echopype 0.3.1

Enhancing the interoperability and scalability in analyzing ocean sonar data

Echopype

Echopype is a package built for enhancing the interoperability and scalability in ocean sonar data processing. These data are widely used for obtaining information about the distribution and abundance of marine animals, such as fish and krill. Our ability to collect large volumes of sonar data from a variety of ocean platforms has grown significantly in the last decade. However, most of the new data remain under-utilized. echopype aims to address the root cause of this problem - the lack of interoperable data format and scalable analysis workflows that adapt well with increasing data volume - by providing open-source tools as entry points for scientists to make discovery using these new data.

Installation

Echopype currently supports file conversion and computation of data produced by:

• Simrad EK60 echosounder (.raw files)

• ASL Environmental Sciences AZFP echosounders (.01A files)

Support for .raw files from the broadband Simrad EK80 echosounder is currently in the development branch combine-refactor and we will merge it to the master branch once it’s ready for alpha testing.

The file conversion functionality converts data from manufacturer-specific binary formats into a standardized netCDF files, based on which all subsequent computations are performed. The data processing routines include calibration (instrument-specific), noise removal, and mean volume backscattering strength (MVBS) calculation.

Echopype can be installed from PyPI:

$ pip install echopype

or through conda:

$ conda install -c conda-forge echopype

When creating an conda environment to work with echopype, use the supplied environment.yml or do

$ conda create -c conda-forge -n echopype python=3.8 --file requirements.txt

Usage

Check out the echopype documentation for more details on installation and usage.

Watch the echopype talk at SciPy 2019 for background, discussions and a quick demo!

Contributors

Wu-Jung Lee (@leewujung) leads this project and along with Kavin Nguyen (@ngkavin) are primary developers of this package. Valentina Staneva (@valentina-s) and Emilio Mayorga (@emiliom) provide consultation and also contribute to the development. Other contributors are listed here.

We thank Dave Billenness of ASL Environmental Sciences for providing the AZFP Matlab Toolbox as reference for our development of AZFP support in echopype. We also thank Rick Towler of the Alaska Fisheries Science Center for providing low-level file parsing routines for Simrad EK60 and EK80 echosounders.

License

Echopype is licensed under the open source Apache 2.0 license.

---

Copyright (c) 2018–, echopype Developers.