User Resources

The following section contains various examples for SeaBASS submitters and users.

Standardized Fields and Units

Below is a table of the standard field names and associated units for use in submitting data to the SeaBASS bio-optical archive. The field names are NOT case sensitive. Use the search bar or the find function in your browser to search the table for words or patterns found in the field names, units or descriptions.

 

Special notes regarding wavelength-specific measurements: There are two different ways to indicate wavelengths in a SeaBASS file. If metadata such as date, location or depth vary within a file, then wavelength should be appended to the field name for every measurement combination. For example, downwelling irradiance measured at 412.3 nm would become 'Ed412.3' (listed along with any other Ed measurements, like Ed416.2, Ed419, etc), or aerosol optical thickness measured at 1020 nm would become 'AOT1020'. Alternately, if date, location and depth are assumed to be approximately constant for all measurements in the file, then use the field 'wavelength' to provide a column of the measured wavelengths and don't include them as part of the field names (this organization is commonly used for reporting spectrophotometry measurements).

 

To provide additional information about a field, for example, the standard deviation of the reported average of replicate measurements, refer to the table of field name modifiers below. For example, "chl_sd" or "ag510_sd". More information and examples can be found in the tables of suffixes and modifiers. Please contact SeaBASS staff if you want to discuss adding new fields.

 

Notes on HPLC pigment field names

AERONET Ocean Color

The NASA OBPG routinely downloads data from the AERONET-Ocean Color website for use in satellite sensor validation match-up analysis. As described by Zibordi et al. (2009), the AERONET-OC network consists of globally distributed autonomous radiometer systems maintained at fixed offshore sites. Please refer to the rest of the information in this article for details on how to acknowledge the use of AERONET-OC data and how the OBPG processes these data.

Who We Are

High quality in situ measurements are prerequisite for satellite data product validation, algorithm development, and many climate-related inquiries. As such, the NASA Ocean Biology Processing Group (OBPG) maintains a local repository of in situ oceanographic and atmospheric data to support their regular scientific analyses. The SeaWiFS Project originally developed this system, SeaBASS, to catalog radiometric and phytoplankton pigment data used their calibration and validation activities. To facilitate the assembly of a global data set, SeaBASS was expanded with oceanographic and atmospheric data collected by participants in the SIMBIOS Program, under NASA Research Announcements NRA-96 and NRA-99, which has aided considerably in minimizing spatial bias and maximizing data acquisition rates. Archived data include measurements of apparent and inherent optical propertiesphytoplankton pigment concentrations, and other related oceanographic and atmospheric data, such as water temperature, salinity, stimulated fluorescence, and aerosol optical thickness. Data are collected using a number of different instrument packages, such as profilers, buoys, and hand-held instruments, and manufacturers on a variety of platforms, including ships and moorings.

readsb (Python)

SB_support_v##.py is a Python module containing a set of classes designed to open, read, and manipulate data files that are in a SeaBASS format. While many of Python's built-in functions may be used to read SeaBASS files, this module leverages Python libraries and tools, including NumPy and Ordered Dictionaries, to efficiently read, sort, mask, and return the contained data for easy use without errors or significant intervention. Using this function, data outputs will be returned as data structures containing the file's header information (metadata) as an array of strings, the file's comments as an array of strings, the file's missing data, above detection limit, and below detection limit values (if present), the file's variable and unit lists as an Ordered Dictionary indexed by variable name, and the file's data as an Ordered Dictionary indexed by variabile name. Additionally, optional arguments flags that may be toggled are mask_missing, mask_above_detection_limit, and mask_below_detection_limit (all set true by default), which remove the header-defined values for these fill values, replacing them with NaN.

readsb (MATLAB)

readsb.m is a MATLAB function designed to open and read data files that are in a SeaBASS format. Some SeaBASS files can be opened using MATLAB's various built-in import functions, however many of the built-in methods are unsuited to efficiently open SeaBASS files without errors or significant manual intervention. Using this function, data outputs can simply be returned as either a cell array or as a structure where the names of the data field headers from the SeaBASS file are array field names (e.g. dataStructure.DEPTH, dataStructure.CHL, dataStructure.LW412). File metadata information is also returned in a separate structure and array.

Data Format and Submission

To account for the continuous growth of the bio-optical data set and the wide variety of supported data types, the NASA Ocean Biology Processing Group felt it essential to develop efficient data ingestion and storage techniques. While this requires a specific data file format, the data protocols were designed to be as straightforward and effortless as possible on the part of the contributor, while still offering a useful format for internal efforts. The system was intended to meet the following conditions: simple data format, easily expandable and flexible enough to accommodate large data sets; global portability across multiple computer platforms; and web accessible data holdings with sufficient security to limit access to authorized users.

FCHECK

To assist with the standardization of SeaBASS data files, the SIMBIOS Project developed feedback software, named FCHECK, to evaluate the format of submitted data files. Since then, it has been rebuilt from the ground up by the SeaBASS development team to make it available to the end-users. Using FCHECK, contributors may evaluate the format of their SeaBASS-compatible files prior to submission.

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.