h5_dump: Dump the content of an HDF5 file.

In grimbough/rhdf5: R Interface to HDF5

Dump the content of an HDF5 file.

Description

Dump the content of an HDF5 file.

Usage

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. 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.
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.
all	If TRUE, a longer list of information on each entry is provided.
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.
...	Arguments passed to h5read()
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

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 dataset with the dataset header information (load=FALSE).

Author(s)

Bernd Fischer, Mike L. Smith

See Also

h5ls()

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
h5dump(h5File)

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

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

grimbough/rhdf5 documentation built on April 16, 2024, 8:22 p.m.