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

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):

monai/deploy/operators/monai_bundle_inference_operator.py

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.

monai/deploy/operators/monet_bundle_inference_operator.py

Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Add the newly introduced example to readme.md This is a a bit of a chicken-and-egg problem, since the readme.md refers to the published latest version of the doc with which can only happen when the release build is done, and this particular doc is part of the build, included in the package to be pushed to pypi.org. Next time, need to consider add the entry, with a placeholder/no-existent URL prior to the release build, so that the content will show up in the new package, and URL leads to valid content post build. Signed-off-by: mmelqin <mingmelvinq@nvidia.com> * Added verbiage to name but a few tutorials. Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…ONAI#316) * DOC: Use upstream/downstream instead of source/destination For monai.deploy.core.Operator, instead of sometimes using "upstream" and "downstream" and sometimes using "source" and "destination", consistently use former. Signed-off-by: Lee Newberg <lee.newberg@kitware.com> * DOC: Use source/destination instead of upstream/downstream For monai.deploy.core.Operator, instead of sometimes using "upstream" and "downstream" and sometimes using "source" and "destination", consistently use the latter. Signed-off-by: Lee Newberg <lee.newberg@kitware.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Implement highdicom seg operator Signed-off-by: Chris Bridge <chrisbridge44@googlemail.com> * Formatting fixes Signed-off-by: Chris Bridge <chrisbridge44@googlemail.com> * Typing fixes Signed-off-by: Chris Bridge <chrisbridge44@googlemail.com> * Update the Spleen App to use HighDicom Seg Writer. The app is still not compatible with monai v0.9.1 as the app testing revealed that to its Invert transform failed resample the predicted image back to input image spacings. Also, the new Seg Writer impl is strict on DICOM attribute VR conformance, and would throw exception when the input DICOM instances have non-conformant attribute VR values. Signed-off-by: mmelqin <mingmelvinq@nvidia.com> * Fix isort error for ordering of imports Signed-off-by: mmelqin <mingmelvinq@nvidia.com> * Update doc strings and comments for seg label and algorithm name and version Signed-off-by: mmelqin <mingmelvinq@nvidia.com> * Pin moani==0.9.0 for now as 0.9.1 causes issues. Also pydicom to 2.3.0 as the use of highdicom require pydicom>=2.3.0 Signed-off-by: mmelqin <mingmelvinq@nvidia.com> * Updated apps that have multiple segments Signed-off-by: mmelqin <mingmelvinq@nvidia.com> * Found the few missing codes, so avoided use of generic "Organ" Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Chris Bridge <chrisbridge44@googlemail.com> Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Co-authored-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…thers Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…roject-MONAI#337) * Improve STL operator so the enclosing app obj can run repetitively with the new sample code Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fixing Flake8 complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> * Ignore Flake8 B024: abstract base class, but it has no abstract methods Signed-off-by: M Q <mingmelvinq@nvidia.com> * Silence mypy complaint on types Signed-off-by: M Q <mingmelvinq@nvidia.com> * Quiet another mypy error. Signed-off-by: M Q <mingmelvinq@nvidia.com> * MyPy complaint fix Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…roject-MONAI#345) * Added support of matching instance level tags, and update liver seg Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix Flake8 complaint Signed-off-by: M Q <mingmelvinq@nvidia.com> * Still enable publish intermediate nii files. Signed-off-by: M Q <mingmelvinq@nvidia.com> * Corrections per review comments 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>

* Added support of matching instance level tags, and update liver seg Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix Flake8 complaint Signed-off-by: M Q <mingmelvinq@nvidia.com> * Still enable publish intermediate nii files. Signed-off-by: M Q <mingmelvinq@nvidia.com> * Corrections per review comments Signed-off-by: M Q <mingmelvinq@nvidia.com> * Enhance attribute settings Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fixed styling complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix MyPy complaint Signed-off-by: M Q <mingmelvinq@nvidia.com> * Use content sequence for section of text 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: kavink <kavink@nvidia.com> Signed-off-by: kavink <kavink@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…roject-MONAI#360) * Updated to be compitable with monai 1.0.0 and its MetaTensor Signed-off-by: M Q <mingmelvinq@nvidia.com> * Made bundle inference operator compatible with MetaTensor Signed-off-by: M Q <mingmelvinq@nvidia.com> * Removed the use of ToTensor from all apps. Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix MyPy complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix isort complaint Signed-off-by: M Q <mingmelvinq@nvidia.com> * Use a constant for repeated use of monai.utils str literal; SonarCloud code smell. Signed-off-by: M Q <mingmelvinq@nvidia.com> * Updated Seg Writer and Spleen Seg Jupyter notebooks Signed-off-by: M Q <mingmelvinq@nvidia.com> * Minor to address comments and checker complaint Signed-off-by: M Q <mingmelvinq@nvidia.com> * Updated clara-viz Jupyter notebook and fixed checking complaint 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: Andres <diazandr3s@gmail.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

…SR Writer (Project-MONAI#366) * Created dicom_utils for common obj and func, and added DICOM PDF Writer Signed-off-by: M Q <mingmelvinq@nvidia.com> * Formatting update Signed-off-by: M Q <mingmelvinq@nvidia.com> * Fix flake8 complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> * Address mypy complaints Signed-off-by: M Q <mingmelvinq@nvidia.com> * Formatting Signed-off-by: M Q <mingmelvinq@nvidia.com> * Change to use full path of dicom_utils Signed-off-by: M Q <mingmelvinq@nvidia.com> * Replace Union with Optional Signed-off-by: M Q <mingmelvinq@nvidia.com> * Replace unused Union Signed-off-by: M Q <mingmelvinq@nvidia.com> * Update the year in the copyright notice Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

* Add the missing python package, PyPDF2 Signed-off-by: M Q <mingmelvinq@nvidia.com> * Add PyPDF2>=2.11.1 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: M Q <mingmelvinq@nvidia.com> Signed-off-by: M Q <mingmelvinq@nvidia.com> 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 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>

…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>

* 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>

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

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

* series selector improvements Signed-off-by: bluna301 <luna.bryanr@gmail.com> * PatientPosition tag check Signed-off-by: bluna301 <luna.bryanr@gmail.com> * exclusion matching for set type Signed-off-by: bluna301 <luna.bryanr@gmail.com> --------- Signed-off-by: bluna301 <luna.bryanr@gmail.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

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

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

sonarqubecloud · 2025-08-08T06:33:45Z

Quality Gate failed

Failed conditions
32.0% Duplication on New Code (required ≤ 3%)

See analysis details on SonarQube Cloud

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

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

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

Copilot AI reviewed Jun 27, 2025

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SimoneBendazzoli93 force-pushed the main branch from 3f1b3a2 to 5cf7679 Compare July 17, 2025 07:23

MMelQin and others added 20 commits July 17, 2025 07:24

Bump version: 0.3.0 → 0.4.0

ed2a45c

Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Update release notes for v0.4.0

f84493f

Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Fix the setting of init state in its own PR, instead of rolled into o…

60de91b

…thers Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Add highdicom license to the Third Party Notices (Project-MONAI#334)

5384e7d

Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: mmelqin <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Nuance PIN MONAI Integration Example App (Project-MONAI#328)

7053478

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

minor adjustment for proper result alignment (Project-MONAI#354)

eb97cd4

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

Nuance pin integration minor adjustments (Project-MONAI#355)

aa4e52f

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

Update executor path to new version (Project-MONAI#135)

ff526eb

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

Minor typo in property method

c6548f9

Signed-off-by: Andres <diazandr3s@gmail.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Update method name

cc98293

Signed-off-by: Andres <diazandr3s@gmail.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

Enhanced multi-value DateElement parsing (Project-MONAI#370)

1c76efa

Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

MMelQin and others added 22 commits July 17, 2025 07:24

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

3d9f752

- 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

9036d24

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

Refactor nnUNet bundle inference operator to MONetBundleInferenceOper…

292c70c

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

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

58f7a29

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

Refactor import statements in app.py and monet_bundle_inference_opera…

8656d2d

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

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

d08f35f

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

Refactor NiftiDataLoader to return transposed numpy array from NIfTI …

7941da9

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

Remove NiftiDataWriter operator and clean up imports in __init__.py

f6e3e64

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

Remove SimpleITK image handling from MonaiBundleInferenceOperator

3ff1250

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

Fix import statement for MONetBundleInferenceOperator to use the corr…

8b4d4ac

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

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

d8da34f

- 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…

56155c0

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

Enhance predict method to support multimodal data concatenation and u…

343e5fd

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

Regression tests with HSDK 3.4 and CLI 3.4.1 (Project-MONAI#545)

3b127ed

Signed-off-by: M Q <mingmelvinq@nvidia.com> Signed-off-by: Simone Bendazzoli <simben@kth.se>

SimoneBendazzoli93 force-pushed the main branch 2 times, most recently from 677f748 to 3b127ed Compare July 17, 2025 07:57

SimoneBendazzoli93 added 2 commits July 17, 2025 09:58

Merge branch 'main' into main

dcc20c8

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

Remove unused import

44803a2

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

SimoneBendazzoli93 force-pushed the main branch from 12c4c49 to 44803a2 Compare July 17, 2025 08:16

SimoneBendazzoli93 added 2 commits July 17, 2025 08:19

Add method to set model network for nnUNet predictor and validate inp…

7804d84

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

Merge branch 'Project-MONAI:main' into main

fe15cf6

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MONet Bundle Integration into MONAI Deploy #543

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