MONet Bundle Integration into MONAI Deploy #543

SimoneBendazzoli93 · 2025-06-17T12:40:32Z

This PR introduces support for the MONet Bundle (an nnUNet wrapper for the MONAI Bundle) into MONAI Deploy.

Key Features:

Added a new operator: MONetBundleInferenceOperator, extending MonaiBundleInferenceOperator
Included an example application demonstrating spleen segmentation using the MONetBundleInferenceOperator

Signed-off-by: Simone Bendazzoli <simben@kth.se>

* hugging_face_integration_app dependency cleanup Signed-off-by: bluna301 <luna.bryanr@gmail.com> * cchmc_ped_abd_ct_seg example app Signed-off-by: bluna301 <luna.bryanr@gmail.com> * license update + code optimizations Signed-off-by: bluna301 <luna.bryanr@gmail.com> * cleanup Signed-off-by: bluna301 <luna.bryanr@gmail.com> * spelling + dependency cleanup Signed-off-by: bluna301 <luna.bryanr@gmail.com> * model DICOM tag cleanup Signed-off-by: bluna301 <luna.bryanr@gmail.com> --------- Signed-off-by: bluna301 <luna.bryanr@gmail.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…efaults to an empty dict Signed-off-by: Simone Bendazzoli <simben@kth.se>

… Inference Operator Signed-off-by: Simone Bendazzoli <simben@kth.se>

…pleITK image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: bluna301 <luna.bryanr@gmail.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…roject-MONAI#536) * Adding requirements for Triton client impl Signed-off-by: M Q <mingmelvinq@nvidia.com> * Updated/added core classes to support Triton remote inference, and added a new example Signed-off-by: M Q <mingmelvinq@nvidia.com> * GitHub build server complains about conflicts for tritonclient[]>=2.54 for no specific reasons Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix flake8 complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix pytype complaints by simplifying code Signed-off-by: M Q <mingmelvinq@nvidia.com> * Remove now unused imports Signed-off-by: M Q <mingmelvinq@nvidia.com> * Addressed all pytype and mypy complaint in new code in the dev env Signed-off-by: M Q <mingmelvinq@nvidia.com> * No complaint in local dev env, but on GitHub Signed-off-by: M Q <mingmelvinq@nvidia.com> * Add model confgi.pbtxt and example env settings Signed-off-by: M Q <mingmelvinq@nvidia.com> * Doc update Signed-off-by: M Q <mingmelvinq@nvidia.com> * update license dates Signed-off-by: M Q <mingmelvinq@nvidia.com> * Updated the copyright year of new files Signed-off-by: M Q <mingmelvinq@nvidia.com> --------- Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* fix casting, add check Signed-off-by: will tepe <will.tepe@cchmc.org> * code review changes Signed-off-by: will tepe <will.tepe@cchmc.org> * fix fir slope as well --------- Signed-off-by: will tepe <will.tepe@cchmc.org> Co-authored-by: will tepe <will.tepe@cchmc.org> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…#537) * The tag value for usinged int is 0 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix formmating complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> --------- Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Prepared changes for releasing v3 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Bump the required version to 3.9 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Update Python version references to 3.9 in documentation and configuration files - Updated .gitignore to include new input and test directories. - Changed Python version from 3.8 to 3.9 in .readthedocs.yml, setup.cfg, and run script. - Updated documentation to reflect the use of Python 3.9 in various tutorials. Signed-off-by: M Q <mingmelvinq@nvidia.com> --------- Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Bump version: 2.0.0 → 3.0.0 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Bump version: 2.0.0 -> 3.0.0 with __init__.py fix Signed-off-by: M Q <mingmelvinq@nvidia.com> * Remove blank line complained by black Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix more formatting complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> --------- Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: Simone Bendazzoli <simben@kth.se>

…ator and add implementation Signed-off-by: Simone Bendazzoli <simben@kth.se>

…nference operator Signed-off-by: Simone Bendazzoli <simben@kth.se>

…tor.py for clarity Signed-off-by: Simone Bendazzoli <simben@kth.se>

…undle Signed-off-by: Simone Bendazzoli <simben@kth.se>

…image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: Simone Bendazzoli <simben@kth.se>

…ect module path

…ploy-app-sdk

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Bump version: 2.0.0 → 3.0.0 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Bump version: 2.0.0 -> 3.0.0 with __init__.py fix Signed-off-by: M Q <mingmelvinq@nvidia.com> * Remove blank line complained by black Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix more formatting complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> --------- Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: Simone Bendazzoli <simben@kth.se>

…ator and add implementation Signed-off-by: Simone Bendazzoli <simben@kth.se>

…nference operator Signed-off-by: Simone Bendazzoli <simben@kth.se>

…tor.py for clarity Signed-off-by: Simone Bendazzoli <simben@kth.se>

…undle Signed-off-by: Simone Bendazzoli <simben@kth.se>

…image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: Simone Bendazzoli <simben@kth.se>

…ect module path Signed-off-by: Simone Bendazzoli <simben@kth.se>

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Bump version: 2.0.0 → 3.0.0 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Bump version: 2.0.0 -> 3.0.0 with __init__.py fix Signed-off-by: M Q <mingmelvinq@nvidia.com> * Remove blank line complained by black Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix more formatting complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> --------- Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…NetBundleInferenceOperator Signed-off-by: Simone Bendazzoli <simben@kth.se>

…pdate docstring Signed-off-by: Simone Bendazzoli <simben@kth.se>

…pleITK image Signed-off-by: Simone Bendazzoli <simben@kth.se>

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Bump version: 2.0.0 → 3.0.0 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Bump version: 2.0.0 -> 3.0.0 with __init__.py fix Signed-off-by: M Q <mingmelvinq@nvidia.com> * Remove blank line complained by black Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix more formatting complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> --------- Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: Simone Bendazzoli <simben@kth.se>

…undle Signed-off-by: Simone Bendazzoli <simben@kth.se>

…image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: Simone Bendazzoli <simben@kth.se>

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Bump version: 2.0.0 → 3.0.0 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Bump version: 2.0.0 -> 3.0.0 with __init__.py fix Signed-off-by: M Q <mingmelvinq@nvidia.com> * Remove blank line complained by black Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix more formatting complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> --------- Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…ploy-app-sdk

sonarqubecloud · 2025-06-26T20:39:37Z

Quality Gate failed

Failed conditions
32.9% Duplication on New Code (required ≤ 3%)

See analysis details on SonarQube Cloud

MMelQin · 2025-06-27T00:28:49Z

@SimoneBendazzoli93 Please sign off the commits with the steps shown in the details of the DECO check error. Thanks.

Copilot

Pull Request Overview

This PR integrates the new MONetBundleInferenceOperator for nnUNet-based MONAI Bundles into MONAI Deploy and provides an example application demonstrating spleen segmentation.

Adds MONetBundleInferenceOperator subclassing the existing bundle inference operator to support nnUNet predictors.
Updates core operator file to fix a string method misuse and handle missing metadata.
Supplies a complete example app with requirements, pipeline code, and entrypoints.

Comments suppressed due to low confidence (2)

monai/deploy/operators/monet_bundle_inference_operator.py:1

[nitpick] The copyright year appears incorrect (2002); update to the current year or range (e.g., 2023).

# Copyright 2002 MONAI Consortium

examples/apps/ai_spleen_nnunet_seg_app/app.py:33

[nitpick] The class name has a typo with triple 'n' in AISpleennnUNetSegApp; consider renaming to AISpleenNnunetSegApp for clarity.

class AISpleennnUNetSegApp(Application):

Copilot · 2025-06-27T00:31:06Z

monai/deploy/operators/monai_bundle_inference_operator.py


+import SimpleITK


Duplicate import of SimpleITK (also imported on line 25); please remove redundant imports to clean up the code.

Suggested change

import SimpleITK

Copilot · 2025-06-27T00:31:06Z

examples/apps/ai_spleen_nnunet_seg_app/requirements.txt

+nibabel>=3.2.1
+torch>=1.12.0
+nvflare
+git+https://github.com/SimoneBendazzoli93/dynamic-network-architectures.git


[nitpick] Including dependencies directly from forks may hinder reproducibility; consider pinning to a stable release or official package versions.

Copilot · 2025-06-27T00:31:07Z

monai/deploy/operators/monet_bundle_inference_operator.py

+        """Predicts output using the inferer. If multimodal data is provided as keyword arguments,
+        it concatenates the data with the main input data."""
+
+        self._nnunet_predictor.predictor.network = self._model_network


[nitpick] Mutating the predictor's internal predictor.network may couple implementation details; consider providing the model via constructor or a dedicated setter.

Suggested change

self._nnunet_predictor.predictor.network = self._model_network

self._set_model_network(self._model_network)

SimoneBendazzoli93 and others added 22 commits June 17, 2025 12:47

Add nnUNet segmentation application and dependencies

dacfaa9

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix meta_data handling in MonaiBundleInferenceOperator to ensure it d…

cbbc7a4

…efaults to an empty dict Signed-off-by: Simone Bendazzoli <simben@kth.se>

Update requirements and fix data shape handling in Monai nUNet Bundle…

d587183

… Inference Operator Signed-off-by: Simone Bendazzoli <simben@kth.se>

Add NiftiDataWriter operator and update NiftiDataLoader to return Sim…

e2591dc

…pleITK image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Add nvflare to requirements for ai_spleen_nnunet_seg_app

c235691

Signed-off-by: Simone Bendazzoli <simben@kth.se>

duplicate ipps non-loaded (Project-MONAI#535)

54ef91b

Signed-off-by: bluna301 <luna.bryanr@gmail.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

ModelInfo arg added to DICOMSegWriterOp (Project-MONAI#533)

aa93ce9

Signed-off-by: bluna301 <luna.bryanr@gmail.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix _version.py and various version-related issues (Project-MONAI#539)

b49964d

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix NiftiDataWriter spacing handling for 1mm pixel dimensions

ebfe2ea

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Refactor nnUNet bundle inference operator to MONetBundleInferenceOper…

7d4fb4e

…ator and add implementation Signed-off-by: Simone Bendazzoli <simben@kth.se>

Update documentation to reflect changes from nnUNet to MONet Bundle i…

a7ba89f

…nference operator Signed-off-by: Simone Bendazzoli <simben@kth.se>

Refactor import statements in app.py and monet_bundle_inference_opera…

3511186

…tor.py for clarity Signed-off-by: Simone Bendazzoli <simben@kth.se>

Update application title and fix operator name in imports for MONet B…

9b01862

…undle Signed-off-by: Simone Bendazzoli <simben@kth.se>

Refactor NiftiDataLoader to return transposed numpy array from NIfTI …

25e9a85

…image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Remove NiftiDataWriter operator and clean up imports in __init__.py

6496e55

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Remove SimpleITK image handling from MonaiBundleInferenceOperator

b01a3a8

Signed-off-by: Simone Bendazzoli <simben@kth.se>

SimoneBendazzoli93 force-pushed the main branch from 045f47d to b01a3a8 Compare June 17, 2025 12:48

SimoneBendazzoli93 marked this pull request as ready for review June 17, 2025 12:50

SimoneBendazzoli93 added 3 commits June 17, 2025 14:52

Merge branch 'Project-MONAI:main' into main

bade974

Fix import statement for MONetBundleInferenceOperator to use the corr…

7418c93

…ect module path

Merge branch 'main' of https://github.com/SimoneBendazzoli93/monai-de…

fb7efc2

…ploy-app-sdk

MMelQin requested review from bluna301, MMelQin and Copilot June 25, 2025 15:41

MMelQin and others added 26 commits June 26, 2025 20:32

Fix _version.py and various version-related issues (Project-MONAI#539)

57f378a

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix NiftiDataWriter spacing handling for 1mm pixel dimensions

f8fbea0

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Refactor nnUNet bundle inference operator to MONetBundleInferenceOper…

26b1244

…ator and add implementation Signed-off-by: Simone Bendazzoli <simben@kth.se>

Update documentation to reflect changes from nnUNet to MONet Bundle i…

16b110c

…nference operator Signed-off-by: Simone Bendazzoli <simben@kth.se>

Refactor import statements in app.py and monet_bundle_inference_opera…

a44803f

…tor.py for clarity Signed-off-by: Simone Bendazzoli <simben@kth.se>

Update application title and fix operator name in imports for MONet B…

1f51edc

…undle Signed-off-by: Simone Bendazzoli <simben@kth.se>

Refactor NiftiDataLoader to return transposed numpy array from NIfTI …

96ab7cb

…image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Remove NiftiDataWriter operator and clean up imports in __init__.py

420fe54

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Remove SimpleITK image handling from MonaiBundleInferenceOperator

22ca8e5

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix import statement for MONetBundleInferenceOperator to use the corr…

326c859

…ect module path Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix _version.py and various version-related issues (Project-MONAI#539)

71c2e7e

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix formatting in docstring and remove unused import statements in MO…

3246307

…NetBundleInferenceOperator Signed-off-by: Simone Bendazzoli <simben@kth.se>

Enhance predict method to support multimodal data concatenation and u…

d650d7a

…pdate docstring Signed-off-by: Simone Bendazzoli <simben@kth.se>

Add NiftiDataWriter operator and update NiftiDataLoader to return Sim…

8e15803

…pleITK image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix _version.py and various version-related issues (Project-MONAI#539)

bafd869

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix NiftiDataWriter spacing handling for 1mm pixel dimensions

d5d4477

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Update application title and fix operator name in imports for MONet B…

39f66cd

…undle Signed-off-by: Simone Bendazzoli <simben@kth.se>

Refactor NiftiDataLoader to return transposed numpy array from NIfTI …

f1e0dbb

…image Signed-off-by: Simone Bendazzoli <simben@kth.se>

Remove NiftiDataWriter operator and clean up imports in __init__.py

d035ab3

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Remove SimpleITK image handling from MonaiBundleInferenceOperator

8bfc852

Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix _version.py and various version-related issues (Project-MONAI#539)

7141271

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Merge branch 'main' of https://github.com/SimoneBendazzoli93/monai-de…

84b61f4

…ploy-app-sdk

MMelQin requested a review from Copilot June 27, 2025 00:29

Copilot AI reviewed Jun 27, 2025

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MONet Bundle Integration into MONAI Deploy #543

MONet Bundle Integration into MONAI Deploy #543

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	self._nnunet_predictor.predictor.network = self._model_network
	self._set_model_network(self._model_network)

MONet Bundle Integration into MONAI Deploy #543

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