1.1. Convert a file to access bathymetry and backscatter

This is a tutorial on how to use CoFFee to convert a file to access 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));

Set folder of raw data files:

dataFolder = 'C:\Users\Schimel_Alexandre\Data\MBES\Kongsberg all\EM2040C\Deakin_2014_EM2040c_Kelp-Pilot-Study\300kHz';

Get the first '.all' file in folder:

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 file:

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

Access bathymetry and backscatter:

bathymetry = -fData.X8_BP_DepthZ; % in m
backscatter = fData.X8_BP_ReflectivityBS; % in dB

Display:

figure; 

ax(1) = subplot(211);
imagesc(bathymetry); 
grid on; colorbar; colormap(ax(1),'jet');
xlabel('ping number'); ylabel('beam number'); title('bathymetry (m)');

ax(2) = subplot(212);
imagesc(backscatter); 
caxis([prctile(backscatter(:),10) prctile(backscatter(:),90)]);
grid on; colorbar; colormap(ax(2),'gray');
xlabel('ping number'); ylabel('beam number'); title('backscatter (dB)')

sgtitle(rawFileName ,'Interpreter','none');