mbari-pbp

Process ocean audio data archives to daily analysis products of hybrid millidecade spectra using PyPAM.

https://github.com/mbari-org/pbp

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 4 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary

Keywords

audio-processing cloud docker hybrid-millidecade-bands notebook pypam soundscape

Keywords from Contributors

mesh interpretability sequences projection interactive hacking network-simulation

Last synced: 6 months ago · JSON representation ·

Repository

Process ocean audio data archives to daily analysis products of hybrid millidecade spectra using PyPAM.

Basic Info

Host: GitHub
Owner: mbari-org
License: apache-2.0
Language: Python
Default Branch: main
Homepage: https://docs.mbari.org/pbp
Size: 3.48 MB

Statistics

Stars: 16
Watchers: 8
Forks: 7
Open Issues: 21
Releases: 0

Topics

audio-processing cloud docker hybrid-millidecade-bands notebook pypam soundscape

Created about 3 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

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.

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

Documentation

Official documentation is available at 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. shell python3.11 -m venv virtenv source virtenv/bin/activate

Install the package: shell 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

API documentation is available at docs.mbari.org/pbp/api.

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.

Owner

Name: Monterey Bay Aquarium Research Institute
Login: mbari-org
Kind: organization

Website: https://www.mbari.org/
Repositories: 25
Profile: https://github.com/mbari-org

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: PBP – PyPAM-Based Processing
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Carlos
    name-particle: A.
    family-names: Rueda
    email: carueda@mbari.org
    affiliation: MBARI
    orcid: 'https://orcid.org/0000-0002-5440-0638'
  - given-names: Danelle
    family-names: Cline
    email: dcline@mbari.org
    affiliation: MBARI
    orcid: 'https://orcid.org/0000-0002-2599-6567'
  - given-names: John
    name-particle: P.
    family-names: Ryan
    email: ryjo@mbari.org
    affiliation: MBARI
    orcid: 'https://orcid.org/0000-0001-7954-5369'
abstract: >-
  Process ocean audio data archives to daily analysis products
  of hybrid millidecade spectra using PyPAM.
keywords:
  - audio-processing
  - cloud
  - hybrid-millidecade-bands
  - netcdf
  - notebook
  - pypam
  - soundscape
license: GPL-3.0
references:
  - authors:
      - family-names: Parcerisas
        given-names: Clea
        orcid: https://orcid.org/0000-0001-7466-0288
    title: "PyPAM: a package to process long-term underwater acoustics data in chunks"
    doi: 10.5281/zenodo.7584847
    type: software

GitHub Events

Total

Issues event: 34
Watch event: 3
Delete event: 9
Member event: 1
Issue comment event: 118
Push event: 67
Pull request review event: 5
Pull request event: 37
Fork event: 5
Create event: 21

Last Year

Issues event: 34
Watch event: 3
Delete event: 9
Member event: 1
Issue comment event: 118
Push event: 67
Pull request review event: 5
Pull request event: 37
Fork event: 5
Create event: 21

Committers

Last synced: 8 months ago

All Time

Total Commits: 453
Total Committers: 7
Avg Commits per committer: 64.714
Development Distribution Score (DDS): 0.203

Past Year

Commits: 159
Committers: 7
Avg Commits per committer: 22.714
Development Distribution Score (DDS): 0.428

Top Committers

Name	Email	Commits
Carlos Rueda	c**a@m**g	361
danellecline	d**e@m**g	61
Michael C Ryan	s**r@g**m	17
John Ryan	3****i	8
dependabot[bot]	4****]	3
Clea Parcerisas	c**s@g**m	2
Joe Duprey	4****y	1

Committer Domains (Top 20 + Academic)

mbari.org: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 46
Total pull requests: 51
Average time to close issues: about 1 month
Average time to close pull requests: 16 days
Total issue authors: 9
Total pull request authors: 6
Average comments per issue: 2.76
Average comments per pull request: 1.8
Merged pull requests: 35
Bot issues: 0
Bot pull requests: 5

Past Year

Issues: 28
Pull requests: 40
Average time to close issues: 28 days
Average time to close pull requests: 9 days
Issue authors: 9
Pull request authors: 6
Average comments per issue: 2.82
Average comments per pull request: 2.0
Merged pull requests: 25
Bot issues: 0
Bot pull requests: 5

View more stats

Top Authors

Issue Authors

carueda (15)
danellecline (10)
ryjombari (6)
cparcerisas (5)
xaviermouy (5)
jdduprey (2)
spacetimeengineer (1)
JMcCordic (1)
sahav (1)

Pull Request Authors

carueda (23)
spacetimeengineer (17)
cparcerisas (9)
danellecline (8)
dependabot[bot] (5)
jdduprey (2)

Top Labels

Issue Labels

bug (10) enhancement (7) HMB-gen (5) documentation (4) question (3) API (3) performance (2) META-gen (2) idea (2) p1 (1) plot (1) windows (1) UX (1) AI (1)

Pull Request Labels

dependencies (5) python (3) documentation (2) enhancement (2)

Packages

Total packages: 1
Total downloads:
- pypi 344 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 60
Total maintainers: 1

pypi.org: mbari-pbp

PyPAM based Processing

Homepage: https://docs.mbari.org/pbp/
Documentation: https://mbari-pbp.readthedocs.io/
License: Apache-2.0
Latest release: 1.7.4
published 6 months ago

Versions: 60
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 344 Last month

Rankings

Dependent packages count: 9.7%

Average: 36.8%

Dependent repos count: 63.9%

Maintainers (1)

caruedambari

Last synced: 6 months ago

Dependencies

.github/workflows/ci.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

requirements.txt pypi

boto3 ==1.26.156
dataclasses-json ==0.5.8
h5netcdf ==1.2.0
marshmallow ==3.19.0
mypy ==1.4.0
pylint ==2.17.4
pytest ==7.3.2
python-dateutil ==2.8.2
ruff ==0.0.272
soundfile ==0.12.1
syrupy ==4.0.4
ufmt ==2.1.0

docker/Dockerfile docker

continuumio/miniconda3 latest build

pyproject.toml pypi

.github/workflows/release-docker.yml actions

actions/checkout v3 composite
docker/build-push-action v2 composite
docker/build-push-action v5 composite
docker/login-action v3 composite
docker/metadata-action v5 composite

docker/docker-compose.yml docker

mbari/pbp 1

mbari-pbp

Science Score: 57.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

PyPAM based data processing

Documentation

Installation

Programs and API

CLI Programs

API

References

Development

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: mbari-pbp

Rankings

Maintainers (1)

Dependencies