detectors/slsDetectorPackage
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Format (#506)

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Formatted package
This commit is contained in:
Dhanya Thattil
2022-08-05 15:39:34 +02:00
committed by GitHub
parent 7173785b29
commit 6bf9dbf6d3
89 changed files with 1366 additions and 1210 deletions
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97
slsReceiverSoftware/src/HDF5DataFile.cpp
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@ -28,18 +28,18 @@ HDF5DataFile::HDF5DataFile(int index, std::mutex *hdf5Lib)
};
H5::StrType strdatatype(H5::PredType::C_S1, sizeof(bitset_storage));
parameterDataTypes = std::vector<H5::DataType>{
H5::PredType::STD_U64LE, H5::PredType::STD_U32LE, H5::PredType::STD_U32LE,
H5::PredType::STD_U64LE, H5::PredType::STD_U64LE, H5::PredType::STD_U16LE,
H5::PredType::STD_U16LE, H5::PredType::STD_U16LE, H5::PredType::STD_U16LE,
H5::PredType::STD_U32LE, H5::PredType::STD_U16LE, H5::PredType::STD_U8LE,
H5::PredType::STD_U64LE, H5::PredType::STD_U32LE,
H5::PredType::STD_U32LE, H5::PredType::STD_U64LE,
H5::PredType::STD_U64LE, H5::PredType::STD_U16LE,
H5::PredType::STD_U16LE, H5::PredType::STD_U16LE,
H5::PredType::STD_U16LE, H5::PredType::STD_U32LE,
H5::PredType::STD_U16LE, H5::PredType::STD_U8LE,
H5::PredType::STD_U8LE, strdatatype};
}
HDF5DataFile::~HDF5DataFile() { CloseFile(); }
std::string HDF5DataFile::GetFileName() const {
return fileName;
}
std::string HDF5DataFile::GetFileName() const { return fileName; }
uint32_t HDF5DataFile::GetFilesInAcquisition() const {
return numFilesInAcquisition;
@ -54,9 +54,7 @@ std::vector<H5::DataType> HDF5DataFile::GetParameterDataTypes() const {
return parameterDataTypes;
}
slsDetectorDefs::fileFormat HDF5DataFile::GetFileFormat() const {
return HDF5;
}
slsDetectorDefs::fileFormat HDF5DataFile::GetFileFormat() const { return HDF5; }
void HDF5DataFile::CloseFile() {
std::lock_guard<std::mutex> lock(*hdf5Lib);
@ -68,8 +66,7 @@ void HDF5DataFile::CloseFile() {
fd = nullptr;
}
} catch (const H5::Exception &error) {
LOG(logERROR) << "Could not close data HDF5 handles of index "
<< index;
LOG(logERROR) << "Could not close data HDF5 handles of index " << index;
error.printErrorStack();
}
if (dataSpace) {
@ -90,9 +87,8 @@ void HDF5DataFile::CloseFile() {
}
void HDF5DataFile::CreateFirstHDF5DataFile(
const std::string& fNamePrefix,
const uint64_t fIndex, const bool owEnable, const bool sMode,
const uint32_t uPortNumber, const uint32_t mFramesPerFile,
const std::string &fNamePrefix, const uint64_t fIndex, const bool owEnable,
const bool sMode, const uint32_t uPortNumber, const uint32_t mFramesPerFile,
const uint64_t nImages, const uint32_t nX, const uint32_t nY,
const uint32_t dr) {
@ -134,8 +130,7 @@ void HDF5DataFile::CreateFile() {
numFilesInAcquisition++;
std::ostringstream os;
os << fileNamePrefix << "_f" << subFileIndex
<< '_' << fileIndex << ".h5";
os << fileNamePrefix << "_f" << subFileIndex << '_' << fileIndex << ".h5";
fileName = os.str();
std::lock_guard<std::mutex> lock(*hdf5Lib);
@ -160,10 +155,10 @@ void HDF5DataFile::CreateFile() {
fd = nullptr;
if (!overWriteEnable)
fd = new H5::H5File(fileName.c_str(), H5F_ACC_EXCL,
H5::FileCreatPropList::DEFAULT, fapl);
H5::FileCreatPropList::DEFAULT, fapl);
else
fd = new H5::H5File(fileName.c_str(), H5F_ACC_TRUNC,
H5::FileCreatPropList::DEFAULT, fapl);
H5::FileCreatPropList::DEFAULT, fapl);
// attributes - version
double dValue = HDF5_WRITER_VERSION;
@ -193,14 +188,14 @@ void HDF5DataFile::CreateFile() {
H5::DSetCreatPropList plistPara;
int fill_value = -1;
plist.setFillValue(dataType, &fill_value);
//plistPara.setFillValue(dataType, &fill_value);
// plistPara.setFillValue(dataType, &fill_value);
plist.setChunk(DATA_RANK, dimsChunk);
plistPara.setChunk(PARA_RANK, dimsChunkPara);
// dataset
dataSet = nullptr;
dataSet = new H5::DataSet(fd->createDataSet(
DATASET_NAME, dataType, *dataSpace, plist));
dataSet = new H5::DataSet(
fd->createDataSet(DATASET_NAME, dataType, *dataSpace, plist));
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
H5::DataSet *ds = new H5::DataSet(fd->createDataSet(
parameterNames[i].c_str(), parameterDataTypes[i],
@ -210,8 +205,7 @@ void HDF5DataFile::CreateFile() {
} catch (const H5::Exception &error) {
error.printErrorStack();
CloseFile();
throw RuntimeError("Could not create HDF5 handles in object " +
index);
throw RuntimeError("Could not create HDF5 handles in object " + index);
}
if (!silentMode) {
LOG(logINFO) << "[" << udpPortNumber
@ -219,7 +213,10 @@ void HDF5DataFile::CreateFile() {
}
}
void HDF5DataFile::WriteToFile(char *imageData, sls_receiver_header& header, const int imageSize, const uint64_t currentFrameNumber, const uint32_t numPacketsCaught) {
void HDF5DataFile::WriteToFile(char *imageData, sls_receiver_header &header,
const int imageSize,
const uint64_t currentFrameNumber,
const uint32_t numPacketsCaught) {
// check if maxframesperfile = 0 for infinite
if (maxFramesPerFile && (numFramesInFile >= maxFramesPerFile)) {
@ -250,15 +247,15 @@ void HDF5DataFile::Convert12to16Bit(uint16_t *dst, uint8_t *src) {
}
void HDF5DataFile::WriteImageDatasets(const uint64_t currentFrameNumber,
char *buffer) {
char *buffer) {
// expand 12 bit to 16 bits
char *revBuffer = buffer;
if (dynamicRange == 12) {
revBuffer = (char *)malloc(EIGER_16_BIT_IMAGE_SIZE);
if (revBuffer == nullptr) {
throw RuntimeError("Could not allocate memory for 12 bit to "
"16 bit conversion in object " +
std::to_string(index));
"16 bit conversion in object " +
std::to_string(index));
}
Convert12to16Bit((uint16_t *)revBuffer, (uint8_t *)buffer);
}
@ -267,7 +264,7 @@ void HDF5DataFile::WriteImageDatasets(const uint64_t currentFrameNumber,
uint64_t nDimx =
((maxFramesPerFile == 0) ? currentFrameNumber
: currentFrameNumber % maxFramesPerFile);
: currentFrameNumber % maxFramesPerFile);
uint32_t nDimy = nPixelsY;
uint32_t nDimz = ((dynamicRange == 4) ? (nPixelsX / 2) : nPixelsX);
@ -291,7 +288,7 @@ void HDF5DataFile::WriteImageDatasets(const uint64_t currentFrameNumber,
LOG(logERROR) << "Could not write to file in object " << index;
error.printErrorStack();
throw RuntimeError("Could not write to file in object " +
std::to_string(index));
std::to_string(index));
}
}
@ -301,7 +298,7 @@ void HDF5DataFile::WriteParameterDatasets(const uint64_t currentFrameNumber,
uint64_t fnum =
((maxFramesPerFile == 0) ? currentFrameNumber
: currentFrameNumber % maxFramesPerFile);
: currentFrameNumber % maxFramesPerFile);
sls_detector_header header = rheader.detHeader;
hsize_t count[PARA_RANK] = {1};
@ -312,50 +309,50 @@ void HDF5DataFile::WriteParameterDatasets(const uint64_t currentFrameNumber,
dataSpacePara->selectHyperslab(H5S_SELECT_SET, count, start);
H5::DataSpace memspace(H5S_SCALAR);
dataSetPara[0]->write(&header.frameNumber, parameterDataTypes[0],
memspace, *dataSpacePara);
memspace, *dataSpacePara);
i = 1;
dataSetPara[1]->write(&header.expLength, parameterDataTypes[1],
memspace, *dataSpacePara);
memspace, *dataSpacePara);
i = 2;
dataSetPara[2]->write(&header.packetNumber, parameterDataTypes[2],
memspace, *dataSpacePara);
memspace, *dataSpacePara);
i = 3;
dataSetPara[3]->write(&header.bunchId, parameterDataTypes[3],
memspace, *dataSpacePara);
dataSetPara[3]->write(&header.bunchId, parameterDataTypes[3], memspace,
*dataSpacePara);
i = 4;
dataSetPara[4]->write(&header.timestamp, parameterDataTypes[4],
memspace, *dataSpacePara);
memspace, *dataSpacePara);
i = 5;
dataSetPara[5]->write(&header.modId, parameterDataTypes[5], memspace,
*dataSpacePara);
*dataSpacePara);
i = 6;
dataSetPara[6]->write(&header.row, parameterDataTypes[6], memspace,
*dataSpacePara);
*dataSpacePara);
i = 7;
dataSetPara[7]->write(&header.column, parameterDataTypes[7], memspace,
*dataSpacePara);
*dataSpacePara);
i = 8;
dataSetPara[8]->write(&header.reserved, parameterDataTypes[8],
memspace, *dataSpacePara);
dataSetPara[8]->write(&header.reserved, parameterDataTypes[8], memspace,
*dataSpacePara);
i = 9;
dataSetPara[9]->write(&header.debug, parameterDataTypes[9], memspace,
*dataSpacePara);
*dataSpacePara);
i = 10;
dataSetPara[10]->write(&header.roundRNumber, parameterDataTypes[10],
memspace, *dataSpacePara);
memspace, *dataSpacePara);
i = 11;
dataSetPara[11]->write(&header.detType, parameterDataTypes[11],
memspace, *dataSpacePara);
memspace, *dataSpacePara);
i = 12;
dataSetPara[12]->write(&header.version, parameterDataTypes[12],
memspace, *dataSpacePara);
memspace, *dataSpacePara);
i = 13;
// contiguous bitset
if (sizeof(sls_bitset) == sizeof(bitset_storage)) {
dataSetPara[13]->write((char *)&(rheader.packetsMask),
parameterDataTypes[13], memspace,
*dataSpacePara);
parameterDataTypes[13], memspace,
*dataSpacePara);
}
// not contiguous bitset
@ -368,7 +365,7 @@ void HDF5DataFile::WriteParameterDatasets(const uint64_t currentFrameNumber,
storage[i >> 3] |= (bits[i] << (i & 7));
// write bitmask
dataSetPara[13]->write((char *)storage, parameterDataTypes[13],
memspace, *dataSpacePara);
memspace, *dataSpacePara);
}
i = 14;
} catch (const H5::Exception &error) {
@ -403,7 +400,7 @@ void HDF5DataFile::ExtendDataset() {
} catch (const H5::Exception &error) {
error.printErrorStack();
throw RuntimeError("Could not extend dataset in object " +
std::to_string(index));
std::to_string(index));
}
if (!silentMode) {
LOG(logINFO) << index << " Extending HDF5 dataset by " << extNumImages