PyVista

Introduction#

Matplotlib and Plotly make charts for you. PyVista does something else: three-dimensional objects that rotate, with light, with surfaces and with volume.

It’s what you need when your data isn’t a series of numbers but a shape — a mechanical part, a terrain, an MRI scan, the markers from a motion capture.

PyVista is a Python layer over VTK, the scientific visualization engine behind programs like ParaView. VTK is written in C++ and is twenty-five years old; PyVista is what makes it bearable.

It draws on your machine, which is what lets you move millions of triangles — and it’s also what makes it need a graphics card that actually works. For molecules, and especially for teaching them to someone else, py3Dmol draws in the browser and doesn’t depend on anything.

Working environment#

uv init viz
Initialized project `viz` at `C:\Users\eva\viz`

cd viz
uv add pyvista imageio
Using CPython 3.14.3
Resolved 32 packages in 337ms
Installed 31 packages in 95ms
 + imageio==2.37.4
 + pyvista==0.48.4

You only need imageio to save animations; to just look at things on screen, pyvista is enough.

Shapes#

A Plotter is the window. You add meshes to it with add_mesh and open it with show.

import pyvista as pv

plotter = pv.Plotter()
plotter.set_background("white")

plotter.add_mesh(pv.Sphere(radius=1, center=(0, 0, 0)), color="#dd3333")
plotter.add_mesh(pv.Cube(center=(3, 0, 0)), color="#3366ee")
plotter.add_mesh(pv.Cone(center=(6, 0, 0), direction=(1, 0, 0)), color="#ddaa22")

plotter.show()

Drag the mouse to rotate it and the wheel to zoom in.

Notice that you haven’t placed any camera: show() looks at where things are and faces them on its own.

A point cloud#

The most common form of scientific data isn’t a mesh but a list of points, each point with a measured value.

A PolyData is exactly that, and glyph places the same figure at each point — a sphere, repeated, that VTK draws in one go no matter how many there are.

from math import cos, sin

import pyvista as pv

points = []
heights = []
for i in range(600):
    angle = i * 0.12
    radius = 0.02 * i
    points.append([radius * cos(angle), radius * sin(angle), 0.01 * i])
    heights.append(0.01 * i)

cloud = pv.PolyData(points)
cloud["height"] = heights

spheres = cloud.glyph(geom=pv.Sphere(radius=0.25), orient=False, scale=False)
plotter = pv.Plotter()
plotter.set_background("white")
plotter.add_mesh(spheres, scalars="height", cmap="viridis", smooth_shading=True)
plotter.show()