104 lines
5.3 KiB
Markdown
104 lines
5.3 KiB
Markdown
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# junifer - JUelich NeuroImaging FEature extractoR
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[](https://anaconda.org/conda-forge/junifer)
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[](https://github.com/charliermarsh/ruff)
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[](https://github.com/pre-commit/pre-commit)
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[](https://doi.org/10.5281/zenodo.8176570)
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[](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
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## About
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`junifer` is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.
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It is currently being developed and maintained at the [Applied Machine Learning](https://www.fz-juelich.de/en/inm/inm-7/research-groups/applied-machine-learning-aml) group at [Forschungszentrum Juelich](https://www.fz-juelich.de/en), Germany. Although the library is designed for people working at [Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7)](https://www.fz-juelich.de/en/inm/inm-7), it is designed to be as modular as possible thus enabling others to extend it easily.
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The documentation is available at [https://juaml.github.io/junifer](https://juaml.github.io/junifer/main/index.html).
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## Repository Organization
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* `docs`: Documentation, built using sphinx.
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* `examples`: Examples, using sphinx-gallery. File names of examples that create visual output must start with `plot_`, otherwise, with `run_`.
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* `junifer`: Main library directory.
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* `api`: User API module.
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* `configs`: Module for pre-defined configs for most used computing clusters.
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* `data`: Module that handles data required for the library to work (e.g. parcels, coordinates).
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* `datagrabber`: DataGrabber module.
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* `datareader`: DataReader module.
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* `external`: Module for external libraries and tools.
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* `markers`: Markers module.
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* `onthefly`: Transformation components (on-the-fly) module.
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* `pipeline`: Pipeline module.
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* `preprocess`: Preprocessing module.
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* `storage`: Storage module.
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* `testing`: Testing components module.
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* `typing`: Type hints module.
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* `utils`: Utilities module (e.g. logging).
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## Installation
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Use `pip` to install from PyPI like so:
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```
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pip install junifer
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```
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You can also install via `conda`, like so:
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```
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conda install -c conda-forge junifer
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```
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### Optional dependencies
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`junifer` supports a few optional dependencies to enable certain features. You can
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install them by specifying a comma separated list within square brackets, like so:
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```
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pip install "junifer[bct,dev]"
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```
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* `bct` installs [bctpy](https://github.com/aestrivex/bctpy) to enable use of `onthefly` module.
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* `neurokit2` installs [neurokit2](https://github.com/neuropsychology/NeuroKit) to enable use of [complexity markers](https://juaml.github.io/junifer/main/api/markers.html#module-junifer.markers.complexity).
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* `all` includes all of the above.
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* `dev` installs packages needed for development.
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* `docs` installs packages needed for building documentation.
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## Citation
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If you use `junifer` in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project's [Zenodo URL](https://doi.org/10.5281/zenodo.8176569).
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## Funding
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We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
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[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`. Development of this software was funded, in part, by the European Union’s Horizon Europe Framework Programme for Research infrastructures under the [specific grant agreement no. 101147319](https://cordis.europa.eu/project/id/101147319) (EBRAINS 2.0).
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(The funding sources had no role in the design, implementation and evaluation of the pipeline.)
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## Contribution
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Contributions are welcome and greatly appreciated. Please read the [guidelines](https://juaml.github.io/junifer/main/contributing.html) to get started.
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## License
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junifer is released under the AGPL v3 license:
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junifer, FZJuelich AML neuroimaging feature extraction library.
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Copyright (C) 2023, authors of junifer.
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU Affero General Public License as published by
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the Free Software Foundation, either version 3 of the License, or any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU Affero General Public License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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