Release update - #259

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Commits on Mar 5, 2026

Hot-fix for OptimizerMixin bug with or statement
cedriclim1
committed
d96808b
Merge branch 'dev' of https://github.com/electronmicroscopy/quantem into optimizer_mixin_hotfix
cedriclim1
committed
0404bf9
Hotfix from tomo_refactor
cedriclim1
committed
895cb1b
Hotfix w/ better name or type checking
cedriclim1
committed
8f5d3cb
Optimizer mixin hotfix fastforward
cedriclim1
committed
b40f946
Added new tests as well
cedriclim1
committed
aacd82d
Merge pull request #187 from electronmicroscopy/optimizer_mixin_hotfix
arthurmccray
authored
9dbeb5b
Merge remote-tracking branch 'upstream/dev' into diffractive_imaging
arthurmccray
committed
58d853d
Added DatasetConstraintParams, works with dictionary inputs still
cedriclim1
committed
1fb2ca9
Merge branch 'dev' into tomography_refactor
cedriclim1
authored
2967c9d
OptimizerMixin fix tests
cedriclim1
committed
f5d6351
Merge pull request #183 from electronmicroscopy/chore/update-lockfile-20260302
gvarnavi
authored
9f92931
Docstrings for dataset_models and object_models
cedriclim1
committed
c1a7e23
Readded dataset models type back in
cedriclim1
committed
2c91064
Bug
cedriclim1
committed
882d9e9
NumPy style docstrings
cedriclim1
committed
64ee01e
Some typos in the docstrings
cedriclim1
committed
47f31ea
Added some __str__ for the OptimizerParams; not sure if needed but better for printing?
cedriclim1
committed
586f3bc
Merge remote-tracking branch 'upstream/dev' into diffractive_imaging
arthurmccray
committed
f628b20
updating Vector save to call compact() first
arthurmccray
committed
9693b11
reorganizing methods and attributes
arthurmccray
committed
f72bea2

Commits on Mar 6, 2026

Commits on Mar 10, 2026

in ptycho, visualize scan positions, get real-space sampling
bobleesj
committed
568fe35
add show_scan_position print output in the api doc
bobleesj
committed
9ce62df
bin, crop API doc improvement
bobleesj
committed
66ec915
add bin tests for 4dstem
bobleesj
committed
72ecdf7
maintain original api doc for some
bobleesj
committed
b9b3ed3
remove free memory part
bobleesj
committed
cbb3e54
do not free memory part in API
bobleesj
committed
e57def2
add Object FOV instead of FOV per PR feedback
bobleesj
committed
1590fac
Verbose, if false will just start printing
cedriclim1
committed
922dc12

Commits on Mar 11, 2026

Commits on Mar 17, 2026

Commits on Mar 18, 2026

updating example to best practices for INR make equispaced grid
arthurmccray
committed
b089e55

Commits on Mar 19, 2026

show_2d, add api description and examples for color, norm, scale bar
bobleesj
committed
e860c03
use the most common api
bobleesj
committed
7b5eaf7
Minor formatting changes
darshan-mali
committed
eda4b9d
Merge remote-tracking branch 'upstream/dev' into imaging_refactor
darshan-mali
committed
876e7b1
Updated Errors. Removed assert from src and replaced with raise.
darshan-mali
committed
ec87cbe
Updated pytest
darshan-mali
committed
023b6cf
DDP dist.all_reduce for scheduler stepping
cedriclim1
committed
614ffa1

Commits on Mar 20, 2026

.to() for object_models fixed; Note should check if world_size > 1 and only do distribute_model if model is not already a DDP
cedriclim1
committed
8772d89

Commits on Mar 22, 2026

Commits on Mar 23, 2026

TomographyLite updated to match ObjConstraints and DatasetConstraints
cedriclim1
committed
c7be969
Merge pull request #194 from bobleesj/show_2d-example-api
cedriclim1
authored
471a851
show_2d upstream
cedriclim1
committed
df9d6f8
chore: update lock file
quantem-bot
committed
bcf6ee4
Merge pull request #200 from electronmicroscopy/chore/update-lockfile-20260323
gvarnavi
authored
a38f0c1
Merge remote-tracking branch 'upstream/dev' into imaging_refactor
darshan-mali
committed
51ca601
Fix for TomographyLite when reloading
cedriclim1
committed
a7f9b5d

Commits on Mar 24, 2026

Show metrics total loss + lrs from different optimizers after finished training
cedriclim1
committed
73c282f
Added show_metrics to SIRT reconstructions as well
cedriclim1
committed
70ecd70
updating viz with ShowParams
arthurmccray
committed
1517b33
Added a check to make sure that if a list(tuple) is given it should match the number of iterations, otherwise raises an error
cedriclim1
committed
c91148f
Merge branch 'dev' into tomography_refactor
cedriclim1
authored
fd13a8e
Setting up DDP for obj_model print statement in TomographyBase now only set to global_rank = 0
cedriclim1
committed
c2f46fe
Merge branch 'tomography_refactor' of https://github.com/electronmicroscopy/quantem into tomography_refactor
cedriclim1
committed
3d74da8
uv.lock fix?
cedriclim1
committed
8e1c1ef
num_samples_per_ray schedule provided set to only global_rank 0 print
cedriclim1
committed
b922cbb
Type-hinting ignore fix in inr.py
cedriclim1
committed
c81b2b5
to_numpy() added in tomography_utils.py, and edited background_subtract
cedriclim1
committed
62616d7
tomography_utils.py diff_shift_2d updated docstring
cedriclim1
committed
3567b4e
plot_losses() function implemented both for conventional and INR algorithms
cedriclim1
committed
5923624
Quick fix on object_models DDP instantiation, global_rank is not defined yet
cedriclim1
committed
0ec02df
logger_tomography fixed linting
cedriclim1
committed
8afb028
TomographyDataset quantile linter error fixed
cedriclim1
committed
4ebb1d9
Linter error in .reconstruct
cedriclim1
committed
435e623
Fixed all linter issues in top-level tomography.py
cedriclim1
committed
5c10509
logger_tomography.py type-hinting fix
cedriclim1
committed
fc0c675
dataset_models.py type-hinting
cedriclim1
committed
462e7a0
radon.py type-hinting fix
cedriclim1
committed
238bffd
tomography_opt.py linting errors fixed by Claude
cedriclim1
committed
1b3b0cd
Removed tomography_old and put forkserver back in instead of spawn.
cedriclim1
committed
ab44488
Nevermind back to spawn, DataLoader doesn't like to be in forkserver
cedriclim1
committed
8d85f30
forgot to include the new file whoops
arthurmccray
committed
96c1665
adding checks for incompatible arguments and validators
arthurmccray
committed
c60a130
updating type hinting to 3.11+
arthurmccray
committed
ccaf70c
bugfix vmax and refactor list to combine
arthurmccray
committed
390a81c
fixing type hinting and potential circular import
arthurmccray
committed
7c2735f
fixing arg passing to _show_combined
arthurmccray
committed
ee204ab
adding inverse units picking
arthurmccray
committed
b63997e
Zero-pad docs fixed
cedriclim1
committed
d6e2aa8
Merge branch 'tomography_refactor' of https://github.com/electronmicroscopy/quantem into tomography_refactor
cedriclim1
committed
9ebc845

Commits on Mar 25, 2026

fixing linescan returns, improving complex cbar labels
arthurmccray
committed
56c44e5
fixing couple typehints
arthurmccray
committed
28021af
Merge pull request #167 from electronmicroscopy/tomography_refactor
arthurmccray
authored
6b40b52

Commits on Mar 30, 2026

chore: update lock file
quantem-bot
committed
e482d76
Merge pull request #203 from electronmicroscopy/chore/update-lockfile-20260330
gvarnavi
authored
a9b9608

Commits on Apr 4, 2026

Commits on Apr 6, 2026

fix
smribet
committed
dd12d60

Commits on Apr 7, 2026

updating slicing too
smribet
committed
7dfb38b

Commits on Apr 8, 2026

adding doc strings
smribet
committed
d92e5c4

Commits on Apr 13, 2026

chore: update lock file
quantem-bot
committed
ea6cfa3

Commits on Apr 15, 2026

Commits on Apr 16, 2026

Commits on Apr 17, 2026

Commits on Apr 18, 2026

TV volume -- needs significant refactoring everywhere
cedriclim1
committed
aebf801

Commits on Apr 19, 2026

DDP Fixes for PPLR stuff
cedriclim1
committed
2579847

Commits on Apr 21, 2026

Commits on Apr 22, 2026

Changes
cedriclim1
committed
a59baac

Commits on Apr 23, 2026

Commits on Apr 24, 2026

Fixed typo
cedriclim1
committed
99fdd88
Small change to set_optimizer in OptimizerMixin to allow for dictionary parsing
cedriclim1
committed
4a44826
Pretraining warning on ObjectTensorDecomp
cedriclim1
committed
ede9d56
Delete .vscode directory
bobleesj
authored
d0b6e84
Merge pull request #214 from electronmicroscopy/vscode-dir-delete
arthurmccray
authored
5b34b3e
Merge pull request #198 from darshan-mali/imaging_refactor
wwmills
authored
0370e29
enable branch PR CI pytest and move pull request template
bobleesj
committed
24468cc

Commits on Apr 27, 2026

Commits on Apr 28, 2026

Small changes
cedriclim1
committed
9a96415
Merge branch 'dev' of github.com:electronmicroscopy/quantem into optmixin_pplr
cedriclim1
committed
e444164

Commits on May 2, 2026

Commits on May 3, 2026

initial demo of Show2D and Show4DSTEM
bobleesj
committed
43b54b2

Commits on May 4, 2026

chore: update lock file
quantem-bot
committed
ff510f9
fix: track widget/scripts/build.mjs (required for npm run build)
bobleesj
committed
e004a23
enable build mjs cli
bobleesj
committed
e29096a

Commits on May 5, 2026

perf: use WebGPU for faster fft colormap and toggle
bobleesj
committed
49c679b
update uv lock with all deps listed for now
bobleesj
committed
88bbaec

Commits on May 6, 2026

Merge pull request #219 from electronmicroscopy/chore/update-lockfile-20260504
arthurmccray
authored
ac17d2a

Commits on May 7, 2026

Commits on May 9, 2026

remove set_image()
henryhng
committed
5b364c6
Merge pull request #7 from henryhng/pr218
bobleesj
authored
eb437bf
remove set_image() from Show2D
henryhng
committed
c57d1d0
invalidate virtual image cache on calibration change, mkdir in save_state_file
henryhng
committed
c36be76
lazy import torch in array_utils
henryhng
committed
5a6e8a8
Merge pull request #8 from henryhng/pr218
bobleesj
authored
f53c7c9
Merge pull request #9 from henryhng/pr218-ruff
bobleesj
authored
4988054

Commits on May 11, 2026

Commits on May 12, 2026

Merge pull request #223 from electronmicroscopy/filter-4dstemload
cedriclim1
authored
290d153

Commits on May 18, 2026

chore: update lock file
quantem-bot
committed
a495a97
Created a BaseContext class - totally optional, not sure if anyone uses this class anyways currently. Type-hinting error fixed in tomography_otp.py
cedriclim1
committed
adcc26d
Merge branch 'optmixin_pplr' of github.com:electronmicroscopy/quantem into optmixin_pplr
cedriclim1
committed
044f446
Removed import in constraints.py
cedriclim1
committed
af33b96
PPLR description changed to multi-parameter optimization
cedriclim1
committed
03da610
SO3 Rotations paper citation in SO3params.py
cedriclim1
committed
a62295c
Type-hinting fix in So3params
cedriclim1
committed
e222512
Load parameters added .to(self.device)
cedriclim1
committed
91d6056
Volume added to reconstruction context
cedriclim1
committed
f37ca9f
Citations for the kplanes models
cedriclim1
committed
8072fa6
Explanation in object_models.py for different types of tv loss.
cedriclim1
committed
eafca0c
Refactor type hinting in _unwrap function to use cast for improved type safety
cedriclim1
committed
e4c8dbe
Some type-hinting fix for Contexts
cedriclim1
committed
136a65f

Commits on May 19, 2026

dataset4d, dataset4dstem hold torch array
bobleesj
committed
98ddd0d
bring original docstring back
bobleesj
committed
d2dc32b
remove need for cached numpy array
bobleesj
committed
6b7319d
further cleaup api docstring
bobleesj
committed
7f9913f
use _array _tensor duck typing for show4dstem
bobleesj
committed
9c93ae9
use row, col convention in docstring
bobleesj
committed
40878d3

Commits on May 21, 2026

Merge pull request #227 from electronmicroscopy/chore/update-lockfile-20260518
arthurmccray
authored
3834e79

Commits on May 23, 2026

fix: tolerate missing _tensor slot on autoserialize-loaded datasets
bobleesj
committed
21b684f

Commits on May 25, 2026

chore: update lock file
quantem-bot
committed
4be1be7

Commits on May 27, 2026

Merge pull request #232 from electronmicroscopy/chore/update-lockfile-20260525
arthurmccray
authored
7645c08

Commits on May 28, 2026

Commits on Jun 1, 2026

Commits on Jun 2, 2026

Tomography Slow/Fast Tests
cedriclim1
committed
0773481
Merge pull request #240 from electronmicroscopy/tomography-tests
arthurmccray
authored
e2dba3e

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