Muscle Fiber Workflow¶

Load the synthetic rectus_femoris dataset, inspect its fiber-direction vector field, and export line glyphs for visualization in ParaView/OpenSim.

In [ ]:

import numpy as np

from pyfieldml import datasets

doc = datasets.load_rectus_femoris()
print("Region:", doc.region.name)

import numpy as np from pyfieldml import datasets doc = datasets.load_rectus_femoris() print("Region:", doc.region.name)

Inspect the fiber field¶

In [ ]:

fibers = doc.evaluators["fiber_direction"]
fv = fibers.as_ndarray()
print("fiber vectors shape:", fv.shape)
print("norm check:", np.allclose(np.linalg.norm(fv, axis=1), 1.0, atol=1e-6))
print("dominant axis (argmax of |component|):")
print("  axis count:", np.bincount(np.argmax(np.abs(fv), axis=1), minlength=3))

fibers = doc.evaluators["fiber_direction"] fv = fibers.as_ndarray() print("fiber vectors shape:", fv.shape) print("norm check:", np.allclose(np.linalg.norm(fv, axis=1), 1.0, atol=1e-6)) print("dominant axis (argmax of |component|):") print(" axis count:", np.bincount(np.argmax(np.abs(fv), axis=1), minlength=3))

Export fiber glyphs as VTK¶

export_fiber_lines writes a short line segment at each node along the fiber direction. Open the result in ParaView to see the fiber arrangement.

In [ ]:

import tempfile
from pathlib import Path

from pyfieldml.interop.opensim import export_fiber_lines

out_dir = Path(tempfile.mkdtemp(prefix="rectus_"))
out = export_fiber_lines(
    doc,
    field="fiber_direction",
    out_path=out_dir / "fibers.vtu",
    length_scale=0.01,
)
print("wrote", out, f"({out.stat().st_size} bytes)")

import tempfile from pathlib import Path from pyfieldml.interop.opensim import export_fiber_lines out_dir = Path(tempfile.mkdtemp(prefix="rectus_")) out = export_fiber_lines( doc, field="fiber_direction", out_path=out_dir / "fibers.vtu", length_scale=0.01, ) print("wrote", out, f"({out.stat().st_size} bytes)")

Licensing note¶

The bundled rectus_femoris dataset is a synthetic spindle shape authored for demonstration (CC0). Real Physiome-project muscle meshes require separate licensing; see the datasets.info('rectus_femoris') metadata.