polyxios

Fast, clean mesh I/O for Python. Read and write 3D mesh files in one line - no hidden surprises, no silent data corruption.

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Install

pip install polyxios

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Usage

import polyxios as px

# Read any supported format
mesh = px.read("brain.vtk")

# Inspect
print(mesh.vertices.shape)      # (n_verts, 3)
print(len(mesh.element_types))  # number of elements

# Write to a different format
px.write(mesh, "brain.ply")
px.write(mesh, "brain.vtp")

Need binary output or format-specific options?

px.write(mesh, "brain.vtk", binary=True)
px.write(mesh, "brain.ply", binary=True, endian="little")

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Lazy loading - work with large files without filling RAM

For large meshes (gigabytes of binary data), pass lazy=True. polyxios memory-maps the file and only loads the pages you actually touch - the rest stays on disk until needed.

# File is opened but data is not loaded into RAM yet
mesh = px.read("huge_brain.vtk", lazy=True)

# Only the vertices are pulled from disk here
first_vertex = mesh.vertices[0]

# Element connectivity is still on disk until you access it

Lazy loading is supported for binary .vtk, .ply, and .stl files. ASCII formats load eagerly (the whole file must be parsed to extract values). Binary STL lazy mode skips vertex deduplication — vertices are returned as-is (3 per triangle), avoiding the extra pass over the data.

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Supported formats

Format	Extension	Read	Write	Lazy load
VTK Legacy	.vtk	✓	✓	binary only
VTK RectilinearGrid	.vtr	✓	✓	-
VTK PolyData	.vtp	✓	✓	-
Wavefront OBJ	.obj	✓	✓	-
Stanford PLY	.ply	✓	✓	binary only
STL	.stl	✓	✓	binary only
Abaqus	.inp	✓	✓	-
AVS-UCD	.avs	✓	✓	-
Medit binary	.meshb	✓	✓	binary only
DOLFIN/FEniCS XML	.xml	✓	✓	-

10 formats supported - more coming via the plugin system.

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Transforms

from polyxios.transforms import pipeline, merge, filter_element_type, remove_orphan_vertices

# Compose transforms into a single function
clean = pipeline(
    filter_element_type(keep="triangle"),
    remove_orphan_vertices,
)
result = clean(mesh)

# Merge two meshes into one
combined = merge(mesh_a, mesh_b)

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Add your own format

Any third-party package can teach polyxios to read and write a new format - no fork required, no pull request needed.

Step 1 - write a codec (two functions, nothing more):

# mypackage/abc_codec.py
from polyxios._registry import Codec
from polyxios._types import PolyData

def read(path, *, lazy=False) -> PolyData:
    ...

def write(poly: PolyData, path, **opts) -> None:
    ...

def register():
    return ".abc", Codec(read, write)

Step 2 - declare an entry point in your pyproject.toml:

[project.entry-points."polyxios.codecs"]
abc = "mypackage.abc_codec:register"

After pip install mypackage, polyxios picks up .abc automatically - no configuration, no restart needed:

mesh = px.read("model.abc")   # works out of the box

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Contributing / Development

Clone the repo, then use spin to manage the development workflow:

pip install spin
spin setup       # add upstream remote + install dev deps (libomp on macOS)
spin install     # build Cython extensions and install
spin install -e  # editable install (source changes reflected immediately)

Command	Description
spin setup	First-time setup: upstream remote, dev deps, OpenMP on macOS
spin build	Build with Meson/ninja
spin install	Regular install (compiled)
spin install -e	Editable install for development
spin test	Run the full test suite
spin test -k <pattern>	Run tests matching a name pattern
spin lint	ruff linter + formatter check + codespell
spin lint --fix	Auto-fix lint and formatting issues
spin docs	Build Sphinx documentation
spin docs --clean	Wipe _build/ before building
spin docs --open	Build and open docs in the browser
spin clean	Remove build artifacts and __pycache__
spin release <version>	Cut a release: bump version, tag, push, start next dev cycle

See docs/contributing.rst for commit message conventions and the full contributor guide. For the full release workflow see docs/development.rst.

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Why polyxios?

• No silent data corruption - large mesh indices raise an error instead of truncating
• All element groups preserved - a face belonging to multiple tags stays in all of them
• Safe on untrusted files - header counts validated before any memory allocation
• Memory-efficient - lazy mmap loading for large binary files
• Works without a compiler - pure Python fallbacks included; Cython hot-paths optional

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License

See LICENSE.