2.2. Georeference water‐column data

This is a tutorial on how to use CoFFee to georeference water-column data. Replace the paths appropriately.

Start from a clean slate:

clear all
close all
restoredefaultpath();
clc

Set location of CoFFee code root folder and add to path:

coffeeFolder = 'C:\Users\Schimel_Alexandre\Code\MATLAB\CoFFee';
addpath(genpath(coffeeFolder));

Select a raw data file with water-column data and convert it. For Kongsberg data acquired in file pairs (i.e. *.all and *.wcd, or *.kmall and *.kmwcd), ensure the pair of files are in the same folder.

dataFolder = 'C:\Users\Schimel_Alexandre\Data\MBES\Kongsberg all\EM2040C\Deakin_2014_EM2040c_Kelp-Pilot-Study\300kHz';
rawFile = CFF_list_raw_files_in_dir(dataFolder, 'filesType', '.all/.wcd', 'nFilesWanted', 1);
rawFileName = CFF_file_name(char(CFF_onerawfileonly(rawFile)));
fData = CFF_convert_raw_files(rawFile,'conversionType','WCD',...
    'forceReconvert',1);

Access water-column data:

iPing = 1;
WCD = CFF_get_WC_data(fData,'WC_SBP_SampleAmplitudes','iPing',iPing);

At this stage, the water-column data is not yet georeferenced. We can only display it in its native format, aka as beam/sample:

figure; 

imagesc(WCD'); 
grid on; colorbar; colormap jet
xlabel('sample number'); ylabel('beam number');

titleStr = sprintf('%s water-column (dB), ping %i',rawFileName,iPing);
title(titleStr,'Interpreter','none');

To calculate the coordinates of each water-column data sample in the swathe frame (that is, distances across and upwards), use CFF_get_WCD_swathe_coordinates:

nSamples = size(WCD,1);
[sampleAcrossDist,sampleUpDist] = CFF_get_WCD_swathe_coordinates(fData,iPing,nSamples);

With this new information, we can display the water-column data as a wedge (or fan):

figure;

h = pcolor(sampleAcrossDist, sampleUpDist, WCD);
set(h,'AlphaData',~isnan(WCD),'facealpha','flat','LineStyle','none');
grid on; axis equal; colorbar; colormap jet
xlabel('across-track distance (m)'); ylabel('height above sonar (m)');

titleStr = sprintf('%s water-column (dB), ping %i',rawFileName,iPing);
title(titleStr,'Interpreter','none');

To calculate the coordinates of each water-column data sample in the projected frame (that is, easting, northing, and height), we first need to process navigation data with CFF_compute_ping_navigation_v2:

fData = CFF_compute_ping_navigation_v2(fData);

Using CFF_compute_ping_navigation_v2 without input parameters selected a default ellipsoid and projection for all future georeferencing:

ellipsoid = fData.MET_ellips;
projection = fData.MET_tmproj;

Then, the coordinates in the projected frame can be obtained using CFF_get_WCD_projected_coordinates:

[sampleEasting, sampleNorthing, sampleHeight] = CFF_get_WCD_projected_coordinates(fData,iPing,nSamples);

With this new information, we can display the water-column data in "3D":

figure;

idxValidWCD = ~isnan(WCD);
h = scatter3(sampleEasting(idxValidWCD), sampleNorthing(idxValidWCD), sampleHeight(idxValidWCD), 10, WCD(idxValidWCD), 'filled');
grid on; axis equal; colorbar; colormap jet
xlabel('easting (m)'); ylabel('northing (m)'); ylabel('height (m)');
CFF_nice_easting_northing(); % pretify the axes labels

titleStr = sprintf('%s water-column (dB), ping %i\n(%s-%s)',rawFileName,iPing,ellipsoid,projection);
title(titleStr,'Interpreter','none');