rhdf5 (version 2.16.0)

h5ls: 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"))
h5dump (file, recursive = TRUE,
	load = TRUE,
	all = FALSE, index_type = h5default("H5_INDEX"), order = h5default("H5_ITER"), ...)

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.

...

Arguments passed to h5read

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.

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

References

http://www.hdfgroup.org/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")