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update readme
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carueda committed Apr 1, 2024
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Expand Up @@ -6,31 +6,40 @@ process ocean audio data archives to daily analysis products of hybrid millideca

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

- [x] JSON generation of timekeeping
- [x] Timekeeping based on given JSON indicating start and duration of every available (recognized) sound file
- [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)
- [x] Calibration with given flat sensitivity value
- [x] Calibration with given sensitivity file (NetCDF), or flat sensitivity value
- [x] Data products
- [x] NetCDF with metadata
- [x] Summary plot (optional)
- [x] Summary plot
- [x] Cloud processing
- [x] Inputs can be downloaded from S3
- [x] Outputs can be uploaded to S3
- [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

TODO more details

## Setup
## Installation

### Install PBP
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.

pip install mbari-pbp
[^1]: As currently [required by PyPAM](https://github.com/lifewatch/pypam/blob/29e82f0c5c6ce43b457d76963cb9d82392740654/pyproject.toml#L16).

### Programs
As a general practice, it is recommended to use a virtual environment for the installation.
```shell
python3.9 -m venv virtenv
source virtenv/bin/activate
```

Install the package:
```shell
pip install mbari-pbp
```

## Programs

The package includes the following CLI programs:

Expand All @@ -41,7 +50,7 @@ The package includes the following CLI programs:
| [`pbp-cloud`](pbp-cloud/) | Program for cloud based processing. |
| [`pbp-plot`](pbp-plot/) | Utility program to plot resulting HMB product. |

## Refs
## References

- PyPAM - Python tool for Passive Acoustic Monitoring –
<https://doi.org/10.5281/zenodo.6044593>
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