Published June 14, 2024
| Version 0.7.0
Software
Open
SBC-Utrecht/pytom-match-pick: 0.7.0
- 1. Utrecht University
- 2. Max Planck Institute for Molecular Physiology
Description
This is a big one! And probably containts the last major api changes before the 1.0.0 release.
Wiki/tutorial will soon be updated to correspond with latest changes.
Main updates
- Thanks to @sroet the package now supports arbitrary angular sampling generation via healpix. This now makes it possible to provide a particle diameter as input and let pytom-match-pick figure out the correct angular sampling!
- A bug was fixed in the particle symmetry option as it was not applied to the correct euler angle.
- CTF parameters can now only be applied in
pytom_match_template.py
and no longer for template creation. This makes input more consistent and logical. - Particle lists can be written out to be Relion5 compatible: centered coordinates in angstrom and proper star file column names.
- A tomogram mask can be provided during template matching and will skip subvolumes where the mask is empty.
PRs
- Readme illustration by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/156
- Phase plate ctf and argparse grouping by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/157
- default value phase shift entry point by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/159
- Update cupy requirements by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/167
- wait longer to prevent leaked processes by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/168
- small speedboost by precalculating conjugation by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/165
- expose tophat kernel connectivity and make n-false-postives a float by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/166
- make template non-symmetrical for template matching test to prevent race condition by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/169
- refactor volume splitting by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/170
- auto generate sampling angles by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/163
- Ctf rework by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/174
- Relion5 compatibility by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/178
- Center of mass fix by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/179
- calculate angular search from particle diameter by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/181
- fix symmetry bug by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/184
- phase randomization score map correction by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/182
- pre-commit with ruff by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/183
- Add tomogram mask option for template matching by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/185
Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.6.0...0.7.0
Files
SBC-Utrecht/pytom-match-pick-0.7.0.zip
Files
(880.6 kB)
Name | Size | Download all |
---|---|---|
md5:5b5b0ad2368e0ba64d74733c6a2120c2
|
880.6 kB | Preview Download |
Additional details
Related works
- Is supplement to
- Software: https://github.com/SBC-Utrecht/pytom-match-pick/tree/0.7.0 (URL)