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Hdf5 para (#505)

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* incorrect dimensions for virtual hdf5 parameter set

* fix for corner case bug in hdf5 virtual parameter dataset when frames caught is not a multiple of framesperfile

* reafctoring for readability and error prone hard numbers
This commit is contained in:
Dhanya Thattil
2022-08-05 09:09:00 +02:00
committed by GitHub
parent 89e293cb5a
commit 7173785b29
4 changed files with 71 additions and 61 deletions
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67
slsReceiverSoftware/src/HDF5DataFile.cpp
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@ -172,41 +172,39 @@ void HDF5DataFile::CreateFile() {
"version", H5::PredType::NATIVE_DOUBLE, dataspace_attr);
attribute.write(H5::PredType::NATIVE_DOUBLE, &dValue);
// dataspace
hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
dataSpace = nullptr;
dataSpace = new H5::DataSpace(3, srcdims, srcdimsmax);
// dataset
// fill value
H5::DSetCreatPropList plist;
int fill_value = -1;
plist.setFillValue(dataType, &fill_value);
// dimensions
hsize_t dims[DATA_RANK] = {nDimx, nDimy, nDimz};
hsize_t dimsMax[DATA_RANK] = {H5S_UNLIMITED, nDimy, nDimz};
hsize_t dimsPara[PARA_RANK] = {nDimx};
hsize_t dimsMaxPara[PARA_RANK] = {H5S_UNLIMITED};
// 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);
hsize_t dimsChunk[DATA_RANK] = {MAX_CHUNKED_IMAGES, nDimy, nDimz};
hsize_t dimsChunkPara[PARA_RANK] = {MAX_CHUNKED_IMAGES};
// dataspace
dataSpace = nullptr;
dataSpace = new H5::DataSpace(DATA_RANK, dims, dimsMax);
dataSpacePara = nullptr;
dataSpacePara = new H5::DataSpace(PARA_RANK, dimsPara, dimsMaxPara);
// property list
H5::DSetCreatPropList plist;
H5::DSetCreatPropList plistPara;
int fill_value = -1;
plist.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));
// create parameter datasets
hsize_t dims[1] = {nDimx};
hsize_t dimsmax[1] = {H5S_UNLIMITED};
dataSpacePara = nullptr;
dataSpacePara = new H5::DataSpace(1, dims, dimsmax);
// always create chunked dataset as unlimited is only
// supported with chunked layout
H5::DSetCreatPropList paralist;
hsize_t chunkpara_dims[3] = {MAX_CHUNKED_IMAGES};
paralist.setChunk(1, chunkpara_dims);
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
H5::DataSet *ds = new H5::DataSet(fd->createDataSet(
parameterNames[i].c_str(), parameterDataTypes[i],
*dataSpacePara, paralist));
*dataSpacePara, plistPara));
dataSetPara.push_back(ds);
}
} catch (const H5::Exception &error) {
@ -237,7 +235,7 @@ void HDF5DataFile::WriteToFile(char *imageData, sls_receiver_header& header, con
ExtendDataset();
}
WriteDataFile(currentFrameNumber, imageData);
WriteImageDatasets(currentFrameNumber, imageData);
WriteParameterDatasets(currentFrameNumber, header);
}
@ -251,7 +249,7 @@ void HDF5DataFile::Convert12to16Bit(uint16_t *dst, uint8_t *src) {
}
}
void HDF5DataFile::WriteDataFile(const uint64_t currentFrameNumber,
void HDF5DataFile::WriteImageDatasets(const uint64_t currentFrameNumber,
char *buffer) {
// expand 12 bit to 16 bits
char *revBuffer = buffer;
@ -306,8 +304,8 @@ void HDF5DataFile::WriteParameterDatasets(const uint64_t currentFrameNumber,
: currentFrameNumber % maxFramesPerFile);
sls_detector_header header = rheader.detHeader;
hsize_t count[1] = {1};
hsize_t start[1] = {fnum};
hsize_t count[PARA_RANK] = {1};
hsize_t start[PARA_RANK] = {fnum};
int i = 0;
try {
H5::Exception::dontPrint(); // to handle errors
@ -387,18 +385,17 @@ void HDF5DataFile::ExtendDataset() {
try {
H5::Exception::dontPrint(); // to handle errors
hsize_t dims[3];
hsize_t dims[DATA_RANK];
dataSpace->getSimpleExtentDims(dims);
dims[0] += numImages;
dataSet->extend(dims);
delete dataSpace;
dataSpace = nullptr;
dataSpace = new H5::DataSpace(dataSet->getSpace());
hsize_t dims_para[1] = {dims[0]};
hsize_t dimsPara[PARA_RANK] = {dims[0]};
for (unsigned int i = 0; i < dataSetPara.size(); ++i)
dataSetPara[i]->extend(dims_para);
dataSetPara[i]->extend(dimsPara);
delete dataSpacePara;
dataSpacePara = nullptr;
dataSpacePara = new H5::DataSpace(dataSetPara[0]->getSpace());