VIIRS Ocean Color Data Visualization and Processing

With IDL-Based NOAA-SeaDAS

Xiaolong Wang1,2, Xiaoming Liu1,2, Lide Jiang1,2, Menghua Wang1,*, and Junqiang Sun1,3
1
NOAA/NESDIS Center for Satellite Applications and Research
E/RA3, 5830 University Research Ct., College Park, MD 20740, USA
2
CIRA, Colorado State University, Fort Collins, CO, USA
3
Global Science and Technology, Greenbelt, MD 20770, USA
*Contact: Menghua.Wang@noaa.gov

ABSTRACT
The NOAA Sea-viewing Data Analysis System (NOAA-SeaDAS) is an Interactive Data Language (IDL)-based satellite
data visualization, analysis, and processing system based on the version 6.4 of the NASA’s Sea-viewing Wide Field-of-
view (SeaWiFS) Data Analysis System (SeaDAS) released in 2012. NOAA-SeaDAS inherited all the original
functionalities of SeaDAS 6.4 and was upgraded with many new functions and new sensor supports, particularly the
support of the Visible Infrared Imaging Radiometer Suite (VIIRS) onboard the Suomi National Polar-Orbiting
Partnership (SNPP). The main goal of the NOAA-SeaDAS development is primarily in support of NOAA ocean color
team’s calibration and validation activities. The current version of NOAA-SeaDAS can visualize, analyze, and process
VIIRS Sensor Data Records (SDR or Level-1B data) produced by the NOAA Interface Data Processing System (IDPS),
ocean color Environmental Data Records (EDR or Level-2 data) produced by the NOAA Multi-Sensor Level-1 to Level-
2 (MSL12) ocean color data processing system, and Level-3 data binned or mapped from Level-2 data produced by
NOAA-MSL12. NOAA-SeaDAS is currently serving an active IDL user group at NOAA and will serve other
institutions and universities in the future. The goal is to allow various scientific users to visualize, analyze, and process
VIIRS data from Level-1B through Level-2 and Level-3. In addition, NOAA-SeaDAS can also visualize satellite images
from the Korean Geostationary Ocean Color Imager (GOCI), as well as many other satellite ocean color sensors, e.g.,
SeaWiFS, the Moderate Resolution Imaging Spectroradiometer (MODIS), etc. NOAA-SeaDAS is under constant
development to create new system functionalities and enhance user experience. With constantly increasing volume in the
global ocean color data archive, NOAA-SeaDAS will play an important role in support of global marine environment
data analysis and various scientific applications.
Keywords: NOAA-SeaDAS, VIIRS, MODIS, GOCI, IDL, ocean color remote sensing, image visualization

1. INTRODUCTION
The Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Data Analysis System (SeaDAS) was a comprehensive image
analysis package for the processing, display, analysis, and quality control of ocean color data [1] developed at NASA
Goddard Space Flight Center (GSFC). NOAA Sea-viewing Dada Analysis System (NOAA-SeaDAS) is a continuous
development of Interactive Data Language (IDL)-based SeaDAS 6.4 at NOAA Center for Satellite Applications and
Research (STAR). NASA SeaDAS was the primary data analysis software for SeaWiFS Project starting 1995. Later
system upgrades added support for the Moderate-Resolution Imaging Spectroradiometer (MODIS) [2, 3], Medium
Resolution Imaging Spectrometer (MERIS) [4], and other earlier ocean color sensors [5]. SeaDAS through version 6.4
released in 2012 was based on IDL. The IDL-based SeaDAS provides a user-friendly interface that meets the needs of
novice users of data analysis software, as well as more advanced IDL users who want capabilities for algorithm
modification and new method or model exploration on various satellite sensors. The IDL-based SeaDAS was award-
winning system software with a fully functional Linux/Mac platform version and PC platform version via virtual
machine applications and was widely used by the ocean color community.
SeaDAS 6.4, however, was the last IDL-based release by NASA Ocean Biology Processing Group (OBPG). Beginning
with SeaDAS 7.0 release in 2013, Java and Python have been used to replace IDL as the programming language, and all
IDL-based functions were removed. Although Java and Python have their advantages in the software development
process, heritage SeaDAS users familiar with IDL-based functions and scripts may not want to switch to Java and

Ocean Remote Sensing and Monitoring from Space, edited by Robert J. Frouin, Delu Pan,
Hiroshi Murakami, Young Baek Son, Proc. of SPIE Vol. 9261, 92611H · © 2014 SPIE
CCC code: 0277-786X/14/$18 · doi: 10.1117/12.2070478

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 Python, and may prefer to continue using an IDL-based SeaDAS. Therefore in 2012, the ocean color team at
NOAA/STAR decided to continue to develop IDL-based SeaDAS, primarily in support of NOAA ocean color team
activities for satellite data visualization, analysis, manipulation, and processing.
NOAA’s SeaDAS development (renamed as NOAA-SeaDAS) inherited all functionalities of SeaDAS 6.4 and all IDL-
based capabilities for further development and enhancement. With the successful launch of Visible Infrared Imaging
Radiometer Suite (VIIRS) [6, 7] on the Suomi National Polar-orbiting Partnership (SNPP) satellite on October 28, 2011,
there was an emergent need for visualization, analyzing, and processing VIIRS ocean color data, thus adding VIIRS
support became the highest priority of NOAA-SeaDAS development. VIIRS is now fully supported in NOAA-SeaDAS:
all VIIRS Sensor Data Records (SDR or Level-1B data), Environmental Data Records (EDR or Level-2 data), and
Level-3 binned data products can now be visualized, displayed, and remapped with various map projections. Pixel-level
quality flags for SDR and EDR data can be evaluated, displayed, and overlaid on ocean color products images. For
advanced IDL users, all IDL-based batch processing functionalities are also fully supported for VIIRS.
In addition to VIIRS support, NOAA-SeaDAS also supports the Korean Geostationary Ocean Color Imager (GOCI)
onboard the Communication, Ocean and Meteorological Satellite (COMS) [8-11]. Support for upcoming ocean color
sensors will be added in the future. Furthermore, many new data manipulation and visualization functionalities, such as
granule aggregation, true color image generation, and bowtie pixel mitigation, etc., have been added into the system.
NOAA-SeaDAS has become a powerful IDL-based tool for ocean color scientists and data users.

2. VIIRS SUPPORT IN NOAA-SEADAS

VIIRS is a new generation Earth-observing sensor with global ocean color capability similar to MODIS-Aqua. It was
placed on an 824-km sun-synchronous polar orbit with a node of about 13:30 pm. VIIRS swath width is broader than
MODIS (3000 km versus 2330 km), and the spatial resolution at nadir is finer than MODIS (750 m versus 1 km) [6].
The ocean color EDR [7, 12, 13] is a key product suite derived from VIIRS. Normalized water-leaving radiance at
various spectral wavelengths, nLw(λ) [14], chlorophyll-a concentration [15], and water diffuse attenuation coefficient at
the wavelength of 490 nm, Kd(490) [16-18] are in demand among ocean science community and marine resource
managers.
NOAA-SeaDAS (inherited from original SeaDAS) provides various functionalities for image visualization and data
manipulation. These powerful IDL-based functionalities had been well-tested and heavily used for SeaWiFS, MODIS
and other ocean color sensors since 1995, and they can be easily upgraded for VIIRS support by adding an interface for
read/load of VIIRS data into NOAA-SeaDAS. VIIRS SDR, EDR, and Level-3 binned data are now all fully supported in
NOAA-SeaDAS to take of advantage of these functionalities.
2.1. VIIRS Data Source and Format
There are two different sources of VIIRS SDR data: the operational SDR data from the NOAA Interface Data Processing
System (IDPS), and reprocessed SDR data generated from the Algorithm Development Libraries (ADL). Data files from
these two sources are similar and both are in HDF-5 format. VIIRS ocean color EDR data also come from two different
sources. The NOAA operational ocean color EDR data from the IDPS are in HDF-5 format, which is similar to IDPS
SDR data. However, the ocean color EDR data generated from the NOAA’s Multi-Sensor Level-1 to Level-2 (NOAA-
MSL12) ocean color data processing system is in HDF-4 format. It is noted that MSL12 was developed as a consistent
and common ocean color data processing system to produce ocean color data from multiple ocean color sensors [19-21].
All of these SDR and EDR data from different sources can be visualized and manipulated in NOAA-SeaDAS. The
VIIRS Level-3 data is essentially in the same format as the SeaWiFS and MODIS Level-3 data and thus is also
supported.
2.2. VIIRS Image Visualization and Manipulation
The general appearance of the graphical user interface (GUI) (Fig. 1) for VIIRS support in NOAA-SeaDAS is inherited
from SeaDAS 6.4. At the time of loading VIIRS data into NOAA-SeaDAS, the system will attempt to automatically
detect its file format (HDF-4 or HDF-5), and whether it is an SDR, an EDR or a Level-3 file. Corresponding processing
programs and parameters will then be applied to match the input file types. NOAA-SeaDAS preserves all previous
SeaDAS image visualization and manipulation functions, such as histogram, contours, coastline, text annotation, zoom
window, graphic management, multiple band display and band data arithmetic, etc. All VIIRS images are geo-registered
for image display with all VIIRS quality flags. Additionally, the loaded VIIRS images can be mapped into various map

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 projections, and the remapped image data can be manipulated. Basically, all image visualization and manipulation
functions that were originally developed for SeaWiFS and MODIS are now working for VIIRS.

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Figure 1. General NOAA-SeaDAS GUI for VIIRS EDR image visualization (chlorophyll-a on March 26,
2012). All image quality flags can be checked at pixel level, zoom window was open to focus on Florida
Keys regions.

2.3. VIIRS EDR Data Quality Flag Display

A powerful tool in NOAA-SeaDAS enables the display of pixel-level EDR data quality flags. Users can use quality flags
to find out the triggers of certain abnormal pixels in the EDR data, and tune the processing algorithm accordingly to
further improve the data quality. The quality flags can also be used to mask out unwanted low-quality pixels for various
applications with different quality requirements. NOAA-MSL12 generated Level-2 data have a different quality flag
structure than that associated with the operational IDPS ocean color EDR:
• NOAA-MSL12 Level-2 flags: Each pixel in a Level-2 file generated from NOAA-MSL12 has a 32-bit quality flag
parameter, and each bit is assigned to a certain flag condition (e.g., high sun glint, high sensor-zenith angle, etc.).
• IDPS ocean color EDR quality flags: IDPS EDR file has seven bytes (each byte has 8 bits) of quality flags for each
pixel. In each byte, the binary value of a single or multiple bits is assigned to a certain flag condition
NOAA-SeaDAS provides two different GUIs for the two sources, i.e., NOAA-MSL12 and IDPS, and it automatically
loads the appropriate GUI according to source of flags. Through the GUI, users can select and assign different flags to
different colors, and overlay the flags on ocean color images. Figures 2 and 3 show the examples of flag display for
NOAA-MSL12 Level-2 flags and IDPS EDR flags, respectively.
2.4. Level-3 Binned Data Support
NOAA-SeaDAS has a built-in function to create VIIRS Level-3 binned (L3b) data files from the Level-2/EDR data. The
L3b data are stored in a representation of a global, cylindrical equal-area grid. The bins can be thought of as square grid
elements or grid cells, and the standard bin resolutions can be 1, 2, 4 or 9 km. In the “binning” process, daily Level-2
data are spatially averaged in bins defined in the L3b file, and they can be further averaged temporally into weekly,
monthly, annually or climatology L3b files. The statistical data provided in L3b files allow for the calculation of the
mean, standard deviation, median, and mode for each ocean color product. Additionally, those VIIRS L3b data can be

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 remapped with various map projections and visualized with NOAA-SeaDAS. Figure 4 shows a global chlorophyll-a
images generated from 8-day L3b data.
2.5. Command-Line Mode and Batch Processing
Although the user-friendly GUI is convenient to use in interactive mode, it is not efficient for processing large amounts
of data. Fortunately, VIIRS SDR, EDR, and Level-3 data can all be loaded, displayed, visualized, and remapped in
command-line mode as an IDL command. These commands can also be invoked in IDL scripts and run in batch mode.
Virtually any functionality of NOAA-SeaDAS image visualization, data processing, and graphics operations can be
automated in IDL scripts. These scripts can be combined with Unix/Linux shell scripts to perform complex data
processing, and provide efficient ways for batch processing of a large amount of ocean color data.

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Figure 2. VIIRS NOAA-MSL12 32-bit Level-2 flag display on a mapped image (October 24, 2012).

Figure 3. VIIRS IDPS EDR data display with quality flag display (pink color identified as turbid water regions (April 6, 2012).

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 .

Figure 4. VIIRS global chlorophyll-a concentration generated from 8-day Level-3 binned file (August 29, 2014).

3. NEW FUNCTIONALITIES FOR VIIRS

The image visualization and manipulation functionalities for heritage ocean color sensors work well for VIIRS in
NOAA-SeaDAS. However, the VIIRS sensor has unique features, thus requires new functionalities. For example, bowtie
pixels are included in MODIS files, but they are excluded from the VIIRS SDR and EDR files. Therefore, special
treatment of the bowtie-deleted pixels is needed for VIIRS images. In addition, new functions have been developed for
multiple granule aggregation and true color image generation in support of VIIRS ocean color data analyses.
3.1. Multiple Granule Aggregation
Normally, one VIIRS granule is ~85.7 seconds, which contains 48 scans (768 scan-lines). As a result, each VIIRS
granule covers only ~570 km in the along-track direction. For an application that spans a large distance in the along-
track direction, aggregating multiple granules into a single file is desirable. For this purpose, the NPP Granule
Aggregation and Packaging Utility (NAGG, http://www.hdfgroup.org/projects/jpss/nagg_index.html) created by HDF
Group is integrated into NOAA-SeaDAS. With NAGG, multiple VIIRS granules can be packaged together to make a
larger swath and optimize image coverage for a region of interest.
A GUI was built in NOAA-SeaDAS to guide users for multiple band data aggregation with IDL data array operation
functions. When those multiple adjacent granule images are loaded into NOAA-SeaDAS, multiple granule aggregation
can be implemented with IDL data array operation and manipulation with associated geo-information guide. Because
those granule data aggregations are performed by NOAA-SeaDAS through the loaded band operation, data manipulation
can be applied efficiently and the results can be visualized immediately with new merged band image display. The
process can also be performed in command line operations. Aggregated granule images can be output as generic HDF
files with navigation information embedded or as mapped file with geo-information, which are portable to work on other
computing platforms.
3.2. True Color Image Generation
NOAA-SeaDAS includes a function to generate high quality true color images. This function was developed based on
the previous MODIS true-color method from University of Wisconsin. Specifically, Rayleigh-corrected radiances or
reflectances for VIIRS SDR bands 3, 4, 5, and 7 were applied using the software from the NASA Direct Readout
Laboratory (DRL, http://directreadout.sci.gsfc.nasa.gov/?id=software). Figure 5 shows examples of VIIRS true color
images for the U.S. east coast region and the Great Barrier Reef along the Australia coast.
This true color image generation program in NOAA-SeaDAS is designed to be operated in either interactive GUI mode
or command-line mode. GUI windows interactively provide auto-detected geo-information (i.e., reference center

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 latitude/longitude and image x-y sizes) to help users choosing files for a region of interest. Command-line scripts can be
used for routine production of VIIRS high quality true color images.

Figure 5. VIIRS true color image for the U.S. east coast region acquired on November 25, 2012 and the Great Barrier
Reef, Australia on September 17, 2014 from SDR granule aggregated files (SDR bands 3, 4, 5 & 7 radiance data were
used in processing at 1 km resolution).

3.3. Bowtie Pixel Mitigation

VIIRS SDR or EDR unmapped images are usually in “swath format”, and they often contain bowtie effects. The bowtie
effect is a geometric feature of VIIRS scans, and individual VIIRS scan lines overlap near the edges of the swath. In
order to minimize the bandwidth usage on the broadcast, these overlapping pixels are replaced (using a “bowtie
deletion” algorithm) with −999.7/−999.6 values (i.e., no-data pixels) onboard. The bowtie-deleted pixels are rendered as
black lines in SDR or EDR images. NOAA-SeaDAS provides an option to perform bowtie pixel mitigation for those
SDR/EDR images before mapping. The “bowtie mitigation” function in NOAA-SeaDAS uses data array operations to
find pixel geophysical values in adjacent scan lines (at almost the same geolocation) to replace those bowtie-deleted
pixels. After bowtie mitigation, the images appear smoother without the distracting black lines (Fig. 6).
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Figure 6. VIIRS chlorophyll-a concentration in Gulf of Mexico (March 26, 2012), before (left) and after (right) bowtie
pixel mitigation with two granules aggregation.

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 4. GOCI SUPPORT AND OTHER SYSTEM FEATURES
In addition to VIIRS support, NOAA-SeaDAS also supports GOCI. Other system features in NOAA-SeaDAS are also
described including: improved bathymetry from SeaDAS 6.4, NetCDF4 and HDF5 file format capability, and updates to
IDL routines.
4.1. GOCI Support
GOCI is the first geostationary ocean color satellite sensor [11]. It is centered at around 36°N and 130°E and covers an
area of ~2500 × 2500 km2, and provides large local area coverage in western Pacific Ocean with a spatial resolution of
500 m for ocean color products. GOCI has eight ocean color relevant spectral bands from 412 to 865 nm with hourly
observations during daytime from around 9:00 to 16:00 local time, i.e., eight images per day. The unique capability of
GOCI can provide good temporal resolution to monitor the dynamics of marine environments on an hourly basis [8-11].
In NOAA-SeaDAS, all functionalities for image display, visualization, and manipulation have been enhanced to support
both GOCI level-1B and Level-2 data (Fig. 7).

Figure 7. GOCI Level-2 water diffuse attenuation coefficient at 490 nm, Kd(490), in the west Pacific Ocean (April 5, 2011).

4.2. Improved Bathymetry Database

Bathymetry contours can be overlaid on ocean color image display in NOAA-SeaDAS. The original bathymetry data
used in SeaDAS 6.4 is from an earlier release of ETOPO2, a 2 arc-minute global relief model of the Earth’s surface. To
increase the horizontal resolution and accuracy, the ETOPO1 dataset has been integrated into NOAA-SeaDAS. ETOPO1
database (built from numerous global and regional data sets) has 1 arc-minute resolution for global ocean bathymetry
and land topography (http://www.ngdc.noaa.gov/mgg/global/global.html). In NOAA-SeaDAS, both ocean bathymetry
and land elevation data can be overlaid on an image display. It is useful for study of coastal and inland lake regions to
provide continuous land-sea topography. Figure 8 shows a sample image overlaid with both ocean bathymetry and land
elevation.
4.3. New Data Format Support
NOAA-SeaDAS is adapting to recently introduced file formats such as HDF5 and netCDF4 (including both classic
model and enhanced data models with group structures) with IDL libraries and existing functions. NOAA-SeaDAS is
also flexible enough to support various metadata defined in the HDF5 and netCDF4 files. Since netCDF4 has the
advantage of interoperability and high-performance I/O, it is increasingly becoming a preferred future data format by the
ocean color community. NOAA-SeaDAS is ready for the new netCDF4 standard.

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 Figure 8. Both ocean bathymetric data and land elevation data can be applied to images for potential inland
water studies. Ocean bathymetric contour line was drawn at every 500 m in depth, while land elevation was
drawn at every 50 m above sea-level (on land, gray, yellow, green, purple, and red colors represent 0, 50,
100, 150, 200, 250 m in height individually).

4.4. Obsolete IDL Routine Replacement

During the system development of NOAA-SeaDAS, several hundred obsolete IDL program routines carried over from
SeaDAS 6.4 were replaced with recommended official IDL new functions. Those updates included file search, file I/O,
HDF file memory handling, and error message handling, etc. With those system function file updates, NOAA-SeaDAS
performance is stable and efficient.

5. FUTURE DEVELOPMENT AND SUMMARY

NOAA-SeaDAS is a satellite data visualization, analysis, manipulation, and data processing system developed based on
SeaDAS 6.4. With system enhancements and new developments, NOAA-SeaDAS is capable of supporting both VIIRS
and GOCI ocean color data visualization and processing. Primarily, the system is in support of NOAA ocean color team
calibration and validation activities. Currently, VIIRS SDR, EDR, and Level-3 data can be visualized, displayed, and
remapped with various map projections. Pixel-level quality flags for SDR and EDR data can be evaluated, displayed,
and overlaid on ocean color images. For advanced IDL users, all IDL-based command-line mode and batch processing
functionalities are also fully supported for VIIRS. Taking advantage of convenient IDL programming, NOAA system
developers are continuously building customized applications for satellite image analysis with powerful IDL image and
graphic functions. NOAA-SeaDAS is also adapting new scientific data formats to meet modern data storage and
distribution requirement, such as full support of HDF5 and netCDF4 data formats, etc.
NOAA-SeaDAS will serve active IDL user groups at NOAA and other institutions for various research and scientific
applications. The NOAA/STAR ocean color team will maintain and improve NOAA-SeaDAS support for VIIRS, GOCI,
MODIS, and SeaWiFS satellite data which required for daily routine operations and research studies. In the future,
NOAA-SeaDAS will be adding support for new ocean color sensors such as Sentinel-3 and GCOM-C.

ACKNOWLEDGMENT
This work was supported by the Joint Polar Satellite System (JPSS) and NOAA funding and grants. The motivation for
NOAA-SeaDAS arose from requests of active IDL users at NOAA and stands on the shoulders of the NASA IDL-based
SeaDAS series and its decade-long success and widespread use in the ocean color community. We are grateful for the
sharing of codes and IDL program routines developed under SeaDAS from NASA OBPG. The views, opinions, and
findings contained in this paper are those of the authors and should not be construed as an official NOAA or U.S.
Government position, policy, or decision.

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