h5writeDimnames {HDF5Array} | R Documentation

## Write/read the dimnames of an HDF5 dataset

### Description

`h5writeDimnames` and `h5readDimnames` can be used to write/read the dimnames of an HDF5 dataset to/from the HDF5 file.

Note that `h5writeDimnames` is used internally by `writeHDF5Array(x, ..., with.dimnames=TRUE)` to write the dimnames of `x` to the HDF5 file together with the array data.

`set_h5dimnames` and `get_h5dimnames` are low-level utilities that can be used to attach existing HDF5 datasets along the dimensions of a given HDF5 dataset, or to retrieve the names of the HDF5 datasets that are attached along the dimensions of a given HDF5 dataset.

### Usage

    h5writeDimnames(dimnames, filepath, name, group=NA, h5dimnames=NULL)
    h5readDimnames(filepath, name, as.character=FALSE)

    set_h5dimnames(filepath, name, h5dimnames, dry.run=FALSE)
    get_h5dimnames(filepath, name)

### Arguments

`dimnames` | The dimnames to write to the HDF5 file. Must be supplied as a list (possibly named) with one list element per dimension in the HDF5 dataset specified via the `name` argument. Each list element in `dimnames` must be an atomic vector or a `NULL`. When not a `NULL`, its length must equal the extent of the corresponding dimension in the HDF5 dataset.
`filepath` | For `h5writeDimnames` and `h5readDimnames`: The path (as a single string) to the HDF5 file where the dimnames should be written to or read from. For `set_h5dimnames` and `get_h5dimnames`: The path (as a single string) to the HDF5 file where to set or get the h5dimnames.
`name` | For `h5writeDimnames` and `h5readDimnames`: The name of the dataset in the HDF5 file for which the dimnames should be written or read. For `set_h5dimnames` and `get_h5dimnames`: The name of the dataset in the HDF5 file for which to set or get the h5dimnames.
`group` | `NA` (the default) or the name of the HDF5 group where to write the dimnames. If set to `NA` then the group name is automatically generated from `name`. If set to the empty string (`""`) then no group will be used. Except when `group` is set to the empty string, the names in `h5dimnames` (see below) must be relative to the group.
`h5dimnames` | For `h5writeDimnames`: `NULL` (the default) or a character vector containing the names of the HDF5 datasets (one per list element in `dimnames`) where to write the dimnames. Names associated with `NULL` list elements in `dimnames` are ignored and should typically be NAs. If set to `NULL` then the names are automatically set to numbers indicating the associated dimensions (`"1"` for the first dimension, `"2"` for the second, etc...) For `set_h5dimnames`: A character vector containing the names of the HDF5 datasets to attach as dimnames of the dataset specified in `name`. The vector must have one element per dimension in dataset `name`. NAs are allowed and indicate dimensions along which nothing should be attached.
`as.character` | Even though the dimnames of an HDF5 dataset are usually stored as datasets of type `"character"` (H5 datatype `"H5T_STRING"`) in the HDF5 file, this is not a requirement. By default `h5readDimnames` will return them as-is. Set `as.character` to `TRUE` to make sure that they are returned as character vectors. See example below.
`dry.run` | When set to `TRUE`, `set_h5dimnames` doesn't make any change to the HDF5 file but will still raise errors if the operation cannot be done.

### Value

`h5writeDimnames` and `set_h5dimnames` return nothing.

`h5readDimnames` returns a list (possibly named) with one list element per dimension in HDF5 dataset `name` and containing its dimnames retrieved from the file.

`get_h5dimnames` returns a character vector containing the names of the HDF5 datasets that are currently set as the dimnames of the dataset specified in `name`. The vector has one element per dimension in dataset `name`. NAs in the vector indicate dimensions along which nothing is set.

### See Also

- `writeHDF5Array` for a high-level function to write an array-like object and its dimnames to an HDF5 file.

- `h5write` in the rhdf5 package that `h5writeDimnames` uses internally to write the dimnames to the HDF5 file.

- `h5mread` in this package (HDF5Array) that `h5readDimnames` uses internally to read the dimnames from the HDF5 file.

- `h5ls` to list the content of an HDF5 file.

- HDF5Array objects.

### Examples

    ## ---------------------------------------------------------------------
    ## BASIC EXAMPLE
    ## ---------------------------------------------------------------------
    library(rhdf5)  # for h5write()

    m0 <- matrix(1:60, ncol=5)
    colnames(m0) <- LETTERS[1:5]

    h5file <- tempfile(fileext=".h5")
    h5write(m0, h5file, "M0")  # h5write() ignores the dimnames
    h5ls(h5file)

    h5writeDimnames(dimnames(m0), h5file, "M0")
    h5ls(h5file)

    get_h5dimnames(h5file, "M0")
    h5readDimnames(h5file, "M0")

    ## Reconstruct 'm0' from HDF5 file:
    m1 <- h5mread(h5file, "M0")
    dimnames(m1) <- h5readDimnames(h5file, "M0")
    stopifnot(identical(m0, m1))

    ## Create an HDF5Array object that points to HDF5 dataset M0:
    HDF5Array(h5file, "M0")

    ## Sanity checks:
    stopifnot(identical(dimnames(m0), h5readDimnames(h5file, "M0")))
    stopifnot(identical(dimnames(m0), dimnames(HDF5Array(h5file, "M0"))))

    ## ---------------------------------------------------------------------
    ## SHARED DIMNAMES
    ## ---------------------------------------------------------------------
    ## If a collection of HDF5 datasets share the same dimnames, the
    ## dimnames only need to be written once in the HDF5 file. Then they
    ## can be attached to the individual datasets with set_h5dimnames():

    h5write(array(runif(240), c(12, 5:4)), h5file, "A1")
    set_h5dimnames(h5file, "A1", get_h5dimnames(h5file, "M0"))
    get_h5dimnames(h5file, "A1")
    h5readDimnames(h5file, "A1")
    HDF5Array(h5file, "A1")

    h5write(matrix(sample(letters, 60, replace=TRUE), ncol=5), h5file, "A2")
    set_h5dimnames(h5file, "A2", get_h5dimnames(h5file, "M0"))
    get_h5dimnames(h5file, "A2")
    h5readDimnames(h5file, "A2")
    HDF5Array(h5file, "A2")

    ## Sanity checks:
    stopifnot(identical(dimnames(m0), h5readDimnames(h5file, "A1")[1:2]))
    stopifnot(identical(dimnames(m0), h5readDimnames(h5file, "A2")))

    ## ---------------------------------------------------------------------
    ## USE h5writeDimnames() AFTER A CALL TO writeHDF5Array()
    ## ---------------------------------------------------------------------
    ## After calling writeHDF5Array(x, ..., with.dimnames=FALSE) the
    ## dimnames on 'x' can still be written to the HDF5 file by doing the
    ## following:

    ## 1. Write 'm0' to the HDF5 file and ignore the dimnames (for now):
    writeHDF5Array(m0, h5file, "M2")

    ## 2. Use h5writeDimnames() to write 'dimnames(m0)' to the file and
    ##    associate them with the "M2" dataset:
    h5writeDimnames(dimnames(m0), h5file, "M2")

    ## 3. Use the HDF5Array() constructor to make an HDF5Array object that
    ##    points to the "M2" dataset:
    HDF5Array(h5file, "M2")

    ## Note that at step 2. you can use the extra arguments of
    ## h5writeDimnames() to take full control of where the dimnames
    ## should be stored in the file:
    writeHDF5Array(m0, h5file, "M3")
    h5writeDimnames(dimnames(m0), h5file, "M3",
                     group="a_secret_place", h5dimnames=c("NA", "M3_dim2"))
    h5ls(h5file)
    ## h5readDimnames() and HDF5Array() still "finds" the dimnames:
    h5readDimnames(h5file, "M3")
    HDF5Array(h5file, "M3")

    ## Sanity checks:
    stopifnot(identical(dimnames(m0), h5readDimnames(h5file, "M3")))
    stopifnot(identical(dimnames(m0), dimnames(HDF5Array(h5file, "M3"))))

    ## ---------------------------------------------------------------------
    ## STORE THE DIMNAMES AS NON-CHARACTER TYPES
    ## ---------------------------------------------------------------------
    writeHDF5Array(m0, h5file, "M4")
    dimnames <- list(1001:1012, as.raw(11:15))
    h5writeDimnames(dimnames, h5file, "M4")
    h5ls(h5file)

    h5readDimnames(h5file, "M4")
    h5readDimnames(h5file, "M4", as.character=TRUE)

    ## Sanity checks:
    stopifnot(identical(dimnames, h5readDimnames(h5file, "M4")))
    dimnames(m0) <- dimnames
    stopifnot(identical(
        dimnames(m0),
        h5readDimnames(h5file, "M4", as.character=TRUE)
    ))

[Package HDF5Array version 1.22.1 Index]