Fixes for strain mapping - #271

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cophus wants to merge 141 commits into

electronmicroscopy:fitting_models_cleanfrom

cophus:strain-fitting-multi-optimizer

Commits on Dec 2, 2025

adding support for 3d dm4 files --> 4dstem
cophus
committed
2cb302d

Commits on Dec 3, 2025

initial construction of polar4dstem class
cophus
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d88ffb5

Commits on Dec 4, 2025

Changing sampling direction for polar4dstem
cophus
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13b8d3d
initial commit for RDF class
cophus
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9b1ecbf

Commits on Jan 1, 2026

initial commit for StrainMap
cophus
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1d0ec61

Commits on Jan 2, 2026

all basic functions implemented
cophus
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5ace6c7

Commits on Jan 3, 2026

Commits on Jan 19, 2026

temp removing function for merge
cophus
committed
0852c49
Merge remote-tracking branch 'origin/dev' into nanobeam
cophus
committed
a1ebf1d
adding rotate_image back
cophus
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53ac2d5
strain mapping updates
cophus
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22804b2
renaming parent .py file
cophus
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a154aa6

Commits on Jan 29, 2026

initial class
cophus
committed
d3d3aa5

Commits on Feb 1, 2026

fixing DFT upsampling / image correlation, adding tests
cophus
committed
ed44789
initial maped class commit
cophus
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f249c6c
Updating with weighted correlation
cophus
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494dc24

Commits on Feb 2, 2026

maped output
cophus
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38a3fc2
datatype control for merged data
cophus
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1e14d70
adding docstrings
cophus
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3196aca

Commits on Feb 16, 2026

initial commit for model based refinment
cophus
committed
bf4b2b8

Commits on Feb 17, 2026

fitting model working!
cophus
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9bb0a56
adding docstrings
cophus
committed
8cc8132

Commits on Feb 20, 2026

fixing CoM behaviour
cophus
committed
7dd327a
updates
cophus
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9bfaa7f

Commits on Feb 22, 2026

slight tweaks
cophus
committed
73d1236

Commits on Feb 24, 2026

Merge remote-tracking branch 'upstream/dev' into fitting_models
arthurmccray
committed
20f210b

Commits on Feb 25, 2026

dataset4dstem.from_file consistent with read_4dstem args
arthurmccray
committed
57563fb

Commits on Feb 26, 2026

refactor in progress, base and rendering largely done, working not perfect
arthurmccray
committed
b2f5253

Commits on Feb 27, 2026

adding state saving to ModelDiffraction
arthurmccray
committed
c7f32a5
switching to state_dict saving
arthurmccray
committed
2a9d640
first version of FitBase
arthurmccray
committed
a9b4eaa

Commits on Feb 28, 2026

Commits on Mar 2, 2026

adding hard constraints like force_center for DiskTemplate
arthurmccray
committed
59aba08
adding docstrings and cleaning
arthurmccray
committed
7443869

Commits on Mar 3, 2026

adding visualizations and overlays
arthurmccray
committed
136f626
adding turning on/off individual components and parameters
arthurmccray
committed
6429e25
fixing center disk duplication and a couple viz bugs
arthurmccray
committed
5588609
adding back parameter bounds
arthurmccray
committed
1fbc76c
updating colormaps
arthurmccray
committed
20b2c58
more consistent hard constraints of ranges
arthurmccray
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f68742e
cleaning up naming of Components
arthurmccray
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b787564
Merge branch 'dev' into fitting_models
arthurmccray
committed
451fba6
Merge pull request #185 from arthurmccray/fitting_models
arthurmccray
authored
7bed26f

Commits on Mar 6, 2026

Individual pattern fitting function for fitting_models
Miti Shah
committed
41b5e90

Commits on Mar 10, 2026

adding normalization constraint, updating individual fitting to fit intensity per disk
Miti Shah
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b22d4cd

Commits on Mar 26, 2026

independant pattern fitting and inital strain calculation
Miti Shah
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451ca80
adding independant optimizers
Miti Shah
committed
9aff08f
updated strain plotting, fixed hard circular mask constraint, fixed bug for get_optimization_parameters() so it doesn't include subcomponents
Miti Shah
committed
1f99fe5

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
f993261

Commits on Apr 16, 2026

updated multiple optimizer
mitis1
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1b1c30e
new loss function
mitis1
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dce5546
cosine optimizer
mitis1
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496f86c
changing chosen loss function
mitis1
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9820b6b

Commits on Apr 17, 2026

adding preprocess square root of image
mitis1
committed
5c33ead

Commits on Apr 19, 2026

updated preprocessing
mitis1
committed
5ffe505

Commits on Apr 24, 2026

new loss functions
mitis1
committed
b74fa93
new loss functions
mitis1
committed
2991a1a

Commits on Apr 30, 2026

fixed sloped intensity peak fitting
mitis1
committed
7126174

Commits on May 4, 2026

changing synthetic disk lattice plotting and lr save to speed up model training
Miti Shah
committed
173c3ce

Commits on May 5, 2026

merging with upstream fitting_models_clean
mitis1
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2aa3676
updated multi optimizer to match upstream
mitis1
committed
77e4715
post-merge cleanup
mitis1
committed
9db1d9c

Commits on May 7, 2026

merging dev
mitis1
committed
bbed474

Commits on May 11, 2026

Add batched single-GPU per-pattern fit path

cedriclim1
and
claude
committed
7efc845
Additiona Claude updates to add soft/schedulers/hard-constraints back into the reconstruction loop
cedriclim1
committed
40052b9
Merge pull request #1 from cedriclim1/cedric-changes
mitis1
authored
d90df27
updating base to match with new optimizer mixin
Miti Shah
committed
2f4e69e

Commits on May 14, 2026

adding windowing for mean pattern calculation
Miti Shah
committed
f69e0bf

Commits on May 15, 2026

adding plot masking
Miti Shah
committed
2067546

Commits on May 19, 2026

changing plotting of strain map and labeling
Miti Shah
committed
04e91bd

Commits on May 20, 2026

adding radial masking function and scalebar option
Miti Shah
committed
df77299
updated scalebar plotting
Miti Shah
committed
4a27332
merging with dev
Miti Shah
committed
02d0e42
updated dev merge
Miti Shah
committed
945ee2d

Commits on May 22, 2026

adding cepstral multi peak implementation
Miti Shah
committed
3887cca

Commits on May 25, 2026

creating strain fitting mixin for plotting and calculation
Miti Shah
committed
864bd57

Commits on May 26, 2026

strain fitting class, updated cepstral and plotting
Miti Shah
committed
3062f15

Commits on May 27, 2026

updated strain class and implementation in model_fitting
Miti Shah
committed
a9df335
editing model fitting to match with strain visualization class
Miti Shah
committed
a3d9a25
merging updated dev
Miti Shah
committed
85e1b49
merge with dev
Miti Shah
committed
be4cf85

Commits on May 29, 2026

fixing typos
Miti Shah
committed
5e6a74c
updated model fitting so it doesn't train parameters where grad=False
Miti Shah
committed
925b44c
remote additional comments
Miti Shah
committed
85de2fd

Commits on May 30, 2026

Merge dev into strain-fitting-multi-optimizer
Miti Shah
committed
3b0414e

Commits on Jun 1, 2026

current strain
cophus
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703e631
minor fixes
cophus
committed
c9faf13
cepstral updates
cophus
committed
2b81d10
updates to cepstral pipeline
cophus
committed
d21b50a
fixes and speed up
cophus
committed
836887b
strain model fitting updates
cophus
committed
00edf7c
few more fixes
cophus
committed
071355a

Commits on Jun 2, 2026

Merge pull request #3 from cophus/strain-fitting-multi-optimizer
mitis1
authored
5381b95
Merge branch 'dev' into strain-fitting-multi-optimizer
Miti Shah
committed
1225c3a
updating imports
Miti Shah
committed
990e25d
fixing code to match new dev updates
Miti Shah
committed
947d3af
Merge remote-tracking branch 'upstream/fitting_models_clean' into strain-fitting-multi-optimizer
Miti Shah
committed
8131d36

Commits on Jun 8, 2026

Commits on Jun 15, 2026

chore: update lock file
quantem-bot
committed
868fad3
Merge pull request #250 from electronmicroscopy/chore/update-lockfile-20260615
gvarnavi
authored
4d02da1

Commits on Jun 19, 2026

Test fixes
cedriclim1
committed
3c29c6e
Test fixes
cedriclim1
committed
e00aeda
Merge pull request #252 from cedriclim1/tomodataset_hotfix
wwmills
authored
24c2d35

Commits on Jun 29, 2026

Commits on Jul 6, 2026

Commits on Jul 9, 2026

Commits on Jul 13, 2026

Commits on Jul 14, 2026

some possible updates
cophus
committed
2d0d720

Commits on Jul 20, 2026

chore: update lock file
quantem-bot
committed
2128aa8

Commits on Jul 22, 2026

Merge pull request #266 from electronmicroscopy/chore/update-lockfile-20260720
arthurmccray
authored
746d919

Commits on Jul 27, 2026

chore: update lock file
quantem-bot
committed
fdb2c86
Merge pull request #270 from electronmicroscopy/chore/update-lockfile-20260727
gvarnavi
authored
1563c4a

Commits on Jul 28, 2026

Commits on Jul 29, 2026

Subtract smooth correlation background before disk peak finding

cophus
and
claude
committed
e84e46f
Default to a unit-sum positive correlation template

cophus
and
claude
committed
ef4c6b5
initial rotation implementation
mitis1
committed
d5812bd
Add BraggVectors.correct_peak_origins for descan calibration

cophus
and
claude
committed
0121149

Commits on Jul 30, 2026