Visualization

This page summarizes the visualization entry points and options. Visualization is one part of the broader swctools toolbox for SWC parsing, modeling, analysis, and geometry.

Global configuration

Use set_config(...) to set defaults for all figures:

from swctools import set_config
set_config(width=800, height=600, force_equal_axes=True, template="plotly_white")

• force_equal_axes ensures identical units along x/y/z (applies aspectmode="data").
• Other options: scene_aspectmode (if you disable force_equal_axes), margins, legend.

Centroid (skeleton)

from swctools import plot_centroid
fig = plot_centroid(gm, show_nodes=True)
fig.show()

Volumetric frusta

from swctools import plot_frusta, FrustaSet
fr = FrustaSet.from_general_model(gm, sides=16, end_caps=False)
fig = plot_frusta(fr, radius_scale=0.8)
fig.show()

Overlay centroid + frusta

from swctools import plot_frusta_with_centroid
fig = plot_frusta_with_centroid(gm, fr, radius_scale=1.0)
fig.show()

Master function: plot_model

from swctools import plot_model

fig = plot_model(
    gm=gm,
    frusta=fr,              # optional; built from gm if omitted
    show_frusta=True,
    show_centroid=True,
    radius_scale=0.8,       # static scale for radii
)
fig.show()

Interactive slider for radius scale

fig = plot_model(
    gm=gm,
    frusta=fr,
    slider=True,            # enables a 0..1 slider by default
    min_scale=0.0,
    max_scale=1.0,
    steps=21,
)
fig.show()

Overlay arbitrary points as spheres (PointSet)

from swctools import PointSet

# Build from a list of xyz points
ps = PointSet.from_points([(0, 0, 0), (3, 0, 0)], base_radius=0.05)
# or from a text file with "x y z" per line (comments starting with '#')
ps = PointSet.from_txt("points.txt", base_radius=0.05)

fig = plot_model(gm=gm, frusta=fr, point_set=ps, point_size=1.5, point_color="crimson")
fig.show()

Notes:

• point_size scales the base_radius uniformly.
• Spheres are low-res by default (stacks=6, slices=12) to keep rendering fast.