Extracting Cholorophyll a concentration for one station and 1000 km around of it

[bluesky1987]

Dear all,
I have a station that it has latitude and longitude (-64N , -56W). I want to extract ‘cholorophyll a concentration’ for 1000km around of this area from January 2018 to end of February 2018.
What is the best way for doing it?
Downloading whole data from MODIS and then extract this area
https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua/L2/

or
Do you know another option? Can I use seaDAS for it?
Actually, I do not know how much data I can have per day over my station.
Cheers,
Marjan

[gnwiii]

It would be helpful to know the spatial and temporal scales you need.  Dealing with level-2 data is complicated as each pass has different mapping between sensor pixels and locations on the ocean surface.  Binning was introduced to put the files on a common spatial mapping while aggregating over space and time.   NASA standard products include daily binned level-3 data at "4km" (actually 1/24th of a degree).  

If you have the OCSSW processing system, you can use the l3bin program to aggregate over time and space and the l3bindump program to extract data within a given radius of a central location:

l3bindump 3.1.1-044d4967 (May 31 2018 12:44:44)
Usage: l3bindump argument-list

  The argument-list is a set of keyword=value pairs. The arguments can
  be specified on the command line, or put into a parameter file, or the
  two methods can be used together, with command line overriding.

  return value: 0=OK, 1=error, 110=requested bin(s) not found
  file data.

  There are 3 use cases:
        1) bin_number
        2) region defined by lat, lon, and radius (in km)
        3) region defined by north, south, west, east
The list of valid keywords follows:

   help (boolean) (alias=h) (default=false) = print usage information
   version (boolean) (default=false) = print the version
        information
   dump_options (boolean) (default=false) = print
        information about each option
   dump_options_paramfile (ofile) = print
        information about each option to paramfile
   dump_options_xmlfile (ofile) = print
        information about each option to XML file
   par (ifile) = input parameter file
   ifile (ifile) = input L1 file name
   ofile (ofile) = output file name
   oformat (string) (default=txt) = output file format
        txt:  plain text columnar format
    seabass:  SeaBASS format
   l3bprod (string) (default=Unspecified) = binned product to extract
   bin_number (int) (default=-1) = bin number
   north (float) (default=-999) = north boundary
   south (float) (default=-999) = south boundary
   east (float) (default=-999) = east boundary
   west (float) (default=-999) = west boundary
   lat (float) (default=-999) = latitude
   lon (float) (default=-999) = longitude
   radius (float) (default=-999) = radius in km
   verbose (boolean) (default=0) = verbose output


The output includes the number of passes and the number of level-2 pixels that contribute to each bin.

[bluesky1987]

Thanks for your answer. What do you mean with the spatial and temporal scales? As I know I have to work with Level 2 data for retrieving cholorophyl for my location. Am I right? Or Shall I use another type of data? binned level-3 data?
I did not know about OCSSW processing system. I only start working with SeaDAS..
Would you please introduce a tutorial or utube manual for doing that.
Sorry, I am a new member, would you please explain more?
Cheers,
Marjan

[OB SeaDAS - knowles]

Hi Marjan,

The level-3 data is here:
https://oceancolor.gsfc.nasa.gov/cgi/l3

Some details about it is here:
https://oceancolor.gsfc.nasa.gov/docs/format/
https://oceancolor.gsfc.nasa.gov/atbd/

Many SeaDAS tutorials can be found here:
https://seadas.gsfc.nasa.gov/tutorials/presentations/
https://seadas.gsfc.nasa.gov/tutorials/video_tutorials/

Here's some useful Earthdata webinars:
https://www.youtube.com/watch?v=2UOvkubct-M
https://www.youtube.com/watch?v=J4V8c4hfw3g

Danny

[OB WebDev - norman]

Marjan,

The OCSSW processing programs are distributed with SeaDAS.

You may wish to spend some time perusing our site to learn about
ocean-color remote sensing.

https://oceancolor.gsfc.nasa.gov/
https://oceancolor.gsfc.nasa.gov/products/
https://oceancolor.gsfc.nasa.gov/atbd/
https://www.youtube.com/user/nasaoceancolor
https://seadas.gsfc.nasa.gov/help/

... and so on.

Norman

[bluesky1987]

Dear @Danny and @Norman and @gnwiii
Thank you for suggestions. I read and watched most of them but still continuing….

1. There are two cholorophyl concentration; one of them by ‘ocx’ algorithm and another one with ‘ocI’alrorithm and I do not know which one I should download?
https://oceancolor.gsfc.nasa.gov/cgi/l3

2. I downloaded 7days data that are listed in below:
A2018015.L3b_DAY_CHL.nc
A2018016.L3b_DAY_CHL.nc
A2018017.L3b_DAY_CHL.nc
A2018018.L3b_DAY_CHL.nc
A2018019.L3b_DAY_CHL.nc
A2018020.L3b_DAY_CHL.nc
A2018021.L3b_DAY_CHL.nc

I started to do it like below link:

https://www.youtube.com/watch?v=5dIwCK7IDXE&start=132

And put their name in a text file and then I tried to calculate weekly average by using ‘l3bin’ (you can see my steps in ‘image1’, ‘image2’, ‘image3’) but I got below error.

execution exception: java.io.IOException: l3bin failed with exit code 1.
Check log for more details.
-E- clo_getOptionString: option=ofile needs to be set with only one value
L3BIN 5.12 (May 31 2018 12:45:20)

Why I got this error?

Cheers,
Marjan

[OB SeaDAS - knowles]

Marjan,

It is the presence of the spaces in your directory named "Satellite Remote Sensing Methods in Aerosols Science" which is causing your error.  Replace them with underscores and it should work ...

... well, additionally, your directory path is significantly long causing the file name (with full path) to be a large numbers of characters.  This factor may also cause a breakage, if not in l3bin, then perhaps in another processor.

Danny

[OB SeaDAS - knowles]

Marjan,

Regarding OCI versus OCX, use OCI as it is the current default (chlor_a).

See the algorithm description for a more on this:
https://oceancolor.gsfc.nasa.gov/atbd/chlor_a/

Danny

[bluesky1987]

Dear Dany,

Yes. You are right.

1. I runned it and I think it worked (you can see my steps in attachment_image1 to 4). Did I do averaging?

2. I do not know why I can not open result and see it. I tried to open result (it is titled ‘average_weekly’ ) by using (file ----open) but I got this error (image4):

No appropriate reader find: /home/marjan/15_1_2018_CHL_cox/mar/weekly_average

you can also find my result in here:

https://drive.google.com/open?id=1p-xP7O41rfiPzXilOsagTHNGKFaxyOzr

Thanks

[gnwiii]

Level-3 binned files store values for small areas (the "bins") on the surface of the earth.   They require mapping (e.g., using l3mapgen) to produce an array that can be viewed as an image.   Note that you can get not only the averages, but other useful statistics:

   product (string) = comma separated list of products.
        Each product can have an optional colon and modifier appended.
        For example, "product=chlor_a,chlor_a:stdev,Kd_490:nobs"
        Available modifiers:
            avg       average value (default)
            stdev     standard deviation
            var       variance
            nobs      number of observations in the bin
            nscenes   number of contributing scenes
            obs_time  average observation time (TAI93)
            bin_num   bin ID number