Overview
This project contains the common functions used in the context of brain atlases. It is used by the projects:
- https://github.com/BlueBrain/atlas-densities
- https://github.com/BlueBrain/atlas-direction-vectors
- https://github.com/BlueBrain/atlas-placement-hints
- https://github.com/BlueBrain/atlas-splitter
Installation
git clone https://github.com/BlueBrain/atlas-commons
cd atlas-commons
pip install -e .
Examples
Create a mask for the region defined by query
from atlas_commons import utils
from voxcell.nexus.voxelbrain import Atlas
# see voxcell documentation for more more information
atlas = Atlas.open('.')
annotation = atlas.load_data('brain_regions')
region_map = atlas.load_region_map()
region = {
"query": "Isocortex",
"attribute": "acronym",
"with_descendants": True,
}
mask = utils.query_region_mask(region, annotation, region_map)
Split input 3D volume into two halves using the middle plane orthogonal to the z-axis
from atlas_commons import utils
import numpy as np
volume = np.array(
[
[[0, 1, 2], [2, 3, 4]],
[[4, 5, 6], [7, 8, 9]],
],
dtype=np.int64,
)
halves = utils.split_into_halves(volume)
Instructions for developers
Run the following commands before submitting your code for review:
cd atlas-commons
isort -l 100 --profile black atlas_commons tests setup.py
black -l 100 atlas_commons tests setup.py
These formatting operations will help you pass the linting check testenv:lint defined in tox.ini.
Acknowledgements
The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.
For license and authors, see LICENSE.txt and AUTHORS.txt respectively.
Copyright © 2022 Blue Brain Project/EPFL