https://github.com/bluebrain/atlas-commons
Common functions used in the context of brain atlases.
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 3 committers (66.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.3%) to scientific vocabulary
Keywords
atlas
build
Last synced: 5 months ago
·
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Repository
Common functions used in the context of brain atlases.
Basic Info
Statistics
- Stars: 1
- Watchers: 39
- Forks: 3
- Open Issues: 0
- Releases: 3
Archived
Topics
atlas
build
Created about 4 years ago
· Last pushed 12 months ago
Metadata Files
Readme
Changelog
Contributing
License
Authors
README.rst
.. warning::
The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
Future development will take place at: https://github.com/openbraininstitute/atlas-commons
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
============
.. code-block:: bash
git clone https://github.com/BlueBrain/atlas-commons
cd atlas-commons
pip install -e .
Examples
========
Create a mask for the region defined by `query`
-----------------------------------------------
.. code-block:: python
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
-------------------------------------------------------------------------------------
.. code-block:: python
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:
.. code-block:: bash
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
Owner
- Name: The Blue Brain Project
- Login: BlueBrain
- Kind: organization
- Email: bbp.opensource@epfl.ch
- Location: Geneva, Switzerland
- Website: https://portal.bluebrain.epfl.ch/
- Repositories: 226
- Profile: https://github.com/BlueBrain
Open Source Software produced and used by the Blue Brain Project
GitHub Events
Total
- Fork event: 1
Last Year
- Fork event: 1
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 14
- Total Committers: 3
- Avg Commits per committer: 4.667
- Development Distribution Score (DDS): 0.5
Top Committers
| Name | Commits | |
|---|---|---|
| Mike Gevaert | m****t@e****h | 7 |
| Luc Guyot | l****t@e****h | 6 |
| Leonardo Cristella | l****a@g****m | 1 |
Committer Domains (Top 20 + Academic)
epfl.ch: 2
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 0
- Total pull requests: 11
- Average time to close issues: N/A
- Average time to close pull requests: 8 days
- Total issue authors: 0
- Total pull request authors: 4
- Average comments per issue: 0
- Average comments per pull request: 1.64
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- mgeplf (10)
- bbpgithubaudit (3)
- alTeska (1)
- lecriste (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 149 last-month
- Total dependent packages: 0
- Total dependent repositories: 4
- Total versions: 4
- Total maintainers: 2
pypi.org: atlas-commons
Library containing common functions to build atlases
- Homepage: https://github.com/BlueBrain/atlas-commons
- Documentation: https://atlas-commons.readthedocs.io/
- License: Apache-2
-
Latest release: 0.1.5
published over 2 years ago
Rankings
Dependent repos count: 7.5%
Dependent packages count: 10.0%
Average: 19.1%
Forks count: 19.1%
Downloads: 26.7%
Stargazers count: 31.9%
Maintainers (2)
Last synced:
7 months ago
Dependencies
setup.py
pypi
- click >=7.0
- numpy >=1.15.0
- voxcell >=3.0.0
.github/workflows/publish-sdist.yml
actions
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish master composite
.github/workflows/run-tox.yml
actions
- actions/checkout v3 composite
- actions/setup-python v4 composite
- codecov/codecov-action v2 composite