koronascript 0.2.1

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-2.18.0-alpha-20240918-0847-linux.zip

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

https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-windows.zip

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

apt-get install libnetcdf or sudo apt install libnetcdf-dev

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

The LSSS environment variable should point to the root directory of your LSSS installation. It can be set at run time either by setting the LSSS environment variable in the shell

export LSSS=~/lsss-2.16.0-alpha

before running your script, or by adding it manually from inside Python:

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

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.