h5cat: preview the contents of HDF5 files in the command line.

h5cat is a Python script to quickly preview the contents of an HDF5 file. It is designed to be used in situations where hdfview is overkill. It is distributed under the open-source MIT license.

NOTE: h5cat is no longer maintained

See the excellent h5glance for a more modern replacement:

https://pypi.org/project/h5glance/#description

Requirements (tested versions)

• Python 2.7, 3.5+
• numpy (<2.0)
• h5py (<3.0)

All of the above are included in the Enthought Python Distribution, so I would recommend you just install that if you can. argparse is required if you are on Python 2.6 (but it is built in with 2.7).

Installation

pip install h5cat

Usage

Agglomeration

Run h5cat -h for a helpful message.

Here are a couple of examples to get you started.

By default, h5cat gives you the shape and type of every dataset in an HDF5 file.

$ h5cat single-channel-tr[0-3]-0-0.00.lzf.h5
>>> single-channel-tr1-0-0.00.lzf.h5

    stack
      shape:  (250, 250, 250) 
      type:  int32

    vi
      shape:  (3, 1) 
      type:  float64
>>> single-channel-tr2-0-0.00.lzf.h5

    stack
      shape:  (250, 250, 250) 
      type:  int32

    vi
      shape:  (3, 1) 
      type:  float64
>>> single-channel-tr3-0-0.00.lzf.h5

    stack
      shape:  (250, 250, 250) 
      type:  int32

    vi
      shape:  (3, 1) 
      type:  float64

If you want more details, use -v or --verbose to get a printout of the array. For large arrays this will be ...ed to show only the edges of the array as can be fit on screen. Use -g or --group to display only a specific group of the .h5 file.

$ h5cat -v -g vi single-channel-tr3-0-0.00.lzf.h5
>>> single-channel-tr3-0-0.00.lzf.h5

    vi
      shape:  (3, 1) 
      type:  float64
[[ 0.        ]
 [ 0.06224902]
 [ 2.23062383]]