8328 nnunet bundle integration #8469

SimoneBendazzoli93 · 2025-06-03T08:05:30Z

Updates to #8328 and PR #8329

Description

Fixed nnUNet to MONAI Bundle functionalities:

Support for trained checkpoint as a TorchScript
Multi-channel input tensor
Fixed issue on different axis permutation between nnUNet and MONAI loaders

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

…integration tests

…dant method

I, simben <[email protected]>, hereby add my Signed-off-by to this commit: 13bdec5 I, simben <[email protected]>, hereby add my Signed-off-by to this commit: 74aaf73 I, simben <[email protected]>, hereby add my Signed-off-by to this commit: 8e4a66c Signed-off-by: simben <[email protected]>

I, simben <[email protected]>, hereby add my Signed-off-by to this commit: 5a04fe0 Signed-off-by: simben <[email protected]>

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…arameter type in tests

…ration

…n ModelnnUNetWrapper

I, simben <[email protected]>, hereby add my Signed-off-by to this commit: 43c694b I, simben <[email protected]>, hereby add my Signed-off-by to this commit: 569df7b I, simben <[email protected]>, hereby add my Signed-off-by to this commit: fcf5ac0 I, simben <[email protected]>, hereby add my Signed-off-by to this commit: c846b6d Signed-off-by: simben <[email protected]>

Signed-off-by: simben <[email protected]>

…rapper Signed-off-by: simben <[email protected]>

…egration

…ntegration

I, simben <[email protected]>, hereby add my Signed-off-by to this commit: b61e4e1 I, simben <[email protected]>, hereby add my Signed-off-by to this commit: ea8028f Signed-off-by: simben <[email protected]>

…egration

…imoneBendazzoli93/MONAI into 8328-nnunet-bundle-integration

…at and update dataroot handling in prepare_bundle_api

…dation

…le_api

…abel handling

…n_metrics

…move debug prints

…nsure proper metric aggregation

…acking

… ensure correct metric logging

…ogging reliability

… before loading

…t JSON, plans, and nnUNet configuration; improve loading logic for optional inputs.

…conversion check

…SON creation

…class_order parameters

…nd class labels

…nk line

…del loading

I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: fd12ece I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: d4a9a9e I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: b08d416 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: ff64bd0 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 96df74c I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 6c6346b I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 7a84968 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: b8de5c4 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 665d989 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 6480bba I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: c4b3453 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 2cf94c7 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 2d09694 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: fcf6981 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: b13b3e8 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 397d0eb I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: f819112 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: f8cb161 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: d62fd04 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 3207bb7 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: c5e64c7 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 4a15b97 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 71b30d7 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 188fa53 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: db2f65b I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 6e82b7e I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: e55f2f5 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: d6a7777 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 8c2330d I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 9656483 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: c267fdf I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 460481f I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: a50ef4c I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: f63cc5e I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: ac94578 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 9f9261d I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 2e6f7c9 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 75d6720 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 406923a I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 84d25c6 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: c8104f4 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 78f6650 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 670ff15 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 1cd4312 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: f5ea8e8 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 310745f I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 6611789 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 2f111d5 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: f42840d I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 50faeef I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 0fe60f0 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: f2dbc26 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: db5ae69 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 3b61e9f I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: eae66cb I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 70418a6 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: aba934d I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 9500de1 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: f2dad2c I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: dfeb9fc Signed-off-by: Simone Bendazzoli <[email protected]>

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…rs to Optional[dict] in ModelnnUNetWrapper

…imoneBendazzoli93/MONAI into 8328-nnunet-bundle-integration

I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 92e1108 Signed-off-by: Simone Bendazzoli <[email protected]>

SimoneBendazzoli93 and others added 30 commits January 28, 2025 19:16

Add nnUNet integration and corresponding unit tests

13bdec5

Implement nnUNet model conversion to MONAI bundle format and enhance …

74aaf73

…integration tests

Merge branch 'Project-MONAI:dev' into dev

ccdc76c

Refactor nnUNet bundle integration tests for clarity and remove redun…

b61e4e1

…dant method

Code reformatting

8e4a66c

nibabel importing moved to setUp

5a04fe0

DCO Remediation Commit for simben <[email protected]>

24643b8

I, simben <[email protected]>, hereby add my Signed-off-by to this commit: 5a04fe0 Signed-off-by: simben <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

253dab1

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Add nnUNet Bundle documentation and related functions to bundle.rst

43c694b

Refactor nnUNet documentation and examples for clarity; update fold p…

569df7b

…arameter type in tests

Clean up whitespace in nnunet.py and add test for nnunet bundle integ…

fcf5ac0

…ration

Fix type conversion for folds and improve input_files type checking i…

c846b6d

…n ModelnnUNetWrapper

Fix documentation for output tensor return in ModelnnUNetWrapper

48d53a4

Signed-off-by: simben <[email protected]>

Remove outdated method documentation for forward pass in ModelnnUNetW…

230cb9b

…rapper Signed-off-by: simben <[email protected]>

Merge branch 'dev' into 8328-nnunet-bundle-integration

507bca8

Merge branch 'Project-MONAI:dev' into dev

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Merge branch 'dev' into 8328-nnunet-bundle-integration

8ba37ad

Merge remote-tracking branch 'origin/dev' into 8328-nnunet-bundle-int…

2ec9207

…egration

Merge remote-tracking branch 'upstream/dev' into 8328-nnunet-bundle-i…

bce281e

…ntegration

Add integration tests for nnUNet bundle functionality

ea8028f

Merge branch 'Project-MONAI:dev' into dev

1a1c78d

Merge branch 'Project-MONAI:dev' into 8328-nnunet-bundle-integration

97c98bd

DCO Remediation Commit for simben <[email protected]>

9dc6532

I, simben <[email protected]>, hereby add my Signed-off-by to this commit: b61e4e1 I, simben <[email protected]>, hereby add my Signed-off-by to this commit: ea8028f Signed-off-by: simben <[email protected]>

Merge branch 'Project-MONAI:dev' into dev

a209e25

Merge remote-tracking branch 'origin/dev' into 8328-nnunet-bundle-int…

7b6a247

…egration

Merge branch 'dev' into 8328-nnunet-bundle-integration

d29ff7d

Refactor nnUNet imports for improved module organization

8bbb63b

Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…

2e6bb14

…imoneBendazzoli93/MONAI into 8328-nnunet-bundle-integration

SimoneBendazzoli93 added 22 commits May 27, 2025 07:39

Enhance prepare_data_folder_api to support 'monai-label' dataset form…

c8104f4

…at and update dataroot handling in prepare_bundle_api

Add nnUNetV2Runner initialization in finalize_bundle for dataset vali…

78f6650

…dation

Update finalize_bundle to support federated training in finalize_bund…

670ff15

…le_api

Fix metrics initialization in compute_validation_metrics for proper l…

1cd4312

…abel handling

Add debug prints for HD95, ASD, and Dice metrics in compute_validatio…

f5ea8e8

…n_metrics

Refactor compute_validation_metrics to correct metric indexing and re…

310745f

…move debug prints

Fix initialization of mean summary in compute_validation_metrics to e…

6611789

…nsure proper metric aggregation

Add debug print for labels in finalize_bundle to aid in validation tr…

2f111d5

…acking

Fix label handling in finalize_bundle to ensure correct metric logging

f42840d

Fix label handling in finalize_bundle to support label formatting and…

50faeef

… ensure correct metric logging

Add warning for missing labels in finalize_bundle to improve metric l…

0fe60f0

…ogging reliability

Fix mlflow_params key assignment in prepare_bundle_api for consistency

f2dbc26

Fix model name check in ModelnnUNetWrapper to ensure it ends with .pt…

db5ae69

… before loading

Merge remote-tracking branch 'upstream/dev' into dev

c8471e7

Merge branch 'dev' into 8328-nnunet-bundle-integration

02eec30

Enhance ModelnnUNetWrapper to accept additional parameters for datase…

3b61e9f

…t JSON, plans, and nnUNet configuration; improve loading logic for optional inputs.

Fix error message in MonaiAlgo to remove local weight dict keys from …

eae66cb

…conversion check

Remove unused label and regions_class_order parameters from dataset J…

70418a6

…SON creation

Refactor create_new_dataset_json to remove unused labels and regions_…

aba934d

…class_order parameters

Add background label to new dataset JSON creation and update foregrou…

9500de1

…nd class labels

Fix formatting in create_new_dataset_json by removing unnecessary bla…

f2dad2c

…nk line

Update torch.load calls to include weights_only=False for improved mo…

dfeb9fc

…del loading

SimoneBendazzoli93 requested review from KumoLiu, ericspod and Nic-Ma as code owners June 3, 2025 08:05

SimoneBendazzoli93 and others added 5 commits June 3, 2025 08:06

[pre-commit.ci] auto fixes from pre-commit.com hooks

d6bec33

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Update type hints for dataset_json, plans, and nnunet_config paramete…

92e1108

…rs to Optional[dict] in ModelnnUNetWrapper

Merge branch '8328-nnunet-bundle-integration' of https://github.com/S…

c10b3b6

…imoneBendazzoli93/MONAI into 8328-nnunet-bundle-integration

DCO Remediation Commit for Simone Bendazzoli <[email protected]>

c90e960

I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 92e1108 Signed-off-by: Simone Bendazzoli <[email protected]>

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