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name: pyvista description: | 3D visualization and mesh analysis for geoscience data using PyVista/VTK. Use when the agent needs to: (1) Create 3D visualizations of geological models, (2) Render seismic volumes or voxel data, (3) Visualize point clouds or well paths, (4) Plot surfaces and meshes in 3D, (5) Read/write VTK, STL, OBJ files, (6) Create cross-sections through 3D models, (7) Export publication-quality figures or interactive HTML. license: MIT metadata: version: 1.0.1 author: Geoscience Skills tags: '["3D Visualization", "VTK", "Mesh", "Geological Models", "Point Clouds"]' dependencies: '["pyvista>=0.42.0", "numpy", "vtk"]' complements: '["gempy", "simpeg", "verde", "segyio", "xarray"]' workflow_role: visualization skill_type: domain

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 - PyVista mesh classes and when to use each
• Plotting Options - Plotter settings and rendering options

Scripts

• scripts/visualize_surface.py - Visualize geological surfaces from file