MAPED data merging with Torch#204

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henrygbell wants to merge 159 commits into

electronmicroscopy:nanobeamfrom

henrygbell:nanobeam

Commits on Apr 7, 2026

Added descan alignment using cross correlation
henrygbell
committed

Commits on Apr 15, 2026

Commits on Apr 16, 2026

Optimizing, set_optimizer is just default to Adam now, probably need to do the matching in set_optimizer instead of parsing in optimizer_params maybe?
cedriclim1
committed
KPlanes Tilted claude implementation, need to talk to Corneel. Things to check: Look at object_models.py and see how the optimizer matching should be handled. It seems like set_optimizers doesn't r…
cedriclim1
committed
Added TV loss for PPLR models, I don't like this solution though will probably have to do TV loss computation within the model?
cedriclim1
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Merge branch 'electronmicroscopy:dev' into optmixin_pplr
cedriclim1
authored
object_models.py now has tv_loss for both KPlanes and INR architectures. Also overloaded reconnecting optimizers
cedriclim1
committed

Commits on Apr 17, 2026

Commits on Apr 18, 2026

TV volume -- needs significant refactoring everywhere
cedriclim1
committed

Commits on Apr 19, 2026

DDP Fixes for PPLR stuff
cedriclim1
committed

Commits on Apr 22, 2026

Changes
cedriclim1
committed

Commits on Apr 23, 2026

Commits on Apr 24, 2026

Commits on Apr 28, 2026

Commits on May 1, 2026

Changed docstrings to all be in numpy format
henrygbell
committed

Commits on May 2, 2026

Commits on May 3, 2026

initial demo of Show2D and Show4DSTEM
bobleesj
committed

Commits on May 4, 2026

Commits on May 5, 2026

Commits on May 6, 2026

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

Commits on May 12, 2026

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

Commits on May 18, 2026

Commits on May 21, 2026

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

Commits on May 23, 2026

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

Commits on May 25, 2026

Commits on May 27, 2026

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

Commits on May 28, 2026

Commits on Jun 1, 2026

Commits on Jun 2, 2026

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

cophus
authored and
henrygbell
committed
initial construction of polar4dstem class

cophus
authored and
henrygbell
committed
Changing sampling direction for polar4dstem

cophus
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henrygbell
committed
initial commit for RDF class

cophus
authored and
henrygbell
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initial commit for StrainMap

cophus
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henrygbell
committed
all basic functions implemented

cophus
authored and
henrygbell
committed
faster strain, adding h5plugin to read arina data

cophus
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henrygbell
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faster strain calc, adding h5plugin to read arina data

cophus
authored and
henrygbell
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temp removing function for merge

cophus
authored and
henrygbell
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adding rotate_image back

cophus
authored and
henrygbell
committed
strain mapping updates

cophus
authored and
henrygbell
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renaming parent .py file

cophus
authored and
henrygbell
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initial class

cophus
authored and
henrygbell
committed
fixing DFT upsampling / image correlation, adding tests

cophus
authored and
henrygbell
committed
initial maped class commit

cophus
authored and
henrygbell
committed
Updating with weighted correlation

cophus
authored and
henrygbell
committed
maped output

cophus
authored and
henrygbell
committed
datatype control for merged data

cophus
authored and
henrygbell
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adding docstrings

cophus
authored and
henrygbell
committed
Converted MAPED code to torch, added batching
henrygbell
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Cleaned up comments, getting ready for PR
henrygbell
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Removed some imports that we don't need
henrygbell
committed
Fixed hann_filter line in real_space_align
henrygbell
committed
Added descan alignment using cross correlation
henrygbell
committed
Changed docstrings to all be in numpy format
henrygbell
committed
Changed the plotting of MAPED.real_space_align to be consistent with numpy version.
henrygbell
committed
initial construction of polar4dstem class

cophus
authored and
henrygbell
committed
Changing sampling direction for polar4dstem

cophus
authored and
henrygbell
committed
initial commit for RDF class

cophus
authored and
henrygbell
committed
initial pdf code + f parameters

ehrhardtkm
authored and
henrygbell
committed
origin finding and pdf updates

ehrhardtkm
authored and
henrygbell
committed
pixel calibration bug fix

ehrhardtkm
authored and
henrygbell
committed
make torch native and general cleanup

ehrhardtkm
authored and
henrygbell
committed
additional cleanup

ehrhardtkm
authored and
henrygbell
committed
added comments for increased clarity

ehrhardtkm
authored and
henrygbell
committed
minor fixes

ehrhardtkm
authored and
henrygbell
committed
origin finding speedup

ehrhardtkm
authored and
henrygbell
committed
make calculate_Gr use precomputed bg

ehrhardtkm
authored and
henrygbell
committed
refactor and row/col convention cleanup

ehrhardtkm
authored and
henrygbell
committed
docstring/API cleanup and origing finding speedup

ehrhardtkm
authored and
henrygbell
committed
remove duplicate gaussian code and restore tomo utils

ehrhardtkm
authored and
henrygbell
committed
Autocorrelation dscan alignment added
henrygbell
committed
Add fast vectorized autocorrelation dscan alignment.
henrygbell
committed
MAPED direct fitting descan correction implemented.
henrygbell
committed
Revert "MAPED direct fitting descan correction implemented."
henrygbell
committed
Merge remote-tracking branch 'henrygbell/nanobeam' into henrygbell-nanobeam
henrygbell
committed
Updates the output merged dataset to use the from_tensor initialization to stop forced switch to CPU memory
henrygbell
committed

Commits on Jun 26, 2026