nnunet-mlx 0.5.1__tar.gz

nnunet_mlx-0.5.1/.gitignore

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+.DS_Store
+.venv
+__pycache__/
+*.py[cod]
+*.egg-info/
+.pytest_cache/
+.ruff_cache/
+.pyright/
+build/
+dist/
+artifacts/
+/data/
+models/
+*.nii
+*.nii.gz
+*.pth
+*.pt
+*.safetensors
+*.gputrace

nnunet_mlx-0.5.1/LICENSE

@@ -0,0 +1,202 @@
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nnunet_mlx-0.5.1/PKG-INFO

@@ -0,0 +1,166 @@
+Metadata-Version: 2.5
+Name: nnunet-mlx
+Version: 0.5.1
+Summary: MLX-native nnU-Net v2 inference on Apple Silicon
+Project-URL: Repository, https://github.com/MedMLX/nnunet-mlx
+Project-URL: Issues, https://github.com/MedMLX/nnunet-mlx/issues
+Project-URL: Documentation, https://github.com/MedMLX/nnunet-mlx/tree/main/docs
+Author: Joseph Sandoval
+License-Expression: Apache-2.0 AND MIT
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Keywords: apple-silicon,image-segmentation,medical-imaging,mlx,nnunet
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: <3.15,>=3.13
+Requires-Dist: blosc2<5,>=3.3.2
+Requires-Dist: imagecodecs<2027,>=2025
+Requires-Dist: medmlx-core==0.2.3
+Requires-Dist: mlx==0.32.4; platform_system == 'Darwin' and platform_machine == 'arm64'
+Requires-Dist: nibabel<6,>=5.3
+Requires-Dist: numpy<3,>=2.0
+Requires-Dist: pillow<14,>=13.0.0
+Requires-Dist: safetensors<1,>=0.6
+Requires-Dist: scikit-image==0.26.0
+Requires-Dist: scipy==1.18.1
+Requires-Dist: simpleitk==2.5.6
+Requires-Dist: tifffile<2027,>=2025
+Requires-Dist: typer==0.27.1
+Provides-Extra: conversion
+Requires-Dist: torch==2.13.0; extra == 'conversion'
+Provides-Extra: dev
+Requires-Dist: hypothesis<7,>=6; extra == 'dev'
+Requires-Dist: matplotlib<4,>=3.10; 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'
+Provides-Extra: oracle
+Requires-Dist: dynamic-network-architectures==0.4.4; extra == 'oracle'
+Requires-Dist: nnunetv2==2.8.1; extra == 'oracle'
+Requires-Dist: torch==2.13.0; extra == 'oracle'
+Requires-Dist: urllib3<3,>=2.8; extra == 'oracle'
+Description-Content-Type: text/markdown
+
+# nnunet-mlx
+
+[nnU-Net v2](https://github.com/MIC-DKFZ/nnUNet) inference in native MLX
+for Apple Silicon. Run existing nnU-Net models locally on Mac.
+
+- Convert and run pretrained nnU-Net v2 model folders
+- 2D and 3D `PlainConvUNet` and `ResidualEncoderUNet`
+- FP32 using MLX; PyTorch is only needed to convert `.pth` checkpoints
+
+Part of [MedMLX](https://github.com/MedMLX).
+[Technical notes](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/technical.md) · [Compatibility](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/compatibility.md)
+
+[Quick start](#quick-start) · [Input and output](#input-and-output) · [Technical details](#technical-details) · [License](#license)
+
+## Requirements
+
+Apple Silicon Mac with Metal, [uv](https://docs.astral.sh/uv/), and conda or mamba
+(setup uses it to build a pinned Python 3.13 environment).
+
+## Quick start
+
+Prepare the source checkout:
+
+```bash
+git clone https://github.com/MedMLX/nnunet-mlx.git
+cd nnunet-mlx
+make env                     # creates .venv with MLX on Metal
+uv pip install --python .venv/bin/python -e '.[conversion]'   # to convert .pth checkpoints
+```
+
+Use `.venv/bin/nnunet-mlx`, or activate `.venv`. Every command accepts `--help`.
+
+Convert an upstream nnU-Net model folder once:
+
+```bash
+nnunet-mlx convert model-folder \
+  --source-model-folder /path/to/upstream-model \
+  --output-model-folder mlx-model
+```
+
+Predict one case, passing one `--input` per modality in channel order:
+
+```bash
+nnunet-mlx model predict \
+  --model-folder mlx-model \
+  --input case_0000.nii.gz \
+  --output-prefix predictions/case
+```
+
+Use `nnunet-mlx model predict-folder` for a whole folder. Add `--overwrite` to replace
+existing output, or `--continue-existing` to skip finished cases.
+
+Only convert checkpoints you trust: `.pth` files are pickles. See [SECURITY.md](https://github.com/MedMLX/nnunet-mlx/blob/main/SECURITY.md).
+
+### Python
+
+```python
+from nnunet_mlx import ModelFolderPredictor, load_model_bundle
+
+bundle = load_model_bundle("mlx-model", configuration="3d_fullres")
+predictor = ModelFolderPredictor(bundle)
+result = predictor.predict_case(
+    ["case_0000.nii.gz"], "predictions/case", save_probabilities=False, overwrite=False,
+)
+```
+
+For a single-channel 3D class model,
+`predictor.predict_nifti(image)` accepts a NiBabel NIfTI-1 image and returns local
+labels on its original grid without intermediate files. Fold logits stay on Metal
+except where restoration needs the host route (separate-Z or non-linear
+resampling). Cascades and regions use the file APIs above.
+
+The model is also discoverable by [medmlx](https://github.com/MedMLX/medmlx)
+as `nnunet`; see [docs/technical.md](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/technical.md) for the runner.
+
+## Input and output
+
+Supply one NIfTI file per input channel in the model's channel order. Prediction
+commands write segmentation files under the selected output prefix or directory;
+probability export is optional. Supported models and configurations are listed
+below and in the [compatibility notes](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/compatibility.md).
+
+| Area | Supported |
+| --- | --- |
+| Networks | 2D and 3D `PlainConvUNet` and `ResidualEncoderUNet` |
+| Configurations | `2d`, `3d_lowres`, `3d_fullres`, cascades |
+| Inference | Gaussian sliding window, mirroring, fold and configuration ensembles, probabilities |
+| Precision | FP32 |
+
+Anything else fails with a clear error rather than falling back. Pretrained-model
+support varies; see [Compatibility](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/compatibility.md).
+
+## Technical details
+
+Targets nnU-Net v2.8.1 and dynamic-network-architectures v0.4.4. Networks, conversion
+and the prediction path are compared against the upstream PyTorch implementation on
+seeded-weight and synthetic inputs and on selected released models (see
+[Compatibility](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/compatibility.md)); agreement on other models or data is not implied.
+Development, parity testing, the PancCTMultiTalentV2 staging recipe and the runner
+contract are in [docs/technical.md](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/technical.md); see also
+[Architecture](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/architecture.md) and [Roadmap](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/roadmap.md).
+
+## Intended use
+
+Intended for research and education, not clinical diagnosis or treatment decisions.
+Outputs require human review.
+
+## License
+
+Apache-2.0; see [LICENSE](https://github.com/MedMLX/nnunet-mlx/blob/main/LICENSE) and [THIRD_PARTY_NOTICES.md](https://github.com/MedMLX/nnunet-mlx/blob/main/THIRD_PARTY_NOTICES.md). Kernels derived from MLX keep
+their MIT license. Pretrained nnU-Net weights have their own licenses and are not
+distributed here. Please cite via [CITATION.cff](https://github.com/MedMLX/nnunet-mlx/blob/main/CITATION.cff) and cite
+[nnU-Net](https://github.com/MIC-DKFZ/nnUNet).
+
+## Implementation mapping
+
+[Central implementation map](https://github.com/MedMLX/Med-MLX/blob/main/implementation-maps/nnunet-mlx.json) records upstream-to-native changes, source references and qualification scope.

nnunet_mlx-0.5.1/README.md

@@ -0,0 +1,117 @@
+# nnunet-mlx
+
+[nnU-Net v2](https://github.com/MIC-DKFZ/nnUNet) inference in native MLX
+for Apple Silicon. Run existing nnU-Net models locally on Mac.
+
+- Convert and run pretrained nnU-Net v2 model folders
+- 2D and 3D `PlainConvUNet` and `ResidualEncoderUNet`
+- FP32 using MLX; PyTorch is only needed to convert `.pth` checkpoints
+
+Part of [MedMLX](https://github.com/MedMLX).
+[Technical notes](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/technical.md) · [Compatibility](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/compatibility.md)
+
+[Quick start](#quick-start) · [Input and output](#input-and-output) · [Technical details](#technical-details) · [License](#license)
+
+## Requirements
+
+Apple Silicon Mac with Metal, [uv](https://docs.astral.sh/uv/), and conda or mamba
+(setup uses it to build a pinned Python 3.13 environment).
+
+## Quick start
+
+Prepare the source checkout:
+
+```bash
+git clone https://github.com/MedMLX/nnunet-mlx.git
+cd nnunet-mlx
+make env                     # creates .venv with MLX on Metal
+uv pip install --python .venv/bin/python -e '.[conversion]'   # to convert .pth checkpoints
+```
+
+Use `.venv/bin/nnunet-mlx`, or activate `.venv`. Every command accepts `--help`.
+
+Convert an upstream nnU-Net model folder once:
+
+```bash
+nnunet-mlx convert model-folder \
+  --source-model-folder /path/to/upstream-model \
+  --output-model-folder mlx-model
+```
+
+Predict one case, passing one `--input` per modality in channel order:
+
+```bash
+nnunet-mlx model predict \
+  --model-folder mlx-model \
+  --input case_0000.nii.gz \
+  --output-prefix predictions/case
+```
+
+Use `nnunet-mlx model predict-folder` for a whole folder. Add `--overwrite` to replace
+existing output, or `--continue-existing` to skip finished cases.
+
+Only convert checkpoints you trust: `.pth` files are pickles. See [SECURITY.md](https://github.com/MedMLX/nnunet-mlx/blob/main/SECURITY.md).
+
+### Python
+
+```python
+from nnunet_mlx import ModelFolderPredictor, load_model_bundle
+
+bundle = load_model_bundle("mlx-model", configuration="3d_fullres")
+predictor = ModelFolderPredictor(bundle)
+result = predictor.predict_case(
+    ["case_0000.nii.gz"], "predictions/case", save_probabilities=False, overwrite=False,
+)
+```
+
+For a single-channel 3D class model,
+`predictor.predict_nifti(image)` accepts a NiBabel NIfTI-1 image and returns local
+labels on its original grid without intermediate files. Fold logits stay on Metal
+except where restoration needs the host route (separate-Z or non-linear
+resampling). Cascades and regions use the file APIs above.
+
+The model is also discoverable by [medmlx](https://github.com/MedMLX/medmlx)
+as `nnunet`; see [docs/technical.md](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/technical.md) for the runner.
+
+## Input and output
+
+Supply one NIfTI file per input channel in the model's channel order. Prediction
+commands write segmentation files under the selected output prefix or directory;
+probability export is optional. Supported models and configurations are listed
+below and in the [compatibility notes](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/compatibility.md).
+
+| Area | Supported |
+| --- | --- |
+| Networks | 2D and 3D `PlainConvUNet` and `ResidualEncoderUNet` |
+| Configurations | `2d`, `3d_lowres`, `3d_fullres`, cascades |
+| Inference | Gaussian sliding window, mirroring, fold and configuration ensembles, probabilities |
+| Precision | FP32 |
+
+Anything else fails with a clear error rather than falling back. Pretrained-model
+support varies; see [Compatibility](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/compatibility.md).
+
+## Technical details
+
+Targets nnU-Net v2.8.1 and dynamic-network-architectures v0.4.4. Networks, conversion
+and the prediction path are compared against the upstream PyTorch implementation on
+seeded-weight and synthetic inputs and on selected released models (see
+[Compatibility](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/compatibility.md)); agreement on other models or data is not implied.
+Development, parity testing, the PancCTMultiTalentV2 staging recipe and the runner
+contract are in [docs/technical.md](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/technical.md); see also
+[Architecture](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/architecture.md) and [Roadmap](https://github.com/MedMLX/nnunet-mlx/blob/main/docs/roadmap.md).
+
+## Intended use
+
+Intended for research and education, not clinical diagnosis or treatment decisions.
+Outputs require human review.
+
+## License
+
+Apache-2.0; see [LICENSE](https://github.com/MedMLX/nnunet-mlx/blob/main/LICENSE) and [THIRD_PARTY_NOTICES.md](https://github.com/MedMLX/nnunet-mlx/blob/main/THIRD_PARTY_NOTICES.md). Kernels derived from MLX keep
+their MIT license. Pretrained nnU-Net weights have their own licenses and are not
+distributed here. Please cite via [CITATION.cff](https://github.com/MedMLX/nnunet-mlx/blob/main/CITATION.cff) and cite
+[nnU-Net](https://github.com/MIC-DKFZ/nnUNet).
+
+## Implementation mapping
+
+[Central implementation map](https://github.com/MedMLX/Med-MLX/blob/main/implementation-maps/nnunet-mlx.json) records upstream-to-native changes, source references and qualification scope.

nnunet_mlx-0.5.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,82 @@
+# Third-party notices
+
+This repository implements compatibility with the following upstream projects.
+Their licenses apply to upstream code and dependencies; the repository's own
+license remains in `LICENSE`.
+
+## nnU-Net
+
+- Project: MIC-DKFZ nnU-Net
+- Source: <https://github.com/MIC-DKFZ/nnUNet>
+- Compatibility pin: v2.8.1,
+  `468cf803df9b267150ae2b6c0c59b8ac84f16227`
+- License: Apache License 2.0
+
+Selected later changes are adapted for the MLX project without changing that
+reference pin: foreground sampling store v1 at
+[the September 14 merge](https://github.com/MIC-DKFZ/nnUNet/commit/ded2aa3a4c81a9caae37054224d8ebac2d19a061)
+and [float32 resampling intermediates](https://github.com/MIC-DKFZ/nnUNet/commit/54c7480e2a8dc1798856b6463ca8fe11197d7e36).
+See the [data-update contract](docs/port/nnunet-v2/spec.md#selected-upstream-data-and-io-updates).
+
+## dynamic-network-architectures
+
+- Project: MIC-DKFZ dynamic-network-architectures
+- Source: <https://github.com/MIC-DKFZ/dynamic-network-architectures>
+- Reference pin: v0.4.4, `d35f85c7b92cbf3e9443b412fdc7c81f8e2e7b12`
+- License: Apache License 2.0
+
+## MLX
+
+- Project: Apple MLX
+- Source: <https://github.com/ml-explore/mlx>
+- Historical MLX reference recorded for this port: v0.32.3,
+  `64ea011cb65f14d9ce2737e60db9a4ae91ed7441`
+- Declared runtime dependency: `mlx==0.32.4` (see `pyproject.toml`).
+  This runtime version is separate from the historical source reference above.
+- Derived kernels retain Apple copyright and MIT terms in
+  `THIRD_PARTY_NOTICES.md`; per-file source notes also record
+  the MLX fork revision for the migrated label-reduction kernel.
+- License: MIT
+
+Pretrained nnU-Net weights remain subject to the licenses and terms of their
+training datasets and distributors. This repository does not redistribute
+weights.
+
+## Project notice
+
+nnU-Net MLX
+
+This product includes software developed by Joseph Sandoval and is licensed
+under the Apache License, Version 2.0 (see LICENSE).
+
+Kernels in src/nnunet_mlx/kernels/ are derived in part from Apple MLX,
+Copyright 2023 Apple Inc., licensed under the MIT License
+(see THIRD_PARTY_NOTICES.md).
+
+See THIRD_PARTY_NOTICES.md for the upstream projects this software is
+compatible with.
+
+
+## Full license: MLX-LICENSE
+
+MIT License
+
+Copyright © 2023 Apple Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.