Moving Isovalue

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Animate an isovalue moving through a volumetric dataset.

Uses download_brain() and open_gif()/write_frame() to create the animation.

import numpy as np
import pyvista as pv
from pyvista import examples

vol = examples.download_brain()
vol

ImageData (0x7f93fdc5dba0)
  N Cells:      6998400
  N Points:     7109137
  X Bounds:     0.000e+00, 1.800e+02
  Y Bounds:     0.000e+00, 2.160e+02
  Z Bounds:     0.000e+00, 1.800e+02
  Dimensions:   181, 217, 181
  Spacing:      1.000e+00, 1.000e+00, 1.000e+00
  N Arrays:     1

ImageData 7,109,137 points 6,998,400 cells 6.8 MiB

Bounds⧉X [0.000e+00, 1.800e+02]Y [0.000e+00, 2.160e+02]Z [0.000e+00, 1.800e+02]

Griddims 181 x 217 x 181spacing (1.000e+00, 1.000e+00, 1.000e+00)

• Point Data: (1)
  image_data active
  • image_data⧉
    scalar
    uint8
    [0.000e+00, 2.550e+02]
    active

Now lets make an array of all of the isovalues for which we want to show.

values = np.linspace(5, 150, num=15)

Now let’s create an initial isosurface that we can plot and move

surface = vol.contour(values[:1])

Pre-compute the surfaces

surfaces = [vol.contour([v]) for v in values]

Set a single surface as the one being plotted that can be overwritten

surface = surfaces[0].copy()

filename = 'isovalue.gif'

pl = pv.Plotter(off_screen=True)
# Open a movie file
pl.open_gif(filename)

# Add initial mesh
pl.add_mesh(
    surface,
    opacity=0.5,
    clim=vol.get_data_range(),
    show_scalar_bar=False,
)
# Add outline for reference
pl.add_mesh(vol.outline_corners(), color='k')

print('Orient the view, then press "q" to close window and produce movie')
pl.camera_position = pv.CameraPosition(
    position=(393.0, 556.4, 235.5),
    focal_point=(88.7, 119.1, 72.62),
    viewup=(-0.1928, -0.2219, 0.9558),
)

# initial render and do NOT close
pl.show(auto_close=False)

# Run through each frame
for surf in surfaces:
    surface.copy_from(surf)
    pl.write_frame()  # Write this frame
# Run through backwards
for surf in surfaces[::-1]:
    surface.copy_from(surf)
    pl.write_frame()  # Write this frame

# Be sure to close the plotter when finished
pl.close()

Orient the view, then press "q" to close window and produce movie

Tags: plot