UPDATED June 2012 to be compatible with ODV 4.x on Mac OS X

This excercise is to help familarize you to plot with Ocean Data View a set of
data along a short oceanographic transect, similar to the type you might
generate during the C-MORE summer school cruise. 

1. THE TEST DATA


Simple flat ascii text file with data from cruise (Florida Straits section of
Atlantic cruise led by Chief Scientist Dennis Hansell, May 2001). Selected
data only. Space separator, no dummy values. File is called
"Oceanus360-10-FloridaStraits-Hansell.txt".

The data include CTD measurements of temperature, salinity and bottle depth
along with associated bottle measurements of nitrate+nitrite, total nitrogen
and organic nitrogen. In addition, cruise label, date, time, latitude and
longitude info are given for each sample.

A single line header defines the columns of variables. Here "spaces" define
the columns - alternatively a "comma-separated values" (csv) format could be
used. These formats are easily exported from a spreadsheet. 


2. START ODV 

    Double-click on ODV icon   (or type "run_odv" in terminal)

3. IMPORT YOUR DATA

    File --> Open --> Navigate to directory where you have data file
   
    From "Files of type" drop-down list select "*.txt, *csv, *jos, *o4x"

    Select/highlight file of interest
(Oceanus360-10-FloridaStraits-Hansell.txt) and click "Open"

    You now see the "Spreadsheet File Properties" dialog: 
    From the "Column Separator" drop-down list select "SPACE"

    (All else should be fine - you can define the "Missing Value Indicators" here if needed)

    Click "OK"


4. "COLLECTION VARIABLES" panel

    Just click "OK" 

5. "COLLECTION PROPERTIES" panel

    For "Primary Variable" select "bottle" from the drop down list
    Click "OK"

4. "METAVARIABLE ASSOCIATION" panel
 
    Make sure ODV knows which variables in the table are latitude and longitude

    Click "Lat(N)" in left column
    Click "Latitude [degrees_north]" in right column
    Click "Associate" button

    Click "Lon(E)" in left column
    Click "Longitude [degrees_east]" in right column
    Click "Associate" button

5. "IMPORT" panel

    Click "OK"

8. A map will open and a window should pop up saying 
   "8 stations imported from ... */*/Oceanus360-10-FloridaStraits-Hansell.txt"

    Click "OK"

9. The screen will now show a regional map indicating the location of the casts

10. DEFINE THE TRANSECT YOU WISH TO PLOT

    Right mouse-click on the MAP:
    From the menu choose "Manage Section" --> "Define Section" and click
 
    The map now fills the workspace. The locations of the casts are shown as blue dots.

    Left mouse-click on the blue dot at one end of the row then move along the row clicking on each dot until the last. Double left-click on the last blue dot.
    (You do not need to be extremely precise about clicking exactly on the dots. Nor do you need to click on each and every dot if the section is very dense.)

11. SECTION PROPERTIES panel

    Give a "Section Title"

    Choose your "Section Coordinate" - I suggest, for this case, "Longitude"

    Choose how the bathymetry of the section will be defined. If you have installed them, pre-defined maps of bathymetry are useful. Click on "File" then "Browse" and choose either "GEBCO1.nc" or "ETOPO2.nc" to use a pre-defined bathymetry. If neither is there, click "cancel" and choose "no bathymetry" for now. You can download and install the bathymetry files from the ODV web site.

    Click "OK"

    Now you probably see several windows: The map is at bottom left, with station points showing and the defined transect indicated by a red contour.



12. CHOOSE AN ODV "VIEW" WHICH SUITS YOUR NEEDS

    On the toolbar at the top, left mouse-click on "View" --> "Layout Templates" --> "1 Section Window" and select

    Now the bottom window shows the map again and the top window some depiction of variables from your section data.



13. ORGANIZE THE PLOT TO PLOT THE SECTION YOU ARE INTERESTED IN

    Right mouse-click on the top figure and select "Properties"

    A dialog box should open up. 
(If it doesnt, leave the cursor over that window and hit the keyboard shortcut
"Alt-P" which should open the dialog.)

    When the dialog box is open choose the "Data" tab

    From the drop down menu's choose variables for the x-  and y- axes: 
    
    For example "Section Longitude" on x and Depth on y 
    When choosing Depth as the y-axis, click the button for "reverse ranges" to get it the right way up.

    Select the variable to be mapped (i.e. z-axis) - whatever you like, e.g. NO3+NO2

    Hit "OK" and you will see a section plotted with coloured dots at the observation points.


14. MAKE A SHADED PLOT WITH CONTOURS

    Right click on the section window and select "Properties" (or hit Alt-P)
    Select the Display Style dialog
    Click on "DIVA gridding" 

    (You can play with the x-scale-length and y-scale-length which changes the smoothing)


    Click on "Contours" tab
    Select the properties of the contours you would like (an automatic suggestion is already there) and click "<<" to add them
    Click "OK"

    If you just see large coloured patches then try opening the "Properties" menu again, go to "Display Style" and try increasing x-scale-length and y-scale-length

15. EXPLORE!

    Almost everything about the plot can be modified by right-clicking and choosing "Properties"


16. To save your work: Click on "View" on top bar. Select "Save View" and save it. You can select this view later to return to the same plot.

17. To export your figure: Right click on the background and select "Save Canvas as" - you will get options to save as .eps, .png etc...


18. Adding additional plots/overlaying plots:

Right click in the blank space on the main window and select "window layout"

Right clicking on the rectangle where your data plot lies will allow you to 
choose to resize the window. Right clicking again and choosing "create a new
window" creates an identical window which you can place. Choosing "create an
overlay window" creates a new plot directly over your original plot. This will
be transparent and you can select a different variable which will be plotted
in contours over your original data plot. So you could plot, for example,
contours of temperature over a colour map of nitrate.

Explore these options.



EXPLORE THE HOT DATA SET IN ODV


-  Download the HOT (Hawaii Ocean Time-series) data set in ODV format from the ODV web site (zip file)

- unzip it

- start ODV, select "File" then "open" from the toolbar, navigate to the  HOT data
(named HOT_bottle_data_1998-2008.odv) and select

- click "open"

- ODV opens with a map in the lower left corner, and several profile plots

- SELECT STATION ALOHA 
   Right click on the map
   Select "Manage section"
          "Define Section"

    a larger map appears - double click on the Northernmost dot (Station Aloha (??)) and click "OK"

   Returns to small map with several profile views….


- SET THE TIME VARIABLE

 In the toolbar, click on  "View", then "Derived Variables", in the right hand column (Choices) scroll down, click on "time" to expand the menu, and select "Time (station date&time)" derived variable --- CLICK "Add", then "OK" and "OK" again

      -- now a useful time variable is available to be one of the axes


- SIMPLIFY THE PLOT

     From toolbar, select "View", "Layout Templates" and select "1 Scatter Plot"

     You should now get just one map and one profile plot

- PLOT a variable with depth and time

     Right click on the graph
     Select "Properties"
     Go to "data" tab and set the Y-axis to Pressure (with reverse range checked)
                          set the X-axis to Time (Station data& time…)
                          set the Z-axis to Phosphate

                        click "OK"

   You should now see a graph of phosphate as a function of depth and time, where the phosphate concentration is represented by colored dots.

Follow steps as above (for Oceanus Section) to change axis ranges, change to an interpolated and contoured plot…

Try overlaying windows with other data sets contoured… etc…