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.

If you have a really big file:

  • The --layer option can be much faster than searching the entire file.

  • Search only --datasets when folding can be much faster. The getgroups function does search the entire depth.

usage: G5list [-h] [--min-attrs MIN_ATTRS] [--link-type] [-D] [-d MAX_DEPTH]
              [-f FOLD] [-i] [-L LAYER] [-l] [-r ROOT] [--links] [-s SORT]
              [-v]
              source

Positional Arguments#

source

Named Arguments#

--min-attrs

Filter based on min. number of attributes

--link-type

Print the link-type

Default: False

-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: “/”

--links

Show destination of soft links

Default: False

-s, --sort

Sort by some column

Default: “path”

-v, --version

show program’s version number and exit

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.

Deal with renamed paths:

G5compare a.h5 b.h5 -r "/a" "/b"  -r "/c" "/d"

usage: G5compare [-h] [-t] [--close] [--shallow] [-D] [-d MAX_DEPTH] [-f FOLD]
                 [-r RENAMED RENAMED] [-R RENAMED_YAML] [-c COLORS]
                 [--table TABLE] [-I] [-v]
                 a b

Positional Arguments#

a

Path to HDF5-file.

b

Path to HDF5-file.

Named Arguments#

-t, --dtype

Verify that the type of the datasets match.

Default: False

--close

Use np.isclose also on float-int matches.

Default: False

--shallow

Only check for the presence of datasets and attributes. Do not check their values.

Default: False

-D, --datasets

Print only datasets

Default: False

-d, --max-depth

Maximum depth to display

-f, --fold

Fold paths

-r, --renamed

Renamed paths.

-R, --renamed-yaml

YAML file with renamed paths.

-c, --colors

Color theme: dark/light/none

Default: “dark”

--table

Table theme

Default: “SINGLE_BORDER”

-I, --input

Header identical to input

Default: False

-v, --version

show program’s version number and exit

G5check#

G5repair#

G5repack#