koronascript 0.1

Wrapper around Korona modules for processing echosounder data

Running Korona through Python

Prerequisites

Install LSSS/Korona.

This version of the KoronaScript is tested against lsss-2.16.0-alpha version. LSSS and korona is usually placed at ~/lsss/lsss-2.16.0-alpha or a similar directory.

Download the appropriate version from here:

https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-linux.zip

https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-windows.zip

If you run linux you need to install the netcdf library separately:

apt-get install libnetcdf

Add license

You need an LSSS licence. The licence have to be added according to the LSSS manual. the licence files are typically placed at the ~/marec/license directory.

Set system variables

This can be set at run time either by setting the LSSS environment variable in the shell

export LSSS=~/lsss-2.16.0-alpha/korona

before running your script, or by adding to path

lsss = '~/lsss-2.16.0-alpha/korona'
os.environ["LSSS"] = lsss

pointing at the LSSS environment to your script.

Usage

Import the modules:

import KoronaScript as ks
import KoronaScript.Modules as ksm

Create a script object:

ks = ks.KoronaScript(Categorization='categorization.xml',
                 HorizontalTransducerOffsets='HorizontalTransducerOffsets.xml')

Add some modules:

ks.add(ksm.EmptyPingRemoval())
ks.add(ksm.Comment(LineBreak='false', Label='CW_0256ms'))
ks.add(ksm.ChannelRemoval(Channels=[1,5,9,13,17],KeepSpecified='true'))
ks.add(ksm.Writer(RelativeDirectory='CW_0256ms'))

Write out the resulting configuration:

ks.write()

Run the script:

ks.run(src="input_dir", dst="output_dir")

The list of modules and their parameters can be found in the configuration/korona-info.json file.