A collection of scripts, notebooks and workflows for working with GNATS (Gulf of Maine North Atlantic Time Series) Slocum glider data.

GNATS glider data

The GNATS glider data are collected along a transect runnning from approximately Portland, Maine to Yarmouth, Nova Scotia:

There are two gliders: Henry and Grampus. Both have CTDs, radiometers for measuring upwelling radiance (L_u) and downwelling irradiance (E_d), a WETLabs ECO Puck for chlorophyll-a and colored dissolved organic matter fluorescence and the backscattering coefficient at 532 nm. Grampus also has a Sea-Bird SUNA nitrate sensor and Aanderaa oxygen sensor. Henry's radiometers are at 412 nm, 443 nm, 490 nm, 510 nm, 532 nm, 555 nm & 670 nm, and Grampus's are at 4 380 nm, 443 nm, 490 nm and 532 nm.

Initial data processing step

Raw data from the gliders are in \*.dbd \*.mbd or \*.sbd files. The \*.mbd files are initially processed into a MATLAB \*.mat file using mbd2matlab.m.

Binning

These scripts bin the glider crossings by depth and longitude. The data are binned into 1 m depth intervals, and 0.01° longitude intervals. For the speed of the gliders, 1 - 3 profiles fall within a 0.01° bin.

binMatFile.py is a module that is used to bin data for a glider mission, and output it into a netCDF file.

binGliderMatFile.py calls binMatFile and for a specified glider mission i.e. it processes an individual mission. Will need to update data file directories.

batchBinGliderMissions.py calls binMatFile for all existing glider missions. Will need to update data file directories.

Dark Count Correction

This script does a dark count correction on the chlorophyll-a fluorometer data. This is a mission wide correction based on the counts in the deepest, darkest waters encountered in the Gulf of Maine: it assumes darkness below 150 m (in the Gulf of Maine, this is within Jordan Basin). Will need to update data file directories.

Quenching Correction

This directory contains two workflows:

1. 01-ApplyDifferentQuenchingCorrections applys six different quenching correction methods to all the glider data.
2. 02-AddCorrectedDataToMissionFiles corrects all the glider chlorophyll fluorescence data with the best performing correction method and adds it to the binned, dark-corrected, mission files.

Creating Secondary Glider Parameters

The notebook CalculatingGliderParams provides a workflow for creating a host of secondary parameters from the measured glider data e.g. mixed layer depth, euphotic depth.