fingal - 3D Geophysical Inversion in python

A python package for geohpysical inversion in 3D for galvanic data based on the finite element method (FEM) supporting unstructured meshes. Data sets supported are electric potential data as well as electric field data for DC and IP surveys.

It is based in the esys-escript with python3 and supports parallel execution with domain decomposition for threading as well as MPI.

Installation

For installation (sorry no setup.py yet) clone the fingal repository

mkdir fingal
git clone https://github.com/LutzGross/fingal.git fingal

and add the path to the fingal to your executable and python path:

export PATH=${PATH}:${HOME}/fingal/bin
export PYTHONPATH=${PYTHONPATH}:${HOME}/fingal/bin

Depending on your esys-escript installation you also have to add the path to the esys-escript installation to PATH, LD_LIBRARY_PATH and PYTHONPATH.

Examples

• As simple example for ERT inversion using syntehtic data: ERTSynthetics
• Synthetic FullWaver data inversion: SyntheticFW
• Volcano with FullWaver data: VolcanoFW

List of Command Line Functions

This is a list of some of the command line function provided. Use the command line option -h to see the options.

• mkConfig.py : creates an initial configuartion file that need to be adjudted to the specific case.
• mkMeshFromStations.py: uses a station file to set up a gmsh geo file to generate finite element mesh
• runSynthetic.py: run a synthetic survey using a given schedule.
• convertZZ.py: converts a ZZ survey file into a station and data file.
• fly2silo.py: creates a silo 3D visualization file from fly mesh file.
• gmsh2fly.py: converts a gmsh msh file to fly mesh file.
• mph2fly.py: converts a COMSOL mph file to fly mesh file.
• plotStations.py: plot the survey stations in plane view.
• runERTinversion.py: runs ERT (an IP) inversion using potential fields.
• runIPFieldinversion.py: runs ERT (an IP) inversion using electric field data (aka FullWaver).

Some Visualization

With VTK files you can use 3D visualization packages such as

• VisIt
• paraview
• mayavi

The switch --xyx activates the creation of a CSV file giving ccordinates and conductivity in core region set in the configuartion file via the core variable. The name of the created file is sigma.csv where again sigma is taken from the output variable set in ex1.py. You can read and plot this file for instance using a 3D scatter plot in matplotlib:

import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits import mplot3d
data= np.loadtxt('sigma.csv',skiprows=1, delimiter=',')
volume=data[data[:,3]>0.04]
xyz=volume[:,:3]
sigma=volume[:,3]
ax = plt.axes(projection='3d')
ax.scatter(xyz[:,0], xyz[:,1], xyz[:,2], c = sigma, s=0.01)
plt.show()

by @LutzGross