Batch Processing in SeaDAS 7

[kimlotte]

Hello.
My OS - Ubuntu 16.04 LTS

Issues: 1) Error creating a Color Bar in L2 generated files
             2) Difficulty in translating SeaDAS 6.4 commands to SeaDAS 7

Problem 1
My L1A Script in SeaDAS 7

#!/bin/csh -f
set sptDir = /home/mycomp/seadas/ocssw/run/scripts
set ocsDir = /home/servir1/seadas/ocssw
set runCmd = `echo "$sptDir/ocssw_runner --ocsswroot $ocsDir"`
set srcDIR = /media/mycomp/Transcend/modis

cd ${srcDIR}
# Products to process
set l2prod1 = "chlor_a"
@ counter = 2002
while ($counter <= 2002)

mkdir $srcDIR/$counter

@ counter2 = 229
while ($counter2 <= 366)
  mkdir $srcDIR/$counter/l2
  set dataDIR = $srcDIR/$counter/l2

  foreach l1afile (A*$counter$counter2*L1A_LAC.x.hdf)
    # generate appropriate file names
    set gran = `echo $l1afile | cut -c 1-14` #sed 's/\.L1A_LAC$//'`
    set geofile = $gran.GEO
    set l1bfile = $gran.L1B_LAC.x.hdf
    set l2file = $gran.L2_LAC.x.hdf

    # generate GEO & L1B files
    $runCmd modis_GEO.py $l1afile -o $geofile
    $runCmd modis_L1B.py $l1afile $geofile

    # generate L2 file ofile=$dataDIR$l2file
    $runCmd l2gen ifile=$l1bfile geofile=$geofile ifile=$l1bfile ofile=$dataDIR/$l2file l2prod1=\"$l2prod1\" resolution=500 proc_land=1 albedo=0.054 maskstlight=1 maskland=1 proc_ocean=1 maskhilt=0 maskglint=0 aer_opt=0 aer_opt=-99 cloud_thresh=1.0

  end
@ counter2 = $counter2 + 1
end
@ counter = $counter + 1
end

Question: What is the problem in my L1A-L2 script since when I try to visualize these files, first, I cannot apply a colour scheme to the file, second if I try to add grid lines, I am not able to change the settings or even see the graticule in the file manager, these and others

Problem 2
In SeaDAS 6.4 here is what I used to do for batch processing.
        a) L1A to L2 (1km files)
        b) L2 to L3
             1)mapped daily HDF/ ASCII files,
             2)L2 (temporal and spatial binning) to L3 (weekly, monthly, and seasonal) files (HDF/ASCII)
        c) Merging L3 HDF files to a NetCDF-4 file using another software other than SeaDAS6.4

Question: Kindly, explain to me how I can achieve these steps in SeaDAS 7.4. I am stuck at L1A - L2 processing which is not even working properly.

[gnwiii]

Your description of the problem does not provide enough detail for anyone trying to help to be able to duplicate the problem on another system.   How to report bugs effectively is also good advice when asking for help.

The first step is to make sure basic OCSSW processing works properly on your installation.  It can be helpful to run the SeaDAS benchmark script after installing the OCSSW Processing System.   The benchmark script also serves to provide examples for each of the main processing steps, and if you can demonstrate a problem using the benchmark files it is easy for others to obtain the same files.

Assuming the basic processing isn't the problem, there are some issues with your script.  You set a value for l1bfile, but fail to set the name of the output files
in the modis_L1B.py argument list, so you should see an error like:

-E- /Users/seadas/seadas-viirs-v2.0/seadas/build/src/l2gen/getformat.c: Input file 'A2006167181000.L1B_LAC.x.hdf' does not exist or cannot open.

Since you request 500m resolution in the l2gen options, you also need to add the HKM output file to the  modis_L1B.py argument list.

If you really want hdf4 output from l2gen, you need to set oformat appropriately.

Hopefully this will get you closer to step a) in your workflow.  Are you using HDF so you can visualize mapped data with existing SeaDAS 6 batch commands? 
Since you are already using 3rd party tools with netCDF format mapped files, you may find it easier to stick with a netcdf workflow.   You may also want to look into the Graph Processing Framework for batch processing of mapped data.