A PyVista (and VTK) interface for the Geoh5 file format providing Python 3D visualization and useable data structures for processing datasets in the geoh5 specification. This library allows geologists to access the powerful tools available in the PyVista ecosystem for their data stored in the Geoh5 format.
The structure and interfaces of this project are heavily inspired by the 'omfvista' package, which provides a similar interface for the 'omf' format.
omfvista package: https://github.com/OpenGeoVis/omfvista
Geoh5 Python interface package: https://mirageoscience-geoh5py.readthedocs-hosted.com/en/stable/index.html
Documentation is hosted at https://github.com/derek-kinakin/geoh5vista
From PyPI
pip install geoh5vistaFrom Github
pip install git+https://github.com/derek-kinakin/geoh5vista.gitThis table provides the list of supported entities. Read from and write to Geoh5 support is the goal for each entity.
| Geoh5 Entity | PyVista Object | Read from Geoh5 | Write to Geoh5 | Notes |
|---|---|---|---|---|
| Workspace | MultiBlock | Yes | Yes | A multiblock containing several object can be written to Geoh5 |
| Points | PointSet | Yes | Yes | |
| Curve | PolyData | Yes | Yes | |
| Surface | PolyData | Yes | Yes | |
| 2D Grid | ImageData | Yes | Yes | 2D grid with dimensions nU x nV x 1 |
| Block model | ImageData or StructuredGrid | Yes | Yes | 3D grid with dimensions nU x nV x nZ |
| Drillholes | PolyData | Yes | No | Drillholes can be round-tripped back to geoh5 as curves |
| Slicer | PolyData | Yes | No | Geometry available as object metadata |
import pyvista as pv
import geoh5vista
project = geoh5vista.read_geoh5('test_file.geoh5')
projectOnce the data is loaded as a pyvista.MultiBlock dataset from geoh5vista,
that object can be directly used for interactive 3D visualization from PyVista:
An interactive scene can be created and manipulated to create a figure. First, grab the elements from the project:
# Grab a few elements of interest and plot em up!
vol = project["Block Model"]
topo = project["Topography"]
dacite = project["Dacite"]Then create a 3D scene with these spatial data and apply a filtering tool from PyVista to the volumetric data:
# Create a plotting window
p = pv.Plotter(notebook=False)
# Add our datasets
p.add_mesh(topo, cmap="gist_earth", opacity=0.5)
p.add_mesh(dacite, color=dacite["gh5_colour"], opacity=0.6)
# Add the volumetric dataset with a thresholding tool
p.add_mesh_threshold(vol)
# Add the bounds axis
p.show_bounds()
# Render the scene in a pop out window
p.show()Writing PyVista objects to a Geoh5 file can be as simple as:
# Write a single object to geoh5
geoh5vista.write_geoh5(topo, "new_gh5_topo_file.geoh5")
# Write a multiblock to geoh5
new_project = pv.MultiBlock()
new_project["Topo"] = topo
new_project["Dacite"] = dacite
geoh5vista.write_geoh5(new_project, "new_project.geoh5")
