How to Use SeaBASS

The SeaBASS website contains several tools and options to help you find data files and products. The main options for aquiring data can be found under the "Get Data" drop-down in the main menu. The "File Search" is a good starting place as it allows you to perform custom searches for data files based on parameters such as particular measurement types (e.g. CTD, Chl, etc), investigator names, date, location and other options. Alternately, you can manually browse through files and folders using the "Archive" option, but it is generally recommended to use the File Search which simplifies downloading multiple files. The "Validation Search" allows you to search for and download post-processed datasets of successful match-ups between satellite sensors and field measurements. "NOMAD" will direct you to a specific subset of co-located measurements that were organized for algorithm development.
 
The "Lists" main menu option provides links to pages that contain alphabetically sorted lists of different types of information archived in SeaBASS. Visit those pages to view all contributing Investigators, Affiliations, Cruises and Experiment. These options can be useful for cross-referencing, for example, you can click on a particular cruise page to see a summary of all the associated data, or you can click on a particular investigator to see a sortable list of all the experiments and cruises they have contributed to.
 
The "Wiki" includes a number of articles and documents related to a variety of SeaBASS topics. You can browse through the articles or else use the search bar to look for articles that match particular keywords. For example, use the search to find an article containing a MATLAB SeaBASS file reader or a small dataset containing examples of hyperspectral Rrs measurements.
 
If you are interested in contributing data to SeaBASS, please visit the links under "Contribute Data" in the main menu for more information. You are also welcome to reach out with questions to the people listed under "Contact Us."


Table of Contents


 

Use the File Search to find and download data from SeaBASS. Its options help narrow search results by parameters such as date, location, experiment name or particular measurement types. By default, none of these options are specified so your search will look for all files in the database. To find more specific results, narrow your search by specifying one or more search options. Next, click the Search button at the bottom of the page (it has 2 buttons allowing you the choice of opening the results in a new browser tab, which is useful in case you want to modify your search settings without starting from scratch.) On the search results page, you can preview, map and/or plot files, and you can choose to download some or all of the files.

The following General Search Parameters are available for all of the Data Search types:
 
Date Ranges
Click on the boxes following "between the dates of" and a calendar tool will pop up. You may enter dates to limit your search results.
 
Search Tip: The search engine rounds certain dates to the nearest month, so you might wish to pad your search range to ensure you do not miss results of interest.
 
Location
The map and corresponding NESW coordinate boxes following "within the coordinates" allow you to narrow search results to those found within the coordinates of a rectangular region. You can use your mouse to click and drag a rectangle around a region on the map, or you can click on the NESW boxes and type the decimal degrees. Search results will be limited to files containing at least one value within the selected boundaries.
 
Search Tip: The search engine rounds certain locations to the nearest 0.5 degrees, so consider broadening your search accordingly.
 
Keyword Search Filters
You may limit your search results by typing keywords that must be matched. This is a good way to search for results from: particular affiliations, primary investigators (PI), or experiment or cruise names. Type only one affiliation/PI/experiment per box. Auto-complete will offer suggestions based on what you have started to type, however you do not have to use the complete word that it suggests. For example, you can search for just "Smith" even if the auto-complete suggests several specific first names to go with Smith. If you want to perform a search using multiple terms, then click the green plus "+" found to the right of the search string box and type addition terms in new boxes. There is a radial button below the search strings that allows you to toggle any or all. "Any" will find data associated with at least one of your search strings while "all" will restrict results to those meeting all criteria.
 
Examples:

1) Search for all “BATS” cruises (Bermuda Atlantic Time Series). Type “bats” in the search string. Results will include all cruise names that include bats, such as bats108 or bats204.

 

2) Search for data files from the ICESCAPE experiment but only those collected by a group whose primary investigator's name was Mitchell. Click the plus button (+) so there are 2 search boxes. Type “Mitchell” in one and type “ICESCAPE” in the other. Make sure that the "all" radial button is selected so that only results satisfying both search strings are displayed.

 

The Search Type is set by the link you used to reach the search page and can also be changed at the top of the search page. File Search and Validation use the same General Search Parameters, but their other options are different. Here is a brief description of the special search options that are distinct to the different search types.

 

The File Search returns files and documentation that were submitted to SeaBASS. Its adjustable search parameters include:

 

Water Depth: Select a minimum and/or maximum water depth (in meters). In the search engine, water depths are based on ETOPO2 depths derived from the measurement's coordinates.

 

Data Type: Make a selection if you wish to narrow results based on a specific type of file (e.g. scans, pigment files, etc.) Click here for more information on data types.

 

Products: By default, the search results aren't narrowed by a specific product or measurement type, but you can use these options to limit your results to groups of measurements, one or more specific product names or even limit your search results to multiple measurement types that must have both been measured during the same cruise.

 

The "Grouped Products" allows you to check one or more boxes to search for results containing at least one of the measurement types in the groups you picked. Hover your mouse over the name of a particular box for a tooltip describing which measurements it includes. For example, searching with the AOP box checked will find files containing any AOP measurements such as Lu, Lw, Lsky, Ed, Es or Rrs.


If you choose to customize your search for one specific product, first determine its field name abbreviation. Next, check the "specific product" check box and type the abbreviation in the field. Only enter one abbreviation per box. If you want to search for multiple fields, then click the plus ( + ) to the right of the field and enter a field on the following line. Searching for multiple products uses a logical "or" (i.e. results will include any files with at least one of the products), unless you change the option to "Find files where all the specific products entered below were measured in the same cruise".

          

          Downloading Search Results:

        

Your search results will be displayed on a page with two tabs (Results and Download Selection). Use the "download all" button above those tabs if you would like to download all the associated files and documents. Once the progress bar reads "completed" you can click the link under the "file" column to save the tar to your local computer.

 

If you want to only download a subset of your search results, then click the "Download Selection" tab, highlight the files you want to download, then click the "download" button. The files and any accompanying documentation will be bundled after you click "submit query."

 

Previewing Individual Files:

 

The "results" tab has several options that allow you to preview the files:

 

Link / Archive / Documents: Left click the name of a file to try to open it in your browser. To the right of each file name are the words "archive", and "documents" which will can be used to browse the data archive where those files are stored.

 

Map: Clicking "map" will create a pop-up map.

 

Plot: This link creates a pop-up with a simple plotting options. Choose appropriate parameters for one or more of: x, y and z then click create plot.

 

 

Validation

The Validation search returns a file containing match-ups between water measurements and coincident satellite products (plots and basic statistics are also returned). Water leaving values are calculated by SeaBASS staff using some data files submitted to SeaBASS. For more information on methods used, refer to: S.W. Bailey and P.J. Werdell, "A multi-sensor approach for the on-orbit validation of ocean color satellite data products", Rem. Sens. Environ. 102, 12-23 (2006).

 

Sensor Selection: Pick to either compare satellite vs. in situ match-ups or satellite vs. satellite (at points where there was also a concurrent in situ measurement).

 

Water Depth: Select a minimum and/or maximum water depth. In the search engine, water depths are based on ETOPO2 depths derived from the measurement's coordinates.

 

Exclusion Criteria: Default values are given for exclusion criteria, such as the minimum number of valid pixels in the match-up (5x5 pixel box) or the maximum number of hours between the satellite and in situ measurement. You may choose a number anywhere between the range that appears in a tooltip when you hover your mouse over the boxes where you can type in numbers. Broadening the range of acceptable values may increase the total number of match-ups returned by your search, however the agreement of the additional match-ups is likely to decrease.

 

Satellite Version: This drop-down menu allows you to select different processing versions used to derive satellite products, if available.

 

Products: At least one box must be selected.

 

Data Sources: Select one of the following options as the source of the in situ data:

 

SeaBASS Only is the default and relies on standard SeaBASS data rather than special datasets. AERONET and MOBY return match-ups from those alternate data sources.

 

Search results are displayed in a new tab that is created after you click the search button. Scroll down the page to view plots, statistics and a map of your search results. If you searched for multiple products (e.g. Rrs and Chl) then use the drop-down menu to select which results to view. Click "Download Stats/Plots" to locally save a copy of the figures and overall statistics. To save a data file with the values of the results, click "Generate CSV". Wait until the system finishes creating your file at which time you can click the "Download CSV" button to save them to your local computer.

 

Download satellite files used for validation
When you download validation search results, the text file contains paired satellite and in situ values and other information, including a column called  "file_name." Using the file name information, you can download the original satellite file or smaller "extracts" of the original satellite granule (i.e., extracts are small "cutouts" of the original granule created to save space and processing time.) Satellite files can be used in conjunction with software such as SeaDAS to view or perform your own analysis.
 

validation_download_picture

Steps to obtain satellite files corresponding to validation matchups:
 
1) After performing a validation search, download the results (via the "Download CSV" button pictured above.)
 
2) Create a plain text file with the list of one or more file names* you want to download, 1 name per row. Some modification of the file name may be required, described below.

3) Download those files using a script: The Ocean Color forum contains information on how to obtain and use satellite files. Refer to the scripting data downloading FAQ post and download the script of your choice. Use it in combination with the list of file names you just made to download the files.

*Some modification of the file name is necessary. The "file_name" provided is the name of the L2 extract or .tgz text file corresponding to the individual data point. However, the file names are always created with consistent patterns, so it is possible to edit the list of names to search for either the original satellite file or .L1A extract.
 
Example validation "file_name"
A2009292183000.L2_LAC.R0000018533_38N_38N_76W_76W.hdf_OCVAL.nc_2009oct_chesapeake_281555_B5.tgz
 
To generate the name of the validation L1A extract, start with the "file_name", search for ".L2" and replace with ".L1A", then delete the everything past ".nc".
Validation "L1A extract" name:
A2009292183000.L2_LAC.R0000018533_38N_38N_76W_76W.hdf_OCVAL.nc
 
Alternately, to obtain the base name of the parent L2 file, delete everything past "_LAC" and replace with "_OC.nc".
L2 parent name:
A2009292183000.L2_LAC_OC.nc
 
To find the parent L1A file, delete everything past "_LAC" and replace with ".bz2". Finally, change "L2" to "L1A".
L1A parent name:
A2009292183000.L1A_LAC.bz2
 

Data Archive

Click Data Archive in the main menu to browse the directory of folders that contain the data files and documentation submitted to SeaBASS. An explanation of the way these files are organized can be found at the top of the Data Archive page. The archive can be a helpful way to investigate a particular folder or subfolder of data from a particular institution or experiment. However, due to the complexity of understanding various abbreviations and the way files are sorted, the Data Archive is considered an advanced tool only for users who are familiar with SeaBASS. For most situations, it is recommended that you use the Data Search to locate files.
 

NOMAD

NOMAD (the NASA bio-Optical Marine Algorithm Dataset) 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. NOMAD can be downloaded as a single file. The data points contained in it were calculated from carefully selected SeaBASS files. The latest version of NOMAD was last updated in 2008. For the complete description, or to download the data set, please click the NOMAD button in the main menu.
 

Use Lists to look up information

The "Lists" options found in the main menu of the SeaBASS website provides several ways to cross reference information and look up lists of different types of information archived in SeaBASS.
 
  • Affiliations lists the different agencies and institutions from which investigators have submitted data
  • Investigators lists all the different primary investigators who have submitted data. Sortable lists of their associated submissions are provided.
  • Experiments lists all the long term research projects in SeaBASS. Experiment pages include DOI information (once registered) as well as maps and links to the associated cruises.
  • Cruises lists all the specific cruises (or deployments). Individual cruise pages include summary information and a map, as well as links to the data files and their location in the archive. Some cruises were used for validation-only, and those pages do not have summary information.

SeaBASS Wiki

The SeaBASS Wiki can be found in the main menu. Many of the content pages on the SeaBASS website (including this article) are Wiki entries. You can browse through the different articles in the Wiki (sorted by those that were changed recently) using the "next" and "last" buttons at the bottom of the page to see additional entries, or else use the search bar if you are looking for a specific topic.
 
There is a search bar in the upper left corner of the Wiki. Type keywords into the search and press enter to see all articles that match.

Working with Files

SeaBASS formatted files can be opened with text editors, spreadsheet programs, or more advanced analysis software such as MATLAB or IDL.
 

MATLAB reader

A MATLAB script for reading SeaBASS files is available. Please refer to the readsb (MATLAB) Wiki article for more information or to download it.

Perl reader and writer

A Perl module for reading and writing SeaBASS files is available from the CPAN website. Visit its page for more information and to download it.

Python reader

A Python script for reading SeaBASS files is available. Please refer to the readsb (Python) Wiki article for more information or to download it.
Last edited by Chris Proctor on 2017-10-11
Created by Jason Lefler on 2012-10-24