Class File¶

Defined in File h5ppFile.h

Class Documentation¶

class h5pp::File¶

Writes and reads data to a binary hdf5-file.

Public Functions

File()¶

File(const File &other)¶

File(const std::string &filePath_, h5pp::FilePermission permission_ = h5pp::FilePermission::RENAME, size_t logLevel_ = 2, bool logTimestamp_ = false)¶

File(const std::string &filePath_, unsigned int H5F_ACC_FLAGS, size_t logLevel_ = 2, bool logTimestamp_ = false)¶

~File()¶

File &operator=(const File &other)¶

void flush()¶

hid::h5f openFileHandle() const¶

h5pp::FilePermission getFilePermission() const¶

std::string getFileName() const¶

std::string getFilePath() const¶

void setFilePermission(h5pp::FilePermission permission_)¶

void setDriver_sec2()¶

void setDriver_stdio()¶

void setDriver_core(bool writeOnClose = true, size_t bytesPerMalloc = 10240000)¶

fs::path copyFileTo(const std::string &targetFilePath, const FilePermission &perm = FilePermission::COLLISION_FAIL) const¶

fs::path moveFileTo(const std::string &targetFilePath, const FilePermission &perm = FilePermission::COLLISION_FAIL)¶

void copyLinkToFile(const std::string &localLinkPath, const std::string &targetFilePath, const std::string &targetLinkPath, const FilePermission &targetFileCreatePermission = FilePermission::READWRITE) const¶

void copyLinkFromFile(const std::string &localLinkPath, const std::string &sourceFilePath, const std::string &sourceLinkPath)¶

template<typename h5x_tgt, typename = h5pp::type::sfinae::enable_if_is_h5_loc<h5x_tgt>> void copyLinkToLocation(const std::string &localLinkPath, const h5x_tgt &targetLocationId, const std::string &targetLinkPath) const¶

template<typename h5x_src, typename = h5pp::type::sfinae::enable_if_is_h5_loc<h5x_src>> void copyLinkFromLocation(const std::string &localLinkPath, const h5x_src &sourceLocationId, const std::string &sourceLinkPath)¶

size_t getLogLevel() const¶

void setLogLevel(size_t logLevelZeroToFive)¶

void setCompressionLevel(unsigned int compressionLevelZeroToNine)¶

unsigned int getCompressionLevel() const¶

unsigned int getCompressionLevel(std::optional<unsigned int> desiredCompressionLevel) const¶

void createGroup(std::string_view group_relative_name)¶

void resizeDataset(DsetInfo &info, const DimsType &newDimensions, std::optional<h5pp::ResizeMode> mode_override = std::nullopt)¶

template<typename DsetDimsType = std::initializer_list<hsize_t>, typename = h5pp::type::sfinae::enable_if_is_integral_iterable_or_num<DsetDimsType>> DsetInfo resizeDataset(std::string_view dsetPath, const DsetDimsType &newDimensions, std::optional<h5pp::ResizeMode> mode = std::nullopt)¶

void createDataset(DsetInfo &info)¶

DsetInfo createDataset(const Options &options)¶

DsetInfo createDataset(std::optional<hid::h5t> h5Type, std::string_view dsetPath, const DimsType &dsetDims, std::optional<H5D_layout_t> h5Layout = std::nullopt, const OptDimsType &dsetDimsChunk = std::nullopt, const OptDimsType &dsetDimsMax = std::nullopt, std::optional<unsigned int> compression = std::nullopt)¶

template<typename DataType> DsetInfo createDataset(const DataType &data, const Options &options)¶

template<typename DataType> DsetInfo createDataset(const DataType &data, std::string_view dsetPath, const OptDimsType &dataDims = std::nullopt, std::optional<H5D_layout_t> h5Layout = std::nullopt, const OptDimsType &dsetDimsChunk = std::nullopt, const OptDimsType &dsetDimsMax = std::nullopt, std::optional<unsigned int> compression = std::nullopt)¶

template<typename DataType> void writeDataset(const DataType &data, DsetInfo &dsetInfo, const Options &options = Options())¶

template<typename DataType> void writeDataset(const DataType &data, const DataInfo &dataInfo, DsetInfo &dsetInfo)¶

template<typename DataType> DsetInfo writeDataset(const DataType &data, const Options &options)¶

template<typename DataType> DsetInfo writeDataset(const DataType &data, std::string_view dsetPath, const OptDimsType &dataDims = std::nullopt, std::optional<H5D_layout_t> h5Layout = std::nullopt, const OptDimsType &dsetDimsChunk = std::nullopt, const OptDimsType &dsetDimsMax = std::nullopt, std::optional<hid::h5t> h5Type = std::nullopt, std::optional<ResizeMode> resizeMode = std::nullopt, std::optional<unsigned int> compression = std::nullopt)¶

Parameters

data: Eigen, stl-like object or pointer to data buffer
dsetPath: Path to HDF5 dataset relative to the file root
dataDims: Data dimensions hint. Required for pointer data
h5Layout: (On create) Layout of dataset. Choose between H5D_CHUNKED,H5D_COMPACT and H5D_CONTIGUOUS
dsetDimsChunk: (On create) Chunking dimensions. Only valid for H5D_CHUNKED datasets
dsetDimsMax: (On create) Maximum dimensions. Only valid for H5D_CHUNKED datasets
h5Type: (On create) Type of dataset. Override automatic type detection.
resizeMode: Type of resizing if needed. Choose INCREASE_ONLY, RESIZE_TO_FIT,DO_NOT_RESIZE
compression: (On create) Compression level 0-9, 0 = off, 9 is gives best compression and is slowest

template<typename DataType> DsetInfo writeDataset(const DataType &data, std::string_view dsetPath, hid::h5t &h5Type, const OptDimsType &dataDims = std::nullopt, std::optional<H5D_layout_t> h5Layout = std::nullopt, const OptDimsType &dsetDimsChunk = std::nullopt, const OptDimsType &dsetDimsMax = std::nullopt, std::optional<ResizeMode> resizeMode = std::nullopt, std::optional<unsigned int> compression = std::nullopt)¶

Parameters

data: Eigen, stl-like object or pointer to data buffer
dsetPath: Path to HDF5 dataset relative to the file root
h5Type: (On create) Type of dataset. Override automatic type detection.
dataDims: Data dimensions hint. Required for pointer data
h5Layout: (On create) Layout of dataset. Choose between H5D_CHUNKED,H5D_COMPACT and H5D_CONTIGUOUS
dsetDimsChunk: (On create) Chunking dimensions. Only valid for H5D_CHUNKED datasets
dsetDimsMax: (On create) Maximum dimensions. Only valid for H5D_CHUNKED datasets
resizeMode: Type of resizing if needed. Choose INCREASE_ONLY, RESIZE_TO_FIT,DO_NOT_RESIZE
compression: (On create) Compression level 0-9, 0 = off, 9 is gives best compression and is slowest

template<typename DataType> DsetInfo writeDataset(const DataType &data, std::string_view dsetPath, H5D_layout_t h5Layout, const OptDimsType &dataDims = std::nullopt, const OptDimsType &dsetDimsChunk = std::nullopt, const OptDimsType &dsetDimsMax = std::nullopt, std::optional<hid::h5t> h5Type = std::nullopt, std::optional<ResizeMode> resizeMode = std::nullopt, std::optional<unsigned int> compression = std::nullopt)¶

Parameters

data: Eigen, stl-like object or pointer to data buffer
dsetPath: Path to HDF5 dataset relative to the file root
h5Layout: (On create) Layout of dataset. Choose between H5D_CHUNKED,H5D_COMPACT and H5D_CONTIGUOUS
dataDims: Data dimensions hint. Required for pointer data
dsetDimsChunk: (On create) Chunking dimensions. Only valid for H5D_CHUNKED datasets
dsetDimsMax: (On create) Maximum dimensions. Only valid for H5D_CHUNKED datasets
h5Type: (On create) Type of dataset. Override automatic type detection.
resizeMode: Type of resizing if needed. Choose INCREASE_ONLY, RESIZE_TO_FIT,DO_NOT_RESIZE
compression: (On create) Compression level 0-9, 0 = off, 9 is gives best compression and is slowest

template<typename DataType> DsetInfo writeDataset_compact(const DataType &data, std::string_view dsetPath, const OptDimsType &dataDims = std::nullopt, std::optional<hid::h5t> h5Type = std::nullopt)¶

template<typename DataType> DsetInfo writeDataset_contiguous(const DataType &data, std::string_view dsetPath, const OptDimsType &dataDims = std::nullopt, std::optional<hid::h5t> h5Type = std::nullopt)¶

template<typename DataType> DsetInfo writeDataset_chunked(const DataType &data, std::string_view dsetPath, const OptDimsType &dataDims = std::nullopt, const OptDimsType &dsetDimsChunk = std::nullopt, const OptDimsType &dsetDimsMax = std::nullopt, std::optional<hid::h5t> h5Type = std::nullopt, std::optional<unsigned int> compression = std::nullopt)¶

void writeSymbolicLink(std::string_view src_path, std::string_view tgt_path)¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> void readDataset(DataType &data, const DataInfo &dataInfo, const DsetInfo &dsetInfo) const¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> DataType readDataset(const DataInfo &dataInfo, const DsetInfo &dsetInfo) const¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> void readDataset(DataType &data, const DsetInfo &dsetInfo, const Options &options = Options()) const¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> DataType readDataset(DsetInfo &dsetInfo, const Options &options = Options()) const¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> DataType readDataset(DsetInfo &dsetInfo, const DimsType &dataDims) const¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> void readDataset(DataType &data, const Options &options) const¶

template<typename DataType> void readDataset(DataType &data, std::string_view dsetPath, const OptDimsType &dataDims = std::nullopt) const¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> DataType readDataset(std::string_view datasetPath, const OptDimsType &dataDims = std::nullopt) const¶

template<typename DataType> void appendToDataset(DataType &data, const DataInfo &dataInfo, DsetInfo &dsetInfo, size_t axis)¶

template<typename DataType> void appendToDataset(DataType &data, DsetInfo &dsetInfo, size_t axis, const OptDimsType &dataDims = std::nullopt)¶

template<typename DataType> DsetInfo appendToDataset(DataType &data, size_t axis, const Options &options = Options())¶

template<typename DataType> DsetInfo appendToDataset(DataType &data, std::string_view dsetPath, size_t axis, const OptDimsType &dataDims = std::nullopt)¶

void createAttribute(AttrInfo &attrInfo)¶

template<typename DataType> AttrInfo createAttribute(const DataType &data, const Options &options)¶

template<typename DataType> void createAttribute(const DataType &data, const DimsType &dataDims, std::string_view attrName, std::string_view linkPath)¶

template<typename DataType> void writeAttribute(const DataType &data, const Options &options)¶

template<typename DataType> void writeAttribute(const DataType &data, std::string_view attrName, std::string_view linkPath, const OptDimsType &dataDims = std::nullopt, std::optional<hid::h5t> h5Type = std::nullopt)¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> void readAttribute(DataType &data, const Options &options) const¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> void readAttribute(DataType &data, std::string_view attrName, std::string_view linkPath, const OptDimsType &dataDims = std::nullopt) const¶

template<typename DataType, typename = std::enable_if_t<not std::is_const_v<DataType>>> DataType readAttribute(std::string_view attrName, std::string_view linkPath, const OptDimsType &dataDims = std::nullopt) const¶

std::vector<std::string> getAttributeNames(std::string_view linkPath) const¶

TableInfo createTable(const hid::h5t &h5EntryType, std::string_view tableName, std::string_view tableTitle, const std::optional<hsize_t> desiredChunkSize = std::nullopt, const std::optional<unsigned int> desiredCompressionLevel = std::nullopt)¶

template<typename DataType> TableInfo appendTableEntries(const DataType &data, std::string_view tableName)¶

void addTableEntriesFrom(const h5pp::TableInfo &srcInfo, h5pp::TableInfo &tgtInfo, TableSelection tableSelection, const std::optional<hsize_t> desiredChunkSize = std::nullopt, const std::optional<unsigned int> desiredCompressionLevel = std::nullopt)¶

TableInfo addTableEntriesFrom(const h5pp::TableInfo &srcInfo, std::string_view tgtTableName, TableSelection tableSelection, const std::optional<hsize_t> desiredChunkSize = std::nullopt, const std::optional<unsigned int> desiredCompressionLevel = std::nullopt)¶

template<typename h5x_src, typename = h5pp::type::sfinae::enable_if_is_h5_loc<h5x_src>> TableInfo addTableEntriesFrom(const h5x_src &srcLocation, std::string_view srcTableName, std::string_view tgtTableName, TableSelection tableSelection, const std::optional<hsize_t> desiredChunkSize = std::nullopt, const std::optional<unsigned int> desiredCompressionLevel = std::nullopt)¶

void addTableEntriesFrom(const h5pp::TableInfo &srcInfo, h5pp::TableInfo &tgtInfo, hsize_t srcStartEntry, hsize_t tgtStartEntry, hsize_t numEntries, const std::optional<hsize_t> desiredChunkSize = std::nullopt, const std::optional<unsigned int> desiredCompressionLevel = std::nullopt)¶

template<typename h5x_src, typename = h5pp::type::sfinae::enable_if_is_h5_loc<h5x_src>> TableInfo addTableEntriesFrom(const h5pp::TableInfo &srcInfo, std::string_view tgtTableName, hsize_t srcStartEntry, hsize_t tgtStartEntry, hsize_t numEntries, const std::optional<hsize_t> desiredChunkSize = std::nullopt, const std::optional<unsigned int> desiredCompressionLevel = std::nullopt)¶

template<typename h5x_src, typename = h5pp::type::sfinae::enable_if_is_h5_loc<h5x_src>> TableInfo addTableEntriesFrom(const h5x_src &srcLocation, std::string_view srcTableName, std::string_view tgtTableName, hsize_t srcStartIdx, hsize_t tgtStartIdx, hsize_t numRecords, const std::optional<hsize_t> desiredChunkSize = std::nullopt, const std::optional<unsigned int> desiredCompressionLevel = std::nullopt)¶

template<typename DataType> void readTableEntries(DataType &data, std::string_view tableName, std::optional<size_t> startEntry = std::nullopt, std::optional<size_t> numEntries = std::nullopt) const¶

template<typename DataType> DataType readTableEntries(std::string_view tablePath, std::optional<size_t> startEntry = std::nullopt, std::optional<size_t> numEntries = std::nullopt) const¶

template<typename DataType> void readTableField(DataType &data, std::string_view tablePath, std::string_view fieldNames, std::optional<size_t> startEntry = std::nullopt, std::optional<size_t> numEntries = std::nullopt) const¶

template<typename DataType> DataType readTableField(std::string_view tablePath, std::string_view fieldName, std::optional<size_t> startEntry = std::nullopt, std::optional<size_t> numEntries = std::nullopt) const¶

template<typename DataType> void readTableField(DataType &data, std::string_view tablePath, std::string_view fieldNames, TableSelection tableSelection) const¶

template<typename DataType> DataType readTableField(std::string_view tablePath, std::string_view fieldName, TableSelection tableSelection) const¶

int getDatasetRank(std::string_view datasetPath) const¶

std::vector<hsize_t> getDatasetDimensions(std::string_view datasetPath) const¶

std::optional<std::vector<hsize_t>> getDatasetMaxDimensions(std::string_view datasetPath) const¶

std::optional<std::vector<hsize_t>> getDatasetChunkDimensions(std::string_view datasetPath) const¶

bool linkExists(std::string_view link) const¶

std::vector<std::string> findLinks(std::string_view searchKey = "", std::string_view searchRoot = "/", long maxHits = -1, long maxDepth = -1) const¶

std::vector<std::string> findDatasets(std::string_view searchKey = "", std::string_view searchRoot = "/", long maxHits = -1, long maxDepth = -1) const¶

std::vector<std::string> findGroups(std::string_view searchKey = "", std::string_view searchRoot = "/", long maxHits = -1, long maxDepth = -1) const¶

DsetInfo getDatasetInfo(std::string_view dsetPath) const¶

AttrInfo getAttributeInfo(std::string_view linkPath, std::string_view attrName) const¶

TableInfo getTableInfo(std::string_view tablePath) const¶

TypeInfo getTypeInfoDataset(std::string_view dsetPath) const¶

TypeInfo getTypeInfoAttribute(std::string_view linkPath, std::string_view attrName) const¶

std::vector<TypeInfo> getTypeInfoAttributes(std::string_view linkPath) const¶

bool fileIsValid() const¶

Public Members

PropertyLists plists¶