Return detailed information on chunks of an HDF5 dataset

Returns the offset, filter mask, file address, and byte size of every stored chunk in a chunked HDF5 dataset. This is a specific application of the HDF5 H5Dchunk_iter function and requires that the dataset uses chunked storage; contiguous or compact datasets will raise an error.

Usage

h5getAllChunkInfo(h5dataset)

Arguments

h5dataset

An object of class H5IdComponent representing an open HDF5 dataset, as returned by H5Dopen().

Value

A named list with four elements, one entry per stored chunk:

offset

Numeric matrix with one row per chunk and one column per dataset dimension, giving the chunk's logical origin in element coordinates.

filter_mask

Numeric vector of per-chunk filter pipeline bitmasks. A value of 0 means all filters were applied.

addr

Numeric vector of byte offsets within the HDF5 file at which each chunk's data begins.

size

Numeric vector of compressed (on-disk) byte sizes for each chunk.

See also

H5Dopen(), H5Dget_num_chunks()

Examples

## chunked dataset: szip-compressed 2-D integer array
h5file <- system.file("testfiles", "h5ex_d_szip.h5", package = "rhdf5")
fid <- H5Fopen(h5file, flags = "H5F_ACC_RDONLY")
did <- H5Dopen(fid, "DS1")

ci <- h5getAllChunkInfo(did)
head(ci$offset)   # logical chunk origins (element coordinates)
#>      [,1] [,2]
#> [1,]    0    0
#> [2,]    0    8
#> [3,]    0   16
#> [4,]    0   24
#> [5,]    0   32
#> [6,]    0   40
ci$addr[1]        # file offset of first chunk in bytes
#> [1] 4016
ci$size[1]        # compressed size of first chunk in bytes
#> [1] 59

H5Dclose(did)
H5Fclose(fid)