mbari-pbp 1.5.0

PyPAM based Processing

PyPAM based data processing

The mbari-pbp package allows to process ocean audio data archives to daily analysis products of hybrid millidecade spectra using PyPAM.

Status: Functional version, including support for cloud based processing.

• JSON generation of timekeeping with indication of start and duration of recognized sound files
• Audio file processing
  • Frequency and psd array output
  • Concatenation of processed 1-minute segments for daily product
  • Calibration with given sensitivity file (NetCDF), or flat sensitivity value
• Data products
  • NetCDF with metadata
  • Summary plot
• Cloud processing
  • Inputs can be downloaded from and uploaded to S3
  • Inputs can be downloaded from public GCS bucket
  • Outputs can be uploaded to GCS

Documentation

docs.mbari.org/pbp.

Installation

The only requirement is Python 3.9, 3.10, or 3.11 on your environment.[^1] You can run python3 --version to check the version of Python installed.

[^1]: As currently required by PyPAM.

As a general practice, it is recommended to use a virtual environment for the installation.

python3.11 -m venv virtenv
source virtenv/bin/activate

Install the package:

pip install mbari-pbp

Programs and API

The mbari-pbp package includes command line interface (CLI) programs, and also provides APIs you can use in your Python scripts or notebooks.

CLI Programs

The package includes the following CLI programs:

Program	Description
pbp-meta-gen	Generate JSON files with audio metadata
pbp-hmb-gen	Main HMB generation program
pbp-cloud	Program for cloud based processing
pbp-hmb-plot	Utility program to plot HMB product

API

TODO link to the API documentation.

References

• PyPAM - Python tool for Passive Acoustic Monitoring – https://doi.org/10.5281/zenodo.6044593
• Computation of single-sided mean-square sound pressure spectral density with 1 Hz resolution follows ISO 18405 3.1.3.13 (International Standard ISO 18405:2017(E), Underwater Acoustics – Terminology. Geneva: ISO) – https://www.iso.org/standard/62406.html
• Hybrid millidecade spectra: A practical format for exchange of long-term ambient sound data – https://asa.scitation.org/doi/10.1121/10.0003324
• Erratum: Hybrid millidecade spectra – https://asa.scitation.org/doi/10.1121/10.0005818

Development

See DEVELOPMENT.md for details.