docker-compose build
docker-compose run --rm bash
app/$ ipython
In [1]: from rapidkrill.desktop import desktop
In [2]: desktop('./echosounder/')
Sometimes the echopy installation fails. In this case run the following in container:
pip install git+https://github.com/bas-acoustics/echopy.git/#egg=echopy
We expect processing results like:
2021-08-13 19:58:55,538 root INFO Reading File JR230-D20091215-T121917 copy.raw...
2021-08-13 19:58:55,845 root WARNING no preceding RAW file
2021-08-13 19:58:56,384 root INFO Processing transect 001 : 0.00 - 4.00 nmi...
+----------+-----------+-------------------------+--------+-------------+-----------+
| Transect | N. miles | Time | Seabed | NASC | % samples |
+----------+-----------+-------------------------+--------+-------------+-----------+
| 1 | 0.000 | 2009-12-15T12:19:16.311 | nan | 6.72 | 100.0 |
| 1 | 1.000 | 2009-12-15T12:24:01.986 | nan | 0.00 | 100.0 |
| 1 | 2.000 | 2009-12-15T12:28:47.391 | nan | 61.17 | 100.0 |
| 1 | 3.000 | 2009-12-15T12:33:31.618 | nan | 8967.00 | 93.7 |
+----------+-----------+-------------------------+--------+-------------+-----------+
/app/src/echopy/echopy/cmaps.py:37: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("coolwarm").copy()
self.coolwarm.set_bad(color='k', alpha=1)
RAPIDKRILL is a Python application for processing echosounder data to derive krill distribution and biomass estimates in near real-time. The software is intended to operate onboard ships of opportunity (e.g. fishing vessels) and relay metrics to land-based scientists.
RAPIDKRILL reads RAW files generated by a SIMRAD EK60 echosounder, processes them and sends summary metrics back to scientists via periodic emails. The software has primarily been designed to run on small, cheap single-board computers such as the Raspberry Pi but can also run on desktop computers (We have tested with Linux and OS X systems).
Further information:
- Alejandro Ariza - British Antarctic Survey - github
- Robert Blackwell - British Antarctic Survey - github
- Sophie Fielding - British Antarctic Survey
Our thanks to the officers, crew and scientists onboard the RRS James Clark Ross for their assistance in collecting the data. The Western Core Box cruises and SF are funded as part of the Ecosystems Programme at the British Antarctic Survey, Natural Environment Research Council, a part of UK Research and Innovation.
This work was supported by the Antarctic Wildlife Research Fund and the Natural Environment Research Council grant NE/N012070/1.
This software is licensed under the MIT License - see the LICENSE.md file for details