, generalData->nPixelsX,
|
|
||||||
generalData->nPixelsY, silentMode);
|
|
||||||
}
|
|
||||||
break;
|
|
||||||
#endif
|
|
||||||
default:
|
|
||||||
// data file
|
|
||||||
if (!skipDataFileWriting) {
|
|
||||||
file = new BinaryFile(index, maxf, nd, fname, fpath, findex,
|
|
||||||
owenable, dindex, nunits, nf, dr, portno,
|
|
||||||
silentMode);
|
|
||||||
}
|
|
||||||
// master file
|
|
||||||
if ((index == 0) && (*dindex == 0)) {
|
|
||||||
masterFile = new BinaryFile(index, maxf, nd, fname, fpath,
|
|
||||||
findex, owenable, dindex, nunits,
|
|
||||||
nf, dr, portno, silentMode);
|
|
||||||
}
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::CreateMasterFile(MasterAttributes *attr) {
|
|
||||||
if (masterFile == nullptr) {
|
|
||||||
throw sls::RuntimeError("master file object not contstructed");
|
|
||||||
}
|
|
||||||
masterFile->CloseMasterFile();
|
|
||||||
masterFile->CreateMasterFile(attr);
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::CreateFirstDataFile() {
|
|
||||||
if (file == nullptr) {
|
|
||||||
throw sls::RuntimeError("file object not contstructed");
|
|
||||||
}
|
|
||||||
file->CloseCurrentDataFile();
|
|
||||||
file->resetSubFileIndex();
|
|
||||||
file->StartofAcquisition();
|
|
||||||
// do not create file if deactivated and no padding
|
|
||||||
if (myDetectorType == EIGER && !activated && !deactivatedPaddingEnable) {
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
file->CreateFile();
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::CloseFiles() {
|
|
||||||
if (file != nullptr)
|
|
||||||
file->CloseAllFiles();
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::EndofAcquisition(bool anyPacketsCaught, uint64_t numf) {
|
|
||||||
if ((file != nullptr) && file->GetFileType() == HDF5) {
|
|
||||||
try {
|
|
||||||
file->EndofAcquisition(anyPacketsCaught, numf);
|
|
||||||
} catch (const sls::RuntimeError &e) {
|
|
||||||
; // ignore for now //TODO: send error to client via stop receiver
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::ThreadExecution() {
|
|
||||||
char *buffer = nullptr;
|
|
||||||
fifo->PopAddress(buffer);
|
|
||||||
LOG(logDEBUG5) << "DataProcessor " << index
|
|
||||||
<< ", "
|
|
||||||
"pop 0x"
|
|
||||||
<< std::hex << (void *)(buffer) << std::dec << ":" << buffer;
|
|
||||||
|
|
||||||
// check dummy
|
|
||||||
auto numBytes = (uint32_t)(*((uint32_t *)buffer));
|
|
||||||
LOG(logDEBUG1) << "DataProcessor " << index << ", Numbytes:" << numBytes;
|
|
||||||
if (numBytes == DUMMY_PACKET_VALUE) {
|
|
||||||
StopProcessing(buffer);
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
uint64_t fnum = 0;
|
|
||||||
try {
|
|
||||||
fnum = ProcessAnImage(buffer);
|
|
||||||
} catch (const std::exception &e) {
|
|
||||||
fifo->FreeAddress(buffer);
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
// stream (if time/freq to stream) or free
|
|
||||||
if (*dataStreamEnable && SendToStreamer()) {
|
|
||||||
// if first frame to stream, add frame index to fifo header (might
|
|
||||||
// not be the first)
|
|
||||||
if (firstStreamerFrame) {
|
|
||||||
firstStreamerFrame = false;
|
|
||||||
(*((uint32_t *)(buffer + FIFO_DATASIZE_NUMBYTES))) =
|
|
||||||
(uint32_t)(fnum - firstIndex);
|
|
||||||
}
|
|
||||||
fifo->PushAddressToStream(buffer);
|
|
||||||
} else {
|
|
||||||
fifo->FreeAddress(buffer);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::StopProcessing(char *buf) {
|
|
||||||
LOG(logDEBUG1) << "DataProcessing " << index << ": Dummy";
|
|
||||||
|
|
||||||
// stream or free
|
|
||||||
if (*dataStreamEnable)
|
|
||||||
fifo->PushAddressToStream(buf);
|
|
||||||
else
|
|
||||||
fifo->FreeAddress(buf);
|
|
||||||
|
|
||||||
if (file != nullptr)
|
|
||||||
file->CloseCurrentFile();
|
|
||||||
StopRunning();
|
|
||||||
LOG(logDEBUG1) << index << ": Processing Completed";
|
|
||||||
}
|
|
||||||
|
|
||||||
uint64_t DataProcessor::ProcessAnImage(char *buf) {
|
|
||||||
|
|
||||||
auto *rheader = (sls_receiver_header *)(buf + FIFO_HEADER_NUMBYTES);
|
|
||||||
sls_detector_header header = rheader->detHeader;
|
|
||||||
uint64_t fnum = header.frameNumber;
|
|
||||||
currentFrameIndex = fnum;
|
|
||||||
uint32_t nump = header.packetNumber;
|
|
||||||
if (nump == generalData->packetsPerFrame) {
|
|
||||||
numFramesCaught++;
|
|
||||||
}
|
|
||||||
|
|
||||||
LOG(logDEBUG1) << "DataProcessing " << index << ": fnum:" << fnum;
|
|
||||||
|
|
||||||
if (!startedFlag) {
|
|
||||||
RecordFirstIndex(fnum);
|
|
||||||
if (*dataStreamEnable) {
|
|
||||||
// restart timer
|
|
||||||
clock_gettime(CLOCK_REALTIME, &timerBegin);
|
|
||||||
timerBegin.tv_sec -= (*streamingTimerInMs) / 1000;
|
|
||||||
timerBegin.tv_nsec -= ((*streamingTimerInMs) % 1000) * 1000000;
|
|
||||||
|
|
||||||
// to send first image
|
|
||||||
currentFreqCount = *streamingFrequency - *streamingStartFnum;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// frame padding
|
|
||||||
if (activated && *framePadding && nump < generalData->packetsPerFrame)
|
|
||||||
PadMissingPackets(buf);
|
|
||||||
|
|
||||||
// deactivated and padding enabled
|
|
||||||
else if (!activated && deactivatedPaddingEnable)
|
|
||||||
PadMissingPackets(buf);
|
|
||||||
|
|
||||||
// rearrange ctb digital bits (if ctbDbitlist is not empty)
|
|
||||||
if (!(*ctbDbitList).empty()) {
|
|
||||||
RearrangeDbitData(buf);
|
|
||||||
}
|
|
||||||
|
|
||||||
try {
|
|
||||||
// normal call back
|
|
||||||
if (rawDataReadyCallBack != nullptr) {
|
|
||||||
rawDataReadyCallBack((char *)rheader,
|
|
||||||
buf + FIFO_HEADER_NUMBYTES +
|
|
||||||
sizeof(sls_receiver_header),
|
|
||||||
(uint32_t)(*((uint32_t *)buf)), pRawDataReady);
|
|
||||||
}
|
|
||||||
|
|
||||||
// call back with modified size
|
|
||||||
else if (rawDataModifyReadyCallBack != nullptr) {
|
|
||||||
auto revsize = (uint32_t)(*((uint32_t *)buf));
|
|
||||||
rawDataModifyReadyCallBack((char *)rheader,
|
|
||||||
buf + FIFO_HEADER_NUMBYTES +
|
|
||||||
sizeof(sls_receiver_header),
|
|
||||||
revsize, pRawDataReady);
|
|
||||||
(*((uint32_t *)buf)) = revsize;
|
|
||||||
}
|
|
||||||
} catch (const std::exception &e) {
|
|
||||||
throw sls::RuntimeError("Get Data Callback Error: " +
|
|
||||||
std::string(e.what()));
|
|
||||||
}
|
|
||||||
|
|
||||||
// write to file
|
|
||||||
if (file != nullptr) {
|
|
||||||
try {
|
|
||||||
file->WriteToFile(
|
|
||||||
buf + FIFO_HEADER_NUMBYTES,
|
|
||||||
sizeof(sls_receiver_header) +
|
|
||||||
(uint32_t)(*((uint32_t *)buf)), //+ size of data (resizable
|
|
||||||
// from previous call back
|
|
||||||
fnum - firstIndex, nump);
|
|
||||||
} catch (const sls::RuntimeError &e) {
|
|
||||||
; // ignore write exception for now (TODO: send error message
|
|
||||||
// via stopReceiver tcp)
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return fnum;
|
|
||||||
}
|
|
||||||
|
|
||||||
bool DataProcessor::SendToStreamer() {
|
|
||||||
// skip
|
|
||||||
if ((*streamingFrequency) == 0u) {
|
|
||||||
if (!CheckTimer())
|
|
||||||
return false;
|
|
||||||
} else {
|
|
||||||
if (!CheckCount())
|
|
||||||
return false;
|
|
||||||
}
|
|
||||||
return true;
|
|
||||||
}
|
|
||||||
|
|
||||||
bool DataProcessor::CheckTimer() {
|
|
||||||
struct timespec end;
|
|
||||||
clock_gettime(CLOCK_REALTIME, &end);
|
|
||||||
|
|
||||||
LOG(logDEBUG1) << index << " Timer elapsed time:"
|
|
||||||
<< ((end.tv_sec - timerBegin.tv_sec) +
|
|
||||||
(end.tv_nsec - timerBegin.tv_nsec) / 1000000000.0)
|
|
||||||
<< " seconds";
|
|
||||||
// still less than streaming timer, keep waiting
|
|
||||||
if (((end.tv_sec - timerBegin.tv_sec) +
|
|
||||||
(end.tv_nsec - timerBegin.tv_nsec) / 1000000000.0) <
|
|
||||||
((double)*streamingTimerInMs / 1000.00))
|
|
||||||
return false;
|
|
||||||
|
|
||||||
// restart timer
|
|
||||||
clock_gettime(CLOCK_REALTIME, &timerBegin);
|
|
||||||
return true;
|
|
||||||
}
|
|
||||||
|
|
||||||
bool DataProcessor::CheckCount() {
|
|
||||||
if (currentFreqCount == *streamingFrequency) {
|
|
||||||
currentFreqCount = 1;
|
|
||||||
return true;
|
|
||||||
}
|
|
||||||
currentFreqCount++;
|
|
||||||
return false;
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::SetPixelDimension() {
|
|
||||||
if (file != nullptr) {
|
|
||||||
if (file->GetFileType() == HDF5) {
|
|
||||||
file->SetNumberofPixels(generalData->nPixelsX,
|
|
||||||
generalData->nPixelsY);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::registerCallBackRawDataReady(void (*func)(char *, char *,
|
|
||||||
uint32_t, void *),
|
|
||||||
void *arg) {
|
|
||||||
rawDataReadyCallBack = func;
|
|
||||||
pRawDataReady = arg;
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::registerCallBackRawDataModifyReady(
|
|
||||||
void (*func)(char *, char *, uint32_t &, void *), void *arg) {
|
|
||||||
rawDataModifyReadyCallBack = func;
|
|
||||||
pRawDataReady = arg;
|
|
||||||
}
|
|
||||||
|
|
||||||
void DataProcessor::PadMissingPackets(char *buf) {
|
|
||||||
LOG(logDEBUG) << index << ": Padding Missing Packets";
|
|
||||||
|
|
||||||
uint32_t pperFrame = generalData->packetsPerFrame;
|
|
||||||
auto *header = (sls_receiver_header *)(buf + FIFO_HEADER_NUMBYTES);
|
|
||||||
uint32_t nmissing = pperFrame - header->detHeader.packetNumber;
|
|
||||||
sls_bitset pmask = header->packetsMask;
|
|
||||||
|
|
||||||
uint32_t dsize = generalData->dataSize;
|
|
||||||
if (myDetectorType == GOTTHARD2 && index != 0) {
|
|
||||||
dsize = generalData->vetoDataSize;
|
|
||||||
}
|
|
||||||
uint32_t fifohsize = generalData->fifoBufferHeaderSize;
|
|
||||||
uint32_t corrected_dsize =
|
|
||||||
dsize - ((pperFrame * dsize) - generalData->imageSize);
|
|
||||||
LOG(logDEBUG1) << "bitmask: " << pmask.to_string();
|
|
||||||
|
|
||||||
for (unsigned int pnum = 0; pnum < pperFrame; ++pnum) {
|
|
||||||
|
|
||||||
// not missing packet
|
|
||||||
if (pmask[pnum])
|
|
||||||
continue;
|
|
||||||
|
|
||||||
// done with padding, exit loop earlier
|
|
||||||
if (nmissing == 0u)
|
|
||||||
break;
|
|
||||||
|
|
||||||
LOG(logDEBUG) << "padding for " << index << " for pnum: " << pnum
|
|
||||||
<< std::endl;
|
|
||||||
|
|
||||||
// missing packet
|
|
||||||
switch (myDetectorType) {
|
|
||||||
// for gotthard, 1st packet: 4 bytes fnum, CACA + CACA, 639*2 bytes
|
|
||||||
// data
|
|
||||||
// 2nd packet: 4 bytes fnum, previous 1*2 bytes data +
|
|
||||||
// 640*2 bytes data !!
|
|
||||||
case GOTTHARD:
|
|
||||||
if (pnum == 0u)
|
|
||||||
memset(buf + fifohsize + (pnum * dsize), 0xFF, dsize - 2);
|
|
||||||
else
|
|
||||||
memset(buf + fifohsize + (pnum * dsize), 0xFF, dsize + 2);
|
|
||||||
break;
|
|
||||||
case CHIPTESTBOARD:
|
|
||||||
case MOENCH:
|
|
||||||
if (pnum == (pperFrame - 1))
|
|
||||||
memset(buf + fifohsize + (pnum * dsize), 0xFF, corrected_dsize);
|
|
||||||
else
|
|
||||||
memset(buf + fifohsize + (pnum * dsize), 0xFF, dsize);
|
|
||||||
break;
|
|
||||||
default:
|
|
||||||
memset(buf + fifohsize + (pnum * dsize), 0xFF, dsize);
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
--nmissing;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/** ctb specific */
|
|
||||||
void DataProcessor::RearrangeDbitData(char *buf) {
|
|
||||||
// TODO! (Erik) Refactor and add tests
|
|
||||||
int totalSize = (int)(*((uint32_t *)buf));
|
|
||||||
int ctbDigitalDataBytes =
|
|
||||||
totalSize - (*ctbAnalogDataBytes) - (*ctbDbitOffset);
|
|
||||||
|
|
||||||
// no digital data
|
|
||||||
if (ctbDigitalDataBytes == 0) {
|
|
||||||
LOG(logWARNING)
|
|
||||||
<< "No digital data for call back, yet dbitlist is not empty.";
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
const int numSamples = (ctbDigitalDataBytes / sizeof(uint64_t));
|
|
||||||
const int digOffset = FIFO_HEADER_NUMBYTES + sizeof(sls_receiver_header) +
|
|
||||||
(*ctbAnalogDataBytes);
|
|
||||||
|
|
||||||
// ceil as numResult8Bits could be decimal
|
|
||||||
const int numResult8Bits =
|
|
||||||
ceil((double)(numSamples * (*ctbDbitList).size()) / 8.00);
|
|
||||||
std::vector<uint8_t> result(numResult8Bits);
|
|
||||||
uint8_t *dest = &result[0];
|
|
||||||
|
|
||||||
auto *source = (uint64_t *)(buf + digOffset + (*ctbDbitOffset));
|
|
||||||
|
|
||||||
// loop through digital bit enable vector
|
|
||||||
int bitoffset = 0;
|
|
||||||
for (auto bi : (*ctbDbitList)) {
|
|
||||||
// where numbits * numsamples is not a multiple of 8
|
|
||||||
if (bitoffset != 0) {
|
|
||||||
bitoffset = 0;
|
|
||||||
++dest;
|
|
||||||
}
|
|
||||||
|
|
||||||
// loop through the frame digital data
|
|
||||||
for (auto ptr = source; ptr < (source + numSamples);) {
|
|
||||||
// get selected bit from each 8 bit
|
|
||||||
uint8_t bit = (*ptr++ >> bi) & 1;
|
|
||||||
*dest |= bit << bitoffset;
|
|
||||||
++bitoffset;
|
|
||||||
// extract destination in 8 bit batches
|
|
||||||
if (bitoffset == 8) {
|
|
||||||
bitoffset = 0;
|
|
||||||
++dest;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// copy back to buf and update size
|
|
||||||
memcpy(buf + digOffset, result.data(), numResult8Bits * sizeof(uint8_t));
|
|
||||||
(*((uint32_t *)buf)) = numResult8Bits * sizeof(uint8_t);
|
|
||||||
}
|
|
||||||
@ -1,343 +0,0 @@
|
|||||||
#pragma once
|
|
||||||
/************************************************
|
|
||||||
* @file DataProcessor.h
|
|
||||||
* @short creates data processor thread that
|
|
||||||
* pulls pointers to memory addresses from fifos
|
|
||||||
* and processes data stored in them & writes them to file
|
|
||||||
***********************************************/
|
|
||||||
/**
|
|
||||||
*@short creates & manages a data processor thread each
|
|
||||||
*/
|
|
||||||
|
|
||||||
#include "ThreadObject.h"
|
|
||||||
#include "receiver_defs.h"
|
|
||||||
|
|
||||||
class GeneralData;
|
|
||||||
class Fifo;
|
|
||||||
class File;
|
|
||||||
class DataStreamer;
|
|
||||||
struct MasterAttributes;
|
|
||||||
|
|
||||||
#include <atomic>
|
|
||||||
#include <vector>
|
|
||||||
|
|
||||||
class DataProcessor : private virtual slsDetectorDefs, public ThreadObject {
|
|
||||||
|
|
||||||
public:
|
|
||||||
/**
|
|
||||||
* Constructor
|
|
||||||
* Calls Base Class CreateThread(), sets ErrorMask if error and increments
|
|
||||||
* NumberofDataProcessors
|
|
||||||
* @param ind self index
|
|
||||||
* @param dtype detector type
|
|
||||||
* @param f address of Fifo pointer
|
|
||||||
* @param act activated
|
|
||||||
* @param depaden deactivated padding enable
|
|
||||||
* @param dsEnable pointer to data stream enable
|
|
||||||
* @param dr pointer to dynamic range
|
|
||||||
* @param freq pointer to streaming frequency
|
|
||||||
* @param timer pointer to timer if streaming frequency is random
|
|
||||||
* @param sfnum pointer to streaming starting fnum
|
|
||||||
* @param fp pointer to frame padding enable
|
|
||||||
* @param sm pointer to silent mode
|
|
||||||
* @param qe pointer to quad Enable
|
|
||||||
* @param cdl pointer to vector or ctb digital bits enable
|
|
||||||
* @param cdo pointer to digital bits offset
|
|
||||||
* @param cad pointer to ctb analog databytes
|
|
||||||
*/
|
|
||||||
DataProcessor(int ind, detectorType dtype, Fifo *f, bool act, bool depaden,
|
|
||||||
bool *dsEnable, uint32_t *freq, uint32_t *timer,
|
|
||||||
uint32_t *sfnum, bool *fp, bool *sm, std::vector<int> *cdl,
|
|
||||||
int *cdo, int *cad);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Destructor
|
|
||||||
* Calls Base Class DestroyThread() and decrements NumberofDataProcessors
|
|
||||||
*/
|
|
||||||
~DataProcessor() override;
|
|
||||||
|
|
||||||
//*** getters ***
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Get acquisition started flag
|
|
||||||
* @return acquisition started flag
|
|
||||||
*/
|
|
||||||
bool GetStartedFlag();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Get Frames Complete Caught
|
|
||||||
* @return number of frames
|
|
||||||
*/
|
|
||||||
uint64_t GetNumFramesCaught();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Gets Actual Current Frame Index (that has not been subtracted from
|
|
||||||
* firstIndex) thats been processed
|
|
||||||
* @return -1 if no frames have been caught, else current frame index
|
|
||||||
*/
|
|
||||||
uint64_t GetCurrentFrameIndex();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Get Current Frame Index thats been processed
|
|
||||||
* @return -1 if no frames have been caught, else current frame index
|
|
||||||
*/
|
|
||||||
uint64_t GetProcessedIndex();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Set Fifo pointer to the one given
|
|
||||||
* @param f address of Fifo pointer
|
|
||||||
*/
|
|
||||||
void SetFifo(Fifo *f);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Reset parameters for new acquisition
|
|
||||||
*/
|
|
||||||
void ResetParametersforNewAcquisition();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Set GeneralData pointer to the one given
|
|
||||||
* @param g address of GeneralData (Detector Data) pointer
|
|
||||||
*/
|
|
||||||
void SetGeneralData(GeneralData *g);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Set up file writer object and call backs
|
|
||||||
* @param ftype file format
|
|
||||||
* @param fwe file write enable
|
|
||||||
* @param act activated
|
|
||||||
* @param depad deactivated padding enable
|
|
||||||
* @param nd pointer to number of detectors in each dimension
|
|
||||||
* @param maxf pointer to max frames per file
|
|
||||||
* @param fname pointer to file name prefix
|
|
||||||
* @param fpath pointer to file path
|
|
||||||
* @param findex pointer to file index
|
|
||||||
* @param owenable pointer to over write enable
|
|
||||||
* @param dindex pointer to detector index
|
|
||||||
* @param nunits pointer to number of threads/ units per detector
|
|
||||||
* @param nf pointer to number of images in acquisition
|
|
||||||
* @param dr pointer to dynamic range
|
|
||||||
* @param portno pointer to udp port number
|
|
||||||
* @param g address of GeneralData (Detector Data) pointer
|
|
||||||
*/
|
|
||||||
void SetupFileWriter(fileFormat ftype, bool fwe, int act, int depaden,
|
|
||||||
int *nd, uint32_t *maxf, std::string *fname,
|
|
||||||
std::string *fpath, uint64_t *findex, bool *owenable,
|
|
||||||
int *dindex, int *nunits, uint64_t *nf, uint32_t *dr,
|
|
||||||
uint32_t *portno, GeneralData *g = nullptr);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Create Master File (also virtual if hdf5)
|
|
||||||
* @param attr master file attributes
|
|
||||||
*/
|
|
||||||
void CreateMasterFile(MasterAttributes *attr);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Create First Data File
|
|
||||||
*/
|
|
||||||
void CreatFirsteDataFile();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Closes files
|
|
||||||
*/
|
|
||||||
void CloseFiles();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* End of Acquisition
|
|
||||||
* @param anyPacketsCaught true if any packets are caught, else false
|
|
||||||
* @param numf number of images caught
|
|
||||||
*/
|
|
||||||
void EndofAcquisition(bool anyPacketsCaught, uint64_t numf);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Update pixel dimensions in file writer
|
|
||||||
*/
|
|
||||||
void SetPixelDimension();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Call back for raw data
|
|
||||||
* args to raw data ready callback are
|
|
||||||
* sls_receiver_header frame metadata
|
|
||||||
* dataPointer is the pointer to the data
|
|
||||||
* dataSize in bytes is the size of the data in bytes.
|
|
||||||
*/
|
|
||||||
void registerCallBackRawDataReady(void (*func)(char *, char *, uint32_t,
|
|
||||||
void *),
|
|
||||||
void *arg);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Call back for raw data (modified)
|
|
||||||
* args to raw data ready callback are
|
|
||||||
* sls_receiver_header frame metadata
|
|
||||||
* dataPointer is the pointer to the data
|
|
||||||
* revDatasize is the reference of data size in bytes.
|
|
||||||
* Can be modified to the new size to be written/streamed. (only smaller
|
|
||||||
* value).
|
|
||||||
*/
|
|
||||||
void registerCallBackRawDataModifyReady(void (*func)(char *, char *,
|
|
||||||
uint32_t &, void *),
|
|
||||||
void *arg);
|
|
||||||
|
|
||||||
private:
|
|
||||||
/**
|
|
||||||
* Record First Index
|
|
||||||
* @param fnum frame index to record
|
|
||||||
*/
|
|
||||||
void RecordFirstIndex(uint64_t fnum);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Thread Exeution for DataProcessor Class
|
|
||||||
* Pop bound addresses, process them,
|
|
||||||
* write to file if needed & free the address
|
|
||||||
*/
|
|
||||||
void ThreadExecution() override;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Frees dummy buffer,
|
|
||||||
* reset running mask by calling StopRunning()
|
|
||||||
* @param buf address of pointer
|
|
||||||
*/
|
|
||||||
void StopProcessing(char *buf);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Process an image popped from fifo,
|
|
||||||
* write to file if fw enabled & update parameters
|
|
||||||
* @param buf address of pointer
|
|
||||||
* @returns frame number
|
|
||||||
*/
|
|
||||||
uint64_t ProcessAnImage(char *buf);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Calls CheckTimer and CheckCount for streaming frequency and timer
|
|
||||||
* and determines if the current image should be sent to streamer
|
|
||||||
* @returns true if it should to streamer, else false
|
|
||||||
*/
|
|
||||||
bool SendToStreamer();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* This function should be called only in random frequency mode
|
|
||||||
* Checks if timer is done and ready to send to stream
|
|
||||||
* @returns true if ready to send to stream, else false
|
|
||||||
*/
|
|
||||||
bool CheckTimer();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* This function should be called only in non random frequency mode
|
|
||||||
* Checks if count is done and ready to send to stream
|
|
||||||
* @returns true if ready to send to stream, else false
|
|
||||||
*/
|
|
||||||
bool CheckCount();
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Pad Missing Packets from the bit mask
|
|
||||||
* @param buf buffer
|
|
||||||
*/
|
|
||||||
void PadMissingPackets(char *buf);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Align corresponding digital bits together (CTB only if ctbDbitlist is not
|
|
||||||
* empty)
|
|
||||||
*/
|
|
||||||
void RearrangeDbitData(char *buf);
|
|
||||||
|
|
||||||
/** type of thread */
|
|
||||||
static const std::string TypeName;
|
|
||||||
|
|
||||||
/** GeneralData (Detector Data) object */
|
|
||||||
const GeneralData *generalData{nullptr};
|
|
||||||
|
|
||||||
/** Fifo structure */
|
|
||||||
Fifo *fifo;
|
|
||||||
|
|
||||||
// individual members
|
|
||||||
/** Detector Type */
|
|
||||||
detectorType myDetectorType;
|
|
||||||
|
|
||||||
/** File writer implemented as binary or hdf5 File */
|
|
||||||
File *file{nullptr};
|
|
||||||
|
|
||||||
/** master file */
|
|
||||||
File *masterFile{nullptr};
|
|
||||||
|
|
||||||
/** virtual file (for hdf5) */
|
|
||||||
File *virtualFile{nullptr};
|
|
||||||
|
|
||||||
/** Data Stream Enable */
|
|
||||||
bool *dataStreamEnable;
|
|
||||||
|
|
||||||
/** Activated/Deactivated */
|
|
||||||
bool activated;
|
|
||||||
|
|
||||||
/** Deactivated padding enable */
|
|
||||||
bool deactivatedPaddingEnable;
|
|
||||||
|
|
||||||
/** Pointer to Streaming frequency, if 0, sending random images with a timer
|
|
||||||
*/
|
|
||||||
uint32_t *streamingFrequency;
|
|
||||||
|
|
||||||
/** Pointer to the timer if Streaming frequency is random */
|
|
||||||
uint32_t *streamingTimerInMs;
|
|
||||||
|
|
||||||
/** Pointer to streaming starting fnum */
|
|
||||||
uint32_t *streamingStartFnum;
|
|
||||||
|
|
||||||
/** Current frequency count */
|
|
||||||
uint32_t currentFreqCount{0};
|
|
||||||
|
|
||||||
/** timer beginning stamp for random streaming */
|
|
||||||
struct timespec timerBegin;
|
|
||||||
|
|
||||||
/** Silent Mode */
|
|
||||||
bool *silentMode;
|
|
||||||
|
|
||||||
/** frame padding */
|
|
||||||
bool *framePadding;
|
|
||||||
|
|
||||||
/** ctb digital bits enable list */
|
|
||||||
std::vector<int> *ctbDbitList;
|
|
||||||
|
|
||||||
/** ctb digital bits offset */
|
|
||||||
int *ctbDbitOffset;
|
|
||||||
|
|
||||||
/** ctb analog databytes */
|
|
||||||
int *ctbAnalogDataBytes;
|
|
||||||
|
|
||||||
// acquisition start
|
|
||||||
/** Aquisition Started flag */
|
|
||||||
std::atomic<bool> startedFlag{false};
|
|
||||||
|
|
||||||
/** Frame Number of First Frame */
|
|
||||||
std::atomic<uint64_t> firstIndex{0};
|
|
||||||
|
|
||||||
// for statistics
|
|
||||||
/** Number of complete frames caught */
|
|
||||||
uint64_t numFramesCaught{0};
|
|
||||||
|
|
||||||
/** Frame Number of latest processed frame number */
|
|
||||||
std::atomic<uint64_t> currentFrameIndex{0};
|
|
||||||
|
|
||||||
/** first streamer frame to add frame index in fifo header */
|
|
||||||
bool firstStreamerFrame{false};
|
|
||||||
|
|
||||||
// call back
|
|
||||||
/**
|
|
||||||
* Call back for raw data
|
|
||||||
* args to raw data ready callback are
|
|
||||||
* sls_receiver_header frame metadata
|
|
||||||
* dataPointer is the pointer to the data
|
|
||||||
* dataSize in bytes is the size of the data in bytes.
|
|
||||||
*/
|
|
||||||
void (*rawDataReadyCallBack)(char *, char *, uint32_t, void *) = nullptr;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Call back for raw data (modified)
|
|
||||||
* args to raw data ready callback are
|
|
||||||
* sls_receiver_header frame metadata
|
|
||||||
* dataPointer is the pointer to the data
|
|
||||||
* revDatasize is the reference of data size in bytes. Can be modified to
|
|
||||||
* the new size to be written/streamed. (only smaller value).
|
|
||||||
*/
|
|
||||||
void (*rawDataModifyReadyCallBack)(char *, char *, uint32_t &,
|
|
||||||
void *) = nullptr;
|
|
||||||
|
|
||||||
void *pRawDataReady{nullptr};
|
|
||||||
};
|
|
||||||
@ -1,71 +0,0 @@
|
|||||||
/************************************************
|
|
||||||
* @file File.cpp
|
|
||||||
* @short sets/gets properties for the file,
|
|
||||||
* creates/closes the file and writes data to it
|
|
||||||
***********************************************/
|
|
||||||
|
|
||||||
#include "File.h"
|
|
||||||
|
|
||||||
#include <iostream>
|
|
||||||
|
|
||||||
File::File(int ind, slsDetectorDefs::fileFormat type, uint32_t *maxf, int *nd,
|
|
||||||
std::string *fname, std::string *fpath, uint64_t *findex,
|
|
||||||
bool *owenable, int *dindex, int *nunits, uint64_t *nf, uint32_t *dr,
|
|
||||||
uint32_t *portno, bool *smode)
|
|
||||||
: index(ind), formatType(type), maxFramesPerFile(maxf), numDetX(nd[0]),
|
|
||||||
numDetY(nd[1]), fileNamePrefix(fname), filePath(fpath), fileIndex(findex),
|
|
||||||
overWriteEnable(owenable), detIndex(dindex), numUnitsPerDetector(nunits),
|
|
||||||
numImages(nf), dynamicRange(dr), udpPortNumber(portno), silentMode(smode)
|
|
||||||
|
|
||||||
{
|
|
||||||
master = ((index == 0) && (*detIndex == 0)) ? true : false;
|
|
||||||
}
|
|
||||||
|
|
||||||
File::~File() {}
|
|
||||||
|
|
||||||
slsDetectorDefs::fileFormat File::GetFileType() { return formatType; }
|
|
||||||
|
|
||||||
std::string File::GetCurrentFileName() { return currentFileName; }
|
|
||||||
|
|
||||||
void File::resetSubFileIndex() { subFileIndex = 0u; }
|
|
||||||
|
|
||||||
void File::PrintMembers(TLogLevel level) {
|
|
||||||
LOG(level) << "\nGeneral Writer Variables:" << std::endl
|
|
||||||
<< "Index: " << index << std::endl
|
|
||||||
<< "Max Frames Per File: " << *maxFramesPerFile << std::endl
|
|
||||||
<< "Number of Detectors in x dir: " << numDetX << std::endl
|
|
||||||
<< "Number of Detectors in y dir: " << numDetY << std::endl
|
|
||||||
<< "File Name Prefix: " << fileNamePrefix << std::endl
|
|
||||||
<< "File Path: " << filePath << std::endl
|
|
||||||
<< "File Index: " << *fileIndex << std::endl
|
|
||||||
<< "Over Write Enable: " << *overWriteEnable << std::endl
|
|
||||||
|
|
||||||
<< "Detector Index: " << *detIndex << std::endl
|
|
||||||
<< "Number of Units Per Detector: " << *numUnitsPerDetector
|
|
||||||
<< std::endl
|
|
||||||
<< "Number of Images in Acquisition: " << *numImages << std::endl
|
|
||||||
<< "Dynamic Range: " << *dynamicRange << std::endl
|
|
||||||
<< "UDP Port number: " << *udpPortNumber << std::endl
|
|
||||||
<< "Master File Name: " << masterFileName << std::endl
|
|
||||||
<< "Current File Name: " << currentFileName << std::endl
|
|
||||||
<< "Silent Mode: " << *silentMode;
|
|
||||||
}
|
|
||||||
|
|
||||||
void File::GetMemberPointerValues(int *nd, uint32_t *&maxf, std::string *&fname,
|
|
||||||
std::string *&fpath, uint64_t *&findex,
|
|
||||||
bool *&owenable, int *&dindex, int *&nunits,
|
|
||||||
uint64_t *&nf, uint32_t *&dr,
|
|
||||||
uint32_t *&portno) {
|
|
||||||
nd[0] = numDetX;
|
|
||||||
nd[1] = numDetY;
|
|
||||||
maxf = maxFramesPerFile;
|
|
||||||
fname = fileNamePrefix;
|
|
||||||
fpath = filePath;
|
|
||||||
findex = fileIndex;
|
|
||||||
owenable = overWriteEnable;
|
|
||||||
dindex = detIndex;
|
|
||||||
nunits = numUnitsPerDetector;
|
|
||||||
nf = numImages;
|
|
||||||
dr = dynamicRange;
|
|
||||||
portno = udpPortNumber;
|
|
||||||
}
|
|
||||||
@ -1,142 +0,0 @@
|
|||||||
#pragma once
|
|
||||||
/************************************************
|
|
||||||
* @file File.h
|
|
||||||
* @short sets/gets properties for the file,
|
|
||||||
* creates/closes the file and writes data to it
|
|
||||||
***********************************************/
|
|
||||||
/**
|
|
||||||
*@short sets/gets properties for the file, creates/closes the file and writes
|
|
||||||
*data to it
|
|
||||||
*/
|
|
||||||
|
|
||||||
#include "receiver_defs.h"
|
|
||||||
#include "sls/logger.h"
|
|
||||||
#include "sls/sls_detector_defs.h"
|
|
||||||
|
|
||||||
#include <string>
|
|
||||||
|
|
||||||
struct MasterAttributes;
|
|
||||||
|
|
||||||
class File : private virtual slsDetectorDefs {
|
|
||||||
|
|
||||||
public:
|
|
||||||
/**
|
|
||||||
* Constructor
|
|
||||||
* creates the File Writer
|
|
||||||
* @param ind self index
|
|
||||||
* @param type file format type
|
|
||||||
* @param maxf pointer to max frames per file
|
|
||||||
* @param nd pointer to number of detectors in each dimension
|
|
||||||
* @param fname pointer to file name prefix
|
|
||||||
* @param fpath pointer to file path
|
|
||||||
* @param findex pointer to file index
|
|
||||||
* @param owenable pointer to over write enable
|
|
||||||
* @param dindex pointer to detector index
|
|
||||||
* @param nunits pointer to number of theads/ units per detector
|
|
||||||
* @param nf pointer to number of images in acquisition
|
|
||||||
* @param dr pointer to dynamic range
|
|
||||||
* @param portno pointer to udp port number for logging
|
|
||||||
* @param smode pointer to silent mode
|
|
||||||
*/
|
|
||||||
File(int ind, slsDetectorDefs::fileFormat type, uint32_t *maxf, int *nd,
|
|
||||||
std::string *fname, std::string *fpath, uint64_t *findex,
|
|
||||||
bool *owenable, int *dindex, int *nunits, uint64_t *nf, uint32_t *dr,
|
|
||||||
uint32_t *portno, bool *smode);
|
|
||||||
|
|
||||||
virtual ~File();
|
|
||||||
fileFormat GetFileType();
|
|
||||||
std::string GetCurrentFileName();
|
|
||||||
void resetSubFileIndex();
|
|
||||||
virtual void PrintMembers(TLogLevel level = logDEBUG1);
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Get Member Pointer Values before the object is destroyed
|
|
||||||
* @param nd pointer to number of detectors in each dimension
|
|
||||||
* @param maxf pointer to max frames per file
|
|
||||||
* @param fname pointer to file name prefix
|
|
||||||
* @param fpath pointer to file path
|
|
||||||
* @param findex pointer to file index
|
|
||||||
* @param owenable pointer to over write enable
|
|
||||||
* @param dindex pointer to detector index
|
|
||||||
* @param nunits pointer to number of theads/ units per detector
|
|
||||||
* @param nf pointer to number of images in acquisition
|
|
||||||
* @param dr pointer to dynamic range
|
|
||||||
* @param portno pointer to dynamic range
|
|
||||||
*/
|
|
||||||
void GetMemberPointerValues(int *nd, uint32_t *&maxf, std::string *&fname,
|
|
||||||
std::string *&fpath, uint64_t *&findex,
|
|
||||||
bool *&owenable, int *&dindex, int *&nunits,
|
|
||||||
uint64_t *&nf, uint32_t *&dr,
|
|
||||||
uint32_t *&portno);
|
|
||||||
|
|
||||||
virtual void CreateFile() = 0;
|
|
||||||
virtual void CloseCurrentDataFile() = 0;
|
|
||||||
virtual void CloseAllFiles() = 0;
|
|
||||||
virtual void CloseMasterFile() = 0;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Write data to file
|
|
||||||
* @param buffer buffer to write from
|
|
||||||
* @param buffersize size of buffer
|
|
||||||
* @param fnum current image number
|
|
||||||
* @param nump number of packets caught
|
|
||||||
*/
|
|
||||||
virtual void WriteToFile(char *buffer, int buffersize, uint64_t fnum,
|
|
||||||
uint32_t nump) = 0;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Create master file
|
|
||||||
* @param attr master file attributes
|
|
||||||
*/
|
|
||||||
virtual void CreateMasterFile(MasterAttributes *attr) = 0;
|
|
||||||
|
|
||||||
// HDf5 specific
|
|
||||||
/**
|
|
||||||
* Set Number of pixels
|
|
||||||
* @param nx number of pixels in x direction
|
|
||||||
* @param ny number of pixels in y direction
|
|
||||||
*/
|
|
||||||
virtual void SetNumberofPixels(uint32_t nx, uint32_t ny) {
|
|
||||||
LOG(logERROR) << "This is a generic function SetNumberofPixels that "
|
|
||||||
"should be overloaded by a derived class";
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Start of Acquisition
|
|
||||||
*/
|
|
||||||
virtual void StartofAcquisition() {
|
|
||||||
LOG(logERROR) << "This is a generic function StartofAcquisition that "
|
|
||||||
"should be overloaded by a derived class";
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* End of Acquisition
|
|
||||||
* @param anyPacketsCaught true if any packets are caught, else false
|
|
||||||
* @param numf number of images caught
|
|
||||||
*/
|
|
||||||
virtual void EndofAcquisition(bool anyPacketsCaught, uint64_t numf) {
|
|
||||||
LOG(logERROR) << "This is a generic function EndofAcquisition that "
|
|
||||||
"should be overloaded by a derived class";
|
|
||||||
}
|
|
||||||
|
|
||||||
protected:
|
|
||||||
bool master;
|
|
||||||
int index;
|
|
||||||
slsDetectorDefs::fileFormat formatType;
|
|
||||||
uint32_t *maxFramesPerFile;
|
|
||||||
std::string masterFileName;
|
|
||||||
std::string currentFileName;
|
|
||||||
int numDetX;
|
|
||||||
int numDetY;
|
|
||||||
std::string *fileNamePrefix;
|
|
||||||
std::string *filePath;
|
|
||||||
uint64_t *fileIndex;
|
|
||||||
uint64_t subFileIndex{0};
|
|
||||||
bool *overWriteEnable;
|
|
||||||
int *detIndex;
|
|
||||||
int *numUnitsPerDetector;
|
|
||||||
uint64_t *numImages;
|
|
||||||
uint32_t *dynamicRange;
|
|
||||||
uint32_t *udpPortNumber;
|
|
||||||
bool *silentMode;
|
|
||||||
};
|
|
||||||
@ -1,378 +0,0 @@
|
|||||||
/************************************************
|
|
||||||
* @file HDF5File.cpp
|
|
||||||
* @short sets/gets properties for the HDF5 file,
|
|
||||||
* creates/closes the file and writes data to it
|
|
||||||
***********************************************/
|
|
||||||
#include "HDF5File.h"
|
|
||||||
#include "Fifo.h"
|
|
||||||
#include "MasterAttributes.h"
|
|
||||||
#include "receiver_defs.h"
|
|
||||||
|
|
||||||
#include <iomanip>
|
|
||||||
#include <iostream>
|
|
||||||
#include <libgen.h> //basename
|
|
||||||
#include <string.h>
|
|
||||||
|
|
||||||
void HDF5File::EndofAcquisition(bool anyPacketsCaught,
|
|
||||||
uint64_t numImagesCaught) {
|
|
||||||
// not created before
|
|
||||||
if (!virtualfd && anyPacketsCaught) {
|
|
||||||
// called only by the one maser receiver
|
|
||||||
if (master && masterfd != nullptr) {
|
|
||||||
// only one file and one sub image (link current file in master)
|
|
||||||
if (((numFilesinAcquisition == 1) && (numDetY * numDetX) == 1)) {
|
|
||||||
// dataset name
|
|
||||||
std::ostringstream oss;
|
|
||||||
oss << "/data";
|
|
||||||
if ((*numImages > 1)) {
|
|
||||||
oss << "_f" << std::setfill('0') << std::setw(12) << 0;
|
|
||||||
}
|
|
||||||
std::string dsetname = oss.str();
|
|
||||||
|
|
||||||
LinkVirtualInMaster(currentFileName, dsetname);
|
|
||||||
}
|
|
||||||
// create virutal file
|
|
||||||
else {
|
|
||||||
CreateVirtualDataFile(
|
|
||||||
// infinite images in 1 file, then maxfrperfile =
|
|
||||||
// numImagesCaught
|
|
||||||
((*maxFramesPerFile == 0) ? numImagesCaught + 1
|
|
||||||
: *maxFramesPerFile),
|
|
||||||
numImagesCaught + 1);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
numFilesinAcquisition = 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CreateVirtualDataFile(uint32_t maxFramesPerFile, uint64_t numf) {
|
|
||||||
|
|
||||||
std::ostringstream osfn;
|
|
||||||
osfn << *filePath << "/" << *fileNamePrefix;
|
|
||||||
osfn << "_virtual";
|
|
||||||
osfn << "_" << *fileIndex;
|
|
||||||
osfn << ".h5";
|
|
||||||
std::string vname = osfn.str();
|
|
||||||
|
|
||||||
if (!(*silentMode)) {
|
|
||||||
LOG(logINFO) << "Virtual File: " << vname;
|
|
||||||
}
|
|
||||||
|
|
||||||
int numDetz = numDetX;
|
|
||||||
uint32_t nDimy = nPixelsY;
|
|
||||||
uint32_t nDimz = ((*dynamicRange == 4) ? (nPixelsX / 2) : nPixelsX);
|
|
||||||
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
|
|
||||||
try {
|
|
||||||
// file
|
|
||||||
hid_t dfal = H5Pcreate(H5P_FILE_ACCESS);
|
|
||||||
if (dfal < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create file access property for virtual file " +
|
|
||||||
vname);
|
|
||||||
if (H5Pset_fclose_degree(dfal, H5F_CLOSE_STRONG) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not set strong file close degree for virtual file " +
|
|
||||||
vname);
|
|
||||||
virtualfd = H5Fcreate(vname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
|
|
||||||
if (virtualfd < 0)
|
|
||||||
throw sls::RuntimeError("Could not create virtual file " + vname);
|
|
||||||
|
|
||||||
// attributes - version
|
|
||||||
hid_t dataspace_attr = H5Screate(H5S_SCALAR);
|
|
||||||
if (dataspace_attr < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create dataspace for attribute in virtual file " +
|
|
||||||
vname);
|
|
||||||
hid_t attrid = H5Acreate2(virtualfd, "version", H5T_NATIVE_DOUBLE,
|
|
||||||
dataspace_attr, H5P_DEFAULT, H5P_DEFAULT);
|
|
||||||
if (attrid < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create attribute in virtual file " + vname);
|
|
||||||
double attr_data = HDF5_WRITER_VERSION;
|
|
||||||
if (H5Awrite(attrid, H5T_NATIVE_DOUBLE, &attr_data) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not write attribute in virtual file " + vname);
|
|
||||||
if (H5Aclose(attrid) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not close attribute in virtual file " + vname);
|
|
||||||
|
|
||||||
// virtual dataspace
|
|
||||||
hsize_t vdsdims[3] = {numf, numDetY * nDimy, numDetz * nDimz};
|
|
||||||
hid_t vdsDataspace = H5Screate_simple(3, vdsdims, nullptr);
|
|
||||||
if (vdsDataspace < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create virtual dataspace in virtual file " + vname);
|
|
||||||
hsize_t vdsdims_para[2] = {numf, (unsigned int)numDetY * numDetz};
|
|
||||||
hid_t vdsDataspace_para = H5Screate_simple(2, vdsdims_para, nullptr);
|
|
||||||
if (vdsDataspace_para < 0)
|
|
||||||
throw sls::RuntimeError("Could not create virtual dataspace "
|
|
||||||
"(parameters) in virtual file " +
|
|
||||||
vname);
|
|
||||||
|
|
||||||
// fill values
|
|
||||||
hid_t dcpl = H5Pcreate(H5P_DATASET_CREATE);
|
|
||||||
if (dcpl < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create file creation properties in virtual file " +
|
|
||||||
vname);
|
|
||||||
int fill_value = -1;
|
|
||||||
if (H5Pset_fill_value(dcpl, GetDataTypeinC(datatype), &fill_value) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create fill value in virtual file " + vname);
|
|
||||||
std::vector<hid_t> dcpl_para(parameterNames.size());
|
|
||||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
|
||||||
dcpl_para[i] = H5Pcreate(H5P_DATASET_CREATE);
|
|
||||||
if (dcpl_para[i] < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create file creation properties (parameters) in "
|
|
||||||
"virtual file " +
|
|
||||||
vname);
|
|
||||||
if (H5Pset_fill_value(dcpl_para[i],
|
|
||||||
GetDataTypeinC(parameterDataTypes[i]),
|
|
||||||
&fill_value) < 0)
|
|
||||||
throw sls::RuntimeError("Could not create fill value "
|
|
||||||
"(parameters) in virtual file " +
|
|
||||||
vname);
|
|
||||||
}
|
|
||||||
|
|
||||||
// hyperslab
|
|
||||||
int numMajorHyperslab = numf / maxFramesPerFile;
|
|
||||||
if (numf % maxFramesPerFile)
|
|
||||||
numMajorHyperslab++;
|
|
||||||
uint64_t framesSaved = 0;
|
|
||||||
for (int j = 0; j < numMajorHyperslab; j++) {
|
|
||||||
|
|
||||||
uint64_t nDimx = ((numf - framesSaved) > maxFramesPerFile)
|
|
||||||
? maxFramesPerFile
|
|
||||||
: (numf - framesSaved);
|
|
||||||
hsize_t offset[3] = {framesSaved, 0, 0};
|
|
||||||
hsize_t count[3] = {nDimx, nDimy, nDimz};
|
|
||||||
hsize_t offset_para[2] = {framesSaved, 0};
|
|
||||||
hsize_t count_para[2] = {nDimx, 1};
|
|
||||||
|
|
||||||
for (int i = 0; i < numDetY * numDetz; ++i) {
|
|
||||||
|
|
||||||
// setect hyperslabs
|
|
||||||
if (H5Sselect_hyperslab(vdsDataspace, H5S_SELECT_SET, offset,
|
|
||||||
nullptr, count, nullptr) < 0) {
|
|
||||||
throw sls::RuntimeError("Could not select hyperslab");
|
|
||||||
}
|
|
||||||
if (H5Sselect_hyperslab(vdsDataspace_para, H5S_SELECT_SET,
|
|
||||||
offset_para, nullptr, count_para,
|
|
||||||
nullptr) < 0) {
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not select hyperslab for parameters");
|
|
||||||
}
|
|
||||||
|
|
||||||
// source file name
|
|
||||||
std::ostringstream os;
|
|
||||||
os << *filePath << "/" << *fileNamePrefix << "_d"
|
|
||||||
<< (*detIndex * (*numUnitsPerDetector) + i) << "_f" << j
|
|
||||||
<< '_' << *fileIndex << ".h5";
|
|
||||||
std::string srcFileName = os.str();
|
|
||||||
|
|
||||||
LOG(logDEBUG1) << srcFileName;
|
|
||||||
// find relative path
|
|
||||||
std::string relative_srcFileName = srcFileName;
|
|
||||||
{
|
|
||||||
size_t i = srcFileName.rfind('/', srcFileName.length());
|
|
||||||
if (i != std::string::npos)
|
|
||||||
relative_srcFileName = (srcFileName.substr(
|
|
||||||
i + 1, srcFileName.length() - i));
|
|
||||||
}
|
|
||||||
|
|
||||||
// source dataset name
|
|
||||||
std::ostringstream osfn;
|
|
||||||
osfn << "/data";
|
|
||||||
if (*numImages > 1)
|
|
||||||
osfn << "_f" << std::setfill('0') << std::setw(12) << j;
|
|
||||||
std::string srcDatasetName = osfn.str();
|
|
||||||
|
|
||||||
// source dataspace
|
|
||||||
hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
|
|
||||||
hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
|
|
||||||
hid_t srcDataspace = H5Screate_simple(3, srcdims, srcdimsmax);
|
|
||||||
if (srcDataspace < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create source dataspace in virtual file " +
|
|
||||||
vname);
|
|
||||||
hsize_t srcdims_para[1] = {nDimx};
|
|
||||||
hsize_t srcdimsmax_para[1] = {H5S_UNLIMITED};
|
|
||||||
hid_t srcDataspace_para =
|
|
||||||
H5Screate_simple(1, srcdims_para, srcdimsmax_para);
|
|
||||||
if (srcDataspace_para < 0)
|
|
||||||
throw sls::RuntimeError("Could not create source dataspace "
|
|
||||||
"(parameters) in virtual file " +
|
|
||||||
vname);
|
|
||||||
|
|
||||||
// mapping
|
|
||||||
if (H5Pset_virtual(dcpl, vdsDataspace,
|
|
||||||
relative_srcFileName.c_str(),
|
|
||||||
srcDatasetName.c_str(), srcDataspace) < 0) {
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not set mapping for paramter 1");
|
|
||||||
}
|
|
||||||
|
|
||||||
for (unsigned int k = 0; k < parameterNames.size(); ++k) {
|
|
||||||
if (H5Pset_virtual(dcpl_para[k], vdsDataspace_para,
|
|
||||||
relative_srcFileName.c_str(),
|
|
||||||
parameterNames[k].c_str(),
|
|
||||||
srcDataspace_para) < 0) {
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not set mapping for paramter " +
|
|
||||||
std::to_string(k));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// H5Sclose(srcDataspace);
|
|
||||||
// H5Sclose(srcDataspace_para);
|
|
||||||
offset[2] += nDimz;
|
|
||||||
if (offset[2] >= (numDetz * nDimz)) {
|
|
||||||
offset[2] = 0;
|
|
||||||
offset[1] += nDimy;
|
|
||||||
}
|
|
||||||
offset_para[1]++;
|
|
||||||
}
|
|
||||||
framesSaved += nDimx;
|
|
||||||
}
|
|
||||||
|
|
||||||
// dataset
|
|
||||||
std::string virtualDatasetName = "data";
|
|
||||||
hid_t vdsdataset = H5Dcreate2(virtualfd, virtualDatasetName.c_str(),
|
|
||||||
GetDataTypeinC(datatype), vdsDataspace,
|
|
||||||
H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
|
||||||
if (vdsdataset < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create virutal dataset in virtual file " + vname);
|
|
||||||
|
|
||||||
// virtual parameter dataset
|
|
||||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
|
||||||
hid_t vdsdataset_para = H5Dcreate2(
|
|
||||||
virtualfd, parameterNames[i].c_str(),
|
|
||||||
GetDataTypeinC(parameterDataTypes[i]), vdsDataspace_para,
|
|
||||||
H5P_DEFAULT, dcpl_para[i], H5P_DEFAULT);
|
|
||||||
if (vdsdataset_para < 0)
|
|
||||||
throw sls::RuntimeError("Could not create virutal dataset "
|
|
||||||
"(parameters) in virtual file " +
|
|
||||||
vname);
|
|
||||||
}
|
|
||||||
|
|
||||||
// close
|
|
||||||
H5Fclose(virtualfd);
|
|
||||||
virtualfd = 0;
|
|
||||||
|
|
||||||
// link
|
|
||||||
LinkVirtualInMaster(vname, virtualDatasetName);
|
|
||||||
} catch (const sls::RuntimeError &e) {
|
|
||||||
if (virtualfd > 0)
|
|
||||||
H5Fclose(virtualfd);
|
|
||||||
virtualfd = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::LinkVirtualInMaster(std::string fname, std::string dsetname) {
|
|
||||||
|
|
||||||
if (fname == currentFileName) {
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
}
|
|
||||||
|
|
||||||
char linkname[100];
|
|
||||||
hid_t vfd = 0;
|
|
||||||
|
|
||||||
try {
|
|
||||||
hid_t dfal = H5Pcreate(H5P_FILE_ACCESS);
|
|
||||||
if (dfal < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create file access property for link");
|
|
||||||
if (H5Pset_fclose_degree(dfal, H5F_CLOSE_STRONG) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not set strong file close degree for link");
|
|
||||||
|
|
||||||
// open master file
|
|
||||||
hid_t mfd = H5Fopen(masterFileName.c_str(), H5F_ACC_RDWR, dfal);
|
|
||||||
if (mfd < 0)
|
|
||||||
throw sls::RuntimeError("Could not open master file");
|
|
||||||
|
|
||||||
// open virtual file
|
|
||||||
vfd = H5Fopen(fname.c_str(), H5F_ACC_RDWR, dfal);
|
|
||||||
if (vfd < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
throw sls::RuntimeError("Could not open virtual file");
|
|
||||||
}
|
|
||||||
|
|
||||||
// find relative path
|
|
||||||
std::string relative_virtualfname = fname;
|
|
||||||
{
|
|
||||||
size_t i = fname.rfind('/', fname.length());
|
|
||||||
if (i != std::string::npos)
|
|
||||||
relative_virtualfname =
|
|
||||||
(fname.substr(i + 1, fname.length() - i));
|
|
||||||
}
|
|
||||||
|
|
||||||
//**data dataset**
|
|
||||||
hid_t vdset = H5Dopen2(vfd, dsetname.c_str(), H5P_DEFAULT);
|
|
||||||
if (vdset < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
throw sls::RuntimeError("Could not open virtual data dataset");
|
|
||||||
}
|
|
||||||
sprintf(linkname, "/entry/data/%s", dsetname.c_str());
|
|
||||||
if (H5Lcreate_external(relative_virtualfname.c_str(), dsetname.c_str(),
|
|
||||||
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
throw sls::RuntimeError("Could not create link to data dataset");
|
|
||||||
}
|
|
||||||
H5Dclose(vdset);
|
|
||||||
|
|
||||||
//**paramter datasets**
|
|
||||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
|
||||||
hid_t vdset_para = H5Dopen2(
|
|
||||||
vfd, (std::string(parameterNames[i])).c_str(), H5P_DEFAULT);
|
|
||||||
if (vdset_para < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not open virtual parameter dataset to create link");
|
|
||||||
}
|
|
||||||
sprintf(linkname, "/entry/data/%s",
|
|
||||||
(std::string(parameterNames[i])).c_str());
|
|
||||||
|
|
||||||
if (H5Lcreate_external(relative_virtualfname.c_str(),
|
|
||||||
parameterNames[i].c_str(), mfd, linkname,
|
|
||||||
H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create link to virtual parameter dataset");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
H5Fclose(vfd);
|
|
||||||
vfd = 0;
|
|
||||||
} catch (...) {
|
|
||||||
if (vfd > 0)
|
|
||||||
H5Fclose(vfd);
|
|
||||||
vfd = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
hid_t HDF5File::GetDataTypeinC(DataType dtype) {
|
|
||||||
if (dtype == PredType::STD_U8LE)
|
|
||||||
return H5T_STD_U8LE;
|
|
||||||
else if (dtype == PredType::STD_U16LE)
|
|
||||||
return H5T_STD_U16LE;
|
|
||||||
else if (dtype == PredType::STD_U32LE)
|
|
||||||
return H5T_STD_U32LE;
|
|
||||||
else if (dtype == PredType::STD_U64LE)
|
|
||||||
return H5T_STD_U64LE;
|
|
||||||
else {
|
|
||||||
hid_t s = H5Tcopy(H5T_C_S1);
|
|
||||||
H5Tset_size(s, MAX_NUM_PACKETS);
|
|
||||||
return s;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
@ -1,92 +0,0 @@
|
|||||||
#pragma once
|
|
||||||
/************************************************
|
|
||||||
* @file HDF5File.h
|
|
||||||
* @short sets/gets properties for the HDF5 file,
|
|
||||||
* creates/closes the file and writes data to it
|
|
||||||
***********************************************/
|
|
||||||
/**
|
|
||||||
*@short sets/gets properties for the HDF5 file, creates/closes the file and
|
|
||||||
*writes data to it
|
|
||||||
*/
|
|
||||||
|
|
||||||
#include "File.h"
|
|
||||||
|
|
||||||
#include "H5Cpp.h"
|
|
||||||
#ifndef H5_NO_NAMESPACE
|
|
||||||
using namespace H5;
|
|
||||||
#endif
|
|
||||||
#include <mutex>
|
|
||||||
|
|
||||||
class HDF5File : private virtual slsDetectorDefs, public File {
|
|
||||||
|
|
||||||
public:
|
|
||||||
/**
|
|
||||||
* Constructor
|
|
||||||
* creates the File Writer
|
|
||||||
* @param ind self index
|
|
||||||
* @param maxf pointer to max frames per file
|
|
||||||
* @param nd pointer to number of detectors in each dimension
|
|
||||||
* @param fname pointer to file name prefix
|
|
||||||
* @param fpath pointer to file path
|
|
||||||
* @param findex pointer to file index
|
|
||||||
* @param owenable pointer to over write enable
|
|
||||||
* @param dindex pointer to detector index
|
|
||||||
* @param nunits pointer to number of theads/ units per detector
|
|
||||||
* @param nf pointer to number of images in acquisition
|
|
||||||
* @param dr pointer to dynamic range
|
|
||||||
* @param portno pointer to udp port number for logging
|
|
||||||
* @param nx number of pixels in x direction
|
|
||||||
* @param ny number of pixels in y direction
|
|
||||||
* @param smode pointer to silent mode
|
|
||||||
*/
|
|
||||||
HDF5File(int ind, uint32_t *maxf, int *nd, std::string *fname,
|
|
||||||
std::string *fpath, uint64_t *findex, bool *owenable, int *dindex,
|
|
||||||
int *nunits, uint64_t *nf, uint32_t *dr, uint32_t *portno,
|
|
||||||
uint32_t nx, uint32_t ny, bool *smode);
|
|
||||||
~HDF5File();
|
|
||||||
void SetNumberofPixels(uint32_t nx, uint32_t ny);
|
|
||||||
void CreateFile() override;
|
|
||||||
void CloseAllFiles() override;
|
|
||||||
void CloseCurrentDataFile() override;
|
|
||||||
void CloseMasterFile() override;
|
|
||||||
void WriteToFile(char *buffer, int bufferSize, uint64_t currentFrameNumber,
|
|
||||||
uint32_t numPacketsCaught) override;
|
|
||||||
void CreateMasterFile(MasterAttributes *attr) override;
|
|
||||||
void StartofAcquisition() override;
|
|
||||||
void EndofAcquisition(bool anyPacketsCaught, uint64_t numImagesCaught);
|
|
||||||
|
|
||||||
private:
|
|
||||||
void CloseFile(H5File *&fd, bool masterFile);
|
|
||||||
void WriteDataFile(uint64_t currentFrameNumber, char *buffer);
|
|
||||||
void WriteParameterDatasets(uint64_t currentFrameNumber,
|
|
||||||
sls_receiver_header *rheader);
|
|
||||||
void ExtendDataset();
|
|
||||||
void CreateDataFile();
|
|
||||||
void CreateMasterDataFile(MasterAttributes *attr);
|
|
||||||
void CreateVirtualDataFile(uint32_t maxFramesPerFile, uint64_t numf);
|
|
||||||
void LinkVirtualInMaster(std::string fname, std::string dsetname);
|
|
||||||
hid_t GetDataTypeinC(DataType dtype);
|
|
||||||
|
|
||||||
static std::mutex hdf5Lib;
|
|
||||||
|
|
||||||
H5File *masterfd;
|
|
||||||
/** Virtual File handle ( only file name because
|
|
||||||
code in C as H5Pset_virtual doesnt exist yet in C++) */
|
|
||||||
hid_t virtualfd;
|
|
||||||
H5File *filefd;
|
|
||||||
DataSpace *dataspace;
|
|
||||||
DataSet *dataset;
|
|
||||||
DataType datatype;
|
|
||||||
|
|
||||||
uint32_t nPixelsX;
|
|
||||||
uint32_t nPixelsY;
|
|
||||||
uint32_t numFramesInFile;
|
|
||||||
int numFilesinAcquisition;
|
|
||||||
|
|
||||||
std::vector<std::string> parameterNames;
|
|
||||||
std::vector<DataType> parameterDataTypes;
|
|
||||||
DataSpace *dataspace_para;
|
|
||||||
std::vector<DataSet *> dataset_para;
|
|
||||||
|
|
||||||
uint64_t extNumImages;
|
|
||||||
};
|
|
||||||
@ -1,830 +0,0 @@
|
|||||||
/************************************************
|
|
||||||
* @file HDF5File.cpp
|
|
||||||
* @short sets/gets properties for the HDF5 file,
|
|
||||||
* creates/closes the file and writes data to it
|
|
||||||
***********************************************/
|
|
||||||
#include "HDF5File.h"
|
|
||||||
#include "Fifo.h"
|
|
||||||
#include "MasterAttributes.h"
|
|
||||||
#include "receiver_defs.h"
|
|
||||||
|
|
||||||
#include <iomanip>
|
|
||||||
#include <iostream>
|
|
||||||
#include <libgen.h> //basename
|
|
||||||
#include <string.h>
|
|
||||||
|
|
||||||
std::mutex HDF5File::hdf5Lib;
|
|
||||||
|
|
||||||
HDF5File::HDF5File(int ind, uint32_t *maxf, int *nd, std::string *fname,
|
|
||||||
std::string *fpath, uint64_t *findex, bool *owenable,
|
|
||||||
int *dindex, int *nunits, uint64_t *nf, uint32_t *dr,
|
|
||||||
uint32_t *portno, uint32_t nx, uint32_t ny, bool *smode)
|
|
||||||
:
|
|
||||||
|
|
||||||
File(ind, HDF5, maxf, nd, fname, fpath, findex, owenable, dindex, nunits,
|
|
||||||
nf, dr, portno, smode),
|
|
||||||
masterfd(nullptr), virtualfd(0), filefd(nullptr), dataspace(nullptr),
|
|
||||||
dataset(nullptr), datatype(PredType::STD_U16LE), nPixelsX(nx),
|
|
||||||
nPixelsY(ny), numFramesInFile(0), numFilesinAcquisition(0),
|
|
||||||
dataspace_para(nullptr), extNumImages(0) {
|
|
||||||
PrintMembers();
|
|
||||||
dataset_para.clear();
|
|
||||||
parameterNames.clear();
|
|
||||||
parameterDataTypes.clear();
|
|
||||||
|
|
||||||
parameterNames = std::vector<std::string>{
|
|
||||||
"frame number",
|
|
||||||
"exp length or sub exposure time",
|
|
||||||
"packets caught",
|
|
||||||
"bunch id",
|
|
||||||
"timestamp",
|
|
||||||
"mod id",
|
|
||||||
"row",
|
|
||||||
"column",
|
|
||||||
"reserved",
|
|
||||||
"debug",
|
|
||||||
"round robin number",
|
|
||||||
"detector type",
|
|
||||||
"detector header version",
|
|
||||||
"packets caught bit mask",
|
|
||||||
};
|
|
||||||
StrType strdatatype(PredType::C_S1, sizeof(bitset_storage));
|
|
||||||
parameterDataTypes = std::vector<DataType>{
|
|
||||||
PredType::STD_U64LE, PredType::STD_U32LE, PredType::STD_U32LE,
|
|
||||||
PredType::STD_U64LE, PredType::STD_U64LE, PredType::STD_U16LE,
|
|
||||||
PredType::STD_U16LE, PredType::STD_U16LE, PredType::STD_U16LE,
|
|
||||||
PredType::STD_U32LE, PredType::STD_U16LE, PredType::STD_U8LE,
|
|
||||||
PredType::STD_U8LE, strdatatype};
|
|
||||||
}
|
|
||||||
|
|
||||||
HDF5File::~HDF5File() { CloseAllFiles(); }
|
|
||||||
|
|
||||||
void HDF5File::SetNumberofPixels(uint32_t nx, uint32_t ny) {
|
|
||||||
nPixelsX = nx;
|
|
||||||
nPixelsY = ny;
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CreateFile() {
|
|
||||||
numFilesinAcquisition++;
|
|
||||||
numFramesInFile = 0;
|
|
||||||
|
|
||||||
// first time
|
|
||||||
if (subFileIndex == 0u) {
|
|
||||||
switch (*dynamicRange) {
|
|
||||||
case 16:
|
|
||||||
datatype = PredType::STD_U16LE;
|
|
||||||
break;
|
|
||||||
case 32:
|
|
||||||
datatype = PredType::STD_U32LE;
|
|
||||||
break;
|
|
||||||
default:
|
|
||||||
datatype = PredType::STD_U8LE;
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
CreateDataFile();
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CloseAllFiles() {
|
|
||||||
CloseCurrentDataFile();
|
|
||||||
CloseMasterFile();
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CloseMasterFile() {
|
|
||||||
if (master) {
|
|
||||||
CloseFile(masterfd, true);
|
|
||||||
// close virtual file
|
|
||||||
// c code due to only c implementation of H5Pset_virtual available
|
|
||||||
if (virtualfd != 0) {
|
|
||||||
if (H5Fclose(virtualfd) < 0) {
|
|
||||||
LOG(logERROR) << "Could not close virtual HDF5 handles";
|
|
||||||
}
|
|
||||||
virtualfd = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CloseCurrentDataFile() {
|
|
||||||
CloseFile(filefd, false);
|
|
||||||
for (unsigned int i = 0; i < dataset_para.size(); ++i)
|
|
||||||
delete dataset_para[i];
|
|
||||||
dataset_para.clear();
|
|
||||||
if (dataspace_para) {
|
|
||||||
delete dataspace_para;
|
|
||||||
dataspace_para = nullptr;
|
|
||||||
}
|
|
||||||
if (dataset) {
|
|
||||||
delete dataset;
|
|
||||||
dataset = nullptr;
|
|
||||||
}
|
|
||||||
if (dataspace) {
|
|
||||||
delete dataspace;
|
|
||||||
dataspace = nullptr;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::WriteToFile(char *buffer, int bufferSize,
|
|
||||||
uint64_t currentFrameNumber,
|
|
||||||
uint32_t numPacketsCaught) {
|
|
||||||
|
|
||||||
// check if maxframesperfile = 0 for infinite
|
|
||||||
if ((*maxFramesPerFile) && (numFramesInFile >= (*maxFramesPerFile))) {
|
|
||||||
CloseCurrentFile();
|
|
||||||
++subFileIndex;
|
|
||||||
CreateFile();
|
|
||||||
}
|
|
||||||
numFramesInFile++;
|
|
||||||
|
|
||||||
// extend dataset (when receiver start followed by many status starts
|
|
||||||
// (jungfrau)))
|
|
||||||
if (currentFrameNumber >= extNumImages) {
|
|
||||||
ExtendDataset();
|
|
||||||
}
|
|
||||||
|
|
||||||
WriteDataFile(currentFrameNumber, buffer + sizeof(sls_receiver_header));
|
|
||||||
WriteParameterDatasets(currentFrameNumber, (sls_receiver_header *)(buffer));
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CreateMasterFile(MasterAttributes *attr) {
|
|
||||||
if (master) {
|
|
||||||
virtualfd = 0;
|
|
||||||
CreateMasterDataFile(attr);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::StartofAcquisition() {
|
|
||||||
numFilesinAcquisition = 0;
|
|
||||||
numFramesInFile = 0;
|
|
||||||
extNumImages = *numImages;
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::EndofAcquisition(bool anyPacketsCaught,
|
|
||||||
uint64_t numImagesCaught) {
|
|
||||||
// not created before
|
|
||||||
if (!virtualfd && anyPacketsCaught) {
|
|
||||||
// called only by the one maser receiver
|
|
||||||
if (master && masterfd != nullptr) {
|
|
||||||
// only one file and one sub image (link current file in master)
|
|
||||||
if (((numFilesinAcquisition == 1) && (numDetY * numDetX) == 1)) {
|
|
||||||
// dataset name
|
|
||||||
std::ostringstream oss;
|
|
||||||
oss << "/data";
|
|
||||||
if ((*numImages > 1)) {
|
|
||||||
oss << "_f" << std::setfill('0') << std::setw(12) << 0;
|
|
||||||
}
|
|
||||||
std::string dsetname = oss.str();
|
|
||||||
|
|
||||||
LinkVirtualInMaster(currentFileName, dsetname);
|
|
||||||
}
|
|
||||||
// create virutal file
|
|
||||||
else {
|
|
||||||
CreateVirtualDataFile(
|
|
||||||
// infinite images in 1 file, then maxfrperfile =
|
|
||||||
// numImagesCaught
|
|
||||||
((*maxFramesPerFile == 0) ? numImagesCaught + 1
|
|
||||||
: *maxFramesPerFile),
|
|
||||||
numImagesCaught + 1);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
numFilesinAcquisition = 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CloseFile(H5File *&fd, bool masterFile) {
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
try {
|
|
||||||
Exception::dontPrint(); // to handle errors
|
|
||||||
if (fd) {
|
|
||||||
fd->close();
|
|
||||||
delete fd;
|
|
||||||
fd = nullptr;
|
|
||||||
}
|
|
||||||
} catch (const Exception &error) {
|
|
||||||
LOG(logERROR) << "Could not close " << (masterFile ? "master" : "data")
|
|
||||||
<< " HDF5 handles of index " << index;
|
|
||||||
error.printErrorStack();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::WriteDataFile(uint64_t currentFrameNumber, char *buffer) {
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
|
|
||||||
uint64_t nDimx =
|
|
||||||
((*maxFramesPerFile == 0) ? currentFrameNumber
|
|
||||||
: currentFrameNumber % (*maxFramesPerFile));
|
|
||||||
uint32_t nDimy = nPixelsY;
|
|
||||||
uint32_t nDimz = ((*dynamicRange == 4) ? (nPixelsX / 2) : nPixelsX);
|
|
||||||
|
|
||||||
hsize_t count[3] = {1, nDimy, nDimz};
|
|
||||||
hsize_t start[3] = {nDimx, 0, 0};
|
|
||||||
hsize_t dims2[2] = {nDimy, nDimz};
|
|
||||||
try {
|
|
||||||
Exception::dontPrint(); // to handle errors
|
|
||||||
|
|
||||||
dataspace->selectHyperslab(H5S_SELECT_SET, count, start);
|
|
||||||
DataSpace memspace(2, dims2);
|
|
||||||
dataset->write(buffer, datatype, memspace, *dataspace);
|
|
||||||
memspace.close();
|
|
||||||
} catch (const Exception &error) {
|
|
||||||
LOG(logERROR) << "Could not write to file in object " << index;
|
|
||||||
error.printErrorStack();
|
|
||||||
throw sls::RuntimeError("Could not write to file in object " +
|
|
||||||
std::to_string(index));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::WriteParameterDatasets(uint64_t currentFrameNumber,
|
|
||||||
sls_receiver_header *rheader) {
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
|
|
||||||
uint64_t fnum =
|
|
||||||
((*maxFramesPerFile == 0) ? currentFrameNumber
|
|
||||||
: currentFrameNumber % (*maxFramesPerFile));
|
|
||||||
|
|
||||||
sls_detector_header header = rheader->detHeader;
|
|
||||||
hsize_t count[1] = {1};
|
|
||||||
hsize_t start[1] = {fnum};
|
|
||||||
int i = 0;
|
|
||||||
try {
|
|
||||||
Exception::dontPrint(); // to handle errors
|
|
||||||
dataspace_para->selectHyperslab(H5S_SELECT_SET, count, start);
|
|
||||||
DataSpace memspace(H5S_SCALAR);
|
|
||||||
dataset_para[0]->write(&header.frameNumber, parameterDataTypes[0],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
i = 1;
|
|
||||||
dataset_para[1]->write(&header.expLength, parameterDataTypes[1],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
i = 2;
|
|
||||||
dataset_para[2]->write(&header.packetNumber, parameterDataTypes[2],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
i = 3;
|
|
||||||
dataset_para[3]->write(&header.bunchId, parameterDataTypes[3], memspace,
|
|
||||||
*dataspace_para);
|
|
||||||
i = 4;
|
|
||||||
dataset_para[4]->write(&header.timestamp, parameterDataTypes[4],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
i = 5;
|
|
||||||
dataset_para[5]->write(&header.modId, parameterDataTypes[5], memspace,
|
|
||||||
*dataspace_para);
|
|
||||||
i = 6;
|
|
||||||
dataset_para[6]->write(&header.row, parameterDataTypes[6], memspace,
|
|
||||||
*dataspace_para);
|
|
||||||
i = 7;
|
|
||||||
dataset_para[7]->write(&header.column, parameterDataTypes[7], memspace,
|
|
||||||
*dataspace_para);
|
|
||||||
i = 8;
|
|
||||||
dataset_para[8]->write(&header.reserved, parameterDataTypes[8],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
i = 9;
|
|
||||||
dataset_para[9]->write(&header.debug, parameterDataTypes[9], memspace,
|
|
||||||
*dataspace_para);
|
|
||||||
i = 10;
|
|
||||||
dataset_para[10]->write(&header.roundRNumber, parameterDataTypes[10],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
i = 11;
|
|
||||||
dataset_para[11]->write(&header.detType, parameterDataTypes[11],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
i = 12;
|
|
||||||
dataset_para[12]->write(&header.version, parameterDataTypes[12],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
i = 13;
|
|
||||||
|
|
||||||
// contiguous bitset
|
|
||||||
if (sizeof(sls_bitset) == sizeof(bitset_storage)) {
|
|
||||||
dataset_para[13]->write((char *)&(rheader->packetsMask),
|
|
||||||
parameterDataTypes[13], memspace,
|
|
||||||
*dataspace_para);
|
|
||||||
}
|
|
||||||
|
|
||||||
// not contiguous bitset
|
|
||||||
else {
|
|
||||||
// get contiguous representation of bit mask
|
|
||||||
bitset_storage storage;
|
|
||||||
memset(storage, 0, sizeof(bitset_storage));
|
|
||||||
sls_bitset bits = rheader->packetsMask;
|
|
||||||
for (int i = 0; i < MAX_NUM_PACKETS; ++i)
|
|
||||||
storage[i >> 3] |= (bits[i] << (i & 7));
|
|
||||||
// write bitmask
|
|
||||||
dataset_para[13]->write((char *)storage, parameterDataTypes[13],
|
|
||||||
memspace, *dataspace_para);
|
|
||||||
}
|
|
||||||
i = 14;
|
|
||||||
} catch (const Exception &error) {
|
|
||||||
error.printErrorStack();
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not write parameters (index:" + std::to_string(i) +
|
|
||||||
") to file in object " + std::to_string(index));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::ExtendDataset() {
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
|
|
||||||
try {
|
|
||||||
Exception::dontPrint(); // to handle errors
|
|
||||||
|
|
||||||
hsize_t dims[3];
|
|
||||||
dataspace->getSimpleExtentDims(dims);
|
|
||||||
dims[0] += *numImages;
|
|
||||||
|
|
||||||
dataset->extend(dims);
|
|
||||||
delete dataspace;
|
|
||||||
dataspace = nullptr;
|
|
||||||
dataspace = new DataSpace(dataset->getSpace());
|
|
||||||
|
|
||||||
hsize_t dims_para[1] = {dims[0]};
|
|
||||||
for (unsigned int i = 0; i < dataset_para.size(); ++i)
|
|
||||||
dataset_para[i]->extend(dims_para);
|
|
||||||
delete dataspace_para;
|
|
||||||
dataspace_para = nullptr;
|
|
||||||
dataspace_para = new DataSpace(dataset_para[0]->getSpace());
|
|
||||||
|
|
||||||
} catch (const Exception &error) {
|
|
||||||
error.printErrorStack();
|
|
||||||
throw sls::RuntimeError("Could not extend dataset in object " +
|
|
||||||
std::to_string(index));
|
|
||||||
}
|
|
||||||
if (!(*silentMode)) {
|
|
||||||
LOG(logINFO) << index << " Extending HDF5 dataset by " << extNumImages
|
|
||||||
<< ", Total x Dimension: " << (extNumImages + *numImages);
|
|
||||||
}
|
|
||||||
extNumImages += *numImages;
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::CreateDataFile() {
|
|
||||||
|
|
||||||
std::ostringstream os;
|
|
||||||
os << *filePath << "/" << *fileNamePrefix << "_d"
|
|
||||||
<< (*detIndex * (*numUnitsPerDetector) + index) << "_f" << subFileIndex
|
|
||||||
<< '_' << *fileIndex << ".h5";
|
|
||||||
currentFileName = os.str();
|
|
||||||
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
|
|
||||||
uint64_t framestosave =
|
|
||||||
((*maxFramesPerFile == 0) ? *numImages : // infinite images
|
|
||||||
(((extNumImages - subFileIndex) > (*maxFramesPerFile))
|
|
||||||
? // save up to maximum at a time
|
|
||||||
(*maxFramesPerFile)
|
|
||||||
: (extNumImages - subFileIndex)));
|
|
||||||
|
|
||||||
uint64_t nDimx = framestosave;
|
|
||||||
uint32_t nDimy = nPixelsY;
|
|
||||||
uint32_t nDimz = ((*dynamicRange == 4) ? (nPixelsX / 2) : nPixelsX);
|
|
||||||
|
|
||||||
try {
|
|
||||||
Exception::dontPrint(); // to handle errors
|
|
||||||
|
|
||||||
// file
|
|
||||||
FileAccPropList fapl;
|
|
||||||
fapl.setFcloseDegree(H5F_CLOSE_STRONG);
|
|
||||||
filefd = nullptr;
|
|
||||||
if (!(*overWriteEnable))
|
|
||||||
filefd = new H5File(currentFileName.c_str(), H5F_ACC_EXCL,
|
|
||||||
FileCreatPropList::DEFAULT, fapl);
|
|
||||||
else
|
|
||||||
filefd = new H5File(currentFileName.c_str(), H5F_ACC_TRUNC,
|
|
||||||
FileCreatPropList::DEFAULT, fapl);
|
|
||||||
|
|
||||||
// attributes - version
|
|
||||||
double dValue = HDF5_WRITER_VERSION;
|
|
||||||
DataSpace dataspace_attr = DataSpace(H5S_SCALAR);
|
|
||||||
Attribute attribute = filefd->createAttribute(
|
|
||||||
"version", PredType::NATIVE_DOUBLE, dataspace_attr);
|
|
||||||
attribute.write(PredType::NATIVE_DOUBLE, &dValue);
|
|
||||||
|
|
||||||
// dataspace
|
|
||||||
hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
|
|
||||||
hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
|
|
||||||
dataspace = nullptr;
|
|
||||||
dataspace = new DataSpace(3, srcdims, srcdimsmax);
|
|
||||||
|
|
||||||
// dataset name
|
|
||||||
std::ostringstream osfn;
|
|
||||||
osfn << "/data";
|
|
||||||
if (*numImages > 1)
|
|
||||||
osfn << "_f" << std::setfill('0') << std::setw(12) << subFileIndex;
|
|
||||||
std::string dsetname = osfn.str();
|
|
||||||
|
|
||||||
// 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) {
|
|
||||||
|
|
||||||
std::ostringstream osfn;
|
|
||||||
osfn << *filePath << "/" << *fileNamePrefix;
|
|
||||||
osfn << "_virtual";
|
|
||||||
osfn << "_" << *fileIndex;
|
|
||||||
osfn << ".h5";
|
|
||||||
std::string vname = osfn.str();
|
|
||||||
|
|
||||||
if (!(*silentMode)) {
|
|
||||||
LOG(logINFO) << "Virtual File: " << vname;
|
|
||||||
}
|
|
||||||
|
|
||||||
int numDetz = numDetX;
|
|
||||||
uint32_t nDimy = nPixelsY;
|
|
||||||
uint32_t nDimz = ((*dynamicRange == 4) ? (nPixelsX / 2) : nPixelsX);
|
|
||||||
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
|
|
||||||
try {
|
|
||||||
// file
|
|
||||||
hid_t dfal = H5Pcreate(H5P_FILE_ACCESS);
|
|
||||||
if (dfal < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create file access property for virtual file " +
|
|
||||||
vname);
|
|
||||||
if (H5Pset_fclose_degree(dfal, H5F_CLOSE_STRONG) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not set strong file close degree for virtual file " +
|
|
||||||
vname);
|
|
||||||
virtualfd = H5Fcreate(vname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, dfal);
|
|
||||||
if (virtualfd < 0)
|
|
||||||
throw sls::RuntimeError("Could not create virtual file " + vname);
|
|
||||||
|
|
||||||
// attributes - version
|
|
||||||
hid_t dataspace_attr = H5Screate(H5S_SCALAR);
|
|
||||||
if (dataspace_attr < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create dataspace for attribute in virtual file " +
|
|
||||||
vname);
|
|
||||||
hid_t attrid = H5Acreate2(virtualfd, "version", H5T_NATIVE_DOUBLE,
|
|
||||||
dataspace_attr, H5P_DEFAULT, H5P_DEFAULT);
|
|
||||||
if (attrid < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create attribute in virtual file " + vname);
|
|
||||||
double attr_data = HDF5_WRITER_VERSION;
|
|
||||||
if (H5Awrite(attrid, H5T_NATIVE_DOUBLE, &attr_data) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not write attribute in virtual file " + vname);
|
|
||||||
if (H5Aclose(attrid) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not close attribute in virtual file " + vname);
|
|
||||||
|
|
||||||
// virtual dataspace
|
|
||||||
hsize_t vdsdims[3] = {numf, numDetY * nDimy, numDetz * nDimz};
|
|
||||||
hid_t vdsDataspace = H5Screate_simple(3, vdsdims, nullptr);
|
|
||||||
if (vdsDataspace < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create virtual dataspace in virtual file " + vname);
|
|
||||||
hsize_t vdsdims_para[2] = {numf, (unsigned int)numDetY * numDetz};
|
|
||||||
hid_t vdsDataspace_para = H5Screate_simple(2, vdsdims_para, nullptr);
|
|
||||||
if (vdsDataspace_para < 0)
|
|
||||||
throw sls::RuntimeError("Could not create virtual dataspace "
|
|
||||||
"(parameters) in virtual file " +
|
|
||||||
vname);
|
|
||||||
|
|
||||||
// fill values
|
|
||||||
hid_t dcpl = H5Pcreate(H5P_DATASET_CREATE);
|
|
||||||
if (dcpl < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create file creation properties in virtual file " +
|
|
||||||
vname);
|
|
||||||
int fill_value = -1;
|
|
||||||
if (H5Pset_fill_value(dcpl, GetDataTypeinC(datatype), &fill_value) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create fill value in virtual file " + vname);
|
|
||||||
std::vector<hid_t> dcpl_para(parameterNames.size());
|
|
||||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
|
||||||
dcpl_para[i] = H5Pcreate(H5P_DATASET_CREATE);
|
|
||||||
if (dcpl_para[i] < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create file creation properties (parameters) in "
|
|
||||||
"virtual file " +
|
|
||||||
vname);
|
|
||||||
if (H5Pset_fill_value(dcpl_para[i],
|
|
||||||
GetDataTypeinC(parameterDataTypes[i]),
|
|
||||||
&fill_value) < 0)
|
|
||||||
throw sls::RuntimeError("Could not create fill value "
|
|
||||||
"(parameters) in virtual file " +
|
|
||||||
vname);
|
|
||||||
}
|
|
||||||
|
|
||||||
// hyperslab
|
|
||||||
int numMajorHyperslab = numf / maxFramesPerFile;
|
|
||||||
if (numf % maxFramesPerFile)
|
|
||||||
numMajorHyperslab++;
|
|
||||||
uint64_t framesSaved = 0;
|
|
||||||
for (int j = 0; j < numMajorHyperslab; j++) {
|
|
||||||
|
|
||||||
uint64_t nDimx = ((numf - framesSaved) > maxFramesPerFile)
|
|
||||||
? maxFramesPerFile
|
|
||||||
: (numf - framesSaved);
|
|
||||||
hsize_t offset[3] = {framesSaved, 0, 0};
|
|
||||||
hsize_t count[3] = {nDimx, nDimy, nDimz};
|
|
||||||
hsize_t offset_para[2] = {framesSaved, 0};
|
|
||||||
hsize_t count_para[2] = {nDimx, 1};
|
|
||||||
|
|
||||||
for (int i = 0; i < numDetY * numDetz; ++i) {
|
|
||||||
|
|
||||||
// setect hyperslabs
|
|
||||||
if (H5Sselect_hyperslab(vdsDataspace, H5S_SELECT_SET, offset,
|
|
||||||
nullptr, count, nullptr) < 0) {
|
|
||||||
throw sls::RuntimeError("Could not select hyperslab");
|
|
||||||
}
|
|
||||||
if (H5Sselect_hyperslab(vdsDataspace_para, H5S_SELECT_SET,
|
|
||||||
offset_para, nullptr, count_para,
|
|
||||||
nullptr) < 0) {
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not select hyperslab for parameters");
|
|
||||||
}
|
|
||||||
|
|
||||||
// source file name
|
|
||||||
std::ostringstream os;
|
|
||||||
os << *filePath << "/" << *fileNamePrefix << "_d"
|
|
||||||
<< (*detIndex * (*numUnitsPerDetector) + i) << "_f" << j
|
|
||||||
<< '_' << *fileIndex << ".h5";
|
|
||||||
std::string srcFileName = os.str();
|
|
||||||
|
|
||||||
LOG(logDEBUG1) << srcFileName;
|
|
||||||
// find relative path
|
|
||||||
std::string relative_srcFileName = srcFileName;
|
|
||||||
{
|
|
||||||
size_t i = srcFileName.rfind('/', srcFileName.length());
|
|
||||||
if (i != std::string::npos)
|
|
||||||
relative_srcFileName = (srcFileName.substr(
|
|
||||||
i + 1, srcFileName.length() - i));
|
|
||||||
}
|
|
||||||
|
|
||||||
// source dataset name
|
|
||||||
std::ostringstream osfn;
|
|
||||||
osfn << "/data";
|
|
||||||
if (*numImages > 1)
|
|
||||||
osfn << "_f" << std::setfill('0') << std::setw(12) << j;
|
|
||||||
std::string srcDatasetName = osfn.str();
|
|
||||||
|
|
||||||
// source dataspace
|
|
||||||
hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
|
|
||||||
hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
|
|
||||||
hid_t srcDataspace = H5Screate_simple(3, srcdims, srcdimsmax);
|
|
||||||
if (srcDataspace < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create source dataspace in virtual file " +
|
|
||||||
vname);
|
|
||||||
hsize_t srcdims_para[1] = {nDimx};
|
|
||||||
hsize_t srcdimsmax_para[1] = {H5S_UNLIMITED};
|
|
||||||
hid_t srcDataspace_para =
|
|
||||||
H5Screate_simple(1, srcdims_para, srcdimsmax_para);
|
|
||||||
if (srcDataspace_para < 0)
|
|
||||||
throw sls::RuntimeError("Could not create source dataspace "
|
|
||||||
"(parameters) in virtual file " +
|
|
||||||
vname);
|
|
||||||
|
|
||||||
// mapping
|
|
||||||
if (H5Pset_virtual(dcpl, vdsDataspace,
|
|
||||||
relative_srcFileName.c_str(),
|
|
||||||
srcDatasetName.c_str(), srcDataspace) < 0) {
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not set mapping for paramter 1");
|
|
||||||
}
|
|
||||||
|
|
||||||
for (unsigned int k = 0; k < parameterNames.size(); ++k) {
|
|
||||||
if (H5Pset_virtual(dcpl_para[k], vdsDataspace_para,
|
|
||||||
relative_srcFileName.c_str(),
|
|
||||||
parameterNames[k].c_str(),
|
|
||||||
srcDataspace_para) < 0) {
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not set mapping for paramter " +
|
|
||||||
std::to_string(k));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// H5Sclose(srcDataspace);
|
|
||||||
// H5Sclose(srcDataspace_para);
|
|
||||||
offset[2] += nDimz;
|
|
||||||
if (offset[2] >= (numDetz * nDimz)) {
|
|
||||||
offset[2] = 0;
|
|
||||||
offset[1] += nDimy;
|
|
||||||
}
|
|
||||||
offset_para[1]++;
|
|
||||||
}
|
|
||||||
framesSaved += nDimx;
|
|
||||||
}
|
|
||||||
|
|
||||||
// dataset
|
|
||||||
std::string virtualDatasetName = "data";
|
|
||||||
hid_t vdsdataset = H5Dcreate2(virtualfd, virtualDatasetName.c_str(),
|
|
||||||
GetDataTypeinC(datatype), vdsDataspace,
|
|
||||||
H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
|
||||||
if (vdsdataset < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create virutal dataset in virtual file " + vname);
|
|
||||||
|
|
||||||
// virtual parameter dataset
|
|
||||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
|
||||||
hid_t vdsdataset_para = H5Dcreate2(
|
|
||||||
virtualfd, parameterNames[i].c_str(),
|
|
||||||
GetDataTypeinC(parameterDataTypes[i]), vdsDataspace_para,
|
|
||||||
H5P_DEFAULT, dcpl_para[i], H5P_DEFAULT);
|
|
||||||
if (vdsdataset_para < 0)
|
|
||||||
throw sls::RuntimeError("Could not create virutal dataset "
|
|
||||||
"(parameters) in virtual file " +
|
|
||||||
vname);
|
|
||||||
}
|
|
||||||
|
|
||||||
// close
|
|
||||||
H5Fclose(virtualfd);
|
|
||||||
virtualfd = 0;
|
|
||||||
|
|
||||||
// link
|
|
||||||
LinkVirtualInMaster(vname, virtualDatasetName);
|
|
||||||
} catch (const sls::RuntimeError &e) {
|
|
||||||
if (virtualfd > 0)
|
|
||||||
H5Fclose(virtualfd);
|
|
||||||
virtualfd = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
void HDF5File::LinkVirtualInMaster(std::string fname, std::string dsetname) {
|
|
||||||
|
|
||||||
if (fname == currentFileName) {
|
|
||||||
std::lock_guard<std::mutex> lock(HDF5File::hdf5Lib);
|
|
||||||
}
|
|
||||||
|
|
||||||
char linkname[100];
|
|
||||||
hid_t vfd = 0;
|
|
||||||
|
|
||||||
try {
|
|
||||||
hid_t dfal = H5Pcreate(H5P_FILE_ACCESS);
|
|
||||||
if (dfal < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create file access property for link");
|
|
||||||
if (H5Pset_fclose_degree(dfal, H5F_CLOSE_STRONG) < 0)
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not set strong file close degree for link");
|
|
||||||
|
|
||||||
// open master file
|
|
||||||
hid_t mfd = H5Fopen(masterFileName.c_str(), H5F_ACC_RDWR, dfal);
|
|
||||||
if (mfd < 0)
|
|
||||||
throw sls::RuntimeError("Could not open master file");
|
|
||||||
|
|
||||||
// open virtual file
|
|
||||||
vfd = H5Fopen(fname.c_str(), H5F_ACC_RDWR, dfal);
|
|
||||||
if (vfd < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
throw sls::RuntimeError("Could not open virtual file");
|
|
||||||
}
|
|
||||||
|
|
||||||
// find relative path
|
|
||||||
std::string relative_virtualfname = fname;
|
|
||||||
{
|
|
||||||
size_t i = fname.rfind('/', fname.length());
|
|
||||||
if (i != std::string::npos)
|
|
||||||
relative_virtualfname =
|
|
||||||
(fname.substr(i + 1, fname.length() - i));
|
|
||||||
}
|
|
||||||
|
|
||||||
//**data dataset**
|
|
||||||
hid_t vdset = H5Dopen2(vfd, dsetname.c_str(), H5P_DEFAULT);
|
|
||||||
if (vdset < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
throw sls::RuntimeError("Could not open virtual data dataset");
|
|
||||||
}
|
|
||||||
sprintf(linkname, "/entry/data/%s", dsetname.c_str());
|
|
||||||
if (H5Lcreate_external(relative_virtualfname.c_str(), dsetname.c_str(),
|
|
||||||
mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
throw sls::RuntimeError("Could not create link to data dataset");
|
|
||||||
}
|
|
||||||
H5Dclose(vdset);
|
|
||||||
|
|
||||||
//**paramter datasets**
|
|
||||||
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
|
|
||||||
hid_t vdset_para = H5Dopen2(
|
|
||||||
vfd, (std::string(parameterNames[i])).c_str(), H5P_DEFAULT);
|
|
||||||
if (vdset_para < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not open virtual parameter dataset to create link");
|
|
||||||
}
|
|
||||||
sprintf(linkname, "/entry/data/%s",
|
|
||||||
(std::string(parameterNames[i])).c_str());
|
|
||||||
|
|
||||||
if (H5Lcreate_external(relative_virtualfname.c_str(),
|
|
||||||
parameterNames[i].c_str(), mfd, linkname,
|
|
||||||
H5P_DEFAULT, H5P_DEFAULT) < 0) {
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
throw sls::RuntimeError(
|
|
||||||
"Could not create link to virtual parameter dataset");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
H5Fclose(mfd);
|
|
||||||
mfd = 0;
|
|
||||||
H5Fclose(vfd);
|
|
||||||
vfd = 0;
|
|
||||||
} catch (...) {
|
|
||||||
if (vfd > 0)
|
|
||||||
H5Fclose(vfd);
|
|
||||||
vfd = 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
hid_t HDF5File::GetDataTypeinC(DataType dtype) {
|
|
||||||
if (dtype == PredType::STD_U8LE)
|
|
||||||
return H5T_STD_U8LE;
|
|
||||||
else if (dtype == PredType::STD_U16LE)
|
|
||||||
return H5T_STD_U16LE;
|
|
||||||
else if (dtype == PredType::STD_U32LE)
|
|
||||||
return H5T_STD_U32LE;
|
|
||||||
else if (dtype == PredType::STD_U64LE)
|
|
||||||
return H5T_STD_U64LE;
|
|
||||||
else {
|
|
||||||
hid_t s = H5Tcopy(H5T_C_S1);
|
|
||||||
H5Tset_size(s, MAX_NUM_PACKETS);
|
|
||||||
return s;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
@ -1,92 +0,0 @@
|
|||||||
#pragma once
|
|
||||||
/************************************************
|
|
||||||
* @file HDF5File.h
|
|
||||||
* @short sets/gets properties for the HDF5 file,
|
|
||||||
* creates/closes the file and writes data to it
|
|
||||||
***********************************************/
|
|
||||||
/**
|
|
||||||
*@short sets/gets properties for the HDF5 file, creates/closes the file and
|
|
||||||
*writes data to it
|
|
||||||
*/
|
|
||||||
|
|
||||||
#include "File.h"
|
|
||||||
|
|
||||||
#include "H5Cpp.h"
|
|
||||||
#ifndef H5_NO_NAMESPACE
|
|
||||||
using namespace H5;
|
|
||||||
#endif
|
|
||||||
#include <mutex>
|
|
||||||
|
|
||||||
class HDF5File : private virtual slsDetectorDefs, public File {
|
|
||||||
|
|
||||||
public:
|
|
||||||
/**
|
|
||||||
* Constructor
|
|
||||||
* creates the File Writer
|
|
||||||
* @param ind self index
|
|
||||||
* @param maxf pointer to max frames per file
|
|
||||||
* @param nd pointer to number of detectors in each dimension
|
|
||||||
* @param fname pointer to file name prefix
|
|
||||||
* @param fpath pointer to file path
|
|
||||||
* @param findex pointer to file index
|
|
||||||
* @param owenable pointer to over write enable
|
|
||||||
* @param dindex pointer to detector index
|
|
||||||
* @param nunits pointer to number of theads/ units per detector
|
|
||||||
* @param nf pointer to number of images in acquisition
|
|
||||||
* @param dr pointer to dynamic range
|
|
||||||
* @param portno pointer to udp port number for logging
|
|
||||||
* @param nx number of pixels in x direction
|
|
||||||
* @param ny number of pixels in y direction
|
|
||||||
* @param smode pointer to silent mode
|
|
||||||
*/
|
|
||||||
HDF5File(int ind, uint32_t *maxf, int *nd, std::string *fname,
|
|
||||||
std::string *fpath, uint64_t *findex, bool *owenable, int *dindex,
|
|
||||||
int *nunits, uint64_t *nf, uint32_t *dr, uint32_t *portno,
|
|
||||||
uint32_t nx, uint32_t ny, bool *smode);
|
|
||||||
~HDF5File();
|
|
||||||
void SetNumberofPixels(uint32_t nx, uint32_t ny);
|
|
||||||
void CreateFile() override;
|
|
||||||
void CloseAllFiles() override;
|
|
||||||
void CloseCurrentDataFile() override;
|
|
||||||
void CloseMasterFile() override;
|
|
||||||
void WriteToFile(char *buffer, int bufferSize, uint64_t currentFrameNumber,
|
|
||||||
uint32_t numPacketsCaught) override;
|
|
||||||
void CreateMasterFile(MasterAttributes *attr) override;
|
|
||||||
void StartofAcquisition() override;
|
|
||||||
void EndofAcquisition(bool anyPacketsCaught, uint64_t numImagesCaught);
|
|
||||||
|
|
||||||
private:
|
|
||||||
void CloseFile(H5File *&fd, bool masterFile);
|
|
||||||
void WriteDataFile(uint64_t currentFrameNumber, char *buffer);
|
|
||||||
void WriteParameterDatasets(uint64_t currentFrameNumber,
|
|
||||||
sls_receiver_header *rheader);
|
|
||||||
void ExtendDataset();
|
|
||||||
void CreateDataFile();
|
|
||||||
void CreateMasterDataFile(MasterAttributes *attr);
|
|
||||||
void CreateVirtualDataFile(uint32_t maxFramesPerFile, uint64_t numf);
|
|
||||||
void LinkVirtualInMaster(std::string fname, std::string dsetname);
|
|
||||||
hid_t GetDataTypeinC(DataType dtype);
|
|
||||||
|
|
||||||
static std::mutex hdf5Lib;
|
|
||||||
|
|
||||||
H5File *masterfd;
|
|
||||||
/** Virtual File handle ( only file name because
|
|
||||||
code in C as H5Pset_virtual doesnt exist yet in C++) */
|
|
||||||
hid_t virtualfd;
|
|
||||||
H5File *filefd;
|
|
||||||
DataSpace *dataspace;
|
|
||||||
DataSet *dataset;
|
|
||||||
DataType datatype;
|
|
||||||
|
|
||||||
uint32_t nPixelsX;
|
|
||||||
uint32_t nPixelsY;
|
|
||||||
uint32_t numFramesInFile;
|
|
||||||
int numFilesinAcquisition;
|
|
||||||
|
|
||||||
std::vector<std::string> parameterNames;
|
|
||||||
std::vector<DataType> parameterDataTypes;
|
|
||||||
DataSpace *dataspace_para;
|
|
||||||
std::vector<DataSet *> dataset_para;
|
|
||||||
|
|
||||||
uint64_t extNumImages;
|
|
||||||
};
|
|
||||||
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user