This repository contains the toolkit to create and proocess the database of seizure and seizure-like data that has been contributed by OpenSeizureDetector users to contribute to research to improve seizure detection algorithms (Open Seizure Toolkit, OSTK).
The repository contains a number of python tools that form a toolkit to assist users of the database in working with the JSON files containing the seizure data. The database data itself is stored separately, with access granted on request as described below.
The python tools are licenced under the GNU General Public Licence, V3.
The OpenSeizureDatabase data is licenced under a variation of the Creative Commons Share Alike licence, with an additional licence condition to publish a description of the system developed and results obtained using the data for the benefit of users of the OpenSeizureDetector project - see the LICENCE description for more details.
The following people have access to the anonymised OpenSeizureDatabase data.
| Name | Contact | Research Area | Web Site |
|---|---|---|---|
| Graham Jones | graham@openseizuredetector.org.uk | Development of Improved SeizureDetection Algorithms for OpenSeizureDetector | OpenSeizureDetector |
| Jamie Pordoy | pordjam@uwl.ac.uk | PhD Research into Seizure Detection | IntSaV Group |
| Benjamin Mickler | Research into seizure detection | ||
| Anthony Cuturrufo, UCLA | Machine Learning Seizure Detection | ||
| Bram Regtien | @aroonPro | OSD Development | |
| Jongchan Lee, Mokwon University | @paorisun | Student Project: Multi-Function smartwatch development | |
| Junrun Chen, Hangzhou Dianzi University | @ErHai1 | classification of epilepsy seizure types and the detection of epilepsy classifications |
Researchers who would like access to the data should email osdb@openseizuredetector.org.uk explaining what they intend to use the data for, and confirming that they will comply with the requirements of the LICENCE for the data. They will then be given access to a repository containing the JSON files that make up the Open Seizure Database.
- Create a folder in your home directory called "osd" and change directory into it.
- Clone this repository (git clone https://github.com/OpenSeizureDetector/OpenSeizureDatabase.git)
- change directory to ~/osd/OpenSeizureDatabase
- create a python virtual environment with python -m venv ~/pyEnvs/osdb
- activate the virtual environment with source ~/pyEnvs/osdb/bin/activate [note, I create an alias in ~/.bashrc with alias osdb='source /home/graham/pyEnvs/osdb/bin/activate' - then i just type 'osdb' to activate the environment].
- execute pip install -r requirements.txt (note the tensorflow requirement is not essential so can be removed if you do not intend to use tensorflow to train neural networks).
- Create a folder in your home directory called "osd/osdb"
- Copy the OSDB JSON text files into ~/osd/osdb
- Go to ~osd/OpenSeizureDatabase/user_tools/dataSummariser
- rename osdbCfg.json.template to osdbCfg.json and adapt it to suit your configuration (folder for example)
- execute python ./summariseData.py --index. This should produce a file output/index.html which lists all the data in the database. Note that there will be missing image files because these are only generated when a full summary is created.
- execute python ./summariseData.py --event=5483. This should produce a folder, output/Event_5483_summary which contains an html file (index.html) and associated images to display a summary of the event, similar to the example output in the documentation folder.
For details of the data structure and the software included in this repository, please refer to the Documentation. The documentation folder also contains an Example set of data for a seizure for reference.