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 > 3. Principal Archives > 3.5 WOOD Secchi

3.5 Managing/Repatriating Secchi Disk Depth Data from the Worldwide Ocean Optics Database

  • Exercise Title:  Managing/Repatriating Secchi Disk Depth Data from the Worldwide Ocean Optics Database (WOOD)

  • Abstract:  In this exercise you'll visit the Worldwide Ocean Optics Database, a huge compendium of data at Johns-Hopkins University.  From the over 30 variables you will download a Secchi disk dataset for Liberia, edit it for use in Saga, and then visualize it as a gridded product in Saga.

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

    • N/A

  • Required Software:

  • Other Resources: 

  • Author:  Murray Brown

  • Version:  1-21-2014

1.  Open the WOOD homepage and take a little to read about it.  It is a huge compendium of all the known quality optics data they editor could find.  Unfortunately it is not funded now, and could disappear unless a good agency takes responsibility.  Such as the US NODC.
2.  Some things to know about WOOD:
  • The 30+ datasets range from huge collections of many thousands of measurements (e.g. Secchi disk depths) to very difficult-to-measure parameters represented by only a few stations.
  • It will be surprising to many students how many variables have been identified in the field of marine optics, a result of the many different factors controlling the sunlight field in the sea (particles, dissolved organic and inorganic substances, plankton, etc.).
  • The internal storage format for WOOD data ("bindary STE") is not delivered as a product here, but conversion software is available
  • Data that we can download is in ASCII tables that are not complex but tedious to examine.  Depths and measurements are listed separately in data segments, and the segments are variable in length.  Separating profiles of variables from each segment into easy-to-use files would be a big programming job.
  • The WOOD will not tell you when your request has exceeded the size of textfiles that it can deliver.  If you want to get a large area, say larger than the Liberia AOI, then perform some experiments to see how large a sub-area can be before data are lost.  You must reduce your requests back down to a manageable area.  For example, it was discovered that if you want to download all global Secchi data, then it must be done in bands of latitude no larger than about 2-3 degrees.  So be very careful working with large downloads.
  • We will work only with the Secchi data here, because there is only one measurement at each location, and no profiles. Hence, no programming.
  • Some important standard hydrographic data, such as salinity, temperature, nutrients, are mixed in with the data.
  • There are 2 data interfaces, a graphic one and a text-based one.  We'll use the text one below, because some PCs cannot run the graphical interface, due to scripting limitations and other security blocks.
3.  On the main page, click on DATA LOCATIONS to explore some of the areas where  data are available.  This is just for your information.
4.  Now click on ACCESS DATA.
5.  Enter the necessary data to register.  Then click CONTINUE TO DATA.
6.  You can select the JAVA-BASED GUI, but the author recommends WEB-BASED TEXT QUERY.
7.  At the top of this long form, you can enter the spatial and temporal parameters for your desired data.

For the LATITUDES and LONGITUDES, enter values that extend at least 1 degree outside the Liberia area of interest, as you see here.  You can make other selections however you wish.

8.  Select for now the SECCHI DEPTH.  You can come back later and look at other data on your own time.
9.  For OUTPUT FIELDS, select MULTIPLE QUERIES: STANDARD just for simplicity.

For OUTPUT FORMAT, select TEXT OUTPUT, NO FORMATTING

 

10.  Then click SUBMIT QUERY.
11.  This large text table appears.  There are several problems to note:
  • The multi-line header will not work with many programs, so it must go.
  • There are many different spacings between the data values, ranging from 1 to 3 or 4.  This also won't work with many programs, so they must be simplified.
12.  Save the textfile to your DATA > OCEAN > WOOD folder with the name secchi_all_liberia_plus_wood.txt
13.  Open the file in your best ASCII editor, such as Context.  Then remove the extra leading header lines, as you see here.
14.  Now inside the remaining text, do these tasks:
  • Simplify the variable names in the header, as you see here, removing any spaces.  There are exactly 12 columns of values and 12 distinct variable names.  Each space in the header begins a new name.
    • PROF_NUM is one name, not two because _ is not a space
  • Eliminate extra spaces in the data table, with the REPLACE function in your editor
    • REPLACE 4 spaces with 1 space
    • REPLACE 3 spaces with 1 space
    • REPLACE 2 spaces with 1 space

Now you can save the table, probably with the same name to save space.

15.  Run Saga.  Then select MODULES > IMPORT/EXPORT-TABLES > IMPORT TEXT TABLE.
  • TABLE - Set to CREATE
  • FILE CONTAINS HEADLINE - Check
  • SEPARATOR - Space
  • FILE - Select the edited textfile you just created

Then click OK.

16.  After the new table appears in Saga, you can inspect it with SHOW to make sure that all 12 variables are present, and that everything looks OK.
17.  First we need to make a shape from the table. Select MODULES > SHAPES-POINTS > CONVERT TABLE TO POINTS.  Then make these selections:
  • POINTS - Set to CREATE
  • TABLE - Select the loaded table
  • X - Select LON
  • Y - Select LAT
  • Z - Select SECCHI

Then click OK.

18.  Now you should have both the table and the new point shape, as you see here.
19.  You can use SHOW to see the point shape locations.
20.  But to show the values for each data point, look at the SETTINGS for the shape, and make these selections:
  • COLORS > TYPE > GRADUATED COLORS
  • ATTRIBUTE > SECCHI
21.  Click on COLORS to see this control.  The COUNT control on the right lets you select 100.  The PRESETS control on the right lets you select the palette (see next Panel).
22.  Here is a good palette for Secchi data, because it will go from GREEN (small values) to BLUE (large values).  This is exactly how Secchi values vary with apparent ocean color.
23.  So after all the changes, you have a graduated colors palette of 100 values, ranging from green to blue, based on the Secchi depths

In the lower right corner, click on SETTINGS > APPLY to see the result..

24.  And here are the Secchi data, colored by values.  You can easily see the transition from green (near-shore) to blue (offshore).
25.  Click on the point shape and select HISTOGRAM to see this distribution of values.  There is a hint of 2 overlapping distributions, perhaps reflecting seasonality?
26.  To do any gridding, you'll need at least one dummy grid.  Go ahead and load the 0.5-degree dummy for Liberia, and any others you want to experiment with.
27.  Now, let's quickly grid these points to see the overall pattern, smoothed out.

Select MODULES > GRID-GRIDDING > INVERSE DISTANCE WEIGHTED, then make these selections:

  • POINTS - Point shape you just made
  • ATTRIBUTE - Secchi
  • TARGET GRID - Grid (Saga will ask Which one? later)
  • SEARCH RANGE - Local
  • MAXIMUM POINTS - Try 10; experiment later
  • DISTANCE WEIGHTING - Try inverse distance to a power; experiment later
  • POWER - Try 2; experiment later

Then click OK.

28.  When asked which grid to use for the work, select the 0.5-degree dummy grid for Liberia.

Then click OK.

29.  Make the same settings for this new grid that you used to visualize the point shape.
30.  Here you can see the final grid, with the WORLD BORDERS shape to cover the stray grid cells on land.  There are some strange values in the deep ocean, but overall the result is quite nice. 
  • The expected lower values along the coast correspond to higher chlorophyll in nutrient-rich, fresher waters. 
  • The generally decreased values in the lower right must be associated with nutrient regeneration mechanisms in the Gulf of Guinea (i.e. higher chlorophyll).
31.  Make sure to take the time to save this final grid in the folder PRODUCTS > SAGA > GRIDS with the name secchi_liberia_all_wood_0p5deg.sgrd