mlxradiomics 0.1.0.dev3__tar.gz

mlxradiomics-0.1.0.dev3/.gitignore

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+__pycache__/
+*.py[cod]
+.pytest_cache/
+.ruff_cache/
+.venv
+dist/
+build/
+results/
+*.nii
+*.nii.gz
+*.dcm
+*.npz
+!tests/fixtures/darwin-arm64/*.npz
+*.egg-info/

mlxradiomics-0.1.0.dev3/LICENSE

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mlxradiomics-0.1.0.dev3/PKG-INFO

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+Metadata-Version: 2.5
+Name: mlxradiomics
+Version: 0.1.0.dev3
+Summary: Apple Silicon Metal radiomics with bounded voxel batches.
+License-Expression: Apache-2.0 AND MIT AND BSD-3-Clause
+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==0.32.4; sys_platform == 'darwin' and platform_machine == 'arm64'
+Requires-Dist: numpy<3,>=2.0
+Provides-Extra: io
+Requires-Dist: pyyaml<7,>=6; extra == 'io'
+Requires-Dist: simpleitk==2.5.6; extra == 'io'
+Provides-Extra: lbp
+Requires-Dist: scipy==1.18.1; extra == 'lbp'
+Requires-Dist: trimesh==4.9.0; extra == 'lbp'
+Description-Content-Type: text/markdown
+
+# mlxradiomics
+
+Extract radiomics features and voxel maps on the Apple Silicon GPU with native MLX.
+
+[Docs](docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![Prewindowed CT liver ROI → local entropy, contrast and homogeneity maps.](https://raw.githubusercontent.com/MedMLX/mlxradiomics/main/docs/showcase.png)
+
+*Prewindowed CT liver ROI → local entropy, contrast and homogeneity maps.*
+
+| Input | Output |
+| :--- | :--- |
+| Aligned image + label mask | ROI features or voxel maps |
+
+**Apple Silicon · Metal · Python 3.13 / 3.14** · [uv](https://docs.astral.sh/uv/)
+
+## Quick start
+
+```bash
+git clone https://github.com/MedMLX/mlxradiomics.git
+cd mlxradiomics
+make env
+```
+
+With aligned `image` and `mask` NumPy arrays:
+
+```python
+from mlxradiomics import Settings, extract
+
+# image and mask are aligned NumPy arrays; spacing follows array-axis order.
+result = extract(
+    image, mask, spacing=(3.0, 1.0, 1.0),
+    settings=Settings(label=2, bin_width=25,
+                      features=("firstorder_Mean", "glcm_Contrast")),
+    voxel=True,
+)
+mean_map = result.features["original_firstorder_Mean"]
+```
+
+Use `voxel=False` for ROI features. The optional `io` extra supports NIfTI and NRRD files; see Docs.
+
+## License
+
+[Apache-2.0](LICENSE). See [third-party notices](THIRD_PARTY_NOTICES.md).
+
+For research and education. Outputs require human review.

mlxradiomics-0.1.0.dev3/README.md

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+# mlxradiomics
+
+Extract radiomics features and voxel maps on the Apple Silicon GPU with native MLX.
+
+[Docs](docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![Prewindowed CT liver ROI → local entropy, contrast and homogeneity maps.](https://raw.githubusercontent.com/MedMLX/mlxradiomics/main/docs/showcase.png)
+
+*Prewindowed CT liver ROI → local entropy, contrast and homogeneity maps.*
+
+| Input | Output |
+| :--- | :--- |
+| Aligned image + label mask | ROI features or voxel maps |
+
+**Apple Silicon · Metal · Python 3.13 / 3.14** · [uv](https://docs.astral.sh/uv/)
+
+## Quick start
+
+```bash
+git clone https://github.com/MedMLX/mlxradiomics.git
+cd mlxradiomics
+make env
+```
+
+With aligned `image` and `mask` NumPy arrays:
+
+```python
+from mlxradiomics import Settings, extract
+
+# image and mask are aligned NumPy arrays; spacing follows array-axis order.
+result = extract(
+    image, mask, spacing=(3.0, 1.0, 1.0),
+    settings=Settings(label=2, bin_width=25,
+                      features=("firstorder_Mean", "glcm_Contrast")),
+    voxel=True,
+)
+mean_map = result.features["original_firstorder_Mean"]
+```
+
+Use `voxel=False` for ROI features. The optional `io` extra supports NIfTI and NRRD files; see Docs.
+
+## License
+
+[Apache-2.0](LICENSE). See [third-party notices](THIRD_PARTY_NOTICES.md).
+
+For research and education. Outputs require human review.

mlxradiomics-0.1.0.dev3/THIRD_PARTY_NOTICES.md

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+# Third-party notices
+
+PyRadiomics compatibility reference, development dependency and marching-geometry
+lookup tables in `src/mlxradiomics/mesh_tables.json` (recorded source revision
+`6a761c4eb01905cfcb1139b0b158547c55edd4df`, `radiomics/src/cshape.c`).
+Source: https://raw.githubusercontent.com/AIM-Harvard/pyradiomics/6a761c4eb01905cfcb1139b0b158547c55edd4df/LICENSE.txt
+
+Copyright 2017 Harvard Medical School
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
+following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following
+disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
+disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products
+derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Wavelet coefficient tables in `src/mlxradiomics/wavelet_tables.json` record
+PyWavelets 1.10.0 as their source:
+Copyright (c) 2006-2012 Filip Wasilewski <http://en.ig.ma/>
+Copyright (c) 2012-     The PyWavelets Developers <https://github.com/PyWavelets/pywt>
+
+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.
+
+## Showcase image
+
+The CT images are from [AMOS22](https://doi.org/10.5281/zenodo.7262581),
+Ji, Yuanfeng et al., licensed [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).
+The showcase uses cropped views with model-derived overlays or maps.

mlxradiomics-0.1.0.dev3/pyproject.toml

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+[build-system]
+requires = ["hatchling>=1.27"]
+build-backend = "hatchling.build"
+
+[project]
+classifiers = ["Operating System :: MacOS :: MacOS X"]
+name = "mlxradiomics"
+version = "0.1.0.dev3"
+description = "Apple Silicon Metal radiomics with bounded voxel batches."
+readme = "README.md"
+requires-python = ">=3.13,<3.15"
+license = "Apache-2.0 AND MIT AND BSD-3-Clause"
+license-files = ["LICENSE", "THIRD_PARTY_NOTICES.md"]
+dependencies = [
+  "numpy>=2.0,<3",
+  "mlx==0.32.4; sys_platform == 'darwin' and platform_machine == 'arm64'",
+  "medmlx-core==0.2.3",
+]
+
+[project.optional-dependencies]
+io = ["SimpleITK==2.5.6", "PyYAML>=6,<7"]
+lbp = ["scipy==1.18.1", "trimesh==4.9.0"]
+
+[project.entry-points."medmlx.models"]
+mlxradiomics = "mlxradiomics.medmlx:MODEL"
+
+[project.scripts]
+mlxradiomics-qualify = "mlxradiomics.qualification:main"
+
+[dependency-groups]
+dev = [
+  "pytest==9.1.1",
+  "hypothesis>=6,<7",
+  "PyYAML>=6,<7",
+  "scikit-image==0.26.0",
+  "scipy==1.16.3",
+  "trimesh==4.9.0",
+  "ruff==0.15.21",
+  "pyright==1.1.414",
+  "SimpleITK==2.5.6",
+  "pyradiomics==3.0.1a1+medmlx.1",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/mlxradiomics"]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.uv.sources]
+medmlx-core = { git = "https://github.com/MedMLX/medmlx.git", rev = "e765f0a94aa31e8dfcdc599e4a4206eaca84f8b0", subdirectory = "packages/core" }
+pyradiomics = { path = "reference/pyradiomics" }
+
+[tool.uv]
+environments = ["sys_platform == 'darwin' and platform_machine == 'arm64'"]
+conflicts = [[{ extra = "lbp" }, { group = "dev" }]]
+
+[tool.ruff]
+extend-exclude = ["reference/pyradiomics/radiomics"]
+target-version = "py313"
+line-length = 100
+
+[tool.ruff.lint]
+extend-select = ["TID251", "TID252", "ANN401"]
+select = ["E", "F", "I", "UP", "B", "SIM"]
+
+[tool.pyright]
+include = ["scripts","src","tests","typings"]
+stubPath = "typings"
+extraPaths = ["src"]
+pythonVersion = "3.13"
+typeCheckingMode = "strict"
+enableTypeIgnoreComments = false
+reportUnnecessaryTypeIgnoreComment = "error"
+
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-q"
+
+[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.hatch.build.targets.sdist]
+only-include = [
+  "src/mlxradiomics",
+  "pyproject.toml",
+  "README.md",
+  "LICENSE",
+  "THIRD_PARTY_NOTICES.md",
+]

mlxradiomics-0.1.0.dev3/src/mlxradiomics/__init__.py

@@ -0,0 +1,81 @@
+"""PyRadiomics-compatible radiomics features computed with MLX on the Apple Silicon GPU.
+
+Research software. Feature values are compared with a pinned PyRadiomics revision on
+synthetic inputs (see docs/technical.md); no IBSI or clinical validation is claimed.
+
+Names other than ``FEATURES`` and ``Settings`` are imported on first access, so
+``import mlxradiomics`` does not import MLX, SimpleITK or the PyRadiomics reference.
+"""
+
+from __future__ import annotations
+
+from importlib import import_module
+from typing import TYPE_CHECKING, cast
+
+from mlxradiomics.config import FEATURES, Settings
+
+if TYPE_CHECKING:
+    from mlxradiomics.engine import Result as Result
+    from mlxradiomics.engine import extract as extract
+    from mlxradiomics.io import Volume as Volume
+    from mlxradiomics.lbp import LBPMethod as LBPMethod
+    from mlxradiomics.pipeline import ImageExtraction as ImageExtraction
+    from mlxradiomics.pipeline import extract_images as extract_images
+    from mlxradiomics.spatial import ImagePair as ImagePair
+    from mlxradiomics.spatial import ImageSettings as ImageSettings
+    from mlxradiomics.spatial import Interpolator as Interpolator
+    from mlxradiomics.spatial import extract_files as extract_files
+    from mlxradiomics.spatial import load_image_pair as load_image_pair
+    from mlxradiomics.transforms import FeatureImage as FeatureImage
+    from mlxradiomics.transforms import ImageType as ImageType
+    from mlxradiomics.transforms import TransformSettings as TransformSettings
+    from mlxradiomics.transforms import feature_images as feature_images
+
+__version__ = "0.1.0.dev3"
+
+_EXPORT_MODULES = {
+    "Result": "engine",
+    "extract": "engine",
+    "Volume": "io",
+    "ImagePair": "spatial",
+    "ImageSettings": "spatial",
+    "Interpolator": "spatial",
+    "extract_files": "spatial",
+    "load_image_pair": "spatial",
+    "ImageExtraction": "pipeline",
+    "extract_images": "pipeline",
+    "FeatureImage": "transforms",
+    "ImageType": "transforms",
+    "TransformSettings": "transforms",
+    "feature_images": "transforms",
+    "LBPMethod": "lbp",
+}
+__all__ = [
+    "FEATURES",
+    "Settings",
+    "Result",
+    "extract",
+    "Volume",
+    "ImagePair",
+    "ImageSettings",
+    "Interpolator",
+    "extract_files",
+    "load_image_pair",
+    "ImageExtraction",
+    "extract_images",
+    "FeatureImage",
+    "ImageType",
+    "TransformSettings",
+    "feature_images",
+    "LBPMethod",
+]
+
+
+def __getattr__(name: str) -> object:
+    """Import a public name on first access and cache it in the module namespace."""
+    module = _EXPORT_MODULES.get(name)
+    if module is None:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    value = cast(object, getattr(import_module(f"mlxradiomics.{module}"), name))
+    globals()[name] = value
+    return value

mlxradiomics-0.1.0.dev3/src/mlxradiomics/_runtime.py

@@ -0,0 +1,28 @@
+"""The package executes only on Apple Silicon Metal through the shared runtime."""
+
+from collections.abc import Callable
+from platform import machine, system
+from typing import TYPE_CHECKING, cast
+
+import numpy as np
+from medmlx_core import MissingDependencyError, import_mlx
+from numpy.typing import NDArray
+
+from mlxradiomics._typing import EvaluationRuntime
+
+if TYPE_CHECKING:
+    import mlx.core as mx
+else:
+    if system() != "Darwin" or machine() != "arm64":
+        raise MissingDependencyError(
+            "mlxradiomics requires macOS arm64 with an accessible Metal GPU",
+            hint="Run on Apple Silicon; host preprocessing and upstream recording need no Metal.",
+        )
+    mx = import_mlx()
+
+
+__all__ = ["array_from_bool", "evaluate", "mx"]
+
+# MLX accepts NumPy bool arrays; its DLPack constructor annotation omits them.
+array_from_bool = cast(Callable[[NDArray[np.bool_]], mx.array], mx.array)
+evaluate = cast(EvaluationRuntime, mx).eval