SeaDAS 7.0 beta setup and configuration files

Further notes on my Adventures processing MODIS files

After starting SeaDAS 7.0 beta, via the icon, I opened a terminal window so that I could tail the log.

The first line was

/Users/Kaffkar/seadas/config/seadas.env: No such file or directory

I recently had to reinstall my operating system, as some windows on my bootcamp partition thought destroying the start software would be sensible.

The result is a slightly odd setup where I have one user and 2 user directories

performed a

find . -name seadas* 

and only the expected results were returned.

>env

TERM_PROGRAM=Apple_Terminal
TERM=xterm-256color
SHELL=/bin/bash
TMPDIR=/var/folders/kt/h45k9r0s2lv2x6yd7tn296vr0000gn/T/
Apple_PubSub_Socket_Render=/tmp/launch-jdUITF/Render
TERM_PROGRAM_VERSION=309
TERM_SESSION_ID=34319DE3-BBFF-416A-8949-1E4870045241
USER=Kaffkar
COMMAND_MODE=unix2003
SSH_AUTH_SOCK=/tmp/launch-YsRd2W/Listeners
__CF_USER_TEXT_ENCODING=0x1F5:0:0
Apple_Ubiquity_Message=/tmp/launch-MQI2sO/Apple_Ubiquity_Message
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
PWD=/Users/Kaffkar 1
LANG=en_AU.UTF-8
SHLVL=1
HOME=/Users/Kaffkar 1
LOGNAME=MacGill
_=/usr/bin/env

>java -version

java version "1.6.0_43"

Java(TM) SE Runtime Environment (build 1.6.0_43-b01-447-11M4203)

Java HotSpot(TM) 64-Bit Server VM (build 20.14-b01-447, mixed mode)

>l2gen

-bash: l2gen: command not found

I am only a casual unix user but it appears both SeaDAS Gui may have been installed correctly but not the SeaDAS 

I have been referencing

HOW TO INSTALL SeaDAS 6.4
Creating True Color RGB in SeaDAS 7.0
How do I make true-color images from MODIS or SeaWiFS

2 years ago I was a Senior Java Developer, and utilised Maven to build, test and create packages so the files in GitHub actually make some sense.

SeaDAS GUI Source

my .bashrc file contains the reference

source /Users/Kaffkar/seadas/config/seadas.env

This needs to be change.
Trying this.



export OCSSWROOT=/Applications/seadas-7.0-beta/Processing
source /Applications/seadas-7.0-beta/Processing/OCSSW_bash.env

Closed all terminals and the SeaDAS Gui
Restarted SeaDAS
Opened a terminal

>l2gen

Command recognised

Tried l1bgen through GUI. No luck, at least the command line is working
Tried l1brsgen through GUI

>l1brsgen ifile=MYD021KM.A2003359.1225.005.2010067090806.hdf ofile=MYD021KMrgb.ppm geofile=MYD03.A2003359.1225.005.2010067073507.hdf subsamp=4 outmode=2 atmocor=1

This worked, now I just have to work out what it did.

SeaDAS 7.0-beta

My machine

OSX 10.8.3
Processor 2.2 GHz Intel Core i7
Memory 4 GB 1333 MHz DDR3

Install of SeaDAS 7.0-beta
Online Install

• Base files
• SeaWiFS
• Modis Aqua

Tips and Tricks

• Directories are not relative, after install so don't move the install around

Updates

I was experience so GUI problems, one suggestion was that SeaWiFS module needed to be installed for l2gen windows to configure.

Downloaded everything to ensure this was not the problem.
Still having issues. They are not consistent so have reported a bug yet.

Atmospheric Correction

Another post about my adventures with MODIS data

MODIS aqua appear to have at least 3 post atmospheric correction product

LW_nnn : The water-leaving radiance.

nLw_nnn : Normalised water leaving radiance

Rrs_nn remote sensing refectance

A200xxxxxxxxxxx.L2_LAC_OC

includes these Remote sensing reflectances

Rrs 412 --> Band 8

Rrs 443 --> Band 9

Rrs 469 ---> Band 3

Rrs 488  --> Band 10

Rrs 531 --> Band 11

Rrs 547 --> Band 12

Rrs 555 --> Band4, Band 12

Rrs 645 --> Band 1

Rrs 667 --> Band 13

Rrs 678  --> Band 14

Rrs_nnn = nLw_nn/ F0_nnn;

F0_nnn = extraterrestrial solar irradiance (constant provided in metadata )

Think I need a greater understanding of data available and the processing so I can make reasonable choices.

MODIS Aqua RGB with SeaDAS 7.0 Beta

Another post recording my adventures with MODIS data

Aim :  Create true colour RGB image from MODIS Level 1B

MODIS Level 1B

• Calibrated
• Not atmospherically corrected

Why 

• Atmospheric Correction required for Chlorophyll Algorithms
• RGB image required in write up

Download data Reverb NASA

• MYD021KM.A2003359.1225.005.2003360215150.hdf
• MYD02HKM.A2003359.1225.005.2003360215150.hdf
• MYD02QKM.A2003359.1225.005.2003360215150.hdf
• MYD03.A2003359.1225.005.2003360210518.hdf

• MYD021KM - reflective bands at 1km
• MYD02HKM - reflective bands at 500m.
• MYD02QKM - reflective bands at 250m.
• MYD03 - geolocation’ information required by MODIS Oceans Level 2 
  (i.e., latitude and longitude) for any remapping. 

I know all the above products can be generated from MODIS Level 1A, today I am being trying to be directed. and shall not investigate that area.

Interest link discussing how the different resolution reflective product work with the 1km resolution geolocation file. iCare MODIS_geolocation wiki

Tried to run l2gen from SeaDAS GUI -->  Issue
Known and Fixed Issues

This should have been fixed I believe.

Reinstalled SeaDAS with all modules, --> Issue
Bugger will have to understand the command line.

Back one step
Let's try l2brgen - the gui is throwing NullPointerExceptions. in the good old AWT Event Queue

DId manage to reproject through the GUI which something

WIMsoft trial

A post regarding my adventures with MODIS data

Summary

• Saw images in Window environment
• unable to achieve goal with WIM evaluation software
• WAM required to handle atmospheric correction

---

Aim :  Create true colour RGB image from MODIS Level 1B

MODIS Level 1B

• Calibrated
• Not atmospherically corrected

Why 

• Atmospheric Correction required for Chlorophyll Algorithms
• RGB image required in write up
• Familiarization with WIM software

Exercise : Exercises_modis_250m.pdf

Download data Reverb NASA

Create a control file
Control specifies

• input directory , data file 1 line
• input files, in this case, 4 lines
• flags indicating bands to process, 1 line
• output direction, line 1

Specifies the band to process