Tomography Module#167

Merged

arthurmccray merged 165 commits intodevfrom

tomography_refactor

Mar 25, 2026

Commits on Sep 16, 2025

Tomo base plotting fixes
Cedric Lim
committed

Commits on Sep 17, 2025

Semi-working NeRF implementation; bug where it's not converging correctly
Cedric Lim
committed
NeRF kinda working; bugs with convergence
Cedric Lim
committed
TV loss squeeze axis
Cedric Lim
committed

Commits on Sep 18, 2025

NeRF works, barebones. Start writing into quantem style
Cedric Lim
committed

Commits on Sep 22, 2025

Pre-transferring to quantem code
Cedric Lim
committed

Commits on Sep 23, 2025

Commits on Oct 10, 2025

Switching from @overload to TypeVar
cophus
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Commits on Oct 14, 2025

Merge pull request #109 from cophus/tomo-background
cedriclim1
authored
Tomo changes
Cedric Lim
committed
Merge branch 'dev' into tomography
Cedric Lim
committed

Commits on Oct 16, 2025

Enforcing positivity optional in tomography_dataset with clamp flag
cedriclim1
committed
Added SIREN, HSIREN, and Finer with allowed complex inputs

Cedric Lim
authored and
Cedric Lim
committed
Added FinerActivation to get_activation_function

Cedric Lim
authored and
Cedric Lim
committed
Fixed PtychoLite to call from cnn.py instead of cnn2d (now removed)

Cedric Lim
authored and
Cedric Lim
committed
Siren + HSiren need np.sqrt instead of torch.sqrt for .uniform_

Cedric Lim
authored and
Cedric Lim
committed
net_list fix on Siren models

Cedric Lim
authored and
Cedric Lim
committed
Softplus missing from self.net_list

Cedric Lim
authored and
Cedric Lim
committed

Commits on Oct 23, 2025

Print pred on cross_Correlation align stack
Cedric Lim
committed

Commits on Nov 12, 2025

Adding back in validation set
Cedric Lim
committed

Commits on Nov 21, 2025

Added pretraininig functionality, in core ML added custom loss functions more torchlike (need to ask Arthur's opinion)
Cedric Lim
committed

Commits on Dec 6, 2025

Updates
Cedric Lim
committed

Commits on Dec 15, 2025

Test
cedriclim1
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Commits on Dec 16, 2025

Outlining dataset_models.py, and the top level Tomography class
cedriclim1
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Commits on Dec 17, 2025

Need to think about tomography_ddp a little bit more, also what should live in tomography_base. Need to implement object_models for incorporating different forward calls
cedriclim1
committed

Commits on Dec 19, 2025

Commits on Jan 21, 2026

Commits on Jan 22, 2026

Reworking TomographyINRDatasets; need to figure out what to do for aux params
cedriclim1
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Commits on Jan 23, 2026

Commits on Jan 26, 2026

Various u[dates
cedriclim1
committed

Commits on Jan 27, 2026

Logger implementation
cedriclim1
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DDP bug where some projection idx's don't get optimized.
Cedric Lim
committed

Commits on Jan 28, 2026

Commits on Jan 29, 2026

Starting profiling of the reconstruction loop; need to move stuff over to conventional tomography file for conv recons
cedriclim1
committed

Commits on Jan 30, 2026

Commits on Jan 31, 2026

Implemented a working TomographyLite, need to test AutoSerialize, and move conventional algorithm .forward calls.
cedriclim1
committed

Commits on Feb 1, 2026

Commits on Feb 2, 2026

Commits on Feb 4, 2026

Commits on Feb 23, 2026

Commits on Feb 24, 2026

Commits on Feb 25, 2026

core/ml/loss_functions; Changed everything to modules check if this works at Ptycho
cedriclim1
committed

Commits on Feb 26, 2026

dataset_models.py bug fixes. Distribute model is not working with cudatoolkit/13.0
cedriclim1
committed

Commits on Mar 2, 2026

Commits on Mar 3, 2026

Commits on Mar 5, 2026

Commits on Mar 10, 2026

Verbose, if false will just start printing
cedriclim1
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Commits on Mar 16, 2026

Commits on Mar 17, 2026

Relaxation parameters for SIRT reconstructions
cedriclim1
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Commits on Mar 19, 2026

DDP dist.all_reduce for scheduler stepping
cedriclim1
committed

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

Commits on Mar 22, 2026

Commits on Mar 23, 2026

Commits on Mar 24, 2026

Commits on Mar 25, 2026

fixing couple typehints
arthurmccray
committed