H5D: HDF5 Dataset Interface

In patperry/rhdf5: HDF5 interface to R

Description

These functions create and manipulate dataset objects, and set and retrieve their constant or persistent properties.

Usage

H5Dcreate    (h5loc, name, dtype_id, h5space, internal1 = NULL, internal2 = 6)
H5Dopen      (h5loc, name)
H5Dclose     (h5dataset)
H5Dget_space (h5dataset)
H5Dget_type  (h5dataset)
H5Dread      (h5dataset, h5spaceFile = NULL, h5spaceMem = NULL, buf = NULL, compoundAsDataFrame = TRUE)
H5Dwrite     (h5dataset, buf, h5spaceMem = NULL, h5spaceFile = NULL)

Arguments

h5loc	An object of class H5IdComponent representing a H5 location identifier (file or group). See H5Fcreate, H5Fopen, H5Gcreate, H5Gopen to create an object of this kind.
name	Name of the dataset (character).
dtype_id	A character name of a datatype. See h5const("H5T") for possible datatypes. Can also be an integer representing an HDF5 datatype.
h5space	An object of class H5IdComponent representing a H5 dataspace. See H5Dget_space, H5Screate_simple, H5Screate to create an object of this kind.
h5dataset	An object of class H5IdComponent representing a H5 dataset. See H5Dcreate, H5Dopen to create an object of this kind.
h5spaceFile,h5spaceMem	An object of class H5IdComponent representing a H5 dataspace. See H5Dget_space, H5Screate_simple, H5Screate to create an object of this kind. The dimensions of the dataset in the file and in memory. The dimensions in file and in memory are interpreted in an R-like manner. The first dimension is the fastest changing dimension. When reading the file with a C-program (e.g. HDFView) the order of dimensions will invert, because in C the fastest changing dimension is the last one.
buf	Reading and writing buffer containing the data to written/read. When using the buffer for reading, the buffer size has to fit the size of the memory space h5spaceMem. No extra memory will be allocated for the data. A pointer to the same data is returned.
compoundAsDataFrame	If true, a compound datatype will be coerced to a data.frame. This is not possible, if the dataset is multi-dimensional. Otherwise the compound datatype will be returned as a list. Nested compound data types will be returned as a nested list.
internal1,internal2	For internal usage only. Will be removed in later versions.

Details

Interface to the HDF5 C-library libhdf5. See http://www.hdfgroup.org/HDF5/doc/RM/RM_H5D.html for further details.

Value

H5Dcreate and H5Dopen return an object of class H5IdComponent represinting a H5 dataset identifier.

H5Dget_space returns an object of class H5IdComponent representing a H5 dataspace identifier.

H5Dread returns an array with the read data.

The other functions return the standard return value from their respective C-functions.

Author(s)

Bernd Fischer

References

http://www.hdfgroup.org/HDF5

See Also

rhdf5

Examples

# write a dataset
fid <- H5Fcreate("ex_H5D.h5")
fid
sid <- H5Screate_simple(c(10,5,3))
sid
did <- H5Dcreate(fid, "A", "H5T_STD_I32LE", sid)
did
H5Dwrite(did, 1L:150L, h5spaceMem = sid, h5spaceFile = sid)
H5Dclose(did)
H5Sclose(sid)
H5Fclose(fid)

# read a dataset
fid <- H5Fopen("ex_H5D.h5")
fid
did <- H5Dopen(fid, "A")
did
sid <- H5Dget_space(did)
sid
B <- H5Dread(did)
B
H5Dclose(did)
H5Sclose(sid)
H5Fclose(fid)

# write a subarray
fid <- H5Fopen("ex_H5D.h5")
fid
did <- H5Dopen(fid, "A")
did
sid <- H5Dget_space(did)
sid
H5Sselect_index(sid, list(1:3,2:4,2))
sidmem <- H5Screate_simple(c(3,3,1))
sidmem
A = array(-801:-809,dim=c(3,3,1))
H5Dwrite(did, A, h5spaceMem = sidmem, h5spaceFile = sid)
H5Dread(did)
H5Sclose(sid)
H5Dclose(did)
H5Sclose(sidmem)
H5Fclose(fid)

patperry/rhdf5 documentation built on May 24, 2019, 8:21 p.m.