synthseg-mlx 0.2.1__tar.gz

synthseg_mlx-0.2.1/.gitignore

@@ -0,0 +1,27 @@
+__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/
+!src/synthseg_mlx/data/
+*.nii
+*.nii.gz
+*.dcm
+.DS_Store

synthseg_mlx-0.2.1/LICENSE

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

@@ -0,0 +1,66 @@
+Metadata-Version: 2.5
+Name: synthseg-mlx
+Version: 0.2.1
+Summary: Native MLX implementation of SynthSeg for Apple Silicon (macOS arm64, Metal)
+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: h5py<4,>=3.12
+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: scipy<2,>=1.14
+Provides-Extra: dev
+Requires-Dist: h5py-stubs<0.2,>=0.1.2; extra == 'dev'
+Requires-Dist: hypothesis<7,>=6.100; 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: scipy-stubs<1.19,>=1.18.1; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# synthseg-mlx
+
+Segment brain MRI or CT with SynthSeg in native MLX. Includes cortical parcellation, structure volumes and QC scores.
+
+[Docs](docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![synthseg-mlx example output](https://raw.githubusercontent.com/MedMLX/synthseg-mlx/main/docs/example.png)
+
+*SynthSeg 2.0 parcellation of an NV-Generate synthetic T1 MR.*
+
+| Input | Output |
+| :--- | :--- |
+| 3D brain MRI or CT · NIfTI | Brain labels, volumes and QC |
+
+**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/synthseg-mlx"
+uv pip install "synthseg-mlx @ git+$repo"
+```
+
+Download and unzip the author’s [SynthSeg models](https://github.com/BBillot/SynthSeg#installation), then run:
+
+```python
+from synthseg_mlx.medmlx import run
+
+result = run(image_path="brain.nii.gz", weights_path="SynthSeg_models", output_dir="out")
+print(result["outputs"]["mask"])
+```
+
+Reads the original Keras checkpoints without TensorFlow. Output masks use the resampled 1 mm grid, rather than the original voxel grid.
+
+## 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.

synthseg_mlx-0.2.1/README.md

@@ -0,0 +1,41 @@
+# synthseg-mlx
+
+Segment brain MRI or CT with SynthSeg in native MLX. Includes cortical parcellation, structure volumes and QC scores.
+
+[Docs](docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![synthseg-mlx example output](https://raw.githubusercontent.com/MedMLX/synthseg-mlx/main/docs/example.png)
+
+*SynthSeg 2.0 parcellation of an NV-Generate synthetic T1 MR.*
+
+| Input | Output |
+| :--- | :--- |
+| 3D brain MRI or CT · NIfTI | Brain labels, volumes and QC |
+
+**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/synthseg-mlx"
+uv pip install "synthseg-mlx @ git+$repo"
+```
+
+Download and unzip the author’s [SynthSeg models](https://github.com/BBillot/SynthSeg#installation), then run:
+
+```python
+from synthseg_mlx.medmlx import run
+
+result = run(image_path="brain.nii.gz", weights_path="SynthSeg_models", output_dir="out")
+print(result["outputs"]["mask"])
+```
+
+Reads the original Keras checkpoints without TensorFlow. Output masks use the resampled 1 mm grid, rather than the original voxel grid.
+
+## 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.

synthseg_mlx-0.2.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,309 @@
+# Third-party notices
+
+MedMLX-authored additions are licensed under [Apache-2.0](LICENSE).
+The upstream attribution and license notices are retained below.
+
+synthseg-mlx includes portions of SynthSeg and its ext/lab2im utilities.
+
+Copyright 2020 Benjamin Billot
+Original upstream: https://github.com/BBillot/SynthSeg
+lab2im upstream: https://github.com/BBillot/lab2im
+Licensed under the Apache License, Version 2.0; see THIRD_PARTY_NOTICES.md.
+
+Source: the SynthSeg fork at revision
+d6a64db19ec7b8b71c64edd59e7e485e0235c26c.
+Copied numerical code: SynthSeg/{predict_synthseg,labels}.py and
+ext/lab2im/{utils,edit_volumes}.py. Bundled data: the seven SynthSeg 2.0
+label, topology and name arrays listed in synthseg_mlx/label_data.py.
+
+Changes: extracted the required NumPy/SciPy functions, adapted imports and
+package layout, moved image I/O to caller-owned array inputs and an optional
+resampled-image hook, removed framework tensor adapters, and made the
+orientation and label helpers' one-element integer assignments explicit for NumPy 2.
+The MedMLX runner also uses the copied NIfTI and CSV helpers (load_volume,
+save_volume, get_volume_info, get_list_labels without its label-folder branch,
+mkdir, write_csv).
+Original
+copyright and citation headers are retained in the copied Python files.
+
+If you use this code, please cite the SynthSeg papers identified at
+https://github.com/BBillot/SynthSeg/blob/master/bibtex.bib and
+https://github.com/BBillot/lab2im/blob/master/bibtex.bib.
+
+The extracted numerical files listed above retain their upstream Apache-2.0
+headers. The label arrays come from the same source repository and revision,
+whose top-level `LICENSE.txt` is Apache-2.0.
+
+## Network and reference provenance
+
+The native MLX network and array engine were moved from RadNN `cbaa1ac` in
+synthseg-mlx commit `333f57dcd5dc821231e922b466d0d9755c1e8768`. The MLX model
+first appears in RadNN commit `b35a3ac0eda371978bb1481bc8663a8e0bcc8393`.
+The native graph uses MLX classes and operators, retaining the SynthSeg network
+structure, checkpoint layer names and operation order described in
+`docs/technical.md`.
+
+The independent reference recorder `scripts/make_variant_fixtures.py` executes
+selected definitions from the external SynthSeg reference revision
+`2a2aa3bbfccb83f8253a51ca8b329b9938a2646d`, including:
+
+- `ext/neuron/models.py`: the `unet`, `conv_enc` and `conv_dec` builders; its
+  file header states `License: GPLv3`.
+- `ext/neuron/utils.py`: coordinate helpers used by the reference graph; its
+  file header also states `License: GPLv3`.
+
+These file-specific headers differ from that reference repository's top-level
+Apache-2.0 `LICENSE.txt`. The external neuron files are not vendored in this
+checkout or included in its wheel or source archive. The reference recorder
+executes them from an explicitly selected source checkout; its numerical source
+revision remains unchanged.
+
+### Historical Neurite attribution
+
+Copyright 2020 Adrian V. Dalca
+
+The historical Neurite source provides an explicit Apache-2.0 grant for relevant
+network builders and coordinate helpers. Adrian Dalca's commit
+`b8efac0fcfceec8017c324b3b4de61c16b6903f2` added the Apache-2.0 license;
+commit `c516287431d37ba6f2e0f5fcfc69d87cda552f5e` changed the notices in
+`neurite/tf/models.py` and `neurite/tf/utils/utils.py` from GPLv3 to Apache-2.0.
+See the full Apache-2.0 license below.
+
+The `unet`, `conv_enc`, `conv_dec`, `volshape_to_meshgrid` and `meshgrid` function
+bodies are unchanged by that file-notice commit, apart from documentation. The
+two coordinate helpers have identical function bodies and signatures in the
+SynthSeg reference revision and this Apache-headered Neurite revision. The three
+builders share network-construction code but are not identical: the SynthSeg
+fork changes input composition, dropout handling and decoder skip selection.
+The native MLX graph retains the fixed network schedules and checkpoint layer
+names; the Apache-headered `SynthSeg/predict_synthseg.py` also declares the
+standard, robust, parcellation and QC architectures, including the denoiser's
+omitted skip connections. The native QC crop and Gaussian coefficient generation
+follow the Apache-headered `MakeShape` and `ext/lab2im/edit_tensors.py` helpers,
+with local MLX array and Metal implementations.
+
+This provenance description distinguishes the extracted numerical files,
+external reference builders and native graph implementation. It does not make
+a determination about copied or translated source expression, independent
+implementation of the architecture, or the license scope of the native graph.
+
+Pinned source headers:
+
+- https://github.com/BBillot/SynthSeg/blob/2a2aa3bbfccb83f8253a51ca8b329b9938a2646d/ext/neuron/models.py#L10
+- https://github.com/BBillot/SynthSeg/blob/2a2aa3bbfccb83f8253a51ca8b329b9938a2646d/ext/neuron/utils.py#L16
+- https://github.com/BBillot/SynthSeg/blob/2a2aa3bbfccb83f8253a51ca8b329b9938a2646d/LICENSE.txt
+
+Historical Apache sources:
+
+- https://github.com/adalca/neurite/commit/b8efac0fcfceec8017c324b3b4de61c16b6903f2
+- https://github.com/adalca/neurite/commit/c516287431d37ba6f2e0f5fcfc69d87cda552f5e
+- https://github.com/adalca/neurite/blob/c516287431d37ba6f2e0f5fcfc69d87cda552f5e/neurite/tf/models.py
+- https://github.com/adalca/neurite/blob/c516287431d37ba6f2e0f5fcfc69d87cda552f5e/neurite/tf/utils/utils.py
+
+Dependencies declared in [pyproject.toml](pyproject.toml) are installed separately
+and retain their respective licenses.
+
+
+## Full license: LICENSE_SynthSeg.txt
+
+                                 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."
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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
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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.
+
+   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)
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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
+
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+          that You distribute, all copyright, patent, trademark, 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
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
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