Hello,

I have recently come across an issue when comparing MODIS-Aqua sea surface temperature data from the 2005 reprocessing 1.1 and the 2009 reprocessing R2009.1. I'm assuming the reprocessing R2010.0 only affects the data from 2009 on.

Previously I downloaded the data at L2 from 2002-2008 and processed it to SMI using SeaDas version 5.3.0. I used the default flags. An example of the L2bin code looks like this:

indir='/home/geiger/MODIS/2003/'
outdir='/home/geiger/MODIS/2003/L3/'
files=findfile(indir+'A*.L2_LAC*')

for i=0,n_elements(files)-1 do begin & $
    filename=strmid(files(i),24,27) & $
    base=strmid(filename,0,14) & $
    outfile=outdir+filename+'.L3b_GAC'& $
    infile=files(i)& $
    l2bin, ifile=infile, ofile=outfile, resolve=2, noext=1 & $

endfor

I have since downloaded the later reprocessing for the same years at L2 and did the same methods in SeaDAS 6.1 update 02. The L2bin code looked like this:
indir='/home/geiger/MODIS/2003/'
outdir='/home/geiger/MODIS/2003/L3/'
files=findfile(indir+'A*.L2_LAC_SST*')

for i=0,n_elements(files)-1 do begin & $
    filename=strmid(files(i),24,31) & $
    outfile=outdir+filename+'.L3b_GAC' & $
    infile=files(i) & $

l2bin, ifile=infile, ofile=outfile, flaguse='ATMFAIL,LAND,HIGLINT,HILT,HISATZEN,STRAYLIGHT,CLDICE,COCCOLITH,HISOLZEN,LOWLW,CHLFAIL,NAVWARN,MAXAERITER,CHLWARN,ATMWARN,NAVFAIL,FILTER', l3bprod=['sst','qual_sst'], resolve=1, noext=1, daynight=0, prodmins=[-2.00000,0.00000] & $

endfor

Upon mapping the old and new image next to each other I noticed some differences. The pass was A2003330175000 and an image comparing the old and new files is here: http://modata.ceoe.udel.edu/dev/egeiger/old_new_A2003330175000.nc.png

Did the default flags change between SeaDAS versions or reprocessings? I get more data in some of the new images compared to the old ones, but in some I get less.
What were the default flags in the old version of SeaDAS?

The file A2003330175000.L2_LAC_SST on our site was produced on Dec 31, 2005, so it hasn't changed since then.  Do you not have the old L2 file for comparison. 

These flags are used by default for masking Ocean Color, they are not intended to be applied as masks in SST:
flaguse='ATMFAIL,LAND,HIGLINT,HILT,HISATZEN,STRAYLIGHT,CLDICE,COCCOLITH,HISOLZEN,LOWLW,CHLFAIL,NAVWARN,MAXAERITER,CHLWARN,ATMWARN,NAVFAIL,FILTER',

The standard flags applied in SST processing are just:
flaguse='LAND,HISOLZ'

Unfortunately, you are running l2bin via the SeaDAS IDL interface, and I don't know what flags SeaDAS uses or previously used by default.  I'll let one of the SeaDAS gurus respond to that one. 

You're also changing the resolution and allowing values to go negative (-2).  Perhaps you should start by eliminating such differences.

-- bryan