User Name
Password  
Remember my login
Create new account 
Forget your password?
tab inactive left border CHRONOS tab inactive right border tab inactive left border Searches tab inactive right border tab active left border Tools tab active right border tab inactive left border Resources tab inactive right border 
 Index   3rd Party Tools   Age Depth Plot   Age Range Chart   TimeScale Creator   TimeScale Converter   WorkFlows 
 
CHRONOS Age Depth Plot

Background

The CHRONOS Age-Depth plotting program, ADP, is a Java re-implementation of the ADP program written by Dave Lazarus for the Macintosh ( Lazarus, 1992, Lazarus, 1995). It reads paleontological age-depth data from the Neptune database or from local files, plots those data, and allows interactive fitting of a line of correlation or age model. The plot may be saved in Scalable Vector Graphics (SVG) format or as PNG or JPEG file.

Downloading and starting the program

ADP runs under the Java runtime environment (1.4 or higher) and is downloaded and launched from the CHRONOS web site via Java WebStart. With the initial download, the application is actually cached on your hard drive and run locally. Thereafter, you can run the program offline (without an internet connection). However, if you are online when you start the program, WebStart will automatically check whether an updated version is available from the CHRONOS website. Of course, you will not be able to connect to the Neptune database if you are working offline.

Explanation

Changing axis limits

The plot's axis limits may be changed using the following three buttons.


Zoom in.  When this button is activated you may zoom in to a rectangular region of interest by clicking and dragging on the plot.



Zoom out.  Click this button to zoom the plot back out to the default limits (based on the data range).



Change axis parameters.  Click this button to launch a dialog box allowing you to enter numeric values for the axis limits and tick intervals along each axis.


Modifying the plot

The plot legend includes checkboxes for toggling the display of the different plot groups. Click in a box to remove the corresponding group from the plot and click it again to re-display that group.

The Edit menu contains items for modifying the main plot title axis titles and for showing and hiding the stratigraphic event labels, which are short character strings read from the stratigraphic event data file. Generally, event labels will overlap unless the density of data in the plot window is fairly low. Lower data densities can be achieved by toggling plot groups off or by zooming in to a more detailed view.


Saving the plot

Select Save plot... from the File menu to save the current plot to a file. The current format options for the output file are SVG (Scalable Vector Graphics), PNG, and JPEG. The latter two options use Java's Robot and ImageIO packages to generate an automatic screen capture of the plot region and write the image to a file. Thus, the output file will contain a raster image of plot region as you see it on the screen. SVG is an XML specification for describing vector graphics and the output SVG file (a plain text file) is designed for convenient editing of various plot characteristics, with font and line characteristics for various plot elements and the palette of plotting symbols defined at the top of the file.


Saving data

Use the Save projected data... item on the File menu to write out a file containing the stratigraphic event data projected to the LOC. You will be asked to enter your name or initials and then a header line comment, both of which will be written to the output file. Then you will be presented with a standard dialog box for specifying the location and name of the output file.

The projection consists of replacing the input age value(s) for each event with the ages on the LOC corresponding to the minimum and maximum depth for that event. The data file will be written in the same format as an input stratigraphic data file, meaning you can read the projected data back in and diplay them. All the depths in the output file will be in mbsf, so you do not need a core-depth data file to interpret a projected stratigraphic event data file.

Use the Save LOC... item to write out the current LOC data to a file. In this case you only get the "save file" dialog box. The first line of the LOC file will contain the hole id and the current date.

Reading line-of-correlation (LOC) data

Whenever you read in new stratigraphic event data, ADP automatically calculates a line-of-correlation (LOC) consisting of a single straight segment connecting the extreme age and depth values in the dataset. At this point you may either use the palette of buttons to modify the LOC or read in a previously existing LOC from a LOC data file. To do the latter, select Read LOC... from the File menu and using the resulting dialog box to navigate to and open the desired LOC data file.

Once the file is read, the program will display the LOC on the plot and will also display the opening comment line from the LOC file after the LOC file info label.

Modifying the line-of-correlation

The LOC is represented on the plot as a green line, with open green squares representing the control points for the line. You may move, add, or delete points using the first three buttons in the palette at the left. (Let the mouse hover briefly over a button to see a brief description of its function.) The buttons work as follows:


Move a control point.  When this button is activated you may use the mouse to grab and drag an existing control point to a new location (click on the point, drag, release). Use the age-depth coordinate label at the bottom of the plot to keep track of the mouse location. Once you grab a point, the program displays light gray lines delimiting the boundaries for a legal move for that point. These boundaries prevent you from creating an age model where age decreases with increasing depth. You may, however, create a hiatus by dragging the mouse beyond the upper or lower bounding line. In this case, the control point will stick at the boundary and will be assigned the bounding depth.



Add a control point.  When this button is activated you may add a control point with a single click on the plot. Light gray lines delimit the legal locations for control point additions, again allowing only non-decreasing age with increasing depth.



Delete a control point.  When this button is activated you may delete a control point by clicking on it.



Reading stratigraphic data from the Neptune database

To retrieve data from the Neptune database, select Get Neptune Data... from the File menu. Momentarily, you should be presented with a world map showing locations of DSDP and ODP holes represented in the database. Initially, the hole selection tool (pointer) is activated. While this button is activated, you can click on the map to select holes near the cursor location. The information for the selected holes will appear in the data table at the bottom. To retrieve the data for one of these holes, select the appropriate row in the table with a single click on any cell in that row and then click Retrieve Selected Data. A text window will then appear, displaying the stratigraphic event data as they are retrieved from the database. Once the all the events for the hole are found, the title of the text window changes from Retrieving Neptune data... to Neptune data retrieved and the plot is made. You can get the data window out of the way either by closing it (click on the x in the corner) or repositioning it or by clicking on the main application (plot) window to bring it to the front. Later, you can re-display the data window by selecting Show Data Window from the Edit menu.

The data window displays data as tab-delimited fields, in the same format as a local stratigraphic event file. On most systems you should be able to select and copy the data and then paste them into a text editor to create a local file. A right-click (Windows) or ctrl-click (Mac) on the text area should bring up an editing pop-up menu.

In the map window, choose the Zoom in button (magnifying glass with "+") and then drag a rectangle on the map and release to zoom in to that region. Then click on the pointer button to return to hole-selection mode. The Zoom out button (magnifying glass with "-") will automatically zoom back out to global extent, leaving the current mode (selection or zoom-in) unchanged. For any zooming operation, there will be a bit of a pause while the code retrieves a new world relief image at the appropriate scale.

The code will also attempt to retrieve an age model from the Neptune database and display it, along with information regarding the age model quality and the date it was developed (in the LOC file info line at the top of the application). If it cannot find an age model for the selected hole, it will generate the default straight-line LOC connecting the extreme depth and age values.


Reading stratigraphic data from local files

To read data from local files, select Read data... from the File menu to initiate data input. You will then be presented with two dialog boxes in succession, the first asking you to locate and open a core-depth data file and the second asking you to locate and open a stratigraphic event data file. The captions at the top of each dialog box indicate what they are asking for, but you have to pay close attention to notice them.

All ADP data files are plain text files, but the program enforces no file-naming conventions. Use names that help you remember what is in each file.

The information in the core-depth data file is used to interpret any stratigraphic event depths that are in core-section,cm format in the stratigraphic event data file. However, the core-depth data are not required to interpret stratigraphic event depths that are already presented in meters below sea floor (mbsf). You may skip input of core-depth data by clicking Cancel on the first dialog box. In this case, the program will still present you with the stratigraphic event data file dialog box and will still read and plot events with depths in mbsf.

As the stratigraphic event file is processed, the data window will show the resulting data values, with the depths in mbsf (rather than core-section,cm format). Once the data have been processed, the plot will update. Again, you can either close the data window or simply switch to the main application (plot) window by clicking on it. The opening comment lines from both the core-depth and stratigraphic data files are displayed at the top of the application. You should check these to make sure that you have read the files you intended to read.


References

D. Lazarus, 1992, Age Depth Plot and Age Maker: Age Modeling of Stratigraphic Sections on the Macintosh Series of Computers, Geobyte, February 1992, pages 7-13.

D. Lazarus, 1995, User's Guide to Age-Depth Plot and Age Maker, Version 2.08, August 15, 1995 (unpublished report).