Adding various strain mapping algorithms - #284

Draft

mitis1 wants to merge 58 commits into

electronmicroscopy:devfrom

mitis1:strain-multi-optimizer-fitting-models

Commits on Mar 18, 2026

Initial plan
Copilot
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9cabc82
initial commit for model based refinment

cophus
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Copilot
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7739850
fitting model working!

cophus
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Copilot
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6e90b3a
adding docstrings

cophus
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Copilot
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f63af0c
fixing CoM behaviour

cophus
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Copilot
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24c47b4
updates

cophus
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Copilot
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984637c
slight tweaks

cophus
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Copilot
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1a4c121
dataset4dstem.from_file consistent with read_4dstem args

arthurmccray
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Copilot
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9ff42ca
refactor in progress, base and rendering largely done, working not perfect

arthurmccray
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Copilot
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207ba98
adding state saving to ModelDiffraction

arthurmccray
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9ba0541
switching to state_dict saving

arthurmccray
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Copilot
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fb8aae4
first version of FitBase

arthurmccray
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Copilot
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f00f255
cleaning up FitBase and ModelDiffraction

arthurmccray
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22227c4
moving more stuff to FitBase

arthurmccray
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f91142f
reorganizing classes -- no functional change

arthurmccray
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5e08803
splitting off ModelDiffractionVisualizations into separate file

arthurmccray
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c604a9f
adding hard constraints like force_center for DiskTemplate

arthurmccray
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Copilot
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f48e691
adding docstrings and cleaning

arthurmccray
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Copilot
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fad203b
adding visualizations and overlays

arthurmccray
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Copilot
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fd34ae5
adding turning on/off individual components and parameters

arthurmccray
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Copilot
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38cb7bd
fixing center disk duplication and a couple viz bugs

arthurmccray
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fb4315d
adding back parameter bounds

arthurmccray
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cf7f801
updating colormaps

arthurmccray
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Copilot
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3f54795
more consistent hard constraints of ranges

arthurmccray
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Copilot
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f12f53e
cleaning up naming of Components

arthurmccray
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Copilot
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fa8ca66
Fix docstring type hint for file_type parameter in from_file
Copilot
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46e83cd
Merge pull request #1 to make create-clean-fittings-branch
arthurmccray
authored
8cc3389
Merge pull request #193 from arthurmccray/fitting_models_clean
arthurmccray
authored
4b15483

Commits on Mar 25, 2026

Merge branch 'dev' into fitting_models_clean
arthurmccray
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fbf631c
updating types for OptimizerParams and SchedulerParams
arthurmccray
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e7a94ef

Commits on Jun 2, 2026

Merge remote-tracking branch 'upstream/dev' into HEAD
Miti Shah
committed
220fc01

Commits on Jun 5, 2026

strain multi-optimizer and bragg disk detection
Miti Shah
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ba74d62
bug fixes for model fititng code transfer
Miti Shah
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9153164

Commits on Jun 6, 2026

fixing rotation plot spacing
Miti Shah
committed
5ee6b5e

Commits on Jun 10, 2026

updating imaging-utils to match fitting_models_clean
Miti Shah
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78111c4
Revert "updating imaging-utils to match fitting_models_clean"
Miti Shah
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9d3b539

Commits on Jun 22, 2026

adding ability to set batch size for cepstral
Mitis User
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9ea871c

Commits on Jun 23, 2026

changing data upload for using more gpu
Mitis User
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0dc871f

Commits on Jun 24, 2026

adding data preloading for slightly faster computation
mitis1
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d26b402

Commits on Jun 25, 2026

changing error function and adding a varible to gaussian background for elliptical distortion
mitis1
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7799d83

Commits on Jul 6, 2026

adding gpu save for template generation and setting device for probe calculation
mitis1
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c44fe6c

Commits on Jul 9, 2026

allowing for multiple gaussian backgrounds and lattice in batched updates and updating strain plotting
mitis1
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0e68ef5

Commits on Jul 12, 2026

allowing for plotting arguments to be set by user
mitis1
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882d052

Commits on Jul 19, 2026

Adding L1 loss, fixing mask + lattice
cophus
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3e60343

Commits on Jul 20, 2026

Commits on Jul 28, 2026

Commits on Jul 29, 2026

initial rotation implementation
mitis1
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d5812bd

Commits on Jul 30, 2026

fixing subpixel dft fit for cepstral, batched mask implementation for model fitting, and optimizer batched implementation
mitis1
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5e66014

Commits on Jul 31, 2026

Commits on Aug 9, 2026

initial data consistency implementation
mitis1
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c2a9d73

Commits on Aug 21, 2026

fixing sign for shear and rotation strain
mitis1
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0b7b301

Commits on Aug 27, 2026

adding condition for calculating strain consistency
mitis1
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dbed7fe

Commits on Aug 29, 2026