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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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104
slsReceiverSoftware/src/MasterFileUtility.cpp
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@ -47,30 +47,30 @@ std::string CreateMasterBinaryFile(const std::string &filePath,
}
#ifdef HDF5C
void LinkHDF5FileInMaster(const std::string &masterFileName,
const std::string &dataFilename,
const std::string &dataSetname,
const std::vector<std::string> parameterNames,
void LinkHDF5FileInMaster(std::string &masterFileName,
std::string &dataFilename,
std::string &dataSetname,
std::vector<std::string> parameterNames,
const bool silentMode, std::mutex *hdf5LibMutex) {
std::lock_guard<std::mutex> lock(*hdf5LibMutex);
std::unique_ptr<H5File> fd{nullptr};
std::unique_ptr<::H5::H5File> fd{nullptr};
try {
Exception::dontPrint(); // to handle errors
::H5::Exception::dontPrint(); // to handle errors
FileAccPropList flist;
::H5::FileAccPropList flist;
flist.setFcloseDegree(H5F_CLOSE_STRONG);
// open master file
H5File masterfd(masterFileName.c_str(), H5F_ACC_RDWR,
FileCreatPropList::DEFAULT, flist);
::H5::H5File masterfd(masterFileName.c_str(), H5F_ACC_RDWR,
::H5::FileCreatPropList::DEFAULT, flist);
// open data file
fd = make_unique<H5File>(dataFilename.c_str(), H5F_ACC_RDONLY,
FileCreatPropList::DEFAULT, flist);
fd = make_unique<::H5::H5File>(dataFilename.c_str(), H5F_ACC_RDONLY,
::H5::FileCreatPropList::DEFAULT, flist);
// create link for data dataset
DataSet dset = fd->openDataSet(dataSetname.c_str());
::H5::DataSet dset = fd->openDataSet(dataSetname.c_str());
std::string linkname = std::string("/entry/data/") + dataSetname;
if (H5Lcreate_external(dataFilename.c_str(), dataSetname.c_str(),
masterfd.getLocId(), linkname.c_str(),
@ -81,7 +81,7 @@ void LinkHDF5FileInMaster(const std::string &masterFileName,
// create link for parameter datasets
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
DataSet pDset = fd->openDataSet(parameterNames[i].c_str());
::H5::DataSet pDset = fd->openDataSet(parameterNames[i].c_str());
linkname = std::string("/entry/data/") + parameterNames[i];
if (H5Lcreate_external(dataFilename.c_str(),
parameterNames[i].c_str(),
@ -93,7 +93,7 @@ void LinkHDF5FileInMaster(const std::string &masterFileName,
}
fd->close();
masterfd.close();
} catch (const Exception &error) {
} catch (const ::H5::Exception &error) {
error.printErrorStack();
if (fd != nullptr)
fd->close();
@ -118,38 +118,38 @@ std::string CreateMasterHDF5File(const std::string &filePath,
std::lock_guard<std::mutex> lock(*hdf5LibMutex);
std::unique_ptr<H5File> fd{nullptr};
std::unique_ptr<::H5::H5File> fd{nullptr};
try {
Exception::dontPrint(); // to handle errors
::H5::Exception::dontPrint(); // to handle errors
FileAccPropList flist;
::H5::FileAccPropList flist;
flist.setFcloseDegree(H5F_CLOSE_STRONG);
unsigned int createFlags = H5F_ACC_EXCL;
if (overWriteEnable) {
createFlags = H5F_ACC_TRUNC;
}
fd = make_unique<H5File>(fileName.c_str(), createFlags,
FileCreatPropList::DEFAULT, flist);
fd = make_unique<::H5::H5File>(fileName.c_str(), createFlags,
::H5::FileCreatPropList::DEFAULT, flist);
// 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);
// Create a group in the file
Group group1(fd->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"));
::H5::Group group1(fd->createGroup("entry"));
::H5::Group group2(group1.createGroup("data"));
::H5::Group group3(group1.createGroup("instrument"));
::H5::Group group4(group3.createGroup("beam"));
::H5::Group group5(group3.createGroup("detector"));
::H5::Group group6(group1.createGroup("sample"));
attr->WriteHDF5Attributes(fd.get(), &group5);
fd->close();
} catch (const Exception &error) {
} catch (const ::H5::Exception &error) {
error.printErrorStack();
if (fd != nullptr)
fd->close();
@ -169,9 +169,9 @@ std::array<std::string, 2> CreateVirtualHDF5File(
const uint32_t maxFramesPerFile, const uint64_t numImages,
const uint32_t nPixelsX, const uint32_t nPixelsY,
const uint32_t dynamicRange, const uint64_t numImagesCaught,
const int numModX, const int numModY, const DataType dataType,
const int numModX, const int numModY, const ::H5::DataType dataType,
const std::vector<std::string> parameterNames,
const std::vector<DataType> parameterDataTypes, std::mutex *hdf5LibMutex,
const std::vector<::H5::DataType> parameterDataTypes, std::mutex *hdf5LibMutex,
bool gotthard25um) {
// virtual file name
@ -189,42 +189,42 @@ std::array<std::string, 2> CreateVirtualHDF5File(
std::lock_guard<std::mutex> lock(*hdf5LibMutex);
std::unique_ptr<H5File> fd{nullptr};
std::unique_ptr<::H5::H5File> fd{nullptr};
try {
Exception::dontPrint(); // to handle errors
::H5::Exception::dontPrint(); // to handle errors
// file
FileAccPropList fapl;
::H5::FileAccPropList fapl;
fapl.setFcloseDegree(H5F_CLOSE_STRONG);
if (!overWriteEnable)
fd = make_unique<H5File>(fileName.c_str(), H5F_ACC_EXCL,
FileCreatPropList::DEFAULT, fapl);
fd = make_unique<::H5::H5File>(fileName.c_str(), H5F_ACC_EXCL,
::H5::FileCreatPropList::DEFAULT, fapl);
else
fd = make_unique<H5File>(fileName.c_str(), H5F_ACC_TRUNC,
FileCreatPropList::DEFAULT, fapl);
fd = make_unique<::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);
// virtual dataspace
hsize_t vdsDims[3] = {numImagesCaught, numModY * nDimy,
numModZ * nDimz};
DataSpace vdsDataSpace(3, vdsDims, nullptr);
::H5::DataSpace vdsDataSpace(3, vdsDims, nullptr);
hsize_t vdsDimsPara[2] = {numImagesCaught,
(unsigned int)numModY * numModZ};
DataSpace vdsDataSpacePara(2, vdsDimsPara, nullptr);
::H5::DataSpace vdsDataSpacePara(2, vdsDimsPara, nullptr);
// property list (fill value and datatype)
int fill_value = -1;
DSetCreatPropList plist;
::H5::DSetCreatPropList plist;
plist.setFillValue(dataType, &fill_value);
// property list for parameters (datatype)
std::vector<DSetCreatPropList> plistPara(paraSize);
std::vector<::H5::DSetCreatPropList> plistPara(paraSize);
// hyperslab (files)
int numFiles = numImagesCaught / maxFramesPerFile;
@ -296,10 +296,10 @@ std::array<std::string, 2> CreateVirtualHDF5File(
// source dataspace
hsize_t srcDims[3] = {nDimx, nDimy, nDimz};
hsize_t srcDimsMax[3] = {H5S_UNLIMITED, nDimy, nDimz};
DataSpace srcDataSpace(3, srcDims, srcDimsMax);
::H5::DataSpace srcDataSpace(3, srcDims, srcDimsMax);
hsize_t srcDimsPara[1] = {nDimx};
hsize_t srcDimsMaxPara[1] = {H5S_UNLIMITED};
DataSpace srcDataSpacePara(1, srcDimsPara, srcDimsMaxPara);
::H5::DataSpace srcDataSpacePara(1, srcDimsPara, srcDimsMaxPara);
// mapping of property list
plist.setVirtual(vdsDataSpace, relative_srcFileName.c_str(),
@ -325,17 +325,17 @@ std::array<std::string, 2> CreateVirtualHDF5File(
framesSaved += nDimx;
}
// datasets
DataSet vdsDataSet(fd->createDataSet(dataSetName.c_str(), dataType,
::H5::DataSet vdsDataSet(fd->createDataSet(dataSetName.c_str(), dataType,
vdsDataSpace, plist));
for (unsigned int p = 0; p < paraSize; ++p) {
DataSet vdsDataSetPara(fd->createDataSet(
::H5::DataSet vdsDataSetPara(fd->createDataSet(
parameterNames[p].c_str(), parameterDataTypes[p],
vdsDataSpacePara, plistPara[p]));
}
fd->close();
} catch (const Exception &error) {
} catch (const ::H5::Exception &error) {
error.printErrorStack();
if (fd) {
fd->close();