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

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
h5dump(h5File)
#> $foo
#> $foo$B
#> , , 1
#> 
#>      [,1] [,2]
#> [1,]  0.1  0.6
#> [2,]  0.2  0.7
#> [3,]  0.3  0.8
#> [4,]  0.4  0.9
#> [5,]  0.5  1.0
#> 
#> , , 2
#> 
#>      [,1] [,2]
#> [1,]  1.1  1.6
#> [2,]  1.2  1.7
#> [3,]  1.3  1.8
#> [4,]  1.4  1.9
#> [5,]  1.5  2.0
#> 
#> 
#> $foo$foobaa
#> NULL
#> 
#> 

# list content of an hdf5 file in a public S3 bucket
# \donttest{
h5dump(file = "https://rhdf5-public.s3.eu-central-1.amazonaws.com/h5ex_t_array.h5", s3 = TRUE)
#> $DS1
#> , , 1
#> 
#>      [,1] [,2] [,3]
#> [1,]    0    0    0
#> [2,]    0   -1   -2
#> [3,]    0   -2   -4
#> [4,]    0   -3   -6
#> [5,]    0   -4   -8
#> 
#> , , 2
#> 
#>      [,1] [,2] [,3]
#> [1,]    0    1    2
#> [2,]    1    1    1
#> [3,]    2    1    0
#> [4,]    3    1   -1
#> [5,]    4    1   -2
#> 
#> , , 3
#> 
#>      [,1] [,2] [,3]
#> [1,]    0    2    4
#> [2,]    2    3    4
#> [3,]    4    4    4
#> [4,]    6    5    4
#> [5,]    8    6    4
#> 
#> , , 4
#> 
#>      [,1] [,2] [,3]
#> [1,]    0    3    6
#> [2,]    3    5    7
#> [3,]    6    7    8
#> [4,]    9    9    9
#> [5,]   12   11   10
#> 
#> 
# }

Dump the content of an HDF5 file.

Usage

Arguments

Value

See also

Author

Examples