echoshader 0.1.0

Open Source Python package for building ocean sonar data visualizations.

Welcome to echoshader

Open Source Python package for building ocean sonar data visualizations based on the HoloViz suite of Python tools.

What are ocean sonar systems?

Ocean sonar systems, such as echosounders, are the workhorse to study life in the ocean. They provide continuous observations of fish and zooplankton by transmitting sounds and analyzing the echoes bounced off these animals, just like how medical ultrasound images the interior of human body. In recent years these systems are widely deployed on ships, autonomous vehicles, or moorings, bringing in a lot of data that allow scientists to study the change of the marine ecosystem.

What is echoshader?

Echoshader aims to enhance the capability to interactively visualize large volumes of ocean sonar data to accelerate the data exploration and discovery process. The project will go hand-in-hand with ongoing development of the echopype package that handles the standardization, pre-processing, and organization of these data.

By providing an accessible and customizable platform for echo data visualization, the project can accelerate advancements in oceanographic research for the benefit of conservation and sustainable resource management like fishery.

Installation

First it is best to create a new environment:

mamba create -c conda-forge -n echoshader --yes python=3.10

mamba activate echoshader

To install from PyPi:

pip install echoshader

The latest branch can be installed via the following:

pip install git+https://github.com/OSOceanAcoustics/echoshader.git

To run in development mode, fork and clone the repository at Echoshader:

mamba create -c conda-forge -n echoshader-dev --yes python=3.10 --file requirements.txt --file requirements-dev.txt
pip install -e

We recommend use mamba to manage conda's environments, which is a re-implementation of conda offering additional benefits.

Creating a development environment

This section is intended for those who are actively developing this package.

mamba create -n echoshader-dev -c pyviz -c conda-forge echopype hvplot geoviews pyvista ipykernel

Note: Users may already have echopype installed, but it should be at a version greater than or equal to 0.7.1.

To link this environment with a Jupyter kernel:

conda activate echoshader-dev
python -m ipykernel install --user --name echoshader-dev --display-name "echoshader-dev"