SeaWiFS. Estimate average chlorophyll

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st10873
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SeaWiFS. Estimate average chlorophyll

by st10873 » Mon Apr 01, 2019 10:14 am America/New_York

I have downloaded two SeaWiFS level-3 .nc-file sets for chlorophyll a for a specified lat/lon boundary within the period 1998-2010; one is for 8-day periods (8D), and the other for monthly periods (MO). I read and process the files in Matlab, and would like to calculate the monthly averages (all years combined) for some given bins.

I thought the MO data would work best, but the chlor_a variable is denoted as sum and sum_square. However, I can not find the appropriate way to estimate the mean chlor_a based on the sum. What do I divide by - days in the month? I can't find any weight or N variable in the file. Likewise for the 8D files. Are these chlor_a variables also sums, or are they averages? I have always assumed the 8D was already averaged over 8 days - although I've never used them before.

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OB WebDev - norman
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SeaWiFS. Estimate average chlorophyll

by OB WebDev - norman » Mon Apr 01, 2019 11:17 am America/New_York

Hi,

To get the mean values you need to divide each "sum" value  by the corresponding
"weights" value.  You will find those two data sets in two different places in the
level-3 file.

h5dump -A S19980011998031.L3b_MO_CHL.nc |grep -A 8 BinList|head -8
      DATASET "BinList" {
         DATATYPE  H5T_COMPOUND {
            H5T_STD_U32LE "bin_num";
            H5T_STD_I16LE "nobs";
            H5T_STD_I16LE "nscenes";
            H5T_IEEE_F32LE "weights";
            H5T_IEEE_F32LE "time_rec";
         }

h5dump -A S19980011998031.L3b_MO_CHL.nc |grep -A 4 'DATASET "chlor_a"'
      DATASET "chlor_a" {
         DATATYPE  H5T_COMPOUND {
            H5T_IEEE_F32LE "sum";
            H5T_IEEE_F32LE "sum_squared";
         }

Regards,
Norman

P.S. Do not attempt to use the "time_rec" data for anything.  That field is present
for historical reasons, but it has never contained the information that it was originally
intended to contain.

st10873
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Joined: Wed Apr 15, 2015 8:19 am America/New_York

SeaWiFS. Estimate average chlorophyll

by st10873 » Mon Apr 01, 2019 11:21 am America/New_York

Thank you for the fast reply.
Does "weights" represent a weighted observation count?
I.e. can I divide the sum_square by the same "weights" to get the variance?

OB WebDev - norman
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SeaWiFS. Estimate average chlorophyll

by OB WebDev - norman » Mon Apr 01, 2019 11:30 am America/New_York

To get the variance, you need to divide the "sum_squared" value by the "weights"
value and then subtract the square of the mean from that.

Norman

P.S.  Note that rounding errors can sometimes cause the variance to go
slightly negative when you subtract the mean squared.  In those cases,
I just set the variance to zero.

st10873
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Joined: Wed Apr 15, 2015 8:19 am America/New_York

SeaWiFS. Estimate average chlorophyll

by st10873 » Mon Apr 01, 2019 11:38 am America/New_York

Great.
PS. Are the chlor_a sum and sum_squared values straight up sums, or are they natural log transformed?

gnwiii
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Answers: 1

SeaWiFS. Estimate average chlorophyll

by gnwiii » Mon Apr 01, 2019 7:01 pm America/New_York

You may find Guide to the Creation and Use of Ocean-Colour, Level-3, Binned Data Products. IOCCG Report Number 4, 2004 helpful.    The OBPG binned data use an extended version of the Naïve Algorithm for single pass variances.  As Norman remarked,
this method has some numerical limitations.   In those cases it may be useful to define new level-2 products (rescaled, centered values).  With
the NetCDF4-CF format it is relatively simple to do this with any "matrix" language that supports NetCDF4-CF.  You will need to add an entry for your new product to the product.xml file.  Working with level-2 data does, however, require more compute time and storage than using OBPG binned data prodcuts.

OB WebDev - norman
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SeaWiFS. Estimate average chlorophyll

by OB WebDev - norman » Tue Apr 02, 2019 8:58 am America/New_York

Volume 32 of the SeaWiFS Prelaunch Technical Memorandum series, where the binning
scheme we use was first described, does indicate that data should be log-transformed
before they are binned.  Even before the SeaWiFS mission got underway, however,
the log transformations and maximum likelihood estimator were found to be undesirable
and were abandoned.  So, our sum and sum_squared values are straight up sums with
no log transformation.

Norman

reghe1984
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SeaWiFS. Estimate average chlorophyll

by reghe1984 » Mon Apr 08, 2019 4:59 am America/New_York

Hi all,

I am a PhD student at Stockholm University working on eastern equatorial Pacific Ocean paleoceanography. I am about to finish to write my PhD thesis and I would like to have an image of the eastern equatorial Pacific Ocean in the cover page. The image should be as the ones in the "Image gallery" folder in this web page showing phytoplankton blooms but of the area comprised between ±20° latitude from the equator and between 70°W and 160°W of longitude. 

My thesis would greatly benefit from such an image. I would adequately acknowledge Ocean Color and NASA for this.
Thank you Very much.

Best Wishes,
Daniele Reghellin

OB WebDev - norman
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SeaWiFS. Estimate average chlorophyll

by OB WebDev - norman » Mon Apr 08, 2019 9:53 am America/New_York

Hi Daniele,

It would probably be better to start a new topic on the forum for
new questions.

Have you considered using imagery from our level-3 browser?
The following is a recent example.
https://oceancolor.gsfc.nasa.gov/showimages/VIIRS/IMAGES/CHL/L3/2019/041/V20190412019072.L3m_R32_SNPP_CHL_chl_ocx_4km.nc.png

Regards,
Norman

reghe1984
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SeaWiFS. Estimate average chlorophyll

by reghe1984 » Wed Apr 17, 2019 2:29 am America/New_York

Hi Norman,

Thank you very much for the reply. The level-3 browser look good but how about getting an image like the one here: https://oceancolor.gsfc.nasa.gov/gallery/ps://oceancolor.gsfc.nasa.gov/gallery/

I'll try to make a new topic.

Best Wishes,
Daniele

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