process_dir = '/Users/ncouto/Library/CloudStorage/Dropbox/SIO/projects/comcepts/data/25_0908_sproul_test';
yaml_file = '25_0908_sproul_test.yml';

depth_array = 0:1:200;

%% Process and plot the data
Meta_Data_yaml = fullfile(process_dir,yaml_file);
ec = epsi_class_yaml(process_dir,Meta_Data_yaml);

%%
fprintf('Reading data...\\n')
ec.f_readData;

%%
fprintf('Making new profiles...\\n')
ec.f_makeNewProfiles;

%%
fprintf('Computing turbulence...\\n')
ec.f_computeTurbulence

%%
fprintf('Gridding profiles...\\n')
ec.f_gridProfiles(depth_array);

Change 25_0908_sproul_test to whatever your top level deployment directory is. Inside that you have /raw with the .modraw files and the .yml file.

You should change what's in the .yml to match your deployment. This top section is what you want to edit to match your deployment:

# Mission and deployment info
cruise_name: COMCEPTS
experiment_name: COMCEPTS_2025  #ex) cross-Gulf Stream, post-storm survey
deployment_name: 25_0908_sproul_test
vehicle_name: MINNOW1
telemetry_case: 
pressure_case: MINNOW_PC1
fish_flag: FCTD #EPSI  or FCTD
profiling_direction: down #up or down for turbulence profiles, CTD data will be processed both directions
latitude: 32.7

# Use file headers
use_file_headers: 0 #Set this to 1 if you want to read Meta_Data from each file header. Set to 0 if you always want to use the values in this file.

# CTD info in modraw file headers
ctd_in_modraw: 0 #generally 0 for minnow, 1 for mako

# Serial numbers
sn:
  ctd: '0131' 
  t1: '452'
  t2: '453'
  s1: '405'
  s2: '403'
  f1: '' #fluorometer
  c1: '' #conductivity
  alt: '' #altimeter

# Directory info - these directories are from the point of view of the machine doing the processing. There is a 
# script to parse this file and create a 'Setup' file that ./fctd_epsi will read on the acquisition computer and 
# there is another script on the processing computer that will read this file to do the processing in Matlab. Each 
# computer needs to know the directories from its own point of view
#   process_library = path to MODFISH directory. 'CALIBRATION' directory should be inside this directory.
#   raw_incoming    = directory where raw data are streaming into (for realtime) or where raw data are downloaded (for standalone)
#   processed_data  = top level directory where data will be processed. The library will create a directory inside this directory with a name specified by  'survey_name'
paths_from_processing_machine: #Used for both Mako and Minnow
  process_library: '/Users/ncouto/GitHub/modscripps/MOD_fish_lib'
  raw_incoming_process: '/Users/ncouto/Library/CloudStorage/Dropbox/SIO/projects/comcepts/data/25_0823_test002/raw'
  processed_data: '/Users/ncouto/Library/CloudStorage/Dropbox/SIO/projects/comcepts/data' #top level where deployment directories will be created, each with raw, mat, profiles, etc
  calibrations: 
    ctd: '/Users/ncouto/GitHub/modscripps/MOD_fish_lib/Acquisition/SBECAL'
    shear: '/Users/ncouto/GitHub/modscripps/MOD_fish_lib/EPSILOMETER/CALIBRATION/SHEAR_PROBES'
    fpo7: '/Users/ncouto/GitHub/modscripps/MOD_fish_lib/EPSILOMETER/CALIBRATION/FPO7'