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 <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

* 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 <[email protected]> * Added verbiage to name but a few tutorials. Signed-off-by: mmelqin <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

…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 <[email protected]> * 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 <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

* Implement highdicom seg operator Signed-off-by: Chris Bridge <[email protected]> * Formatting fixes Signed-off-by: Chris Bridge <[email protected]> * Typing fixes Signed-off-by: Chris Bridge <[email protected]> * 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 <[email protected]> * Fix isort error for ordering of imports Signed-off-by: mmelqin <[email protected]> * Update doc strings and comments for seg label and algorithm name and version Signed-off-by: mmelqin <[email protected]> * 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 <[email protected]> * Updated apps that have multiple segments Signed-off-by: mmelqin <[email protected]> * Found the few missing codes, so avoided use of generic "Organ" Signed-off-by: mmelqin <[email protected]> Signed-off-by: Chris Bridge <[email protected]> Signed-off-by: mmelqin <[email protected]> Co-authored-by: mmelqin <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

…thers Signed-off-by: mmelqin <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Signed-off-by: mmelqin <[email protected]> Signed-off-by: mmelqin <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

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

Signed-off-by: Simone Bendazzoli <[email protected]>

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

Signed-off-by: kavink <[email protected]> Signed-off-by: kavink <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

Signed-off-by: Andres <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

* Add the missing python package, PyPDF2 Signed-off-by: M Q <[email protected]> * Add PyPDF2>=2.11.1 Signed-off-by: M Q <[email protected]> Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Signed-off-by: M Q <[email protected]> Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

* fix casting, add check Signed-off-by: will tepe <[email protected]> * code review changes Signed-off-by: will tepe <[email protected]> * fix fir slope as well --------- Signed-off-by: will tepe <[email protected]> Co-authored-by: will tepe <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

…#537) * The tag value for usinged int is 0 Signed-off-by: M Q <[email protected]> * Fix formmating complaints Signed-off-by: M Q <[email protected]> --------- Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

* Prepared changes for releasing v3 Signed-off-by: M Q <[email protected]> * Bump the required version to 3.9 Signed-off-by: M Q <[email protected]> * 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 <[email protected]> --------- Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

* Bump version: 2.0.0 → 3.0.0 Signed-off-by: M Q <[email protected]> * Bump version: 2.0.0 -> 3.0.0 with __init__.py fix Signed-off-by: M Q <[email protected]> * Remove blank line complained by black Signed-off-by: M Q <[email protected]> * Fix more formatting complaints Signed-off-by: M Q <[email protected]> --------- Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Signed-off-by: Simone Bendazzoli <[email protected]>

…ator and add implementation Signed-off-by: Simone Bendazzoli <[email protected]>

…nference operator Signed-off-by: Simone Bendazzoli <[email protected]>

…tor.py for clarity Signed-off-by: Simone Bendazzoli <[email protected]>

…undle Signed-off-by: Simone Bendazzoli <[email protected]>

…image Signed-off-by: Simone Bendazzoli <[email protected]>

Signed-off-by: Simone Bendazzoli <[email protected]>

…ect module path Signed-off-by: Simone Bendazzoli <[email protected]>

* hugging_face_integration_app dependency cleanup Signed-off-by: bluna301 <[email protected]> * cchmc_ped_abd_ct_seg example app Signed-off-by: bluna301 <[email protected]> * license update + code optimizations Signed-off-by: bluna301 <[email protected]> * cleanup Signed-off-by: bluna301 <[email protected]> * spelling + dependency cleanup Signed-off-by: bluna301 <[email protected]> * model DICOM tag cleanup Signed-off-by: bluna301 <[email protected]> --------- Signed-off-by: bluna301 <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

* Prepared changes for releasing v3 Signed-off-by: M Q <[email protected]> * Bump the required version to 3.9 Signed-off-by: M Q <[email protected]> * 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 <[email protected]> --------- Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

- Removed unnecessary logic in setup.py - Fix versioneer issues Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

* Bump version: 2.0.0 → 3.0.0 Signed-off-by: M Q <[email protected]> * Bump version: 2.0.0 -> 3.0.0 with __init__.py fix Signed-off-by: M Q <[email protected]> * Remove blank line complained by black Signed-off-by: M Q <[email protected]> * Fix more formatting complaints Signed-off-by: M Q <[email protected]> --------- Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

…NetBundleInferenceOperator Signed-off-by: Simone Bendazzoli <[email protected]>

…pdate docstring Signed-off-by: Simone Bendazzoli <[email protected]>

* series selector improvements Signed-off-by: bluna301 <[email protected]> * PatientPosition tag check Signed-off-by: bluna301 <[email protected]> * exclusion matching for set type Signed-off-by: bluna301 <[email protected]> --------- Signed-off-by: bluna301 <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Signed-off-by: Simone Bendazzoli <[email protected]>

…ut type Signed-off-by: Simone Bendazzoli <[email protected]>

sonarqubecloud · 2025-07-17T08:19:47Z

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 <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Update release notes for v0.4.0

f84493f

Signed-off-by: mmelqin <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

60de91b

…thers Signed-off-by: mmelqin <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

5384e7d

Signed-off-by: mmelqin <[email protected]> Signed-off-by: mmelqin <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

7053478

Signed-off-by: Simone Bendazzoli <[email protected]>

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

eb97cd4

Signed-off-by: Simone Bendazzoli <[email protected]>

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

aa4e52f

Signed-off-by: Simone Bendazzoli <[email protected]>

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

ff526eb

Signed-off-by: kavink <[email protected]> Signed-off-by: kavink <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Minor typo in property method

c6548f9

Signed-off-by: Andres <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Update method name

cc98293

Signed-off-by: Andres <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

1c76efa

Signed-off-by: M Q <[email protected]> Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

WillButAgain and others added 23 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 <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

Fix NiftiDataWriter spacing handling for 1mm pixel dimensions

9036d24

Signed-off-by: Simone Bendazzoli <[email protected]>

Refactor nnUNet bundle inference operator to MONetBundleInferenceOper…

292c70c

…ator and add implementation Signed-off-by: Simone Bendazzoli <[email protected]>

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

58f7a29

…nference operator Signed-off-by: Simone Bendazzoli <[email protected]>

Refactor import statements in app.py and monet_bundle_inference_opera…

8656d2d

…tor.py for clarity Signed-off-by: Simone Bendazzoli <[email protected]>

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

d08f35f

…undle Signed-off-by: Simone Bendazzoli <[email protected]>

Refactor NiftiDataLoader to return transposed numpy array from NIfTI …

7941da9

…image Signed-off-by: Simone Bendazzoli <[email protected]>

Remove NiftiDataWriter operator and clean up imports in __init__.py

f6e3e64

Signed-off-by: Simone Bendazzoli <[email protected]>

Remove SimpleITK image handling from MonaiBundleInferenceOperator

3ff1250

Signed-off-by: Simone Bendazzoli <[email protected]>

Fix import statement for MONetBundleInferenceOperator to use the corr…

8b4d4ac

…ect module path Signed-off-by: Simone Bendazzoli <[email protected]>

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 <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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

56155c0

…NetBundleInferenceOperator Signed-off-by: Simone Bendazzoli <[email protected]>

Enhance predict method to support multimodal data concatenation and u…

343e5fd

…pdate docstring Signed-off-by: Simone Bendazzoli <[email protected]>

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

3b127ed

Signed-off-by: M Q <[email protected]> Signed-off-by: Simone Bendazzoli <[email protected]>

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 <[email protected]>

Remove unused import

44803a2

Signed-off-by: Simone Bendazzoli <[email protected]>

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

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

7804d84

…ut type Signed-off-by: Simone Bendazzoli <[email protected]>

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MONet Bundle Integration into MONAI Deploy #543

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