Metadata-Version: 2.1
Name: okapi-em
Version: 0.0.8
Summary: napari plugin to deal with charging artifacts in tomography electron microscopy data
Author: Luis Perdigao
Author-email: luis.perdigao@rfi.ac.uk
License: Apache-2.0
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Framework :: napari
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: Apache Software License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: magicgui
Requires-Dist: chafer
Requires-Dist: napari[all]
Requires-Dist: opencv-python
Requires-Dist: quoll (>=0.0.4)
Requires-Dist: pyqt5
Provides-Extra: all
Requires-Dist: imageio-ffmpeg ; extra == 'all'
Provides-Extra: testing
Requires-Dist: tox ; extra == 'testing'
Requires-Dist: pytest ; extra == 'testing'
Requires-Dist: pytest-cov ; extra == 'testing'
Requires-Dist: pytest-qt ; extra == 'testing'

# okapi-em

https://github.com/rosalindfranklininstitute/okapi-em

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A napari plugin for processing serial-FIB-SEM data.

Powered by [chafer] and [quoll].

This [napari] plugin contains the following tools:

- slice alignment using constrained SIFT
- two charge artifact suppression filters
    - directional fourier bandapass filter
    - line-by-line filter function optimiser and subtraction (requires charge artifact labels) - uses [chafer]
- fourier ring correlation (FRC) resolution estimation - uses [quoll]

----------------------------------

This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.

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Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started

and review the napari docs for plugin developers:
https://napari.org/plugins/stable/index.html
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## Installation

You can install `okapi-em` via [pip]:

`pip install okapi-em`

For development mode it can be installed, clone this package then navigate to the cloned `okapi-em` folder and run:

`pip install -e .`

This should install in any machine, however ...

Currently the FRC calculation provided by the [quoll] package which is optional because
of its stringent environmemt requirements from miplib package. These currently are:

- python 3.7
- linux OS

This issue will be addressed in future version.


To install okapi-em with quoll included:

`pip install okapi-em[all]`

Note that to launch napari in python 3.7 you will need to use the command:

`python -m napari`



## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [Apache Software License 2.0] license,
"okapi-em" is free and open source software

## Issues

If you encounter any problems, please file an issue along with a detailed description.

[quoll]: https://github.com/rosalindfranklininstitute/quoll
[chafer]: https://github.com/rosalindfranklininstitute/chafer
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin


[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
