8328 nnunet bundle integration by SimoneBendazzoli93 · Pull Request #8329 · Project-MONAI/MONAI

SimoneBendazzoli93 · 2025-02-05T15:39:47Z

Description

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]>

SimoneBendazzoli93 · 2025-02-06T15:09:28Z

/black

SimoneBendazzoli93 · 2025-02-06T15:13:25Z

The corresponding Notebook tutorial is added trough the issue: Project-MONAI/tutorials#1938

…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

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…trainer classes

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

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I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 8e510e1 Signed-off-by: Simone Bendazzoli <[email protected]>

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

…orted trainer link

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I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 5422368 Signed-off-by: Simone Bendazzoli <[email protected]>

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

monai/apps/nnunet/nnunet_bundle.py

KumoLiu · 2025-04-02T07:16:09Z

Hi @ericspod, let me know if you have any other concerns on this PR, thanks!

No code changes detected. ```

…o dev

I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 7d60fd7 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 3b13218 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: fbf6105 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: d1035ca I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 47798af I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 0578b22 I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 6d3fb0c Signed-off-by: Simone Bendazzoli <[email protected]>

ericspod

Looks good to me now!

KumoLiu · 2025-04-07T02:32:52Z

/build

KumoLiu · 2025-04-07T02:53:25Z

/build

SimoneBendazzoli93 and others added 16 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

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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]>

SimoneBendazzoli93 marked this pull request as ready for review February 6, 2025 15:08

SimoneBendazzoli93 added 11 commits February 12, 2025 18:34

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

507bca8

Merge branch 'Project-MONAI:dev' into dev

e7a44f5

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

pre-commit-ci bot and others added 10 commits March 30, 2025 14:09

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Update docstring in get_nnunet_trainer to include link for supported …

8e510e1

…trainer classes

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

f74a39c

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

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

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

7d86a73

I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 8e510e1 Signed-off-by: Simone Bendazzoli <[email protected]>

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

a346719

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

Update docstring in get_nnunet_trainer for better readability of supp…

5422368

…orted trainer link

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

aff9cbe

for more information, see https://pre-commit.ci

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

5527ac8

I, Simone Bendazzoli <[email protected]>, hereby add my Signed-off-by to this commit: 5422368 Signed-off-by: Simone Bendazzoli <[email protected]>

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

d969b79

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

SimoneBendazzoli93 requested a review from KumoLiu March 31, 2025 06:37

SimoneBendazzoli93 added 2 commits March 31, 2025 12:57

nvflare support

7d60fd7

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

ed2360c

KumoLiu reviewed Apr 1, 2025

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monai/apps/nnunet/nnunet_bundle.py Outdated Show resolved Hide resolved

SimoneBendazzoli93 added 2 commits April 1, 2025 13:53

Update requirements.txt

3b13218

Add nnunet_root_folder parameter to train function

fbf6105

SimoneBendazzoli93 added 7 commits April 2, 2025 14:36

```

d1035ca

No code changes detected. ```

Merge branch 'dev' of https://github.com/SimoneBendazzoli93/MONAI int…

a8b0a23

…o dev

Remove conditional print statement for torch.compile in nnUNetWrapper

47798af

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

c04cc05

Remove unused nvflare module files

0578b22

Update torch version requirement in requirements.txt

6d3fb0c

ericspod approved these changes Apr 4, 2025

View reviewed changes

KumoLiu enabled auto-merge (squash) April 7, 2025 02:35

KumoLiu merged commit 90ead4b into Project-MONAI:dev Apr 7, 2025
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SimoneBendazzoli93 mentioned this pull request Jun 3, 2025

8328 nnunet bundle integration #8469

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8328 nnunet bundle integration#8329

8328 nnunet bundle integration#8329
KumoLiu merged 97 commits intoProject-MONAI:devfrom
SimoneBendazzoli93:8328-nnunet-bundle-integration

SimoneBendazzoli93 commented Feb 5, 2025 •

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SimoneBendazzoli93 commented Feb 5, 2025 •

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