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 > 3.8 Transmissometry

3.8 Visualizing the Global Transmissometer Database Collection in Ocean Data View

  • Exercise Title:  Visualizing the Global Transmissometer Database Collection in Ocean Data View (ODV)

  • Abstract:  In this exercise you'll visit and obtain the transmissometer collection for ODV, the major single-source archive for these data.  [The WOOD transmissometer archive may rival it, but no objective comparison has been performed.]  This collection is immediately able to be visualized in ODV, but some refinements concerning the color palette selection are suggested for better viewing.  The method for exporting data of interest (to an ASCII spreadsheet) is practiced.

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

    • N/A

  • Required Software:

  • Other Resources: 

  • Author:  Murray Brown

  • Version:  3-2-2014

1.  Open the ODV website, which should be very familiar to you if  you've been a student of the MDL exercises.  Take some time to read through the informational pages if you're new.  [While here, make sure that you already have the latest version of ODV installed; you can check that at the SOFTWARE tab].

2.  Click on the DATA tab to open this library of existing special data collections that have been created by Prof. Schlitzer or by ODV contributors.  Take the time to read through it, and you'll be amazed at the extremely wide range of data types that have already been covered.  Some collections are generalized datasets, sometimes from notable historic programs, that have been subjected to thorough quality control (e.g. WOCE, GEOSECS); others are very narrowly defined data types (e.g. transmissometer data; alkalinity & TCO2).  It goes without saying that if you chose to work with one or more of these collections, there will be significant overlap with the World Ocean Database stations, perhaps even complete duplication.

3.  We're going to work with the transmissometer database, so click on that menu item.  You'll see this page of metadata items.  Take the time to read about these data.
4.  Click on the STATION MAP to see this chart of the station locations.  They have been assembled from multiple major programs and/or cruise tracks from WOCE.
5.  Click on the DATA FILE link to save the global file as cmeter_global_odv.zip in the folder LIBERIA > DATA > OCEAN.  Then unzip this file and name the contents:
  • cmeter_global_odv.odv (a file) and
  • cmeter_global_odv.dat (a folder)

As you probably already know, an ODV file and a .DAT folder usually constitute an ODV collection, and that's what you now have.

6.  To open this collection, you can:
  • Run ODV, then use FILE > OPEN
  • Double-click on the .odv file you just made to open the collection automatically
7.  In ODV, select VIEW > LAYOUT TEMPLATES > FULL SCREEN MAP

8.  And here is the map of the whole collection.  Take the time to click on various random points and to see the related metadata in the right-side panel.

9.  If you want to extract data (e.g. an ODV ASCII spreadsheet) for use in another program, then you should perform the actions in the next 4 panels.  If not, then skip over the next 5 panels. 
10. We have discovered that the ASCII exports from this collection are HUGE and you probably need to limit the data, as we now will do.

Use your cursor to select one of the stations in the transect you want to use.

11.  Look in the metadata panel to see the name of the cruise.  It is "save" which stands for the South Atlantic Ventilations Experiment.
12.  Right-click on the collection map, and select STATION SELECTION CRITERIA.
13.  Find and select NAME/RANGE > SAVE and click OK.
14.  Now you only have the SAVE stations.  This will be a very considerable reduction in overall data points.
15.  Now we'll specify a "section" of the stations for direct visualization of the transmissometer data.

Right-click on the data map, and select MANAGE SECTION.

16.  Now a lot of things are going on in this panel, so please look carefully:
  • Designate the section with a CLICK at the first point, and CLICKs at any turns (as you see here). Then DOUBLE-CLICK at the final point.  Here we've gone from Liberia to South America, but you can go in the opposite direction also.
  • For SECTION COORDINATE select DISTANCE
  • For BATHYMETRY, select FILE > GEBCO1.NC, which is a file already available inside ODV.
  • For MEAN WIDTH, choose a large enough value to include all the desired stations inside the section frame

Now you can click OK to create this section.

 

17.  To see the section, select VIEW > LAYOUT TEMPLATES > 1 SECTION WINDOW
18.  Here, the section appears.  But the default variable, TEMPERATURE, appears.  We really want the TRANSMISSOMETER values.
19.  Right-click on the map, and select Z-VARIABLE.
20.  To reverse the direction of the section, so that Liberia is on the right,  right-click on the map and select X-AXIS > SECTION DISTANCE and check REVERSE RANGE.
21.  To specify the mapped variable, right-click on the map and select Z-AXIS > BEAMCP, and click OK.

NOTE:  The term BEAMCP is a mixed name, including the word BEAM to designate the instrument used in WOCE, a 25-cm beam transmissometer.  The C part of the name is possibly an homage to Jerlov's terminology:

  • a = absorption
  • b = scattering
  • c = total attenuation

The units are per meter, so the data values refer to the fraction of light lost during transit through the water, over a distance of one meter.

22.  Now you can see the first view of the section.  The C values don't show much, probably because the color scale is too large, i.e. most of the values are very small.
23.  To examine the data values, right click on the map and select EXTRAS > STATISTICS.
24.  There are many statistical values to examine.  We want to see what are the Z values, so we can select a reasonable color palette range.

Click on Z HISTOGRAM.

25.  This histogram of Z values (the BEAMC) show that 0-01 would be a good range.  You can close this graph.
26.  Right-click on the map, and select SET AXIS RANGES.  Change to range for the Z values to 0-0.1, then click OK.
27.  Now you can see much more detail.  The waters with higher values (indicating more light-absorbing material in the water ) extend at least to 2000 m in certain areas.  The deep sea is uniformly very clear.
28.  Now to see the patters better, we need to grid the data.  Right-click on the map and select PROPERTIES.  Make these settings:
  • DATA DISPLAY STYLE > GRIDDED FIELD > DIVA GRIDDING
  • AUTOMATIC SCALE LENGTHS - Not checked
  • X SCALE - Set to 100 (i.e. 10% of map width)
  • Y SCALE - Set to 20

Then click OK.

 

29.  You'll see this section plot, showing that most of the water column has extremely low values, and only the very shallowest water has any interesting details.

With Saga, if we were gridding, then this is an occasion where a LOG viewing scale would be better.  But in ODV we do it slightly differently

29.  Right-click on the section plot and select PROPERTIES.

Click the COLOR MAPPING tab, and move the NONLINEARITY slider all the way to the top.  Then click OK.

30.  Now you can see much more detail in the upper sea.  On your own time, you can investigate the use of these color mapping options and zooming to discover other optical features in the mid-Atlantic.
31.  To "freeze" this view of the data, with these settings, select VIEW > SAVE VIEW AS and save it with the name cmeter_liberia_sw_section_odv_collection.xview.
32.  Now, to export these data, select EXPORT > STATION DATA > ODV SPREADSHEET FILE.

NOTE:  In section mode, when you export the data, you will get all data currently selected, shown in Panel 14, above.  This is somewhat more than the section, but it's a good place to begin.

33.  Navigate to PRODUCTS > ODV > SUBSETS and enter the filename data_from_cmeter_odv_liberia_sw_section.txt for the data export.
34.  When you see SELECT VARIABLES FOR EXPORT, select any or all, as you wish.  Then click OK.
35.  Make these usual choices for the SPREADSHEET PROPERTIES.  Then click OK.
36.  When asked for SAMPLE SELECTION CRITERIA, make sure select GOOD QUALITY, click on APPLY TO ALL VARIABLES, and then click OK.
37.  After a moment, this message confirms that you have exported the desired spreadsheet.

38.  Here you can see the spreadsheet in Excel.  If you want to work with these data in other program (including also Excel itself) then you should perform this import to see the actual values and check that everything looks OK.  The first 11 lines are usually deleted here for work in programs that cannot handle so many extra header lines.

39.  After Excel work, you can save the file in a format that will be most easily used.  Tab-separated variables would be perfect for Saga, etc. etc.