swctools

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.

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