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Refac(MSplit): LVAE module #1033

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8fceef0
cleanup
CatEek Jul 29, 2026
78e8894
blocks cleanup
CatEek Jul 29, 2026
7ea8ffe
layers fix + some tests
CatEek Aug 1, 2026
23f1983
cleanup + fixes
CatEek Aug 1, 2026
0d20dd7
precoms
CatEek Aug 1, 2026
40bf1fa
comments fix
CatEek Aug 1, 2026
43edcfe
Merge branch 'dev/microsplit_api' into iz/feat/lvae_model_refac
CatEek Aug 2, 2026
83f7b82
precoms fix
CatEek Aug 2, 2026
9760071
Update src/careamics/models/lvae/layers.py
CatEek Aug 11, 2026
3d82a28
Merge branch 'dev/microsplit_api' into iz/feat/lvae_model_refac
CatEek Aug 11, 2026
f8c5e70
Merge branch 'dev/microsplit_api' into iz/feat/lvae_model_refac
jdeschamps Aug 17, 2026
6ff0f3d
Merge branch 'dev/microsplit_api' into iz/feat/lvae_model_refac
CatEek Aug 18, 2026
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6 changes: 3 additions & 3 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ repos:
rev: v0.16.1
hooks:
- id: ruff
exclude: "^(docs/.*|src/careamics/lvae_training/.*|src/careamics/models/lvae/(?!noise_models\\.py).*|scripts/.*|demos/.*)"
exclude: "^(docs/.*|src/careamics/lvae_training/.*|src/careamics/models/lvae/noise_models.py|scripts/.*|demos/.*)"

- repo: https://github.com/psf/black-pre-commit-mirror
rev: 26.5.1
Expand All @@ -30,7 +30,7 @@ repos:
hooks:
- id: mypy
files: "^src/"
exclude: "^(docs/.*|src/careamics/lvae_training/.*|src/careamics/models/lvae/(?!noise_models\\.py).*|src/careamics/config/likelihood_model.py|src/careamics/losses/lvae/.*)"
exclude: "^(docs/.*|src/careamics/lvae_training/.*|src/careamics/models/lvae/noise_models.py|src/careamics/config/likelihood_model.py|src/careamics/losses/lvae/.*)"
args: ["--config-file", "mypy.ini"]
additional_dependencies:
- numpy
Expand All @@ -44,7 +44,7 @@ repos:
rev: v1.11.0rc0
hooks:
- id: numpydoc-validation
exclude: "^(tests/.*|docs/.*|src/careamics/lvae_training/.*|src/careamics/models/lvae/(?!noise_models\\.py).*|src/careamics/losses/lvae/.*|scripts/.*)"
exclude: "^(tests/.*|docs/.*|src/careamics/lvae_training/.*|src/careamics/models/lvae/noise_models.py|src/careamics/losses/lvae/.*|scripts/.*)"
# data_module: overloads and config params (val_percentage etc.) don't match signature; see https://github.com/numpy/numpydoc/issues/559

# # jupyter linting and formatting
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14 changes: 0 additions & 14 deletions src/careamics/config/architectures/lvae_config.py
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Expand Up @@ -142,20 +142,6 @@ def validate_z_dims(cls, z_dims: tuple) -> tuple:

return z_dims

def set_3D(self, is_3D: bool) -> None:

@jdeschamps jdeschamps Aug 3, 2026

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We should also have another look at the UNet and whether this set 3D is ever used or necessary. Maybe a small clean up issue.

@CatEek CatEek Aug 11, 2026

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created issue

@jdeschamps jdeschamps Aug 20, 2026

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Following #1038, this should not be removed and we should see what else needs to be updated for the LVAE architecture to be set to 3D.

Indeed, we need to have an HDN napari plugin for a grant.

"""
Set 3D model by setting the `conv_dims` parameters.

Parameters
----------
is_3D : bool
Whether the algorithm is 3D or not.
"""
if is_3D:
self.conv_dims = 3
else:
self.conv_dims = 2

def is_3D(self) -> bool:
"""
Return whether the model is 3D or not.
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2 changes: 2 additions & 0 deletions src/careamics/models/lvae/__init__.py
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@@ -1,3 +1,5 @@
"""LVAE model package."""

__all__ = ["LadderVAE"]

from .lvae import LadderVAE
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