KeyError: 'longitude' when using raw2nc with EK60 data

[PierrePriou]

I received the following error when trying to convert raw EK60 data into NetCDF using raw2nc

The data was collected in the Arctic and, generally, had bad GPS fixes. I am currently using Echopype version 0.4.0.

To reproduce the error, I attached the code that I used and a link for downloading the raw data file.

import os
os.chdir("C:/Users/cfer/PhD/Echopype_test")
os.getcwd()

file_name = "EK60_2019_LEG_02-D20190717-T095103"

from echopype import Convert
dc = Convert('data/raw/acoustics/' + file_name + '.raw') 
dc.raw2nc() # KeyError: longitude

Thank you.

[leewujung]

@PierrePriou: thanks for reporting this.

When you said "bad GPS fixes", do you know if the GPS was actually sending messages? If the GPS message stream was empty, this is something we had put in a fix for (see #185). I still have to do a release for that to be formal, hopefully in the coming few days.

If you could give the latest master branch a try by pip install git+https://github.com/OSOceanAcoustics/echopype that'll be great. If there's additional problem please kindly let us know.

[cyrf0006]

@leewujung: I tested @PierrePriou 's problem with he latest echopype version. The problem remains. It looks like the NMEA message is troncated in his files:

$INGGA,095105.067,7244.26485,N,06646 [...]

instead of

$INGGA,144001.10,6759.823526,N,00517.812805,E,xxx*7C

This causes an error L.369 of ek60.py because pynmea2 do not parse longitude (only latitude in this case). I think that you already got a sense of the problem L. 365:

# TODO: use NaN when nmea_msg is empty

In addition to test for empty message, I think that testing for broken message is also needed. Hopefully that would solve the problem down the road. I am sorry I wish I could help, but I am too busy at the moment!

[leewujung]

@cyrf0006 : turns out that we did fix that, but on a different branch... I've added the fix as a patch (#197 ) to the master as part of a minor release along with a few other, before the other one is ready.

@PierrePriou : you should be able to parse the file now, but it appears that the file you provided have partially correct readings and a large number of empty ones and a large erroneous spike.

@ngkavin : please check here for the case when only one valid NMEA message is found in the datagrams and add that to class-redesign. Without that it errored out for me for the test file 2019118 group2survey-D20191214-T081342.raw.

[cyrf0006]

I confirm that it works now! Thanks @leewujung & @ngkavin!

[PierrePriou]

It is working! Unfortunately, the GPS malfunctioned during that cruise so that may be the reason behind the lack of data. Thank you @leewujung, @ngkavin and @cyrf0006 for the help!

[leewujung]

@PierrePriou hopefully you had other backups to get the info! I'll close this now. :)