1. SeaDAS Training Course
NASA Ocean Biology Processing Group
*** Venue line 1 ***
*** Venue line 2 ***
***Date***

2. What is SeaDAS?
-The SeaWiFS Data Analysis System (SeaDAS) is a comprehensive image analysis package for the processing, display, analysis, and quality control of ocean color data. -SeaDAS is intended for use with all of the OBPG supported sensors: MODIS/Aqua, MODIS/Terra, SeaWiFS, OCTS, CZCS. -SeaDAS can also be very useful as a general scientific imagery/data analysis package.

3. SeaDAS - Processing and Display

7. SeaDAS Functionalities
Processing -All sensors L0 or L1A to SMI -subscening -browse products Data Visualization -image package (reads many formats) -geolocated display (coastline, gridlines, etc.) -various image/data functions Data Manipulation -projection -band operations -output data

8. UNIX Microsoft Windows UNIX Mac OS X linux SGI IRIX Sun Solaris
-SeaDAS runs on “UNIX-like” systems (UNIX/linux/OS X) -This means it does NOT run on Windows. -Dedicated UNIX computer best, but there are options for Windows users.
Mac OS X
Microsoft
Windows
UNIX
linux
SGI IRIX
Sun Solaris

9. What is UNIX?
-UNIX is a fully featured modern Operating System -History (AT&T Bell Labs, Berkeley, UNIX, linux, OS X) -It is available in a variety of ‘flavors’ -It is comprised of simple tools (commands) that perform a single function well -These tools can be used together to perform complex tasks -Powerful Command line -GUI

10. Sample linux directory structure

12. The UNIX Command Line

13. UNIX Basics
UNIX Directory Structure: -At login, you are in your home directory. -This is your “current working directory”. -All files and directories below your home directory usually belong to you. -You change your working directory by changing to another directory with the “cd” command.

14. SeaDAS is made up of binaries and libraries, UNIX shell scripts, and IDL code.
Binaries and Libraries -binaries are executable files created by compiling code -mainly used for data processing (e.g. msl12 = L1->L2 processing) -made from C and/or Fortran code -SeaDAS also includes HDF binaries and libraries UNIX Shell Scripts -Shell scripts are executable text files containing many commands -mainly used as “wrappers” for processing -there are also stand-alone utility scripts IDL Code

15. IDL (Interactive Data Language)
-IDL stands for the Interactive Data Language -Made by ITT Visual Information Solutions, ITT VIS (formerly RSI) -It is a scientific programming language (similar to Matlab) -It is also a “scientific environment” -SeaDAS GUI written in IDL -SeaDAS also uses IDL for data display and analysis functions -non-SeaDAS IDL functionalities are also available! Runtime SeaDAS - free, but no SeaDAS command line or procedures Purchasing IDL - command line, procedures, full IDL environment

16. SeaDAS Directory Structure
seadas/ SeaDAS root directory
bin/ C and Fortran processing binaries
config/ SeaDAS config files (Imake and default files)
data/ Data files used for processing and display
common/benchmarks/ - Data files/scripts for running SeaDAS benchmarks
common/luts/ Color LUTs directory (store custom LUTs here)
common/metoz/ MET/OZONE ancillary files storage directory
common/oisst/ OISST ancillary files storage directory
modis/atteph/ MODIS attitude and ephemeris storage directory
demo/ Demo and test data files
doc/ SeaDAS HTML documentation files
etc/ Stand-alone data processing wrapper scripts
examples/ Example batch scripts
hdf/ HDF software (binaries and libraries)
idl_lib/ Copy of all SeaDAS IDL routines
idl_rt/ Required directory for Runtime SeaDAS mode
inc/ Include files for C and Fortran routines
lib/ C and Fortran compiled libraries
src/ Root directory of all SeaDAS source code
c4idl/ C routines used within IDL programs
c_procs/ Main data processing C routines
idl_procs/ IDL routines
idl_utils/ IDL utility routines
lib/ C and Fortran routines for SeaDAS libraries
utils/ Utility programs used by wrapper scripts
util/ SeaDAS general utilities directory
var/ Miscellaneous ancillary navigation files

17. SeaDAS Requirements
Operating Systems: -linux (Red Hat, Fedora, CentOS, etc.) -Mac OS X 10.3, 10.4 (PPC or Intel) -Sun Solaris 2.7, 2.8 -SGI IRIX 6.5 -Vmware on Windows / Knoppix Live CD RAM: 128MB minimum, 1GB+ best Display: 1024x768 minimum, millions of colors Disk space: 1.5GB for SeaDAS install plus space for data Optional: full IDL license Optional: gcc and fortran compilers

19. SeaDAS Modes
There are 3 ways to use SeaDAS: 1. Graphical User Interface (GUI) 2. Command Line: -IDL command line -UNIX command line 3. Automated: -IDL command (batch) files -IDL procedures -UNIX shell scripts

20. Understanding the SeaDAS Environment
Exercise
Understanding the SeaDAS Environment
On the server: -Change directory into your home (~/) directory: cd -List the contents of your home (~/) directory: ls -l Change directory into your home (~/) directory: cd $SEADAS -List the contents of the SeaDAS directory: ls -l -List the contents of the SeaDAS bin directory: ls bin -List the contents of the SeaDAS etc directory: ls etc -List your shell environment variables: env -change directory into your data directory: cd data -List the contents of your data directory: ls -l data

21. Displaying data with SeaDAS
Exercise
Displaying data with SeaDAS
-On the server: cd ~/data/process seadas Display the SeaWiFS Level 1 subscene S L1A_MLAC.x.hdf: -Click Display -Select the S L1A_MLAC.x.hdf file and click Ok -Select the 555nm product and click Load -In the Band List Selection window click Display -Resize display window by dragging the lower right corner -Using the Functions menu: *overlay a Coastline and latitude/longitude Grid *turn on the Color Bar *turn on the Cursor Position window *Select Color LUT->Load LUT and select different color LUTs

22. Review of OBPG
Satellite Data

23. Data Processing

25. Data Processing using
the SeaDAS GUI

26. Operational MODIS Ocean Band Suite
VIS/NIR
Ocean Color
Thermal
SST

27. Data Levels & Flow Level 0 raw digital counts native binary format
ATT & EPH
spacecraft attitude
spacecraft position
Level 1A
raw digital counts
HDF formatted
GEO
geolocation
radiant path geometry
Level 1B
calibrated reflectances
converted telemetry
Ancillary data
wind speed
surface pressure
total ozone
Reynolds SST
Level 2
geolocated geophysical products for each pixel

28. Data Levels & Flow Level 0 raw digital counts native binary format
ATT & EPH
spacecraft attitude
spacecraft position
Level 1A
raw digital counts
HDF formatted
GEO
geolocation
radiant path geometry
Level 1A Subset
reduced to standard ocean bands only
Level 1B
calibrated reflectances
converted telemetry
Ancillary data
wind speed
surface pressure
total ozone
Reynolds SST
Level 2
geolocated geophysical products for each pixel

29. L0 to L1A

30. L1A Subscene
1. Display A L1A (choose EV_3959_22) 2. Functions -> Cursor Position 3. Process -> MODIS -> modis_subscene 4. Enter SW-Corner: 40, / NE-Corner: 43, -65

31. L1A to L1B

32. MSL12 Multi-Sensor Level-1 to Level-2
Common software for Level-2 processing of MODIS, SeaWiFS and other sensors in a consistent manner.
Supports a multitude of product algorithms and processing methodologies.
standard and non-standard, validated and experimental
run-time selection of output product suite
For MODIS, replaced:
PGE09, PGE10
products MOD18 - MOD28

33. L1B to L2
(msl12)

34. Level 2 Processing Flags
-As data is processed by msl12 from Level 1 to Level 2, checks are made for different defined conditions. -When certain tests and conditions are met for a given pixel, a flag is set for that pixel for that condition. -A total of 31 flags can be set for each pixel. -These msl12 Level 2 processing flags are stored in the Level 2 data file as the "l2_flags" product. -The storage method sets bits to 0 or 1 in 32-bit integers that correspond to each pixel.

35. Level 2 Processing Flags
(flags in red are masked during Level 3 processing)

36. Level-2 Flags and Masking
RGB Image
Chlorophyll
Sediments
Only masking is for clouds
Physical saturation, no retrieval
Can eliminate or change cloud masking, but can’t change saturation
Chlorophyll looks good, even near in glint (band ratio) What about radiances?
Glint
Cloud

37. Level-2 Flags and Masking
RGB Image
nLw (443)
Add masking for straylight
Add masking for high glint
Sediments
Only masking is for clouds
Physical saturation, no retrieval
Can eliminate or change cloud masking, but can’t change saturation
Chlorophyll looks good, even near in glint (band ratio) What about radiances?
Glint
Cloud

38. Processing Masks
-For Level 1 to Level 2 processing (msl12), masked pixels are not processed and are typically set to zero so as to eliminate them from future analysis. -For products where zero could be a valid data value, a number outside the possible data range is substituted. -For SeaWiFS and MODIS, msl12 currently has 8 predefined L1A processing masks (each comprised of only one flag) that can be turned on (1) or off (0) by the user. These 8 masks and their default settings are: maskland=1 maskcloud=1 maskhilt=1 maskbath=0 maskglint=0 masksatzen=0 masksunzen=0 maskstlight=0

39. SeaDAS Level 2 Flags Display Function

41. SST Quality Tests
SST Quality Levels

42. SeaDAS Data Functions

43. Importing and Exporting
Data using SeaDAS
SeaDAS can export data files as HDF, SeaDAS Mapped, flat binary, ascii text, png, and postscript

44. SeaDAS can read / display / analyse:
-All OBPG HDF Data files (MODIS, SeaWiFS, OCTS, CZCS)
-Some non-OBPG legacy Ocean HDF formats
-General HDF (any 2D SDS in an HDF file)
-Navigated HDF (a 2D SDS plus a “lat” SDS and “lon” SDS)
-“SeaDAS Mapped” HDF files
-AVHRR V5 w/ standard NASA or NOAA SDS attribute names
-AVHRR V4 SST/JPL PO.DAAC HDF Pathfinder Best SST
-AVHRR V4 SST/JPL PO.DAAC HDF MCSST
-Binary flat files
-PNG files
-True Color files
-Multi-column ascii text files

45. Data Product Geographic Resolution, Mapping and Binning

46. Definitions
Projection - any process which transforms a spatially organized data set from one coordinate system to another. For MODIS Ocean data products this will refer to two-dimensional data sets.
Mapping - a process of transforming a data set from an arbitrary spatial organization to a uniform (rectangular, row-by-column) organization, by processes of projection and resampling.
Binning - a process of projecting and aggregating data from an arbitrary spatial and temporal organization, to a uniform spatial scale over a defined time range. Ideally the binning process will preserve both the central tendency (e.g., average) and the variation in the data points that contribute to a bin.

47. Ocean Product Projections
Equal-area: sinusoidal, with equally space rows and number of bins per row proportional to sine of latitude; resolutions of 4.6 and 9.2 km
Equal-angle: rectangular (Platte Carre) with rows and columns equally spaced in latitude and longitude; resolutions of 24 and 12 points per degree.
Ocean equal-area and equal-angle projections are equivalent at the equator.

48. Sinusoidal Equal-Area Projection

49. Level-3 Binned vs Mapped
bin file grid
bin files
multiple products
stored as float
sampling statistics included
map files
single product
stored as scaled integer
map file grid

50. MODIS “Bowtie” Effect
Increasing Pixel Size

51. One MODIS scan at ~45 degrees scan angle

52. Two MODIS scans showing overlap of pixels

53. Multiple MODIS scans showing pixel overlap

54. Bin boundaries overlaid on pixel locations

55. Ocean coverage over time for binned files

56. Binned and Mapped Products
Binned products: generated daily from Level-2, and then aggregated to:
-8 days
-monthly
-seasonal
-annual
-mission
Standard mapped image (SMI) products are generated at each temporal resolution by projecting binned files to the equal-angle grid.

57. Level-3 Processing Standard Products 0.042-deg 0.084-deg Daily 8-day
geolocated geophysical products for each pixel
Standard Products
Bin resolution 4.6 x 4.6 km2
Mapped resolution
0.042-deg
0.084-deg
Composite Periods
Daily
8-day
Monthly
Seasonal
Yearly
Mission
Level 3 binned
geophysical products averaged spatially and/or temporally
sinusoidally distributed, equal area bins
Level 3 mapped
images created by mapping and scaling binned products
user-friendly, cylindrical equiangular projection

58. Level 2 Processing Flags
(flags in red are masked during Level 3 processing)

59. SeaDAS Command Line Processing

60. SeaDAS/IDL Command Line
-All SeaDAS processing can also be done using the SeaDAS (IDL) command line. -Virtually everything you can do via the GUI can be done using the SeaDAS command line. -IDL commands can be intermixed with SeaDAS commands. -If you haven’t purchased IDL, you can still use command (batch) files to access the command line functionality.

61. SeaDAS/IDL Command Line
SeaDAS> modis_l1bgen,/help Usage: modis_l1bgen, ifile="ifile", geofile="geofile", ofile="ofile", filehkm="filehkm", fileqkm="fileqkm", refllutfile="refllutfile", emislutfile="emislutfile", qalutfile="qalutfile", delete1km=delete1km, deletehkm=deletehkm, deleteqkm=deleteqkm, savelog=savelog, wait=wait (Note use of quotes around path/filenames) Example: modis_l1bgen, ifile="$SDSDEMO/A L1A_LAC", geofile="./A GEO", /wait SeaDAS>

62. Processing using the SeaDAS command line
Example
Processing using the SeaDAS command line
SeaDAS> print, “Hello World!” Hello World! SeaDAS> SeaDAS> modis_l1bgen, ifile="A L1A_sub”, geofile="A GEO_sub", /wait % seadas -em -b simple_commands.txt

63. UNIX Command Line
% modis_L1A_to_L1B.csh Usage: modis_L1A_to_L1B.csh L1A_file GEO_file [OPTIONS] Options: -o L1B_1KM_filename Output MODIS L1B 1KM HDF filename -h L1B_HKM_filename Output MODIS L1B HKM HDF filename -q L1B_QKM_filename Output MODIS L1B QKM HDF filename -rlut REFL_LUT_filepath Full path and filename of Reflective LUT file -elut EMIS_LUT_filepath Full path and filename of Emissive LUT file -qlut QA_LUT_filepath Full path and filename of QA LUT file -delete-1km Delete 1km resolution L1B file -delete-hkm Delete 500m resolution L1B file -delete-qkm Delete 250m resolution L1B file -save-log Save the Level 1B processing log %

64. Processing using the UNIX command line
Example
Processing using the UNIX command line
Level 1B processing example: % modis_L1A_to_L1B.csh A L1A_sub \ A GEO_sub -delete-hkm -delete-qkm

65. Processing using the UNIX command line
Example (cont’):
Processing using the UNIX command line
Level 2 processing example: % ms_met.csh A L1B_LAC % ms_ozone.csh A L1B_LAC % ms_oisst.csh A L1B_LAC ...this will create three files: A L1B_LAC.met_list A L1B_LAC.ozone_list A L1B_LAC.sst_list ...then you could run msl12 on the UNIX command line: % msl12 \ par=A L1B_LAC.met_list \ par=A L1B_LAC.ozone_list \ par=A L1B_LAC.sst_list \ ifile=A L1B_LAC \ geofile=A GEO_sub \ ofile1=A L2

66. Automating SeaDAS Processing
SeaDAS can be completely automated using: -IDL command files, and/or -IDL procedures, and/or -UNIX shell scripts For certain things it makes sense to use IDL, other things can be done more simply and quickly using UNIX.

67. Using an IDL command file to automate processing
Example
Using an IDL command file to automate processing
;;; this is an IDL command file ;;; ; modify "*L2_LAC" to match the filename pattern of your L2 files filenames=findfile('*L2_LAC') for i=0, n_elements(filenames)-1 do begin & $ base=strmid(filenames,0,14) & $ outfile = base+'.L3b' & $ print, "Running l2bin on ", filenames(i) & $ l2bin, ifile=filenames(i), $ ofile=outfile(i), resolve=4, $ FLAGUSE='ATMFAIL,LAND,HILT,HISATZEN,STRAYLIGHT,CLDICE,COCCOLITH, HISOLZEN,LOWLW,CHLFAIL,NAVWARN,ABSAER,MAXAERITER,CHLWARN,ATMWARN, NAVFAIL,FILTER' & $ endfor print, "Finished!”

68. Using a UNIX shell script to automate processing
Example
Using a UNIX shell script to automate processing
#!/bin/sh for FILE in *L2_LAC do BASE=`echo $FILE |awk -F. '{ print $1 }'` echo "Running l2bin on $FILE" l2bin infile=$FILE ofile=$BASE.L3b resolve=4 >/dev/null done ls -1r *.L3b >list.txt echo "Running l3bin" l3bin in=list.txt out=M L3b noext=1 >/dev/null echo "Running smigen" smigen ifile=M L3b prod=chlor_a \ ofile=M _smi_CHLOR_A_auto.hdf \ resolution=4km latnorth= latsouth= \ lonwest= loneast= echo "Finished!"

69. fin

71. SeaDAS Server Login
When you are assigned a guest # and server, please log onto your server and test SeaDAS: ssh -X username: guest# password: guest123
Execute: seadas

72. MERIS Support for Processing and Display