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Add scale factor to idealized mesh #5

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Merged
finsberg merged 1 commit into from
Nov 17, 2025
Merged

Add scale factor to idealized mesh #5

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8 changes: 8 additions & 0 deletions src/mri2mesh/mesh/idealized_brain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,6 +144,12 @@ def add_arguments(parser):
action="store_true",
help="Manifold surface",
)
parser.add_argument(
"--scale-factor",
type=float,
default=1.0,
help="Scale factor",
)


def main(
Expand Down Expand Up @@ -171,6 +177,7 @@ def main(
use_floodfill: bool = False,
smooth_open_boundary: bool = False,
manifold_surface: bool = False,
scale_factor: float = 1.0,
) -> None:
logger.info("Generating idealized brain surface")
from ..surface.idealized_brain import main as main_surface
Expand All @@ -189,6 +196,7 @@ def main(
skull_y1=skull_y1,
skull_z0=skull_z0,
skull_z1=skull_z1,
scale_factor=scale_factor,
)
from .basic import create_mesh, CSGTree, convert_mesh_dolfinx

Expand Down
15 changes: 12 additions & 3 deletions src/mri2mesh/surface/idealized_brain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,12 @@ def add_arguments(parser: argparse.ArgumentParser) -> None:
default=0.154949,
help="Skull z1",
)
parser.add_argument(
"--scale-factor",
type=float,
default=1.0,
help="Scale factor",
)


def main(
Expand All @@ -104,6 +110,7 @@ def main(
skull_y1: float = 0.173221,
skull_z0: float = 0.001,
skull_z1: float = 0.154949,
scale_factor: float = 1.0,
) -> None:
import pyvista as pv

Expand All @@ -113,10 +120,10 @@ def main(
z = np.array([0, 0, 1])
skull = pv.Box((skull_x0, skull_x1, skull_y0, skull_y1, skull_z0, skull_z1))
c = skull.center_of_mass()
par = pv.Sphere(r * parenchyma_factor, center=c)
LV = pv.Sphere(r * lv_factor, center=c)
par = pv.Sphere(radius=r * parenchyma_factor, center=c)
LV = pv.Sphere(radius=r * lv_factor, center=c)
V34 = pv.Cylinder(
c - v34_center_factor * r * z,
center=c - v34_center_factor * r * z,
direction=z,
height=r * v34_height_factor,
radius=v34_radius_factor * r,
Expand All @@ -127,6 +134,7 @@ def main(
[V34, LV, par, skull, ventricles],
["V34", "LV", "parenchyma_incl_ventr", "skull", "ventricles"],
):
s.scale(scale_factor, inplace=True)
pv.save_meshio(outdir / f"{n}.ply", s)

from .. import __version__
Expand All @@ -148,6 +156,7 @@ def main(
"skull_z1": skull_z1,
"version": __version__,
"timestamp": datetime.datetime.now().isoformat(),
"scale_factor": scale_factor,
},
indent=2,
)
Expand Down
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