What's new in Java OceanAtlas 4.0

This is perhaps the most major upgrade to this program since it was initially developed. Along with many quality fixes there are many new features and enhancements to the user interface. The most notable internal change has been support for the Java 2 Graphics platform. Java 2 graphics give JOA access to multiple, high quality fonts, anti-aliased text and graphics, true rotated text, and superior printing. All of JOA's plots are much closer to "presentation quality" when printed.

New or Improved Features in JOA 4.0

• Spreadsheet File Improvements

  1. Argo Import: Fixes/changes to spreadsheet file reader to accommodate Argo drifter data files created by NODC (.jos files):
     1. Date and Time can now be in separate columns
     2. Station observations are automatically sorted by pressure (as needed) to be in order of increasing pressure.
  2. Export: When exporting to a spreadsheet file, one can now select from a variety of built-in and user-definable missing value indicators and field delimiters. Missing values can be -99 (JOA default), -999.0 (WOCE default), 1e35 (EPIC default), space character, or a user-defined value. Field delimiters can be tab (JOA default), comma, space character, or user-defined.
  3. Import Preview: Opening a spreadsheet file (.jos), presents a new window to preview the spreadsheet file and select missing values and field delimiters. JOA displays the first 10 lines of the file in a scrolling text field.
  4. Import: JOA now accepts -99, -999.0, 1e35, the space character, and a user-defined string as missing value indicators. JOA now accepts tab, comma, and user defined (non-space) field delimiters. Note: space can be used as an output field delimiter but not as an input delimiter.

• Metadata Color bars

  Color bars can be created for four common types of station metadata: date/time, month, latitude, and longitude. The color bar creation dialog has been modified to accommodate these new types of color bars. Metadata color bars are dynamic; they do not correspond to a specific range but are scaled according to the metadata ranges of the currently open data files. Adding data to an existing data window will cause all metadata ranges to be recomputed and any plots colored by metadata to be redrawn. Metadata colorbars can be applied to property-property plots, profile plots, and map plots.

• Interactive Data Enhancement/Filtering

  A range of the color parameter can be highlighted on property-property and profile plots to highlight the points that fall in that range of the color parameter. We call this feature ÒenhancementÓ but it is really a form of an observation filter. A "real" observation filter (i.e., one created through the observation filter dialog) will take precedence over an enhancement. Enhanced values are drawn on top of other values for better visibility. There is a new preference panel for setting the behavior of plot enhancement.

• Map Improvements

  JOA maps are greatly enhanced in this version. Improvements include:
  1. Presentation quality improvements: Maps have "cartographic" borders and graticule labels.
  2. Map Station Symbol Coloring Enhancements: Map plots have major new options for coloring station symbols including coloring station locations by station calculations values (e.g., depth of mixed layer, or value interpolated onto a neutral surface) or by metadata. Station coloring by isosurface value can now interpolate missing values of an isosurface.
  3. Map Improvements for Float Data: Other map improvements to accommodate drifter data (smarter station connection line) and bug fixes.
  4. Station labels: Maps can show the station number or the value of a station calculation parameter or station metadata next to a station symbol. User has control of label size, offset, angle, and display precision.

• Color Bar Improvements

  Color bar legends now are sized dynamically--they will resize as one resizes windows with color bar legends. The color bar editor has been enhanced to allow creation of metadata colorbars and easier editing of existing colorbars.

• Data Window Cross-section Improvements

  Cross-sections can now be zoomed by click-dragging in the depth dimension or setting explicit ranges in its "Properties" dialog. Click browsing is now more accurate in selecting the closest observation to the click point. Observation symbols can now be colored by presence/absence of a specific parameter (in addition to quality code). User interface has been improved to allow more than 6 station calculations.

• Station Calculations

  This area of JOA has changed dramatically. In addition to a new user interface, there are these new calculations:
  1. Neutral Surface: Salinity, temperature, and pressure (and optional error terms) can be interpolated onto user-defined values of gamma.
  2. Station Extrema: Calculate the extrema (max, min) of a parameter over a whole profile or in a user-defined range of another parameter (e.g., max of O2 between 1000 and 2000 decibars). Can return the values of other parameters at the extremum.
  3. Interpolation: Calculate the value of a parameter interpolated onto the value of a surface (e.g., salinity on a density surface). If pressure is the surface variable, can optionally interpolate to the surface or bottom.
  Results of all station calculations can be plotted as a station line plots or used to color map symbols on a map plot. Exporting station calculation values now allows you to select a delimiter and a missing value indicator. Exported station calculation files now include fields for latitude, longitude, and date for better compatibility with external analysis/plotting tools.

• Enhanced Section Manager

  1. Custom mean Casts: Mean casts are interpolated onto a user-selectable interpolation surface and displayed in a new data window. Mean casts can be saved in any of JOA's output formats. Custom mean casts can be used to create residual contour plots (described below). Custom mean casts can optionally include computed statistics, n and variance (in addition to the mean).
  2. Add Ocean Bottom: JOA can add the depth of the ocean at a station's location by interpolation from an etopo bathymetry file.
  3. Merge Stations: An option has been added to merge all stations from all sections into one new section.

• Contour Plot Improvements

  This is another are area of major improvement in JOA 4.0:
  1. Residual Contour Plots with Custom Mean Casts: Residual contour plots can be based upon custom mean casts files created from other data collections with the Section Manager. When creating a residual contour plot, JOA allows one to select a mean cast from any open data window in addition to using a mean cast calculated from the stations in the current data window. JOA will automatically regrid a mean cast if it is not on the same grid as the residual contour plot one has specified. For example, you can compute a mean cast for a large number of stations in the Pacific Ocean and then plot a contour plot of residuals for a WOCE section line from this basin-mean cast.
  2. Improved Interpolation: Improvements to the built-in interpolators produce better contour plots. We have renamed and improved how JOA deals with missing values when interpolating observations onto standard levels. Note: JOA interpolates to standard levels one station at a time. JOA now includes three options for dealing with missing values:
     1. No interpolation of missing values
     2. Vertical or "local" interpolation: In this case JOA attempts to fill missing values by looking a user-selectable maximum number of observations above or below (depending upon the interpolation direction) the standard level for a non-missing value. JOA does not use values from surrounding casts to fill missing values.
     3. Horizontal or "far-field" interpolation: Before interpolating a standard level, JOA will compute for each cast a set of "virtual" bottles based upon the values of surrounding casts. This is done by connecting bounding observations by a line, computing the horizontal gradient, and interpolating where that line intersects the current cast. The number of surrounding stations to use when computing virtual bottles is a user-settable option (defaults to +- 2 stations). Virtual bottles are weighted by their distance from the cast being interpolated. The user also sets how far from a standard level to look for a real observation. When interpolating a standard level, if a real observation is not found within n standard levels (defaults to 2 standard levels) above/below this level, JOA will use the virtual bottle within this range with the highest weight value. This technique is particularly valuable when there are stations with sparse sampling intermingled with more densely sampled stations
  3. Edge Processing in Interpolations: The JOA interpolator includes an option to extend interpolations to the reported ocean bottom by extrapolating the vertical gradient to the bottom and then computing horizontal gradients. This produces a much more pleasing contour plot along the bottom but must be used with caution as false extrema can be created in certain circumstances.
  4. Plot symbols for missing values: JOA no longer plots an observation symbol if the contoured parameter is missing at that observation (bottle).
  5. Plot Symbol Color: User can now select the color of observation/level symbols.

• Other Plot Improvements

  1. Plot toolbars: All JOA plots now have a toolbar at the top of the plot window. The number of capabilities available in the toolbar varies by plot type. All plots have a lock button for "locking" a plot. A locked plot does not allow browsing, resizing, adding data, or filtering. With the exception of contour plots, all toolbars include a value browser that shows the value of the plotted parameters at the cursor location.
  2. Constrained zooming in property-property plots: Holding the shift key down when zooming a property plot will only zoom the plot in the x-axis parameter.
  3. Multiple browsing cursors in mutiple-axes property-property plots
  4. Improved click browsing on property-property plots with multiple x axes. Click browsing in multiple axes plots now searches for the closest matching observation for the primary x axis. The primary x axis can be changed using a plot's settings dialog.
  5. Isopycnal contours and labels have better presentation quality appearance Contour lines are continuous and plot labels are antialiased.

• New Preferences

  1. New Font Preferences: Allows user to select fonts, text styles, text size, and text color for labels used in JOA plots. Currently can set styles for: axis values, axis labels, isopycnal labels, plot titles (printed plots only), colorbar labels, map graticule labels, and map station labels. Text styles can be saved in preferences and independent style files.
  2. Default Autoscale Color Scheme: select which color scheme to use when creating autoscaled colorbars.
  3. User-defined browsing cursor: User can select symbol style (cross, circle, box, etc) and size of linked browsing cursor in JOA Preferences.
  4. Better Text Metadata Display: User-settable date and location formats in Preferences dialog. User can select between a variety of different date formats and between decimal or degrees-minutes-seconds format for locations. Formats are used wherever dates and/or locations are presented (data window, maps, latitude axes, metadata colorbars, etc...).

• Other Improvements

  1. Improved Page Setup: New Page Setup command for selecting printer settings.
  2. Edit Plot Settings Command: Because of a shortcoming in Java, right clicking (ctrl-clicking on the Mac) to display a plots contextual menu will often move the browsing cursor. There is now a Edit Plot Settings command in the Edit menu for displaying a plot's setup dialog without using the mouse.
  3. NODC Argo netCDF Data files: JOA can read netCDF files that adhere to the NODC Argo convention.
  4. Mac OS X Look and Feel: JOA adheres closely to user interface conventions for Mac OS X with respect to menu layout and general look and feel. JOA is integrated with the Finder and supports custom document types (.joa extension), drag and drop of data files to JOA's icon open file and launches JOA if necessary, and double clicking a document launches JOA and opens document.