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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
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49dbb5d
DCO Remediation Commit for simben <[email protected]>
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nibabel importing moved to setUp
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43c694b
Add nnUNet Bundle documentation and related functions to bundle.rst
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569df7b
Refactor nnUNet documentation and examples for clarity; update fold p…
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fcf5ac0
Clean up whitespace in nnunet.py and add test for nnunet bundle integ…
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Fix type conversion for folds and improve input_files type checking i…
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DCO Remediation Commit for simben <[email protected]>
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48d53a4
Fix documentation for output tensor return in ModelnnUNetWrapper
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230cb9b
Remove outdated method documentation for forward pass in ModelnnUNetW…
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507bca8
Merge branch 'dev' into 8328-nnunet-bundle-integration
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e7a44f5
Merge branch 'Project-MONAI:dev' into dev
SimoneBendazzoli93 Feb 12, 2025
8ba37ad
Merge branch 'dev' into 8328-nnunet-bundle-integration
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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…
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ea8028f
Add integration tests for nnUNet bundle functionality
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1a1c78d
Merge branch 'Project-MONAI:dev' into dev
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Merge branch 'Project-MONAI:dev' into 8328-nnunet-bundle-integration
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Merge remote-tracking branch 'origin/dev' into 8328-nnunet-bundle-int…
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d29ff7d
Merge branch 'dev' into 8328-nnunet-bundle-integration
ericspod Mar 4, 2025
8bbb63b
Refactor nnUNet imports for improved module organization
SimoneBendazzoli93 Mar 10, 2025
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a7cad28
Update nnUNet import paths and comment out Transposed transform in in…
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6e1a2bd
Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…
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e099b08
Merge branch 'Project-MONAI:dev' into dev
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Merge remote-tracking branch 'origin/dev' into 8328-nnunet-bundle-int…
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10aa0ce
Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…
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c107015
DCO Remediation Commit for simben <[email protected]>
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3b5e80b
Update documentation for nnUNet Bundle integration
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1da18e1
Refactor imports and improve code formatting in nnUNet bundle
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Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…
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Refactor forward method in ModelnnUNetWrapper for clarity and type co…
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Remove commented-out code in ModelnnUNetWrapper for improved readability
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1032c9b
Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…
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30cb6c5
Comment out the torch.compile line in ModelnnUNetWrapper to prevent p…
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2c24a6d
Merge branch 'Project-MONAI:dev' into dev
SimoneBendazzoli93 Mar 24, 2025
568d25a
Merge branch '8328-nnunet-bundle-integration' into dev
SimoneBendazzoli93 Mar 24, 2025
1a30a0b
Add JSON generation widgets for nnUNet and update requirements
SimoneBendazzoli93 Mar 24, 2025
ca851cd
Add modality_list parameter to nnUNetExecutor and related functions
SimoneBendazzoli93 Mar 25, 2025
fee1bb0
Fix modality_list check in prepare_config and add debug print statement
SimoneBendazzoli93 Mar 25, 2025
1972504
Rename nnUNetMONAIModelWrapper to ModelnnUNetWrapper for consistency
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5c633f2
SimoneBendazzoli93 Mar 28, 2025
052ef64
Add original_dataset_name to nnunet_plans in preprocess function
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1c41164
Remove unused nvflare module files and restore polygraphy in requirem…
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Add new functions to nnunet_bundle for converting between MONAI and n…
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Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…
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6178082
Add ModelnnUNetWrapper import to nnunet bundle
SimoneBendazzoli93 Mar 30, 2025
2a83641
Merge branch 'Project-MONAI:dev' into dev
SimoneBendazzoli93 Mar 30, 2025
570d068
Merge remote-tracking branch 'origin/dev' into 8328-nnunet-bundle-int…
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78a7d14
DCO Remediation Commit for Simone Bendazzoli <[email protected]>
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88a5e5a
Refactor nnUNet integration: update type hints and improve parameter …
SimoneBendazzoli93 Mar 30, 2025
49d0897
Refactor nnUNet bundle: clean up import order and improve code format…
SimoneBendazzoli93 Mar 30, 2025
0f8335b
Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…
SimoneBendazzoli93 Mar 30, 2025
18d5a4c
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4ca028a
Enhance nnUNet bundle: add nnUNetPredictor import and update type hin…
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050651c
DCO Remediation Commit for Simone Bendazzoli <[email protected]>
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b881cd3
Refactor nnUNet bundle: remove unused nnUNetTrainer and nnUNetPredict…
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Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…
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Merge branch 'dev' into 8328-nnunet-bundle-integration
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3b13218
Update requirements.txt
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Add nnunet_root_folder parameter to train function
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```
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Merge branch 'dev' of https://github.com/SimoneBendazzoli93/MONAI int…
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47798af
Remove conditional print statement for torch.compile in nnUNetWrapper
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Merge branch 'dev' into 8328-nnunet-bundle-integration
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0578b22
Remove unused nvflare module files
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6d3fb0c
Update torch version requirement in requirements.txt
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12 changes: 12 additions & 0 deletions docs/source/apps.rst
Original file line number Diff line number Diff line change
Expand Up @@ -277,3 +277,15 @@ FastMRIReader

.. autoclass:: monai.apps.nnunet.nnUNetV2Runner
:members:

`nnUNet Bundle`
---------------
.. autoclass:: monai.apps.nnunet.ModelnnUNetWrapper
:members:
:special-members:

.. autofunction:: monai.apps.nnunet.get_nnunet_trainer
.. autofunction:: monai.apps.nnunet.get_nnunet_monai_predictor
.. autofunction:: monai.apps.nnunet.convert_nnunet_to_monai_bundle
.. autofunction:: monai.apps.nnunet.convert_monai_bundle_to_nnunet
.. autofunction:: monai.apps.nnunet.get_network_from_nnunet_plans
1 change: 1 addition & 0 deletions docs/source/bundle.rst
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ Model Bundle
:members:
:special-members:


`Scripts`
---------
.. autofunction:: ckpt_export
Expand Down
8 changes: 8 additions & 0 deletions monai/apps/nnunet/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,5 +11,13 @@

from __future__ import annotations

from .nnunet_bundle import (
ModelnnUNetWrapper,
convert_monai_bundle_to_nnunet,
convert_nnunet_to_monai_bundle,
get_network_from_nnunet_plans,
get_nnunet_monai_predictor,
get_nnunet_trainer,
)
from .nnunetv2_runner import nnUNetV2Runner
from .utils import NNUNETMode, analyze_data, create_new_data_copy, create_new_dataset_json
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