SeaBASS Software Tools

A number of custom tools have been developed to work with SeaBASS formatted files in a few programming languages, including Perl, Python, MATLAB, etc.

SeaBASS Validation Description

The SeaBASS validation system is designed to provide ground-truth comparisons between in situ measurements and coincident satellite-borne ocean color instrument observations. The results are displayed and distributed via a web-based search engine, available for assessments of satellite measurements and algorithm performance. This article briefly summarizes the following steps involved in this system of creating match-ups: 1) Assembly of in situ data; 2) Reduction of in situ data to relevant observations; and 3) Preparation of coincident satellite imagery.

NASA Particle Absorption Workshop

This page has been set up for documents and information that will be shared at the NASA Particle Absorption Workshop (June 2014).

NOMAD: NASA bio-Optical Marine Algorithm Dataset

NOMAD is a publicly available, global, high quality in situ bio-optical data set for use in ocean color algorithm development and satellite data product validation activities. Data products include coincident observations of water-leaving radiances and chlorophyll a concentrations, along with relevant metadata, such as the date, time, and coordinates of data collection and binary processing flags. Inherent optical properties (IOPs; e.g., spectral absorption and backscattering coefficients) and aerosol optical thicknesses have been or will be included in the near future. The entire dataset is available via a digital text file provided below under Downloads. Additional background details, such as the motivation for creating such a data set, and a historical perspective of such data sets, are provided in the Werdell and Bailey reference listed below.

 

NOMAD is available for research uses only. It was compiled by the NASA Ocean Biology Processing Group at Goddard Space Flight Center, Maryland, USA, using generous data contributions from the ocean color research community. Source bio-optical data are available online via a suite of SeaBASS Search Engines. Optimum interpolation (OI) sea surface temperature (SST) data were acquired from the NOAA Climate Diagnostics Center. ETOPO2 water depths were acquired from the NOAA National Geophysical Data Center. NOMAD Data access and use are governed by the SeaBASS Data Access Policy. Please direct comments, questions, and identified outliers to the SeaBASS Administrator.

Hyperspectral Rrs Examples

The following file contains seven examples of hyperspectral remote sensing reflectance (Rrs) spectra. These spectra were subjectively selected and compiled with the goal of providing examples of a variety of spectral shapes from different waters. Please read below for more information on the file contents.
 
This data file is available for research uses only. It was compiled by the NASA Ocean Biology Processing Group at Goddard Space Flight Center, Maryland, USA, using generous data contributions from the ocean color research community. Source bio-optical data are available online via a suite of SeaBASS Search Engines. Access and use are governed by the SeaBASS Data Access Policy. Please direct comments, questions, and identified issues to the SeaBASS Administrator.

Perl Tips

This article was written to provide a few Perl tips and examples that can help you quickly edit single or batch data files from a command line.
 
Perl is a general-purpose language that is very powerful at manipulating data files containing text and numbers. Often it is necessary for SeaBASS data submitters or users to search and replace patterns found throughout many text files, which can be very time consuming if you manually open, change and resave each file individually. If you've ever accidentally misformatted a header, or need to get rid of extra spaces at the beginning of every line, or faced some other repetitive task involving search-and-replace, then don't fret; continue reading to learn some simple ways to fix those issues in a single command.
 
Perl is free and is even installed by default on several operating systems (e.g. most Macs). If you don't already have it, it can be downloaded from www.perl.org for most flavors of Windows, Mac and Linux operating systems. Of the options available, Windows users might wish to try Strawberry Perl (though we do not officially endorse any particular version.) Many Perl guides and tutorials already exist on the Internet so the content on this page will focus only on a few tips that are relevant to SeaBASS data. You can accomplish extremely complex tasks by writing longer amounts of code in Perl, but those are beyond the scope of this article. If Perl is new to you then you might also want to read a more comprehensive introduction such as the one found on the official Perl site, but you should be able to get started with the examples below.

Datasets

SeaBASS contains several special datasets that are not indexed in the file search engine. These datasets either contain files with atypical formats, unusual measurement types, or other special considerations that do not quite conform to the standardized SeaBASS format. This page provides a centralized listing of such datasets, as those files can still be accessed and manually downloaded from the archive. Please refer to individual pages for more information.

Perl SeaBASS to netCDF Converter (sb2nc)

sb2nc is a Perl script designed to open and read data files that are in a SeaBASS format and convert them to netCDF4 files. Using this script, nearly CF-compliant netCDF files may be simply generated from valid SeaBASS files that have passed FCHECK. This Perl script takes care of determining and defining netCDF file dimensions, global attributes, variables, and variable sub-attributes, including _Fillvalue, valid_min, valid_max, units, etc