Strain mapping improvements: adding independent optimizers for model fitting and multipeak fitting for cepstral calculation#235

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mitis1 wants to merge 102 commits into

electronmicroscopy:fitting_models_cleanfrom

mitis1:strain-fitting-multi-optimizer

Commits on Dec 2, 2025

adding support for 3d dm4 files --> 4dstem
cophus
committed

Commits on Dec 3, 2025

initial construction of polar4dstem class
cophus
committed

Commits on Dec 4, 2025

Commits on Jan 1, 2026

initial commit for StrainMap
cophus
committed

Commits on Jan 2, 2026

all basic functions implemented
cophus
committed

Commits on Jan 3, 2026

Commits on Jan 29, 2026

initial class
cophus
committed

Commits on Feb 1, 2026

Commits on Feb 2, 2026

Commits on Feb 16, 2026

initial commit for model based refinment
cophus
committed

Commits on Feb 17, 2026

Commits on Feb 20, 2026

Commits on Feb 22, 2026

slight tweaks
cophus
committed

Commits on Feb 24, 2026

Merge remote-tracking branch 'upstream/dev' into fitting_models
arthurmccray
committed

Commits on Feb 25, 2026

dataset4dstem.from_file consistent with read_4dstem args
arthurmccray
committed

Commits on Feb 26, 2026

refactor in progress, base and rendering largely done, working not perfect
arthurmccray
committed

Commits on Feb 27, 2026

Commits on Mar 2, 2026

Commits on Mar 3, 2026

Commits on Mar 6, 2026

Individual pattern fitting function for fitting_models
Miti Shah
committed

Commits on Mar 10, 2026

adding normalization constraint, updating individual fitting to fit intensity per disk
Miti Shah
committed

Commits on Mar 26, 2026

Commits on Mar 27, 2026

editing strain code for better cmaps, changing diffraction and base for allowing user setting of constraint parameters, fixing bug in get_parameters so it doesn't include submodules
Miti Shah
committed

Commits on Apr 16, 2026

Commits on Apr 17, 2026

adding preprocess square root of image
mitis1
committed

Commits on Apr 19, 2026

updated preprocessing
mitis1
committed

Commits on Apr 24, 2026

Commits on Apr 30, 2026

fixed sloped intensity peak fitting
mitis1
committed

Commits on May 4, 2026

changing synthetic disk lattice plotting and lr save to speed up model training
Miti Shah
committed

Commits on May 5, 2026

Commits on May 7, 2026

merging dev
mitis1
committed

Commits on May 11, 2026

Commits on May 14, 2026

adding windowing for mean pattern calculation
Miti Shah
committed

Commits on May 15, 2026

adding plot masking
Miti Shah
committed

Commits on May 19, 2026

changing plotting of strain map and labeling
Miti Shah
committed

Commits on May 20, 2026

adding radial masking function and scalebar option
Miti Shah
committed
updated scalebar plotting
Miti Shah
committed
merging with dev
Miti Shah
committed
updated dev merge
Miti Shah
committed

Commits on May 22, 2026

adding cepstral multi peak implementation
Miti Shah
committed

Commits on May 25, 2026

creating strain fitting mixin for plotting and calculation
Miti Shah
committed

Commits on May 26, 2026

strain fitting class, updated cepstral and plotting
Miti Shah
committed

Commits on May 27, 2026

updated strain class and implementation in model_fitting
Miti Shah
committed
editing model fitting to match with strain visualization class
Miti Shah
committed
merging updated dev
Miti Shah
committed
merge with dev
Miti Shah
committed

Commits on May 29, 2026

fixing typos
Miti Shah
committed
updated model fitting so it doesn't train parameters where grad=False
Miti Shah
committed
remote additional comments
Miti Shah
committed

Commits on May 30, 2026

Merge dev into strain-fitting-multi-optimizer
Miti Shah
committed

Commits on Jun 1, 2026

Commits on Jun 2, 2026

Merge pull request #3 from cophus/strain-fitting-multi-optimizer
mitis1
authored
Merge branch 'dev' into strain-fitting-multi-optimizer
Miti Shah
committed
updating imports
Miti Shah
committed
fixing code to match new dev updates
Miti Shah
committed
Merge remote-tracking branch 'upstream/fitting_models_clean' into strain-fitting-multi-optimizer
Miti Shah
committed