Command-line tools

G5print

Print (one, several, or all) datasets in a HDF5-file.

usage: G5print [-h] [--full] [--no-data] [--regex] [-a] [-d MAX_DEPTH]
               [-f FOLD] [-i] [-r ROOT] [-v]
               source [dataset ...]

Positional Arguments

source: File path
dataset: Path to datasets to print (default: all)

Named Arguments

--full

Print full array

Default: False

--no-data

Don’t print data

Default: False

--regex

Evaluate dataset name as a regex

Default: False

-a, --attrs

Print attributes

Default: False

-d, --max-depth

Maximum depth to display

-f, --fold

Fold paths

-i, --info

Print information: shape, dtype

Default: False

-r, --root

Start somewhere in the path-tree

Default: “/”

-v, --version

show program’s version number and exit

G5list

List datasets (or groups of datasets) in a HDF5-file.: Note that if you have a really big file the --layer option can be much faster than searching the entire file.

usage: G5list [-h] [-D] [-d MAX_DEPTH] [-f FOLD] [-i] [-L LAYER] [-l]
              [-r ROOT] [-s] [-v]
              source

Positional Arguments

source

Named Arguments

-D, --datasets

Print only datasets

Default: False

-d, --max-depth

Maximum depth to display

-f, --fold

Fold paths

-i, --info

Print info: shape, dtype

Default: False

-L, --layer

Print paths at a specific layer

-l, --long

–info but with attributes

Default: False

-r, --root

Start somewhere in the path-tree

Default: “/”

-s, --links

Show destination of soft links

Default: False

-v, --version

show program’s version number and exit

Overview

`GooseHDF5.cli.G5check`	Try reading datasets.
`GooseHDF5.cli.G5repair`	Extract readable data from a HDF5-file and copy it to a new HDF5-file.
`GooseHDF5.cli.G5compare`	Compare two HDF5 files.
`GooseHDF5.cli.G5repack`	Read and write a HDF5 file.

G5check

Try reading datasets.: In case of reading failure the path is printed (otherwise nothing is printed).

usage

G5check [options] <source>

arguments

<source>: HDF5-file.

options

-b, --basic: Only try getting a list of datasets, skip trying to read them.
-h, --help: Show help.
--version: Show version.

(c - MIT) T.W.J. de Geus | tom@geus.me | www.geus.me | github.com/tdegeus/GooseHDF5

G5repair

Extract readable data from a HDF5-file and copy it to a new HDF5-file.

usage

G5repair [options] <source> <destination>

arguments

<source>: Source HDF5-file, possibly containing corrupted data.
<destination>: Destination HDF5-file.

options

-f, --force: Force continuation, overwrite existing files.
-h, --help: Show help.
--version: Show version.

(c - MIT) T.W.J. de Geus | tom@geus.me | www.geus.me | github.com/tdegeus/GooseHDF5

G5compare

Compare two HDF5 files.: If the function does not output anything all datasets are present in both files, and all the content of the datasets is equal. Each output line corresponds to a mismatch between the files.

usage

G5compare [options] <source> <other>

arguments

<source>: HDF5-file.
<other>: HDF5-file.

options

-t, --dtype: Verify that the type of the datasets match.
-r, --renamed=ARG: Renamed paths: this option takes two arguments, one for source and one for other. It can repeated, e.g. G5compare a.h5 b.h5 -r /a /b -r /c /d

-c, –color=STR (none, dark): Color theme. default: dark.

-h, --help: Show help.
--version: Show version.

(c - MIT) T.W.J. de Geus | tom@geus.me | www.geus.me | github.com/tdegeus/GooseHDF5

G5repack

Read and write a HDF5 file.: This allows a compacter file by removing features like extendible datasets.

usage

G5repack [options] <source>…

arguments

<source>: HDF5-file.

options

-c, --compress: Apply compression (using the loss-less GZip algorithm).
-f, --float: Store doubles as floats.
-h, --help: Show help.
--version: Show version.

(c - MIT) T.W.J. de Geus | tom@geus.me | www.geus.me | github.com/tdegeus/GooseHDF5