detectors/slsDetectorPackage
25
0
Fork 0
mirror of https://github.com/slsdetectorgroup/slsDetectorPackage.git synced 2025-06-18 15:57:13 +02:00
Code Issues Actions Packages Releases Activity

H5 one dataset name (#484)

Browse Source 
* rename all datasets in hdf5 files to just 'data'

* removing the global qualifier H5

* update release notes
This commit is contained in:
Dhanya Thattil
2022-06-09 12:35:33 +02:00
committed by GitHub
parent 89aa0760c6
commit 8ca8185d41
12 changed files with 380 additions and 399 deletions
Download Patch File Download Diff File Expand all files Collapse all files

118
slsReceiverSoftware/src/MasterFileUtility.cpp
View File

@ -49,30 +49,29 @@ std::string CreateMasterBinaryFile(const std::string &filePath,
#ifdef HDF5C
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<::H5::H5File> fd{nullptr};
std::unique_ptr<H5::H5File> fd{nullptr};
try {
::H5::Exception::dontPrint(); // to handle errors
H5::Exception::dontPrint(); // to handle errors
::H5::FileAccPropList flist;
H5::FileAccPropList flist;
flist.setFcloseDegree(H5F_CLOSE_STRONG);
// open master file
::H5::H5File masterfd(masterFileName.c_str(), H5F_ACC_RDWR,
::H5::FileCreatPropList::DEFAULT, flist);
H5::H5File masterfd(masterFileName.c_str(), H5F_ACC_RDWR,
H5::FileCreatPropList::DEFAULT, flist);
// open data file
fd = make_unique<::H5::H5File>(dataFilename.c_str(), H5F_ACC_RDONLY,
::H5::FileCreatPropList::DEFAULT, flist);
fd = make_unique<H5::H5File>(dataFilename.c_str(), H5F_ACC_RDONLY,
H5::FileCreatPropList::DEFAULT, flist);
// create link for data dataset
::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(),
H5::DataSet dset = fd->openDataSet(DATASET_NAME);
std::string linkname = std::string("/entry/data/") + std::string(DATASET_NAME);
if (H5Lcreate_external(dataFilename.c_str(), DATASET_NAME,
masterfd.getLocId(), linkname.c_str(),
H5P_DEFAULT, H5P_DEFAULT) < 0) {
throw RuntimeError(
@ -81,7 +80,7 @@ void LinkHDF5FileInMaster(std::string &masterFileName,
// create link for parameter datasets
for (unsigned int i = 0; i < parameterNames.size(); ++i) {
::H5::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 +92,7 @@ void LinkHDF5FileInMaster(std::string &masterFileName,
}
fd->close();
masterfd.close();
} catch (const ::H5::Exception &error) {
} catch (const H5::Exception &error) {
error.printErrorStack();
if (fd != nullptr)
fd->close();
@ -118,38 +117,38 @@ std::string CreateMasterHDF5File(const std::string &filePath,
std::lock_guard<std::mutex> lock(*hdf5LibMutex);
std::unique_ptr<::H5::H5File> fd{nullptr};
std::unique_ptr<H5::H5File> fd{nullptr};
try {
::H5::Exception::dontPrint(); // to handle errors
H5::Exception::dontPrint(); // to handle errors
::H5::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<::H5::H5File>(fileName.c_str(), createFlags,
::H5::FileCreatPropList::DEFAULT, flist);
fd = make_unique<H5::H5File>(fileName.c_str(), createFlags,
H5::FileCreatPropList::DEFAULT, flist);
// attributes - version
double dValue = HDF5_WRITER_VERSION;
::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);
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
::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"));
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 ::H5::Exception &error) {
} catch (const H5::Exception &error) {
error.printErrorStack();
if (fd != nullptr)
fd->close();
@ -162,16 +161,16 @@ std::string CreateMasterHDF5File(const std::string &filePath,
return fileName;
}
std::array<std::string, 2> CreateVirtualHDF5File(
std::string CreateVirtualHDF5File(
const std::string &filePath, const std::string &fileNamePrefix,
const uint64_t fileIndex, const bool overWriteEnable, const bool silentMode,
const int modulePos, const int numUnitsPerReadout,
const uint32_t maxFramesPerFile, const uint64_t numImages,
const uint32_t maxFramesPerFile,
const uint32_t nPixelsX, const uint32_t nPixelsY,
const uint32_t dynamicRange, const uint64_t numImagesCaught,
const int numModX, const int numModY, const ::H5::DataType dataType,
const int numModX, const int numModY, const H5::DataType dataType,
const std::vector<std::string> parameterNames,
const std::vector<::H5::DataType> parameterDataTypes, std::mutex *hdf5LibMutex,
const std::vector<H5::DataType> parameterDataTypes, std::mutex *hdf5LibMutex,
bool gotthard25um) {
// virtual file name
@ -180,8 +179,6 @@ std::array<std::string, 2> CreateVirtualHDF5File(
<< "_" << fileIndex << ".h5";
std::string fileName = osfn.str();
std::string dataSetName = "data";
unsigned int paraSize = parameterNames.size();
uint64_t numModZ = numModX;
uint32_t nDimy = nPixelsY;
@ -189,42 +186,42 @@ std::array<std::string, 2> CreateVirtualHDF5File(
std::lock_guard<std::mutex> lock(*hdf5LibMutex);
std::unique_ptr<::H5::H5File> fd{nullptr};
std::unique_ptr<H5::H5File> fd{nullptr};
try {
::H5::Exception::dontPrint(); // to handle errors
H5::Exception::dontPrint(); // to handle errors
// file
::H5::FileAccPropList fapl;
H5::FileAccPropList fapl;
fapl.setFcloseDegree(H5F_CLOSE_STRONG);
if (!overWriteEnable)
fd = make_unique<::H5::H5File>(fileName.c_str(), H5F_ACC_EXCL,
::H5::FileCreatPropList::DEFAULT, fapl);
fd = make_unique<H5::H5File>(fileName.c_str(), H5F_ACC_EXCL,
H5::FileCreatPropList::DEFAULT, fapl);
else
fd = make_unique<::H5::H5File>(fileName.c_str(), H5F_ACC_TRUNC,
::H5::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;
::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);
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};
::H5::DataSpace vdsDataSpace(3, vdsDims, nullptr);
H5::DataSpace vdsDataSpace(3, vdsDims, nullptr);
hsize_t vdsDimsPara[2] = {numImagesCaught,
(unsigned int)numModY * numModZ};
::H5::DataSpace vdsDataSpacePara(2, vdsDimsPara, nullptr);
H5::DataSpace vdsDataSpacePara(2, vdsDimsPara, nullptr);
// property list (fill value and datatype)
int fill_value = -1;
::H5::DSetCreatPropList plist;
H5::DSetCreatPropList plist;
plist.setFillValue(dataType, &fill_value);
// property list for parameters (datatype)
std::vector<::H5::DSetCreatPropList> plistPara(paraSize);
std::vector<H5::DSetCreatPropList> plistPara(paraSize);
// hyperslab (files)
int numFiles = numImagesCaught / maxFramesPerFile;
@ -286,24 +283,17 @@ std::array<std::string, 2> CreateVirtualHDF5File(
p + 1, srcFileName.length() - p));
}
// source dataset name
std::ostringstream osfn;
osfn << "/data";
if (numImages > 1)
osfn << "_f" << std::setfill('0') << std::setw(12) << iFile;
std::string srcDatasetName = osfn.str();
// source dataspace
hsize_t srcDims[3] = {nDimx, nDimy, nDimz};
hsize_t srcDimsMax[3] = {H5S_UNLIMITED, nDimy, nDimz};
::H5::DataSpace srcDataSpace(3, srcDims, srcDimsMax);
H5::DataSpace srcDataSpace(3, srcDims, srcDimsMax);
hsize_t srcDimsPara[1] = {nDimx};
hsize_t srcDimsMaxPara[1] = {H5S_UNLIMITED};
::H5::DataSpace srcDataSpacePara(1, srcDimsPara, srcDimsMaxPara);
H5::DataSpace srcDataSpacePara(1, srcDimsPara, srcDimsMaxPara);
// mapping of property list
plist.setVirtual(vdsDataSpace, relative_srcFileName.c_str(),
srcDatasetName.c_str(), srcDataSpace);
DATASET_NAME, srcDataSpace);
for (unsigned int p = 0; p < paraSize; ++p) {
plistPara[p].setVirtual(
vdsDataSpacePara, relative_srcFileName.c_str(),
@ -325,17 +315,17 @@ std::array<std::string, 2> CreateVirtualHDF5File(
framesSaved += nDimx;
}
// datasets
::H5::DataSet vdsDataSet(fd->createDataSet(dataSetName.c_str(), dataType,
H5::DataSet vdsDataSet(fd->createDataSet(DATASET_NAME, dataType,
vdsDataSpace, plist));
for (unsigned int p = 0; p < paraSize; ++p) {
::H5::DataSet vdsDataSetPara(fd->createDataSet(
H5::DataSet vdsDataSetPara(fd->createDataSet(
parameterNames[p].c_str(), parameterDataTypes[p],
vdsDataSpacePara, plistPara[p]));
}
fd->close();
} catch (const ::H5::Exception &error) {
} catch (const H5::Exception &error) {
error.printErrorStack();
if (fd) {
fd->close();
@ -346,7 +336,7 @@ std::array<std::string, 2> CreateVirtualHDF5File(
if (!silentMode) {
LOG(logINFO) << "Virtual File: " << fileName;
}
return std::array<std::string, 2>{fileName, dataSetName};
return fileName;
}
#endif