List the content of an HDF5 file.

Source: R/h5ls.R

List the content of an HDF5 file.

h5ls(
  file,
  recursive = TRUE,
  all = FALSE,
  datasetinfo = TRUE,
  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. You can also 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.

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

Value

h5ls returns a data.frame with the file content.

See also

h5dump()

Author

Bernd Fischer, Mike L. Smith

Examples


h5File <- tempfile(pattern = "ex_dump.h5")
h5createFile(h5File)

# create groups
h5createGroup(h5File, "foo")
h5createGroup(h5File, "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, h5File, "foo/B")

# list content of hdf5 file
h5ls(h5File, all = TRUE)
#>   group   name         ltype cset       otype num_attrs dclass          dtype
#> 0     /    foo H5L_TYPE_HARD    0   H5I_GROUP         0                      
#> 1  /foo      B H5L_TYPE_HARD    0 H5I_DATASET         1  FLOAT H5T_IEEE_F64LE
#> 2  /foo foobaa H5L_TYPE_HARD    0   H5I_GROUP         0                      
#>    stype rank       dim    maxdim
#> 0           0                    
#> 1 SIMPLE    3 5 x 2 x 2 5 x 2 x 2
#> 2           0                    

# list content of an hdf5 file in a public S3 bucket
# \donttest{
h5ls(file = "https://rhdf5-public.s3.eu-central-1.amazonaws.com/h5ex_t_array.h5", s3 = TRUE)
#>   group name       otype dclass dim
#> 0     /  DS1 H5I_DATASET  ARRAY   4
# }