PyWaveLearn (PWL)

Machine learning for wave enthusiasts.

Warning: This repository mainly contains legacy code developed during my PhD. Unfortunately, I currently do not have time to maintain this repository and most of the research presented here has already been supersede by more recent publications.

This repository makes available some useful tools for coastal scientists to handle common nearshore data with special focus on data mining, machine learning, and big data.

The work presented here was originally designed as supporting material for the paper: "A Novel Machine Learning Algorithm for Tracking Remotely Sensed Waves in the Surf Zone".

The accepted manuscript can be obtained here.

The main task handled here is to detect wave breaking, as explained in this notebook, and shown in this animation (click to play):

Installation:

At the moment, pywavelearn can only be installed from the source code.

We strongly recommend to use Anaconda (available from here) to handle all the dependencies.

Make sure you have all the dependencies:

# create a new environment
conda create --name pwl python=3.6  # netCDF4 DOES NOT work with python 3.7 yet
# activate
source activate pwl
# install the netCDF4 and xarray
conda install netCDF4 xarray
# install seaborn for better plots
conda install seaborn
# colour analysis
pip install colorspacious
conda install -c conda-forge colour-science
# OpenCV
conda install -c menpo opencv
# science kits
conda install scikit-image scikit-learn
# heavy machine learning machinery - not needed for the basic tools
sudo apt-get install gcc gfortran
conda install cython tensorflow keras
pip install xgboost
# a nice progress bar
conda install -c conda-forge tqdm
# peak detection
pip install peakutils
# dealig with shapefiles - Fiona is too unstable to be trusted...
pip install pyshp simpledbf
conda install pytables sqlalchemy

You may also want ffmpeg and some codecs to process raw video data (Ubuntu-only).

sudo apt install ffmpeg ubuntu-restricted-extras

Now, install pywavelearn:

git clone https://github.com/caiostringari/pywavelearn.git
cd pywavelearn
sudo python setup.py install

pwl.image

The module image was designed to make it easier to rectify ARGUS-like images using the OpenCV and scikit-image packages. Most of the heavy lifting is done using Flamingo. This module has the companion script extract_timestack.py which extracts space-time transects (timestacks) from a set of coastal images and also has the option to store rectified frames in a netCDF4 structure suitable for big data analysis.

Usage examples are available here.

pwl.colour

The module colour is the basis for most of the machine learn tasks available in this package. It exploits the fact that unbroken waves, broken waves, and the shoreline have different colour signatures that can be used to "learn" information about these features.

The wave breaking detection script shows the full potential of the colour module.

Usage examples are available here.

pwl.stats, pwl.spectral and pwl.linear

The modules stats, spectral and linear contain tools to deal with the most common wave analysis problems. They provide ways to calculate wave heights, periods, spectral densities, and most of the parameters derived from the linear wave theory.

Usage examples are available here.

scripts

Most of the functions available across the various modules have a Command Line Interface (CLI) companion. The most important ones are:

1. calibrate_camera.py
2. extract_frames.py
3. get_gcp_uvcoords.py
4. extract_timestack.py
5. learn_wavebreaking.py

The full help for these scripts can be seen using python script_name.py --help.

TODOS:

1. Improve documentation
2. Add continuous integration (CI)