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Hdf5fix (#483)

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* hdf5 fix for string reference

* fix hdf5 compilation after namespace change
This commit is contained in:
Dhanya Thattil
2022-06-09 11:42:32 +02:00
committed by GitHub
parent 3cee36a3db
commit 89aa0760c6
8 changed files with 376 additions and 381 deletions
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82
slsReceiverSoftware/src/HDF5DataFile.cpp
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@ -26,13 +26,13 @@ HDF5DataFile::HDF5DataFile(int index, std::mutex *hdf5Lib)
"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};
::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_U8LE, strdatatype};
}
HDF5DataFile::~HDF5DataFile() { CloseFile(); }
@ -45,25 +45,25 @@ uint32_t HDF5DataFile::GetFilesInAcquisition() const {
return numFilesInAcquisition_;
}
DataType HDF5DataFile::GetPDataType() const { return dataType_; }
::H5::DataType HDF5DataFile::GetPDataType() const { return dataType_; }
std::vector<std::string> HDF5DataFile::GetParameterNames() const {
return parameterNames_;
}
std::vector<DataType> HDF5DataFile::GetParameterDataTypes() const {
std::vector<::H5::DataType> HDF5DataFile::GetParameterDataTypes() const {
return parameterDataTypes_;
}
void HDF5DataFile::CloseFile() {
std::lock_guard<std::mutex> lock(*hdf5Lib_);
try {
Exception::dontPrint(); // to handle errors
::H5::Exception::dontPrint(); // to handle errors
if (fd_) {
fd_->close();
delete fd_;
fd_ = nullptr;
}
} catch (const Exception &error) {
} catch (const ::H5::Exception &error) {
LOG(logERROR) << "Could not close data HDF5 handles of index "
<< index_;
error.printErrorStack();
@ -116,13 +116,13 @@ void HDF5DataFile::CreateFirstHDF5DataFile(
switch (dynamicRange_) {
case 12:
case 16:
dataType_ = PredType::STD_U16LE;
dataType_ = ::H5::PredType::STD_U16LE;
break;
case 32:
dataType_ = PredType::STD_U32LE;
dataType_ = ::H5::PredType::STD_U32LE;
break;
default:
dataType_ = PredType::STD_U8LE;
dataType_ = ::H5::PredType::STD_U8LE;
break;
}
@ -153,31 +153,31 @@ void HDF5DataFile::CreateFile() {
uint32_t nDimz = ((dynamicRange_ == 4) ? (nPixelsX_ / 2) : nPixelsX_);
try {
Exception::dontPrint(); // to handle errors
::H5::Exception::dontPrint(); // to handle errors
// file
FileAccPropList fapl;
::H5::FileAccPropList fapl;
fapl.setFcloseDegree(H5F_CLOSE_STRONG);
fd_ = nullptr;
if (!overWriteEnable_)
fd_ = new H5File(fileName_.c_str(), H5F_ACC_EXCL,
FileCreatPropList::DEFAULT, fapl);
fd_ = new ::H5::H5File(fileName_.c_str(), H5F_ACC_EXCL,
::H5::FileCreatPropList::DEFAULT, fapl);
else
fd_ = new H5File(fileName_.c_str(), H5F_ACC_TRUNC,
FileCreatPropList::DEFAULT, fapl);
fd_ = new ::H5::H5File(fileName_.c_str(), H5F_ACC_TRUNC,
::H5::FileCreatPropList::DEFAULT, fapl);
// attributes - version
double dValue = HDF5_WRITER_VERSION;
DataSpace dataspace_attr = DataSpace(H5S_SCALAR);
Attribute attribute = fd_->createAttribute(
"version", PredType::NATIVE_DOUBLE, dataspace_attr);
attribute.write(PredType::NATIVE_DOUBLE, &dValue);
::H5::DataSpace dataspace_attr = ::H5::DataSpace(H5S_SCALAR);
::H5::Attribute attribute = fd_->createAttribute(
"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 DataSpace(3, srcdims, srcdimsmax);
dataSpace_ = new ::H5::DataSpace(3, srcdims, srcdimsmax);
// dataset name
std::ostringstream osfn;
@ -188,7 +188,7 @@ void HDF5DataFile::CreateFile() {
// dataset
// fill value
DSetCreatPropList plist;
::H5::DSetCreatPropList plist;
int fill_value = -1;
plist.setFillValue(dataType_, &fill_value);
// always create chunked dataset as unlimited is only
@ -196,28 +196,28 @@ void HDF5DataFile::CreateFile() {
hsize_t chunk_dims[3] = {MAX_CHUNKED_IMAGES, nDimy, nDimz};
plist.setChunk(3, chunk_dims);
dataSet_ = nullptr;
dataSet_ = new DataSet(fd_->createDataSet(
dataSet_ = new ::H5::DataSet(fd_->createDataSet(
dataSetName_.c_str(), dataType_, *dataSpace_, plist));
// create parameter datasets
hsize_t dims[1] = {nDimx};
hsize_t dimsmax[1] = {H5S_UNLIMITED};
dataSpacePara_ = nullptr;
dataSpacePara_ = new DataSpace(1, dims, dimsmax);
dataSpacePara_ = new ::H5::DataSpace(1, dims, dimsmax);
// always create chunked dataset as unlimited is only
// supported with chunked layout
DSetCreatPropList paralist;
::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) {
DataSet *ds = new DataSet(fd_->createDataSet(
::H5::DataSet *ds = new ::H5::DataSet(fd_->createDataSet(
parameterNames_[i].c_str(), parameterDataTypes_[i],
*dataSpacePara_, paralist));
dataSetPara_.push_back(ds);
}
} catch (const Exception &error) {
} catch (const ::H5::Exception &error) {
error.printErrorStack();
CloseFile();
throw RuntimeError("Could not create HDF5 handles in object " +
@ -287,16 +287,16 @@ void HDF5DataFile::WriteDataFile(const uint64_t currentFrameNumber,
hsize_t start[3] = {nDimx, 0, 0};
hsize_t dims2[2] = {nDimy, nDimz};
try {
Exception::dontPrint(); // to handle errors
::H5::Exception::dontPrint(); // to handle errors
dataSpace_->selectHyperslab(H5S_SELECT_SET, count, start);
DataSpace memspace(2, dims2);
::H5::DataSpace memspace(2, dims2);
dataSet_->write(revBuffer, dataType_, memspace, *dataSpace_);
memspace.close();
if (dynamicRange_ == 12) {
free(revBuffer);
}
} catch (const Exception &error) {
} catch (const ::H5::Exception &error) {
if (dynamicRange_ == 12) {
free(revBuffer);
}
@ -320,9 +320,9 @@ void HDF5DataFile::WriteParameterDatasets(const uint64_t currentFrameNumber,
hsize_t start[1] = {fnum};
int i = 0;
try {
Exception::dontPrint(); // to handle errors
::H5::Exception::dontPrint(); // to handle errors
dataSpacePara_->selectHyperslab(H5S_SELECT_SET, count, start);
DataSpace memspace(H5S_SCALAR);
::H5::DataSpace memspace(H5S_SCALAR);
dataSetPara_[0]->write(&header.frameNumber, parameterDataTypes_[0],
memspace, *dataSpacePara_);
i = 1;
@ -383,7 +383,7 @@ void HDF5DataFile::WriteParameterDatasets(const uint64_t currentFrameNumber,
memspace, *dataSpacePara_);
}
i = 14;
} catch (const Exception &error) {
} catch (const ::H5::Exception &error) {
error.printErrorStack();
throw RuntimeError(
"Could not write parameters (index:" + std::to_string(i) +
@ -395,7 +395,7 @@ void HDF5DataFile::ExtendDataset() {
std::lock_guard<std::mutex> lock(*hdf5Lib_);
try {
Exception::dontPrint(); // to handle errors
::H5::Exception::dontPrint(); // to handle errors
hsize_t dims[3];
dataSpace_->getSimpleExtentDims(dims);
@ -404,16 +404,16 @@ void HDF5DataFile::ExtendDataset() {
dataSet_->extend(dims);
delete dataSpace_;
dataSpace_ = nullptr;
dataSpace_ = new DataSpace(dataSet_->getSpace());
dataSpace_ = new ::H5::DataSpace(dataSet_->getSpace());
hsize_t dims_para[1] = {dims[0]};
for (unsigned int i = 0; i < dataSetPara_.size(); ++i)
dataSetPara_[i]->extend(dims_para);
delete dataSpacePara_;
dataSpacePara_ = nullptr;
dataSpacePara_ = new DataSpace(dataSetPara_[0]->getSpace());
dataSpacePara_ = new ::H5::DataSpace(dataSetPara_[0]->getSpace());
} catch (const Exception &error) {
} catch (const ::H5::Exception &error) {
error.printErrorStack();
throw RuntimeError("Could not extend dataset in object " +
std::to_string(index_));