Java OceanAtlas General Information

Introduction

Java OceanAtlas is a Java application which provides a graphic exploration environment to examine and plot oceanographic vertical profile data. The original root of the application is the program Atlast developed by Peter Rhines (1989), and the MacOS applications OceanAtlas (1990) and Power OceanAtlas (1996). Java OceanAtlas brings many new and improved features, and it will run on any computer operating system which supports the appropriate level of Java, for example MacOS, Windows, and UNIX.

Java OceanAtlas can function as a stand-alone living atlas of oceanographic sections: the data sets supplied include pre-1990s data for pressure, temperature, salinity, dissolved oxygen, and the 'nutrients' nitrate, phosphate, and silicate from more than 2000 ocean sections (including the major pre-WOCE trans-oceanic sections), data extracted from the mean property fields in the Levitus WOA98 compilation, and many multi-parameter basin-scale sections from the 1990-1998 WOCE Hydrographic Program. Additional profiles - as individual profiles, sections, or other collectiosn of profile data - of arbitrary parameter composition can be imported at any time in several standard community formats including spreadsheets, WOCE 'WHP-Exchange', NODC 'SD2', and EPIC netCDF. Java OceanAtlas will work with any type of pressure-indexed data.

Java OceanAtlas plots include property-property plots, offset profiles, contour plots, and maps, using color as a plotted variable to aid interpretation. There is a comprehensive data display window. All Java OceanAtlas plots are linked and may be 'browsed' by sample and/or by station. Plots can be re-scaled, resized or have their colored variable changed. Selected areas of most plots can be made into new plots. Standard levels, scales, contours, and colors can be changed via user interfaces similar to those used in commercial applications. Java OceanAtlas provides data filtering and exporting. Many different types of calculations can be performed, including custom parameter calculations.

The growing 'Atlas of Ocean Sections' electronic atlas of oceanographic sections provides a unique reference and teaching environment. Java OceanAtlas is also a powerful data examination tool, and as such is useful for initial exploration and data quality examination of new expedition data.

What Java OceanAtlas Does Best

Java OceanAtlas (JOA) is great at property-property plots, allowing any original or calculated parameter to be plotted against any other. There is full control over axis ranges, plot point size, etc., plus the plotted points can be colored by any other parameter for which there are values and a color/contour bar. And by selecting "Connect Observations" during plot set-up or modification, on each property-property plot a line will be drawn connecting the values in sequence.

Profile (waterfall) plots, again allowing any original or calculated parameter to be plotted against any other, are colored by the current color/contour bar. Amplitude, line width, and spacing are adjustable.

Java OceanAtlas produces Contour plots without the visually-appealing but occasionally data-obscuring effects of objective analysis, using simple linear interpolation to prepare gridded data and contours. Coloring/contouring can be specified from JOA-supplied, autoscaled, or user-generated colors and intervals.

Station maps can easily be customized to show the regions or underlying bathymetric features of interest. Station dots can optionally be colored in accord with water property values; along with the vertical data browsing tool this provides an effective substitute for contoured lateral data maps.

JOA is an excellent data exploration tool: click the mouse pointer on a data point on one plot and it gets highlighted there, on all other open plots (including Maps and Contour plots), and the actual data are displayed in the Data Window. By using Filters and appropriate plot scales to focus on the data of greatest interest one can get drawn into the data.

Any number of data sets can be combined, or subsets made and re-combined, or multiple data sets can be opened without combining them.

The default plot set-ups will provide a useable plot without further input from the user, but a great range of customization is feasible for every plot.

Limitations of Java OceanAtlas

Java OceanAtlas works with vertical profile data, and is optimized for working with vertical sections. Mainly Java OceanAtlas does not support contoured horizontal mapping. There are good reasons for this, mostly having to do with data density, data noise, and the limits of gridding algorithms. We have experimented with an OceanAtlas version which made contoured data maps, but while it worked fine with carefully prepared pre-gridded data, it left much to be desired for the mixed data which goes into most basin-scale maps such as those made by Professor Joseph Reid of the Scripps Institution of Oceanography.

Java OceanAtlas was not made as a publication plot tool. Other applications are better at that, although some interesting presentation-quality graphics are possible by using a screen capture utility, the 'Save' function, or the clipboard to grab JOA plots and copy them into a graphics program for enhancement and printing.

The present version of Java OceanAtlas does not generate velocity, flux, and transport calculations and related plots.

Java OceanAtlas is a Java application and suffers from the limitations of that environment. In particular memory usage can be high by present day standards (using >100 MB of RAM in a JOA session is not unusual) and some JOA functions are on the slow side. Also, although JOA updates keep pace with Java updates, for the most part this is only with the current lowest common Java version across MacOS, Windows, and Unix.