AreTomo (w)rapper for rln4
Project description
li'l AreTomo
A lightweight Python API for AreTomo.
Installation
It is recommended to install into a fresh virtual environment.
pip install lil_aretomo
Usage
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
pip install -e .[dev]
pre-commit install
Flake8, black and isort will then run automatically on each commit.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
lil_aretomo-0.1.1.tar.gz
(10.0 kB
view details)
Built Distribution
File details
Details for the file lil_aretomo-0.1.1.tar.gz.
File metadata
- Download URL: lil_aretomo-0.1.1.tar.gz
- Upload date:
- Size: 10.0 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.0 CPython/3.12.3
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 02ccb0efbf2c06304570117f142e78331bfffdde46864e22de11c6cd7f30f178 |
|
| MD5 | 9969aa604e174861c215c1b4df0c48c6 |
|
| BLAKE2b-256 | 6a525226ffe39caa5f12ba6ab8172466952c5d4799e8d5d2906529f0d0932731 |
File details
Details for the file lil_aretomo-0.1.1-py2.py3-none-any.whl.
File metadata
- Download URL: lil_aretomo-0.1.1-py2.py3-none-any.whl
- Upload date:
- Size: 6.8 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.0 CPython/3.12.3
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 7318f945626f66b7700eac7b27172849d8991d02e87d55a17ba5d09263c08e8e |
|
| MD5 | c382a962706dfd40a59857a1804167bd |
|
| BLAKE2b-256 | 788510273a7dede1739a6c16062956a4d78db13c5f15f347e3fb580c48ec2538 |
