H5-attributs: Manipulate HDF5 attributes

In hdf5r.Extra: Extensions for 'HDF5' R Interfaces

Manipulate HDF5 attributes

Description

Functions to get, set or delete HDF5 attributes for an existing link.

Usage

h5Attr(x, which, ...)

h5Attributes(x, ...)

h5AttrNames(x, ...)

h5DeleteAttr(x, which, ...)

h5WriteAttr(x, which, robj, ...)

## S3 method for class 'H5D'
h5Attr(x, which, ...)

## S3 method for class 'H5Group'
h5Attr(x, which, name = NULL, ...)

## S3 method for class 'H5File'
h5Attr(x, which, name = NULL, ...)

## S3 method for class 'character'
h5Attr(x, which, name = NULL, ...)

## S3 method for class 'H5D'
h5AttrNames(x, ...)

## S3 method for class 'H5Group'
h5AttrNames(x, name = NULL, ...)

## S3 method for class 'H5File'
h5AttrNames(x, name = NULL, ...)

## S3 method for class 'character'
h5AttrNames(x, name = NULL, ...)

## S3 method for class 'H5D'
h5Attributes(x, ...)

## S3 method for class 'H5Group'
h5Attributes(x, name = NULL, ...)

## S3 method for class 'H5File'
h5Attributes(x, name = NULL, ...)

## S3 method for class 'character'
h5Attributes(x, name = NULL, ...)

## S3 method for class 'H5D'
h5WriteAttr(
  x,
  which,
  robj,
  overwrite = TRUE,
  check.scalar = TRUE,
  stype = c("utf8", "ascii7"),
  ...
)

## S3 method for class 'H5Group'
h5WriteAttr(
  x,
  which,
  robj,
  name = NULL,
  overwrite = TRUE,
  check.scalar = TRUE,
  stype = c("utf8", "ascii7"),
  ...
)

## S3 method for class 'H5File'
h5WriteAttr(
  x,
  which,
  robj,
  name = NULL,
  overwrite = TRUE,
  check.scalar = TRUE,
  stype = c("utf8", "ascii7"),
  ...
)

## S3 method for class 'character'
h5WriteAttr(
  x,
  which,
  robj,
  name = NULL,
  overwrite = TRUE,
  check.scalar = TRUE,
  stype = c("utf8", "ascii7"),
  ...
)

## S3 method for class 'H5D'
h5DeleteAttr(x, which, ...)

## S3 method for class 'H5Group'
h5DeleteAttr(x, which, name = NULL, ...)

## S3 method for class 'H5File'
h5DeleteAttr(x, which, name = NULL, ...)

## S3 method for class 'character'
h5DeleteAttr(x, which, name = NULL, ...)

Arguments

x	An H5File, H5Group, H5D or a path name of HDF5 file.
which	Name of the HDF5 attribute
...	Arguments passed to other methods.
robj	An R object to be written as HDF5 attribute
name	Name of an existing HDF5 sub-link. Default is NULL, which will use current link.
overwrite	Whether or not to overwrite the existing HDF5 attribute.
check.scalar	Whether or not to use scalar space when robj is a scalar. If FALSE, the attribute written will be treated as an array.
stype	Passed to h5GuessDtype

Value

H5Attr:

• If which exists in link name, will return an R object representing the attribute. If which doesn't exist or contains empty data, will return NULL.

• If name doesn't exist, will raise an error from H5File$attr_exists_by_name().

h5AttrNames will return a character vector containing all attribute names for the given link.

h5Attributes will return a list containing all attributes for the given link.

Examples

file <- system.file("extdata", "pbmc_small.h5ad", package = "hdf5r.Extra")

# Read H5 attribute
x <- h5Attr(file, "encoding-version")
x <- h5Attr(file, "column-order", "raw/var") ## An empty attribute
length(x)

h5obj <- h5Open(file, "raw/var", mode = "r")
x <- h5Attr(h5obj, "column-order")

# Read H5 attribute names
h5AttrNames(file)
h5AttrNames(file, "X")
h5AttrNames(h5obj)

# Read all H5 attributes
a1 <- h5Attributes(file, "raw/var")
a2 <- h5Attributes(h5obj)
identical(a1, a2)

# Write H5 attribute
tmp.file <- tempfile(fileext = ".h5")
file.copy(file, tmp.file)

new_a <- character()  # Can write an empty attribute
h5WriteAttr(tmp.file, "new_a", robj = new_a, name = "X")
new_a <- c("a", "b")
h5WriteAttr(tmp.file, "new_a", robj = new_a, name = "X", overwrite = TRUE)
h5Attr(tmp.file, "new_a", name = "X")

# Delete H5 attribute
h5DeleteAttr(tmp.file, "new_a", name = "X")
h5Attr(tmp.file, "new_a", name = "X")

hdf5r.Extra documentation built on Oct. 18, 2024, 9:06 a.m.