Pyvista

PyVista - 3D Visualization

Quick Reference

import pyvista as pv

mesh = pv.read('model.vtk')
plotter = pv.Plotter()
plotter.add_mesh(mesh, scalars='property', cmap='viridis')
plotter.show()

Key Classes

| Class | Purpose | |-------|---------| | pv.Plotter | Main visualization window | | pv.PolyData | Surface meshes, point clouds | | pv.StructuredGrid | Regular 3D grids | | pv.UnstructuredGrid | Irregular meshes | | pv.ImageData | 3D voxel data (seismic) |

Essential Operations

Load and Display Mesh

mesh = pv.read('model.vtk')
plotter = pv.Plotter()
plotter.add_mesh(mesh, scalars='lithology', cmap='Set1')
plotter.show()

Create Structured Grid (Surface)

x, y = np.meshgrid(np.arange(-10, 10, 0.5), np.arange(-10, 10, 0.5))
z = np.sin(np.sqrt(x**2 + y**2))
grid = pv.StructuredGrid(x, y, z)
pv.Plotter().add_mesh(grid, scalars=z.ravel(), cmap='terrain').show()

Visualize Point Cloud

cloud = pv.PolyData(np.random.rand(1000, 3) * 100)
cloud['depth'] = cloud.points[:, 2]
pv.Plotter().add_mesh(cloud, scalars='depth', point_size=5,
                      render_points_as_spheres=True).show()

Volume Rendering (Seismic)

grid = pv.ImageData(dimensions=(nx+1, ny+1, nz+1), spacing=(25, 25, 10))
grid.cell_data['amplitude'] = data.ravel(order='F')
pv.Plotter().add_volume(grid, cmap='seismic', opacity='sigmoid').show()

Slice Through Volume

volume = pv.read('seismic.vti')
slice_x = volume.slice(normal='x', origin=volume.center)
pv.Plotter().add_mesh(slice_x, cmap='seismic').show()

Well Path Visualization

points = np.column_stack([x, y, z])  # Well trajectory
tube = pv.Spline(points, 500).tube(radius=5)
pv.Plotter().add_mesh(tube, color='brown', label='Well').add_legend().show()

Combine Multiple Surfaces

plotter = pv.Plotter()
plotter.add_mesh(horizon1, color='gold', opacity=0.7, label='Top')
plotter.add_mesh(horizon2, color='blue', opacity=0.7, label='Base')
plotter.add_mesh(fault, color='red', opacity=0.5, label='Fault')
plotter.add_legend().show()

Export for Publication

plotter = pv.Plotter(off_screen=True)
plotter.add_mesh(mesh, cmap='terrain')
plotter.screenshot('figure.png', scale=3)   # High-res image
plotter.export_html('model.html')           # Interactive HTML

Color Maps

| Map | Use Case | |-----|----------| | terrain | Topography, elevation | | seismic | Seismic amplitudes (diverging) | | viridis | General scientific | | Set1, Set2 | Categorical (lithology) |

Supported Formats

.vtk, .vtu, .vti, .vtp, .stl, .obj, .ply (read/write)

When to Use vs Alternatives

| Tool | Best For | Limitations | |------|----------|-------------| | pyvista | Pythonic 3D viz, VTK wrapper, mesh operations, scripting | Requires display or off-screen backend | | Mayavi | Scientific 3D visualization, volume rendering | Heavier dependency, less active development | | ParaView | Interactive GUI exploration of large 3D datasets | GUI-focused, scripting is secondary | | matplotlib 3D | Simple 3D scatter/surface plots | Limited interactivity, not true 3D engine |

Use pyvista when you need programmatic 3D visualization of geological models, meshes, or point clouds with VTK power but a Pythonic API.

Consider alternatives when you need a full GUI for exploring large models (use ParaView), legacy scientific visualization (use Mayavi), or only need simple 3D scatter plots (use matplotlib 3D).

Common Workflows

Visualize 3D geological model with multiple surfaces

• [ ] Load mesh files with pv.read() for each surface/horizon
• [ ] Create plotter with pv.Plotter() (use off_screen=True for scripts)
• [ ] Add each surface with plotter.add_mesh() and distinct colors/opacity
• [ ] Add well paths as tubes with pv.Spline().tube()
• [ ] Add axes and legend with plotter.add_axes() and plotter.add_legend()
• [ ] Set camera position for desired view angle
• [ ] Export screenshot with plotter.screenshot() or HTML with plotter.export_html()

Tips

• Use off_screen=True for batch processing
• Add axes with plotter.add_axes() for publication
• Export to HTML for interactive sharing
• Use opacity to show internal structure

References

• [Mesh Types](references/mesh_types.md) - PyVista mesh classes and when to use each
• [Plotting Options](references/plotting_options.md) - Plotter settings and rendering options

Scripts

• [scripts/visualizesurface.py](scripts/visualizesurface.py) - Visualize geological surfaces from file

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: SteadfastAsArt
• Source: SteadfastAsArt/geoscience-skills
• License: MIT

Install and usage instructions live in the source repository linked above.