diff --git a/slsReceiverSoftware/src/DataProcessor.cpp b/slsReceiverSoftware/src/DataProcessor.cpp index 517f062e5..d5ad4203c 100644 --- a/slsReceiverSoftware/src/DataProcessor.cpp +++ b/slsReceiverSoftware/src/DataProcessor.cpp @@ -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); } diff --git a/slsReceiverSoftware/src/File.h b/slsReceiverSoftware/src/File.h index c9cebb276..259bfb1e7 100644 --- a/slsReceiverSoftware/src/File.h +++ b/slsReceiverSoftware/src/File.h @@ -7,15 +7,12 @@ #include -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 GetParameterNames() const { @@ -55,11 +52,11 @@ class File : private virtual slsDetectorDefs { return std::vector{}; }; - virtual std::vector GetParameterDataTypes() const { + virtual std::vector GetParameterDataTypes() const { LOG(logERROR) << "This is a generic function GetFilesInAcquisition that " "should be overloaded by a derived class"; - return std::vector{}; + return std::vector{}; }; virtual void CreateFirstHDF5DataFile( diff --git a/slsReceiverSoftware/src/HDF5DataFile.cpp b/slsReceiverSoftware/src/HDF5DataFile.cpp index 2d30b90c3..a3885f705 100644 --- a/slsReceiverSoftware/src/HDF5DataFile.cpp +++ b/slsReceiverSoftware/src/HDF5DataFile.cpp @@ -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{ - 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 HDF5DataFile::GetParameterNames() const { return parameterNames_; } -std::vector HDF5DataFile::GetParameterDataTypes() const { +std::vector<::H5::DataType> HDF5DataFile::GetParameterDataTypes() const { return parameterDataTypes_; } void HDF5DataFile::CloseFile() { std::lock_guard 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 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_)); diff --git a/slsReceiverSoftware/src/HDF5DataFile.h b/slsReceiverSoftware/src/HDF5DataFile.h index 7c0805ea7..7f2fdb56b 100644 --- a/slsReceiverSoftware/src/HDF5DataFile.h +++ b/slsReceiverSoftware/src/HDF5DataFile.h @@ -16,9 +16,9 @@ class HDF5DataFile : private virtual slsDetectorDefs, public File { std::array GetFileAndDatasetName() const override; uint32_t GetFilesInAcquisition() const override; - DataType GetPDataType() const override; + ::H5::DataType GetPDataType() const override; std::vector GetParameterNames() const override; - std::vector 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 dataSetPara_{nullptr}; + ::H5::DataSpace *dataSpacePara_{nullptr}; + std::vector<::H5::DataSet *> dataSetPara_{nullptr}; std::vector parameterNames_; - std::vector parameterDataTypes_; + std::vector<::H5::DataType> parameterDataTypes_; uint32_t subFileIndex_{0}; uint32_t numFramesInFile_{0}; diff --git a/slsReceiverSoftware/src/MasterAttributes.cpp b/slsReceiverSoftware/src/MasterAttributes.cpp index 8de7e2f9c..b39921f4a 100644 --- a/slsReceiverSoftware/src/MasterAttributes.cpp +++ b/slsReceiverSoftware/src/MasterAttributes.cpp @@ -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 + 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); diff --git a/slsReceiverSoftware/src/MasterAttributes.h b/slsReceiverSoftware/src/MasterAttributes.h index 5fbb0a41a..904512061 100644 --- a/slsReceiverSoftware/src/MasterAttributes.h +++ b/slsReceiverSoftware/src/MasterAttributes.h @@ -11,16 +11,16 @@ #include #include +#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 *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 *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 *w); #ifdef HDF5C - void WriteGotthardHDF5Attributes(H5File *fd, Group *group); + void WriteGotthardHDF5Attributes(::H5::H5File *fd, ::H5::Group *group); #endif void GetJungfrauBinaryAttributes( rapidjson::PrettyWriter *w); #ifdef HDF5C - void WriteJungfrauHDF5Attributes(H5File *fd, Group *group); + void WriteJungfrauHDF5Attributes(::H5::H5File *fd, ::H5::Group *group); #endif void GetEigerBinaryAttributes( rapidjson::PrettyWriter *w); #ifdef HDF5C - void WriteEigerHDF5Attributes(H5File *fd, Group *group); + void WriteEigerHDF5Attributes(::H5::H5File *fd, ::H5::Group *group); #endif void GetMythen3BinaryAttributes( rapidjson::PrettyWriter *w); #ifdef HDF5C - void WriteMythen3HDF5Attributes(H5File *fd, Group *group); + void WriteMythen3HDF5Attributes(::H5::H5File *fd, ::H5::Group *group); #endif void GetGotthard2BinaryAttributes( rapidjson::PrettyWriter *w); #ifdef HDF5C - void WriteGotthard2HDF5Attributes(H5File *fd, Group *group); + void WriteGotthard2HDF5Attributes(::H5::H5File *fd, ::H5::Group *group); #endif void GetMoenchBinaryAttributes( rapidjson::PrettyWriter *w); #ifdef HDF5C - void WriteMoenchHDF5Attributes(H5File *fd, Group *group); + void WriteMoenchHDF5Attributes(::H5::H5File *fd, ::H5::Group *group); #endif void GetCtbBinaryAttributes(rapidjson::PrettyWriter *w); #ifdef HDF5C - void WriteCtbHDF5Attributes(H5File *fd, Group *group); + void WriteCtbHDF5Attributes(::H5::H5File *fd, ::H5::Group *group); #endif }; diff --git a/slsReceiverSoftware/src/MasterFileUtility.cpp b/slsReceiverSoftware/src/MasterFileUtility.cpp index 22ba0400d..b0052e82f 100644 --- a/slsReceiverSoftware/src/MasterFileUtility.cpp +++ b/slsReceiverSoftware/src/MasterFileUtility.cpp @@ -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 parameterNames, +void LinkHDF5FileInMaster(std::string &masterFileName, + std::string &dataFilename, + std::string &dataSetname, + std::vector parameterNames, const bool silentMode, std::mutex *hdf5LibMutex) { std::lock_guard lock(*hdf5LibMutex); - std::unique_ptr 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(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 lock(*hdf5LibMutex); - std::unique_ptr 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(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 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 parameterNames, - const std::vector parameterDataTypes, std::mutex *hdf5LibMutex, + const std::vector<::H5::DataType> parameterDataTypes, std::mutex *hdf5LibMutex, bool gotthard25um) { // virtual file name @@ -189,42 +189,42 @@ std::array CreateVirtualHDF5File( std::lock_guard lock(*hdf5LibMutex); - std::unique_ptr 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(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(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 plistPara(paraSize); + std::vector<::H5::DSetCreatPropList> plistPara(paraSize); // hyperslab (files) int numFiles = numImagesCaught / maxFramesPerFile; @@ -296,10 +296,10 @@ std::array 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 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(); diff --git a/slsReceiverSoftware/src/MasterFileUtility.h b/slsReceiverSoftware/src/MasterFileUtility.h index 4a4b0e136..3aa2427a5 100644 --- a/slsReceiverSoftware/src/MasterFileUtility.h +++ b/slsReceiverSoftware/src/MasterFileUtility.h @@ -4,17 +4,13 @@ #include "MasterAttributes.h" +#include + namespace sls { namespace masterFileUtility { -#ifdef HDF5C -#include "H5Cpp.h" -#include -#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 parameterNames, +void LinkHDF5FileInMaster(std::string &masterFileName, + std::string &dataFilename, + std::string &dataSetname, + std::vector parameterNames, const bool silentMode, std::mutex *hdf5LibMutex); std::string CreateMasterHDF5File(const std::string &filePath, @@ -45,9 +41,9 @@ std::array 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 parameterNames, - const std::vector parameterDataTypes, std::mutex *hdf5LibMutex, + const std::vector<::H5::DataType> parameterDataTypes, std::mutex *hdf5LibMutex, bool gotthard25um); #endif } // namespace masterFileUtility