GeoMapApp User Guide

GeoMapApp is an application created for the discovery, exploration, manipulation, visualization and analysis of a large choice of built-in and user-imported data sets. The application is coded in Java Standard Edition 5 (1.5.0) and runs in most installations of the Windows XP, Vista and Mac OSX operating systems as well as with Solaris and Linux. The application is free and can be downloaded at http://www.geomapapp.org/. The development of GeoMapApp is funded by the US National Science Foundation and the Trustees of Columbia University.

From the base map window, users access the many built-in grids, images and tabular data sets via the menu bar. This can also be used to import new data sets. The GeoMapApp tool bar provides a number of useful functions and shortcuts, including zoom and panning, the profile tool and mask function, and a digitizer. When viewing grids, the grid dialog offers convenient tools for changing the color palette and sun illumination, for drawing contours and taking profiles, and for creating a 3-D perspective view. At all times, GeoMapApp’s layer manager allows the layers to be toggled off and on, their transparency altered, and their order switched. For example, varying the transparency is useful when comparing co-located data sets, and, when viewing multiple data sets, the user can specify which layer is topmost. A number of built-in data sets are shapefiles. The shapefile manager allows individual components of built-in and imported multi-shape shapefiles to be selected.

2) Download and start GeoMapApp

On the GeoMapApp web page (http://www.geomapapp.org/) choose the platform from the Download Links area n the left margin. On the next page, click Agree and then save the application to the local computer. Double-click on the GeoMapApp icon to start the application.

Alternatively, if GeoMapApp was downloaded as a jar file (GeoMapApp.jar), it can be opened from a terminal window by changing to the directory containing the application and typing: java -jar -Xmx1028m GeoMapApp.jar

In this example, 1028 Mbytes are allocated as application memory (the default is 256 Mbytes). Specifying this larger memory size is useful when importing large grids or data sets from the local disk drive.

2.1) Choosing a Map Projection

When GeoMapApp is opened, the user has a choice of three map projections as shown below, left.

The Mercator projection – the leftmost panel – is the pre-selected default. Click the center panel for the southern hemisphere polar projection or the rightmost panel for the northern hemisphere polar projection. Click the button to proceed. An initialisation screen (above, right) is displayed briefly before the GeoMapApp window appears.

Most of the built-in data sets are common to all three projections although some data sets are unique to certain projections.

The Mercator projection conforms to the European Petroleum Survey Group code 3395, the Southern hemisphere polar projection to EPSG 3031 and the Northern hemisphere projection to EPSG 32661. The Mercator projection extends from 81°S to 81°N.

2.2) The GeoMapApp window

When the GeoMapApp map window opens the display shows the shaded color relief from the Global Multi-Resolution Topography (GMRT) compilation of the Marine Geoscience Data System.

Figure: Mercator projection (default)

Figure: Southern hemisphere projection Figure: Northern hemisphere projection

3) Global Multi-Resolution Topography (GMRT)

The GMRT compilation (Ryan et al., 2009) consists of high-resolution bathymetry (~100m grid spacing) from multibeam echo-soundings for ocean areas and comparable resolution (3 arc seconds) elevations from the Shuttle Radar Topography Mission for land areas. For the Mercator and polar projections multibeam swaths are merged with the 1 arc-minute resolution “predicted bathymetry” of Smith and Sandwell (1997).

In addition, the GMRT compilation for the southern hemisphere polar projection incorporates the BEDMAP 2000 Antarctic under-ice topography of Lythe et al. (2000), and GMRT for the northern hemisphere polar projection uses the digital depths of the International Bathymetric Chart of the Arctic Ocean (IBCAO) of Jakobsson et al. (2008).

_·Smith, W. H. F and Sandwell, D.T., 1997. Global seafloor topography from satellite altimetry and ship depth soundings. Science, 277, 1957-1962.

_·Lythe, M.B., Vaughan, D.G. and the BEDMAP Consortium, 2000. BEDMAP bed topography of the Antarctic. 1:10,000,000 scale map. BAS (misc) 9. Cambridge, British Antarctic Survey.

_·Jakobsson, M.R., Macnab, R., Mayer, L., Anderson, R., Edwards, M., Hatzky, J., Schenke, H.W., and Johnson, P., 2008. An improved bathymetric portrayal of the Arctic Ocean: Implications for ocean modeling and geological, geophysical and oceanographic analysis, Geophys. Res. Lett., doi:10.1029/2008GL033520.

Figure: Examples of the GMRT at the East Pacific Rise 9N site. Progressively higher resolution is shown to lower right. (Middle)The mask function indicates areas with multibeam swath bathymetry data. (Right) The underlying grid is shaded from the NW and exaggerated to highlight the strong abyssal hill fabric.

4) The Menu Bar - Overview

Built-in and imported data sets and many other functions are accessed through the menu bar.

Figure: The GeoMapApp menu bar.

The File menu () provides user import options for Excel™ spreadsheets, data tables, grids and shapefiles, and offers connections to import data from a number of national and institutional data repositories including IRIS, NASA, JPL, UNAVO, NSIDC.

The Basemaps menu ()provides a very wide range of global, regional and local data set grids, maps and images with full zoom capabilities.

Figure: Examples of the many base maps available in GeoMapApp (clockwise from upper left): Geology map of France, NASA Blue Marble, AVHRR average sea surface temperatures (1985-1997), Smith-Sandwell satellite altimetry-derived free air gravity anomaly.

The Portals menu () offers customized data access and manipulation interfaces specific to each data type. For example, the Multi-Channel Seismics interface allows users to view and digitize MCS profiles, the seafloor drilling interface provides customized core profiling and searching, and the Photographic Transects portal offers seafloor dive photos arranged along the dive track.

Figure: Examples of Portal customized interfaces: (Clockwise from upper left) Seafloor dive photos on high-resolution bathymetry for the EPR 9N Ridge 2000 study site; the DSDP/ODP interface includes species range charts, down-hole physical measurements and stratigraphic information; Multi-Channel Seismic reflection profiles over the Aleutian trench.

Under the Datasets menu (), a large number of tabular data sets at all scales can be plotted, colored, scaled, graphed, and extracted.

Figure: Examples of Data sets: (Clockwise from upper left) Precipitation isotopes; oceanic water column properties and associated temperature, salinity and oxygen profiles; global heat flow and associated graph of heat flow versus depth; seafloor photos.

The Focus Sites menu () provides quick links to Ridge 2000 and MARGINS Focus Site data sets.

In the Overlays menu (), various overlays an be selected and toggled on/off, including a distance scale, the inset map, coastlines, lakes and rivers and geographic/political names and boundaries.

The Bookmarks menu () allows the current view to be saved, zooms out to global view, and zooms in to selected sites of interest.

Education-related links are given under the Education menu ().

5) The Menu Bar - Details

In this section are the details of each of the menus.

5.1) File

Import data sets, export map images, and set GeoMapApp preferences under the File () menu.

5.1.1) Import data sets – Import Dataset from Web Feature Service (WFS)

A step-by-step multimedia tutorial is available for this function (Web Feature Service): http://www.geomapapp.org/tutorials/index.html

Allows real-time connection to a wide range of database and repository holdings, including those at NGDC, IRIS earthquake location data, UNAVCO station information, the PetDB petrological database and SedDB sediment geochemistry database, DSDP information, and others.

When a WFS is loaded, all functionality associated with tabular data sets is available, such as symbol coloring and scaling, graphing, and lasso selection.

Figure: An IRIS Web Feature Service for earthquake locations showing those around Indonesia, colored according to magnitude.

To graph the down-hole measurements associated with the DSDP WFS, see the data set Special Functionality section.

5.1.2) Import data sets – Import Image from Web Map Service (WMS)

Allows real-time connections to a number of agencies serving images and maps via WMS, including NASA, JPL and NSIDC.

Figure: Web Map Service examples. Clockwise from upper left: Outgoing long wave radiation (NASA, CERES); One month of fires across eastern Africa (NASA, Terra/MODIS); Extent of sea ice in austral summer (NSIDC, for December 1979-2007); Landsat5 pseudo-color mosaic (JPL, CONUS data set).

5.1.3) Import data sets – Import a 2-D Grid File

A step-by-step multimedia tutorial is available for this function (Import Grid): http://www.geomapapp.org/tutorials/index.html

With this function, users load their own grids and have full capability for zooming, grid manipulation and profiling. Various formats of grids can be imported, including the GMT netCDF and ESRI ASCII/binary formats. Multiple grids can be imported at once.

5.1.4) Import data sets – Import Shapefile

A step-by-step multimedia tutorial is available for this function (Import Shapefile): http://www.geomapapp.org/tutorials/index.html

Use this option to import shapefiles. The required shapefile components are listed here.

5.1.5) Import data sets – Import Table or Spreadsheet

A step-by-step multimedia tutorial is available for this function (Import Data Table): http://www.geomapapp.org/tutorials/index.html

Users can import data tables that are in ASCII and Excel^TM formats as well as tables stored on the clipboard or at a given web URL. The table must contain a column for longitude (in decimal degrees) and a column for latitude (in decimal degrees). The imported points are plotted on the map and can be manipulated as for any data set – colored, scaled, graphed, linked to URLs, and so on.

5.1.6) Preferences

Controls the border annotations, and allows users to specify a proxy server. The proxy server setting (under development) allows users to use GeoMapApp in firewall-protected environments.

Tick marks turn on items. Untick boxes to turn them off. Select font type from the drop-down menu. Type a new font size into the box . To check the appearance of changes to the annotations, select . Then, to accept the changes, select .

5.1.7) Save Map Window as Image File

The current map view (including any points, grids, tracks and so on that are being viewed) can be saved in various image formats: JPEG, Bitmap (bmp), KMZ (Google Earth^TM-compatible), and GeoTIFF. The image can also be stored as a PDF file (see Print option below).

5.1.8) Print Map Window

Sends current map view to printer or a PDF file. Click Printer button to choose destination printer (or PDF file).

5.1.9) Exit

Close GeoMapApp.

5.2) Basemaps

A wide range of global and regional data sets covering many disciplines of study are available through the Basemaps menu. New images and grids are added frequently.

Apart from items listed under Global Grids and Regional Grids, which have special functionality, all of the other Basemaps choices are images. When grids and images are added to the GeoMapApp menus, they are compiled at a number of resolution scales to allow zooming.

In the Basemaps menu, data sets are grouped roughly into geology/geophysics, physical oceanography and land-use/anthropogenic divisions.

Select and click one item from the menu for it to load in the map window.

Figure: AVHRR sea surface temperature data set loaded in GeoMapApp. Zoom in to see finer detail.

The map legend appears automatically. The map legend can be resized and moved.

The Layer Manager can be used to turn the map window image off and on, to alter its transparency and to discard it entirely.

Upon loading an item from the Global Grids or Regional Grids menus, the grid is loaded in the map window, and a grid dialog appears. For grids that comprise a multi-shape shapefiles, a Shapefile Manager also comes up.

Figure: Very-high-resolution bathymetry of San Francisco Bay showing fine detail on the 2-3m ripples and a 2m-deep dredge channel. Grid is available under regional bathymetric grids of the US offshore margin (Various NOAA Coastal Grids, scroll to last item in Shapefile Manager – SF Bay).

The Shapefile Manager allows items to be selected or discarded.

The grid dialog provides functions to manipulate the grid including changing the color, sun illumination, contours, and taking profiles.

5.3) Portals

The Portals menu provides customized interfaces for a number of specific data types. The expanded functionality allows greater data manipulation and access.

5.3.1) Bathymetry, Gravity and Magnetic Anomaly Profiles

This customized interface allows users to view underway geophysical profiles for more than 4,900 individual research cruises spanning decades of exploration.

Select this interface from the Portals menu () to display the ship tracks. The default view displays all cruise tracks with any gravity, magnetics or bathymetry data. To select cruises for a particular data type, use the check boxes to the right of the map: tick only those boxes for which data is required.

Figure: Use the check boxes to choose which data tracks to display on the map.

Zoom to an area and click on a track of interest. The selected track turns white. Note that only those cruises falling both within the map area and having the data type selected are displayed in the cruise list. Select View Profile () to load the underway geophysical data. The track turns yellow. The red part of the track shows the extent of the profile displayed in the lower pane. Note that it may be necessary to scroll through the profile window to see profiles for incomplete data sets.

Download the underway geophysical data set in MGD77 format using the Download Data button (). Import an MGD77 file (). Select cruises from the collections of NGDC, LDEO, USAP, SIOExplorer by choosing the radio button in the right pane.

Save the map as an image using -> .

Figure: (Left) Select a cruise track, click View Profile (). (Right) Scroll in profile pane. Choose between gravity, magnetics, bathymetry. Download the MGD77 format file or import your own MGD77 file.

5.3.2) Multibeam Swath Bathymetry

Quickly identify and download multibeam swath data files from the ship track map.

A step-by-step multimedia tutorial is available for this function (Multibeam Tracks): http://www.geomapapp.org/tutorials/index.html

When this interface is selected in Portals (), ship tracks load in the map window. Zoom and click on a track of interest. That ship track turns white. The red part of the track shows the extent of the individual swath file listed in the lower left. Note that the red part of the track may be very short depending upon zoom factor and duration of particular swath files.

Download this multibeam swath data file in its native format (all are MB-SYSTEM compatible files) using the button.

The button opens the MGDS database page for this cruise, if available.

Save the map as an image using -> .

5.3.3) PetDB (Composition of the Oceanic Volcanic Crust)

Explore geochemical analyses and sample locations for samples in the PetDB petrological database. When selected, the PetDB sample locations are plotted as squares on the map.

5.3.3.1) Overview

Click a symbol on the map (it turns red); the data record for this symbol is highlighted in the lower table. The columns list the following information:

- Number of samples associated with the chosen station

- Type of material analyzed. Codes are listed in right panel ()

- Type of data available. Codes are listed in right panel ()

- Type of rock analyzed. Codes are listed in right panel ()

- Coordinates of sample location.

The Compiled Chem tab lists the compiled geochemistry for all samples associated with the chosen station. Click the column heading to sort the values.

5.3.3.2) Filtering the PetDB samples

When the PetDB portal is opened, all samples are displayed. The right-hand panel provides the capability to filter the samples by type of material, type of data, and type of rock. Click an item in the list to de-select it. Click to de-select all items; click to select all items.

In the following example, basaltic glasses with REE and volatiles analyses have been selected. Only those samples that satisfy these parameters are plotted on the map.

The PetDB web page for the selected sample can be accessed using the button.

5.3.3.3) Color, Graph and Lasso data

The button opens a window and the column to color on is chosen from the drop-down menu. Click to open the color palette histogram.

To plot any two numerical columns, click and select the x-axis and y-axis variables from the drop-down lists. If symbols have been colored (on any column) that coloration is preserved in the graph.

Figure: Compiled chemistry for sample 208NMNH113716: Graph shows Ce plotted against La, with coloring on Nd.

The Lasso Tool in the right-hand panel () or the lasso tool in the graph () can both be used to select specific samples.

See this section for more information on coloring and graphing data points.

5.3.4) Earthquake Locations, Epicenter Depths and Magnitudes (ISC)

Display and filter earthquakes from the International Seismological Centre for years 1964-1996.

Use the filters in the right pane for , , to change the displayed range of earthquake depth, magnitude and year. Click the button each time a range is adjusted. Epicenters are color-coded as shallow (green), intermediate (yellow) and deep (red).

Save the map as an image using -> .

5.3.5) Earthquake Focal Mechanism Solutions (CMT)

View as beachballs around 30,000 focal mechanism solutions from The Global Centroid-Moment Tensor Project, formerly the Harvard CMT Project.

When viewing the world, the solutions plot as blue symbols.

Zoom to an area to see the beachballs. They are displayed for zoom factors of 32 or more.

Click to open the Global CMT web page.

Save the map as an image using ->

5.3.6) Location and Timing of Seafloor Earthquakes and Volcanic Eruptions

This portal provides a movie animation function that shows earthquake activity over multiple years for various NOAA/PMEL data sets.

A step-by-step multimedia tutorial is available for this function (Earthquake Swarm): http://www.geomapapp.org/tutorials/

Three data sets are available: the Sound Surveillance System deep-water array (SOSUS, 13 years of data), East Pacific Rise (EPR, 6 years of data) and Mid-Atlantic Ridge (MAR, 4 years of data).

Choose one of the three data sets by ticking the appropriate box (, ) then click to load the selected data set.

The data set displayed can be switched by choosing () and loading () one of the others from the areas box.

The lower pane displays the earthquake activity and the animation parameters.

The histogram shows the number of earthquakes (vertical axis) with time (horizontal axis). Click and drag the grey vertical lines left or right to change the time window.

Reset the time window with the button. Dates ranges are given in (year, day-of-year, time) format. A viewing speed of 5 frames/second usually looks good for animations.

Start the animation with the button. Save the animation as an MPEG file with the button (when choosing a file name, append “.mov”).

Figure: (Left) Watch an earthquake swarm propagate over ten days in 1998 along the MAR axis at 45.75^o N. (Right) View two earthquake swarms at the Wilkes Fracture Zone between 1999-2001, superimposed upon striking EPR axial topography mapped with multibeam echo-sounders.

5.3.7) Multi-Channel Seismic Reflection Profiles

Use this interface to view, compare digitize, annotate, extract Multi-Channel Seismic (MCS) reflection profiles for about sixty MCS cruises.

When this portal is selected, geographical bounding boxes outline the extent of available MCS profiles on the map. Click inside one of the boxes to zoom automatically to the area and display the seismic lines within that box. In the map window click a line to select it, or use the drop-down menus at right to choose a cruise and a seismic line. The chosen line turns white.

Select to load the MCS profile into panel 1. The portion of profile displayed in the lower panel is shown as red on the seismic line map. To load a second line, click on another track in the map and select . Select to display the profiles side-by-side.

Figure: Comparing two Aleutian Trench MCS profiles 800 km apart. Inverse video is used to display EW9409 line 1235.

Scroll through the MCS profile using the horizontal and vertical scroll bars ( ) next to the profiles. Note that the red portion of the seismic line moves with each horizontal scrolling action. Zoom in or out of the MCS profile using the zoom buttons . The MCS profile axes show two-way travel time in seconds (vertical axis) and Common Mid-Point gather number (horizontal axis).

Flip the profile laterally using the twin arrows button ( ).

5.3.7.1) MCS save profile function

Save the profile on display – or the entire scanned profile – using the left-most diskette button (, next to flip-axis button). This diskette button () also allows the seismic line navigation to be saved, and provides a direct link to download the SEG-Y file from UTIG, if available.

5.3.7.2) MCS digitizing function

Reflector horizons can be digitized, annotated and saved to a file using the buttons directly above the MCS profile display.

Figure: Digitized horizon (blue line) for eastern Mediterranean cruise EM-83, seismic line 05. The red circle shows the three control buttons that trigger the Digitize (), Text annotation () and Save Digitized Points () functions.

Activate the Digitize function by selecting . Click firmly with the mouse to digitize each point, and exit the digitizer by clicking the adjacent arrow cursor button .

Annotate with the text () button by clicking twice in the profile window and typing text in the text box that pops up. Select to accept the text.

After digitizing a profile, click the arrow cursor button to exit the digitizer mode. Save the digitized points with the right-most diskette button () next to the profile zoom buttons,. The saved ASCII file contains four tab-separated columns giving longitude, latitude, TWTT, and CMP number.

5.3.8) Single-Channel Seismic Reflection Profiles

Single-Channel Seismic (SCS) reflection profiles can be viewed, digitized, annotated and extracted using this interface. About 260 scanned profiles are available and these were collected on cruises of Lamont-Doherty’s research vessels Robert D. Conrad (for the years 1963-1978), Eltanin (1965-1972) and Vema (1960-1980).

A step-by-step multimedia tutorial is available for this function (SCS Profiles): http://www.geomapapp.org/tutorials/

When the SCS portal is chosen from the Portals menu (), zoom and click on a track line. The selected cruise turns white and is highlighted in the cruise list at right. Note that all of the SCS cruises remain in the list when zooming or panning.

Click to load the SCS profile in the lower pane. The vertical axis gives two-way travel time in seconds. The horizontal axis is distance along profile. The portion of profile shown in the lower window is displayed in red on the track map.

The thin red line that appears at the top of the reflection profile

(not to be confused with the red track line described above) is the seafloor depth taken from the precision depth recorder (PDR) data. This line denoting PDR seafloor depth can be turned off and on by clicking the toolbar button as follows: is on, and is off.

Figure: SCS profile for the 1967 Vema cruise V2407 showing many reflectors in the far western Pacific. The thin red line at the top of the reflectors represents the PDR depth.

5.3.8.1) SCS save profile function

Save the profile on display – or the entire scanned profile – using the right-most diskette button () next to the profile zoom buttons,.

5.3.8.2) SCS digitizing function

Reflector horizons can be digitized, annotated and saved to a file using the buttons to the left of the SCS profile display. Activate the Digitize function by selecting . Click firmly with the mouse to digitize each point, and exit the digitizer by clicking the adjacent arrow cursor button . Annotate with the text () button by clicking twice in the profile window and typing text in the text box that pops up.

Save the digitized points with the left-most diskette button (next to the button). After digitizing a profile, click the arrow cursor button to exit the digitizer mode. Here is an example of a digitized, annotated reflector:

Summary of buttons controlling SCS profile options:. From left to right: Save digitized points ; Turn off/on PDR seafloor depth ; Pointer ; Digitizer ; Text annotation ; Zoom in ; Zoom out ; Save profile image .

5.3.8.3) Note on zooming in the SCS profile window

If the zoom in () or zoom out () button is active, it can be deactivated only by clicking the same button again. The background color of the button indicates zoom active () or inactive ().

5.3.9) Seafloor Magnetic Anomaly Identifiers

Explore isochrons of seafloor magnetic anomalies using Mueller et al’s 1997 data set.

Select this interface under Portals (). When loaded, zoom and select an isochron of interest. Two things happen: The selected isochron turns white, and the isochron name and age are displayed in the lower left.

Figure: Isochrons in the north Atlantic. Anomaly 18 has been selected.

Click on the web page link to open an information page describing the data set. The isochrons can be turned off and on by ticking/unticking the box.

Suggestion: The magnetic isochron interface can be combined with the profile-distance tool to determine distance and age from a spreading ridge, and thus the spreading rate.

Data set reference: Müller, R.D., Roest, W.R., Royer, J.-Y., Gahagan, L.M. and Sclater, J.G., 1997, Digital isochrons of the world's ocean floor, Journal of Geophysical Research, 102, 3211-3214.

5.3.10) Ocean Floor Drilling

This portal offers a wealth of data for drill holes of the Deep Sea Drilling Project (DSDP Legs 1-96), the Ocean Drilling Program (ODP Legs 100-210) and the Integrated Ocean Drilling Program (IODP Legs 301-312).

When this portal is selected, the location of all drill holes in these programs is plotted in the map window. A new window is also created. It displays a scrollable list all of the holes in the current map view.

To select a hole, either click a hole in the map window (turns red), or click a row in the table (turns blue). Multiple holes can be selected by using shift-click in the table.

Figure: DSDP hole 24-238 in the central Indian Ocean has been selected.

Scroll to the right in the table to see columns of common fauna found in cores (nannofossils, foraminifera, diatoms, and so on). The “true”/“false” labels indicate the existence of a range chart for that particular fauna in that particular core. To display all holes with range charts of, say, diatoms, click once on the diatoms column header to sort those records. All holes with diatoms range charts will be highlighted. Their locations turn red in the map window.

Figure: Holes with diatoms range charts.

Note that at times the hole location symbols may become hidden under the symbols of other data sets or under images of other base maps. Click the button make them reappear.

Click to exit this DSDP-ODP-IODP portal.

5.3.10.1) Additional functionality within Ocean Drilling interface

Enhanced features are triggered by these icons in the DSDP-ODP-IODP tool bar.

5.3.10.2) Data types folder

The folder icon opens a new window. In the left pane is a list of various data types. In the right pane are control parameters, including a slider bar to specify age range.

Choose a data type from the drop-down menus and press to illuminate in the map window all holes reporting that data type within the specified age range. In the example shown at right, holes with mica in the 0-2 Ma range have been selected.

The name of the selected data type is given in the upper right corner of the folder window

Click and drag the slider bar to change the age range. This allows relative abundances to be visualized through time. The highlighted holes in the map window change with each chosen age range. Change the time range increment by clicking the button.

Holes that do not contain that data type in the specified age range can be turned off using the icon. Clicking the icon again redisplays these grey symbols.

The color icon uses a color table to display the relative percentage of the data type for the chosen age range. Red indicates high values, blue indicates low values.

More than one data type can be loaded although only one at a time can be visualized. The loaded data types are listed in the drop-down menu in the upper right Switch between loaded data types by selecting them from this drop-down menu. Click the discard icon to remove the selected data type from this list.

Figure: Colored hole symbols showing the relative abundance of carbonate in the 6-8 Ma time range.

Currently, quantitative measurements are available in GeoMapApp for legs 1-96.

5.3.10.3) Faunal Range Charts

The range chart icon opens a window with faunal range information.

Using the drop-down menu choose the type of fauna and flora types to display in the range chart, if reported for the selected hole.

The graphical part of the window contains three areas.

Figure: Range chart structure. On the left, shaded grey boxes show the presence of cores at their respective depths (in meters) below the sea floor. In the middle are the epoch and stage ages with name. Faunal ranges are shown on the right, as thin grey vertical lines.

In the faunal range, black dots () represent the sample depths.

Click a dot to display information about a species, in the lower part of the window.

In detail, the following information is presented.

· The species name ().

· Location of sample within the core (). Here, 16-3-25 cm refers to the core number (16), section (3), and depth in section (25 cm). Followed by reporting author (A.R. Edwards), report volume (21), and page number (650).

· Depth information () lists depth in meters below sea floor (305 mbsf), age at that depth in millions of years before present (25.968 Ma). BTD (3248 mbss) gives the back-track depth of the sea floor of that age expressed in meters below the paleo sea surface (mbss). It is calculated by removing the thermal subsidence since that time and by unloading the lithosphere by the weight of the sediments that have accumulated since that time.

· Further information contained in external databases about this species is given under the three hyperlinks ().

The selected species is highlighted in light blue in the range chart. As the cursor moves in the window, a horizontal red line tracks the cursor giving updated depth/age information.

The four buttons across the top of the range chart window provide links to more information. The Janus button links to the JANUS database at Texas A&M University to display the Hole/Core summary results.

The CHRONOS ARC button goes to the CHRONOS portal and displays age model information for the selected hole.

The Logs button is currently inactive.

The Initial Report button displays the table of contents and links to chapters of the report for the leg during which the hole was drilled.

5.3.10.4) Age-Depth Models

When a hole has been selected, the age-depth model button opens a graph in a new window. The horizontal axis gives the sediment age, and depth is given in meters below seafloor (mbsf) on the vertical axis. Orange rectangles mark the epoch/stage boundaries.

As the cursor moves down the graph, age-depth control points appear as red circles on the depth-age line. These age-depth values can be saved in a text file using the save button .

To change the age range displayed on the horizontal axis move the cursor to hover over either the left or right vertical axis line. When the cursor symbol changes to a double-headed arrow, drag the cursor sideways to change the range. The graph scaling can be reset by clicking the normalizing button .

The fossil ranges, as defined by their first and last occurrence, are turned off and on with the button. The button opens a web page giving CHRONOS portal Line-of-Correlation information.

Users can modify the age-depth model by clicking the icon. When active, click on an age-depth control point and drag it with the mouse to change its age and depth value. To create a new control point, click at the new location in the graph window. The age-depth curve will instantly adjust to include this new control point. The new set of age-depth values can be saved in a text file with the save button . Clear the new points with the graph reset button .

Previously-stored age-depth models created in earlier GeoMapApp sessions can be accessed using the drop-down menu at the top of the window, . The default age-depth model can be reloaded by selecting “Default” from the menu. The current age-depth model can also be saved under this menu. The saved file is stored in the user’s GeoMapApp home directory, or can be stored elsewhere using the file navigation buttons.

The text display () at the base of the graph lists six pieces of information about the control points and age-depth model – three values for the control points, and three values for the age-depth model. From left to right these values are: (a) The number of the control point nearest the cursor; (b) its depth in meters below seafloor (mbsf); (c) its assigned age (Ma). These are followed by values for the age-depth model at the level of the cursor: (d) the depth in meters below seafloor (mbsf) of the cursor position; (e) the corresponding sediment age from the age-depth model (Ma); and, (f) the calculated back-tracked depth (BTD) in meters below the paleo sea surface (mbss).

5.3.10.5) Physical-Chemical Measurements Graphs and Core photos

For each drill core, a range of physical and chemical measurements were made on the recovered core and in many cases, photos of the cores were taken. These can be viewed using the graphing function .

Measured categories are listed in the left-most drop-down menu. Shown in this example is Carbon. Types of measurements within that category are listed in the right-most drop-down menu. Here, “percent total carbon” has been selected and graphed.

To access the core photos, click the button in the lower left corner of the graph window. A blue column appears in the graph window between the epoch/stage names and the depth axis. If hand-drawn visual core descriptions are available, another column of squares appears, one for each core section to display the description. Click one of the small black squares to bring up the core photo in a browser window.

The ASCII table from which the graph is drawn can be viewed using the button which opens a text editor.

The tabular data values are saved to a file using the button.

Where a measurement category has multiple data types, the graph for each type can be viewed side-by-side using the button. From the pop-up menus choose the category and data type to plot. A new graph will be plotted next to the first one. The graphing window is discarded with the button.

Figure: Graphs of total carbon, organic carbon and CaCO₃ plotted side-by-side. The new graphs can be deleted by clicking (upper right corner).

5.3.10.6) Geological Timescale

The Geological Timescale icon opens a window displaying Period, Epoch and Stage boundaries, the geomagnetic polarities time scale and faunal zonal boundaries for foraminifera and calcareous nannofossils as well as the delta ¹⁸O curve of Zachos et al., 2001.

A horizontal red line tracks up and down in this window corresponding to the age of the sediment derived from the age-depth model. This allows the range chart and physical/chemical measurement for the selected hole to be directly correlated with the standard chronology and internationally-recognized epoch/stage boundaries and magnetic reversal time scale.

5.3.10.7) Zooming on graphs

When viewing the graphs (range charts, age-depth graph, and measurements graph) zoom functionality is available: To zoom in, hold down the control key and click the cursor within the graph. To zoom out, hold down the control and shift keys and click the cursor within the graph. The Geological Time Scale display includes separate buttons for zooming.

5.3.10.8) Keeping track of depth in the core section

The vertical position of the cursor creates a horizontal red line that moves in synchronization in all the windows to indicate the same depth below the seafloor. This can assist in correlation between the various data types being graphed. Even if graphs have been zoomed, the red line still shows the corresponding depth in each graph.

5.3.11) Seafloor Photographic Transects

View a wide range of submersible dive photos using this interactive browsing function. Photos from platforms including Alvin and Jason II are available.

A step-by-step multimedia tutorial is available for this function (Dive Photos): http://www.geomapapp.org/tutorials/

Figure: Examples of dive photos at the Ridge 2000 EPR 9N study site.

Example: View Jason-II dive photos at TowCam vent, in the Lau spreading center, with locations superimposed on Jason-II SM2000 25cm very high-resolution bathymetry.

Step 1: Load the hi-res bathymetry grid

Under the Basemaps portal (), select Select From Searchable List, type “TowCam” in the text box, click . Scroll to find the TUIM05MV 25cm grid for TwoCam vent field.

Click once on and click . The bathymetric grid will load, and the Shapefile Manager and grid dialog appear.

Figure: Hi-res grid for TowCam vent field loaded in GeoMapApp. The distance scale bar spans 100m (each division being 20m). If the grid dialog does not automatically pop up, go to the Shapefile Manager window and click the grid name once (circled in red). This makes the light bulb turn yellow (). Click once on the yellow light bulb () and the grid dialog appears.

Step 2: Choose dives for a particular area

Under Portals -> Seafloor Photographic Transects choose one of the geographically-grouped sets of dives. In this example, select Lau:N-ELSC: TowCam NDSF Dive Photos.

The Jason-II navigation tracks appear as black lines on the map. In the Shapefile Manager window select a particular dive from the dive list at right (example: J2-240). The track for that dive turns white, and the light bulb turns yellow ().

Figure: Jason –II dive track J2-240 selected. Track has turned white.

Step 3: Load and view photos for one dive

In the Shapefile Manager shown above, click the yellow light bulb. This loads a list of all photos available for that particular dive (J2-240 in this example). And, in the map view, small black circles show the geographical location of these photos. Click the yellow light bulb again to open the selected photo in an image viewing window.

Figure: (Upper panel) Click light bulb to list the images available for dive J2-240. (Lower panel) Photos available for dive J2-240 are labeled with a time stamp of format (yyyymmdd_hhmmss). Use the scroll bar at right to go through the list. Click the yellow light bulb () to view the photo.

Step 4: Scrolling through photos

In the image viewer window, the arrows () step through the photos. In the map window, the location of the current images is shown by a white circle. However, the Jason-II vehicle carries four cameras and each time-stamped file actually contains four separate images, one from each camera.

To view images in all four cameras, click three more times in the Shapefile Manager window on the yellow light bulb (). This produces three additional image viewer windows, laid on top of each other. Separate the image viewer windows by moving each to a different part of the computer screen to reveal one window for each camera.

In each image-view window, use the drop-down menu to select a specific camera.

Figure (right): Select the camera number from the drop-down menu (circled in red). Arrows scroll through the images in time.

Figure: Jason II’s four cameras show the images captured at one location on dive J2-240.

5.4) Datasets

A wide range of tabulated data covering many aspects of geophysics, geology, physical oceanography, palaeo-climates and much more is available under the Datasets menu (). New data sets are added regularly.

Common to all of these tabular data sets is that each is geographically-referenced by longitude and latitude. This allows individual points to be queried.

Under the Datasets menu, follow the cascading menus. Click the name of a data set to load it.

For large data sets, GeoMapApp displays a notice if there are more than 10,000 points (Figure). All of the points are loaded in GeoMapApp’s memory but only 10,000 will be displayed in the map window. These displayed points are chosen to be representative of the geographical distribution of the entire data set. Upon zooming in, more of the points become visible.

Figure: Notice window appears for large data sets. All points are loaded into GeoMapApp’s memory.

Once the data set has loaded, points can be selected either by clicking one row in the table (row turns blue,) or by clicking one of the grey dots on the map.

To select more than one point, either shift-click to select multiple consecutive points in the table, ctrl-shift-click to select multiple non-consecutive points in the table, or, use the Lasso Tool () and draw around points on the map.

Many of the data set tables contain URL hyperlinks to more information. The link is usually given at the end of the row so scroll to the right in the table to find the URL, if present.

Figure: Example of built-in data set: Lamont Core Repository data tables (clockwise from top left): After selecting one point (highlighted as a red dot north of Brazil), the URL at the end of the row opens a web page containing more information (bottom right). The Lasso Tool () is used to select multiple points (an example is lower left).

Basic functions allow numerical columns in the built-in or imported data sets to be manipulated, including colored by value, scaled, and graphed. See GeoMapApp multimedia tutorials (Symbols, Graphs) and here for examples of manipulating data sets.

Figure: Example of built-in data set: Global continental heatflow from Pollack et al. 1991 compilation. (Clockwise from top left) Data points have been colored according to one of the numerical values, in this case heatflow value (mW/m²). The colors are easily changed by moving the grey vertical lines in the color histogram window (right). Graph of two numerical columns, here heatflow against temperature gradient (bottom).

These data set manipulation functions apply to the built-in tabular data and to imported tabular data.

5.4.1) Special functionality

Under the Datasets menu (), the Water Column Properties -> World Data set of Temperature, Salinity, Oxygen, Nutrient Profiles (Reid and Mantyla, 1994) data records are each associated with a number of water column properties. Click once on a URL in the column to display the water column properties as a table in web browser.

To plot these properties as profiles, select one record in the table and control-shift-click on the URL (hold down the control and shift keys, and at the same time click the URL with the mouse). This brings up a separate graph window.

The y-axis can be flipped () to put the sea surface at the top.

To compare profiles side-by-side, select the Add Graph menu () and choose which parameter to plot. The new graph can be deleted by clicking (upper right corner). Add more graphs as needed. The water column values can be saved to a tabular text file ( button).

Figure: Reid and Mantyla’s water column properties compilation interface has enhanced functionality. Click once on the URL to open the table of data (upper right). Press control-shift-click on the URL to open the graphing window (right middle). Flip the y-axis () and add more graphs (). Multiple profiles are plotted side-by-side (bottom).

5.5) Focus Sites

This menu provides quick links to data and information for the MARGINS Focus Sites and Ridge 2000 Integrated Study Sites.

Examples of available data and information include: field rock/bio/fluid sample descriptions, field station locations, geochemistry data and EarthChem tables, vehicle dive photos, and high-resolution multibeam bathymetry grids. When viewing vehicle dive photos under the Focus Site menu, refer to the Seafloor Photographic Transects section.

Figure: Examples of focus site data sets available directly from the Focus Sites menu. (Upper left: Central America rock samples giving collection information and field descriptions. (Upper right: Weinrebe’s 2008 multibeam bathymetry compilation grid covering the Costa Rican margin, with sun illumination from the NW. (Bottom: At the Ridge 2000 EPR 9N study site, the seismic layer thickness grid of Canales et al. (2003) is made semi-transparent and overlain on the underlying multibeam bathymetry. PetDB rock sample analyses are colored by TiO₂ value and scaled by silica content.

5.6) Overlays

Look in the Overlays menu () to find scale bars for the map distance and color, as well as coastlines and geographical boundaries, and inset map controls. Toggle a feature on and off by selecting it in the menu.

Figure: Overlain on this view of Europe are major lakes and rivers, coastlines, province boundaries, a color scale bar and a distance scale. The inset map and bathymetry credits have been turned off.

Some Overlay menu selections such as Country Administrative Boundaries produce a Shapefile Manager window which allows added functionality. Click the shapefile name (in the example below, countries_and_provinces). This turns the name blue () and lists the shapefile components in the right pane. Click one of these components (here, Bourgogne) to illuminate that feature on the map. The box turns the layer on and off.

The Layer Manager tool (rightmost icon,, in tool bar) contains a tick box that turns the layer on and off (), discards the layer (), and allows the layer transparency to be altered.

Figure: Using the Shapefile Manager window (lower window), the province of Bourgogne has been highlighted. The Layer Manager (upper right) also controls layer transparency.

5.7) Bookmarks

Bookmarks () allow the user to zoom to predetermined map regions.

5.7.1) Create a bookmark for a map region

Here, bookmark refers to a place name/link in the GeoMapApp Bookmarks menu. Use the Add Bookmark for Current Map View function to create a bookmark.

Enter the name for this bookmark and click .

The box, when ticked, makes the new bookmark name instantly appear under the Bookmark menu’s Places menu.

However, the bookmark is temporary and will be lost when GeoMapApp is closed.

To preserve the bookmark for future GeoMapApp sessions, the box must also be ticked. The next time GeoMapApp is started, the new bookmark is available under the Bookmarks menu Places -> My Places menu.

Many bookmarks can be added to the GeoMapApp menu by repeating these steps.

When a bookmark is stored for future use by ticking the box the record information is saved in a text file called My Places.loc in a folder called places which is stored in the location specified when GeoMapApp was started for the very first time (usually this will be the user’s home directory or My Documents folder). To delete a bookmark, manually delete the relevant line of text from the My Places.loc file. The name of the link can be changed by editing this line.

5.7.2) Zoom to the world map

Return to the world map view using Zoom out to Global Scale.

5.7.3) The Places menu

Add Place provides the same function as Add Bookmark for Current Map View described above.

Show Places displays geographical boundary boxes for all listed places as well as for each of the seven focus and auxiliary sites of the NSF MARGINS program and for each of the three Integrated Study sites and allied areas of the NSF Ridge 2000 program. Click once inside a box to automatically zoom in.

Turn off the boxes by clicking once more on the Show Places menu item.

My Places lists the user-specified bookmarks.

5.8) Education

This menu provides links to various education web site resources:

5.9) Help

Links to help documents, web pages and multimedia GeoMapApp tutorials are here. Users can also provide comments and feedback, and sign up for the GeoMapApp announcements e-mailing list.

6) Guide to the Toolbar

6.1) Arrow Cursor

Use the arrow cursor to select items overlain on the map or items from loaded data tables.

6.2) Pan

When selected, click on the map and drag. This pan function offers an alternative to using the map scroll bars.

A step-by-step multimedia tutorial is available for this function (Zoom and Pan): http://www.geomapapp.org/tutorials/

6.3) Save

Offers options to save the map window image in a number of formats. Also, when a grid has been loaded, the grid can be saved in various formats. Equivalent to File -> Save Map Window as Image File.

Figure: Save options when a grid is loaded. If no grid, only the four save-image options are active.

6.4) Zoom

When zooming in either click on the map or click-and-drag the magnifying glass to define a rectangle on the map. When zooming out, click once the map for each zoom out operation.

A step-by-step multimedia tutorial is available for this function (Zoom and Pan): http://www.geomapapp.org/tutorials/

Note: when the cursor is in the map window, the ‘zoom factor’ is shown at the right end of the tool bar.

For most base maps and grids in GeoMapApp, the maximum native resolution is achieved at a zoom factor of 512. Going beyond that value merely stretches the image making the pixels bigger. A number of contributed grids and other high-resolution grids have higher native resolutions. For example, grids derived from scanning sonar devices on dive vehicles have resolutions of meters or better. In these cases, the zoom factor can be very large (around 12,000) before pixilation becomes noticeable.

6.5) Profile/Distance tool

A step-by-step multimedia tutorial is available for this function (Profile Tool): http://www.geomapapp.org/tutorials/

Take profiles across grids and find distance between points using this function.

6.5.1) Basic profile tool functionality

Selecting the profile tool automatically loads the underlying GMRT global elevation-bathymetry base map. The profile is defined by two points. Click once in the map window to specify the start point. Keep the mouse button depressed and move the cursor to the desired end point. Release the mouse button to draw the profile line. A profile window immediately opens.

Figure: Topographic profile across northern Japan. As the cursor is moved in the profile window, the cursor location is displayed on the profile track as a small circle. Save options for the profile are listed under the Save menu.

Geographic position (in formats of degrees-decimal minutes and decimal degrees) and depth/elevation are listed at the top of the profile window.

To change the axes scaling, untick the Auto-fit box, and type a scaling factor into the window. Hit return/enter for the scaling to take effect. In the following example, auto-fitting on the y-axis has been disabled and a y-axis scale of 4000m/inch is specified.

The profile is taken along a great circle line by default. Choose between great circle and straight line:

6.5.2) Taking profiles across other grids

The default setting for the profile tool is to take a profile across the GMRT base map. Profiles can be taken across any other built-in or imported grid regardless of what type of data is represented by the grid. See such an example here.

6.5.3) Distance tool

The profile/distance tool calculates great circle or straight line distance between two points. Proceed as with taking a profile: Click the map at the start point and keep the mouse button depressed. As the cursor is moved, the distance in kilometers from the start point to the cursor’s new location is instantaneously displayed in the upper bar of the main map window (to the right of the zoom factor):

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When the mouse button is released, the end point of the profile line is defined and the profile window pops up.

6.6) Digitizer

A step-by-step multimedia tutorial is available for this function (Digitizer Function): http://www.geomapapp.org/tutorials/

Digitize points along the GMRT base map. Useful for cruise planning, for example.

Select the digitizer tool. Two things happen: Various panels appear in the GeoMapApp window, and the base map GMRT grid is loaded (manifested as a change in the map colors).

Figure: (Left) Zoomed in around New Zealand. (Right) When the digitizer is activated, the colors of the map change, a large empty panel appears below, and a narrow panel appears at right.

Expose the right-hand panel by dragging or clicking once on the stippled grey vertical bar:

To begin digitizing, click once on the line segment button . The cursor becomes a cross-hairs (+). Click points on the map. To finish digitizing, click the digitizer cursor button . The line segments on the map turn white, with small squares at each digitized point. The digitized points are listed in the table below the map.

Figure: Digitized way points for a proposed cruise track leaving Wellington, crossing the Chatham Rise and heading towards the Louisville Ridge.

The digitized points are saved by selecting all of the lines in the table below the map (they turn blue) and copy-pasting them with the mouse into another application.

174.85788863109047	-41.29443217284362	-33.0
181.11586426914155	-45.666576149823726	-3237.0
182.57758120649652	-42.07900314783847	-2715.0
186.50594547563804	-44.505595658541566	-3460.0
192.53552784222737	-39.09659598320126	-975.0

At this stage in this example, only the five digitized points are registered. To create a graphical profile of topography along the digitized line segments, click Make Profile then graph . The profile appears in the lower pane (use the scroll bar in the profile window to view the rest of the profile).

The profile is created by interpolating intermediate locations between the digitized points and sampling the GMRT grid at those interpolated points. The amount of interpolation depends upon the zoom level of the base map. To view the interpolated points, select profile . To save all of these points, select all of the lines in the table and copy-paste with the mouse.

To digitize a new set of points click again on the line segment button . Each set of digitized points is stored in a separate line segments record until the GeoMapApp window is closed.

To select previous digitized segments, click on the relevant record In this way, multiple sets of digitized points can be compared.

The digitized points are lost when the GeoMapApp window is closed. Save them if they are needed for future use!

6.7) Shapefile Manager

A step-by-step multimedia tutorial is available for this function (Import Shapefile): http://www.geomapapp.org/tutorials/

When a shapefile is loaded, the shapefile manager can be used to toggle the shapefile on and off, and, for multi-shape shapefiles, to select individual shapefile components.

In this example, two multi-shape shapefiles are loaded. Choose which one to view by clicking its name in the left pane, then select in the right pane which individual shapefile to view.

Figure: The multi-shape NOAA coastal grids shapefile is selected. Clicking the light bulb loads the grid for shapefile H10974. The multi-shape lakes shapefile, bc_2m_lakes, is also loaded. Click in the left pane to display its component shapefiles. Other examples of multi-shape shapefiles include the built-in seafloor dive photos and geographical boundaries data sets.

For grids, click the light bulb to open the grid dialog and click the zoom button to zoom on the area covered by the shapefile. The information button provides additional on-line information on the data set. The shapefile can be toggled on and off using the visibility buttons . Discard the shapefile using .

6.8) Focus

In rare instances when the map view does not come into focus after zooming, click the focus button to refresh the image.

6.9) Mask function

A step-by-step multimedia tutorial is available for this function (Mask Function): http://www.geomapapp.org/tutorials/

GeoMapApp’s GMRT base map includes a large number of multibeam swath bathymetry data as well as some regional grids. The mask function uses a transparent mask to show the location of these higher resolution multibeam swath bathymetry tracks and bathymetry grids. Grey areas indicate no swath data was added to the GMRT grid. Click the mask function button again to discard the mask.

Figure: (Top row) The GMRT base map (left) and the location of higher resolution multibeam swath bathymetry used in its creation (right). (Bottom row) When zooming, some areas look ‘fuzzy’ or lacking in detail (left, an example on the East Pacific Rise). The mask function (right) reveals areas of multibeam data (transparent mask); the grey areas were not refined using multibeam data.

6.10) Show Contributed Grids

A step-by-step multimedia tutorial is available for this function (Contributed Grids): http://www.geomapapp.org/tutorials/

A large number of grids have been contributed to GeoMapApp, including grids of bathymetry, gravity, magnetics, and sidescan.

After clicking the Contributed Grids button labeled rectangles show the outline of the contributed grids. Zoom to an area and click inside one of the rectangles. The rectangle turns white.

Figure: Contributed grids in the Izu-Bonin-Marianas area. In this example, the box containing the grid of the Marianas western insular margin has been selected – the box outline turns white.

Click once with the right mouse button to load the grid: the grid appears in the map window, and a Layer Manager and Grid Dialog pop up. For clarity, the contributed grid rectangles can be turned off by clicking the Contributed Grids button again or by unticking that item in the Layer Manager.

Modify the grid appearance using the Grid Dialog functions . If this window did not appear automatically, click the light bulb to open it. Discard the grid by selecting its name in the Layers window and clicking .

6.11) Global Grid Dialog

This short cut allows various global grids to be loaded, with minimal clicking. When selected, the GMRT base map grid is loaded in the map window, and a grid dialog comes up.

Open the drop-down menu to see the list of other available global grids.

Click once on a grid name. That grid will load automatically.

Figure: Global grid of geoid height anomaly (Sandwell and Smith, 1997), with ten-meter contours, and a profile showing the remarkable 180m geoid height anomaly between the Indian Ocean and Indonesia.

See the grid manipulation section for more information on grid functionality.

6.12) Layer Manager

Turn layer display on and off, change layer transparency and ordering, and discard layers with the Layer Manager.

Untick/tick the heat flow box (, ) to turn the layer display on and off. Slide the Opacity slider bar () to alter the transparency of the layer. This allows convenient comparison with features on underlying layers. When the bar is all the way to the right the layer is opaque. As the slider bar is moved to the left, the layer transparency increases allowing the underlying layers to become visible. When the bar is all the way to the left (equivalent to unticking the box), the layer is completely transparent (invisible) and the underlying layer is fully visible. Bring layers to the front by changing their order with the vertical arrows . Click the box to discard the layer.

7) Tool tips

Many icons and table column headings contain active tooltips. Allow the cursor to linger over the item for a second or two to see the associated tooltip.

8) Text Displayed on the Toolbar

The displayed text varies with three cases.

Case 1: No grid loaded (default view, or when images are loaded)

From left to right, the text in this example shows:

Longitude in whole degrees, decimal minutes East or West (range is 0-180).

Latitude in whole degrees, decimal minutes North or South (range is 0-90).

Longitude in decimal degrees East or West (range is 0-180).

Latitude in decimal degrees North or South (range is 0-90).

Zoom factor. For GMRT base map, the zoom factor range is 1 (global view) to 512 (maximum native resolution, corresponding to a grid spacing of about 100m).

Case 2: Grid loaded (global, contributed, or imported grids)

Same as case 1, but now shown to the right of the geographic location is the z value of the grid at the cursor location (-2733m).

Note that when contributed grids and other high-resolution grids are loaded, the native grid resolution may support considerably larger zoom factors.

Case 3: Profile tool activated (grid is loaded)

Same as case 2, but now shown to the right of the zoom factor is the distance from the start of the profile to the position of the cursor location (418.45 km).

9) GeoMapApp Tutorials

Short multimedia audio-video tutorials covering a range of GeoMapApp capabilities and functions are available at http://www.geomapapp.org/tutorials/index.html and are linked from the GeoMapApp web page (click Multimedia Tutorials on the left side of the web page).

The tutorials can be viewed in any web browser. Most are about one minute in duration. The Play, Pause, and Stop controls are located at the base of the browser window.

10) Cookbook

10.1) How to Import Data – Spreadsheets

A step-by-step multimedia tutorial is available for this function (Import Data Tables): http://www.geomapapp.org/tutorials/

In addition to ASCII data tables, spreadsheets can be imported to GeoMpaApp. The spreadsheet must contain a column for longitude (in decimal degrees between +/- 180) and a column for latitude (in decimal degrees between +/- 90). The first row of the spreadsheet is expected to be column headings. Spreadsheets containing dozens of columns can be imported successfully.

Figure: Example spreadsheet called TicoFlux2_Processed_Heatflow.xls contains NSF MARGINS-funded heat flow data collected by Andy Fisher in the central America focus site..

Go to the File menu to import the file and select From Excel-formatted (.xls) file.

Locate the file and Open it. After GeoMapApp reads the contents of the file, a Config window appears.

GeoMapApp searches for latitude and longitude column heading (“Latitude”, “latitude”, “lat”). If no match is found, the latitude and longitude columns must be specified in the Config window. Open the drop-down menu for Latitude Column and select the latitude column from the list. In this example, it is “Pen_Latitude”.

Similarly, select the longitude column. Click . The GeoMapApp map window will shrink and two panels appear.

The lower panel contains the imported data records.

Widen the columns by clicking on the column border and dragging the double-headed arrow cursor.

The right-side panel contains functions to manipulate, lasso and save the imported data set.

For example, to color the symbols by heat flow value, click The color histogram window shows heat flow along the x-axis and number of values on the y-axis. Drag the vertical grey lines with the cursor (double-headed arrow) to change the color range.

10.2) How to Lasso Data Points

When a data table is loaded, click the lasso tool to activate the selection function. Move the cursor to the map window, click and hold the mouse button, and draw around the points to be selected.

The selected points are highlighted in white on the map, and in blue in the data table below the map window.

Save these chosen points in a range of formats using the Save function.

10.3) How to Import Data – Grids

A step-by-step multimedia tutorial is available for this function (Import Grid): http://www.geomapapp.org/tutorials/index.html

Gridded representations of any type of data set can be imported in GeoMapApp as long as the grid is in one of a number of widely-used format. Current grid format options include the GMT netCDF and ESRI ASCII/binary formats.

Multiple grids can be imported at once, as shown in this example. In this case, the multiple grids must reside in one folder.

Figure: List of netCDF grids constructed from JAMSTEC research vessel Kairei processed multibeam swath bathymetry data collected in 2003.

Activate the import-grid function

Specify the grid type from the drop-down menu:

When the file system navigator window appears, navigate to the folder containing the grids

Use the cursor (shift-click) to select all of the grid files. (To import just one grid, select that grid file name only.) The file names turn blue.

Click

A Confirm Projection and Bounds window appears:

As part of the import process, the Z values in the grid can be scaled by any factor (). This is useful for switching depths from positive downwards to negative downwards, for example. Further, to avoid having to manually scale each of the grids to be imported, tick the box – the scaling factor will be applied automatically.

Click Each grid is processed, and the status is shown in the Import Grid window.

When all of the grids have been processed the folder containing the grids now includes a set of z-folders and a suite of shapefile components. These new files and folders should not be discarded at this stage - the shapefile allows the imported grids to be accessed instantly at a later date, and the z-folders allow zoom capability.

Two new windows appear – a grid dialog and a shapefile manager – and the map window zooms to the gridded area.

The wide range of GeoMapApp grid manipulation functions can now be applied to these imported grids – changing the color palette, sun illumination, vertical exaggeration, adding contours, taking profiles, overlaying imported data points, saving images, and so on.

Note that the grids are loaded for the current GeoMapApp session only. Not to worry: if GeoMapApp is closed, the grids can instantly be reloaded by importing the shapefile (in this case, file - select this file using the -> function).

User-imported grids do not become part of the global bathymetry (GMRT tiles) data set. Grids can be added to the global bathymetry base map if the contributor gives permission. Contact MGDS for this.

10.4) How to manipulate grids

When a grid is loaded, two windows pop up: the grid dialog (shown at left, below) and the Layer Manager (shown at right).

See the Layer Manager section for more information.

In the grid dialog a number of functions are available.

The histogram shows the relative distribution of z-values within the loaded grid. The color table is automatically adjusted to span the full range of z-values. To change the span of the colors, drag the two thin, grey vertical lines to the left or right. The map will refresh instantly with the new range of colors. Reset the color range to the default span by clicking the normalizing button . The chosen limits can be locked with the button. This preserves the limits when the map window is zoomed or panned.

The “ocean palette” button is a shortcut to a color palette suitable for z-values between 0 to about -8000 (typical ocean depth ranges). The “land palette” button is a shortcut to a color palette suitable for z-values between 0 to about +6000 (typical land elevations). The button switches to the default palette that spans positive and negative ranges. The continuous rainbow button spreads the color scheme uniformly across the z-range of the grid. Discrete color changes are specified with the bar chart icon and its associated text box: . Specify the increment for the color change boundaries. Click the button to choose different color palettes or to create or save a custom palette.

In all palette-related functions, the two thin grey vertical lines are displayed in the histogram window and can be dragged left or right to change the colors.

The right-side of the grid dialog contains tools controlling the artificial sun illumination. Use the courser to drag the yellow sun symbol in order to change the illumination angle and brightness, or type the precise declination and inclination angles into the text boxes. The level of shading is determined by the vertical exaggeration which is specified in the box.

To draw contours on the grid, click the contour button. This opens a contour parameters box. Specify the contour interval and the maximum/minimum values to be contoured. When the button is clicked, the contours are processed on the local CPU and displayed on the map. The contours can be turned off by clicking the contour button again.

Figure (to right): Hawaiian free air gravity anomaly grid with contours displayed at 10mGal intervals.

With a grid loaded, profiles across the grid are captured using the profile function . Select the profile button and use the cursor to draw the profile line in the map window: click on the start of the line and keeping the mouse button depressed click another point on the map to define the end of the profile. Follow this link for more information on the profile tool.

Figure: Flexural moats around the Hawaiian islands shown in this profile of the Sandwell-Smith satellite-derived free air gravity anomaly.

In the grid dialog, click the information button ( upper left) to open a web page with more information on the loaded grid.

To reload or discard the grid, click the buttons.

The grid that is visible in the map window can be saved in many different formats using the save button . The map window can also be saved here as an image. Note that the when a grid is saved, it is saved at the resolution of the map window.

The grid can be viewed in 2-D or 3-D which is controlled with the selection. To switch to the 3-D perspective view, select to open the 3-D preview window. This window shows a low-resolution version of the grid and allows various parameters to be altered before viewing the full-resolution version.

Rotate the grid using the button (drag cursor left or right in the preview image). Tilt the surface with (drag cursor up or down in the preview image). Zoom in or out with the zoom button (in preview image, drag cursor to the right to zoom out, and to the left to zoom in). Change the vertical exaggeration by typing the factor into the box. Check the size of the final image (700x500 pixels works well with most laptop screens). Click the button to produce the full-resolution 3-D perspective plot.

10.5) How to use the Layer Transparency

Layer transparency can be changed to allow underlying layers to be made visible. This is very useful for comparing data sets in different layers. For example, compare satellite-derived free-air gravity anomalies with bathymetry around Hawaii.

Zoom to the Hawaii region and load the Smith-Sandwell FAA gravity data set.

Click the Layer Manager button in the toolbar to activate the Layer Manager window.

Toggle the gravity data set off and on by unticking/ticking the , box.

Slide the Opacity slider bar () to alter the transparency of the layer. This allows convenient comparison with features on underlying layers. When the bar is all the way to the right the layer is opaque. As the slider bar is moved to the left, the layer transparency increases allowing the underlying layers to become visible. When the bar is all the way to the left (equivalent to unticking the box), the layer is completely transparent (invisible) and the underlying layer is fully visible.

Figure: (Left) Layer is opaque. (Middle) As the transparency is increased (opacity decreased), the underlying GMRT bathymetry becomes visible. (Right) When fully transparent, the original layer is no longer visible, allowing the GMRT layer to be displayed fully.

Click the discard box to discard the layer.

10.6) How to Import Data – Shapefiles

A step-by-step multimedia tutorial is available for this function (Import Shapefile): http://www.geomapapp.org/tutorials/index.html

Shapefiles comprise a number of component files. To import a shapefile to GeoMapApp, the following component files must be present: .shp, .shx, .dbf.

Activate the import-shapefile function:

Navigate to the folder containing the shapefile component files.

Figure: After browsing to the folder containing the shapefile, check that the .shp, .shx, .dbf are present. In this example, the shapefile contains outlines of lakes at 2m resolution for British Columbia.

Select the .shp file (). Click A Shapefile Manager window appears, the shapefile contents are listed in the right panel, and the layer is displayed on the map.

In the right panel, click on an item in the list to highlight that feature – on the map, the feature turns white.

Figure: Close-up of British Columbia lake outlines. (Left) Shapefile item is selected (highlighted in white). (Right) item is de-selected (outlined in black).

10.7) How to Import Data – Shapefiles of grids

When grids are imported to GeoMapApp, a shapefile is created automatically. This shapefile of the grid can be imported at a later date without having to re-import the grid.

Follow the steps above for importing shapefiles of polygonal layers and select the shapefile name. Since the shapefile content is a grid, the grid dialog also appears.

10.8) How to use the Tear-Off Menus

Frequently, users need to load multiple built-in GeoMapApp data sets from the many drop-down menus. Having to navigate repeatedly through the menus can be frustrating. Tear-off menus help avoid this. They allow a drop-down menu and its sub-menus to remain open and active throughout a GeoMapApp session.

Tear-off menus are available for the Basemaps, Datasets and Focus Sites menus.

To activate the tear-off function, select one of these menus and click

A search window appears.

Either click on one of the top-level folder symbols () or navigate into a top-level folder () and click on a folder symbol () there. With the mouse button depressed, drag the folder out of the search window. When the mouse button is released that chosen folder opens as a menu in a new, active window.

Example: Choose Drag the folder symbol out of the window. When the mouse button is released, the Water Column Properties menu opens in a new window.

This window remains active throughout this GeoMapApp session.

Submenus (here, ) are also active:

10.9) How to move/sort tabular columns

With any tabular data set loaded, the order of columns can be changed by clicking on the column header and dragging the column left or right. The rows within a column can be sorted in ascending or descending order by clicking once on the column header.

Figure: For this ISC data set, the original configuration of the tabular data is shown in the upper panel. Beneath it, the latitude, longitude, magnitude and depth columns have been moved to the left, and the magnitude column has been sorted in ascending order.

10.10) How to Detach-Attach Tables

When any tabular data set is viewed, click in the upper right. This detaches the table, allowing the map window to become larger and the self-contained table to be moved around the screen.

Example of free-floating, detached table, in this case for the IODP web feature service.

Click to re-connect the table to the map window.

11) Miscellaneous

11.1) Loading data sets with many points

Due to memory limitations with some older computers, GeoMapApp implements a decimation scheme when loading large data sets. For this, all of the data points are first read from the data set. Then, they are decimated based upon their geographical distribution. In any given GeoMapApp map view, up to 10,000 points from the geographically-decimated data set are displayed. Do not worry – the other points have not been lost. Instead, as a user zooms to an area, more points (up to 10,000) are displayed.

The following notice appears when the decimation process is active. Click to proceed with loading.

11.2) GeoMapApp Image Gallery

A number of images from GeoMapApp are available at http://www.geomapapp.org/gallery/index.html and are linked from the GeoMapApp web page (click Image Gallery on the left side of the web page).

11.3) Contact us, and the GeoMapApp listserv

Questions about GeoMapApp, as well as suggestions for improvements and notification of any bug, should be sent to info@marine-geo.org

To join the GeoMapApp mailing list, go to the Mailing List link under the Help menu.