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Workspace

Python module for handling HDF5 variables in ipython console.
Created variables are stored using h5py.

Main Features

  • Provides a set of tools for handling variables, i.e. objects being instances of the Variable class.
  • Variables are created in the interactive namespace, which is by default a current __main__ module.
  • When running in IPython, variables are available through the interactive namespace.
  • Each variable is paired with an associated HDF5 root group and exposes convenient interface for it.
  • Created variables are stored in the HDF5 binary data format.
  • Explore variables using tab completion mechanism. For IPython it is recommended to have greedy completion enabled.
  • Dataset compression is enabled by default. Compression parameters can be changed through the interactive namespace.

Motivation

A goal of this project is to provide environment for handling HDF5 files in Python console (preferably in IPython). Main application of this module is to store and organize large amount of measurement data.

Prerequisites

Workspace requires the following software installed for your platform:

  1. Python
  2. NumPy
  3. H5py
  4. IPython (optional)

The easiest way of getting all required software is to install Anaconda

Basic Usage

This chapter assumes that all required packages are installed.

ENVIRONMENT CONFIGURATION

In order to start working with Workspace module following steps are needed:

  1. Run Python interpreter in the directory containing project files.
  2. Import ui module: import workspace.ui
  3. Create an instance of the Interface() class: ws = workspace.ui.Interface()
  4. Enable tab completion mechanism: (optional, IPython only) get_ipython().magic('config IPCompleter.greedy = True')
CREATING/OPENING A HDF5 FILE

HDF5 file are being created by calling add method on the ws object, which is an instance of the workspace.ui.Interface() class.

Example:

In: ws.add("example_file.h5")

CREATING VARIABLES

Variables are being created by calling a propercreate method on the ws[file_index], which points to HDF5 file with index = [file_index] in the interactive namespace. As for now there is only basic type supported. More information could be found in the API Reference

Example:

In: ws[0].create.basic("var1")

It is also possible to specify parent of variable that is being created: Following code creates variable var2 as a children of var1.

In: ws[0].create.basic("var2",var1)

REMOVING VARIABLES

In order to remove variable from the HDF5 file and the interactive namespace, method remove() should be called on it.

Example:

In: var1.remove()

DISPLAYING LIST OF HDF5 FILES

List of HDF5 files that are loaded in current session is available through ws object, which is an instance of the workspace.ui.Interface() class.

Example:

In: ws Out:

0) HDF5 file "file_0.h5" (mode r+)
1) HDF5 file "file_1.h5" (mode r+)
2) HDF5 file "file_2.h5" (mode r+)
DISPLAYING LIST OF VARIABLES

List of variables contained in all HDF5 files that are loaded in current session, is available through ws.vars, where ws is an instance of the workspace.ui.Interface() class.

Example:

In: ws.vars Out:

0) Variable var_0 (-) from HDF5 group "/var_0" (1 members) in HDF5 file "file_0.h5" (mode r+)
1) Variable var_1 (var_0) from HDF5 group "/var_1" (1 members) in HDF5 file "file_0.h5" (mode r+)
2) Variable var_2 (var_1) from HDF5 group "/var_2" (1 members) in HDF5 file "file_1.h5" (mode r+)
2) Variable var_3 (-) from HDF5 group "/var_3" (1 members) in HDF5 file "file_2.h5" (mode r+)

For each variable there is also name of the parent of associated HDF5 group displayed in bracket. If the group does not have parent, (-) is showed.

API Documentation

API documentation is available on the web: API Reference

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.