/LISST_toolbox

MATLAB toolbox to process LISST (Sequoia Scientific, Inc.)

Primary LanguageMATLAB

Welcome to the LISST_toolbox!

This toolbox was created to read, process, plot, and write data from profiling LISST (Laser In-Situ Scattering and Transmissometry) instruments manufactured by Sequoia Scientific, Inc.

Currently, the toolbox has only been used to process LISST-Deep Type B and Type C instruments.

Setup

See Setup wiki page for details on how to organize your data and configuration scripts to utilize this toolbox.

https://github.com/britairving/LISST_toolbox/wiki/Setup

Table of Contents

Before running this toolbox, you must organize your data as described in LISST_processing_config.m and configure your project in a script [project]_config.m, where "project" is the unique name of your project. See the setup wiki page for more details.

LISST_processing_workflow.m

wrapper script that calls all subsequent scripts

[project]_config.m

See Setup wiki for information on how to set up this configuration script.

  • Defines metadata used in file header (SeaBASS), instrument specifications, ctd type, and available background files.

LISST_processing_config.m

  • Builds paths to LISST data and instrument files based on expected folder hierarchy
  • Reads/defines instrument information important for data processing and metadata storage
  • Aside from path_length, and inversion model used to process data, variables are read from instrument files lisst.ini and InstrumentData.txt using paths built in the beginning part of this script
  • Defines data processing model (spherical or random shaped particles), and grid settings
  • Defines QC flags
  • Defines automatic QC tests.

LISST_read_raw_data.m

  • Defines structures "meta_raw" and "data_raw"
  • Converts raw data (*.DAT) files in cfg.path.dir_raw using Sequoia's tt2mat.m script

LISST_write_Level1.m

  • Writes raw data in ascii format.

LISST_preprocess_data.m

  • Defines structures "meta_pre" and "data_pre"
  • Calculates date (matlab's datenum format)
  • Calculates temperature and depth based on lisst.ini file contents
  • read_ctd_data_by_type.m | Reads in CTD data (subsequent steps much easier if this is upcast and downcast data with true timestamp!)
  • LISST_match_ctd_cast.m | Matches LISST profile to CTD cast #
  • LISST_correct_time_depth_lag.m | Corrects LISST depth and time based on CTD data
  • LISST_identify_downcast.m | Identifies limits of downcast (decending) in LISST profile
  • Saves data to cfg.path.file_pre

LISST_process_data.m

  • Defines structures "meta_proc" and "data_proc"
  • Limits data to downcasts only
  • LISST_select_background_scatterfiles.m | Select which background files to use for processing
  • getscat_v2.m | Sequoia's function to process raw data to get scattering and transmission
  • invert.p | Sequoia's function that inverts raw data to get uncalibrated volume distribution and midpoint of size bins in microns.
  • Calculates other parameters such as volume distribution, particle size distribution, mean particle size, forward scatter coefficient, beam attenuation, etc.

LISST_data_qaqc_auto.m

  • Performs automated quality control on processed LISST data
  • Performs qc tests described in manual and defined in LISST_processing_config.m

LISST_grid_data.m

  • Defines structures "meta_grid" and "data_grid"
  • Grids data (downcasts only) to depth bins defined by cfg.grid_options.bin_depth_m

LISST_data_qaqc_expert.m

This is not ready yet but will be done in the future!

LISST_write_Level2.m

  • Copies raw files (.dat) and background scatterfiles (.asc) to submit directory
  • writes QC'ed data full resolution and gridded data to formatted files based on cfg.write_format

Citation/acknowledgement

If you use this toolbox, please cite as follows: Brita Irving, LISST_toolbox, (2021), GitHub repository, https://github.com/britairving/LISST_toolbox/

References & Resources