lung-nodule-mlx 0.2.1__tar.gz

lung_nodule_mlx-0.2.1/.gitignore

@@ -0,0 +1,26 @@
+__pycache__/
+*.py[cod]
+.venv/
+*.egg-info/
+dist/
+build/
+.pytest_cache/
+.ruff_cache/
+
+# Checkpoints and converted weights are never committed.
+checkpoints/
+weights/
+*.safetensors
+*.npz
+!tests/fixtures/*.npz
+!tests/fixtures/*/*.npz
+*.pt
+*.pth
+*.ckpt
+
+# Imaging data is never committed.
+data/
+*.nii
+*.nii.gz
+*.dcm
+.DS_Store

lung_nodule_mlx-0.2.1/LICENSE

@@ -0,0 +1,202 @@
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lung_nodule_mlx-0.2.1/PKG-INFO

@@ -0,0 +1,84 @@
+Metadata-Version: 2.5
+Name: lung-nodule-mlx
+Version: 0.2.1
+Summary: MONAI 3D RetinaNet lung nodule detector for Apple Silicon (macOS arm64, Metal)
+Author: Joseph Sandoval, Alfredo Sandoval Jr.
+License-Expression: Apache-2.0 AND BSD-3-Clause
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: <3.15,>=3.13
+Requires-Dist: medmlx-core==0.2.3
+Requires-Dist: nibabel<6,>=5.3
+Requires-Dist: numpy<3,>=2.0
+Provides-Extra: conversion
+Requires-Dist: torch<3,>=2.13; extra == 'conversion'
+Provides-Extra: dev
+Requires-Dist: hypothesis<7,>=6.140; extra == 'dev'
+Requires-Dist: monai==1.6.1; extra == 'dev'
+Requires-Dist: pyright==1.1.414; extra == 'dev'
+Requires-Dist: pytest<10,>=8.4; extra == 'dev'
+Requires-Dist: ruff<1,>=0.13; extra == 'dev'
+Requires-Dist: torch<2.14,>=2.13; extra == 'dev'
+Requires-Dist: torchvision<0.29,>=0.28; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# lung-nodule-mlx
+
+Detect lung nodule candidates in 3D chest CT with MONAI RetinaNet and native MLX.
+
+[Docs](docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![A 3D nodule candidate localized in axial, coronal and sagittal CT views.](https://raw.githubusercontent.com/MedMLX/lung-nodule-mlx/main/docs/showcase.png)
+
+*A 3D nodule candidate localized in axial, coronal and sagittal CT views.*
+
+| Input | Output |
+| :--- | :--- |
+| 3D chest CT · NIfTI | Candidate boxes and scores in RAS mm |
+
+**Apple Silicon · Metal · Python 3.13 / 3.14** · [uv](https://docs.astral.sh/uv/)
+
+## Quick start
+
+```bash
+uv venv --python 3.13
+source .venv/bin/activate
+repo="https://github.com/MedMLX/lung-nodule-mlx"
+uv pip install \
+  "lung-nodule-mlx[conversion] @ git+$repo" \
+  huggingface-hub
+```
+
+Download and convert the checkpoint once, then run:
+
+```bash
+python -c 'from pathlib import Path; from huggingface_hub import hf_hub_download; import lung_nodule_mlx as m; m.convert_weights(Path(hf_hub_download("MONAI/lung_nodule_ct_detection", "models/model.pt")), Path("network.safetensors"))'
+
+c++ -std=c++17 -O2 -dynamiclib \
+  "$(python -c 'import lung_nodule_mlx, pathlib; print(pathlib.Path(lung_nodule_mlx.__file__).with_name("selection.cpp"))')" \
+  -o selection.dylib
+```
+
+```python
+from lung_nodule_mlx.medmlx import run
+
+result = run(
+    image_path="ct.nii.gz",
+    weights_path="network.safetensors",
+    selector_path="selection.dylib",
+    output_dir="out",
+    resample_raw_input=True,
+)
+print(result["outputs"]["detections"])
+```
+
+Requires Apple’s command-line developer tools for box selection. Keep `resample_raw_input=True` for ordinary CT.
+
+## License
+
+[Apache-2.0](LICENSE). See [third-party notices](THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

lung_nodule_mlx-0.2.1/README.md

@@ -0,0 +1,57 @@
+# lung-nodule-mlx
+
+Detect lung nodule candidates in 3D chest CT with MONAI RetinaNet and native MLX.
+
+[Docs](docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![A 3D nodule candidate localized in axial, coronal and sagittal CT views.](https://raw.githubusercontent.com/MedMLX/lung-nodule-mlx/main/docs/showcase.png)
+
+*A 3D nodule candidate localized in axial, coronal and sagittal CT views.*
+
+| Input | Output |
+| :--- | :--- |
+| 3D chest CT · NIfTI | Candidate boxes and scores in RAS mm |
+
+**Apple Silicon · Metal · Python 3.13 / 3.14** · [uv](https://docs.astral.sh/uv/)
+
+## Quick start
+
+```bash
+uv venv --python 3.13
+source .venv/bin/activate
+repo="https://github.com/MedMLX/lung-nodule-mlx"
+uv pip install \
+  "lung-nodule-mlx[conversion] @ git+$repo" \
+  huggingface-hub
+```
+
+Download and convert the checkpoint once, then run:
+
+```bash
+python -c 'from pathlib import Path; from huggingface_hub import hf_hub_download; import lung_nodule_mlx as m; m.convert_weights(Path(hf_hub_download("MONAI/lung_nodule_ct_detection", "models/model.pt")), Path("network.safetensors"))'
+
+c++ -std=c++17 -O2 -dynamiclib \
+  "$(python -c 'import lung_nodule_mlx, pathlib; print(pathlib.Path(lung_nodule_mlx.__file__).with_name("selection.cpp"))')" \
+  -o selection.dylib
+```
+
+```python
+from lung_nodule_mlx.medmlx import run
+
+result = run(
+    image_path="ct.nii.gz",
+    weights_path="network.safetensors",
+    selector_path="selection.dylib",
+    output_dir="out",
+    resample_raw_input=True,
+)
+print(result["outputs"]["detections"])
+```
+
+Requires Apple’s command-line developer tools for box selection. Keep `resample_raw_input=True` for ordinary CT.
+
+## License
+
+[Apache-2.0](LICENSE). See [third-party notices](THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

lung_nodule_mlx-0.2.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,305 @@
+# Third-party notices
+
+MedMLX-authored additions are licensed under [Apache-2.0](LICENSE).
+The upstream attribution and license notices are retained below.
+
+selection.cpp specializes the ATen CPU top-k algorithm from PyTorch.
+
+From PyTorch:
+
+Copyright (c) 2016-     Facebook, Inc            (Adam Paszke)
+Copyright (c) 2014-     Facebook, Inc            (Soumith Chintala)
+Copyright (c) 2011-2014 Idiap Research Institute (Ronan Collobert)
+Copyright (c) 2012-2014 Deepmind Technologies    (Koray Kavukcuoglu)
+Copyright (c) 2011-2012 NEC Laboratories America (Koray Kavukcuoglu)
+Copyright (c) 2011-2013 NYU                      (Clement Farabet)
+Copyright (c) 2006-2010 NEC Laboratories America (Ronan Collobert, Leon Bottou, Iain Melvin, Jason Weston)
+Copyright (c) 2006      Idiap Research Institute (Samy Bengio)
+Copyright (c) 2001-2004 Idiap Research Institute (Ronan Collobert, Samy Bengio, Johnny Mariethoz)
+
+From Caffe2:
+
+Copyright (c) 2016-present, Facebook Inc. All rights reserved.
+
+All contributions by Facebook:
+Copyright (c) 2016 Facebook Inc.
+
+All contributions by Google:
+Copyright (c) 2015 Google Inc.
+All rights reserved.
+
+All contributions by Yangqing Jia:
+Copyright (c) 2015 Yangqing Jia
+All rights reserved.
+
+All contributions by Kakao Brain:
+Copyright 2019-2020 Kakao Brain
+
+All contributions by Cruise LLC:
+Copyright (c) 2022 Cruise LLC.
+All rights reserved.
+
+All contributions by Tri Dao:
+Copyright (c) 2024 Tri Dao.
+All rights reserved.
+
+All contributions by Arm:
+Copyright (c) 2021, 2023-2025 Arm Limited and/or its affiliates
+
+All contributions from Caffe:
+Copyright(c) 2013, 2014, 2015, the respective contributors
+All rights reserved.
+
+All other contributions:
+Copyright(c) 2015, 2016 the respective contributors
+All rights reserved.
+
+Caffe2 uses a copyright model similar to Caffe: each contributor holds
+copyright over their contributions to Caffe2. The project versioning records
+all such contribution and copyright details. If a contributor wants to further
+mark their specific copyright on a particular contribution, they should
+indicate their copyright solely in the commit message of the change when it is
+committed.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution.
+
+3. Neither the names of Facebook, Deepmind Technologies, NYU, NEC Laboratories America
+   and IDIAP Research Institute nor the names of its contributors may be
+   used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+Native network and detector adapters follow MONAI and the lung_nodule_ct_detection
+0.6.10 bundle. Copyright (c) MONAI Consortium. Licensed under Apache-2.0.
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
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+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
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+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
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+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
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+      cross-claim or counterclaim in a lawsuit) alleging that the Work
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+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
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+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
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+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
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+## Showcase image
+
+The CT images are from LIDC-IDRI via [LUNA16](https://doi.org/10.5281/zenodo.3723295),
+Bram van Ginneken and Colin Jacobs, [CC BY 3.0](https://creativecommons.org/licenses/by/3.0/).
+The showcase adds model predictions and cropped views.