2.1. Georeference seafloor data

This is a tutorial on how to use CoFFee to georeference bathymetry and backscatter 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:

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', 'nFilesWanted', 1);
rawFileName = CFF_file_name(char(rawFile));
CFF_print_raw_files_list(rawFile);

Convert raw data file:

fData = CFF_convert_raw_files(rawFile,'conversionType','seafloor',...
    'forceReconvert',1);

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;

Georeference all seafloor data with CFF_georeference_bottom_detect:

fData = CFF_georeference_bottom_detect(fData);

Access bathymetry, backscatter, and the coordinates of the soundings:

bathymetry = -fData.X8_BP_DepthZ; % in m
backscatter = fData.X8_BP_ReflectivityBS; % in dB
easting = fData.X_BP_bottomEasting; % in m
northing = fData.X_BP_bottomNorthing; % in m

Display:

figure; 

ax(1) = subplot(121);
scatter(easting(:), northing(:), 10, bathymetry(:),'filled'); 
grid on; axis equal; colorbar; colormap(ax(1),'jet');
xlabel('easting (m)'); ylabel('northing (m)'); title('bathymetry (m)');
CFF_nice_easting_northing(); % pretify the axes labels

ax(2) = subplot(122);
scatter(easting(:), northing(:), 10, backscatter(:),'filled'); 
caxis([prctile(backscatter(:),10) prctile(backscatter(:),90)]);
grid on; axis equal; colorbar; colormap(ax(2),'gray');
xlabel('easting (m)'); ylabel('northing (m)'); title('backscatter (dB)')
CFF_nice_easting_northing(); % pretify the axes labels

sgtitle(sprintf('%s\n(%s-%s)',rawFileName,ellipsoid,projection) ,'Interpreter','none');