Acoustic Analysis Software

PAMGuard

The SAEL Lab uses PAMGuard for several analysis processes.

Matlab

Matlab

Triton

Triton

Raven

Raven

Python

Our lab uses Python to run soundscape analyses using PyPAM and PBP

These directions are written by a new Python user. If you are an experienced user, please make suggestions/corrections as needed!

Downloading and Installing Python

There are several different ways to install and use Python, use what works best for you!

  1. Go to Anaconda distribution website
  2. Select your operating system and download the installer (standard/default settings are ok). Anaconda Navigator comes bundled with a Python distributor and will automatically install the latest Python version (currently 3.12), see ‘Creating New Environments’ steps below to use a different version of Python
  3. You’re ready to use Python!

Python Environments

Python environments allow you to manage packages and Python versions, and ensures your project has the necessary dependencies. Anaconda Navigator allows you to set and work in different environments.

Creating New Environments

PyPAM requires a specific Python version (3.9-3.11) and some analyses require specific packages that are not included in the base Anaconda channels or Python Package Index (PyPI). Follow the directions below to set up a custom environment for PyPAM (the same directions can be applied to make other environments)

  1. Open Anaconda Navigator and click on the ‘Environments’ tab on the left

  2. Click the ‘Create’ button on bottom left

  3. Set the Environment name (PyPAM for example) and ensure the Python box is checked with 3.9-3.11 version. You can also select the R box and choose a version

  4. Click ‘Create’ and the environment will establish itself (Note: This may take a few minutes to set up)

  5. Once established you can see your new environment in the list and all of the packages that are installed

  6. Click on the green arrow and select “Open Terminal”

  7. This will open a command prompt where you can write Python code to edit the environment

  8. Double check the python version by typing python –version, this should return a version between 3.9-3.11

  9. To install packages more packages type conda install <package name> or pip install <package name>. If the package is included in the base libraries, you can use the conda install format (i.e. conda install netcdf4). If the package is not included, use the pip format (i.e. pip install mbari-pbp)

  10. Installing mbari-pbp should also automatically install PyPAM, if you are still missing the PyPAM package type pip install lifewatch-pypam into the environment command window

  11. You should now be ready to use PyPAM and PBP functions!

Python IDEs

There are also several ways to interact with Python code through Integrated Development Environments (IDEs). These allow you to write, execute, and visualize Python Code within a user friendly interface. Anaconda Navigator has several IDEs included in the bundle, including Jupyter Notebook (PyPAM PBP example scripts).

LFDCS

Low Frequency Detection and Classification System (LFDCS) is a software built by Dr. Mark Baumgartner at the Woods Hole Oceanographic Institution (WHOI). It was designed for automated detection and classification of low-frequency baleen whale vocalizations in real-time acoustic data. It was recently adapted to a LFDCS Desktop program to process archival data as well.

The SAEL Lab has begun taking some initial steps to use LFDCS Desktop for our data and develop/contribute to a west coast call library.

More information here