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description: How to make 3D Volume Plots in Python with Plotly.

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layout: user-guide

name: 3D Volume Plots

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permalink: python/3d-volume-plots/

thumbnail: thumbnail/3d-volume-plots.jpg

title: Python 3D Volume Plots | plotly

A volume plot with `go.Volume` shows several partially transparent isosurfaces for volume rendering. The API of `go.Volume` is close to the one of `go.Isosurface`. However, whereas [isosurface plots](./3d-isosurface-plots/) show all surfaces with the same opacity, tweaking the `opacityscale` parameter of `go.Volume` results in a depth effect and better volume rendering.

In the three examples below, note that the default colormap is different whether isomin and isomax have the same sign or not.

import plotly.graph_objects as go

import numpy as np

X, Y, Z = np.mgrid[-8:8:40j, -8:8:40j, -8:8:40j]

values = np.sin(X*Y*Z) / (X*Y*Z)

fig = go.Figure(data=go.Volume(

x=X.flatten(),

y=Y.flatten(),

z=Z.flatten(),

value=values.flatten(),

isomin=0.1,

isomax=0.8,

opacity=0.1, # needs to be small to see through all surfaces

surface_count=17, # needs to be a large number for good volume rendering

))

fig.show()

import plotly.graph_objects as go

import numpy as np

X, Y, Z = np.mgrid[-1:1:30j, -1:1:30j, -1:1:30j]

values = np.sin(np.pi*X) * np.cos(np.pi*Z) * np.sin(np.pi*Y)

fig = go.Figure(data=go.Volume(

x=X.flatten(),

y=Y.flatten(),

z=Z.flatten(),

value=values.flatten(),

isomin=-0.1,

isomax=0.8,

opacity=0.1, # needs to be small to see through all surfaces

surface_count=21, # needs to be a large number for good volume rendering

))

fig.show()

import numpy as np

import plotly.graph_objects as go

np.random.seed(0)

l = 30

X, Y, Z = np.mgrid[:l, :l, :l]

vol = np.zeros((l, l, l))

pts = (l * np.random.rand(3, 15)).astype(np.int)

vol[tuple(indices for indices in pts)] = 1

from scipy import ndimage

vol = ndimage.gaussian_filter(vol, 4)

vol /= vol.max()

fig = go.Figure(data=go.Volume(

x=X.flatten(), y=Y.flatten(), z=Z.flatten(),

value=vol.flatten(),

isomin=0.2,

isomax=0.7,

opacity=0.1,

surface_count=25,

))

fig.update_layout(scene_xaxis_showticklabels=False,

scene_yaxis_showticklabels=False,

scene_zaxis_showticklabels=False)

fig.show()

In order to see through the volume, the different isosurfaces need to be partially transparent. This transparency is controlled by a global parameter, `opacity`, as well as an opacity scale mapping scalar values to opacity levels. The figure below shows that changing the opacity scale changes a lot the visualization, so that `opacityscale` should be chosen carefully (`uniform` corresponds to a uniform opacity, `min`/`max` maps the minimum/maximum value to a maximal opacity, and `extremes` maps both the minimum and maximum values to maximal opacity, with a dip in between).

import plotly.graph_objects as go

from plotly.subplots import make_subplots

fig = make_subplots(

rows=2, cols=2,

specs=[[{'type': 'volume'}, {'type': 'volume'}],

[{'type': 'volume'}, {'type': 'volume'}]])

import numpy as np

X, Y, Z = np.mgrid[-8:8:30j, -8:8:30j, -8:8:30j]

values = np.sin(X*Y*Z) / (X*Y*Z)

fig.add_trace(go.Volume(

opacityscale="uniform",

), row=1, col=1)

fig.add_trace(go.Volume(

opacityscale="extremes",

), row=1, col=2)

fig.add_trace(go.Volume(

opacityscale="min",

), row=2, col=1)

fig.add_trace(go.Volume(

opacityscale="max",

), row=2, col=2)

fig.update_traces(x=X.flatten(), y=Y.flatten(), z=Z.flatten(), value=values.flatten(),

isomin=0.15, isomax=0.9, opacity=0.1, surface_count=15)

fig.show()

It is also possible to define a custom opacity scale, mapping scalar values to relative opacity values (between 0 and 1, the maximum opacity is given by the opacity keyword). This is useful to make a range of values completely transparent, as in the example below between -0.2 and 0.2.

import plotly.graph_objects as go

import numpy as np

X, Y, Z = np.mgrid[-1:1:30j, -1:1:30j, -1:1:30j]

values = np.sin(np.pi*X) * np.cos(np.pi*Z) * np.sin(np.pi*Y)

fig = go.Figure(data=go.Volume(

x=X.flatten(),

y=Y.flatten(),

z=Z.flatten(),

value=values.flatten(),

isomin=-0.5,

isomax=0.5,

opacity=0.1, # max opacity

opacityscale=[[-0.5, 1], [-0.2, 0], [0.2, 0], [0.5, 1]],

surface_count=21,

colorscale='RdBu'

))

fig.show()

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. Compare below with and without caps.

import numpy as np

import plotly.graph_objects as go

X, Y, Z = np.mgrid[:1:20j, :1:20j, :1:20j]

vol = (X - 1)**2 + (Y - 1)**2 + Z**2

fig = go.Figure(data=go.Volume(

x=X.flatten(), y=Y.flatten(), z=Z.flatten(),

value=vol.flatten(),

isomin=0.2,

isomax=0.7,

opacity=0.2,

surface_count=21,

caps= dict(x_show=True, y_show=True, z_show=True, x_fill=1), # with caps (default mode)

))

fig.update_layout(scene_camera = dict(

up=dict(x=0, y=0, z=1),

center=dict(x=0, y=0, z=0),

eye=dict(x=0.1, y=2.5, z=0.1)

))

fig.show()

import numpy as np

import plotly.graph_objects as go

X, Y, Z = np.mgrid[:1:20j, :1:20j, :1:20j]

vol = (X - 1)**2 + (Y - 1)**2 + Z**2

fig = go.Figure(data=go.Volume(

x=X.flatten(), y=Y.flatten(), z=Z.flatten(),

value=vol.flatten(),

isomin=0.2,

isomax=0.7,

opacity=0.2,

surface_count=21,

caps= dict(x_show=False, y_show=False, z_show=False), # no caps

))

fig.update_layout(scene_camera = dict(

up=dict(x=0, y=0, z=1),

center=dict(x=0, y=0, z=0),

eye=dict(x=0.1, y=2.5, z=0.1)

))

fig.show()

Slices through the volume can be added to the volume plot. In this example the isosurfaces are only partially filled so that the slice is more visible, and the caps were removed for the same purpose.

import numpy as np

import plotly.graph_objects as go

X, Y, Z = np.mgrid[:1:20j, :1:20j, :1:20j]

vol = (X - 1)**2 + (Y - 1)**2 + Z**2

fig = go.Figure(data=go.Volume(

x=X.flatten(), y=Y.flatten(), z=Z.flatten(),

value=vol.flatten(),

isomin=0.2,

isomax=0.7,

opacity=0.2,

surface_count=21,

slices_z=dict(show=True, locations=[0.4]),

surface=dict(fill=0.5, pattern='odd'),

caps= dict(x_show=False, y_show=False, z_show=False), # no caps

))

fig.show()

See https://plot.ly/python/reference/#volume for more information and chart attribute options!

[3D isosurface documentation](./3d-isosurface-plots/)