Marine Data Literacy 2.0

Providing instruction for managing, converting, analyzing and displaying oceanographic station data, marine meteorological data, GIS-compatible marine and coastal data or model simulations, and mapped remote sensing imagery





Home > 9. Operational/Synoptic > 9.24 GlobColour

9.24 Visualizing Satellite-Measured Optical Properties and Pigments in IDV: GlobColour

  • Exercise Title:  Visualizing Satellite-Measured Optical Properties and Pigments in IDV: GlobColour

  • Abstract:  In this exercise you'll learn how to find marine optical data (especially chlorophyll) at the GlobColour project website and visualize it in IDV.  These data are available in two formats (NetCDF and CDF).  NetCDF (all current versions)  is compatible with IDV and other widely used NetCDF visualization programs.  CDF is not compatible with IDV.

  • Preliminary Reading (in OceanTeacher, unless otherwise indicated):

  • Required Software:

  • Other Resources: 

  • Author:  Murray Brown

  • Version:  February 2013

IMPORTANT NEW INFORMATION:  Recently the Saga GIS software has been shown to deal quite adequately with most NetCDF (NC) data grids (and possibly also GRIB files).  This should be viewed as a useful addition to the rapid, direct NC analysis and display capabilities of IDV (see below).  If you are also interested in this route for your data, then please check Viewing and Managing Well-Formed NetCDF Grids in Saga.
1.  Open the GlobColour website and take the time to read through the explanatory materials.  It is particularly important that you read the Products Description, because the analyses here are derived from a variety of methods and satellite sources, and the processing includes multiple pathways.

After you are familiar with the overall picture, then click on the DATA ACCESS link.

2.  This is a portion of the data access page.  Also read this page.  Then click on the FULL PRODUCT SET link (top of the list).

NOTE:  The large green rectangle with HERMES on it is a link to that server.  It produces CDF files that are improperly labeled as NetCDF.

3.  Here is a quotation from the full product set page, showing the many available products.  Case I denotes clear oceanic waters, and Case II denotes "coastal" waters affected by many input processes.

The Full Product Set (FPS), also called GLOB_4KM, covers the merged Level-3 ocean color products in the time period 1997-today. Distributed merged products are:

  • Chlorophyll-a, case I water (CHL1),

  • Chlorophyll-a, case II water (CHL2),

  • Total Suspended Matter (TSM),

  • Coloured dissolved and detrital organic materials (CDM),

  • Particulate back-scattering coefficient (bbp),

  • Diffuse attenuation coefficient (KD490),

  • Fully normalised water leaving radiances at 412, 443, 490, 510, 531, 550-565, 620, 665-670, 681 and 709 nm (Lxxx),

  • Relative excess of radiance at 555 nm (EL555),

  • Aerosol optical thickness over water (T865),

  • Cloud Fraction (CF).

4.  Lower down the same page, you'll see this notice about the availability of the data through FTP.  There is even a link where you can click FTP SERVICE.
5.  If you check the not-shown contents of the link, you'll see that it actually already contains the login globcolour_data and the password fgh678.  Just click on it to enter.
6.  Here is the top level folder in the data collection.  Click on GLOB_4KM.
7.  Here you find choices of data product to browse:
  • DT - "Delayed time"; up to approximately 1 month before the current date; only 1-day options
  • NRT - "Near-real-time"; up to about 1 day before the current date; only 1-day options
  • NRT3 - Up to about 3 days before the current date; only 1-day options
  • RAN - Up to approximately 1 month before the current date; includes 8-day and 1-month product options
  • V1 - Validation data

Click on NRT.

8.  Here is the top of the list of folders in the NRT folder.  They are in date order, so scroll to the bottom and open the latest folder (2012-11-15 in the author's experiment).
9.  Here is the top of the contents of the latest folder.  You must read the Products Description (link above) to understand the contents of each file.

The files that begin L3b are in the CDF format.  The files that begin L3m are in the IDV-compatible NetCDF 3 format.

10.  Scroll to the bottom of the folder to find the latest data.  We want chlorophyll at the highest resolution (4 km).

NOTE:  Of course you are passing over a wonderful assortment of other marine optical products, which you can work with later on your own time.

11.  Download the file to the folder DATA > OCEAN > GLOBCOLOUR.  Then unzip it in place.
12  DEPRECATED Panoply inspection.
13.  Run IDV.
14.  On the dashboard, select DATA CHOOSERS > FILES > GRID FILES (NetCDF).  Then navigate to the new NetCDF file you unzipped.

Select that file, and click ADD SOURCE.

15.  Before you do anything else, because these GlobColour files are very large, let's pick a spatial subset.

Right-click on the loaded file in the DATA SOURCES list, and select PROPERTIES.

16.  Select SPATIAL SUBSET and draw a rectangle around the Gulf of Mexico (or any interesting area you see; perhaps even Liberia if your own data file has something there).

Then click OK.

17.  Now you're ready to map the data subset.  Open these menus by clicking them, and make these selections.


18.  This is the initial image.  As usual with chlorophyll data, you don't see much detail with the full data range.
19.  On the dashboard, select DISPLAYS > COLOR TABLE > DEFAULT and change the palette to RADAR > DbZ to get a nice rainbow palette.
20  Also click COLOR TABLE > DEFAULT > CHANGE RANGE to get this small window.  Change the range to the values shown.  Then click OK.
21.  Here is the final image, with the improved palette and data range.
22.  You can select FILE > SAVE AS to save this IDV product as L3m_20121115__GLOB_4_GSM-MERMOD_CHL1_DAY_00.xidv
23.  This excellent site will be the centerpiece for all future operational training involving ocean optics.  We are indebted to the European marine community for such a great resource.