meniscus2brep 0.1.0__tar.gz

meniscus2brep-0.1.0/LICENSE

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meniscus2brep-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: meniscus2brep
+Version: 0.1.0
+Summary: Convert meniscus images to B-rep geometry
+Author: Scott Sibole
+Author-email: Scott Sibole <scott.sibole@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Requires-Dist: gmsh>=4.15.2
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: numpy>=2.5.4
+Requires-Dist: pydantic>=2.14.3
+Requires-Dist: scipy>=1.18.1
+Requires-Dist: simpleitk>=2.5.7
+Requires-Dist: vtk>=9.7.2
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+
+# meniscus2brep
+
+[![PyPI](https://img.shields.io/pypi/v/meniscus2brep)](https://pypi.org/project/meniscus2brep/)
+[![Coverage](https://img.shields.io/endpoint?url=https://comporthobiomech.github.io/meniscus2brep/coverage.json)](https://github.com/CompOrthoBiomech/meniscus2brep/actions/workflows/release.yml)
+[![Docs](https://img.shields.io/badge/docs-gh--pages-blue)](https://comporthobiomech.github.io/meniscus2brep/)
+
+Generate B-rep geometry of a meniscus from a segmentation LabelMap, and mesh it with high-quality elements:
+
+- **B-rep from segmentation labels.** Reads a LabelMap (`.nii`, `.nrrd`, or `.mhd`), fits a centerline through the labeled meniscus, slices its smoothed surface into cross-section contours, and lofts them into a solid B-spline B-rep (`.brep`) with planar or smooth end caps.
+- **Tetrahedral meshing** with linear 4-node or quadratic 10-node tetrahedra.
+- **Hexahedral meshing** with block-structured 8-node, 20-node, or 27-node hexahedra. The solid is split into a butterfly (O-grid) of five blocks, so elements stay well shaped at the meniscus's sharp corners.
+
+Meshes are written in any format gmsh infers from the file extension, such as `.msh`, `.vtk`, or `.inp`.
+
+**Documentation:** <https://comporthobiomech.github.io/meniscus2brep/>
+
+## Installation
+
+```sh
+pip install meniscus2brep
+```
+
+## Usage
+
+Two command-line pipelines take a JSON configuration, `--option value` overrides, or both. Run either with `--help` to list every option and its default.
+
+```sh
+meniscus2brep-brep --label-map knee.nii --output meniscus.brep --cap planar
+meniscus2brep-mesh --brep meniscus.brep --output meniscus.msh --max-size 1.0
+```
+
+Each run saves the configuration it used, so it can be repeated with `--config`. Without `--config` it is saved as `settings<timestamp>.json` in the working directory. With `--config` and overrides, the changed configuration is saved beside the original as `<name>_modified.json`.
+
+### Element types
+
+| Elements | B-rep options | Mesh options |
+|---|---|---|
+| 4-node tetrahedra | | `--element tetrahedral` (the default) |
+| 10-node tetrahedra | | `--element tetrahedral --element-order 2` |
+| 8-node hexahedra | `--hex-blocks true --points-per-slice 10` | `--element hexahedral` |
+| 20-node hexahedra | `--hex-blocks true --points-per-slice 10` | `--element hexahedral --element-order 2 --second-order-incomplete true` |
+| 27-node hexahedra | `--hex-blocks true --points-per-slice 10` | `--element hexahedral --element-order 2` |
+
+## Development
+
+Requires [uv](https://docs.astral.sh/uv/).
+
+```sh
+uv sync
+uv run pytest
+```
+
+Build the documentation into `docs/_build/html`:
+
+```sh
+uv run --group docs sphinx-build -W -b html docs docs/_build/html
+```
+
+## License
+
+Licensed under the [Apache License 2.0](LICENSE).

meniscus2brep-0.1.0/README.md

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+# meniscus2brep
+
+[![PyPI](https://img.shields.io/pypi/v/meniscus2brep)](https://pypi.org/project/meniscus2brep/)
+[![Coverage](https://img.shields.io/endpoint?url=https://comporthobiomech.github.io/meniscus2brep/coverage.json)](https://github.com/CompOrthoBiomech/meniscus2brep/actions/workflows/release.yml)
+[![Docs](https://img.shields.io/badge/docs-gh--pages-blue)](https://comporthobiomech.github.io/meniscus2brep/)
+
+Generate B-rep geometry of a meniscus from a segmentation LabelMap, and mesh it with high-quality elements:
+
+- **B-rep from segmentation labels.** Reads a LabelMap (`.nii`, `.nrrd`, or `.mhd`), fits a centerline through the labeled meniscus, slices its smoothed surface into cross-section contours, and lofts them into a solid B-spline B-rep (`.brep`) with planar or smooth end caps.
+- **Tetrahedral meshing** with linear 4-node or quadratic 10-node tetrahedra.
+- **Hexahedral meshing** with block-structured 8-node, 20-node, or 27-node hexahedra. The solid is split into a butterfly (O-grid) of five blocks, so elements stay well shaped at the meniscus's sharp corners.
+
+Meshes are written in any format gmsh infers from the file extension, such as `.msh`, `.vtk`, or `.inp`.
+
+**Documentation:** <https://comporthobiomech.github.io/meniscus2brep/>
+
+## Installation
+
+```sh
+pip install meniscus2brep
+```
+
+## Usage
+
+Two command-line pipelines take a JSON configuration, `--option value` overrides, or both. Run either with `--help` to list every option and its default.
+
+```sh
+meniscus2brep-brep --label-map knee.nii --output meniscus.brep --cap planar
+meniscus2brep-mesh --brep meniscus.brep --output meniscus.msh --max-size 1.0
+```
+
+Each run saves the configuration it used, so it can be repeated with `--config`. Without `--config` it is saved as `settings<timestamp>.json` in the working directory. With `--config` and overrides, the changed configuration is saved beside the original as `<name>_modified.json`.
+
+### Element types
+
+| Elements | B-rep options | Mesh options |
+|---|---|---|
+| 4-node tetrahedra | | `--element tetrahedral` (the default) |
+| 10-node tetrahedra | | `--element tetrahedral --element-order 2` |
+| 8-node hexahedra | `--hex-blocks true --points-per-slice 10` | `--element hexahedral` |
+| 20-node hexahedra | `--hex-blocks true --points-per-slice 10` | `--element hexahedral --element-order 2 --second-order-incomplete true` |
+| 27-node hexahedra | `--hex-blocks true --points-per-slice 10` | `--element hexahedral --element-order 2` |
+
+## Development
+
+Requires [uv](https://docs.astral.sh/uv/).
+
+```sh
+uv sync
+uv run pytest
+```
+
+Build the documentation into `docs/_build/html`:
+
+```sh
+uv run --group docs sphinx-build -W -b html docs docs/_build/html
+```
+
+## License
+
+Licensed under the [Apache License 2.0](LICENSE).

meniscus2brep-0.1.0/pyproject.toml

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+[project]
+name = "meniscus2brep"
+version = "0.1.0"
+description = "Convert meniscus images to B-rep geometry"
+readme = "README.md"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Scott Sibole", email = "scott.sibole@gmail.com" }
+]
+requires-python = ">=3.13"
+dependencies = [
+    "gmsh>=4.15.2",
+    "loguru>=0.7.3",
+    "numpy>=2.5.4",
+    "pydantic>=2.14.3",
+    "scipy>=1.18.1",
+    "simpleitk>=2.5.7",
+    "vtk>=9.7.2",
+]
+
+[project.scripts]
+meniscus2brep-brep = "meniscus2brep.pipeline:brep_main"
+meniscus2brep-mesh = "meniscus2brep.pipeline:mesh_main"
+
+[build-system]
+requires = ["uv_build>=0.8.13,<0.9.0"]
+build-backend = "uv_build"
+
+[dependency-groups]
+dev = [
+    "pytest>=9.2.0",
+    "pytest-cov>=7.1.0",
+]
+docs = [
+    "autodoc-pydantic>=2.2.0",
+    "furo>=2025.12.19",
+    "myst-parser>=5.2.0",
+    "sphinx>=9.2.0",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = ["--import-mode=importlib"]

meniscus2brep-0.1.0/src/meniscus2brep/__init__.py

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+"""meniscus2brep."""
+
+from importlib.metadata import version
+
+from loguru import logger
+
+__version__ = version("meniscus2brep")
+
+# A library stays silent unless its user opts in with logger.enable("meniscus2brep").
+logger.disable("meniscus2brep")

meniscus2brep-0.1.0/src/meniscus2brep/config.py

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+"""Configuration models and parsing them from JSON."""
+
+from os import PathLike
+from pathlib import Path
+from typing import Annotated, Any, Literal, Self
+
+from pydantic import BaseModel, BeforeValidator, ConfigDict, Field
+
+from meniscus2brep.mesh import Algorithm2D, Algorithm3D
+from meniscus2brep.vol import DEFAULT_SMOOTHING_ITERATIONS, DEFAULT_SMOOTHING_PASS_BAND
+
+
+class BaseConfig(BaseModel):
+    """Base class for configuration models.
+
+    Unknown fields are rejected so that misspelled options fail at load time
+    instead of being silently ignored.
+    """
+
+    model_config = ConfigDict(extra="forbid")
+
+    @classmethod
+    def from_json(cls, path: str | PathLike[str]) -> Self:
+        """Parse and validate a configuration from a JSON file."""
+        return cls.model_validate_json(Path(path).read_bytes())
+
+
+def _none_from_text(value: Any) -> Any:
+    """Read "none" or "null" as None, so command-line overrides can clear optional values."""
+    return None if isinstance(value, str) and value.strip().lower() in ("none", "null") else value
+
+
+OptionalFloat = Annotated[float | None, BeforeValidator(_none_from_text)]
+
+
+class BrepConfig(BaseConfig):
+    """Settings for building a B-rep from a segmented LabelMap, with the defaults of each step."""
+
+    label_map: Path = Field(default=Path("label_map.nii"), description="LabelMap to read: .nii, .nrrd, or .mhd")
+    output: Path = Field(default=Path("meniscus.brep"), description="B-rep file to write")
+    label: int = Field(default=1, description="Value of the meniscus in the LabelMap")
+    sigma: OptionalFloat = Field(
+        default=None,
+        description="Gaussian smoothing of the distance field in physical units. None spans 3 voxel edges per axis, 0 disables",
+    )
+    level: float = Field(default=0.0, description="Distance of the surface from the label boundary; positive is outside")
+    smoothing_iterations: int = Field(
+        default=DEFAULT_SMOOTHING_ITERATIONS, ge=0, description="Windowed sinc smoothing iterations on the surface before slicing; 0 disables"
+    )
+    smoothing_pass_band: float = Field(
+        default=DEFAULT_SMOOTHING_PASS_BAND, gt=0, le=2, description="Windowed sinc pass band in (0, 2]; lower smooths and shrinks more"
+    )
+    spacing: float = Field(default=5.0, description="Arc-length distance between slices along the centerline, in physical units")
+    points_per_slice: int = Field(default=32, description="Points on each slice contour. Use about 10 for hexahedral blocks")
+    spline_order: int = Field(default=3, description="Polynomial degree of the B-spline geometry")
+    cap: Literal["none", "planar", "smooth"] = Field(default="planar", description="How to close the ends; ignored for hexahedral blocks")
+    cap_offset: OptionalFloat = Field(
+        default=None, description="Apex offset of smooth caps in physical units. None is a quarter of the equivalent radius"
+    )
+    hex_blocks: bool = Field(default=False, description="Build the five-block butterfly solid with planar caps that hexahedral meshing needs")
+
+
+class MeshConfig(BaseConfig):
+    """Settings for meshing a B-rep, with the defaults of each meshing function."""
+
+    brep: Path = Field(default=Path("meniscus.brep"), description="B-rep file to read")
+    output: Path = Field(default=Path("meniscus.msh"), description="Mesh file to write; gmsh infers the format from the extension")
+    element: Literal["tetrahedral", "hexahedral"] = Field(
+        default="tetrahedral", description="Element shape. Hexahedral needs a B-rep built with hex_blocks"
+    )
+    element_order: int = Field(default=1, description="Polynomial order of the elements")
+    second_order_incomplete: bool = Field(default=False, description="Omit face and interior nodes from high-order elements")
+    min_size: float = Field(default=0.0, description="Smallest tetrahedron size in physical units")
+    max_size: OptionalFloat = Field(default=None, description="Largest tetrahedron size in physical units. None lets gmsh choose")
+    elements_per_circle: int = Field(default=0, description="Tetrahedra per circle of surface curvature; 0 disables curvature sizing")
+    algorithm_2d: Algorithm2D = Field(default=Algorithm2D.FRONTAL_DELAUNAY, description="gmsh surface algorithm for tetrahedral meshing")
+    algorithm_3d: Algorithm3D = Field(default=Algorithm3D.DELAUNAY, description="gmsh volume algorithm for tetrahedral meshing")
+    elements_per_edge: int = Field(default=4, description="Hexahedra along each edge of a cap")
+    elements_along: int = Field(default=20, description="Hexahedra along the solid between the caps")

meniscus2brep-0.1.0/src/meniscus2brep/disk.py

@@ -0,0 +1,160 @@
+"""Reading and writing LabelMaps as .nii, .nrrd, or .mhd + .raw, poly data as .vtp, and B-reps as .brep, and writing meshes."""
+
+from os import PathLike
+from pathlib import Path
+
+import gmsh
+import numpy as np
+import SimpleITK as sitk
+from loguru import logger
+from vtkmodules.vtkCommonDataModel import vtkPolyData
+from vtkmodules.vtkIOXML import vtkXMLPolyDataReader, vtkXMLPolyDataWriter
+
+from meniscus2brep.geo import BRep, gmsh_session
+from meniscus2brep.mesh import Mesh
+from meniscus2brep.vol import LABEL_MAP_PIXEL_IDS
+
+SUPPORTED_SUFFIXES = frozenset({".nii", ".nrrd", ".mhd"})
+POLY_DATA_SUFFIXES = frozenset({".vtp"})
+BREP_SUFFIXES = frozenset({".brep"})
+
+
+def read_label_map(path: str | PathLike[str]) -> sitk.Image:
+    """Read a segmented LabelMap from disk.
+
+    For a .mhd file, the .raw file it references must also exist.
+
+    Raises:
+        ValueError: If the file format is unsupported or the image is not
+            sitkUInt8, sitkUInt16, or sitkInt16.
+    """
+    path = _validated_path(path)
+    image = sitk.ReadImage(str(path))
+    _require_label_map(image)
+    logger.debug("Read {} LabelMap of size {} and spacing {} from {}", image.GetPixelIDTypeAsString(), image.GetSize(), image.GetSpacing(), path)
+    return image
+
+
+def write_label_map(image: sitk.Image, path: str | PathLike[str]) -> None:
+    """Write a segmented LabelMap to disk, overwriting any existing file.
+
+    A .mhd path also writes a .raw file alongside it.
+
+    Raises:
+        ValueError: If the file format is unsupported or the image is not
+            sitkUInt8, sitkUInt16, or sitkInt16.
+    """
+    path = _validated_path(path)
+    _require_label_map(image)
+    sitk.WriteImage(image, str(path), useCompression=False)
+
+
+def read_poly_data(path: str | PathLike[str]) -> vtkPolyData:
+    """Read poly data from a VTK XML .vtp file.
+
+    Raises:
+        ValueError: If the suffix is not .vtp or the file is not VTK XML poly data.
+        FileNotFoundError: If the file does not exist.
+    """
+    path = _validated_path(path, POLY_DATA_SUFFIXES)
+    if not path.is_file():
+        raise FileNotFoundError(f"No such file: {path}")
+
+    # The reader logs failures and returns empty output without any error state.
+    reader = vtkXMLPolyDataReader()
+    if not reader.CanReadFile(str(path)):
+        raise ValueError(f"Not a VTK XML poly data file: {path}")
+    reader.SetFileName(str(path))
+    reader.Update()
+    return reader.GetOutput()
+
+
+def write_poly_data(poly_data: vtkPolyData, path: str | PathLike[str]) -> None:
+    """Write poly data to a VTK XML .vtp file, overwriting any existing file.
+
+    Raises:
+        ValueError: If the suffix is not .vtp.
+        OSError: If the file cannot be written.
+    """
+    path = _validated_path(path, POLY_DATA_SUFFIXES)
+
+    writer = vtkXMLPolyDataWriter()
+    writer.SetFileName(str(path))
+    writer.SetInputData(poly_data)
+    if not writer.Write():
+        raise OSError(f"Could not write poly data to {path}")
+
+
+def read_brep(path: str | PathLike[str]) -> BRep:
+    """Read a B-rep from an Open Cascade .brep file.
+
+    Raises:
+        ValueError: If the suffix is not .brep or the file holds no valid shape.
+        FileNotFoundError: If the file does not exist.
+    """
+    path = _validated_path(path, BREP_SUFFIXES)
+    if not path.is_file():
+        raise FileNotFoundError(f"No such file: {path}")
+
+    with gmsh_session():
+        try:
+            shapes = gmsh.model.occ.importShapes(str(path))
+        except Exception as error:  # gmsh raises only the bare Exception type.
+            raise ValueError(f"Not a valid B-rep file: {path}") from error
+    if not shapes:
+        raise ValueError(f"Not a valid B-rep file: {path}")
+    return BRep(path.read_text(encoding="utf-8"))
+
+
+def write_brep(brep: BRep, path: str | PathLike[str]) -> None:
+    """Write a B-rep to an Open Cascade .brep file, overwriting any existing file.
+
+    Raises:
+        ValueError: If the suffix is not .brep.
+        OSError: If the file cannot be written.
+    """
+    path = _validated_path(path, BREP_SUFFIXES)
+    path.write_text(brep.text, encoding="utf-8")
+    logger.debug("Wrote B-rep to {}", path)
+
+
+def write_mesh(mesh: Mesh, path: str | PathLike[str]) -> None:
+    """Write a mesh in the format gmsh infers from the extension, overwriting any existing file.
+
+    Volume formats include .msh, .vtk, .inp, .unv, .bdf, .med, .mesh, and
+    .su2. The mesh has only volume elements, so surface formats such as .stl
+    hold no elements.
+
+    Raises:
+        ValueError: If gmsh does not recognize the extension.
+        OSError: If the file cannot be written.
+    """
+    path = Path(path)
+    with gmsh_session():
+        volume = gmsh.model.addDiscreteEntity(3)
+        gmsh.model.mesh.addNodes(3, volume, np.arange(1, len(mesh.nodes) + 1).tolist(), mesh.nodes.ravel().tolist())
+        first_tag = 1
+        for name, connectivity in mesh.elements.items():
+            element_tags = np.arange(first_tag, first_tag + len(connectivity))
+            gmsh.model.mesh.addElementsByType(volume, mesh.element_types[name], element_tags.tolist(), (connectivity + 1).ravel().tolist())
+            first_tag += len(connectivity)
+        try:
+            gmsh.write(str(path))
+        except Exception as error:  # gmsh raises only the bare Exception type.
+            if "Unknown output file format" in str(error):
+                raise ValueError(f"gmsh cannot write meshes in the format of {path.name!r}") from error
+            raise OSError(f"Could not write mesh to {path}") from error
+    logger.debug("Wrote mesh to {}", path)
+
+
+def _validated_path(path: str | PathLike[str], suffixes: frozenset[str] = SUPPORTED_SUFFIXES) -> Path:
+    path = Path(path)
+    if path.suffix.lower() not in suffixes:
+        supported = ", ".join(sorted(suffixes))
+        raise ValueError(f"Unsupported file format {path.name!r}; expected one of: {supported}")
+    return path
+
+
+def _require_label_map(image: sitk.Image) -> None:
+    if image.GetPixelID() not in LABEL_MAP_PIXEL_IDS:
+        raise ValueError(f"LabelMap must be sitkUInt8, sitkUInt16, or sitkInt16, got {image.GetPixelIDTypeAsString()}")