How to open netcdf4 file in MATLAB

Hello there!

I am trying to open file - A20021822002212.L3b_MO_CHL.nc in MATLAB. After issuing the command -

 ncdisp('/home/xyz/Desktop/abc/chlorophyl_Data/A20021822002212.L3b_MO_CHL.nc'),

I see the following details:

Source:
           /home/xyz/Desktop/abc/chlorophyll_Data/A20021822002212.L3b_MO_CHL.nc

Format:
           netcdf4

Global Attributes:

* product_name                     = 'A20021822002212.L3b_MO_CHL.nc'
*            title                            = 'MODIS Level-3 Binned Data'
*            instrument                       = 'MODIS'
*            platform                         = 'Aqua'
*            temporal_range                   = '26-day'
*            start_orbit_number               = 885
*            end_orbit_number                 = 1.26e+03
*            date_created                     = '2015177112310000'
*            processing_version               = '2014.0'
*            history                          = 'l3bin 
* par=A20021822002212.L3b_MO_CHL.param'
*            time_coverage_start              = '2002-07-03T22:55:06.000Z'
*            time_coverage_end                = '2002-07-29T18:40:05.000Z'
*            northernmost_latitude            = 83.7
*            southernmost_latitude            = -49
*            easternmost_longitude            = 180
*            westernmost_longitude            = -180
*            geospatial_lat_max               = 83.7
*            geospatial_lat_min               = -49
*            geospatial_lon_max               = 180
*            geospatial_lon_min               = -180
*            geospatial_lat_units             = 'degrees_north'
*            geospatial_lon_units             = 'degrees_east'
*            geospatial_lon_resolution        = 0.0417
*            geospatial_lat_resolution        = 0.0417
*            spatialResolution                = '4.6 km'
*            data_bins                        = 1.11e+07
*            percent_data_bins                = 46.9
*            units                            = 'chlor_a:mg m^-3,chl_ocx:mg m^-3'
*            binning_scheme                   = 'Integerized Sinusoidal Grid'
*            project                          = 'Ocean Biology Processing Group (NASA/GSFC/OBPG)'
*            institution                      = 'NASA Goddard Space Flight Center, Ocean Ecology Laboratory, Ocean Biology Processing Group'
*            standard_name_vocabulary         = 'NetCDF Climate and Forecast (CF) Metadata Conventions'
*            Metadata_Conventions             = 'Unidata Dataset Discovery v1.0'
*            Conventions                      = 'CF-1.6, Unidata Dataset Discovery v1.0'
*            naming_authority                 = 'gov.nasa.gsfc.sci.oceandata'
*            id                               = 'A20021822002212.L3b_MO_CHL.nc/L3/A20021822002212.L3b_MO_CHL.nc'
*            license                          = 'http://science.nasa.gov/earth-science/earth-science-data/data-information-policy/'
*            creator_name                     = 'NASA/GSFC/OBPG'
*            publisher_name                   = 'NASA/GSFC/OBPG'
*            creator_email                    = '[e-mail]'
*            publisher_email                  = '[e-mail]'
*            creator_url                      = 'http://oceandata.sci.gsfc.nasa.gov'
*            publisher_url                    = 'http://oceandata.sci.gsfc.nasa.gov'
*            processing_level                 = 'L3 Binned'
*            cdm_data_type                    = 'point'
*            identifier_product_doi_authority = 'http://dx.doi.org'
*            identifier_product_doi           = '10.5067/AQUA/MODIS_OC.2014.0'
*            keywords                         = 'Oceans > Ocean Chemistry > Chlorophyll; Oceans > Ocean Optics > Ocean Color'
*            keywords_vocabulary              = 'NASA Global Change Master Directory (GCMD) Science Keywords'
* 

Groups:
    /level-3_binned_data/
        Dimensions:

* binListDim  = 11145203 (UNLIMITED)
*                    binDataDim  = 11145203 (UNLIMITED)
*                    binIndexDim = 4320  (UNLIMITED)
        Variables:
            BinList 

*  Size:       11145203x1
*                    Dimensions: binListDim
*                    Datatype:   UNSUPPORTED DATATYPE
            chlor_a 

* Size:       11145203x1
*                    Dimensions: binDataDim
*                    Datatype:   UNSUPPORTED DATATYPE
            chl_ocx 

* Size:       11145203x1
*                    Dimensions: binDataDim
*                    Datatype:   UNSUPPORTED DATATYPE
            BinIndex

*  Size:       4320x1
*                    Dimensions: binIndexDim
*                    Datatype:   UNSUPPORTED DATATYPE

      /processing_control/
          Attributes:

* software_name    = 'L3BIN'
*                    software_version = '4.03'
*                    source           = 'A20021852002192.L3b_8D_CHL.nc,A20021932002200.L3b_8D_CHL.nc,A20022012002208.L3b_8D_CHL.nc,A2002184.L3b_DAY_CHL.nc,A2002209.L3b_DAY_CHL.nc,A2002210.L3b_DAY_CHL.nc'
                   l2_flag_names    = 'ATMFAIL,LAND,HILT,HISATZEN,STRAYLIGHT,CLDICE,COCCOLITH,LOWLW,CHLWARN,CHLFAIL,NAVWARN,MAXAERITER,ATMWARN,HISOLZEN,NAVFAIL,FILTER,HIGLINT'
        Groups:
            /processing_control/input_parameters/
                Attributes:

*  infile             = '/data2/sdpsoper/vdc/vpu1/workbuf/l3inlist.dat'
*                            ofile              = 'A20021822002212.L3b_MO_CHL.nc'
*                            pfile              = 'A20021822002212.L3b_MO_CHL.nc'
*                            oformat            = 'netCDF4'
*                            syear              = '2002'
*                            eyear              = '2002'
*                            sday               = '182'
*                            eday               = '212'
*                            sorbit             = '-1'
*                            eorbit             = '-1'
*                            out_parm           = 'DEFAULT'
*                            processing_version = '2014.0'
*                            reduce_fac         = '1'
*                            merged             = ''
*                            loneast            = '180.000000'
*                            lonwest            = '-180.000000'
*                            latnorth           = '90.000000'
*                            latsouth           = '-90.000000'
*                            verbose            = '0'
*                            unit_wgt           = '0'
*                            median             = '0'
*                            deflate            = '4'

But, When I issue the command :

cc=ncread('/home/xyz/Desktop/abc/chlorophyll_Data/A20021822002212.L3b_MO_CHL.nc','/level-3_binned_data/chlor_a');

I see the following error:

Error using netcdf.getVar (line 134)
33 is not a recognized netCDF datatype.

Error in internal.matlab.imagesci.nc/read (line 606)
                data = netcdf.getVar(gid, varid);

Error in ncread (line 59)
vardata = ncObj.read(varName, varargin{:});

Please help me to rectify this error.

I have also tried h5read, but no use.

Thanks

Answer 1

[Chad Greene]

If the NetCDF file you are using is one of the ones found here, I was able to access the data like this:

A = h5read('A20021822002212.L3b_MO_CHL.nc','/level-3_binned_data/chlor_a');

then there seems to be two arrays in a structure. They're called sum and sum_squared. Plotting them against each other looks like this:

plot(A.sum,A.sum_squared,'b.')

[Priya Patil]

Thanks. It worked for me. What is 'b.' here in the plot command? Also, Can you please tell me how to access attributes such as loneast or latnorth in this data? I need to plot the chlorophyll concentration for in Indian ocean region (35E-110E, 40S-20N). I need help regarding the same. Thanks in advance.

[Chad Greene]

The 'b.' is just shorthand for "blue dots". It's the same as writing this:

plot(A.sum,A.sum_squared,,'color','blue','marker','.')

The georeferencing problem is less straightforward. It's an interesting problem, so I wrote a function for it and used your example in the documentation. The function is now on File Exchange here.

[Priya Patil]

Thanks a lot.

Answer 2

[Priya Patil]

Thanks Chad. I went through the function - binind2latlon(binind,varargin) written by you. It proved to be helpful in getting a 2D plot for the variable chlor_a. Now, I need to perform an analysis (eof, correlation, etc.) upon this data.I am thinking to convert monthly satellite data for a specific time range (for example, year 2002- 2008) into the gridded data form and store it in a single file.

So, can I save this data in a simple netcdf form, so that I can access it with utility such as GrADS or with simple ncread command of MATLAB? I mean, instead of running this function everytime to get a 2D plot for a single month, can I run it once to get the 'chlor_a' variable and store it in a (.dat) file so that next time I can simply access it using ncread command?

Again, I want to aggregate/merge these files of different months into a single .dat file so that I can perform monthly/seasonal analysis of the data. can you give any clue/direction upon both of these questions?

Thanks