Ctf3d ci - #2

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bHimes wants to merge 151 commits into

mainfrom

Commits on Dec 21, 2023

whole buncha shit
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82beb30

Commits on Jan 18, 2024

Hella Wip
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6ec2881

Commits on Jan 19, 2024

Removes previously deprecated stage of alignment NoAlignment
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81fbf3f
Removes StageOfAlignment ClassAlignment, as well as old functions to align classes to each other and related functionality that is years long broken
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1d8e27d
Remove SOA RefAlignment
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d46a1a2
Replace all pBH parameter structs with emc in prep for moving all optional parameters into the parser function
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6b4671b
Move nPeaks to parser
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e65636e
Move whitenPS to parser and remove old commented out function from ctf3d
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1846ede
Remove all optional refs to sf3d_v2 (always on now)
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be41dad
Manually formated all files, primarily to fix nesting indent inconsitencies that make editing code hard. The formater did some things I don't like, and will rever like alignment of function input/o…
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5404ede
Continue moving optional parameters and also create EMC_assert functions to check for correctness.
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a202e1b
Add parsing function to check and replace deprecated parameter names so old parameter files do not break.
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82f5a13
Added range checks for asserts and change microscope parameters.
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76c2191
Remove load tomo parameter
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8f7984a
Whole pile of parameteres moved
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6cd5840
basic parsing passes
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3e0e727
through basic avg and fsc, single ref align is running
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d9ef47d
Align, Avg for classification seem to be working, pca with single ref is running.
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8d32303

Commits on Jan 30, 2024

wip
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a65b243

Commits on Feb 2, 2024

WIP: Basic update to classification working, needs to be parameterized.
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7a7517f

Commits on Feb 12, 2024

Commits on Feb 15, 2024

Commits on Feb 16, 2024

Commits on Feb 18, 2024

mapBack WIP
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fb8b20f
Fix indexing problem in substack saving for toCistem
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7ccd09c

Commits on Feb 19, 2024

Commits on Feb 21, 2024

Commits on Feb 22, 2024

Breaking changes, breaking code, breaking my fast
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71ea25c
working for init and ctf3d, though the newstack op still is inverted
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8bb68df
well
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79b0dfb

Commits on Feb 23, 2024

Commits on Feb 26, 2024

hate
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4336ae1

Commits on Feb 28, 2024

Commits on Feb 29, 2024

Commits on Mar 1, 2024

Commits on Mar 4, 2024

wip
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44fea65

Commits on Mar 5, 2024

It seems there was no major flaw with correcting the x inversion in ctf 3d. Setting the default mtf to 1 (from 2) since the later maps seem to be oversharpened. This may be a contributor to overfit…
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2821a37

Commits on Mar 7, 2024

Commits on Mar 19, 2024

wipo
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e23aab1

Commits on Mar 22, 2024

Updates to make pca with random subset work again, set boundary errors in cross-correlation to ignore (i'm processing more data by the edges) and other wip
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a0cd087
WIP adding gpu conversions to and from half
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e401a3b
wip fix tracking of mexfiles
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e25bbd4
Fix non-tracking of mex files
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e395826
other things
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83b3a23
CPU to GPU swap during half cast seems to be working
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04906e2

Commits on Mar 24, 2024

Fixes bug in ctf update where new xform was used but not saved, turn off epxerimental flag in template search, more work on halfcast with gpu/cpu transfer embedded.
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bcb9c96

Commits on Mar 25, 2024

broken, but almost re-ordered alignRawv2
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991d3a7

Commits on Mar 26, 2024

multi-ref 2 seems to be working weith refactor
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364d9b0
Fix HP output when using colormap
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45317dd

Commits on Jun 17, 2024

With broken refactored alignRaw_v2, weird z-shifts, reverting that file to 44fea6575cf221d02897799b96e6eb46374a123c
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b68e74c

Commits on Jun 18, 2024

Keeping the reverted alignRaw. Note tomoCPR is still not running the alignments at the end
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33690d3

Commits on Jul 10, 2024

Roughed in a very basic prallelization for PCA over scaleSpace or multiRef.
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ae26c94

Commits on Jul 19, 2024

Add a more rigrous check on file validity to catch the case where the header is intact but the image file is still truncated. Add an (untested) method to remove all -9999 ignored particles from the…
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510d5d5

Commits on Sep 27, 2024

I think this fixes the parallel multi ref pca
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1858b35

Commits on Sep 30, 2024

Revert pca to single threaded as the results are not correct, and the acceleration is ~10-15% which is not worth trouble shooting right now.
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9be8302

Commits on Oct 5, 2024

Fix classIdx -> iRef in alignRaw
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3bb5c58

Commits on Jan 20, 2025

wip: making eigenvolumes more useful when symmetry contraints are applied by re-symmetrizing the outputs for visualization. Note: When reviewing, it looks like the options for PCA masking using a p…
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501e199

Commits on Jan 25, 2025

Wip: fixes bug where CTF/sf3d missing in -z presumably related to uint int conversion collapse
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1d81d4e

Commits on Feb 28, 2025

wip: working out a better handedness check
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837c76c

Commits on Mar 4, 2025

allow ctf 3d in parallel and a bunch of other shit including revamped ctf estimation/hand check
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2dbb839
forgot a debug breakpoint
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915f0c5
swapped order of loop in TM for big speed up
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695eaea

Commits on Mar 5, 2025

Commits on Aug 17, 2025

whole lotta chains in this mutha
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84a53cf

Commits on Aug 26, 2025

feat: Implement comprehensive tilt-series asset management and alignment system
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335a3b7

Commits on Aug 27, 2025

feat: Implement rubber band selection tool and enhance GUI architecture
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83c24c4

Commits on Sep 3, 2025

feat: Implement CUDA utilities and PaddedArray class with memory management
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6b8b15b
feat: Integrate emC auto-alignment with shell script functionality and establish emc_ naming convention

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GitHub Copilot
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638f4a6
wip
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4498177
ci: Streamline CI workflows to reduce queue times
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97d7fdd
ci: Switch to ubuntu-latest for better runner availability
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e72fb7b
ci: Remove unnecessary X11 dependencies for headless testing
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88e6c00
Fix Python linting issues
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964e428
Fix Black formatting for tilt_series_assets.py
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f5cbb89
Complete Black formatting for all Python files
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ff7c230
Fix Black/isort compatibility issues
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53905f0
Fix critical flake8 errors blocking CI
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1ac5602
Fix critical test import issues - use proper package structure
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c3c20c2
Update test_components.py import (WIP)
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71fe793
Add comprehensive Python .gitignore and context documentation
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643aafe
Progress on flake8 cleanup - major improvements
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995d13f
Continue flake8 cleanup - remove line length restrictions
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9a961fe

Commits on Sep 4, 2025

working on linting
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76d53db
Restructure CI workflows for focused granular checks
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1cac963
Add comprehensive CI status badges
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37748e3
wip
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9df16e4
Add comprehensive YAML comments explaining workflow efficiency
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a0b538d
wip
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3dfc2be
test gpu ci
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9b77a15
simplify runs-on
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a2b0cf4
fix cupy issue
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69ad2de
let unit tests fail
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a2af93b
feat: Enhance CUDA operations with memory layout fixes and diagnostics
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7d3e579

Commits on Sep 18, 2025

feat: Improve emClarity compilation output and error handling

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claude
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b2d11aa
fixes for alt_cache
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5d696b7

Commits on Sep 19, 2025

feat: Implement universal metadata wrapper with three-mode system

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28fe3d6
feat: Implement basic metadata wrapper with legacy support

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cee84c6
docs: Add wrapper usage guide

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889cf30
feat: Implement metadata wrapper system and improve compilation output

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71ba6de
fixes
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b351317

Commits on Sep 20, 2025

refactor: Major parameter handling and help menu cleanup

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claude
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0fe8102
feat: Comprehensive help message improvements for emClarity commands

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6c4c101
feat: Fix plotFSC command implementation and variable scope issues

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claude
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44883bc

Commits on Sep 22, 2025

feat: Implement atomic MAT file saves with integrity checking and retry logic

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fb3b5c4
fix: Improve error handling and debugging in atomic MAT file saves

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a6cef0a
feat: Add comprehensive MAT file corruption protection and safe copy utility

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af6d327
debug: Add comprehensive verbose debugging to atomic MAT file saves

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8bbd600
fix: Eliminate MAT file corruption by refactoring metadata I/O architecture

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claude
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51ffc86
wipo
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1b02e06

Commits on Sep 23, 2025

WIP: Implement parallel processing for BH_to_cisTEM_mapBack

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claude
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4df2a4d

Commits on Sep 25, 2025

fix: Resolve 54-particle validation error in BH_to_cisTEM_mapBack

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062fd3f
wip
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f2bc8a9
fix: Remove undefined variable reference from debug output

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ac2ae86

Commits on Sep 29, 2025

fix: Improve MAT file save reliability and fix mask command parameter parsing

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claude
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483e5fd

Commits on Dec 23, 2025

add basics for multislice (no water though or movement)
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cbf6620

Commits on Dec 30, 2025

wip: Add Y-shift handling and GPU memory optimization for synthetic projections

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681ebac
feat: Add in-plane rotation support to synthetic projections

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0782c2d
feat: Add emClarity simulate command for synthetic data generation

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7f0cecb