flexible-unet-mlx 0.2.1__tar.gz

flexible_unet_mlx-0.2.1/.gitignore

@@ -0,0 +1,10 @@
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.ruff_cache/
+.venv/
+dist/
+work/
+checkpoints/
+*.safetensors
+*.pt

flexible_unet_mlx-0.2.1/LICENSE

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

@@ -0,0 +1,110 @@
+Metadata-Version: 2.5
+Name: flexible-unet-mlx
+Version: 0.2.1
+Summary: Native FP32 MLX FlexibleUNet released-checkpoint network
+Author: Joseph Sandoval, Alfredo Sandoval Jr.
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Classifier: Operating System :: MacOS :: MacOS X
+Requires-Python: <3.15,>=3.13
+Requires-Dist: medmlx-core==0.2.3
+Requires-Dist: numpy<3,>=2.0
+Requires-Dist: pillow<14,>=13
+Provides-Extra: conversion
+Requires-Dist: torch<2.14,>=2.13; extra == 'conversion'
+Provides-Extra: dev
+Requires-Dist: hypothesis<7,>=6.140; extra == 'dev'
+Requires-Dist: mlx==0.32.4; (platform_machine == 'arm64' and sys_platform == 'darwin') and 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: safetensors<1,>=0.6; extra == 'dev'
+Requires-Dist: torch<2.14,>=2.13; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# flexible-unet-mlx
+
+Native MLX port of the MONAI
+[endoscopic tool segmentation](https://huggingface.co/MONAI/endoscopic_tool_segmentation)
+model (FlexibleUNet, EfficientNet-B2) for Apple Silicon. Segment surgical tools in
+endoscopy frames, locally on Mac.
+
+- RGB endoscopy frame in, tool mask out
+- Apple Silicon GPU acceleration
+- FP32 inference using MLX; PyTorch is only needed once to convert the checkpoint
+
+Part of [MedMLX](https://github.com/MedMLX).
+[Technical notes](https://github.com/MedMLX/flexible-unet-mlx/blob/main/docs/technical.md)
+
+[Quick start](#quick-start) · [Input and output](#input-and-output) · [Technical details](#technical-details) · [License](#license)
+
+## Requirements
+
+Apple Silicon Mac with Metal, Python 3.13 or 3.14 and [uv](https://docs.astral.sh/uv/).
+
+## Quick start
+
+Install with the conversion extra, and install the Hugging Face CLI as a separate
+tool for downloading the checkpoint:
+
+```bash
+uv pip install "flexible-unet-mlx[conversion] @ git+https://github.com/MedMLX/flexible-unet-mlx.git"
+uv tool install huggingface-hub
+```
+
+Download the MONAI checkpoint:
+
+```bash
+hf download MONAI/endoscopic_tool_segmentation models/model.pt \
+  --revision f0416a27d59516d9c1b6bec5181c9c33002c84fa --local-dir tool-bundle
+```
+
+Convert it once, then segment a frame:
+
+```python
+from pathlib import Path
+
+from flexible_unet_mlx import convert_checkpoint
+from flexible_unet_mlx.medmlx import run
+
+convert_checkpoint(Path("tool-bundle/models/model.pt"), Path("model.safetensors"))
+
+result = run(image_path="frame.jpg", weights_path="model.safetensors", output_dir="out")
+print(result["outputs"]["mask"])
+```
+
+Pass `overwrite=True` to replace existing output. The model is also discoverable by
+[medmlx](https://github.com/MedMLX/medmlx) as `flexible-unet`.
+
+## Input and output
+
+Input is one RGB image Pillow can read (the bundle used JPEG frames).
+
+For `frame.jpg`, the mask is written to `out/frame/frame_trans.png`: 8-bit grayscale
+at the original frame size, 255 for tool and 0 for background. `result["details"]`
+holds the frame size, tool pixel counts and timings.
+
+## Technical details
+
+Preprocessing, inference and postprocessing follow the pinned MONAI 1.4.0 bundle,
+including Torch's bilinear resize rounding. The tests compare against recordings of
+the upstream transforms and network made on one Apple Silicon Mac, using synthetic
+frames and seeded random weights. Agreement with the released checkpoint is a
+separate, optional check, and no segmentation accuracy evaluation is included. The
+lower-level network API, tolerances and fixture regeneration are in
+[docs/technical.md](https://github.com/MedMLX/flexible-unet-mlx/blob/main/docs/technical.md).
+
+## Intended use
+
+Intended for research and education, not clinical decisions. Outputs require human review.
+
+## License
+
+Code: Apache-2.0; see [LICENSE](https://github.com/MedMLX/flexible-unet-mlx/blob/main/LICENSE).
+MONAI-derived code is Apache-2.0; see [third-party notices](https://github.com/MedMLX/flexible-unet-mlx/blob/main/THIRD_PARTY_NOTICES.md).
+Checkpoint rights remain with their publishers.
+
+## Implementation mapping
+
+[Central implementation map](https://github.com/MedMLX/Med-MLX/blob/main/implementation-maps/flexible-unet-mlx.json) records upstream-to-native changes, source references and qualification scope.

flexible_unet_mlx-0.2.1/README.md

@@ -0,0 +1,85 @@
+# flexible-unet-mlx
+
+Native MLX port of the MONAI
+[endoscopic tool segmentation](https://huggingface.co/MONAI/endoscopic_tool_segmentation)
+model (FlexibleUNet, EfficientNet-B2) for Apple Silicon. Segment surgical tools in
+endoscopy frames, locally on Mac.
+
+- RGB endoscopy frame in, tool mask out
+- Apple Silicon GPU acceleration
+- FP32 inference using MLX; PyTorch is only needed once to convert the checkpoint
+
+Part of [MedMLX](https://github.com/MedMLX).
+[Technical notes](https://github.com/MedMLX/flexible-unet-mlx/blob/main/docs/technical.md)
+
+[Quick start](#quick-start) · [Input and output](#input-and-output) · [Technical details](#technical-details) · [License](#license)
+
+## Requirements
+
+Apple Silicon Mac with Metal, Python 3.13 or 3.14 and [uv](https://docs.astral.sh/uv/).
+
+## Quick start
+
+Install with the conversion extra, and install the Hugging Face CLI as a separate
+tool for downloading the checkpoint:
+
+```bash
+uv pip install "flexible-unet-mlx[conversion] @ git+https://github.com/MedMLX/flexible-unet-mlx.git"
+uv tool install huggingface-hub
+```
+
+Download the MONAI checkpoint:
+
+```bash
+hf download MONAI/endoscopic_tool_segmentation models/model.pt \
+  --revision f0416a27d59516d9c1b6bec5181c9c33002c84fa --local-dir tool-bundle
+```
+
+Convert it once, then segment a frame:
+
+```python
+from pathlib import Path
+
+from flexible_unet_mlx import convert_checkpoint
+from flexible_unet_mlx.medmlx import run
+
+convert_checkpoint(Path("tool-bundle/models/model.pt"), Path("model.safetensors"))
+
+result = run(image_path="frame.jpg", weights_path="model.safetensors", output_dir="out")
+print(result["outputs"]["mask"])
+```
+
+Pass `overwrite=True` to replace existing output. The model is also discoverable by
+[medmlx](https://github.com/MedMLX/medmlx) as `flexible-unet`.
+
+## Input and output
+
+Input is one RGB image Pillow can read (the bundle used JPEG frames).
+
+For `frame.jpg`, the mask is written to `out/frame/frame_trans.png`: 8-bit grayscale
+at the original frame size, 255 for tool and 0 for background. `result["details"]`
+holds the frame size, tool pixel counts and timings.
+
+## Technical details
+
+Preprocessing, inference and postprocessing follow the pinned MONAI 1.4.0 bundle,
+including Torch's bilinear resize rounding. The tests compare against recordings of
+the upstream transforms and network made on one Apple Silicon Mac, using synthetic
+frames and seeded random weights. Agreement with the released checkpoint is a
+separate, optional check, and no segmentation accuracy evaluation is included. The
+lower-level network API, tolerances and fixture regeneration are in
+[docs/technical.md](https://github.com/MedMLX/flexible-unet-mlx/blob/main/docs/technical.md).
+
+## Intended use
+
+Intended for research and education, not clinical decisions. Outputs require human review.
+
+## License
+
+Code: Apache-2.0; see [LICENSE](https://github.com/MedMLX/flexible-unet-mlx/blob/main/LICENSE).
+MONAI-derived code is Apache-2.0; see [third-party notices](https://github.com/MedMLX/flexible-unet-mlx/blob/main/THIRD_PARTY_NOTICES.md).
+Checkpoint rights remain with their publishers.
+
+## Implementation mapping
+
+[Central implementation map](https://github.com/MedMLX/Med-MLX/blob/main/implementation-maps/flexible-unet-mlx.json) records upstream-to-native changes, source references and qualification scope.

flexible_unet_mlx-0.2.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,220 @@
+# Third-party notices
+
+This package translates FlexibleUNet and its source network semantics from
+[MONAI 1.4.0](https://github.com/Project-MONAI/MONAI/tree/1.4.0), copyright
+MONAI Consortium, licensed under Apache-2.0. The complete notice is preserved
+in [MONAI-Apache-2.0.txt](#monai-apache-2-0-txt-full-text).
+
+The pinned checkpoint bundle is [MONAI/endoscopic_tool_segmentation](https://huggingface.co/MONAI/endoscopic_tool_segmentation/tree/f0416a27d59516d9c1b6bec5181c9c33002c84fa).
+Its publisher's checkpoint license applies separately; weights are not included.
+See specification.json for immutable source/config/checkpoint identities.
+Project-authored code is licensed under Apache-2.0.
+
+
+<a id="monai-apache-2-0-txt-full-text"></a>
+
+## MONAI-Apache-2.0.txt full text
+
+```text
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+
+      "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
+      or by an individual or Legal Entity authorized to submit on behalf of
+      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,
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+      subsequently incorporated within the Work.
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+      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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+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
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+      Contribution(s) alone or by combination of their Contribution(s)
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+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   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
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          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
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
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+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
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+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
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+```