%% (1) Define process directory and data directory
% process_dir = directory containing epsi library
% configFile  = path to config file
process_dir = '~/GitHub/MOD_fish_lib/';
addpath(genpath(process_dir))
md = fullfile(process_dir,'Meta_Data_Process','MDP_norse2023_minnow1_beforeNov19.txt');
data_dir = '/Users/ncouto/Library/CloudStorage/Dropbox/SIO/projects/norse/data/1115_epsi_minnow2_reprocess'; 

%% (2) Initialize epsi class
ec = epsi_class(data_dir,md);

%% (3) Convert raw to mat
ec.f_readData;

%% (4) Create FCTD .mat files
fctd_mat_dir = fullfile(data_dir,'fctd_mat');
mkdir(fctd_mat_dir)

matList = dir(fullfile(data_dir,'mat','EPSI*.mat'));
for iF=1:numel(matList)
		matData = load(fullfile(mat_dir,matList(iF).name));
		base = matList(iF).name(1:end-4);
    [FCTD] =  make_FCTD_mat(matData,fctd_mat_dir,base,'tfo2023');
end
        
%% (5) Concatenate FCTD .mat files into FCTDall
FCTDall_L0 = make_FCTDall_L0(fctd_mat_dir);

%% (6) Correct temperature and conductivity, divide into up and down casts, and process microconductivity data if it exists
FCTDall_L1 = make_FCTDall_L1(FCTDall_L0,fctd_mat_dir);

%% (7) Grid data
FCTDgrid = make_FCTDgrid(FCTDall_L1,fctd_mat_dir);

What this code is doing:

make_FCTDall_L0.m

This function concatenates all the individual FCTD .mat files into a one big FCTDall structure.

make_FCTDall_L1.m