l2gen not using specific settings

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ana_dogliotti
Posts: 28
Joined: Mon Sep 12, 2005 1:16 pm America/New_York

l2gen not using specific settings

by ana_dogliotti » Wed Jan 12, 2022 12:55 pm America/New_York

Hello,

I've just downloaded Seadas installer script and manifest script (install_ocssw 5.2) and installed all the processing programs and required data packages for some missions using --tag V2021.2 . I have Ubuntu 16.04.7

When I try processing using l2gen and specific options, like which wave and threshold to use for cloud detection and the subset lat/lon limits, they are not taken into account. It just takes the default parameters and also the Climatology for OZONE and MET files... but the correponding to the date have already been downloaded using gent_anc and they are located in the corresponding var/anc/ dir...

$PATH-SEADAS/ocssw/bin/l2gen ifile=/home/tele/L1/V2021358181800/V2021358181800.L1B_JPSS1 geofile=/home/tele/V2021358181800/V2021358181800.GEO-M_JPSS1 ofile=/home/tele/L2/V2021358181800/V2021358181800.L2_JPSS1_GW94_SWIR13 l2prod=l2_flags,Rrs_nnn,La_nnn aer_opt=-1 aer_wave_short=1238 aer_wave_long=2257 brdf_opt=0 gas_opt=15 maskland=1 maskcloud=1 maskglint=1 masksunzen=1 masksatzen=1 maskhilt=0 maskstlight=0 sunzen=70.0 satzen=60.0 cloud_wave=2257 cloud_thresh=0.018 resolution=750 north=-34 south=-35.0 west=-58.6 east=-57.35

I've been using this syntax in previous seadas versions and it worked. Has something changed? The installation is ok?
Thanks in advance for your help.

Ana

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OB SeaDAS - xuanyang02
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Re: l2gen not using specific settings

by OB SeaDAS - xuanyang02 » Wed Jan 12, 2022 2:48 pm America/New_York

It might be helpful if you could do "SeaDAS-OCSSW -> SeaDAS/System Info" in SeaDAS GUI, and then copy and paste the result here.

I did l2gen on command line.

Code: Select all

l2gen par=l2gen-forummParFile.par
Here is the content of my par file l2gen-forummParFile.par:

ifile=/Users/bingyang/Scenes/VIIRS_J1/forum/V2021358181800.L1B-M_JPSS1.nc
geofile=/Users/bingyang/Scenes/VIIRS_J1/forum/V2021358181800.GEO-M_JPSS1.nc
ofile=/Users/bingyang/Scenes/VIIRS_J1/forum/V2021358181800.L2_JPSS1.nc
l2prod=l2_flags,Rrs_nnn,La_nnn
aer_opt=-1
aer_wave_short=1238
aer_wave_long=2257
brdf_opt=0
gas_opt=15
maskland=1
maskcloud=1
maskglint=1
masksunzen=1
masksatzen=1
maskhilt=0
maskstlight=0
sunzen=70.0
satzen=60.0
cloud_wave=2257
cloud_thresh=0.018
resolution=750
north=-34
south=-35.0
west=-58.6
east=-57.35

It seems that l2gen took the options except north/south/west/east, see this post -- viewtopic.php?f=7&t=2407&p=8662&sid=eed ... 078c#p8662

If you are calling l2gen from python, maybe this post could be helpful -- viewtopic.php?f=7&t=2619&p=9443&sid=eed ... 078c#p9443

ana_dogliotti
Posts: 28
Joined: Mon Sep 12, 2005 1:16 pm America/New_York

Re: l2gen not using specific settings

by ana_dogliotti » Wed Jan 12, 2022 3:19 pm America/New_York

Hi,

Thanks for your quick reply. I've also tried what you did (build a par file), but I still get the same results, all the default parameters are used.

Regarding the post, has it been fixed? Anyway, it also not taking the lat/lon when processing MODISA images...

Here is the output of the SeaDAS System Info. I should tell you that I first install all the processors using install_ocssw and then installed the GUI (seadas_8.1.0_linux64_installer.sh))

Main Application Platform:
Application Version: SeaDAS 8.1.0
Installation Directory: /home/tele/seadas8
Data Directory: /home/tele/.seadas8
Configuration: /home/tele/seadas8/etc/snap.properties
WARNING!! File '/home/tele/seadas8/etc/snap.properties' does not exist
Configuration2: /home/tele/.seadas8/etc/snap.properties
VM Configuration: /home/tele/seadas8/bin/pconvert.vmoptions
WARNING!! File '/home/tele/seadas8/bin/pconvert.vmoptions' does not exist
VM Configuration (gpt): /home/tele/seadas8/bin/gpt.vmoptions
WARNING!! File '/home/tele/seadas8/bin/gpt.vmoptions' does not exist
Desktop Specification Version: 8.0.3
Engine Specification Version: 8.0.3
JRE: Java(TM) SE Runtime Environment 1.8.0_201-b09
JVM: Java HotSpot(TM) 64-Bit Server VM by Oracle Corporation
Memory: 3641 MiB

OCSSWROOT (Java Env): /home/tele/seadas8/ocssw

Python3 Directory:
/home/tele/anaconda3/bin/python3

SeaDAS Toolbox:
SeaDAS Toolbox Specification Version: 1.1.0
Configuration: /home/tele/.seadas8/etc/seadas.properties
OCSSW Root Directory: /home/tele/seadas8/ocssw
OCSSW Log Directory: /home/tele
OCSSW Location: local
Environment {$OCSSWROOT} (external): /home/tele/seadas8/ocssw

-----------------------------------------------

NASA Science Processing (OCSSW):
Environment {$OCSSWROOT}: /home/tele/seadas8/ocssw
Environment {$OCDATAROOT}: /home/tele/seadas8/ocssw/share
l2gen version: msl12 9.5.1-V2021.2 (Jun 18 2021 11:22:53)
l2bin version: 7.0.1
l3bin version: 5.13
l3mapgen version: l3mapgen 2.3.0-V2021.2 (Jun 18 2021 11:24:42)
Installed Missions: ['meris', 'aqua', 'seawifs', 'viirsn', 'viirsj1']

General System and Software:
Operating system: Ubuntu 16.04.7 LTS
Java version: 9-internal
Python3 version: 3.7.6
Python3 Path: /home/tele/anaconda3/bin/python3
Env: ASAP_PARMS=/home/tele/seadas8/ocssw/share/common/nav
CC=gcc
_CE_CONDA=
_CE_M=
CLUTTER_IM_MODULE=xim
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/tele/anaconda3/bin/conda
CONDA_PREFIX=/home/tele/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/tele/anaconda3/bin/python
_CONDA_SET_PROJ_LIB=/home/tele/seadas8/ocssw/opt/share/proj
CONDA_SHLVL=1
CXX=g++
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-f3pqtRcyMP
DEFAULTS_PATH=/usr/share/gconf/gnome.default.path
DESKTOP_SESSION=gnome
DISPLAY=:0
ELEMENTS=/home/tele/seadas8/ocssw/var/seawifs
EOS_LIB_PREFIX=linux64
FC=gfortran
GCC_TUNE=
GDM_LANG=es_AR
GDMSESSION=gnome
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GNOME_KEYRING_CONTROL=
GNOME_KEYRING_PID=
GPG_AGENT_INFO=/home/tele/.gnupg/S.gpg-agent:0:1
GTK2_MODULES=overlay-scrollbar
GTK_IM_MODULE=ibus
GTK_MODULES=
HDFEOS_LIB=/home/tele/seadas8/ocssw/opt/EOS/lib/linux64
HOME=/home/tele
_=/home/tele/seadas8/ocssw/bin/seadas_info
HRPT_STATION_IDENTIFICATION_FILE=/home/tele/seadas8/ocssw/share/seawifs/station/station_id.dat
IM_CONFIG_PHASE=1
INSTANCE=
J2D_PIXMAPS=shared
JOB=dbus
L2GEN_ANC=/home/tele/seadas8/ocssw/var/anc
LANG=es_AR.UTF-8
LANGUAGE=es_AR:es
LD_LIBRARY_PATH=/home/tele/seadas8/jre1.8.0_201/jre/lib/amd64:/home/tele/seadas8/jre1.8.0_201/jre/lib/i386:
LESSCLOSE=/usr/bin/lesspipe %s %s
LESSOPEN=| /usr/bin/lesspipe %s
LIB3_BIN=/home/tele/seadas8/ocssw/opt/bin
LIB3_CHECK=0
LIB3_DIR=/home/tele/seadas8/ocssw/opt
LIB3_INC=/home/tele/seadas8/ocssw/opt/include
LIB3_LIB=/home/tele/seadas8/ocssw/opt/lib
LOGNAME=tele
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
MANDATORY_PATH=/usr/share/gconf/gnome.mandatory.path
NAVCTL=/home/tele/seadas8/ocssw/share/seawifs/nav
NAVQC=/home/tele/seadas8/ocssw/share/seawifs/nav
OCDATAROOT=/home/tele/seadas8/ocssw/share
OCSSW_ARCH=linux_64
OCSSW_BIN=/home/tele/seadas8/ocssw/bin
OCSSW_DEBUG=0
OCSSWROOT=/home/tele/seadas8/ocssw
OCSSW_SVN=localhost
OCTS_REGISTRATION_TABLES=/home/tele/seadas8/ocssw/share/octs/nav
OCVARROOT=/home/tele/seadas8/ocssw/var
ORBCTL=/home/tele/seadas8/ocssw/share/seawifs/nav
PATH=/home/tele/bin:/home/tele/.local/bin:/home/tele/anaconda3/bin:/home/tele/anaconda3/bin:/home/tele/anaconda3/bin:/home/tele/anaconda3/bin:/home/tele/anaconda3/condabin:/home/tele/seadas8/ocssw/opt/bin:/home/tele/seadas8/ocssw/bin:/home/tele/bin:/home/tele/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PGSINC=/home/tele/seadas8/ocssw/opt/EOS/include
PGSLIB=/home/tele/seadas8/ocssw/opt/EOS/lib/linux64
PROJ_LIB=/home/tele/seadas8/ocssw/opt/share/proj
PWD=/home/tele
QT4_IM_MODULE=xim
QT_ACCESSIBILITY=1
QT_IM_MODULE=ibus
QT_LINUX_ACCESSIBILITY_ALWAYS_ON=1
QT_QPA_PLATFORMTHEME=appmenu-qt5
SESSION=gnome
SESSION_MANAGER=local/acer-anita:@/tmp/.ICE-unix/2212,unix/acer-anita:/tmp/.ICE-unix/2212
SESSIONTYPE=gnome-session
SHELL=/bin/bash
SHLVL=3
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
SWFTBL=/home/tele/seadas8/ocssw/share/seawifs/qc
SWTBL=/home/tele/seadas8/ocssw/share/seawifs
TERM=xterm-256color
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1000/1989
USER=tele
VTE_VERSION=4205
WINDOWID=58726328
XAUTHORITY=/home/tele/.Xauthority
XDG_CONFIG_DIRS=/etc/xdg/xdg-gnome:/usr/share/upstart/xdg:/etc/xdg
XDG_CURRENT_DESKTOP=GNOME
XDG_DATA_DIRS=/usr/share/gnome:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/var/lib/snapd/desktop
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/tele
XDG_MENU_PREFIX=gnome-
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
XDG_SEAT=seat0
XDG_SESSION_DESKTOP=gnome
XDG_SESSION_ID=c2
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SESSION_TYPE=x11
XDG_VTNR=7
XMODIFIERS=@im=ibus

OB SeaDAS - xuanyang02
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Re: l2gen not using specific settings

by OB SeaDAS - xuanyang02 » Wed Jan 12, 2022 4:37 pm America/New_York

Thanks for paste the SeaDAS/System Info here. I don't see anything wrong. I assume you download --viirsdem along with viirsj and viirsn.

I tried
$l2gen ifile=V2021358181800.L1B-M_JPSS1.nc geofile=V2021358181800.GEO-M_JPSS1.nc ofile=V2021358181800.L2_JPSS1_GW94_SWIR13 l2prod=l2_flags,Rrs_nnn,La_nnn aer_opt=-1 aer_wave_short=1238 aer_wave_long=2257 brdf_opt=0 gas_opt=15 maskland=1 maskcloud=1 maskglint=1 masksunzen=1 masksatzen=1 maskhilt=0 maskstlight=0 sunzen=70.0 satzen=60.0 cloud_wave=2257 cloud_thresh=0.018 resolution=750 north=-34 south=-35.0 west=-58.6 east=-57.35

Here is part of the output:
The following products will be included in V2021358181800.L2_JPSS1_GW94_SWIR13. -- these are not default l2prod
0 Rrs_411
1 Rrs_445
2 Rrs_489
3 Rrs_556
4 Rrs_667
5 Rrs_746
6 Rrs_868
7 Rrs_1238
8 Rrs_1604
9 Rrs_2258
10 La_411
11 La_445
12 La_489
13 La_556
14 La_667
15 La_746
16 La_868
17 La_1238
18 La_1604
19 La_2258
20 l2_flags

Aerosol selection bands 1238 and 2258 -- default would be Aerosol selection bands 746 and 868

l2gen is not taking the north/south/west/east options in V2021.2. It is in V2021.1

ana_dogliotti
Posts: 28
Joined: Mon Sep 12, 2005 1:16 pm America/New_York

Re: l2gen not using specific settings

by ana_dogliotti » Wed Jan 12, 2022 5:40 pm America/New_York

Yes, I have installed the viirsdem.

Can you check in your output which band is it using to mask clouds? In the par option I put cloud_wave=2257 cloud_thresh=0.018, but in the output it says

Using 868.0 nm channel for cloud flagging over water.

Thanks

Ana

OB SeaDAS - xuanyang02
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Re: l2gen not using specific settings

by OB SeaDAS - xuanyang02 » Wed Jan 12, 2022 6:26 pm America/New_York

I did get
Using 868.0 nm channel for cloud flagging over water.
Using 411.0 nm channel for cloud flagging over land.

Maybe some options are not working. I'll get back to you

Bing

OB SeaDAS - dshea
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Re: l2gen not using specific settings

by OB SeaDAS - dshea » Thu Jan 13, 2022 10:39 am America/New_York

The bug that you are seeing only happens when you use the north,south,east,west parameters. The bug was introduced between V2021.1 and V2021.2. It was fixed in T2021.11 and later

If you do not want to install a newer version of the code you can
- run lonlat2pixline to find the spix,epix,sline,eline from your north,south,east,west
- pass spix,epix,sline,eline to l2gen instead of north,south,east,west to avoid the l2gen bug.

don

ana_dogliotti
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Joined: Mon Sep 12, 2005 1:16 pm America/New_York

Re: l2gen not using specific settings

by ana_dogliotti » Thu Jan 13, 2022 11:18 am America/New_York

Thank you Don!
I see there is other versions V2021.2 and V2022.0. Is the bug fixed in this later V2022.0 version? There are newer T versions... like T2022. Which is more reliable to use?
Thanks

Ana

gnwiii
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Re: l2gen not using specific settings

by gnwiii » Thu Jan 13, 2022 9:35 pm America/New_York

I think V2022.0 uses the new https://oceancolor.gsfc.nasa.gov/docs/f ... onvention/, so is not a drop-in replacement for existing workflows.

OB SeaDAS - xuanyang02
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Re: l2gen not using specific settings

by OB SeaDAS - xuanyang02 » Thu Jan 13, 2022 10:22 pm America/New_York

Yes, V2022.0 should be reliable, which just came out two days ago.

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