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 files for lil-aretomo 0.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| lil_aretomo-0.1.1.tar.gz | 10.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| lil_aretomo-0.1.1-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 16.9 kB
Release files / lil_aretomo-0.1.1.tar.gz
| Download URL | lil_aretomo-0.1.1.tar.gz |
|---|---|
| Size | 10.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.0 CPython/3.12.3
|
Release files / lil_aretomo-0.1.1-py2.py3-none-any.whl
| Download URL | lil_aretomo-0.1.1-py2.py3-none-any.whl |
|---|---|
| Size | 6.8 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
7318f945626f66b7700eac7b27172849d8991d02e87d55a17ba5d09263c08e8e
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.0 CPython/3.12.3
|
