h5ls {rhdf5} | R Documentation

## List the content of an HDF5 file.

### Description

Lists the content of an HDF5 file.

### Usage

    h5ls   (file,
            recursive = TRUE,
            all = FALSE,
            datasetinfo = TRUE,
            index_type = h5default("H5_INDEX"),
            order = h5default("H5_ITER"),
            s3 = FALSE,
            s3credentials = NULL,
            native = FALSE)

    h5dump (file,
            recursive = TRUE,
            load = TRUE,
            all = FALSE,
            index_type = h5default("H5_INDEX"),
            order = h5default("H5_ITER"),
            s3 = FALSE,
            s3credentials = NULL,
            ...,
            native = FALSE)

### Arguments

`file` | The filename (character) of the file in which the dataset will be located. For advanced programmers it is possible to provide 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.
`recursive` | If TRUE, the content of the whole group hierarchy is listed. If FALSE, Only the content of the main group is shown. If a positive integer is provided this indicates the maximum level of the hierarchy that is shown.
`all` | If TRUE, a longer list of information on each entry is provided.
`datasetinfo` | If FALSE, datatype and dimensionality information is not provided. This can speed up the content listing for large files.
`index_type` | See `h5const("H5_INDEX")` for possible arguments.
`order` | See `h5const("H5_ITER")` for possible arguments.
`load` | If TRUE the datasets are read in, not only the header information. Note, that this can cause memory problems for very large files. In this case choose `load=FALSE` and load the datasets successively.
`s3` | Logical value indicating whether the file argument should be treated as a URL to an Amazon S3 bucket, rather than a local file path.
`s3credentials` | A list of length three, providing the credentials for accessing files in a private Amazon S3 bucket.
`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`

.

`...` | Arguments passed to `h5read`

### Details

`h5ls` lists the content of an HDF5 file including group structure and datasets. It returns the content as a data.frame. You can use `h5dump(file="myfile.h5", load=FALSE)` to obtain the dataset information in a hierarchical list structure. Usually the datasets are loaded individually with `h5read`, but you have the possibility to load the complete content of an HDF5 file with `h5dump`

### Value

`h5ls` returns a data.frame with the file content.

`h5dump` returns a hierarchical list structure representing the HDF5 group hierarchy. It either returns the datasets within the list structure (`load=TRUE`) or it returns a data.frame for each datset with the dataset header information `load=FALSE`.

### Author(s)

Bernd Fischer, Mike L. Smith

### References

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

### See Also

`h5read`, `h5write`, rhdf5

### Examples

    h5createFile("ex_ls_dump.h5")

    # create groups
    h5createGroup("ex_ls_dump.h5","foo")
    h5createGroup("ex_ls_dump.h5","foo/foobaa")

    # write a matrix
    B = array(seq(0.1,2.0,by=0.1),dim=c(5,2,2))
    attr(B, "scale") <- "liter"
    h5write(B, "ex_ls_dump.h5","foo/B")

    # list content of hdf5 file
    h5ls("ex_ls_dump.h5",all=TRUE)
    h5dump("ex_ls_dump.h5")

    # list content of an hdf5 file in a public S3 bucket

    h5ls(file = "https://rhdf5-public.s3.eu-central-1.amazonaws.com/h5ex_t_array.h5", s3 = TRUE)
    h5dump(file = "https://rhdf5-public.s3.eu-central-1.amazonaws.com/h5ex_t_array.h5", s3 = TRUE)

[Package rhdf5 version 2.34.0 Index]