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Adding various strain mapping algorithms - #284

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mitis1 wants to merge 77 commits into

electronmicroscopy:devfrom

mitis1:strain-multi-optimizer-fitting-models

Draft

Adding various strain mapping algorithms#284
mitis1 wants to merge 77 commits into
electronmicroscopy:devfrom
mitis1:strain-multi-optimizer-fitting-models

Commits on Mar 18, 2026
- Initial plan
  Copilot
  committed
  9cabc82
- initial commit for model based refinment
  
  cophus
  authored and
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  7739850
- fitting model working!
  
  cophus
  authored and
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  6e90b3a
- adding docstrings
  
  cophus
  authored and
  Copilot
  committed
  f63af0c
- fixing CoM behaviour
  
  cophus
  authored and
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  24c47b4
- updates
  
  cophus
  authored and
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  984637c
- slight tweaks
  
  cophus
  authored and
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  1a4c121
- dataset4dstem.from_file consistent with read_4dstem args
  
  arthurmccray
  authored and
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  9ff42ca
- refactor in progress, base and rendering largely done, working not perfect
  
  arthurmccray
  authored and
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  207ba98
- adding state saving to ModelDiffraction
  
  arthurmccray
  authored and
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  9ba0541
- switching to state_dict saving
  
  arthurmccray
  authored and
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  fb8aae4
- first version of FitBase
  
  arthurmccray
  authored and
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  committed
  f00f255
- cleaning up FitBase and ModelDiffraction
  
  arthurmccray
  authored and
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  22227c4
- moving more stuff to FitBase
  
  arthurmccray
  authored and
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  f91142f
- reorganizing classes -- no functional change
  
  arthurmccray
  authored and
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  5e08803
- splitting off ModelDiffractionVisualizations into separate file
  
  arthurmccray
  authored and
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  c604a9f
- adding hard constraints like force_center for DiskTemplate
  
  arthurmccray
  authored and
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  committed
  f48e691
- adding docstrings and cleaning
  
  arthurmccray
  authored and
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  committed
  fad203b
- adding visualizations and overlays
  
  arthurmccray
  authored and
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  committed
  fd34ae5
- adding turning on/off individual components and parameters
  
  arthurmccray
  authored and
  Copilot
  committed
  38cb7bd
- fixing center disk duplication and a couple viz bugs
  
  arthurmccray
  authored and
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  committed
  fb4315d
- adding back parameter bounds
  
  arthurmccray
  authored and
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  committed
  cf7f801
- updating colormaps
  
  arthurmccray
  authored and
  Copilot
  committed
  3f54795
- more consistent hard constraints of ranges
  
  arthurmccray
  authored and
  Copilot
  committed
  f12f53e
- cleaning up naming of Components
  
  arthurmccray
  authored and
  Copilot
  committed
  fa8ca66
- Fix docstring type hint for file_type parameter in from_file
  Copilot
  committed
  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
  committed
  fbf631c
- updating types for OptimizerParams and SchedulerParams
  arthurmccray
  committed
  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
  committed
  ba74d62
- bug fixes for model fititng code transfer
  Miti Shah
  committed
  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
  committed
  78111c4
- Revert "updating imaging-utils to match fitting_models_clean"
  Miti Shah
  committed
  9d3b539
Commits on Jun 22, 2026
- adding ability to set batch size for cepstral
  Mitis User
  committed
  9ea871c
Commits on Jun 23, 2026
- changing data upload for using more gpu
  Mitis User
  committed
  0dc871f
Commits on Jun 24, 2026
- adding data preloading for slightly faster computation
  mitis1
  committed
  d26b402
Commits on Jun 25, 2026
- changing error function and adding a varible to gaussian background for elliptical distortion
  mitis1
  committed
  7799d83
Commits on Jul 6, 2026
- adding gpu save for template generation and setting device for probe calculation
  mitis1
  committed
  c44fe6c
Commits on Jul 9, 2026
- allowing for multiple gaussian backgrounds and lattice in batched updates and updating strain plotting
  mitis1
  committed
  0e68ef5
Commits on Jul 12, 2026
- allowing for plotting arguments to be set by user
  mitis1
  committed
  882d052
Commits on Jul 19, 2026
- Adding L1 loss, fixing mask + lattice
  cophus
  committed
  3e60343
Commits on Jul 20, 2026
- add plotting to pattern rotation finder, transpose to strain
  cophus
  committed
  ed242ea
- Merge pull request #4 from cophus/strain-multi-optimizer-fitting-models
  mitis1
  authored
  1a49502
Commits on Jul 28, 2026
- fixing visualize, dilation plot, strain panel labels, and model fitting constraints
  mitis1
  committed
  7f2be6f
- initial strain rotation bug fixes and renaming some variables
  mitis1
  committed
  40c296d
Commits on Jul 29, 2026
- initial rotation implementation
  mitis1
  committed
  d5812bd
Commits on Jul 30, 2026
- fixing subpixel dft fit for cepstral, batched mask implementation for model fitting, and optimizer batched implementation
  mitis1
  committed
  5e66014
Commits on Jul 31, 2026
- adding colin background subtraction and fixing merge commits in model fitting and strain mapping
  mitis1
  committed
  957694f
- bug fixes from previous commit
  mitis1
  committed
  a42311b
Commits on Aug 9, 2026
- initial data consistency implementation
  mitis1
  committed
  c2a9d73
Commits on Aug 21, 2026
- fixing sign for shear and rotation strain
  mitis1
  committed
  0b7b301
Commits on Aug 27, 2026
- adding condition for calculating strain consistency
  mitis1
  committed
  dbed7fe
Commits on Aug 29, 2026
Commits on Sep 5, 2026
- Merge branch 'dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  c533fb9
- adding back upsampled_correlation_numpy to imaging_utils
  mitis1
  committed
  e761648
- fixing imaging-utils
  mitis1
  committed
  856753f
Commits on Sep 16, 2026
- updating function descripitions and fixing plotting
  mitis1
  committed
  cf44585
Commits on Sep 17, 2026
- initial variable rename for consistancy
  mitis1
  committed
  2f65233
Commits on Oct 5, 2026
- strain calculation and cepstral transform updates
  mitis1
  committed
  1fb8121
Commits on Oct 16, 2026
- Merge branch 'dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  572813d
Commits on Oct 20, 2026
- fixing units, updating plotting, fixing code based on PR comments
  mitis1
  committed
  6c09389
- Merge remote-tracking branch 'origin/dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  d18dc00
- renaming variables for consistency and speeding up mp cepstral
  mitis1
  committed
  cc8c580
- updating init function
  mitis1
  committed
  758f6ea
Commits on Oct 21, 2026
- model fitting bug fix and new loss function
  mitis1
  committed
  5d20a9d
Commits on Oct 23, 2026
- Merge branch 'dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  53dfe91
Commits on Oct 26, 2026
- adding independant lr for lattice parameters
  mitis1
  committed
  fa37585
- Merge branch 'dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  4e310db
Commits on Oct 30, 2026
- Merge branch 'dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  3b1beff
Commits on Nov 2, 2026
- Merge branch 'dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  5460af6
Commits on Nov 3, 2026
- Merge branch 'dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  4794aaf
Commits on Nov 4, 2026
- Merge branch 'dev' into strain-multi-optimizer-fitting-models
  mitis1
  committed
  0370e40

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