# li'l AreTomo
A lightweight Python API for [AreTomo](https://www.biorxiv.org/content/10.1101/2022.02.15.480593v1).
## Installation
It is recommended to install into a fresh virtual environment.
```sh
pip install lil_aretomo
```
## Usage
```python
import numpy as np
import mrcfile
from lil_aretomo import align_tilt_series
tilt_series = mrcfile.read('my_tilt_series.mrc')
align_tilt_series(
tilt_series=tilt_series,
tilt_angles=np.linspace(-60, 60, 41),
pixel_size=1.35, # angstroms per pixel
sample_thickness_nanometers=2000, # angstroms
correct_tilt_angle_offset=True,
basename='TS_01', # basename for files passed to AreTomo
output_directory='TS_01_AreTomo',
skip_if_completed=False # set to True to skip if results from a previous alignment are present
)
```
### For developers
We use pre-commit to ensure code style and formatting remains consistent.
To install the package in editable mode development dependencies
```sh
pip install -e .[dev]
pre-commit install
```
Flake8, black and isort will then run automatically on each commit.
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