Creating a Uniform Grid

Create a simple uniform grid from a 3D NumPy array of values.

import numpy as np
import pyvista as pv

Take a 3D NumPy array of data values that holds some spatial data where each axis corresponds to the XYZ cartesian axes. This example will create a pyvista.UniformGrid object that will hold the spatial reference for a 3D grid which a 3D NumPy array of values can be plotted against.

Create the 3D NumPy array of spatially referenced data. This is spatially referenced such that the grid is 20 by 5 by 10 (nx by ny by nz)

values = np.linspace(0, 10, 1000).reshape((20, 5, 10))
values.shape

Create the PyVista object

grid = pv.UniformGrid()

Set the grid dimensions: shape + 1 because we want to inject our values on

the CELL data

grid.dimensions = np.array(values.shape) + 1

Edit the spatial reference

grid.origin = (100, 33, 55.6)  # The bottom left corner of the data set
grid.spacing = (1, 5, 2)  # These are the cell sizes along each axis

Add the data values to the cell data

grid.cell_data["values"] = values.flatten(order="F")  # Flatten the array!
grid

Now plot the grid!

grid.plot(show_edges=True)

Don’t like cell data? You could also add the NumPy array to the point data of a pyvista.UniformGrid. Take note of the subtle difference when setting the grid dimensions upon initialization.

# Create the 3D NumPy array of spatially referenced data
# This is spatially referenced such that the grid is 20 by 5 by 10
#   (nx by ny by nz)
values = np.linspace(0, 10, 1000).reshape((20, 5, 10))
values.shape

Create the PyVista object and set the same attributes like above

grid = pv.UniformGrid()

# Set the grid dimensions: shape because we want to inject our values on the
#   POINT data
grid.dimensions = values.shape

# Edit the spatial reference
grid.origin = (100, 33, 55.6)  # The bottom left corner of the data set
grid.spacing = (1, 5, 2)  # These are the cell sizes along each axis

Add the data values to the cell data

grid.point_data["values"] = values.flatten(order="F")  # Flatten the array!
grid

Now plot the grid!

grid.plot(show_edges=True)

Exercise

Now create your own pyvista.UniformGrid from a 3D NumPy array!

help(pv.UniformGrid)

Here are some example 3D data using random data. Feel free to use your own 3D numpy array here!

arr = np.random.random((100, 100, 100))
arr.shape

Create the pyvista.UniformGrid

Hint, you will likely need to ravel the array with F-ordering: arr.ravel(order="F")

vol = pv.UniformGrid()
# Set attributes and data
...

vol.plot()

Example

Here are some examples of this kind of data in PyVista!

See the PyVista documentation for further details on Volume Rendering

from pyvista import examples

vol = examples.download_knee_full()

p = pv.Plotter()
p.add_volume(vol, cmap="bone", opacity="sigmoid")
p.show()

vol = pv.Wavelet()
vol.plot(volume=True)