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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
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GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 376 additions and 381 deletions
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4
slsReceiverSoftware/src/DataProcessor.cpp
View File

@ -211,14 +211,14 @@ void DataProcessor::LinkFileInMaster(const std::string &masterFileName,
if (receiverRoiEnabled_) {
throw std::runtime_error("Should not be here, roi with hdf5 virtual should throw.");
}
std::string fname{virtualFileName}, datasetName{virtualDatasetName};
std::string fname{virtualFileName}, datasetName{virtualDatasetName}, masterfname{masterFileName};
// if no virtual file, link data file
if (virtualFileName.empty()) {
auto res = dataFile_->GetFileAndDatasetName();
fname = res[0];
datasetName = res[1];
}
masterFileUtility::LinkHDF5FileInMaster(masterFileName, fname, datasetName,
masterFileUtility::LinkHDF5FileInMaster(masterfname, fname, datasetName,
dataFile_->GetParameterNames(),
silentMode, hdf5LibMutex);
}

15
slsReceiverSoftware/src/File.h
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@ -7,15 +7,12 @@
#include <array>
namespace sls {
#ifdef HDF5C
#include "H5Cpp.h"
#ifndef H5_NO_NAMESPACE
using namespace H5;
#endif
#endif
namespace sls {
struct MasterAttributes;
class File : private virtual slsDetectorDefs {
@ -42,10 +39,10 @@ class File : private virtual slsDetectorDefs {
return 0;
};
virtual DataType GetPDataType() const {
virtual H5::DataType GetPDataType() const {
LOG(logERROR) << "This is a generic function GetPDataType that "
"should be overloaded by a derived class";
return PredType::STD_U16LE;
return H5::PredType::STD_U16LE;
}
virtual std::vector<std::string> GetParameterNames() const {
@ -55,11 +52,11 @@ class File : private virtual slsDetectorDefs {
return std::vector<std::string>{};
};
virtual std::vector<DataType> GetParameterDataTypes() const {
virtual std::vector<H5::DataType> GetParameterDataTypes() const {
LOG(logERROR)
<< "This is a generic function GetFilesInAcquisition that "
"should be overloaded by a derived class";
return std::vector<DataType>{};
return std::vector<H5::DataType>{};
};
virtual void CreateFirstHDF5DataFile(

82
slsReceiverSoftware/src/HDF5DataFile.cpp
View File

@ -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_));

18
slsReceiverSoftware/src/HDF5DataFile.h
View File

@ -16,9 +16,9 @@ class HDF5DataFile : private virtual slsDetectorDefs, public File {
std::array<std::string, 2> GetFileAndDatasetName() const override;
uint32_t GetFilesInAcquisition() const override;
DataType GetPDataType() const override;
::H5::DataType GetPDataType() const override;
std::vector<std::string> GetParameterNames() const override;
std::vector<DataType> GetParameterDataTypes() const override;
std::vector<::H5::DataType> GetParameterDataTypes() const override;
void CloseFile() override;
@ -45,17 +45,17 @@ class HDF5DataFile : private virtual slsDetectorDefs, public File {
int index_;
std::mutex *hdf5Lib_;
H5File *fd_{nullptr};
::H5::H5File *fd_{nullptr};
std::string fileName_;
std::string dataSetName_;
DataSpace *dataSpace_{nullptr};
DataSet *dataSet_{nullptr};
DataType dataType_{PredType::STD_U16LE};
::H5::DataSpace *dataSpace_{nullptr};
::H5::DataSet *dataSet_{nullptr};
::H5::DataType dataType_{::H5::PredType::STD_U16LE};
DataSpace *dataSpacePara_{nullptr};
std::vector<DataSet *> dataSetPara_{nullptr};
::H5::DataSpace *dataSpacePara_{nullptr};
std::vector<::H5::DataSet *> dataSetPara_{nullptr};
std::vector<std::string> parameterNames_;
std::vector<DataType> parameterDataTypes_;
std::vector<::H5::DataType> parameterDataTypes_;
uint32_t subFileIndex_{0};
uint32_t numFramesInFile_{0};

430
slsReceiverSoftware/src/MasterAttributes.cpp
View File

@ -1,6 +1,8 @@
// SPDX-License-Identifier: LGPL-3.0-or-other
// Copyright (C) 2021 Contributors to the SLS Detector Package
#include "MasterAttributes.h"
#include <time.h>
namespace sls {
@ -39,7 +41,7 @@ void MasterAttributes::GetBinaryAttributes(
}
#ifdef HDF5C
void MasterAttributes::WriteHDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
WriteCommonHDF5Attributes(fd, group);
switch (detType) {
case slsDetectorDefs::GOTTHARD:
@ -167,40 +169,40 @@ void MasterAttributes::GetFinalBinaryAttributes(
}
#ifdef HDF5C
void MasterAttributes::WriteCommonHDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteCommonHDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
char c[1024]{};
// version
{
double version = BINARY_WRITER_VERSION;
DataSpace dataspace = DataSpace(H5S_SCALAR);
Attribute attribute =
fd->createAttribute("Version", PredType::NATIVE_DOUBLE, dataspace);
attribute.write(PredType::NATIVE_DOUBLE, &version);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::Attribute attribute =
fd->createAttribute("Version", ::H5::PredType::NATIVE_DOUBLE, dataspace);
attribute.write(::H5::PredType::NATIVE_DOUBLE, &version);
}
// timestamp
{
time_t t = time(nullptr);
StrType strdatatype(PredType::C_S1, 256);
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
time_t t = std::time(nullptr);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Timestamp", strdatatype, dataspace);
strcpy_safe(c, std::string(ctime(&t)));
dataset.write(c, strdatatype);
}
// detector type
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Detector Type", strdatatype, dataspace);
strcpy_safe(c, ToString(detType));
dataset.write(c, strdatatype);
}
// timing mode
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Timing Mode", strdatatype, dataspace);
strcpy_safe(c, ToString(timingMode));
dataset.write(c, strdatatype);
@ -208,27 +210,27 @@ void MasterAttributes::WriteCommonHDF5Attributes(H5File *fd, Group *group) {
// TODO: make this into an array?
// geometry x
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Geometry in x axis",
PredType::NATIVE_INT, dataspace);
dataset.write(&geometry.x, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Geometry in x axis",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&geometry.x, ::H5::PredType::NATIVE_INT);
}
// geometry y
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Geometry in y axis",
PredType::NATIVE_INT, dataspace);
dataset.write(&geometry.y, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Geometry in y axis",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&geometry.y, ::H5::PredType::NATIVE_INT);
}
// Image Size
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Image Size", PredType::NATIVE_INT, dataspace);
dataset.write(&imageSize, PredType::NATIVE_INT);
DataSpace dataspaceAttr = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
Attribute attribute =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Image Size", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&imageSize, ::H5::PredType::NATIVE_INT);
::H5::DataSpace dataspaceAttr = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::Attribute attribute =
dataset.createAttribute("Unit", strdatatype, dataspaceAttr);
strcpy_safe(c, "bytes");
attribute.write(strdatatype, c);
@ -236,335 +238,335 @@ void MasterAttributes::WriteCommonHDF5Attributes(H5File *fd, Group *group) {
// TODO: make this into an array?
// npixels x
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Number of pixels in x axis",
PredType::NATIVE_INT, dataspace);
dataset.write(&nPixels.x, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Number of pixels in x axis",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&nPixels.x, ::H5::PredType::NATIVE_INT);
}
// npixels y
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Number of pixels in y axis",
PredType::NATIVE_INT, dataspace);
dataset.write(&nPixels.y, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Number of pixels in y axis",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&nPixels.y, ::H5::PredType::NATIVE_INT);
}
// Maximum frames per file
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Maximum frames per file",
PredType::NATIVE_INT, dataspace);
dataset.write(&maxFramesPerFile, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Maximum frames per file",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&maxFramesPerFile, ::H5::PredType::NATIVE_INT);
}
// Frame Discard Policy
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset = group->createDataSet("Frame Discard Policy",
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset = group->createDataSet("Frame Discard Policy",
strdatatype, dataspace);
strcpy_safe(c, ToString(frameDiscardMode));
dataset.write(c, strdatatype);
}
// Frame Padding
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Frame Padding",
PredType::NATIVE_INT, dataspace);
dataset.write(&framePadding, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Frame Padding",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&framePadding, ::H5::PredType::NATIVE_INT);
}
// Scan Parameters
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Scan Parameters", strdatatype, dataspace);
strcpy_safe(c, ToString(scanParams));
dataset.write(c, strdatatype);
}
// Total Frames
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Total Frames",
PredType::STD_U64LE, dataspace);
dataset.write(&totalFrames, PredType::STD_U64LE);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Total Frames",
::H5::PredType::STD_U64LE, dataspace);
dataset.write(&totalFrames, ::H5::PredType::STD_U64LE);
}
// Receiver Roi xmin
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("receiver roi xmin",
PredType::NATIVE_INT, dataspace);
dataset.write(&receiverRoi.xmin, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("receiver roi xmin",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&receiverRoi.xmin, ::H5::PredType::NATIVE_INT);
}
// Receiver Roi xmax
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("receiver roi xmax",
PredType::NATIVE_INT, dataspace);
dataset.write(&receiverRoi.xmax, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("receiver roi xmax",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&receiverRoi.xmax, ::H5::PredType::NATIVE_INT);
}
// Receiver Roi ymin
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("receiver roi ymin",
PredType::NATIVE_INT, dataspace);
dataset.write(&receiverRoi.ymin, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("receiver roi ymin",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&receiverRoi.ymin, ::H5::PredType::NATIVE_INT);
}
// Receiver Roi ymax
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("receiver roi ymax",
PredType::NATIVE_INT, dataspace);
dataset.write(&receiverRoi.ymax, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("receiver roi ymax",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&receiverRoi.ymax, ::H5::PredType::NATIVE_INT);
}
}
void MasterAttributes::WriteFinalHDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteFinalHDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
char c[1024]{};
// Total Frames in file
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Frames in File",
PredType::STD_U64LE, dataspace);
dataset.write(&framesInFile, PredType::STD_U64LE);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Frames in File",
::H5::PredType::STD_U64LE, dataspace);
dataset.write(&framesInFile, ::H5::PredType::STD_U64LE);
}
// additional json header
if (!additionalJsonHeader.empty()) {
std::string json = ToString(additionalJsonHeader);
StrType strdatatype(PredType::C_S1, json.length());
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Additional JSON Header",
::H5::StrType strdatatype(::H5::PredType::C_S1, json.length());
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Additional JSON Header",
strdatatype, dataspace);
strcpy_safe(c, ToString(additionalJsonHeader));
dataset.write(c, strdatatype);
}
}
void MasterAttributes::WriteHDF5Exptime(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
void MasterAttributes::WriteHDF5Exptime(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Exposure Time", strdatatype, dataspace);
char c[1024]{};
strcpy_safe(c, ToString(exptime));
dataset.write(c, strdatatype);
}
void MasterAttributes::WriteHDF5Period(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
void MasterAttributes::WriteHDF5Period(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Acquisition Period", strdatatype, dataspace);
char c[1024]{};
strcpy_safe(c, ToString(period));
dataset.write(c, strdatatype);
}
void MasterAttributes::WriteHDF5DynamicRange(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Dynamic Range", PredType::NATIVE_INT, dataspace);
dataset.write(&dynamicRange, PredType::NATIVE_INT);
DataSpace dataspaceAttr = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
Attribute attribute =
void MasterAttributes::WriteHDF5DynamicRange(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Dynamic Range", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&dynamicRange, ::H5::PredType::NATIVE_INT);
::H5::DataSpace dataspaceAttr = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::Attribute attribute =
dataset.createAttribute("Unit", strdatatype, dataspaceAttr);
char c[1024] = "bits";
attribute.write(strdatatype, c);
}
void MasterAttributes::WriteHDF5TenGiga(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Ten Giga Enable",
PredType::NATIVE_INT, dataspace);
dataset.write(&tenGiga, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5TenGiga(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Ten Giga Enable",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&tenGiga, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5ROI(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5ROI(::H5::H5File *fd, ::H5::Group *group) {
// Roi xmin
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("roi xmin", PredType::NATIVE_INT, dataspace);
dataset.write(&detectorRoi.xmin, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("roi xmin", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&detectorRoi.xmin, ::H5::PredType::NATIVE_INT);
}
// Roi xmax
{
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("roi xmax", PredType::NATIVE_INT, dataspace);
dataset.write(&detectorRoi.xmax, PredType::NATIVE_INT);
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("roi xmax", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&detectorRoi.xmax, ::H5::PredType::NATIVE_INT);
}
}
void MasterAttributes::WriteHDF5NumUDPInterfaces(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Number of UDP Interfaces",
PredType::NATIVE_INT, dataspace);
dataset.write(&numUDPInterfaces, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5NumUDPInterfaces(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Number of UDP Interfaces",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&numUDPInterfaces, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5ReadNRows(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Number of rows", PredType::NATIVE_INT, dataspace);
dataset.write(&readNRows, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5ReadNRows(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Number of rows", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&readNRows, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5ThresholdEnergy(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5ThresholdEnergy(::H5::H5File *fd, ::H5::Group *group) {
char c[1024]{};
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Threshold Energy",
PredType::NATIVE_INT, dataspace);
dataset.write(&thresholdEnergyeV, PredType::NATIVE_INT);
DataSpace dataspaceAttr = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
Attribute attribute =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Threshold Energy",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&thresholdEnergyeV, ::H5::PredType::NATIVE_INT);
::H5::DataSpace dataspaceAttr = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::Attribute attribute =
dataset.createAttribute("Unit", strdatatype, dataspaceAttr);
strcpy_safe(c, "eV");
attribute.write(strdatatype, c);
}
void MasterAttributes::WriteHDF5ThresholdEnergies(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5ThresholdEnergies(::H5::H5File *fd, ::H5::Group *group) {
char c[1024]{};
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 1024);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 1024);
::H5::DataSet dataset =
group->createDataSet("Threshold Energies", strdatatype, dataspace);
strcpy_safe(c, ToString(thresholdAllEnergyeV));
dataset.write(c, strdatatype);
}
void MasterAttributes::WriteHDF5SubExpTime(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5SubExpTime(::H5::H5File *fd, ::H5::Group *group) {
char c[1024]{};
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Sub Exposure Time", strdatatype, dataspace);
strcpy_safe(c, ToString(subExptime));
dataset.write(c, strdatatype);
}
void MasterAttributes::WriteHDF5SubPeriod(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5SubPeriod(::H5::H5File *fd, ::H5::Group *group) {
char c[1024]{};
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Sub Period", strdatatype, dataspace);
strcpy_safe(c, ToString(subPeriod));
dataset.write(c, strdatatype);
}
void MasterAttributes::WriteHDF5SubQuad(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Quad", PredType::NATIVE_INT, dataspace);
dataset.write(&quad, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5SubQuad(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Quad", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&quad, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5RateCorrections(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5RateCorrections(::H5::H5File *fd, ::H5::Group *group) {
char c[1024]{};
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 1024);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 1024);
::H5::DataSet dataset =
group->createDataSet("Rate Corrections", strdatatype, dataspace);
strcpy_safe(c, ToString(ratecorr));
dataset.write(c, strdatatype);
}
void MasterAttributes::WriteHDF5CounterMask(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Counter Mask", PredType::STD_U32LE, dataspace);
dataset.write(&counterMask, PredType::STD_U32LE);
void MasterAttributes::WriteHDF5CounterMask(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Counter Mask", ::H5::PredType::STD_U32LE, dataspace);
dataset.write(&counterMask, ::H5::PredType::STD_U32LE);
}
void MasterAttributes::WriteHDF5ExptimeArray(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5ExptimeArray(::H5::H5File *fd, ::H5::Group *group) {
for (int i = 0; i != 3; ++i) {
char c[1024]{};
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Exposure Time1", strdatatype, dataspace);
strcpy_safe(c, ToString(exptimeArray[i]));
dataset.write(c, strdatatype);
}
}
void MasterAttributes::WriteHDF5GateDelayArray(H5File *fd, Group *group) {
void MasterAttributes::WriteHDF5GateDelayArray(::H5::H5File *fd, ::H5::Group *group) {
for (int i = 0; i != 3; ++i) {
char c[1024]{};
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Gate Delay1", strdatatype, dataspace);
strcpy_safe(c, ToString(gateDelayArray[i]));
dataset.write(c, strdatatype);
}
}
void MasterAttributes::WriteHDF5Gates(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Gates", PredType::STD_U32LE, dataspace);
dataset.write(&gates, PredType::STD_U32LE);
void MasterAttributes::WriteHDF5Gates(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Gates", ::H5::PredType::STD_U32LE, dataspace);
dataset.write(&gates, ::H5::PredType::STD_U32LE);
}
void MasterAttributes::WriteHDF5BurstMode(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
StrType strdatatype(PredType::C_S1, 256);
DataSet dataset =
void MasterAttributes::WriteHDF5BurstMode(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::StrType strdatatype(::H5::PredType::C_S1, 256);
::H5::DataSet dataset =
group->createDataSet("Burst Mode", strdatatype, dataspace);
char c[1024]{};
strcpy_safe(c, ToString(burstMode));
dataset.write(c, strdatatype);
}
void MasterAttributes::WriteHDF5AdcMask(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("ADC Mask", PredType::NATIVE_INT, dataspace);
dataset.write(&adcmask, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5AdcMask(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("ADC Mask", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&adcmask, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5AnalogFlag(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Analog Flag", PredType::NATIVE_INT, dataspace);
dataset.write(&analog, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5AnalogFlag(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Analog Flag", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&analog, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5AnalogSamples(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Analog Samples", PredType::NATIVE_INT, dataspace);
dataset.write(&analogSamples, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5AnalogSamples(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Analog Samples", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&analogSamples, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5DigitalFlag(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Digital Flag", PredType::NATIVE_INT, dataspace);
dataset.write(&digital, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5DigitalFlag(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Digital Flag", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&digital, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5DigitalSamples(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Digital Samples",
PredType::NATIVE_INT, dataspace);
dataset.write(&digitalSamples, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5DigitalSamples(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Digital Samples",
::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&digitalSamples, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5DbitOffset(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset =
group->createDataSet("Dbit Offset", PredType::NATIVE_INT, dataspace);
dataset.write(&dbitoffset, PredType::NATIVE_INT);
void MasterAttributes::WriteHDF5DbitOffset(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset =
group->createDataSet("Dbit Offset", ::H5::PredType::NATIVE_INT, dataspace);
dataset.write(&dbitoffset, ::H5::PredType::NATIVE_INT);
}
void MasterAttributes::WriteHDF5DbitList(H5File *fd, Group *group) {
DataSpace dataspace = DataSpace(H5S_SCALAR);
DataSet dataset = group->createDataSet("Dbit Bitset List",
PredType::STD_U64LE, dataspace);
dataset.write(&dbitlist, PredType::STD_U64LE);
void MasterAttributes::WriteHDF5DbitList(::H5::H5File *fd, ::H5::Group *group) {
::H5::DataSpace dataspace = ::H5::DataSpace(H5S_SCALAR);
::H5::DataSet dataset = group->createDataSet("Dbit Bitset List",
::H5::PredType::STD_U64LE, dataspace);
dataset.write(&dbitlist, ::H5::PredType::STD_U64LE);
}
#endif
@ -584,7 +586,7 @@ void MasterAttributes::GetGotthardBinaryAttributes(
};
#ifdef HDF5C
void MasterAttributes::WriteGotthardHDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteGotthardHDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
MasterAttributes::WriteHDF5Exptime(fd, group);
MasterAttributes::WriteHDF5Period(fd, group);
MasterAttributes::WriteHDF5ROI(fd, group);
@ -604,7 +606,7 @@ void MasterAttributes::GetJungfrauBinaryAttributes(
}
#ifdef HDF5C
void MasterAttributes::WriteJungfrauHDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteJungfrauHDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
MasterAttributes::WriteHDF5Exptime(fd, group);
MasterAttributes::WriteHDF5Period(fd, group);
MasterAttributes::WriteHDF5NumUDPInterfaces(fd, group);
@ -637,7 +639,7 @@ void MasterAttributes::GetEigerBinaryAttributes(
}
#ifdef HDF5C
void MasterAttributes::WriteEigerHDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteEigerHDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
MasterAttributes::WriteHDF5DynamicRange(fd, group);
MasterAttributes::WriteHDF5TenGiga(fd, group);
MasterAttributes::WriteHDF5Exptime(fd, group);
@ -676,7 +678,7 @@ void MasterAttributes::GetMythen3BinaryAttributes(
}
#ifdef HDF5C
void MasterAttributes::WriteMythen3HDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteMythen3HDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
MasterAttributes::WriteHDF5DynamicRange(fd, group);
MasterAttributes::WriteHDF5TenGiga(fd, group);
MasterAttributes::WriteHDF5Period(fd, group);
@ -699,7 +701,7 @@ void MasterAttributes::GetGotthard2BinaryAttributes(
}
#ifdef HDF5C
void MasterAttributes::WriteGotthard2HDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteGotthard2HDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
MasterAttributes::WriteHDF5Exptime(fd, group);
MasterAttributes::WriteHDF5Period(fd, group);
MasterAttributes::WriteHDF5BurstMode(fd, group);
@ -721,7 +723,7 @@ void MasterAttributes::GetMoenchBinaryAttributes(
}
#ifdef HDF5C
void MasterAttributes::WriteMoenchHDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteMoenchHDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
MasterAttributes::WriteHDF5Exptime(fd, group);
MasterAttributes::WriteHDF5Period(fd, group);
MasterAttributes::WriteHDF5TenGiga(fd, group);
@ -755,7 +757,7 @@ void MasterAttributes::GetCtbBinaryAttributes(
}
#ifdef HDF5C
void MasterAttributes::WriteCtbHDF5Attributes(H5File *fd, Group *group) {
void MasterAttributes::WriteCtbHDF5Attributes(::H5::H5File *fd, ::H5::Group *group) {
MasterAttributes::WriteHDF5Exptime(fd, group);
MasterAttributes::WriteHDF5Period(fd, group);
MasterAttributes::WriteHDF5TenGiga(fd, group);

82
slsReceiverSoftware/src/MasterAttributes.h
View File

@ -11,16 +11,16 @@
#include <rapidjson/stringbuffer.h>
#include <chrono>
#ifdef HDF5C
#include "H5Cpp.h"
#endif
namespace sls {
using ns = std::chrono::nanoseconds;
#ifdef HDF5C
#include "H5Cpp.h"
#ifndef H5_NO_NAMESPACE
using namespace H5;
#endif
#endif
class MasterAttributes {
public:
@ -71,7 +71,7 @@ class MasterAttributes {
void
GetBinaryAttributes(rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteHDF5Attributes(H5File *fd, Group *group);
void WriteHDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
#endif
void GetCommonBinaryAttributes(
@ -79,75 +79,75 @@ class MasterAttributes {
void GetFinalBinaryAttributes(
rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteCommonHDF5Attributes(H5File *fd, Group *group);
void WriteFinalHDF5Attributes(H5File *fd, Group *group);
void WriteHDF5Exptime(H5File *fd, Group *group);
void WriteHDF5Period(H5File *fd, Group *group);
void WriteHDF5DynamicRange(H5File *fd, Group *group);
void WriteHDF5TenGiga(H5File *fd, Group *group);
void WriteHDF5ROI(H5File *fd, Group *group);
void WriteHDF5NumUDPInterfaces(H5File *fd, Group *group);
void WriteHDF5ReadNRows(H5File *fd, Group *group);
void WriteHDF5ThresholdEnergy(H5File *fd, Group *group);
void WriteHDF5ThresholdEnergies(H5File *fd, Group *group);
void WriteHDF5SubExpTime(H5File *fd, Group *group);
void WriteHDF5SubPeriod(H5File *fd, Group *group);
void WriteHDF5SubQuad(H5File *fd, Group *group);
void WriteHDF5RateCorrections(H5File *fd, Group *group);
void WriteHDF5CounterMask(H5File *fd, Group *group);
void WriteHDF5ExptimeArray(H5File *fd, Group *group);
void WriteHDF5GateDelayArray(H5File *fd, Group *group);
void WriteHDF5Gates(H5File *fd, Group *group);
void WriteHDF5BurstMode(H5File *fd, Group *group);
void WriteHDF5AdcMask(H5File *fd, Group *group);
void WriteHDF5AnalogFlag(H5File *fd, Group *group);
void WriteHDF5AnalogSamples(H5File *fd, Group *group);
void WriteHDF5DigitalFlag(H5File *fd, Group *group);
void WriteHDF5DigitalSamples(H5File *fd, Group *group);
void WriteHDF5DbitOffset(H5File *fd, Group *group);
void WriteHDF5DbitList(H5File *fd, Group *group);
void WriteCommonHDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
void WriteFinalHDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5Exptime(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5Period(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5DynamicRange(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5TenGiga(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5ROI(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5NumUDPInterfaces(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5ReadNRows(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5ThresholdEnergy(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5ThresholdEnergies(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5SubExpTime(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5SubPeriod(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5SubQuad(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5RateCorrections(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5CounterMask(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5ExptimeArray(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5GateDelayArray(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5Gates(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5BurstMode(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5AdcMask(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5AnalogFlag(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5AnalogSamples(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5DigitalFlag(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5DigitalSamples(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5DbitOffset(::H5::H5File *fd, ::H5::Group *group);
void WriteHDF5DbitList(::H5::H5File *fd, ::H5::Group *group);
#endif
void GetGotthardBinaryAttributes(
rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteGotthardHDF5Attributes(H5File *fd, Group *group);
void WriteGotthardHDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
#endif
void GetJungfrauBinaryAttributes(
rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteJungfrauHDF5Attributes(H5File *fd, Group *group);
void WriteJungfrauHDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
#endif
void GetEigerBinaryAttributes(
rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteEigerHDF5Attributes(H5File *fd, Group *group);
void WriteEigerHDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
#endif
void GetMythen3BinaryAttributes(
rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteMythen3HDF5Attributes(H5File *fd, Group *group);
void WriteMythen3HDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
#endif
void GetGotthard2BinaryAttributes(
rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteGotthard2HDF5Attributes(H5File *fd, Group *group);
void WriteGotthard2HDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
#endif
void GetMoenchBinaryAttributes(
rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteMoenchHDF5Attributes(H5File *fd, Group *group);
void WriteMoenchHDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
#endif
void
GetCtbBinaryAttributes(rapidjson::PrettyWriter<rapidjson::StringBuffer> *w);
#ifdef HDF5C
void WriteCtbHDF5Attributes(H5File *fd, Group *group);
void WriteCtbHDF5Attributes(::H5::H5File *fd, ::H5::Group *group);
#endif
};

104
slsReceiverSoftware/src/MasterFileUtility.cpp
View File

@ -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();

22
slsReceiverSoftware/src/MasterFileUtility.h
View File

@ -4,17 +4,13 @@
#include "MasterAttributes.h"
#include <mutex>
namespace sls {
namespace masterFileUtility {
#ifdef HDF5C
#include "H5Cpp.h"
#include <mutex>
#ifndef H5_NO_NAMESPACE
using namespace H5;
#endif
#endif
std::string CreateMasterBinaryFile(const std::string &filePath,
@ -25,10 +21,10 @@ std::string CreateMasterBinaryFile(const std::string &filePath,
MasterAttributes *attr);
#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::string CreateMasterHDF5File(const std::string &filePath,
@ -45,9 +41,9 @@ 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);
#endif
} // namespace masterFileUtility