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8328 nnunet bundle integration #8329

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13bdec5
Add nnUNet integration and corresponding unit tests
SimoneBendazzoli93 Jan 28, 2025
74aaf73
Implement nnUNet model conversion to MONAI bundle format and enhance …
SimoneBendazzoli93 Feb 5, 2025
ccdc76c
Merge branch 'Project-MONAI:dev' into dev
SimoneBendazzoli93 Feb 5, 2025
b61e4e1
Refactor nnUNet bundle integration tests for clarity and remove redun…
SimoneBendazzoli93 Feb 5, 2025
8e4a66c
Code reformatting
SimoneBendazzoli93 Feb 5, 2025
49dbb5d
DCO Remediation Commit for simben <[email protected]>
SimoneBendazzoli93 Feb 5, 2025
5a04fe0
nibabel importing moved to setUp
SimoneBendazzoli93 Feb 5, 2025
24643b8
DCO Remediation Commit for simben <[email protected]>
SimoneBendazzoli93 Feb 5, 2025
253dab1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 5, 2025
43c694b
Add nnUNet Bundle documentation and related functions to bundle.rst
SimoneBendazzoli93 Feb 6, 2025
569df7b
Refactor nnUNet documentation and examples for clarity; update fold p…
SimoneBendazzoli93 Feb 6, 2025
fcf5ac0
Clean up whitespace in nnunet.py and add test for nnunet bundle integ…
SimoneBendazzoli93 Feb 6, 2025
c846b6d
Fix type conversion for folds and improve input_files type checking i…
SimoneBendazzoli93 Feb 6, 2025
2da5ca9
DCO Remediation Commit for simben <[email protected]>
SimoneBendazzoli93 Feb 6, 2025
48d53a4
Fix documentation for output tensor return in ModelnnUNetWrapper
SimoneBendazzoli93 Feb 6, 2025
230cb9b
Remove outdated method documentation for forward pass in ModelnnUNetW…
SimoneBendazzoli93 Feb 6, 2025
507bca8
Merge branch 'dev' into 8328-nnunet-bundle-integration
SimoneBendazzoli93 Feb 12, 2025
e7a44f5
Merge branch 'Project-MONAI:dev' into dev
SimoneBendazzoli93 Feb 12, 2025
8ba37ad
Merge branch 'dev' into 8328-nnunet-bundle-integration
SimoneBendazzoli93 Feb 13, 2025
2ec9207
Merge remote-tracking branch 'origin/dev' into 8328-nnunet-bundle-int…
SimoneBendazzoli93 Feb 18, 2025
bce281e
Merge remote-tracking branch 'upstream/dev' into 8328-nnunet-bundle-i…
SimoneBendazzoli93 Feb 18, 2025
ea8028f
Add integration tests for nnUNet bundle functionality
SimoneBendazzoli93 Feb 18, 2025
97c98bd
Merge branch 'Project-MONAI:dev' into 8328-nnunet-bundle-integration
SimoneBendazzoli93 Feb 24, 2025
9dc6532
DCO Remediation Commit for simben <[email protected]>
SimoneBendazzoli93 Feb 24, 2025
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10 changes: 10 additions & 0 deletions docs/source/bundle.rst
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,13 @@ Model Bundle
:members:
:special-members:


`nnUNet Bundle`
---------------
.. autoclass:: ModelnnUNetWrapper
:members:
:special-members:

`Scripts`
---------
.. autofunction:: ckpt_export
Expand All @@ -50,3 +57,6 @@ Model Bundle
.. autofunction:: init_bundle
.. autofunction:: push_to_hf_hub
.. autofunction:: update_kwargs
.. autofunction:: get_nnunet_trainer
.. autofunction:: get_nnunet_monai_predictor
.. autofunction:: convert_nnunet_to_monai_bundle
1 change: 1 addition & 0 deletions monai/bundle/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@

from .config_item import ComponentLocator, ConfigComponent, ConfigExpression, ConfigItem, Instantiable
from .config_parser import ConfigParser
from .nnunet import ModelnnUNetWrapper, convert_nnunet_to_monai_bundle, get_nnunet_monai_predictor, get_nnunet_trainer
from .properties import InferProperties, MetaProperties, TrainProperties
from .reference_resolver import ReferenceResolver
from .scripts import (
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