1. Move .modraw files into a deployment processing directory

%% (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) Compute turbulence variables 
ec.f_processNewProfiles;

% (5) Grid profiles 
z = 0:250; %Choose depth range for gridding
ec.f_gridProfiles(z);

Update probe numbers and calibrations. Then reprocess turbulence data:

% Setup
clear; close all

%paths
deploymentdir = 'C:/Users/ankit/Documents/SIO/Academics/Research/24_ASTRAL/Processed_Data/epsi/24_0602_deployment_17'; 
codedir = 'C:/Users/ankit/Documents/SIO/Academics/Research/GitHub/EPSILOMETER/';
md = fullfile(codedir,'Meta_Data_Process','MDP_norse2023_minnow1_beforeNov19.txt');

%generate path to epsi library
addpath(genpath(codedir)) 

%global parameters
depth_array = 0:500;
deployment = '24_0602_deployment_17';
s1 = '320';
s2 = '304';
t1 = '248';
t2 = '351';

%create new directory
cd(deploymentdir)
if ~exist('profiles_new','dir'); mkdir 'profiles_new'; end
if ~exist('figs_new','dir'); mkdir 'figs_new'; end

%% Reprocess epsi data
ec = epsi_class(deploymentdir,md); %read in epsi functions and metadata

%update paths
ec.Meta_Data.paths.data = deploymentdir;
ec.Meta_Data.paths.raw_data = [deploymentdir, '/raw'];
ec.Meta_Data.paths.mat_data = [deploymentdir, '/mat'];
ec.Meta_Data.paths.profiles = [deploymentdir, '/profiles_test'];
ec.Meta_Data.paths.figures = [deploymentdir, '/figs_new'];
ec.Meta_Data.paths.process_library = codedir;
ec.Meta_Data.paths.calibration = [codedir,'CALIBRATION/ELECTRONICS'];

%update serial numbers
ec.Meta_Data.AFE.s1.SN = s1;    %put in the correct serial number
ec.Meta_Data.AFE.s2.SN = s2;   %put in the correct serial number

%reprocess
ec.f_readData; %Convert raw to mat
ec.f_getSNshear;    %Grab the correct cal numbers based on those serial numbers
ec.f_calibrateTemperature;    %Get the temperature calibration numbers
ec.f_makeNewProfiles; %Create new profiles with measured values
ec.f_computeTurbulence;    %Recompute turbulence parameters for all your profiles 
ec.f_gridProfiles(depth_array); %Regrid data