kneemesh 0.1.0__tar.gz

kneemesh-0.1.0/LICENSE

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kneemesh-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: kneemesh
+Version: 0.1.0
+Summary: B-rep geometry and meshes of knee structures from segmented images
+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
+
+# kneemesh
+
+[![PyPI](https://img.shields.io/pypi/v/kneemesh)](https://pypi.org/project/kneemesh/)
+[![Coverage](https://img.shields.io/endpoint?url=https://comporthobiomech.github.io/kneemesh/coverage.json)](https://github.com/CompOrthoBiomech/kneemesh/actions/workflows/release.yml)
+[![Docs](https://img.shields.io/badge/docs-gh--pages-blue)](https://comporthobiomech.github.io/kneemesh/)
+
+Generate B-rep geometry of knee structures from a segmentation LabelMap, and mesh it with high-quality elements. The meniscus is supported now; lateral and medial tibial, femoral, and patellar cartilage and the bones are planned. For the meniscus:
+
+- **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/kneemesh/>
+
+## Installation
+
+```sh
+pip install kneemesh
+```
+
+## Usage
+
+Two command-line pipelines take the structure as their first argument, then a JSON configuration, `--option value` overrides, or both. Run `kneemesh-brep meniscus --help` to list every option and its default.
+
+```sh
+kneemesh-brep meniscus --label-map knee.nii --output meniscus.brep --cap planar
+kneemesh-mesh meniscus --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).

kneemesh-0.1.0/README.md

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+# kneemesh
+
+[![PyPI](https://img.shields.io/pypi/v/kneemesh)](https://pypi.org/project/kneemesh/)
+[![Coverage](https://img.shields.io/endpoint?url=https://comporthobiomech.github.io/kneemesh/coverage.json)](https://github.com/CompOrthoBiomech/kneemesh/actions/workflows/release.yml)
+[![Docs](https://img.shields.io/badge/docs-gh--pages-blue)](https://comporthobiomech.github.io/kneemesh/)
+
+Generate B-rep geometry of knee structures from a segmentation LabelMap, and mesh it with high-quality elements. The meniscus is supported now; lateral and medial tibial, femoral, and patellar cartilage and the bones are planned. For the meniscus:
+
+- **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/kneemesh/>
+
+## Installation
+
+```sh
+pip install kneemesh
+```
+
+## Usage
+
+Two command-line pipelines take the structure as their first argument, then a JSON configuration, `--option value` overrides, or both. Run `kneemesh-brep meniscus --help` to list every option and its default.
+
+```sh
+kneemesh-brep meniscus --label-map knee.nii --output meniscus.brep --cap planar
+kneemesh-mesh meniscus --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).

kneemesh-0.1.0/pyproject.toml

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+[project]
+name = "kneemesh"
+version = "0.1.0"
+description = "B-rep geometry and meshes of knee structures from segmented images"
+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]
+kneemesh-brep = "kneemesh.pipeline:brep_main"
+kneemesh-mesh = "kneemesh.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"]

kneemesh-0.1.0/src/kneemesh/__init__.py

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+"""kneemesh: B-rep geometry and meshes of knee structures from segmented images."""
+
+from importlib.metadata import version
+
+from loguru import logger
+
+__version__ = version("kneemesh")
+
+# A library stays silent unless its user opts in with logger.enable("kneemesh").
+logger.disable("kneemesh")

kneemesh-0.1.0/src/kneemesh/brep.py

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+"""B-rep values, gmsh sessions, and B-spline construction shared by every structure."""
+
+import tempfile
+import uuid
+from collections.abc import Iterator
+from contextlib import contextmanager
+from dataclasses import dataclass
+from itertools import pairwise
+from pathlib import Path
+
+import gmsh
+import numpy as np
+from loguru import logger
+from scipy.interpolate import BSpline, make_interp_spline
+from vtkmodules.util.numpy_support import numpy_to_vtk
+from vtkmodules.vtkCommonCore import vtkPoints
+from vtkmodules.vtkCommonDataModel import vtkCellArray, vtkPolyData, vtkPolyLine
+
+from kneemesh.vol import ContourSlice
+
+MAX_SPLINE_ORDER = 25  # Open Cascade's limit on B-spline degree.
+
+
+@dataclass(frozen=True)
+class BRep:
+    """A B-rep shape held as the text of an Open Cascade .brep file."""
+
+    text: str
+
+
+@contextmanager
+def gmsh_session() -> Iterator[None]:
+    """Run a block on a temporary gmsh model, leaving gmsh as it was found."""
+    owns_gmsh = not gmsh.isInitialized()
+    if owns_gmsh:
+        gmsh.initialize(readConfigFiles=False, interruptible=False)
+        gmsh.option.setNumber("General.Terminal", 0)
+    previous_model = gmsh.model.getCurrent()
+    gmsh.model.add(f"kneemesh-{uuid.uuid4().hex}")
+    try:
+        yield
+    finally:
+        gmsh.model.remove()
+        if owns_gmsh:
+            gmsh.finalize()
+        else:
+            gmsh.model.setCurrent(previous_model)
+
+
+def export_brep() -> BRep:
+    """Return the current gmsh model's highest-dimension shapes as a BRep. Call inside gmsh_session."""
+    with tempfile.TemporaryDirectory() as directory:
+        path = Path(directory) / "shape.brep"
+        gmsh.write(str(path))
+        text = path.read_text(encoding="utf-8")
+    counts = [len(gmsh.model.getEntities(dim)) for dim in range(4)]
+    logger.debug("B-rep has {} vertices, {} edges, {} faces, and {} volumes ({} kB)", *counts, len(text) // 1024)
+    return BRep(text)
+
+
+def chord_parameters(points: np.ndarray) -> np.ndarray:
+    """Return parameters from 0 to 1 proportional to chord length around a closed contour, ending at the repeated first point."""
+    closed = np.vstack((points, points[:1]))
+    lengths = np.concatenate(([0.0], np.cumsum(np.linalg.norm(np.diff(closed, axis=0), axis=1))))
+    return lengths / lengths[-1]
+
+
+def periodic_spline(points: np.ndarray, spline_order: int) -> BSpline:
+    """Return a periodic B-spline through points, over parameters 0 to 1 proportional to chord length."""
+    return make_interp_spline(chord_parameters(points), np.vstack((points, points[:1])), k=spline_order, bc_type="periodic")
+
+
+def open_chord_parameters(points: np.ndarray) -> np.ndarray:
+    """Return parameters from 0 to 1 proportional to chord length along an open sequence of points."""
+    lengths = np.concatenate(([0.0], np.cumsum(np.linalg.norm(np.diff(points, axis=0), axis=1))))
+    return lengths / lengths[-1]
+
+
+def clamped_interpolation(parameters: np.ndarray, points: np.ndarray, degree: int) -> tuple[np.ndarray, np.ndarray]:
+    """Return the knots and poles of a clamped B-spline through points at parameters.
+
+    Averaged knots make this work at any degree. Both ends are pinned to the
+    exact end points, so curves fitted to the same end points meet exactly.
+    """
+    if degree == 1:
+        knots = np.concatenate(([parameters[0]], parameters, [parameters[-1]]))
+    else:
+        interior = [parameters[index + 1 : index + degree + 1].mean() for index in range(len(parameters) - degree - 1)]
+        knots = np.concatenate(([parameters[0]] * (degree + 1), interior, [parameters[-1]] * (degree + 1)))
+    poles = np.array(make_interp_spline(parameters, points, k=degree, t=knots).c)
+    poles[0], poles[-1] = points[0], points[-1]
+    return knots, poles
+
+
+def add_bspline_curve(knots: np.ndarray, poles: np.ndarray, degree: int) -> int:
+    """Add an open B-spline curve from scipy-style full knots and poles, returning its tag."""
+    unique_knots, multiplicities = np.unique(knots, return_counts=True)
+    tags = [gmsh.model.occ.addPoint(*pole.tolist()) for pole in poles]
+    return gmsh.model.occ.addBSpline(tags, degree=degree, knots=unique_knots.tolist(), multiplicities=multiplicities.tolist())
+
+
+def add_swept_surface(rows: list[tuple[np.ndarray, np.ndarray]], degree: int, along: np.ndarray, along_degree: int) -> int:
+    """Add a B-spline surface through section curves sharing one knot vector, returning its tag.
+
+    Each column of poles is interpolated along the curve at the same
+    parameters, so a surface's edge depends only on that edge's points and
+    matches its neighbor's exactly.
+    """
+    knots = rows[0][0]
+    grid = np.array([poles for _, poles in rows])
+    columns = [clamped_interpolation(along, grid[:, column], along_degree) for column in range(grid.shape[1])]
+    along_knots = columns[0][0]
+    poles = np.stack([column_poles for _, column_poles in columns], axis=1)
+    unique_knots, multiplicities = np.unique(knots, return_counts=True)
+    unique_along, along_multiplicities = np.unique(along_knots, return_counts=True)
+    return gmsh.model.occ.addBSplineSurface(
+        [gmsh.model.occ.addPoint(*pole.tolist()) for row in poles for pole in row],
+        poles.shape[1],
+        degreeU=degree,
+        degreeV=along_degree,
+        knotsU=unique_knots.tolist(),
+        knotsV=unique_along.tolist(),
+        multiplicitiesU=multiplicities.tolist(),
+        multiplicitiesV=along_multiplicities.tolist(),
+    )
+
+
+def periodic_poles_and_knots(spline: BSpline, point_count: int) -> tuple[np.ndarray, list[float]]:
+    """Return a periodic spline's poles and knots as Open Cascade takes them."""
+    # Scipy repeats the first poles at the end of its coefficients and pads its
+    # knots on both sides. Open Cascade takes each only once.
+    return spline.c[:point_count], spline.t[spline.k : len(spline.t) - spline.k].tolist()
+
+
+def add_closed_wire(spline: BSpline, point_count: int) -> int:
+    """Add a closed wire of one periodic B-spline, returning its tag."""
+    poles, knots = periodic_poles_and_knots(spline, point_count)
+    # Repeating the first tag is how gmsh is told the curve is periodic.
+    curve = gmsh.model.occ.addBSpline(add_closed_points(poles), degree=spline.k, knots=knots, multiplicities=[1] * len(knots))
+    return gmsh.model.occ.addWire([curve], checkClosed=True)
+
+
+def split_periodic_spline(spline: BSpline, parameters: np.ndarray) -> list[BSpline]:
+    """Split a periodic spline exactly into clamped splines at parameters.
+
+    parameters must be sorted, distinct, and start at 0, so the last piece ends at 1.
+    """
+    degree = spline.k
+    splits = [float(parameter) for parameter in parameters] + [1.0]
+
+    # Raising a knot's multiplicity to the degree makes the curve pass through
+    # a pole there, so the poles between two such knots define that piece alone.
+    refined = BSpline(spline.t, spline.c, degree)
+    for split in splits:
+        missing = degree - int(np.sum(refined.t == split))
+        if missing > 0:
+            refined = refined.insert_knot(split, missing)
+    # Index from a start knot's last copy and an end knot's first, which also
+    # holds where scipy clamps the ends of a degree 1 spline instead of padding.
+    pieces = []
+    for start, end in pairwise(splits):
+        after_start = int(np.flatnonzero(refined.t == start)[-1]) + 1
+        at_end = int(np.flatnonzero(refined.t == end)[0])
+        knots = np.concatenate(([start] * (degree + 1), refined.t[after_start:at_end], [end] * (degree + 1)))
+        pieces.append(BSpline(knots, refined.c[after_start - 1 - degree : at_end], degree))
+    return pieces
+
+
+def add_closed_points(poles: np.ndarray) -> list[int]:
+    """Add a point per pole, returning their tags with the first repeated at the end.
+
+    gmsh treats a B-spline whose first and last point tags match as periodic.
+    """
+    tags = [gmsh.model.occ.addPoint(*pole.tolist()) for pole in poles]
+    return [*tags, tags[0]]
+
+
+def contours_to_polydata(slices: list[ContourSlice]) -> vtkPolyData:
+    """Assemble contour slices into a single poly data of closed polylines.
+
+    Args:
+        slices: Contours from slice_isocontour.
+
+    Returns:
+        A vtkPolyData with one vtkPolyLine per slice, in the order given. Each
+        polyline ends on its own first point id to close the contour, so no
+        point is duplicated.
+
+    Raises:
+        ValueError: If slices is empty.
+    """
+    if not slices:
+        raise ValueError("No contour slices to assemble")
+
+    points = vtkPoints()
+    points.SetData(numpy_to_vtk(np.vstack([contour.points for contour in slices]), deep=True))
+
+    lines = vtkCellArray()
+    first_id = 0
+    for contour in slices:
+        count = len(contour.points)
+        polyline = vtkPolyLine()
+        ids = polyline.GetPointIds()
+        ids.SetNumberOfIds(count + 1)
+        for index in range(count):
+            ids.SetId(index, first_id + index)
+        ids.SetId(count, first_id)
+        lines.InsertNextCell(polyline)
+        first_id += count
+
+    poly_data = vtkPolyData()
+    poly_data.SetPoints(points)
+    poly_data.SetLines(lines)
+    return poly_data