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ZPLSC Echogram Generator

The ZPLSC Echogram Generator creates echograms (images) from the zooplankton sensor data (signal strength). The plots are arranged by frequency band (typically four) and show signal strength (color) given depth (Y axis) along time (X axis). These plots are individually scaled by band to provide contrast for tracking organisms of various sizes. Note that the depth axis is the distance from the sensor which is typically pointed upward; sea surface up and down swells can thus be seen over the time period.

Execution

Configuration

The necessary python modules must be available for use in the environment. On the test machine this is accomplished by sourcing the engine environment:

source activate engine

The configuration file provides the system defaults, such as the location of the raw data repository and the ZPLSC moorings. This file is named zplsc_echogram_config.yml and should in the current directory in which the generator is run. Here's an example file:

raw_data_dir: /omc_data/whoi/OMC
zplsc_echogram_directory: ~/ZPLSC_Echograms
zplsc_subsites:
  - CE01ISSM
  - CE06ISSM
  - CE07SHSM
  - CE09OSSM
  - CP01CNSM
  - CP03ISSM
  - CP04OSSM

The raw_data_dir must be accessible on the current systems file service and is the base location for the OMC data. The generator will search the directory tree underneath to find raw ZPLS files.

The zplsc_echogram_directory is the output location for the ZPLSC echograms (PNG images).

the zplsc_subsites is the list of all ZPLS files that are intended to be searched in the raw data respository.

Usage

zplsc_echogram_generator.py [<subsites>] [<deployments>] [<dates>] [--keep]
zplsc_echogram_generator.py (-h | --help)

Arguments:

subsites Single or a list of subsites of ZPLSC instruments (delimit lists by "'s and space separated). If omitted, all subsites from the config file are used and yesterday's echograms are generated.

deployments Single or a list of deployment numbers. (ex: 4 or "4 5")

dates Single or a list of dates of the desired 24 hour echograms.

(Ex: 2016-10-01 for one day or 2016-11 for the entire month or "2016-10-01 2016-11") (Note: The date can also be in these formats: YYYY/MM/DD, YYYY/MM, YYYYMMDD or YYYYMM)

Options:

-h --help Print this help message

--keep Keeps the temporary files after the echogram has been created.

For example:

$ zplsc_echogram CE01ISSM 5 20160701
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