BowChain

Overview

Process a all bow chain deployments from a cruise with BowChain_master(cruiseName). Process a specific vessel or deployment with BowChain_master(cruiseName,vesselName,deploymentName).

BowChain_master.m is structured as follows:

Cruise and deployment configuration

The cruise’s configuration function is called using get_config.m. This fills the cruise’s config structure with global default options from config_default.m and checks deployments for missing options.

Deployment processing

Each deployment is processed sequentially with the following steps:

1. Sensor setup (preproc_setup.m)
   • The user-defined sensor serial numbers are passed into get_sensor_info.m. This function acts as a database containing processing instructions for different sensor types.
   • If the instrument type is known and an associated raw datafile is found, the sensor gets an entry in config.sensors containing parsing instructions and an output .mat file name.
2. File conversion (preproc_raw2mat.m)
   • Using the information gathered in preproc_setup.m, each sensor’s raw datafiles are convered to a .mat format. This step is skipped if .mat files already exist.
3. Load data
   • Each sensor’s .mat file is loaded using proc_load_mat.m. This creates a data cell array with raw sensor data in each cell.
4. Sample data onto a uniformly-spaced time base using proc_grid_init.m.
   • This initializes the grided data structure that is passed through the next several functions.
   • If any customizations add additional fields to the ~gridded~ structure, they must be initialized in this function. MATLAB will throw an error if a function tries to add fields to a single entry of a non-scalar struct array. In other words, gridded(i) = some_function(gridded(i)) will not work if some_function tries to add non-initialized fields to gridded(i).
5. Calibrate sensor clocks and pressure sensors
   • Clocks are calibrated using proc_time_offsets.m. The config.time_offset_method and related fields control what this function does.
   • Pressure sensors are calibrated with proc_pressure_cal.m if the config.zero_pressure_interval field is defined.
   • Time and pressure offsets are applied to the raw data, and it is once again sampled onto a uniformly-spaced time base using proc_grid_init.m.
6. Compute positional offsets with a chain shape model
   • proc_chain_model.m uses known instrument positions and measured pressure data to compute positional offsets for each measurement. This fills the x and z fields of the gridded data structure.
7. Apply positional offsets to GPS data
   • proc_gps.m converts positional offsets to arclength on the WGS84 ellipsoid and adds them to the ship’s position in the direction of the ship’s heading.

Setup

BowChain

Clone the git repository:

git clone https://github.com/dswinters/BowChain.git

Copy the user_directories.m.example file to user_directories.m:

cd BowChain/Code
cp user_directories.m.example user_directories.m

RSKtools

Download RSKtools from https://rbr-global.com/support/matlab-tools and add it to MATLAB’s path (typically somewhere like $HOME/Documents/MATLAB). I do this in $HOME/Documents/MATLAB/startup.m:

addpath(genpath(fullfile(userpath,'RSKtools')));

Configuration

Deployment configuration

Within the Code directory, cruise-specific folders contain information needed to locate and process deployment data. Each cruise needs a <cruise>_config file that returns a structure containing configuration information for each deployment.

See the config_SUNRISE.m in the SUNRISE_2021 branch for an example of a cruise configuration file. This function can utilize whatever organizational structure exists for a cruise; it just needs to return a config structure with the following options for each deployment:

Deployment configuration options

Base parameters

Field	Description	Default
config.name	deployment name
config.vessel	vessel name
config.dir.raw	raw deployment data directory
config.sensor_sn	cell array of sensor serial number strings
config.sensor_pos	vector of sensor positions
config.dn_range	time interval for deployment
config.freq_base	frequency of gridded output data	2 Hz
config.time_offset.method	method for sensor clock corrections	‘none’
config.zero_pressure_interval	time interval for zero-pressure calibration	no pressure calibration
config.chain_model	model to use for instrument position corrections	‘cm_straight’
config.file_gps	location of GPS data file

Some configuration options require additional fields in the config structure:

Field	Value	Additional Required Field	Description
config.time_offset_method	‘cohere’	config.cohere_interval	Interval to use for clock calibration
config.time_offset_method	‘known_drift’	config.time_synched	Time (datenum,UTC) that clocks were synched
config.time_offset_method	‘known_drift’	config.drift	Measured clock drift on recovery

Instrument configuration

Each instrument is linked to an instrument type via its serial number, and each instrument type is linked to a parsing function and a raw data file extension. This is all done in get_sensor_info.m, which takes a serial number as input.

Any instruments that I have not encountered will not be included in this list! Fortunately, associating serial numbers to instruments can be easily done by modifying get_sensor_info to include new serial numbers.

Every sensor parsing function is wrapped in a simple function to rename the fields in a consistent manner. The following files in the Code/ParseFunctions/ directory are all examples of such “wrapper” functions:

• Code/ParseFunctions/parse_rbr_concerto.m
• Code/ParseFunctions/parse_rbr_solo.m
• Code/ParseFunctions/parse_sbe39.m
• Code/ParseFunctions/parse_sbe56.m

See the latter half of get_sensor_info.m for associations between instrument types and parsing functions.