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How to make 3D Isosurface Plots in Python with Plotly.
3d_charts
python
base
3D Isosurface Plots
10
u-guide
python/3d-isosurface-plots/
python/isosurfaces-with-marching-cubes/
thumbnail/isosurface.jpg

With go.Isosurface, you can plot isosurface contours of a scalar field value, which is defined on x, y and z coordinates.

Basic Isosurface

In this first example, we plot the isocontours of values isomin=2 and isomax=6. In addition, portions of the sides of the coordinate domains for which the value is between isomin and isomax (named the caps) are colored. Please rotate the figure to visualize both the internal surfaces and the caps surfaces on the sides.

import plotly.graph_objects as go

fig= go.Figure(data=go.Isosurface(
    x=[0,0,0,0,1,1,1,1],
    y=[1,0,1,0,1,0,1,0],
    z=[1,1,0,0,1,1,0,0],
    value=[1,2,3,4,5,6,7,8],
    isomin=2,
    isomax=6,
))

fig.show()

Removing caps when visualizing isosurfaces

For a clearer visualization of internal surfaces, it is possible to remove the caps (color-coded surfaces on the sides of the visualization domain). Caps are visible by default.

import plotly.graph_objects as go
import numpy as np

X, Y, Z = np.mgrid[-5:5:40j, -5:5:40j, -5:5:40j]

# ellipsoid
values = X * X * 0.5 + Y * Y + Z * Z * 2

fig = go.Figure(data=go.Isosurface(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    isomin=10,
    isomax=40,
    caps=dict(x_show=False, y_show=False)
    ))
fig.show()

Modifying the number of isosurfaces

import plotly.graph_objects as go
import numpy as np

X, Y, Z = np.mgrid[-5:5:40j, -5:5:40j, -5:5:40j]

# ellipsoid
values = X * X * 0.5 + Y * Y + Z * Z * 2

fig = go.Figure(data=go.Isosurface(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    isomin=10,
    isomax=50,
    surface_count=5, # number of isosurfaces, 2 by default: only min and max
    colorbar_nticks=5, # colorbar ticks correspond to isosurface values
    caps=dict(x_show=False, y_show=False)
    ))
fig.show()

Changing the opacity of isosurfaces

import plotly.graph_objects as go
import numpy as np

X, Y, Z = np.mgrid[-5:5:40j, -5:5:40j, -5:5:40j]

# ellipsoid
values = X * X * 0.5 + Y * Y + Z * Z * 2

fig = go.Figure(data=go.Isosurface(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    opacity=0.6,
    isomin=10,
    isomax=50,
    surface_count=3,
    caps=dict(x_show=False, y_show=False)
    ))
fig.show()

Isosurface with Additional Slices

Here we visualize slices parallel to the axes on top of isosurfaces. For a clearer visualization, the fill ratio of isosurfaces is decreased below 1 (completely filled).

import plotly.graph_objects as go
import numpy as np

X, Y, Z = np.mgrid[-5:5:40j, -5:5:40j, -5:5:40j]

# ellipsoid
values = X * X * 0.5 + Y * Y + Z * Z * 2

fig = go.Figure(data=go.Isosurface(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    isomin=5,
    isomax=50,
    surface_fill=0.4,
    caps=dict(x_show=False, y_show=False),
    slices_z=dict(show=True, locations=[-1, -3,]),
    slices_y=dict(show=True, locations=[0]),
    ))
fig.show()

Multiple Isosurfaces with Caps

import plotly.graph_objects as go
import numpy as np

X, Y, Z = np.mgrid[-5:5:40j, -5:5:40j, 0:5:20j]

values = X * X * 0.5 + Y * Y + Z * Z * 2

fig = go.Figure(data=go.Isosurface(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    isomin=30,
    isomax=50,
    surface=dict(count=3, fill=0.7, pattern='odd'),
    caps=dict(x_show=True, y_show=True),
    ))
fig.show()

Changing the default colorscale of isosurfaces

import plotly.graph_objects as go
import numpy as np

X, Y, Z = np.mgrid[-5:5:40j, -5:5:40j, -5:5:40j]

# ellipsoid
values = X * X * 0.5 + Y * Y + Z * Z * 2

fig = go.Figure(data=go.Isosurface(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    colorscale='BlueRed',
    isomin=10,
    isomax=50,
    surface_count=3,
    caps=dict(x_show=False, y_show=False)
    ))
fig.show()

Customizing the layout and appearance of isosurface plots

import plotly.graph_objects as go
import numpy as np

X, Y, Z = np.mgrid[-5:5:40j, -5:5:40j, 0:5:20j]

values = X * X * 0.5 + Y * Y + Z * Z * 2

fig = go.Figure(data=go.Isosurface(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    isomin=30,
    isomax=50,
    surface=dict(count=3, fill=0.7, pattern='odd'),
    showscale=False, # remove colorbar
    caps=dict(x_show=True, y_show=True),
    ))

fig.update_layout(
    margin=dict(t=0, l=0, b=0), # tight layout
    scene_camera_eye=dict(x=1.86, y=0.61, z=0.98))
fig.show()

Reference

See https://plotly.com/python/reference/isosurface/ for more information and chart attribute options!