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',
skip_if_completed=False
)
# 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',
skip_if_completed=False
)
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.
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
File details
Details for the file yet-another-imod-wrapper-0.0.9.tar.gz.
File metadata
- Download URL: yet-another-imod-wrapper-0.0.9.tar.gz
- Upload date:
- Size: 17.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.1 CPython/3.11.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 7cf4e180166166ec6e34b83cd5c038f55161b533f13f6c51611e6f5513acccd4 |
|
| MD5 | a0652c62727be8c8fd9d858cfd1609c7 |
|
| BLAKE2b-256 | c444fd71c62a037f59b1bf34772eac7e7cc423f8cd8c9b338045c5dd56f04834 |
File details
Details for the file yet_another_imod_wrapper-0.0.9-py2.py3-none-any.whl.
File metadata
- Download URL: yet_another_imod_wrapper-0.0.9-py2.py3-none-any.whl
- Upload date:
- Size: 13.4 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.1 CPython/3.11.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 97cf1ad02cb8ed67d6e1b4b1401a10d5f7a6541851bcc15543409fb624f84f8f |
|
| MD5 | d5628898d689df6cd7f27d888fd4e38f |
|
| BLAKE2b-256 | dcca0738b8f18a22dab34f7c79fb6c52b69fcc37fdef5cb586bf7ca32568242f |
