ela 0.6.0

A Python package for exploratory lithology analysis

Exploratory Lithology Analysis

master:

Analysing driller’s logs is a tedious and repetitive task in many groundwater modelling projects. Automating the process of extracting useful information from driller’s logs allows spending less time on manual data wrangling, more time on its interpretation, and enhances the reproducibility of the analysis.

This package combines features to:

• perform natural language processing lithology descriptions in the logs, to detect primary and secondary lithologies

• apply supervised machine learning to interpolate lithologies across a 3D grid

• visualise interactively the 3D data

License

MIT (see License.txt)

Documentation

Get a quick tour of the visualisation part of ‘ela’

Installation

Note that ‘ela’ relies on several external packages, and some can be fiddly to install depending on the version of Python and packages. Below are fairly prescriptive instructions, given in the hope of limiting the risk of issues.

Debian packages for spatial projections

cartopy and possibly other python packages require proj4 version 4.9+ to be installed (libproj-dev). If your debian/ubuntu repo does not suffice (older versions) you may try:

sudo apt-get install -y libc6
wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/proj-data_4.9.3-2_all.deb
sudo dpkg -i proj-data_4.9.3-2_all.deb
wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/libproj12_4.9.3-2_amd64.deb
sudo dpkg -i libproj12_4.9.3-2_amd64.deb
wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/proj-bin_4.9.3-2_amd64.deb
sudo dpkg -i proj-bin_4.9.3-2_amd64.deb
wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/libproj9_4.9.2-2_amd64.deb
sudo dpkg -i libproj9_4.9.2-2_amd64.deb
wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/libproj-dev_4.9.3-2_amd64.deb
sudo dpkg -i libproj-dev_4.9.3-2_amd64.deb

Installation of python dependencies with conda

You may want to install Anaconda to install dependencies. Note that I recommend to not let anaconda change your startup file and change the PATH environment. To activate Anaconda you first need: source ~/anaconda3/bin/activate. Then choose a conda environment name.

Optionally you may want to do conda update -n base conda and conda update -n base anaconda-navigator

my_env_name=ELA

conda create --name ${my_env_name} python=3.6
conda activate  ${my_env_name}
conda install --name ${my_env_name} rasterio cartopy geopandas pandas nltk scikit-learn scikit-image matplotlib vtk

As of writing (2018-08) conda does not have pyqt5, and a suitable version of mayavi for python3. We use pip

pip install --upgrade pip

pip search pyqt5
pip search mayavi

pip install pyqt5
pip install mayavi

Windows

Placeholder section. As of Sept 2018 it may be possible to install upon Python 3.6+ with Anaconda 3, and then including mayavi from pip.

Installation of pyela

pip install -r requirements.txt
python setup.py install

For Python 2.7.x pyqt5 is not available:

# Note: not sure if conda-forge needed: conda config --add channels conda-forge
conda create --name  ${my_env_name} python=2.7 mayavi rasterio cartopy geopandas pandas nltk scikit-learn scikit-image matplotlib vtk

Related Geoscience packages

‘ela’ aims to complement other Python packages for geoscience, in particular for handling bore data . It depends on the package ‘striplog’ and is likely to depend on ‘lasio’ in the future.

Known issues

As of 2018-08, using mayavi 4.6 on python 3.6 is buggy, a VTK issue it seems. Python 2.7 with mayavi 4.5 via Anaconda2 is known to work.

Troubleshooting

If in a conda environment trying to use pip you get:

ModuleNotFoundError: No module named 'pip._internal'

consider:

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python3 get-pip.py --force-reinstall