H5S: HDF5 Dataspace Interface

In rhdf5: R Interface to HDF5

Description

These functions create and manipulate the dataspace in which to store the elements of a dataset.

Usage

H5Screate                 (type = h5default("H5S"), native = FALSE)
H5Screate_simple          (dims, maxdims, native = FALSE)
H5Scopy                   (h5space)
H5Sclose                  (h5space)
H5Sis_simple              (h5space)
H5Sget_simple_extent_dims (h5space)
H5Sset_extent_simple      (h5space, dims, maxdims)
H5Sselect_hyperslab       (h5space, op = h5default("H5S_SELECT"), 
                           start = NULL, stride = NULL, count = NULL,
                           block = NULL)
H5Sselect_index           (h5space, index)
H5Sunlimited              ()

Arguments

type	See h5const("H5S") for possible types.
dims	Dimension of the dataspace. This argument is similar to the dim attribute of an array. When viewing the HDF5 dataset with an C-program (e.g. HDFView), the dimensions appear in inverted order, because the fastest changing dimension in R is the first one, and in C its the last one.
maxdims	Maximum extension of the dimension of the dataset in the file. If not provided, it is set to dims.
native	An object of class logical. If TRUE, array-like objects are treated as stored in HDF5 row-major rather than R column-major orientation. Using native = TRUE increases HDF5 file portability between programming languages. A file written with native = TRUE should also be read with native = TRUE

.

h5space	An object of class H5IdComponent representing a H5 dataspace identifier. See H5Dget_space, H5Screate_simple, H5Screate to create an object of this kind.
index	A list of integer indices. The length of the list corresponds to the number of dimensions of the HDF5 array.
op	See h5const("H5S_SELECT") for possible arguments.
start	The start coordinate of a hyperslab (similar to subsetting in R). Counting is R-style 1-based.
stride	The stride of the hypercube. Read the introduction http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html before using this argument. R behaves like Fortran in this example.
count	The number of blocks to be written.
block	The block size of the hyperslab. Read the introduction http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html before using this argument. R behaves like Fortran in this example.

Details

Interface to the HDF5 C-library libhdf5. See https://portal.hdfgroup.org/display/HDF5/Dataspaces for further details.

As an introduction to use hyperslabs see these tutorials: See these introductions to hyperslabs: https://support.hdfgroup.org/HDF5/Tutor/selectsimple.html, https://support.hdfgroup.org/HDF5/Tutor/select.html and http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html. Please note that in R the first dimension is the fastest changing dimension. When viewing the HDF5 datasets with any C-program (e.g. HDFView), the order of dimensions is inverted. In the R interface counting starts with 1, whereas in the C-programs (e.g. HDFView) counting starts with 0.

H5Sselect_index is not part of the standard HDF5 C interface. It performes an iterative call to H5select_points by iterating through the given index positions. This function avoids a for loop in R. If a list element is NULL, all elements of the respective dimension are considered.

Value

H5Screate, H5Screate_simple, and H5Scopy return an object of class H5IdComponent representing a dataspace.

H5Sis_simple returns a boolean.

H5Sget_simple_extent_dims returns an integer vector.

H5Sunlimited is a simple macro to return the constant H5S_UNLIMITED that can be provided to the maxdims arguments of H5Screate_simple to create and extensible dataspace.

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

Author(s)

Bernd Fischer

References

https://portal.hdfgroup.org/display/HDF5

See Also

rhdf5

Examples

sid <- H5Screate_simple(c(10,5,3))
sid
H5Sis_simple(sid)
H5Sget_simple_extent_dims(sid)

# select a subarray (called hyperslab in the hdf5 community).
# The next h5write can use this to write a subarray
H5Sselect_index(sid, list(1:3,2:4,2))

# always close dataspaces after usage to free recources
H5Sclose(sid)
sid

Example output

HDF5 DATASPACE
        rank 3
        size 10 x 5 x 3
     maxsize 10 x 5 x 3
[1] TRUE
$rank
[1] 3

$size
[1] 10  5  3

$maxsize
[1] 10  5  3

HDF5 BADID

No valid identifier.

rhdf5 documentation built on Nov. 8, 2020, 6:56 p.m.