Metadata-Version: 2.4
Name: axonemalyze
Version: 0.0.1
Summary: Calculate the circularity of axoneme picks from cryo-ET images.
Project-URL: repository, https://github.com/ammsa23/axonemalyze
Author-email: Ammaar Saeed <ammaar_saeed@g.harvard.edu>
License: MIT License
License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Typing :: Typed
Requires-Python: >=3.7
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scipy
Provides-Extra: dev
Requires-Dist: black; extra == 'dev'
Requires-Dist: pandas; extra == 'dev'
Requires-Dist: pytest; extra == 'dev'
Requires-Dist: pytest-cov; extra == 'dev'
Provides-Extra: test
Requires-Dist: numpy; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Requires-Dist: pytest>=6.0; extra == 'test'
Requires-Dist: scipy; extra == 'test'
Description-Content-Type: text/markdown

# axonemalyze
Calculate the circularity of axoneme picks from cryo-ET images.

# Functions
The code is split into two command-line functions:
- `segment_axonemes`
- `estimate_circularity`

Installing the package gives access to these functions. The command-line functions are to be run in that order.

For more help with these functions, use the `-h` flag.

## segment_axonemes
The function takes a directory as input. This directory should contain all files in the `.coords` format with the xyz coordinates of the picks.

Here is an example of how to run this function:
```
segment_axonemes test_data/
```

This function outputs a directory (default `segmented/`) in the input directory with a single `.csv` file per axoneme.

## estimate_circularity.py
This function takes a directory as input. This directory should contain all files in the `.csv` format as outputted by `segment_axonemes.py`.

Here is an example of how to run this function:
```
estimate_circularity test_data/segmented/
```

This function prints an average circularity for each axoneme that contains at least five doublets to the standard output.
