segresnet-mlx 0.2.1__tar.gz

segresnet_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

segresnet_mlx-0.2.1/LICENSE

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

@@ -0,0 +1,94 @@
+Metadata-Version: 2.5
+Name: segresnet-mlx
+Version: 0.2.1
+Summary: Native MLX SegResNet with NumPy sliding-window logit inference
+Project-URL: Homepage, https://github.com/MedMLX/segresnet-mlx
+Project-URL: Documentation, https://github.com/MedMLX/segresnet-mlx/blob/main/docs/technical.md
+Project-URL: Repository, https://github.com/MedMLX/segresnet-mlx
+Project-URL: Issues, https://github.com/MedMLX/segresnet-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: nibabel<6,>=5.3
+Requires-Dist: numpy<3,>=2.0
+Provides-Extra: conversion
+Requires-Dist: torch<3,>=2.6; extra == 'conversion'
+Provides-Extra: dev
+Requires-Dist: hypothesis<7,>=6; 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: pytorch-ignite<0.6,>=0.4.11; extra == 'dev'
+Requires-Dist: ruff<1,>=0.13; extra == 'dev'
+Requires-Dist: torch<3,>=2.6; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# segresnet-mlx
+
+Segment brain tumors, renal structures and whole-body CT anatomy with MONAI SegResNet models in native MLX.
+
+[Docs](https://github.com/MedMLX/segresnet-mlx/blob/main/docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![SegResNet brain tumor segmentation in axial, coronal and sagittal views](https://raw.githubusercontent.com/MedMLX/segresnet-mlx/main/docs/example.png)
+
+*BraTS bundle output on a Medical Segmentation Decathlon brain MRI: tumor core
+(red), edema (green) and enhancing tumor (yellow).*
+
+| Input | Output |
+| :--- | :--- |
+| MRI sequences or CT volumes | Segmentation 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 "segresnet-mlx==0.2.1" huggingface-hub
+```
+
+The tagged GitHub release is an alternative installation route:
+
+```bash
+repo="https://github.com/MedMLX/segresnet-mlx.git@v0.2.1"
+python -m pip install "segresnet-mlx @ git+$repo" huggingface-hub
+```
+
+Download the public converted BraTS bundle separately, then run:
+
+```python
+from huggingface_hub import hf_hub_download
+from segresnet_mlx.medmlx import run
+
+bundle = "brats_mri_segmentation"
+weights = hf_hub_download("MedMLX/segresnet-brats-mlx", "segresnet-brats.safetensors")
+
+result = run(
+    bundle=bundle,
+    t1c_path="t1c.nii.gz",
+    t1_path="t1.nii.gz",
+    t2_path="t2.nii.gz",
+    flair_path="flair.nii.gz",
+    weights_path=weights,
+    output_dir="out",
+)
+print(result["outputs"]["mask"])
+```
+
+Keep input volumes on the same voxel grid. The package contains code only.
+Public converted bundles are available separately for
+[BraTS](https://huggingface.co/MedMLX/segresnet-brats-mlx) and
+[renal CECT](https://huggingface.co/MedMLX/segresnet-renal-cect-mlx); follow each
+weight card and its terms. Docs cover local upstream checkpoint conversion and
+whole-body CT bundles. Qualification differs by bundle; see the technical notes.
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/segresnet-mlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/segresnet-mlx/blob/main/THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

segresnet_mlx-0.2.1/README.md

@@ -0,0 +1,65 @@
+# segresnet-mlx
+
+Segment brain tumors, renal structures and whole-body CT anatomy with MONAI SegResNet models in native MLX.
+
+[Docs](https://github.com/MedMLX/segresnet-mlx/blob/main/docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![SegResNet brain tumor segmentation in axial, coronal and sagittal views](https://raw.githubusercontent.com/MedMLX/segresnet-mlx/main/docs/example.png)
+
+*BraTS bundle output on a Medical Segmentation Decathlon brain MRI: tumor core
+(red), edema (green) and enhancing tumor (yellow).*
+
+| Input | Output |
+| :--- | :--- |
+| MRI sequences or CT volumes | Segmentation 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 "segresnet-mlx==0.2.1" huggingface-hub
+```
+
+The tagged GitHub release is an alternative installation route:
+
+```bash
+repo="https://github.com/MedMLX/segresnet-mlx.git@v0.2.1"
+python -m pip install "segresnet-mlx @ git+$repo" huggingface-hub
+```
+
+Download the public converted BraTS bundle separately, then run:
+
+```python
+from huggingface_hub import hf_hub_download
+from segresnet_mlx.medmlx import run
+
+bundle = "brats_mri_segmentation"
+weights = hf_hub_download("MedMLX/segresnet-brats-mlx", "segresnet-brats.safetensors")
+
+result = run(
+    bundle=bundle,
+    t1c_path="t1c.nii.gz",
+    t1_path="t1.nii.gz",
+    t2_path="t2.nii.gz",
+    flair_path="flair.nii.gz",
+    weights_path=weights,
+    output_dir="out",
+)
+print(result["outputs"]["mask"])
+```
+
+Keep input volumes on the same voxel grid. The package contains code only.
+Public converted bundles are available separately for
+[BraTS](https://huggingface.co/MedMLX/segresnet-brats-mlx) and
+[renal CECT](https://huggingface.co/MedMLX/segresnet-renal-cect-mlx); follow each
+weight card and its terms. Docs cover local upstream checkpoint conversion and
+whole-body CT bundles. Qualification differs by bundle; see the technical notes.
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/segresnet-mlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/segresnet-mlx/blob/main/THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

segresnet_mlx-0.2.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,21 @@
+# Third-party notices
+
+MedMLX-authored additions are licensed under [Apache-2.0](LICENSE).
+
+## MONAI SegResNet and model bundles
+
+The native MLX network, inferer and transforms are adapted from
+[MONAI](https://github.com/Project-MONAI/MONAI), with the numerical reference
+pinned to revision `eccefc57550b111ed781d82249dfe77872a0e918` (MONAI 1.6.0).
+Copyright (c) MONAI Consortium. These source portions retain Apache-2.0 terms;
+the full license is included in [LICENSE](LICENSE).
+
+Bundle definitions originate in the
+[MONAI model zoo](https://github.com/Project-MONAI/model-zoo), revision
+`db9eeeef7ba64ce2ced0230d9bd4c524f69b7f0c`. The source files and bundle versions
+are identified in [scripts/upstream_reference.json](scripts/upstream_reference.json).
+The port changes execution to native MLX and host NumPy image processing.
+
+Pretrained checkpoints and input datasets retain their publisher terms.
+Dependencies declared in [pyproject.toml](pyproject.toml) retain their respective
+licenses independently of the package source license.

segresnet_mlx-0.2.1/pyproject.toml

@@ -0,0 +1,90 @@
+[build-system]
+requires = ["hatchling>=1.27"]
+build-backend = "hatchling.build"
+
+[project]
+name = "segresnet-mlx"
+version = "0.2.1"
+description = "Native MLX SegResNet with NumPy sliding-window logit inference"
+readme = "README.md"
+requires-python = ">=3.13,<3.15"
+classifiers = ["Operating System :: MacOS :: MacOS X"]
+license = "Apache-2.0"
+license-files = ["LICENSE", "THIRD_PARTY_NOTICES.md"]
+authors = [{ name = "Joseph Sandoval" }, { name = "Alfredo Sandoval Jr." }]
+dependencies = [
+  "medmlx-core==0.2.3",
+  "nibabel>=5.3,<6",
+  "numpy>=2.0,<3",
+]
+
+[project.entry-points."medmlx.models"]
+segresnet = "segresnet_mlx.medmlx:MODEL"
+
+[project.urls]
+Homepage = "https://github.com/MedMLX/segresnet-mlx"
+Documentation = "https://github.com/MedMLX/segresnet-mlx/blob/main/docs/technical.md"
+Repository = "https://github.com/MedMLX/segresnet-mlx"
+Issues = "https://github.com/MedMLX/segresnet-mlx/issues"
+
+[project.optional-dependencies]
+conversion = ["torch>=2.6,<3"]
+dev = [
+  "pyright==1.1.414",
+  "pytorch-ignite>=0.4.11,<0.6",
+  "hypothesis>=6,<7",
+  "monai==1.6.1", # Pinned upstream reference tests and generation only.
+  "pytest>=8.4,<10",
+  "ruff>=0.13,<1",
+  "torch>=2.6,<3",
+]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/segresnet_mlx"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--strict-config --strict-markers"
+markers = ["mlx: native MLX execution requiring Apple Silicon Metal"]
+
+[tool.uv]
+constraint-dependencies = ["setuptools>=84.1.0", "filelock>=4.2.1", ]
+environments = ["sys_platform == 'darwin' and platform_machine == 'arm64'"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py313"
+
+[tool.ruff.lint]
+extend-select = ["TID251", "TID252", "ANN401"]
+select = ["E", "F", "I", "UP", "B", "SIM", "RUF"]
+
+[tool.pyright]
+include = ["scripts","src","tests"]
+extraPaths = ["src"]
+pythonVersion = "3.13"
+typeCheckingMode = "strict"
+enableTypeIgnoreComments = false
+reportUnnecessaryTypeIgnoreComment = "error"
+
+[tool.ruff.lint.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
+"typing.Any" = {msg = "Use a precise type and parse untyped values at the boundary."}
+"typing_extensions.Any" = {msg = "Use a precise type and parse untyped values at the boundary."}
+
+[tool.uv.sources]
+medmlx-core = { git = "https://github.com/MedMLX/medmlx.git", rev = "e765f0a94aa31e8dfcdc599e4a4206eaca84f8b0", subdirectory = "packages/core" }
+
+[tool.hatch.build.targets.sdist]
+only-include = [
+  "src/segresnet_mlx",
+  "pyproject.toml",
+  "README.md",
+  "LICENSE",
+  "THIRD_PARTY_NOTICES.md",
+]

segresnet_mlx-0.2.1/src/segresnet_mlx/__init__.py

@@ -0,0 +1,67 @@
+"""Explicit MLX port of MONAI SegResNet inference.
+
+Public names load on first access, so importing the package (or the medmlx
+declaration in ``segresnet_mlx.medmlx``) does not import MLX.
+"""
+
+from importlib import import_module
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from segresnet_mlx.inference import forward_patch as forward_patch
+    from segresnet_mlx.network import SegResNet as SegResNet
+    from segresnet_mlx.predictor import BUNDLE_CONFIGS as BUNDLE_CONFIGS
+    from segresnet_mlx.predictor import BundlePredictor as BundlePredictor
+    from segresnet_mlx.predictor import SlidingWindowConfig as SlidingWindowConfig
+    from segresnet_mlx.predictor import predict_logits as predict_logits
+    from segresnet_mlx.telemetry import WindowTelemetry as WindowTelemetry
+    from segresnet_mlx.topology import SegResNetSpec as SegResNetSpec
+    from segresnet_mlx.weights import convert_checkpoint as convert_checkpoint
+    from segresnet_mlx.weights import convert_state_dict as convert_state_dict
+    from segresnet_mlx.weights import load_model as load_model
+    from segresnet_mlx.weights import required_shapes as required_shapes
+
+__version__ = "0.2.1"
+
+_EXPORTS = {
+    "BUNDLE_CONFIGS": "segresnet_mlx.predictor",
+    "BundlePredictor": "segresnet_mlx.predictor",
+    "SegResNet": "segresnet_mlx.network",
+    "SegResNetSpec": "segresnet_mlx.topology",
+    "SlidingWindowConfig": "segresnet_mlx.predictor",
+    "WindowTelemetry": "segresnet_mlx.telemetry",
+    "convert_checkpoint": "segresnet_mlx.weights",
+    "convert_state_dict": "segresnet_mlx.weights",
+    "forward_patch": "segresnet_mlx.inference",
+    "load_model": "segresnet_mlx.weights",
+    "predict_logits": "segresnet_mlx.predictor",
+    "required_shapes": "segresnet_mlx.weights",
+}
+
+__all__ = [
+    "BUNDLE_CONFIGS",
+    "BundlePredictor",
+    "SegResNet",
+    "SegResNetSpec",
+    "SlidingWindowConfig",
+    "WindowTelemetry",
+    "convert_checkpoint",
+    "convert_state_dict",
+    "forward_patch",
+    "load_model",
+    "predict_logits",
+    "required_shapes",
+]
+
+
+def __getattr__(name: str) -> object:
+    module = _EXPORTS.get(name)
+    if module is None:
+        raise AttributeError(f"module 'segresnet_mlx' has no attribute {name!r}")
+    value = getattr(import_module(module), name)
+    globals()[name] = value
+    return value
+
+
+def __dir__() -> list[str]:
+    return sorted({*globals(), *_EXPORTS})

segresnet_mlx-0.2.1/src/segresnet_mlx/_arrays.py

@@ -0,0 +1,36 @@
+"""Host array dtypes at model, checkpoint and image boundaries."""
+
+from __future__ import annotations
+
+from collections.abc import Callable
+from typing import TYPE_CHECKING, cast
+
+import numpy as np
+
+if TYPE_CHECKING:
+    from segresnet_mlx._types import Array
+
+type HostArray = np.ndarray[tuple[int, ...], np.dtype[np.generic]]
+type Float32Array = np.ndarray[tuple[int, ...], np.dtype[np.float32]]
+type Float64Array = np.ndarray[tuple[int, ...], np.dtype[np.float64]]
+type Int64Array = np.ndarray[tuple[int, ...], np.dtype[np.int64]]
+type MaskArray = Float32Array | Int64Array
+
+type NumericScalar = (
+    np.bool_
+    | np.int8
+    | np.int16
+    | np.int32
+    | np.int64
+    | np.uint8
+    | np.uint16
+    | np.uint32
+    | np.uint64
+    | np.float16
+    | np.float32
+    | np.float64
+    | np.complex64
+    | np.complex128
+)
+type NumericArray = np.ndarray[tuple[int, ...], np.dtype[NumericScalar]]
+as_numpy = cast("Callable[[Array], NumericArray]", np.array)

segresnet_mlx-0.2.1/src/segresnet_mlx/_nifti.py

@@ -0,0 +1,63 @@
+"""Typed protocols for the NiBabel NIfTI, header and orientation calls used here."""
+
+from __future__ import annotations
+
+from collections.abc import Sequence
+from os import PathLike
+from typing import Protocol, cast
+
+import nibabel
+import numpy as np
+from nibabel.filebasedimages import ImageFileError as ImageFileError
+
+from segresnet_mlx._arrays import Float64Array, HostArray
+
+type PathArg = str | PathLike[str]
+
+
+class ArrayBuffer(Protocol):
+    def __array__(
+        self, dtype: np.dtype[np.generic] | None = None, copy: bool | None = None
+    ) -> HostArray: ...
+
+
+class NiftiHeader(Protocol):
+    def get_zooms(self) -> tuple[float, ...]: ...
+    def set_zooms(self, zooms: Sequence[float] | Float64Array) -> None: ...
+    def __getitem__(self, key: str) -> HostArray: ...
+
+
+class NiftiImage(Protocol):
+    shape: tuple[int, ...]
+    affine: Float64Array
+    dataobj: ArrayBuffer | HostArray
+    header: NiftiHeader
+
+    def __init__(self, dataobj: HostArray, affine: HostArray) -> None: ...
+    def get_data_dtype(self) -> np.dtype[np.generic]: ...
+    def get_sform(self) -> Float64Array: ...
+    def get_qform(self) -> Float64Array: ...
+    def set_sform(self, affine: Float64Array, code: int | None = None) -> None: ...
+    def set_qform(self, affine: Float64Array, code: int | None = None) -> None: ...
+
+
+class Orientations(Protocol):
+    def axcodes2ornt(self, axcodes: str, labels: tuple[tuple[str, str], ...]) -> Float64Array: ...
+    def ornt_transform(self, start_ornt: Float64Array, end_ornt: Float64Array) -> Float64Array: ...
+    def inv_ornt_aff(self, ornt: Float64Array, shape: Sequence[int]) -> Float64Array: ...
+    def aff2axcodes(
+        self, aff: Float64Array, labels: tuple[tuple[str, str], ...]
+    ) -> tuple[str | None, ...]: ...
+
+
+class Nibabel(Protocol):
+    Nifti1Image: type[NiftiImage]
+    orientations: Orientations
+
+    def load(self, filename: PathArg) -> NiftiImage: ...
+    def save(self, img: NiftiImage, filename: PathArg) -> None: ...
+    def io_orientation(self, affine: Float64Array) -> Float64Array: ...
+
+
+# Bound to the real module; this runner admits only NIfTI images.
+nib = cast(Nibabel, nibabel)