seadas training course nasa ocean biology processing group *** venue line 1 *** *** venue line 2 ***...

SeaDAS Training CourseNASA Ocean Biology Processing Group

*** Venue line 1 ***

*** Venue line 2 ***

***Date***

-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.

What is SeaDAS?

SeaDAS - Processing and Display

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

SeaDAS Functionalities

-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.

UNIX

linux

Mac OS X

SGI IRIX

Sun Solaris

MicrosoftWindowsUNIX

-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

What is UNIX?

Sample linux directory structure

The UNIX Command Line

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.

UNIX Basics

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

SeaDAS is made up of binaries and libraries, UNIX shell scripts, and IDL code.

-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

IDL (Interactive Data Language)

SeaDAS Directory Structureseadas/ - - - - - - - - - - - - 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

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

SeaDAS Requirements

SeaDAS Benchmarks (times are cpu times in seconds)

PLATFORM L1A->GEO L1A->L1B L1B->L2 L2->L3 SMI TOTAL T IME

Apple MacBook Pro 2.2 Laptop CPU: 2.16GHz Intel Core 2 Duo RAM: 2GB OS: OS X 10.4.8 (Intel)

8 18 87 5 118

Sun Fire V40z CPU: Dual 2GHz dual core AMD Opteron 870 RAM: 8GB OS: Rocks 4.1

24 30 146 12 212

Generic PC CPU: Dual Pentium 4 3.0Ghz RAM: 2GB OS: Fedora core 4

32 35 150 24 241

Apple Power Macintosh G5 CPU: Dual 2.5GHz PowerPC G5 RAM: 4GB OS: OS X 10.3.9 (PPC)

18 31 183 22 254

Generic PC CPU: Dual 1.3GHz Pentium III RAM: 1GB OS: Redhat Linux 7.3

29 72 325 26 452

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

SeaDAS Modes

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

Exercise

Understanding the SeaDAS Environment

-On the server:

cd ~/data/process seadas

Display the SeaWiFS Level 1 subscene S2004111164518.L1A_MLAC.x.hdf:

-Click Display -Select the S2004111164518.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

ExerciseDisplaying data with SeaDAS

Review of OBPGSatellite Data

Data Processing

Data Processing usingthe SeaDAS GUI

Band Number

Wavelength (nm)

Band Width

(nm)

Spatial Resolution

(m)

SNR at Ltyp

Ltyp mW cm-2

m-1 sr-1

Lmax mW cm-2

m-1 sr-1 8 412 15 1000 1773 7.84 26.9 9 443 10 1000 2253 6.99 19.0

10 488 10 1000 2270 5.38 14.0 11 531 10 1000 2183 3.87 11.1 12 551 10 1000 2200 3.50 8.8 13 667 10 1000 1962 1.47 4.2 14 678 10 1000 2175 1.38 4.2 15 748 10 1000 1371 0.889 3.5 16 869 15 1000 1112 0.460 2.5

Operational MODIS Ocean Band Suite

Band Number

Wavelength (nm)

Band Width

(nm)

Spatial Resolution

(m)

NEdT

22 3959 60 1000 0.07 23 4050 60 1000 0.07 31 11000 60 1000 0.05 32 12000 60 1000 0.05

VIS/NIR

Ocean Color

Thermal

SST

Data Levels & Flow• Level 0

– raw digital counts– native binary format

• Level 1A – raw digital counts– HDF formatted

• Level 1B

– calibrated reflectances

– converted telemetry

• Level 2

– geolocated geophysical products for each pixel

• Ancillary data– wind speed– surface pressure – total ozone– Reynolds SST

• GEO – geolocation– radiant path geometry

• ATT & EPH – spacecraft attitude– spacecraft position

Data Levels & Flow• Level 0

– raw digital counts– native binary format

• Level 1A – raw digital counts– HDF formatted

• Level 1B

– calibrated reflectances

– converted telemetry

• Level 2

– geolocated geophysical products for each pixel

• Ancillary data– wind speed– surface pressure – total ozone– Reynolds SST

• GEO – geolocation– radiant path geometry

• ATT & EPH – spacecraft attitude– spacecraft position

• Level 1A Subset – reduced to standard

ocean bands only

L0 to L1A

1. Display A2005205180000.L1A (choose EV_3959_22)

2. Functions -> Cursor Position

3. Process -> MODIS -> modis_subscene

4. Enter SW-Corner: 40, -75 / NE-Corner: 43, -65

L1A Subscene

L1A to L1B

MSL12Multi-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

L1B to L2(msl12)

-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.

Level 2 Processing Flags

Level 2 Processing Flags

(flags in red are masked during Level 3 processing)

ChlorophyllRGB Image

Glint

Sediments

Cloud

Level-2 Flags and Masking

nLw (443)RGB Image

Glint

Sediments

Cloud

Level-2 Flags and Masking

Add masking for high glintAdd masking for straylight

-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=1maskcloud=1maskhilt=1maskbath=0maskglint=0masksatzen=0masksunzen=0maskstlight=0

Processing Masks

SeaDAS Level 2 Flags Display Function

SST Quality Tests

SST Quality Levels

SeaDAS Data Functions

Importing and ExportingData using SeaDAS

SeaDAS can export data

files as HDF, SeaDAS

Mapped, flat binary, ascii

text, png, and postscript

-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

SeaDAS can read / display / analyse:

Data Product Geographic Resolution,

Mapping and Binning

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.

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.

Sinusoidal Equal-Area Projection

Level-3 Binned vs Mapped

bin file grid

map file grid

• bin files

– multiple products– stored as float– sampling statistics included

• map files

– single product– stored as scaled integer

Increasing Pixel Size

MODIS “Bowtie” Effect

One MODIS scan at ~45 degrees scan angle

Two MODIS scans showing overlap of pixels

Multiple MODIS scans showing pixel overlap

Bin boundaries overlaid on pixel locations

Ocean coverage over time for binned files

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.

Level-3 Processing

• 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

• Level 2

– 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 2 Processing Flags

(flags in red are masked during Level 3 processing)

SeaDAS Command Line Processing

-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.

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/A2005191123500.L1A_LAC",

geofile="./A2005191123500.GEO", /wait

SeaDAS>

SeaDAS/IDL Command Line

SeaDAS> print, “Hello World!”

Hello World!

SeaDAS>

SeaDAS> modis_l1bgen, ifile="A2005205180000.L1A_sub”,

geofile="A2005205180000.GEO_sub", /wait

% seadas -em -b simple_commands.txt

ExampleProcessing using the SeaDAS 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

%

UNIX Command Line

Level 1B processing example:

% modis_L1A_to_L1B.csh A2005205180000.L1A_sub \

A2005205180000.GEO_sub -delete-hkm -delete-qkm

ExampleProcessing using the UNIX command line

Level 2 processing example:

% ms_met.csh A2005205180000.L1B_LAC

% ms_ozone.csh A2005205180000.L1B_LAC

% ms_oisst.csh A2005205180000.L1B_LAC

...this will create three files:

A2005205180000.L1B_LAC.met_list

A2005205180000.L1B_LAC.ozone_list

A2005205180000.L1B_LAC.sst_list

...then you could run msl12 on the UNIX command line:

% msl12 \

par=A2005205180000.L1B_LAC.met_list \

par=A2005205180000.L1B_LAC.ozone_list \

par=A2005205180000.L1B_LAC.sst_list \

ifile=A2005205180000.L1B_LAC \

geofile=A2005205180000.GEO_sub \

ofile1=A2005205180000.L2

Example (cont’):Processing using the UNIX command line

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.

Automating SeaDAS 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!”

ExampleUsing an IDL command file to automate processing

#!/bin/shfor FILE in *L2_LACdo BASE=`echo $FILE |awk -F. '{ print $1 }'` echo "Running l2bin on $FILE" l2bin infile=$FILE ofile=$BASE.L3b resolve=4 >/dev/nulldone

ls -1r *.L3b >list.txtecho "Running l3bin"l3bin in=list.txt out=M20052022005205.L3b noext=1 >/dev/null

echo "Running smigen"smigen ifile=M20052022005205.L3b prod=chlor_a \ofile=M20052022005205_smi_CHLOR_A_auto.hdf \resolution=4km latnorth=48.0000 latsouth=35.0000 \lonwest=-78.0000 loneast=-62.0000

echo "Finished!"

ExampleUsing a UNIX shell script to automate processing

fin

When you are assigned a guest # and server, please log onto your server and test SeaDAS:

ssh -X guest#@192.168.1.### username: guest# password: guest123

Execute: seadas

SeaDAS Server Login

MERIS Support for Processing and Display