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Recent Releases of pytom-match-pick

pytom-match-pick - 0.10.0

What's Changed

  • drop python 3.10 by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/295
  • add testing for correlation by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/296
  • add testing for create_mask by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/297
  • add --relion5-compat to merge_stars by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/298

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.9.0...0.10.0

- Python
Published by sroet 8 months ago

pytom-match-pick - 0.9.0

What's changed

  • Thanks to @shahpnmlab, pytom-match-pick now supports reading xml metadata from WarpTools to calculate the 3D-CTF!

Overview of PR's

  • update help on particle-diameter to describe intended behavior by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/274
  • Deal with multi column tilt file by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/276
  • Make sure we error with a reasonable message if gpus can't evenly devide number of splits by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/277
  • Fix auto compilation of docs by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/278
  • informative error on mask template shape mismatch by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/283
  • Fix handling of tomogram masks in signed bytes by @rdrighetto in https://github.com/SBC-Utrecht/pytom-match-pick/pull/270
  • update/add citation by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/288
  • add CODEOWNERS file to harden .github directory by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/290
  • make pytom warp xml compatible by @shahpnmlab in https://github.com/SBC-Utrecht/pytom-match-pick/pull/284

New Contributors

  • @rdrighetto made their first contribution in https://github.com/SBC-Utrecht/pytom-match-pick/pull/270
  • @shahpnmlab made their first contribution in https://github.com/SBC-Utrecht/pytom-match-pick/pull/284

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.8.0...0.9.0

- Python
Published by McHaillet 9 months ago

pytom-match-pick - 0.8.0

What's Changed

  • Fix symmetry by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/265
  • Change extract radius to particle diameter for consistency by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/264
  • Revised tutorial by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/261

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.11...0.8.0

- Python
Published by McHaillet about 1 year ago

pytom-match-pick - 0.7.11

What's Changed

  • new ruff version by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/255
  • fix for float16 scores for tophat by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/260

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.10...0.7.11

- Python
Published by McHaillet about 1 year ago

pytom-match-pick - 0.7.10

What's Changed

  • improve center approximation for relion5 by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/250

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.9...0.7.10

- Python
Published by McHaillet about 1 year ago

pytom-match-pick - restructured PyPI workflow

Code should still be identical to 0.7.4, but the release workflow has been changed to hopefully be more robust

What's Changed

  • Restructure release by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/242

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.8...0.7.9

- Python
Published by sroet over 1 year ago

pytom-match-pick - 0.7.8

THIS IS A RE-RELEASE OF 0.7.4 We ran into some issues with deployment to pypi, see #236

Major updates

  • pytommatchtemplate.py now supports relion5 metadata input via the --relion5-tomograms-star option. You can provide a tomograms.star file from a tomogram reconstruction job and pytom-match-pick will fetch the necessary CTF and dose data by the tomogram id.
  • Some small fixes were also made to relion5-style star file particle list to make reading back easier.

What's Changed

  • dont publish attestation to pypi by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/240

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.7...0.7.8

- Python
Published by McHaillet over 1 year ago

pytom-match-pick - 0.7.7

Here we go again...

- Python
Published by McHaillet over 1 year ago

pytom-match-pick - 0.7.5

Test release to get automatic deployment running again.

- Python
Published by McHaillet over 1 year ago

pytom-match-pick - 0.7.4

Major updates

  • pytommatchtemplate.py now supports relion5 metadata input via the --relion5-tomograms-star option. You can provide a tomograms.star file from a tomogram reconstruction job and pytom-match-pick will fetch the necessary CTF and dose data by the tomogram id.
  • Some small fixes were also made to relion5-style star file particle list to make reading back easier.

PR's

  • deal with new ruff version and next try for tutorial-test.yml by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/224
  • Update tutorial-tests.yml by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/225
  • Get tutorial-tests.yml working by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/226
  • Add bins option to both the tophat and extraction plot by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/227
  • add check on input gpu indices by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/228
  • Drop py 39 and upgrade by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/230
  • Relion5 input by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/229

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.2...0.7.4

- Python
Published by McHaillet over 1 year ago

pytom-match-pick - 0.7.2

Major changes

  • We have a site! (It's automatically deployed with changes to the main branch)
  • The tomogram mask supplied to match_template can now be ignored upon extraction to prevent unnecessary recalculation.
  • After some initial issues, reading of starfiles by RELION5 should be fixed when using relion5-compat mode in extract_candidates.
  • Score maps can be written out in float16 mode to save some disk space.
  • Defocus handedness can be specified in match_template and will calculate defocus offsets for each subvolume. The site got a new 'Benchmarks' tab where a post is added that illustrates the effects of specifying defocus handedness (check it out here).

PR overview

  • fix defocus help unit by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/197
  • mkdocs site for pytom-match-pick by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/199
  • fix: strings signs in deploy docs workflow by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/203
  • Update README.md by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/202
  • update workflow permission to write github pages by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/204
  • Update Developers.md by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/205
  • Add ignore tomo mask option by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/209
  • add check on tomo mask shape by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/210
  • site updates: fix some usage informations, make authorship clear, add logo by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/212
  • add E501 check by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/216
  • Create CITATION.cff by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/218
  • Fix relion5 compat by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/220
  • logging.warn will be deprecated by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/223
  • add comment to entry_points that tells developers not to use line bre… by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/219
  • feature: calculate subvolume defocus values by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/217
  • Enable 16 bit output by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/222

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.1...0.7.2

- Python
Published by McHaillet over 1 year ago

pytom-match-pick - 0.7.1

What's Changed

  • Add DOI badge to readme.md by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/186
  • add tutorial test yml by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/187
  • Update pyproject.toml by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/188
  • fix: make output directories for tutorial tests by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/189
  • revert healpix workaround by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/193
  • bug fix: add int type for rng seed by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/192

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.0...0.7.1

- Python
Published by McHaillet over 1 year ago

pytom-match-pick - 0.7.0

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.
  • 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

- Python
Published by McHaillet over 1 year ago

pytom-match-pick - 0.6.0

What's Changed

  • change default mrc permissive to false, try to autorecover, remove userfacing 'permissive' argument by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/140
  • don't make plots for particle extraction in estimate_roc by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/147
  • change 'ptm' to 'rln' in the extraction star file by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/149
  • README.md now points to GitHub Discussions for usage questions by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/154

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.5.0...0.6.0

- Python
Published by McHaillet almost 2 years ago

pytom-match-pick - 0.5.0

What's changed

  • summations of tilts in the per-tilt weighted wedge has been improved leading to less aliasing
  • center of tilt rotation is updated to properly correspond to Fourier space origin
  • install instructions now point to the pip install from pypi!

Pull requests

  • Try to fix race condition in testing by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/138
  • update readme to point to pip install instead of source by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/139
  • ctf model ramp weighting correction and updated interpolation center by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/141

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.4.3...0.5.0

- Python
Published by McHaillet almost 2 years ago

pytom-match-pick - 0.4.3

Third (and hopefully last) release to try to get automatic pypi working

What's Changed

  • Fix release workflow by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/137

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.4.2...0.4.3

- Python
Published by sroet about 2 years ago

pytom-match-pick - 0.4.2

second try for pypi release

What's Changed

  • Update pyproject.toml by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/136

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.4.1...0.4.2

- Python
Published by sroet about 2 years ago

pytom-match-pick - 0.4.1

This is a (of hopefully not too many) test release to see if we can automagickally publish to pypi

What's Changed

  • Enable auto pypi publishing by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/134
  • test updated version by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/135

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.4.0...0.4.1

- Python
Published by sroet about 2 years ago

pytom-match-pick - 0.4.0

What has changed

  • The name has changed to pytom-match-pick for easy distinguishing!
  • Installation has been changed to use entry-points instead of bin scripts.
  • Small fixes for template generation to prevent some nasty artifacts. It can improve results for EM map generated templates.
  • Small improvements to the repository to continuous testing.
  • Coverage reports are now generated for pull requests!

List of PR's

  • Convert bin scripts to entry points by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/109
  • small fixes for template generation and preparation by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/114
  • initual guess for github workflow by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/115
  • get gh workflows working by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/116
  • Add test badge to README.md by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/117
  • add coverage reporting by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/118
  • Update coverage.yml by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/120
  • Update unit-tests.yml by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/121
  • Update coverage.yml by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/122
  • test 80% coverage failing by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/123
  • and back to 75! by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/124
  • enable coverage of the multiprocess code by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/125
  • changing name to pytom-match-pick from pytom-template-matching-gpu by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/126
  • add tests for missing libraries by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/127
  • remove unnecessary 'if name==main:unittest.main()' from testfiles by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/130
  • get tests to 100% coverage by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/131
  • readme update pytom-match-pick by @McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/132
  • Update main branch version to 0.4.0 by @sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/133

Full Changelog: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.3.5...0.4.0

- Python
Published by McHaillet about 2 years ago

pytom-match-pick - 0.3.5

Updates

  • The calculation of standard deviation over the template matching search has been updated, which means the default extraction mode of pytom_extract_candidates.py should work better. This is especially the case for jobs that split the search into subvolumes.
  • Quality of life improvement, but does not change any results: whitening filter is no longer recalculated everytime the TMJob class is initialized, which saves unnecessary calculation for extraction jobs.

List of PRs

  • Slicing for std calculation by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/110
  • Prevent whitening for extraction by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/112

Full Changelog: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.4...0.3.5

- Python
Published by McHaillet about 2 years ago

pytom-match-pick - 0.3.4

Major points

  • We fixed a bug where in template matching the combination of a restricted search in xyz (--search-x option, etc.) and volume split would lead to incorrect merging of subvolumes.
  • Installation instructions favor building cupy against local cuda-toolkit, but for robustness also highlight the option to put a cuda-toolkit with prebuild cupy in the conda environment. However, building cupy can provide almost 2x better performance on our systems.
  • We added a workaround for cupy 13.0.0 which currently broke a custom kernel.

List of PRs

  • Improved installation instructions by @thorstenwagner in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/69
  • Update install instruction p2 by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/71
  • Terminate other processes if one breaks by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/75
  • parallel manager in a separate test file by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/78
  • unittest discover requirest testfiles to start with 'test' by @sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/79
  • calculate spectrum whitening filter only in the search region by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/81
  • Standard deviation cut-off lower threshold by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/82
  • Subvolume indexing bug by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/83
  • Add scipy to requirements in setup.py by @sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/87
  • Add tutorial wiki link to the README.md by @sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/86
  • make json writing OS agnostic in tmjob.py by @sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/90
  • Template.py: make filter warnings conditional and allow for no ctf_params by @sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/98
  • experimental tophat filtering for constraining score volume peaks at extraction by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/91
  • add docstrings to all functions by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/100
  • Convert to pyproject.toml by @sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/104
  • Cupy13 workaround by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/107
  • update install instructions to prefer building cupy by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/108

New Contributors

  • @thorstenwagner made their first contribution in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/69

Full Changelog: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.3...0.3.4

- Python
Published by McHaillet about 2 years ago

pytom-match-pick - 0.3.3

What's Changed

  • update to minimal cutoff value in estimate_roc by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/65
  • Patch unittest inconsistency by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/66
  • Patch single radial average function by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/67
  • Bump version to 0.3.3 by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/68

Full Changelog: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.2...0.3.3

- Python
Published by McHaillet about 2 years ago

pytom-match-pick - 0.3.2

What's Changed

  • Patch for failing extraction at volume edges by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/60
  • Patch band pass unassigned by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/62
  • improve radial average speed with nimdage.mean() by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/63
  • add check for equal scores in merging sub jobs to prevent race condition by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/64

Full Changelog: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.1...0.3.2

- Python
Published by McHaillet over 2 years ago

pytom-match-pick - 0.3.1

What's Changed

  • import pytom_tm now has a pytom_tm.__version__ attribute
  • jobs are now annotated with the module version number
  • the symmetry option is now specific about only covering rotational symmetry around the z-axis
  • whitening filters are now stored to prevent recalculation

by @McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/57

Full Changelog: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.0...0.3.1

- Python
Published by McHaillet over 2 years ago

pytom-match-pick - Per-tilt CTF and dose weighting, spectrum whitening, and rotational symmetry

Version 0.3.0 is out!

Functionality updates to pytom_match_template.py: - The --per-tilt-weighting option has been expanded so it can now model a 3D CTF with tilt and dose weighting (as previously described in methods like Relion subtomo averaging, Warp, and EmClarity). To enable the full weighting 3 files need to be provided: a .rawtlt/.tlt file with tilt angle info, a .defocus/.txt file with per tilt defocus (in nm), and a file with accumulated dose per tilt (in e-/A2). The defocus file and dose file are assumed to have the same ordering as the tlt file. PR #53 - Spectrum whitening is now available (similar to Rickgauer et al., (2017) for 2DTM). The power spectrum radial average is estimated for the full tomogram, and the whitening filter is calculated from it and applied to tomogram and template. It sharpens the correlation peaks! PR #53 - There is now a rotational-symmetry option to reduce the angular search for templates with rotational symmetry. PR #55 - It is now possible to provide a custom angular search file. PR #56

Fixes: - pytom_create_template.py has a more specific warning message for the low pass filter. PR #51

Docs will be updated soon and we are working on a tutorial!

Thanks @rdrighetto for some very useful discussion on the CTF model.

- Python
Published by McHaillet over 2 years ago

pytom-match-pick - IO consistency fixes and cellular masks

Most important updates - starfiles written out by this module now contain all the extraction statistics and header start with _ptm (#43) - tomographic mask to extract particles within cellular regions can now be applied during candidate extraction (#42) - a fix has been added to make the testing of parallel jobs numerically stable (#40) - a few IO fixes for MRC files to make reading more permissive (#33, #38, #41)

Thanks to @hamid13r for the great feedback!

- Python
Published by McHaillet over 2 years ago