totalsegmentator-mlx 0.1.1__tar.gz

totalsegmentator_mlx-0.1.1/.gitignore

@@ -0,0 +1,20 @@
+.venv
+.venv-*
+.cache/
+runs/
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.hypothesis/
+.ruff_cache/
+dist/
+build/
+*.egg-info/
+*.nii
+*.nii.gz
+*.pth
+*.safetensors
+*.npz
+*.npy
+# Generated synthetic CT fixtures carry the independent workflow reference.
+!tests/fixtures/*.nii.gz

totalsegmentator_mlx-0.1.1/LICENSE

@@ -0,0 +1,201 @@
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totalsegmentator_mlx-0.1.1/PKG-INFO

@@ -0,0 +1,70 @@
+Metadata-Version: 2.5
+Name: totalsegmentator-mlx
+Version: 0.1.1
+Summary: TotalSegmentator v2 CT segmentation with native MLX inference on Apple Silicon
+Project-URL: Homepage, https://github.com/MedMLX/totalsegmentator-mlx
+Project-URL: Documentation, https://github.com/MedMLX/totalsegmentator-mlx/blob/main/docs/technical.md
+Project-URL: Repository, https://github.com/MedMLX/totalsegmentator-mlx
+Project-URL: Issues, https://github.com/MedMLX/totalsegmentator-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: nnunet-mlx==0.5.1
+Requires-Dist: numpy<3,>=2.0
+Requires-Dist: scipy==1.18.1
+Provides-Extra: conversion
+Requires-Dist: nnunet-mlx[conversion]; extra == 'conversion'
+Provides-Extra: dev
+Requires-Dist: hypothesis<7,>=6; 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'
+Description-Content-Type: text/markdown
+
+# totalsegmentator-mlx
+
+Segment 117 CT structures with TotalSegmentator v2 in native MLX. Includes standard, fast and coarse modes.
+
+[Docs](https://github.com/MedMLX/totalsegmentator-mlx/blob/main/docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![totalsegmentator-mlx example output](https://raw.githubusercontent.com/MedMLX/totalsegmentator-mlx/main/docs/example.png)
+
+*Fast-mode 3D surfaces and an axial slice from an autoPET CT.*
+
+| Input | Output |
+| :--- | :--- |
+| 3D CT · NIfTI | Multilabel mask 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 "totalsegmentator-mlx[conversion]==0.1.1"
+```
+
+Convert your TotalSegmentator v2 checkpoints once, then segment:
+
+```bash
+totalsegmentator-mlx convert --source-model-dir ~/.totalsegmentator/nnunet/results \
+  --output-model-dir models --models organs vertebrae cardiac muscles ribs
+totalsegmentator-mlx predict -i ct.nii.gz -o mask.nii.gz --model-dir models
+```
+
+The PyPI package contains code only. Obtain trusted TotalSegmentator v2 checkpoints
+from [upstream](https://github.com/wasserth/TotalSegmentator) under their publisher
+terms, then convert your local copies. No checkpoints are downloaded automatically.
+Docs cover model folders, modes and cropping.
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/totalsegmentator-mlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/totalsegmentator-mlx/blob/main/THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

totalsegmentator_mlx-0.1.1/README.md

@@ -0,0 +1,42 @@
+# totalsegmentator-mlx
+
+Segment 117 CT structures with TotalSegmentator v2 in native MLX. Includes standard, fast and coarse modes.
+
+[Docs](https://github.com/MedMLX/totalsegmentator-mlx/blob/main/docs/technical.md) · [MedMLX](https://github.com/MedMLX)
+
+![totalsegmentator-mlx example output](https://raw.githubusercontent.com/MedMLX/totalsegmentator-mlx/main/docs/example.png)
+
+*Fast-mode 3D surfaces and an axial slice from an autoPET CT.*
+
+| Input | Output |
+| :--- | :--- |
+| 3D CT · NIfTI | Multilabel mask 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 "totalsegmentator-mlx[conversion]==0.1.1"
+```
+
+Convert your TotalSegmentator v2 checkpoints once, then segment:
+
+```bash
+totalsegmentator-mlx convert --source-model-dir ~/.totalsegmentator/nnunet/results \
+  --output-model-dir models --models organs vertebrae cardiac muscles ribs
+totalsegmentator-mlx predict -i ct.nii.gz -o mask.nii.gz --model-dir models
+```
+
+The PyPI package contains code only. Obtain trusted TotalSegmentator v2 checkpoints
+from [upstream](https://github.com/wasserth/TotalSegmentator) under their publisher
+terms, then convert your local copies. No checkpoints are downloaded automatically.
+Docs cover model folders, modes and cropping.
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/totalsegmentator-mlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/totalsegmentator-mlx/blob/main/THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

totalsegmentator_mlx-0.1.1/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,46 @@
+# Third-party notices
+
+MedMLX-authored additions are licensed under [Apache-2.0](LICENSE).
+The upstream attribution and license notices are retained below.
+
+totalsegmentator-mlx extracts the existing MedMLX integration and the
+TotalSegmentator v2 CT outer pipeline into a native model package.
+
+TotalSegmentator source and label tables:
+  https://github.com/Alfredo-Sandoval/TotalSegmentator
+  revision 44310d406805032e7056c8c13a2a37456faeaaf7
+  derived from https://github.com/wasserth/TotalSegmentator
+  Apache License, Version 2.0 (included as LICENSE).
+
+The extracted CT path preserves canonical orientation, cubic 1.5 mm CT
+resampling with int32 staging, ordered five-part global label merging,
+nearest-neighbor label restoration and the NIfTI label table. Other upstream
+tasks, backends and application services are not included.
+
+The MedMLX adapter originated in medseg-mlx, by Joseph Sandoval and
+Alfredo Sandoval Jr., under the Apache License, Version 2.0.
+
+nnunet-mlx is a separate dependency and retains its own Apache-2.0 and MIT
+notices. Model checkpoint terms are separate from these source-code licenses.
+
+Dependencies declared in [pyproject.toml](pyproject.toml) are installed separately
+and retain their respective licenses.
+
+## Historical Medical Segmentation Decathlon labels
+
+The inherited Git history contains 32 training masks from the Medical
+Segmentation Decathlon `Task05_Prostate` dataset. Its dataset metadata credits
+Radboud University, Nijmegen Medical Centre. The masks' NIfTI contents are
+unchanged from the dataset's `labelsTr` files.
+
+Upstream commit
+[`29ca422`](https://github.com/wasserth/TotalSegmentator/commit/29ca42220288df4e5080fce501f4025453ebc07e)
+added them under `mnt/nvme/nnunet/preprocessed/Task005_Prostate/gt_segmentations/`;
+[`4d6b53d`](https://github.com/wasserth/TotalSegmentator/commit/4d6b53d859063df5c3d7ace0b019b60c27df19e5)
+removed them from the source tree. They remain in the inherited Git history.
+
+These masks retain the dataset's
+[Creative Commons Attribution-ShareAlike 4.0 International license](https://creativecommons.org/licenses/by-sa/4.0/).
+Source: [Medical Segmentation Decathlon on the AWS Open Data Registry](https://registry.opendata.aws/msd/)
+and its MONAI-hosted [Task05_Prostate archive](https://msd-for-monai.s3-us-west-2.amazonaws.com/Task05_Prostate.tar),
+accessed 2026-10-24.

totalsegmentator_mlx-0.1.1/pyproject.toml

@@ -0,0 +1,86 @@
+[build-system]
+requires = ["hatchling>=1.27"]
+build-backend = "hatchling.build"
+
+[project]
+name = "totalsegmentator-mlx"
+version = "0.1.1"
+description = "TotalSegmentator v2 CT segmentation with native MLX inference on Apple Silicon"
+readme = "README.md"
+classifiers = ["Operating System :: MacOS :: MacOS X"]
+requires-python = ">=3.13,<3.15"
+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",
+  "nnunet-mlx==0.5.1",
+  "nibabel>=5.3,<6",
+  "numpy>=2.0,<3",
+  "scipy==1.18.1",
+]
+
+[project.urls]
+Homepage = "https://github.com/MedMLX/totalsegmentator-mlx"
+Documentation = "https://github.com/MedMLX/totalsegmentator-mlx/blob/main/docs/technical.md"
+Repository = "https://github.com/MedMLX/totalsegmentator-mlx"
+Issues = "https://github.com/MedMLX/totalsegmentator-mlx/issues"
+
+[project.optional-dependencies]
+conversion = ["nnunet-mlx[conversion]"]
+dev = ["hypothesis>=6,<7", "pyright==1.1.414", "pytest>=8.4,<10", "ruff>=0.13,<1"]
+
+[project.scripts]
+totalsegmentator-mlx = "totalsegmentator_mlx.cli:main"
+
+[project.entry-points."medmlx.models"]
+totalsegmentator = "totalsegmentator_mlx.medmlx:MODEL"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/totalsegmentator_mlx"]
+
+[tool.uv]
+constraint-dependencies = ["setuptools>=84.1.0", "filelock>=4.2.1", ]
+environments = ["sys_platform == 'darwin' and platform_machine == 'arm64'"]
+required-environments = ["sys_platform == 'darwin' and platform_machine == 'arm64'"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--strict-config --strict-markers"
+
+[tool.ruff]
+target-version = "py313"
+line-length = 100
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "UP", "B", "SIM", "RUF", "TID251", "TID252", "ANN401"]
+
+[tool.ruff.lint.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
+"typing.Any" = {msg = "Use precise types at external boundaries."}
+"typing_extensions.Any" = {msg = "Use precise types at external boundaries."}
+
+[tool.pyright]
+include = ["src", "tests"]
+pythonVersion = "3.13"
+typeCheckingMode = "strict"
+enableTypeIgnoreComments = false
+reportUnnecessaryTypeIgnoreComment = "error"
+
+[tool.uv.sources]
+medmlx-core = { git = "https://github.com/MedMLX/medmlx.git", rev = "e765f0a94aa31e8dfcdc599e4a4206eaca84f8b0", subdirectory = "packages/core" }
+nnunet-mlx = { git = "https://github.com/MedMLX/nnunet-mlx.git", rev = "ac07d0047a2f6f2e620b52e9d3a512a64d874b6a" }
+
+[tool.hatch.build.targets.sdist]
+only-include = [
+  "src/totalsegmentator_mlx",
+  "pyproject.toml",
+  "README.md",
+  "LICENSE",
+  "THIRD_PARTY_NOTICES.md",
+]

totalsegmentator_mlx-0.1.1/src/totalsegmentator_mlx/__init__.py

@@ -0,0 +1,23 @@
+"""TotalSegmentator v2 ``total`` CT inference on Apple Silicon (MLX), research software.
+
+``segment`` runs a CT through the native workflow and returns uint8 global label IDs
+(1-117) on the input grid; ``convert_model`` converts upstream fold-0 checkpoints to
+the layout ``segment`` reads. Names load on first access, so importing the package
+does not import the MLX engine.
+"""
+
+from importlib import import_module
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from totalsegmentator_mlx.conversion import convert_model
+    from totalsegmentator_mlx.pipeline import segment
+
+__all__ = ["convert_model", "segment"]
+
+
+def __getattr__(name: str) -> object:
+    owner = {"segment": "pipeline", "convert_model": "conversion"}.get(name)
+    if owner is None:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    return getattr(import_module(f"{__name__}.{owner}"), name)

totalsegmentator_mlx-0.1.1/src/totalsegmentator_mlx/__main__.py

@@ -0,0 +1,6 @@
+"""Run the installed command through python -m totalsegmentator_mlx."""
+
+from totalsegmentator_mlx.cli import main
+
+if __name__ == "__main__":
+    main()

totalsegmentator_mlx-0.1.1/src/totalsegmentator_mlx/cli.py

@@ -0,0 +1,128 @@
+"""Lazy command-line entry point for conversion, CT prediction and label discovery."""
+
+from __future__ import annotations
+
+import argparse
+import json
+import sys
+from pathlib import Path
+from typing import TYPE_CHECKING, cast
+
+from totalsegmentator_mlx.labels import LABELS, MODEL_PARTS, QUALITY_MODELS
+
+if TYPE_CHECKING:
+    from totalsegmentator_mlx.models import Mode
+
+
+class Arguments(argparse.Namespace):
+    """Typed namespace for the ``predict``, ``convert`` and ``labels`` subcommands.
+
+    Only the fields of the chosen subcommand are set by argparse.
+    """
+
+    command: str
+    input_path: Path
+    output_path: Path
+    model_dir: Path
+    mode: str
+    model_part: str | None
+    organ: list[str] | None
+    roi_subset: list[str] | None
+    robust_crop: bool
+    body_seg: bool
+    models: list[str] | None
+    force_split: bool
+    overwrite: bool
+    probabilities_path: Path | None
+    source_model_dir: Path
+    output_model_dir: Path
+
+
+def _parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description="Native TotalSegmentator v2 CT inference on Metal")
+    subparsers = parser.add_subparsers(dest="command", required=True)
+    predict = subparsers.add_parser("predict", help="Segment a NIfTI CT on its original grid")
+    predict.add_argument("-i", "--input", dest="input_path", type=Path, required=True)
+    predict.add_argument("-o", "--output", dest="output_path", type=Path, required=True)
+    predict.add_argument("--model-dir", type=Path, required=True)
+    predict.add_argument(
+        "--mode",
+        choices=["standard", *QUALITY_MODELS],
+        default="standard",
+        help="standard: five 1.5 mm parts; fast: 3 mm model; coarse: 6 mm model (upstream fastest)",
+    )
+    predict.add_argument("--model-part", choices=list(MODEL_PARTS))
+    predict.add_argument("--organ", nargs="+", help="Filter canonical organ names after inference")
+    predict.add_argument(
+        "--roi-subset",
+        nargs="+",
+        help="Crop to these structures with a rough 6 mm segmentation and run only their parts",
+    )
+    predict.add_argument(
+        "--robust-crop", action="store_true", help="Locate --roi-subset with the 3 mm model"
+    )
+    predict.add_argument(
+        "--body-seg", action="store_true", help="Crop to the body with the Dataset300 model"
+    )
+    predict.add_argument("--force-split", action="store_true")
+    predict.add_argument("--overwrite", action="store_true")
+    predict.add_argument("--probabilities-path", type=Path)
+    convert = subparsers.add_parser("convert", help="Convert trusted local fold-0 checkpoints")
+    convert.add_argument("--source-model-dir", type=Path, required=True)
+    convert.add_argument("--output-model-dir", type=Path, required=True)
+    convert_models = convert.add_mutually_exclusive_group()
+    convert_models.add_argument("--model-part", choices=[*MODEL_PARTS, *QUALITY_MODELS, "body"])
+    convert_models.add_argument(
+        "--models",
+        nargs="+",
+        choices=[*MODEL_PARTS, *QUALITY_MODELS, "body"],
+        help="Models to convert into one new root (default: the five standard parts)",
+    )
+    subparsers.add_parser("labels", help="Print released global label IDs as JSON")
+    return parser
+
+
+def main(argv: list[str] | None = None) -> None:
+    """Run a subcommand; ``labels`` prints the global ID-to-name table as JSON.
+
+    Exceptions that are ``OSError``, ``ValueError``, ``RuntimeError`` or ``ImportError``
+    (which includes the ``medmlx_core`` errors) are reported on stderr with exit status 2.
+    ``predict`` prints the output path on success and ``convert`` the new model root.
+    """
+    parser = _parser()
+    args = parser.parse_args(argv, namespace=Arguments())
+    if args.command == "labels":
+        print(json.dumps(LABELS, indent=2))
+        return
+    try:
+        if args.command == "convert":
+            from totalsegmentator_mlx.conversion import convert_model
+
+            output = convert_model(
+                args.source_model_dir,
+                args.output_model_dir,
+                model_part=args.model_part,
+                models=args.models,
+            )
+            print(output)
+            return
+        from totalsegmentator_mlx.pipeline import segment
+
+        segment(
+            args.input_path,
+            model_dir=args.model_dir,
+            output_path=args.output_path,
+            mode=cast("Mode", args.mode),
+            model_part=args.model_part,
+            prompt=args.organ,
+            roi_subset=args.roi_subset,
+            robust_crop=args.robust_crop,
+            body_seg=args.body_seg,
+            force_split=args.force_split,
+            overwrite=args.overwrite,
+            probabilities_path=args.probabilities_path,
+            progress=lambda message: print(message, file=sys.stderr, flush=True),
+        )
+        print(args.output_path)
+    except (OSError, ValueError, RuntimeError, ImportError) as error:
+        parser.exit(2, f"{parser.prog}: {error}\n")