File IPNWB_HDF5Helpers.ipf

H5 Wrapper functions for convenient use of the HDF5 operations

Unnamed Group

static const double kHDF5DataInfoVersion = 1000

Taken from HDF5 Browser.ipf

Included here for convenience.

static const double H5S_MAX_RANK = 32
static variable InitHDF5DataInfo(HDF5DataInfo *di)

Functions

variable H5_WriteTextDataset(variable locationID, string name, string str = defaultValue, WaveTextOrNull wvText = defaultValue, variable overwrite = defaultValue, variable compressionMode = defaultValue, variable skipIfExists = defaultValue, variable writeIgorAttr = defaultValue, variable appendData = defaultValue, variable refMode = defaultValue)

Write a string or text wave into a HDF5 dataset.

Only one of str or wvText can be given.

Parameters:

  • locationID – HDF5 identifier, can be a file or group

  • name – Name of the HDF5 dataset

  • str – Contents to write into the dataset

  • wvText – Contents to write into the dataset

  • overwrite – [optional, defaults to false] Should existing datasets be overwritten

  • compressionMode – [optional, defaults to NO_COMPRESSION] Type of compression to use, one of CompressionMode

  • skipIfExists – [optional, defaults to false] Do nothing if the dataset already exists

  • writeIgorAttr – [optional, defaults to false] Add Igor specific attributes to the dataset, see the /IGOR flag of HDF5SaveData

  • appendData – [optional, defaults to -1] Set the dimension to append to within the given dataset (requires compression)

  • refMode – [optional, defaults to NO_REFERENCE] Set refMode, one in ReferenceMode (DisplayHelpTopic “Saving Reference Data”)

variable H5_WriteDataset(variable locationID, string name, variable var = defaultValue, variable varType = defaultValue, WaveOrNull wv = defaultValue, variable overwrite = defaultValue, variable compressionMode = defaultValue, variable skipIfExists = defaultValue, variable writeIgorAttr = defaultValue, variable appendData = defaultValue)

Write a variable or text wave into a HDF5 dataset.

Only one of var or wv can be given.

Parameters:

  • locationID – HDF5 identifier, can be a file or group

  • name – Name of the HDF5 dataset

  • var – Contents to write into the dataset

  • varType – Type of the data, must be given if var is supplied. See IgorTypes

  • wv – Contents to write into the dataset

  • overwrite – [optional, defaults to false] Should existing datasets be overwritten

  • compressionMode – [optional, defaults to NO_COMPRESSION] Type of compression to use, one of CompressionMode

  • skipIfExists – [optional, defaults to false] Do nothing if the dataset already exists

  • writeIgorAttr – [optional, defaults to false] Add Igor specific attributes to the dataset, see the /IGOR flag of HDF5SaveData

  • appendData – [optional, defaults to -1] Set the dimension to append to within the given dataset (requires compression)

static wave H5_GetChunkSizes(wave wv, variable compressionMode)

Return a wave for the valid chunk sizes of each dimension taking into account the compression mode.

static variable H5_WriteDatasetLowLevel(variable locationID, string name, wave wv, variable overwrite, variable compressionMode, variable skipIfExists, variable writeIgorAttr, variable appendData, variable refMode)

See also

H5_WriteTextDataset or H5_WriteDataset

variable H5_WriteTextAttribute(variable locationID, string attrName, string path, string list = defaultValue, string str = defaultValue, variable overwrite = defaultValue, variable refMode = defaultValue)

Attach a text attribute to the given location.

Only one of str or list can be given.

Parameters:

  • locationID – HDF5 identifier, can be a file, group or dataset

  • attrName – Name of the attribute

  • path – Additional path on top of locationID which identifies the object onto which the attribute should be attached.

  • list – Contents to write into the attribute, list will be always written as 1D-array

  • str – Contents to write into the attribute

  • overwrite – [optional, defaults to false] Should existing attributes be overwritten

  • refMode – [optional, defaults to 0] Set refMode, one in ReferenceMode (DisplayHelpTopic “Saving Reference Data”)

variable H5_WriteAttribute(variable locationID, string attrName, string path, variable var, variable varType, variable overwrite = defaultValue)

Attach a numerical attribute to the given location.

Parameters:

  • locationID – HDF5 identifier, can be a file, group or dataset

  • attrName – Name of the attribute

  • path – Additional path on top of locationID which identifies the object onto which the attribute should be attached.

  • var – Contents to write into the attribute

  • varType – Type of the attribute, see IgorTypes

  • overwrite – [optional, defaults to false] Should existing attributes be overwritten

variable H5_CreateSoftLink(variable locationID, string path, string target)

Create a link to a group.

Parameters:

  • locationID – HDF5 identifier, can be a file, group or dataset

  • path – Name of the link

  • target – The linked destination

variable H5_OpenFile(string discLocation, variable write = defaultValue)

Open HDF5 file and return ID.

Parameters:

  • discLocation – full path to nwb file

  • write – open file for writing. default is readonly.

Returns:

ID for referencing open hdf5 file

variable H5_CloseFile(variable fileID)

Close HDF5 file.

Parameters:

fileID – ID of open hdf5 file

Returns:

open state as true/false

variable H5_IsFileOpen(variable fileID)

Return 1 if the given HDF5 file is already open, 0 otherwise.

Parameters:

fileID – HDF5 locationID from HDF5OpenFile.

variable H5_DatasetExists(variable locationID, string name)

Return 1 if the given HDF5 dataset exists, 0 otherwise.

Parameters:

  • locationID – [in] HDF5 identifier, can be a file or group

  • name – [in] Additional path on top of locationID which identifies the dataset

wave H5_LoadDataset(variable locationID, string name)

Load a specified dataset as wave.

Parameters:

  • locationID – [in] HDF5 identifier, can be a file or group

  • name – [in] path on top of locationID which identifies the dataset

Returns:

reference to wave containing loaded data

wave H5_GetDatasetSize(variable locationID, string dataset)

Return the dimension sizes of the given dataset.

Parameters:

  • locationID – HDF5 identifier, can be a file or group

  • dataset – name of the dataset

Returns:

wave with the dimension sizes or an invalid wave reference

variable H5_AttributeExists(variable locationID, string path, string attribute, variable *objectType = defaultValue)

Check if a given attribute exists.

Parameters:

  • locationID – [in] HDF5 identifier, can be a file or group

  • path – [in] Additional path on top of locationID which identifies the group or dataset

  • attribute – [in] Name of the attribute

  • objectType – [out] [optional] Return the type of the element to which the attribute is attached to. Can be used for subsequent HDF5LoadData calls.

wave H5_LoadAttribute(variable locationID, string path, string attribute)

Load the given attribute and return its contents.

Parameters:

  • locationID – [in] HDF5 identifier, can be a file or group

  • path – [in] Additional path on top of locationID which identifies the group or dataset

  • attribute – [in] Name of the attribute to load

variable H5_GroupExists(variable locationID, string path)

Return 1 if the given HDF5 group exists, 0 otherwise.

Parameters:

  • locationID – HDF5 identifier, can be a file or group

  • path – Additional path on top of locationID which identifies the group.

variable H5_CreateGroupsRecursively(variable locationID, string fullPath)

Create all groups along the given path.

Parameters:

  • locationID – HDF5 identifier, can be a file or group

  • fullPath – Additional path on top of locationID which identifies the group

variable H5_IsValidIdentifier(string name)

Return true if name is a valid hdf5 identifier.

This is more restrictive than the actual HDF5 library checks. See the BNF Grammar here.

string H5_ListGroupMembers(variable locationID, string path)

List all datasets at path (non-recursively)

Parameters:

  • locationID – [in] HDF5 identifier, can be a file or group

  • path – [in] Additional path on top of locationID which identifies the group

string H5_ListGroups(variable fileID, string path)

List all groups inside a group (non-recursively)

Parameters:

  • fileID – [in] HDF5 file identifier

  • path – [in] Full path to the group inside fileID

variable H5_OpenGroup(variable locationID, string path)

Open the group reachable via locationID and path and return its ID.

Parameters:

  • locationID – HDF5 identifier, can be a file or group

  • path – Additional path on top of locationID which identifies the group

Returns:

the groupID of the opened group. Return NaN if the group did not exist.

variable H5_FlushFile(variable fileID)

Flush the file contents to disc.

Parameters:

fileID – HDF5 file identifier

string H5_GetLinkTarget(string discLocation, string path)

Todo:

Needs HDF5 XOP support for reading link targets use HDF5LinkInfo

string H5_GetLibraryVersion()

Return the HDF5 Library version.

Variables

static const double H5_ATTRIBUTE_SIZE_LIMIT = 60e3
static const double H5_CHUNK_SIZE = 8192
struct HDF5DataInfo

Public Members

uint32 version
char structName[16]
double datatype_class
char datatype_class_str[32]
double datatype_size
double datatype_sign
double datatype_order
char datatype_str[64]
double dataspace_type
double ndims
double dims[H5S_MAX_RANK]
double maxdims[H5S_MAX_RANK]