contours of bathymetry required

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helga55
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Joined: Tue Mar 08, 2005 9:36 am America/New_York

contours of bathymetry required

by helga55 » Thu May 12, 2022 10:47 am America/New_York

Hi all, A lot seems to have changed about this forum from the last time I visited. Nevertheless, I am desperately in need of help.
I made a figure of the sites that I sampled in the waters around the Korean peninsula using ArcMap. The basemap is VIIRS ocean color .nc image with units of chlorophyll mg-m3 and on which I also added some data as graduated symbols. I have now been asked to draw contour lines of the bathymetry around the Korean peninsula- at least two or three lines to show the depths of the stations that I sampled. I have two problems 1) i dont know what kind of bathymetry file/data to download 2) once I do find the data I dont know how to make these contours. I could do this is Seadas or Arcmap. Thanks a lot.

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OB SeaDAS - xuanyang02
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Re: contours of bathymetry required

by OB SeaDAS - xuanyang02 » Thu May 12, 2022 1:25 pm America/New_York

You can browse VIIRS L2 files here -- https://oceancolor.gsfc.nasa.gov/cgi/browse.pl or directly download the files here --https://oceandata.sci.gsfc.nasa.gov/directaccess/

1. load the L2 file (eg. V2019096034800.L2_JPSS1_OC.nc) in SeaDAS and open the chlor_a band
2. click the Bathymetry icon on the toolbar and create bathymetry mask; Once the bathymetry mask is created, open it.
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3. click the Contour icon on the toolbar and create contour lines.
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helga55
Posts: 8
Joined: Tue Mar 08, 2005 9:36 am America/New_York

Re: contours of bathymetry required

by helga55 » Thu May 12, 2022 1:44 pm America/New_York

Hi xuanyang02,
Thanks for your reply - i did try this but it first asks me to download the ETOPO1_ocssw.nc file and when i hit the Install file button it gives an error.
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OB SeaDAS - knowles
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Re: contours of bathymetry required

by OB SeaDAS - knowles » Thu May 12, 2022 6:57 pm America/New_York

You can add contours in SeaDAS as described in the previous post. Note that you can only make contours on the selected band. So since you want contours of Bathymetry overlaid on chlor_a, you will need to:

1. Load VIIRS file.
2. Create bathymetry (which creates a band called "bathymetry"
3. Click on the "bathymetry" band which opens an image view and selects it as the current active product
4. Click on the Contours tool.
5. Set "levels" = 2 in Contours tool.
6. Click "Preview/Edit" in the Contours tool.
7. Set your desired contour values and click "Save", then click "Create Contour Lines".
8. Click on "chlor_a" band which opens its image view.
9. In the Layer Manager tab click on the checkboxes for the 2 contour line layers which you just created.

You can then right click in the chlor_a image view window and export the image "Export View as Image"

helga55
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Joined: Tue Mar 08, 2005 9:36 am America/New_York

Re: contours of bathymetry required

by helga55 » Fri May 13, 2022 9:39 am America/New_York

Thank you @xuanyang02 and @knowles but I think my earlier reply did not go through.
my current problem is that after I do Layer -> Bathymetry & Elevation, the Menu pops up but when I hit Create Bands and Mask , It asks me "Do you want to install the 'file ETOPO1_ocssw.nc" When I select 'Install File' I get an error "file ETOPO1_ocssw.nc" installation error'. so that is where i am stuck now. Thanks a lot.

OB SeaDAS - xuanyang02
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Re: contours of bathymetry required

by OB SeaDAS - xuanyang02 » Fri May 13, 2022 3:37 pm America/New_York

What version of SeaDAS are you using? Please do SeaDAS-OCSSW -> SeaDAS/System Info and post the result here.

There is a copy of ETOPO1_ocssw.nc in $OCDATAROOT/common. You can manually copy it to ~/.seadas8/seadas-bathymetry-operator/auxdata. That might work.

helga55
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Joined: Tue Mar 08, 2005 9:36 am America/New_York

Re: contours of bathymetry required

by helga55 » Fri May 13, 2022 5:24 pm America/New_York

My apologies but with all the problems that I was having I decided to uninstall and reinstall seadas again.
However, every time I do and after I launch seadas I get the following message "Log File directory is not accessible to write"
Below I also get a "Warning! Processers not installed"
If I go to Seadas-OCSSW ->Install/Update OC processors I get the following error "Remote servor is down. OCSSW is not accessible. Please start OCSSW remote server"

-----------------------------------------------------------
Main Application Platform:
-----------------------------------------------------------
Application Version: SeaDAS 8.2.0
SNAP Engine Version: 8.0.9* (SeaDAS Platform modified)
SNAP Desktop Version: 8.0.9* (SeaDAS Platform modified)
SNAP Engine Build Date: 202203151509
SNAP Desktop Build Date: 202203151517
Installation Directory: C:\Program Files (x86)\SeaDAS
Data Directory: C:\Users\helga\.seadas8
Configuration: C:\Program Files (x86)\SeaDAS\etc\snap.properties
VM Configuration: C:\Program Files (x86)\SeaDAS\etc\snap.conf
VM Configuration (gpt): C:\Program Files (x86)\SeaDAS\bin\gpt.vmoptions
VM Configuration (pconvert): C:\Program Files (x86)\SeaDAS\bin\pconvert.vmoptions
Runtime Configuration: C:\Users\helga\.seadas8\etc\snap.properties
Runtime Configuration (SeaDAS Toolbox): C:\Users\helga\.seadas8\etc\seadas.properties
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): null
WARNING!! Could not retrieve system parameters because 'which python3' failed
java.io.IOException: Cannot run program "bash": CreateProcess error=2, The system cannot find the file specified


-----------------------------------------------------------
SeaDAS Toolbox:
-----------------------------------------------------------
SeaDAS Toolbox Version: 1.2.0
SeaDAS Toolbox Build Date: 202203211503
Configuration: C:\Users\helga\.seadas8\etc\seadas.properties
OCSSW Root Directory: null
OCSSW Log Directory: C:\Program Files (x86)\SeaDAS
OCSSW Location: virtualMachine
Environment {$OCSSWROOT} (external): null


-----------------------------------------------------------
NASA Science Processing (OCSSW):
-----------------------------------------------------------
Warning! Processers not installed



-----------------------------------------------------------
General System and Software (from GUI):
-----------------------------------------------------------

Operating System: Windows 10 10.0
Java Version: 1.8.0_201

OB SeaDAS - xuanyang02
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Re: contours of bathymetry required

by OB SeaDAS - xuanyang02 » Mon May 16, 2022 11:26 am America/New_York

To install and process SeaDAS OCSSW in Windows, you need to set up the client-server configuration following the instructions here https://seadas.gsfc.nasa.gov/client_server/

If you have issues with client-server model, please start a new question on the forum.

helga55
Posts: 8
Joined: Tue Mar 08, 2005 9:36 am America/New_York

Re: contours of bathymetry required

by helga55 » Mon May 16, 2022 1:55 pm America/New_York

Hi xuanyang02, thanks a lot for your response. i understand that installing and processing SeaDAS OCSSW in Windows requires me to build a virtual machine as i am running Windows. I also understand that i require OCSSW only if I want to create new products from raw data , apply atmospheric corrections etc etc but currently i only want to display products in your repository, and do simple data processing etc. Would I need OCSSW to use Bathymetry?

OB SeaDAS - xuanyang02
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Posts: 323
Joined: Tue Feb 09, 2021 5:42 pm America/New_York
Answers: 1

Re: contours of bathymetry required

by OB SeaDAS - xuanyang02 » Mon May 16, 2022 3:42 pm America/New_York

You don't need OCSSW to calculate Bathymetry, so you can ignore the warnings for now.

Are you able to create Bathymetry with newly installed SeaDAS?

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