JOA for Your Work
JOA comes from the "factory" setup for basin-scale "blue water"
oceanography. JOA can be extended with custom "resource packs"
that include custom coastlines and isobaths as well as colorbars,
map settings, and interpolation surfaces developed for specific
areas of the world. For PMEL, we have created a resource pack
useful for research in the Gulf of Alaska and the Bering Sea.
This pack contains a high-resolution coastline for the north
Pacific as well as 50m, 100m, 200m, and 1000m custom isobaths
for the Gulf of Alaska and Bering Sea. To download these resources,
click the following link:
To install these resources into JOA:
1) Extract the files from the zip archive such that folder
names are preserved (Use Folder Names option in WinZip).
This will result in a two folders called Custom_Coastlines and
2) Open your JOA folder. This is where you originally installed
JOA. You should have a folder called JOA_Support.
3) Copy the files from the Custom_Coastlines and Custom_Isobaths
folders from the zip archive to the folders of the same name
in your JOA_Support folder
To best use the contour plots and plot value coloring features
of JOA, it is important that you create JOA colorbar and surface
resources (and perhaps color palettes) for the type and ranges
of the data that you will work with.
A colobar is the JOA term for how values of parameter (e.g.,
salinity) are associated with color (e.g., warm colors for high
salinity and cool colors for low salinity). Colorbars are used
to color observation symbols in property and profile plots and
for defining how a parameter is contoured. The JOA Contour
Editor allows you to select a range of values for a parameter,
how many color steps in this range and whether initial colors
are selected from a palette of colors or algorithmically by
choosing start, end and middle colors. The mapping of values
to color can be anything you chose, linear, logistic, exponential
or any shape you can define. JOA can create initial colorbars
with linear, logistic, or exponential shapes. Contour plots
can use pre-built colorbars or create autoscaled colorbars for
an individual plot. A colorbar can have a maximum of 128 levels.
Click the tutorial link below to learn about creating custom
color bars in JOA
Tutorial on Creating
a Custom Colorbar
JOA contours data by interpolating the values onto a regular
grid. This grid of values is called an interpolation surface
in JOA. The most common interpolation parameter is pressure
but JOA allows interpolation of any parameter onto any defined
surface. Interpolation surfaces need not be linear - you may
want higher resolution in shallow water and lower resolution
in deeper waters. The final choice for your interpolation surfaces
will depend upon the nature of the data you are working with.
If you are using bottle profiles you will want a surface that
will generally match the spacing of the bottles. JOA has a limitation
of 128 levels per interpolation surface. Click the tutorial
link below to learn how to create a custom interpolation surface.
Tutorial on Creating
a Custom Interpolation Surface
JOA allows you to create maps of anywhere on the globe in a
variety of projections. Maps can have optional graticules, coastlines,
or bathymetry (isolines or etopo). After you have created a
map of your study area, you can optionally save it to a settings
file for use in future JOA sessions. You can also save the map
settings as the default map settings for JOA.
JOA comes with built in color palettes that have been created
especially for oceanographic data. However, you are free to
create your own color palettes for use in your own custom colorbars.
Click the tutorial link below to learn how to create custom
Creating a Custom Color Palette
Using the Smith and Sandwell
2-Minute Bathymetry Data with JOA
Smith and Sandwell is a high-resolution bathymetry resource
that is compatible with Java OceanAtlas 3.1. Due to the size
of this data set (around 270MB), we advise you to only use small
To use the Smith and Sandwell 2 minute bathymetry data with
JOA follow these steps:
1. Go to the National Virtual Ocean Data web site at: National Virtual Ocean Data System
2. In the Data Sets list, click on the link for "Smith
and Sandwell 2 min topo"
3. Click the Surface relief link displayed below the
"Smith and Sandwell 2 min topo" link.
4. Using either the map, the region popup, or the latitude/longitude
text fields, define a subarea of the map. Bathymetry data will
be returned for this area.
5. Set these options: Select View: x/y (lat/lon) slice,
Select Product: netCDF
6. Click the red Get Data button. You will be prompted
to save the data file on your local disk drive.
7. Change the name to be compatible with JOA. The name you
choose must contain the text "ETOPO2" and end with an .nc extension.
Example: ETOPO2_Kodiak.nc, etopo2_Bering_Sea.nc
8. Downloaded files and rename them. The files should be installed
in the JOA_Support folder found in your JOA installation folder.
9. You will see the files you downloaded in the Bathymetry
panel of the map dialog. You can use any of the ROSE colorbars
to color the bathymetry.