yet another IMOD wrapper
Project description
yet-another-imod-wrapper
A simple Python API for aligning single axis tilt-series in IMOD.
from yet_another_imod_wrapper import (
align_tilt_series_using_fiducials,
align_tilt_series_using_patch_tracking
)
import mrcfile
import numpy as np
# load tilt series into (n, y, x) numpy array
tilt_series = mrcfile.read('my_tilt_series.mrc')
# align using fiducials
align_tilt_series_using_fiducials(
tilt_series=tilt_series,
tilt_angles=np.arange(-60, 63, 3),
pixel_size=1.35,
fiducial_size=10,
nominal_rotation_angle=85,
basename='my_tilt_series',
output_directory='fiducials'
)
# align using patch-tracking
align_tilt_series_using_patch_tracking(
tilt_series=tilt_series,
tilt_angles=np.arange(-60, 63, 3),
pixel_size=1.35,
patch_size=1000,
patch_overlap_percentage=33,
basename='my_tilt_series',
output_directory='patch_tracking'
)
Installation
This package requires that IMOD>=4.11.0
is installed and on the PATH
.
yet-another-imod-wrapper
can be installed using pip
.
pip install yet-another-imod-wrapper
We recommend installing into a fresh virtual environment.
Project details
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
Built Distribution
Close
Hashes for yet-another-imod-wrapper-0.0.5.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 3efe9e64b032454b6c6e7e828bf19f4f4d4e64521b34445829ddf3f23a4a1f86 |
|
MD5 | e9669a68700c2f75bce2db19d798d643 |
|
BLAKE2b-256 | f126bff79a2ff17f7da409154ea8bc47d35c5058e75e7fbc95fc123da12dc425 |
Close
Hashes for yet_another_imod_wrapper-0.0.5-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 335ac4fb813e4072075f61f11db119c37b950a72e881102b8c3057fe8a2c9616 |
|
MD5 | 113d111a06efe451c26eef9ea0774333 |
|
BLAKE2b-256 | df8f2fb3175fa2065aece6b2ec4fae8e88c0f9cbbb7dfa9c76a5785d9540e4c2 |