Metadata-Version: 2.1
Name: flowshape
Version: 0.1.3
Summary: Cell shape analysis using the spherical harmonics decomposition
Project-URL: Preprint, https://www.biorxiv.org/content/10.1101/2022.12.08.519700v1
Project-URL: Homepage, https://bitbucket.org/pgmsembryogenesis/flowshape/
Project-URL: Bug Tracker, https://bitbucket.org/pgmsembryogenesis/flowshape/issues
Author-email: Casper van Bavel <casper.vanbavel@kuleuven.be>
License-File: LICENSE
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/markdown

# FlowShape
This package provides functionality for the analysis of cell shape using the spherical harmonics decomposition.
Please refer to the [preprint](https://www.biorxiv.org/content/10.1101/2022.12.08.519700v1) for more information.
A local branch of [lie_learn](https://github.com/AMLab-Amsterdam/lie_learn) that does not depend on cython is included (spheremesh/lie_learn). 

## Installation
Currently the package is on pypi, but still requires conda to install libigl. We are working on an easier installation but in the meantime you can follow these steps:

Recommended: create a seperate conda environment and activate it:

`conda create --name flowshape_env`

`conda activate flowshape_env`

Then, install libigl from conda-forge:

`conda install -c conda-forge igl`

Finally, install FlowShape from pip:

`pip install flowshape`

## Demo

For the [demo](./demo/), you will need [JupyterLab](https://jupyter.org/install), as well as [Meshplot](https://skoch9.github.io/meshplot/tutorial/) for plotting.

To install both, run:

`conda install -c conda-forge jupyterlab meshplot`

Then, to open JupyterLab, run:

`jupyter-lab`

Download the demo folder from this repository and open the `demo.ipynb` notebook. 


## How to use
See [demo.ipynb](./demo/) for a basic example. The API consists only of functions operating on NumPy ndarrays and there are no classes. Most functions have docstrings in the source. More documentation to follow.
