geoh5vista: a Geoh5 <> PyVista (VTK) interface

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

Installation

From PyPI

pip install geoh5vista

From Github

pip install git+https://github.com/derek-kinakin/geoh5vista.git

Current Status of Supported Geoh5 Entities

This table provides the list of supported entities. Read from and write to Geoh5 support is the goal for each entity.

Geoh5 Entity Metadata Support

The following metadata are read from the geoh5 entities and attached to the PyVista objects in the "user_dict":

• Entity name (ob.user_dict["gh5_name"]) as a string
• Entity colour (ob.user_dict["gh5_colour"]) as a list [R,G,B]
• Entity type (ob.user_dict["gh5_entity_type"]) as "Points", "Curve", "Surface", "Grid2D", "Grid3D", or "Drillhole"
• Entity visibility (ob.user_dict["gh5_name"]) as True/False

Example Use

import pyvista as pv
import geoh5vista

project = geoh5vista.read_geoh5('test_file.geoh5')
project

Once 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.user_dict["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")