HEDTools - Python

HED (Hierarchical Event Descriptors) is a framework for systematically describing both laboratory and real-world events as well as other experimental metadata. HED tags are comma-separated path strings. HED, itself, is platform-independent, extendable, and data-neutral.

This repository contains the underlying python tools that support validation, summarization, and analysis of datasets using HED tags. Most people will simply annotate their events by creating a spreadsheet or a BIDS JSON sidecar that associates HED tags with event codes or the events themselves. If you have such a spreadsheet or a JSON, you can use the HED Online Validator currently available at https://hedtools.ucsd.edu/hed to validate or transform your files without downloading any tools.

Installation

Use pip to install hedtools from PyPI:

    pip install hedtools

To install directly from the GitHub repository:

    pip install git+https://github.com/hed-standard/hed-python/@master

The HEDTools in this repository require python 3.7 or greater.

Relationship to other repositories

The hed-python repository contains the Python infrastructure for validating and analyzing HED. This repository has two companion repositories:

• hed-web contains the web interface for HED as well as a deployable docker module that supports web services for HED.
• hed-examples contains examples of using HED in Python and MATLAB. The site also contains many Jupyter notes illustrating various aspect of data curation and analysis using HED. The site hosts HED test datasets and the HED user manuals.

Develop versus master branches

Because the three repositories are interrelated, the following conventions are followed. The latest stable version is on the master branches of hed-python and hed-web and the main branch of hed-examples. The documentation link on readthedocs will describe the stable versions.

As features are integrated, they first appear in the develop branches of the three repositories. The develop branches of the three repositories will be kept in sync. If an interface change in hed-python triggers a change in hed-web or hed-examples, every effort will be made to get the stable branches of the respective repositories in sync.

To contribute

Contributions are welcome. Please use the Github issues for suggestions or bug reports. The Github pull request may also be used for contributions. Usually these updates should be made to the develop branch, not the master.

Other links of interest

HED specification documentation: https://hed-specification.readthedocs.io/en/latest/.

Examples: https://hed-examples.readthedocs.io/en/latest/.

Documentation: https://hed-python.readthedocs.io/en/latest/.

Code climate reports: https://codeclimate.com/github/hed-standard/hed-python.