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Marine Data Literacy 2.0

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Home > 9. Operational/Synoptic > 9.4 ColorWeb

9.4 Visualizing Satellite-Measured Optical Properties and Pigments in IDV: ColorWeb

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

  • Abstract:  In this exercise you will learn a method to obtain recent sea surface pigment data (chlorophyll a) and many other optical properties from the MODIS-Aqua instrument.  The method, a global data download from the Ocean Color Web, obtains very recent data (on the order of one day old) as an image that can be imported into IDV, but the image is only qualitative.  The visual color scale is available for rough comparisons, but the raster contains only 256-color palette values, not chlorophyll concentrations. 

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

  • Required Software:

  • Other Resources: 

  • Author:  Murray Brown

  • Version:  05-04-2014

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 Ocean Color Web home page.  This site provides a wide range of remote sensing products, ranging from climatologies to near-real time, at Levels 1, 2 and 3.  Only L3 products can be handled with the software described here.


2.  This graphic and tabular interface opens.  Look along the top row to see the current settings, then change them, as follows:
  • Standard Products
  • Aqua MODIS Chlorophyll Concentration
  • Daily
  • 4 km
  • 24 Thumbnails
2.  The latest image is in the lower-right corner of the 24 thumbnails.  Right-click on the exact middle of the image, and select SAVE LINK AS.

NOTE:  You do NOT want to save the two binary data files which can be saved by clicking on the lower left and right corners of the thumbnail.

3.  Navigate to your folder DATA > OCEAN and save the image as A2011007.L3m_DAY_CHL_chlor_a_4km.png.  In your own case, the date will be different, depending on instructions from your teacher or notes in the course.

NOTE:  The date format is YYYYddd, where ddd is the number of the day in the year.  Sometimes improperly called a Julian Day, the real name for this value is the Year Day.

4.  OPTION:  You can also change the product type from DAILY to 3 DAYS, and save the resulting composite image as A20110052011007.L3m_3D_CHL_chlor_a_4km.png.  In your own case, the date will be different, depending on instructions from your teacher or notes in the course.

NOTE:  The date format is YYYYdddYYYYddd, to capture the beginning and end Year Days of the composite image.

5.  Open any good ASCII text editor and COPY  and PASTE this text into a blank document.

It is a template for the XIMG file format used by IDV to geo-reference plate caree images.

<image name="Display Title for the Image"

6.  Edit the XIMG file to look something like this, with obvious differences for the dates of the images you really are using.
7.  Navigate to the folder DATA > OCEAN, and save the file with the name A2011007.L3m_DAY_CHL_chlor_a_4km_png.ximg, or a similar name, depending on the data dates you are using.
8.  Run IDV.
9.  Select EDIT > PREFERENCES > SYSTEM, and make sure these setting are already made by default:
  • MAX IMAGE SIZE:  1000

This last item is counterintuitive, because the default -1 appears to place no limit on size.  This item is actually the size at which IDV begins subsampling large images to display them, so a finite value is needed to facilitate their display.

Click OK.

10.  Now you can select DATA > CHOOSE DATA > DATA CHOOSERS.  Set the DATA SOURCE TYPE to XML FILES, and navigate to the DATA > OCEAN folder

Select the XIMG file for the single-day image, and click ADD SOURCE.

11.  You should see this set of options under the FIELD SELECTOR tab of the dashboard.


12.  This is the global image.  Notice that it does not have a scale on the right relating the colors to chlorophyll values.  There is only a "gray scale" palette, due to the fact that this raster is not a scientific data set, but merely a georeferenced simple image.

In most cases, the features of interest are obvious, and self explanatory.

NOTE:  You can use the key combination SHIFT-Left Click to drag a zoom box around the main data area for closer viewing.  AND you can use the PROJECTIONS > PREDEFINED controls to look at specific regions.  Some areas don't work very well, though.

13.  You can refer back to the (logarithmic) color scale on the Color Web pages for a rough estimation method.
14.  This is the 3-day composite image, mentioned in Panel 4 above, showing far more area of the sea colored.  Longer time means more coverage.
15.  To save this product for other future work, select FILE > SAVE AS then navigate to PRODUCTS > IDV and save it with the filename A20110052011007.L3m_3D_CHL_chlor_a_4km_png.xidv