silverlabnwb 0.2.0

Python tools for working with Silver Lab data in the NWB2 format

Python tools for working with Silver Lab data in the NWB2 format

• Free software: MIT license

This Python package simplifies access to NWB data for typical Silver Lab experiments, and converts data from Labview format into NWB. It provides a few command-line utilities, as well as supporting access from other Python software.

This work was funded by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under award number U01NS113273 (to Professor R. Angus Silver). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

This work was funded by the Wellcome Trust (101445, 203048) and the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under award number U01NS113273. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. These grants were awarded to Professor R. Angus Silver.

Installation

Some of our dependencies are hard to install, so it’s best to use conda:

conda create -n nwb2 python=3.6 pip numpy pandas hdf5 h5py
conda install -n nwb2 av tifffile -c conda-forge
conda activate nwb2
pip install silverlabnwb[video]

Documentation

https://PySilverLabNWB.readthedocs.io/

Development

Testing uses pytest, along with tox to test on multiple Python installations and do style checks etc.

To install the developer packages, run:

pip install .[test]

To test just on your current Python:

pytest

To run all the tests run:

tox

The automatic tests make use of various environment variables to customise what is run.

No ‘import’ tests will run unless SILVERLAB_DATA_DIR is set and points to a folder containing suitable data. A version of this folder is available through UCL’s OneDrive at present, but only contains smaller sample data. The full datasets are available on Jonathan’s Mac or the SilverLab shared drive.

Set SILVERLAB_TEST_LONG_IMPORTS to 1 to test importing full-size datasets.

Set SILVERLAB_GEN_REF to 1 to regenerate reference signatures.

Note, to combine the coverage data from all the tox environments run:

Windows	set PYTEST_ADDOPTS=--cov-append tox
Other	PYTEST_ADDOPTS=--cov-append tox

Changelog

0.1.0 (2020-06-09)

• First release on PyPI.

0.1.1 (2020-08-06)

• Minor patch to documentation and change log.

0.2.0 (2020-09-03)

• Update to pynwb 1.3.2

• handles up to LabView 2.3.1

• red and green channels now on same imaging plane

• manifold replaced by origin coordinates and grid spacing