Chapter Six Supplement

Instruments and Methods

Example S6C: A Vertical Section Visualized from CTD, Bottle, and Multi-year Averaged Data

It is worthwhile to compare a vertical section made from three different data types:

The bottle and CTD data come from the 2003 and 2005 “A16” expeditions for the US Global Ocean Carbon and Repeat Hydrography program, so match up station to station.

The multi-year averaged data come from the World Ocean Atlas 2005 (WOA05) annual average data, which are available at 1-degree intervals of latitude and longitude over the World Ocean - we picked off the data points that are closest to the A16 track.

Files that may be needed or created in this example:

  • A16_2003_2005_bottle_clean.joa
  • A16_2003_2005_ctd_decimated.joa
  • WOA05_A16.joa
  • A16_2003_2005_CTD_undecimated.joa

We have changed the parameter names in the CTD data file from CTDS to SALT and from CTDO to O2 to make it easier for you to use the same contour/color bars for plots from all three data sets.

Exercise S16C-01: Comparing Data - Multiple Data Types (CTD, Bottle, and Multi-year Averaged Data)

  • File → Open…A16S_2003_2005_bottle_clean.joa
  • FileOpen…A16S_2003_2005_ctd_decimated.joa (Do not Add)
  • FileOpen…WOA05_A16.joa (Do not Add)
  • To calculate potential temperature (“theta”), sigma-0, and sigma-4 for each data file:
  • CalculationsParameters...
  • Select (theta), sigma-0, and sigma-4

The parameters in common to all three data files are now pressure, temperature, salinity, dissolved oxygen, potential temperature, sigma-0, and sigma-4.

Make contoured vertical sections from each of the three A16-related data files of:

  • Potential temperature
  • Salinity
  • Sigma-0
  • Sigma-4
  • oxygen


  • The appearance of the south-to-north and vertical distributions of these parameters when represented by time-averaged bottle-like data, single-expedition bottle data, and single-expedition CTD data.
  • The time-averaged versus single-expedition silicate, nitrate, and phosphate data.

We show the three potential temperature sections below.


FIG s6c-01 Three potential temperature sections


The sections with an eye to how the different data types represent the distributions of seawater properties.

The “big picture” is clearly the same in all three data files, but there are clear differences between the visualizations provided by the A16 bottle, A16 CTD, and WOA05 data files.

But remember, due to the method that JOA uses to plot a contoured vertical section, you cannot see details of smaller vertical extent than allowed by the choice of JOA interpolation surface, so the visual difference between the A16 bottle and CTD vertical sections does not reflect the full difference in resolution of the data files.


On a JOA vertical section (“contour”) plot you can select a subset of the plot by click-drag-releasing the mouse.

The subset of a Contour plot section is a magnification of the same features in the full-range section.

Exercise 6SC-02: High-Resolution Contoured CTD Sections

CTD data almost always have significantly greater vertical resolution than do any existing JOA interpolation surfaces, and so you cannot easily visualize the full vertical resolution of CTD data on a JOA Contour (vertical section) plot.


Here we will demonstrate how you can use a custom interpolation surface with levels onto which the data can be interpolated that match or more closely match the vertical resolution of the CTD data. At this writing JOA has a built-in limit of 128 levels per interpolation surface. Therefore, for example, if you wish to plot a contoured section of CTD data with 2-decibar vertical resolution, you will be restricted to a 254-decibar range of pressure, for example you could make a custom interpolation surface to look at the range 960-1214 decibars.

You can learn more about making custom interpolation surfaces in the JOA User Guide, or simply go to ”Surface Manager“ under the JOA Resources menu and give it a try.

As an example, we have supplied a custom interpolation surface with 128 levels covering 0-254 decibars at even 2-decibar intervals, which you can use with undecimated CTD data to examine fine structure in the upper layer.

We supply an undecimated CTD data file (A16_2003_2005_clean_CTD_undecimated.joa) for those who wish to take a close look at CTD data near or at the vertical resolution the data were reported to the data center:

  • File → Open…A16_2003_2005_CTD_undecimated.joa
  • Prepare a contoured/colored vertical section, choosing the "PRES-0-254_srf.xml" interpolation surface, along with whichever parameter to plot - and corresponding color bar - you wish.

    See note below for instructions on easy methods to make temporary custom color/contour bars for JOA Contour vertical section plots.

  • NOTE:

    Drawing the plot may seriously slow some computers, due to the combination of data file size and computation intensity.

    You may note that the resulting contoured section plot is not all that different in appearance from that of the same pressure range.

  • Making a temporary custom color bar for a JOA Contour Plot (vertical section plot) is deliberately made as simple as we could manage, in order that users could most easily explore a data set:
    • Double-clicking on any JOA color bar - one in a dialog box, on any plot, in the Data Window, etc. - will bring up the JOA Colorbar Editor dialog box, from which you can set new ranges and/or a new “shape” (interval distribution scheme) for the color bar.


      FIG s6c-02 The Colorbar Editor dialog box

    • Experimenting with the various “shapes” will help you decide if you want an alternative to the often-best-choice linear shape.
    • The dark gray histogram in the graph-like area of the Colorbar Editor dialog box is meant to act as a guide to the relative frequency of occurrence of data inside the overall data range in the Y-axis of the graphic.
    • (To achieve a custom distribution of color ranges such as the one shown in the above example, you must use the Contour Manager... under the JOA Resources menu.)

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