medsam2-mlx 0.2.1__tar.gz

medsam2_mlx-0.2.1/.gitignore

@@ -0,0 +1,25 @@
+__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
+*.pt
+*.pth
+*.ckpt
+
+# Imaging data is never committed.
+data/
+*.nii
+*.nii.gz
+*.dcm
+.DS_Store

medsam2_mlx-0.2.1/LICENSE

@@ -0,0 +1,202 @@
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medsam2_mlx-0.2.1/PKG-INFO

@@ -0,0 +1,111 @@
+Metadata-Version: 2.5
+Name: medsam2-mlx
+Version: 0.2.1
+Summary: Native MLX implementation of MedSAM2
+Project-URL: Homepage, https://github.com/MedMLX/medsam2-mlx
+Project-URL: Documentation, https://github.com/MedMLX/medsam2-mlx/blob/main/docs/technical.md
+Project-URL: Repository, https://github.com/MedMLX/medsam2-mlx
+Project-URL: Issues, https://github.com/MedMLX/medsam2-mlx/issues
+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: mlx<0.33,>=0.32.4
+Requires-Dist: nibabel<6,>=5.3
+Requires-Dist: numpy<3,>=2.0
+Requires-Dist: pillow<14,>=13
+Requires-Dist: scipy<2,>=1.13
+Provides-Extra: conversion
+Requires-Dist: torch<3,>=2.6; extra == 'conversion'
+Provides-Extra: dev
+Requires-Dist: hypothesis<7,>=6.156; 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: simpleitk<3,>=2.5.6; extra == 'dev'
+Requires-Dist: torch<3,>=2.6; extra == 'dev'
+Provides-Extra: reference
+Requires-Dist: hydra-core<2,>=1.3.2; extra == 'reference'
+Requires-Dist: iopath<0.2,>=0.1.10; extra == 'reference'
+Requires-Dist: opencv-python-headless==5.0.0.93; extra == 'reference'
+Requires-Dist: pillow<14,>=13; extra == 'reference'
+Requires-Dist: simpleitk<3,>=2.5; extra == 'reference'
+Requires-Dist: torch<3,>=2.6; extra == 'reference'
+Requires-Dist: tqdm<5,>=4.66; extra == 'reference'
+Description-Content-Type: text/markdown
+
+# medsam2-mlx
+
+Segment lesions or organs from a box, point or mask prompt, then track them through a volume with MedSAM2.
+
+[Docs](https://github.com/MedMLX/medsam2-mlx/blob/main/docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![One box prompt → nodule masks propagated across neighboring CT slices.](https://raw.githubusercontent.com/MedMLX/medsam2-mlx/main/docs/showcase.png)
+
+*One box prompt → nodule masks propagated across neighboring CT slices.*
+
+| Input | Output |
+| :--- | :--- |
+| Scan + slice-level prompt | Tracked masks on the input grid |
+
+**Apple Silicon · Metal · Python 3.13 / 3.14** · [uv](https://docs.astral.sh/uv/)
+
+## Quick start
+
+```bash
+uv venv --python 3.13 --seed
+source .venv/bin/activate
+python -m pip install "medsam2-mlx[conversion]==0.2.1" huggingface-hub
+```
+
+The tagged GitHub release is an alternative installation route:
+
+```bash
+repo="https://github.com/MedMLX/medsam2-mlx.git@v0.2.1"
+python -m pip install "medsam2-mlx[conversion] @ git+$repo" huggingface-hub
+```
+
+The package contains code only. Obtain the original checkpoint from
+[wanglab/MedSAM2](https://huggingface.co/wanglab/MedSAM2) under its publisher terms
+and convert it locally. The MedMLX converted CTLesion bundle remains private
+because its weight-card terms conflict; no converted weights are distributed here.
+Download and convert once, then run:
+
+```python
+from pathlib import Path
+
+from huggingface_hub import hf_hub_download
+from medmlx_core import import_mlx
+from medsam2_mlx.conversion import convert_weights
+
+mx = import_mlx()
+weights = convert_weights(Path(hf_hub_download("wanglab/MedSAM2", "MedSAM2_CTLesion.pt")))
+mx.save_safetensors(
+    "MedSAM2_CTLesion.safetensors", {name: mx.array(value) for name, value in weights.items()}
+)
+```
+
+```python
+from medsam2_mlx.medmlx import run
+
+result = run(
+    image_path="ct.nii.gz",
+    weights_path="MedSAM2_CTLesion.safetensors",
+    output_dir="out",
+    box_xyxy=[120, 140, 180, 200],
+    frame_idx=40,
+    propagation="both",
+)
+print(result["outputs"])
+```
+
+For NIfTI, `frame_idx` uses the third voxel axis. Box and point coordinates use the first two stored voxel axes.
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/medsam2-mlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/medsam2-mlx/blob/main/THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

medsam2_mlx-0.2.1/README.md

@@ -0,0 +1,72 @@
+# medsam2-mlx
+
+Segment lesions or organs from a box, point or mask prompt, then track them through a volume with MedSAM2.
+
+[Docs](https://github.com/MedMLX/medsam2-mlx/blob/main/docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![One box prompt → nodule masks propagated across neighboring CT slices.](https://raw.githubusercontent.com/MedMLX/medsam2-mlx/main/docs/showcase.png)
+
+*One box prompt → nodule masks propagated across neighboring CT slices.*
+
+| Input | Output |
+| :--- | :--- |
+| Scan + slice-level prompt | Tracked masks on the input grid |
+
+**Apple Silicon · Metal · Python 3.13 / 3.14** · [uv](https://docs.astral.sh/uv/)
+
+## Quick start
+
+```bash
+uv venv --python 3.13 --seed
+source .venv/bin/activate
+python -m pip install "medsam2-mlx[conversion]==0.2.1" huggingface-hub
+```
+
+The tagged GitHub release is an alternative installation route:
+
+```bash
+repo="https://github.com/MedMLX/medsam2-mlx.git@v0.2.1"
+python -m pip install "medsam2-mlx[conversion] @ git+$repo" huggingface-hub
+```
+
+The package contains code only. Obtain the original checkpoint from
+[wanglab/MedSAM2](https://huggingface.co/wanglab/MedSAM2) under its publisher terms
+and convert it locally. The MedMLX converted CTLesion bundle remains private
+because its weight-card terms conflict; no converted weights are distributed here.
+Download and convert once, then run:
+
+```python
+from pathlib import Path
+
+from huggingface_hub import hf_hub_download
+from medmlx_core import import_mlx
+from medsam2_mlx.conversion import convert_weights
+
+mx = import_mlx()
+weights = convert_weights(Path(hf_hub_download("wanglab/MedSAM2", "MedSAM2_CTLesion.pt")))
+mx.save_safetensors(
+    "MedSAM2_CTLesion.safetensors", {name: mx.array(value) for name, value in weights.items()}
+)
+```
+
+```python
+from medsam2_mlx.medmlx import run
+
+result = run(
+    image_path="ct.nii.gz",
+    weights_path="MedSAM2_CTLesion.safetensors",
+    output_dir="out",
+    box_xyxy=[120, 140, 180, 200],
+    frame_idx=40,
+    propagation="both",
+)
+print(result["outputs"])
+```
+
+For NIfTI, `frame_idx` uses the third voxel axis. Box and point coordinates use the first two stored voxel axes.
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/medsam2-mlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/medsam2-mlx/blob/main/THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

medsam2_mlx-0.2.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,241 @@
+# Third-party notices
+
+The MLX network and session logic in this package (`config.py`, `_ops.py`,
+`image_encoder.py`, `transformer.py`, `prompt_encoder.py`, `mask_decoder.py`,
+`memory_attention.py`, `memory_encoder.py`, `sam2_base.py`, and
+`video_predictor.py` under `src/medsam2_mlx/`) are translated from
+[MedSAM2](https://github.com/bowang-lab/MedSAM2/tree/332f30d420f1d1b08e2a79b3ae6a602458808383)
+at revision `332f30d420f1d1b08e2a79b3ae6a602458808383`, copyright the MedSAM2
+authors (bowang-lab), which is derived from
+[SAM 2](https://github.com/facebookresearch/sam2), copyright Meta Platforms, Inc.
+and affiliates. Both are licensed under the Apache License, Version 2.0. The
+complete license text is preserved in
+[MedSAM2-Apache-2.0.txt](#medsam2-apache-2-0-txt-full-text).
+
+Changes from the upstream source: the PyTorch modules were rewritten for MLX
+(channels-last convolutions, fused attention and layer norm, matrix forms of
+PyTorch's bilinear and bicubic interpolation), restricted to the evaluation-mode
+`sam2.1_hiera_t512` configuration, and the CUDA connected-components kernel used
+for hole filling was replaced by a SciPy host implementation. Each translated
+file names its upstream source files in its header.
+
+No code from any other MLX SAM 2 implementation is used.
+
+The MedSAM2 checkpoints are not included. Their license is set by the original
+publisher and applies separately. Project-authored code is licensed under
+Apache-2.0.
+
+
+<a id="medsam2-apache-2-0-txt-full-text"></a>
+
+## MedSAM2-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
+
+   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
+      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,
+      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."
+
+      "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.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      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.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      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
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      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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+
+## 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.