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Merged
skaliy merged 11 commits into from
Oct 27, 2026
Merged

Chore/repo cleanup #94

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4120375
fix(vision_inference): keep touching labels together in shape-based r…
skaliy Oct 27, 2026
29bd973
fix(vision_augmentation)!: apply GPU affine parameters on the matchin…
skaliy Oct 27, 2026
d5a3d52
fix(vision_metrics)!: score one-channel output and reject non-binary …
skaliy Oct 27, 2026
4f102ae
fix(utils)!: stop tutorials 11d/11e failing at fit and leaking runs
skaliy Oct 27, 2026
45a10b4
refactor(vision_patch)!: remove the unimplemented weighted sampler
skaliy Oct 27, 2026
c1a685a
docs: fix tutorial text, front matter and the readme logo
skaliy Oct 27, 2026
f0cd001
build: raise the xlrd floor and drop unused dev requirements
skaliy Oct 27, 2026
c9805ba
ci: run tests once per pull request commit
skaliy Oct 27, 2026
e77019a
chore: fix gitignore exceptions and ignore local files
skaliy Oct 27, 2026
f5dbdec
fix(research): repair the spine inference script and refresh research…
skaliy Oct 27, 2026
ce6a608
build: bump version to 0.13.0
skaliy Oct 27, 2026
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7 changes: 5 additions & 2 deletions .github/workflows/test.yaml
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@@ -1,5 +1,9 @@
name: CI
on: [workflow_dispatch, pull_request, push]
on:
workflow_dispatch:
pull_request:
push:
branches: [main]

jobs:
test:
Expand All @@ -10,5 +14,4 @@ jobs:
env:
PYTHONPATH: research:research/vestibular_schwannoma
run: |
python -m pip install pytest
python -m pytest -q research/vestibular_schwannoma/tests
8 changes: 3 additions & 5 deletions .gitignore
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Expand Up @@ -3,8 +3,6 @@ _docs/
*.bak
.gitattributes
.last_checked
.gitconfig
*.bak
*.log
*~
~*
Expand Down Expand Up @@ -66,7 +64,6 @@ coverage.xml
*.pot

# Django stuff:
*.log
local_settings.py

# Flask stuff:
Expand Down Expand Up @@ -178,7 +175,7 @@ _proc/

# MLflow
mlruns/
mlruns.db
mlruns.db*
mlflow.db

# Reports
Expand All @@ -189,7 +186,7 @@ reports/
*.nii
*.nii.gz
# Exception: keep test image used in vision_core
!images/IXI002-Guys-0828-T1.nii.gz
!nbs/images/IXI002-Guys-0828-T1.nii.gz

# research/ holds patient data, so it denies by default and allows code back by
# type. PACS exports name DICOM files without an extension, so the *.dcm rule
Expand Down Expand Up @@ -228,3 +225,4 @@ research/vs_seg/

# Local working notes
TODO.md
todo.html
6 changes: 3 additions & 3 deletions CITATION.cff
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Expand Up @@ -13,8 +13,8 @@ authors:
and Mathematical Sciences, Western Norway University
of Applied Sciences, Bergen, Norway
orcid: 'https://orcid.org/0000-0002-0038-5540'
- given-names: Lundervold
family-names: Alexander Selvikvåg
- given-names: Alexander Selvikvåg
family-names: Lundervold
email: allu@hvl.no
affiliation: >-
Department of Computer Science, Electrical Engineering
Expand All @@ -38,7 +38,7 @@ license: Apache-2.0
preferred-citation:
type: article
authors:
- family-names: " Kaliyugarasan"
- family-names: "Kaliyugarasan"
given-names: "Satheshkumar"
orcid: "https://orcid.org/0000-0002-0038-5540"
- family-names: "Lundervold"
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3 changes: 2 additions & 1 deletion CONTRIBUTING.md
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Expand Up @@ -2,10 +2,11 @@
Contributions to the source code are greatly appreciated. If you find any issues or have suggestions for improvements, please open an issue in the corresponding GitHub repository. To contribute code changes, we encourage you to follow these [steps](https://docs.github.com/en/get-started/quickstart/contributing-to-projects).

## Getting Started
1. Install an editable version of the forked project: `pip install -e 'fastMONAI[dev]'`
1. Install an editable version of the forked project from inside the project folder: `pip install -e '.[dev]'`
2. Git hooks are used to run automatic scripts during each commit and merge to strip the notebooks of superfluous metadata and avoid merge conflicts. To set up Git hooks, run the following command inside the project folder: `nbdev_install_hooks`
3. Once you have installed the project and set up the Git hooks, you can start making changes to the notebooks.
4. Run: `nbdev_prepare` to build .py modules from notebooks and test them (if unit tests are written).
5. Write commit messages and pull request titles as [Conventional Commits](https://www.conventionalcommits.org/), for example `fix(vision_patch): handle empty masks`. See `AGENTS.md` for the allowed types.

## Contact
If you have any questions or need further assistance, please contact us at [skaliyugarasan@hotmail.com]. We appreciate your interest and look forward to your contributions.
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -3,7 +3,7 @@

<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->

![](https://raw.githubusercontent.com/skaliy/skaliy.github.io/main/assets/fastmonai_v1.png)
![](https://raw.githubusercontent.com/MMIV-ML/fastMONAI/main/nbs/images/fastmonai_v1.png)

![CI](https://github.com/MMIV-ML/fastMONAI/workflows/CI/badge.svg)
[![Docs](https://github.com/MMIV-ML/fastMONAI/actions/workflows/deploy.yaml/badge.svg)](https://fastmonai.no)
Expand Down
2 changes: 1 addition & 1 deletion fastMONAI/__init__.py
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@@ -1 +1 @@
__version__ = "0.12.0"
__version__ = "0.13.0"
21 changes: 13 additions & 8 deletions fastMONAI/_modidx.py
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Expand Up @@ -22,8 +22,6 @@
'fastMONAI/dataset_info.py'),
'fastMONAI.dataset_info.MedDataset._visualize_single_case': ( 'dataset_info.html#meddataset._visualize_single_case',
'fastMONAI/dataset_info.py'),
'fastMONAI.dataset_info.MedDataset.calculate_target_size': ( 'dataset_info.html#meddataset.calculate_target_size',
'fastMONAI/dataset_info.py'),
'fastMONAI.dataset_info.MedDataset.fingerprint': ( 'dataset_info.html#meddataset.fingerprint',
'fastMONAI/dataset_info.py'),
'fastMONAI.dataset_info.MedDataset.get_size_statistics': ( 'dataset_info.html#meddataset.get_size_statistics',
Expand Down Expand Up @@ -69,8 +67,6 @@
'fastMONAI/external_data.py'),
'fastMONAI.external_data._dataset_available_locally': ( 'external_data.html#_dataset_available_locally',
'fastMONAI/external_data.py'),
'fastMONAI.external_data._df_sort_and_add_columns': ( 'external_data.html#_df_sort_and_add_columns',
'fastMONAI/external_data.py'),
'fastMONAI.external_data._process_ixi_xls': ( 'external_data.html#_process_ixi_xls',
'fastMONAI/external_data.py'),
'fastMONAI.external_data._process_medmnist_img': ( 'external_data.html#_process_medmnist_img',
Expand All @@ -93,8 +89,10 @@
'fastMONAI/utils.py'),
'fastMONAI.utils.MLflowUIManager._kill_process': ( 'utils.html#mlflowuimanager._kill_process',
'fastMONAI/utils.py'),
'fastMONAI.utils.MLflowUIManager.check_mlflow_installed': ( 'utils.html#mlflowuimanager.check_mlflow_installed',
'fastMONAI/utils.py'),
'fastMONAI.utils.MLflowUIManager._log_tail': ( 'utils.html#mlflowuimanager._log_tail',
'fastMONAI/utils.py'),
'fastMONAI.utils.MLflowUIManager._remove_log': ( 'utils.html#mlflowuimanager._remove_log',
'fastMONAI/utils.py'),
'fastMONAI.utils.MLflowUIManager.find_available_port': ( 'utils.html#mlflowuimanager.find_available_port',
'fastMONAI/utils.py'),
'fastMONAI.utils.MLflowUIManager.is_mlflow_running': ( 'utils.html#mlflowuimanager.is_mlflow_running',
Expand All @@ -113,6 +111,8 @@
'fastMONAI/utils.py'),
'fastMONAI.utils.ModelTrackingCallback._extract_training_params': ( 'utils.html#modeltrackingcallback._extract_training_params',
'fastMONAI/utils.py'),
'fastMONAI.utils.ModelTrackingCallback._log_run_setup': ( 'utils.html#modeltrackingcallback._log_run_setup',
'fastMONAI/utils.py'),
'fastMONAI.utils.ModelTrackingCallback._log_split_df': ( 'utils.html#modeltrackingcallback._log_split_df',
'fastMONAI/utils.py'),
'fastMONAI.utils.ModelTrackingCallback._save_model_artifacts': ( 'utils.html#modeltrackingcallback._save_model_artifacts',
Expand All @@ -135,6 +135,7 @@
'fastMONAI/utils.py'),
'fastMONAI.utils._actual_split_df': ('utils.html#_actual_split_df', 'fastMONAI/utils.py'),
'fastMONAI.utils._canonical_tracking_json': ('utils.html#_canonical_tracking_json', 'fastMONAI/utils.py'),
'fastMONAI.utils._check_patch_threshold': ('utils.html#_check_patch_threshold', 'fastMONAI/utils.py'),
'fastMONAI.utils._detect_patch_workflow': ('utils.html#_detect_patch_workflow', 'fastMONAI/utils.py'),
'fastMONAI.utils._die_with_parent': ('utils.html#_die_with_parent', 'fastMONAI/utils.py'),
'fastMONAI.utils._download_model_artifact': ('utils.html#_download_model_artifact', 'fastMONAI/utils.py'),
Expand All @@ -147,9 +148,11 @@
'fastMONAI.utils._extract_size_from_transforms': ( 'utils.html#_extract_size_from_transforms',
'fastMONAI/utils.py'),
'fastMONAI.utils._extract_standard_config': ('utils.html#_extract_standard_config', 'fastMONAI/utils.py'),
'fastMONAI.utils._get_x_column': ('utils.html#_get_x_column', 'fastMONAI/utils.py'),
'fastMONAI.utils._json_round_trip': ('utils.html#_json_round_trip', 'fastMONAI/utils.py'),
'fastMONAI.utils._monai_constructor': ('utils.html#_monai_constructor', 'fastMONAI/utils.py'),
'fastMONAI.utils._normalize_monai_kwargs': ('utils.html#_normalize_monai_kwargs', 'fastMONAI/utils.py'),
'fastMONAI.utils._prefer_raw_column': ('utils.html#_prefer_raw_column', 'fastMONAI/utils.py'),
'fastMONAI.utils._read_preprocessing_manifest': ( 'utils.html#_read_preprocessing_manifest',
'fastMONAI/utils.py'),
'fastMONAI.utils._resolve_backend_store_uri': ( 'utils.html#_resolve_backend_store_uri',
Expand Down Expand Up @@ -457,8 +460,12 @@
'fastMONAI.vision_data.show_results': ('vision_data.html#show_results', 'fastMONAI/vision_data.py')},
'fastMONAI.vision_inference': { 'fastMONAI.vision_inference._do_resize': ( 'vision_inference.html#_do_resize',
'fastMONAI/vision_inference.py'),
'fastMONAI.vision_inference._prediction_save_path': ( 'vision_inference.html#_prediction_save_path',
'fastMONAI/vision_inference.py'),
'fastMONAI.vision_inference._resize_labels': ( 'vision_inference.html#_resize_labels',
'fastMONAI/vision_inference.py'),
'fastMONAI.vision_inference._restore_prediction': ( 'vision_inference.html#_restore_prediction',
'fastMONAI/vision_inference.py'),
'fastMONAI.vision_inference._signed_depth': ( 'vision_inference.html#_signed_depth',
'fastMONAI/vision_inference.py'),
'fastMONAI.vision_inference._to_original_orientation': ( 'vision_inference.html#_to_original_orientation',
Expand Down Expand Up @@ -551,8 +558,6 @@
'fastMONAI/vision_metrics.py'),
'fastMONAI.vision_metrics.calculate_dsc': ( 'vision_metrics.html#calculate_dsc',
'fastMONAI/vision_metrics.py'),
'fastMONAI.vision_metrics.calculate_haus': ( 'vision_metrics.html#calculate_haus',
'fastMONAI/vision_metrics.py'),
'fastMONAI.vision_metrics.calculate_hd95': ( 'vision_metrics.html#calculate_hd95',
'fastMONAI/vision_metrics.py'),
'fastMONAI.vision_metrics.calculate_lesion_detection_rate': ( 'vision_metrics.html#calculate_lesion_detection_rate',
Expand Down
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