PaleoGIS™ for ArcGIS™

The Rothwell Group, L. P.

PaleoGIS User’s Manual

Version 4.2

Table of Contents

Introduction to PaleoGIS

Accessing PaleoGIS in ArcMap

Supported Data Types for Use in PaleoGIS

Basic Reconstruction Work-flow

Preparing for Reconstructions and/or Animations

Add User Data to be Reconstructed

Validate Data Layers

Reconstructing Data Layers

PaleoGIS: Basic Functions Toolbar

Reconstruction Tool

Reconstructing Vector Layers

Reconstructing Raster Layers

Set Fixed Plate Tool

Clear Fixed Plate Tool

Animation Tool

Quick Spin Tool

Configuration Window

Basic Configuration Options

Advanced Configuration Options

Miscellaneous Settings

Application Settings

Model Settings

Models

Timescales

PaleoGIS: Plate Model Tools Toolbar

Genealogist Tool

Pole Finder Tool

Spin and Drop Tool

Drag and Drop Tool

Enter Pole Tool

Pole Saver Tool

Pole Set Maintenance Tool

Time Slice Manager Tool

Plate Model Symbology Tool

Saving Symbology to the Plate Model Geodatabase

Viewing or Deleting Existing Plate Model Symbology

PaleoGIS Analysis Toolbar

Azimuth & Rate vs. Time

Instantaneous Motion

Point Path Visualization

Paleo Calculator

PaleoGIS Data Frame Context Menu

Save Reconstruction

Export to ArcGlobe

Refresh Cache

Empty Scratch Directory

Validate All Layers

PaleoGIS Layer Context Menu

Refresh Cache for Single Layer

Un-Reconstruct

Validate Layer

Repair Layer

Preprocess Raster (warp raster reconstruction method only)

Time Slice Viewer

Using PaleoGIS with a Proxy Server

PaleoGIS Application Settings

T_PaleoGIS_Settings Table

T_PaleoGIS_Timescales Table

T_PaleoGIS_Models Table

PaleoGIS Metadata Keywords

Command Line Tool and Batch Scripting With PaleoGIS

Product Support

Appendix A:  ArcMap Skills

ArcMap Table of Contents

Activating a Data Frame

Setting Layer Properties in ArcMap

Setting Layer Visibility

Setting Display Units for a Layer

Setting Selectable Layers

Select Feature

Selecting more than one Feature in a Layer

Selecting Only One Feature in a Layer with Stacked Polygons

Introduction to PaleoGIS

PaleoGIS is a comprehensive collection of desktop tools allowing the user to create, display, and manipulate plate tectonic reconstructions through the ESRI ArcMap user interface.  This application allows users to incorporate their own data into the reconstructions so the data can be evaluated in its paleogeographic context.

This documentation specifically applies to PaleoGIS 4.2.x running on ArcMap 10.1, 10.2, 10.2.1, 10.2.2, 10.3 or 10.3.1 (PaleoGIS versions 4.2.1, 4.2.2, 4.2.2.1, 4.2.2.2, 4.2.3, and 4.2.3.1, respectively).  If you are using previous versions of PaleoGIS or ArcMap, some of the content and screenshots may not be accurate for the version you are using.

Accessing PaleoGIS in ArcMap

1. Click on the Customize option on the ArcMap main menu and click on Extensions. The following window will display:

2. Click on the PaleoGIS for ArcGIS checkbox to turn on the extension.  It may take several seconds for the extension to turn on.  If the box is already checked, PaleoGIS is already activated.  Note: By clicking on PaleoGIS for ArcGIS to highlight it, the PaleoGIS properties will display in the Description box at the bottom of the window.

3. Click Close.

4. If the PaleoGIS toolbars are not already displayed, open them by clicking on View on the ArcMap main menu, and then click on Customize > Toolbars and select each of the PaleoGIS toolbars - PaleoGIS: Analysis Tools, PaleoGIS: Basic Functions, and PaleoGIS: Plate Model Tools.

Note:  The PaleoGIS: Basic Functions toolbar must be displayed for PaleoGIS to be fully enabled.  The visibility of the other two toolbars can be set according to the user’s needs.

5. The PaleoGIS toolbars will display as follows.  Note: The PaleoGIS toolbars can be anchored to the application frame in ArcMap by dragging them to the desired location.

6. Additional PaleoGIS functions can be accessed via the context menu that appears when right-clicking on a data frame name or layer in the Table of Contents. Selecting PaleoGIS from the context menu displays the menu shown below with the choices enabled when appropriate.

Supported Data Types for Use in PaleoGIS

PaleoGIS supports the reconstruction of point, multi-point, polyline and polygon vector data in shapefile, personal geodatabase, file geodatabase and SDE formats.  Vector data can use any projection or coordinate system.  

PaleoGIS can also reconstruct rasters (single- and multi-band) in grid, .jpg, .gif, .img, .png, .jp2, .tif, .bmp, personal geodatabase, and file geodatabase formats.  There are two raster reconstruction methods available: the “pixel” method (the default method) or the “warp” method.  The pixel method accepts all projections, coordinate systems and datums, and can reliably reconstruct large rasters with global extents.  The warp method can operate on rasters in projected or geographic coordinates, but they must have a WGS84 datum.  Also, for the warp method it is recommended that rasters be trimmed to the smallest acceptable geographic area for analysis, and also that raster be down-sampled to the lowest acceptable resolution.  The warp method is not recommended for use on rasters larger than 10 MBytes in size.

Basic Reconstruction Work-flow

We begin by looking at the most common workflow for using PaleoGIS.  PaleoGIS is a robust software package that can be used to do many plate tectonic modeling tasks, but for many users the goal is to simply reconstruct user data layers back to a particular geologic time using an existing published plate model. The workflow for doing this common task is described below. If you are unfamiliar with any ArcMap terms used in this section, please refer to Appendix A: ArcMap Skills.

Preparing for Reconstructions and/or Animations

First, turn on the PaleoGIS extension and display the PaleoGIS: Basic Functions toolbar as described above in the Introduction to PaleoGIS section. Then open the Configuration window (see figure below) by clicking on the Configuration button on the PaleoGIS: Basic Functions toolbar.

Select the desired plate model from the Select Model dropdown menu and click the Load Selected Plate Model button. The selected model will be loaded into memory and a new data frame containing the model’s plate polygons, and possibly some supporting data, will be added to top of the ArcMap table of contents.   All other data frames that existed before loading the model will remain in the map - they will just be moved below the new data frame. No data frames or data will be removed from the map.

The newly added top data frame will have the name of the plate model that you just loaded. This data frame is the PaleoGIS “present day” data frame because it now contains the present day version of the plate model polygons for the model that you just loaded.  Do not insert any other data frames above this one because PaleoGIS always performs reconstructions and animations based on the top (present day) data frame.

Add User Data to be Reconstructed

One of the key features of PaleoGIS is that it can reconstruct user data back to its paleogeographic location.  To reconstruct your data, simply add the desired data layers to the present day (top) data frame, and make sure that the visibility is turned on for those layers.  Refer to the Supported Data Types for Use in PaleoGIS section for more information about the types of data that are acceptable for use in PaleoGIS.

Validate Data Layers

It is important to validate any data layers (vector or raster) before performing reconstructions on them. This is important because this process will tell you if the layers are not in a PaleoGIS supported format or contain any malformed geometries. Layers that are improperly formatted or contain malformed geometries cannot be reconstructed. You can validate a single layer or all the layers in the present day data frame by using the PaleoGIS context menu options as shown below.

A window will be displayed showing the results of the validation. This window also provides important tips for working with data layers in PaleoGIS.

If the validation windows says that a layer is not in a PaleoGIS supported format, you can create a copy of the data in a supported format (shapefile or a featureclass in a Personal or File Geodatabase) by right-clicking on the layer in the Table of Contents and then choosing the Data > Export Data option.  You can then add the exported data to the map.

If the validation window says that there are malformed geometries, run the Repair Layer tool on the specified layer. This tool calls the ESRI Repair tool and should fix any problems with the data layer.  Note that the Repair Layer tool will change your data when making the repairs, so you should first make a backup copy of the data before running the tool.

Reconstructing Data Layers

After ensuring that the data layers are valid, you are ready to reconstruct your data. In the PaleoGIS: Basic Functions toolbar you can either select a geologic age from the Age drop down or enter a numeric age in (Ma) manually. To execute the reconstruction, click the Go button.

PaleoGIS will display a number of windows as it processes the user data layers and the plate model polygons.  It will then display these reconstructed layers in a new data frame placed at the bottom of the table of contents.  For more detailed information about reconstructing vector and raster layers, see the Reconstruction Tool section.

PaleoGIS: Basic Functions Toolbar

Reconstruction Tool: Used to perform reconstructions to the desired age.

 Set Fixed Plate Tool: Sets the reference frame for reconstructions.

 Clear Fixed Plate Tool: Resets the reference frame to the default value.

 Animation Tool: Allows the user to create animations of plate movement over time.

 Quick Spin Tool: Changes the map projection to "The World From Space", and then re-centers the map to a specified point.

 Configuration Button: Opens the Configuration window.

 Help Button: Opens PaleoGIS Help.  It will first attempt to access an online version of the user documentation.  If that fails, it will access a local copy.

Reconstruction Tool

This is the most commonly used tool in PaleoGIS. It is used to perform plate model reconstructions to the geologic age of interest.

1. Load a plate model and user data layers (vector and/or raster) to be reconstructed. See the sections below for detailed information about reconstructing vector and raster layers, and refer to the Supported Data Types for Use in PaleoGIS section for detailed information about the types of data that are acceptable for use in PaleoGIS.

2. Enter a numeric value in the Age textbox or choose a geologic age from the dropdown list.  Note: All numeric ages must be entered as millions of years ago (Ma), e.g. 1 = 1 million years ago.

3. Press the Go button to begin the reconstruction.

Reconstructing Vector Layers

When you press the Go button, PaleoGIS performs a number of operations as part of the reconstruction process.  First, PaleoGIS compares the list of visible layers in the present day data frame to the list of layers in the data cache. Layers are added and/or deleted from the cache in order to synchronize the cache with the present day data frame.

Next, PaleoGIS performs an intersection routine on any new layers in the cache using the currently loaded plate model polygons. This process is often called “cookie cutting” because the plate model polygons are used like lots of little cookie cutters to slice up the features in the user data layers. The attributes from the plate model polygons (plate code, appearance age, and disappearance age) are transferred to the attribute table of the user data layer during this process. The user data layers are now “coded” with the information necessary for PaleoGIS to reconstruct their features back to a given geologic age.

It is important to understand that PaleoGIS is not directly reconstructing the data layers that are contained in the present day data frame. PaleoGIS is reconstructing the copy of these layers in the cache that has been intersected with the plate model polygons.  The original data is not changed during the intersection or reconstruction process.

You can perform the “caching” process explicitly by right-clicking on the present day data frame and choosing the the PaleoGIS > Refresh Cache option from the context menu. This may be helpful if you are receiving an error while performing a reconstruction and you want to determine if the problem is actually occurring while the layers are being copied to the cache or while being reconstructed.

Also, make sure to run the PaleoGIS > Refresh Cache option if you have edited a data layer and want these edits to be reflected in reconstructions or animations. Otherwise, if you make changes to a data layer that has already been copied to the cache, PaleoGIS will not notice that the layer has been changed and it will reconstruct the layer as it was before the edits were made.

Reconstructing Raster Layers

All versions of PaleoGIS 4.2 except the versions for ArcGIS 10.3 and 10.3.1 (v4.2.3 and v4.2.3.1) provide two methods for raster reconstruction: 1) the “pixel” method (recommended), which is a new algorithm for raster reconstruction and 2) the “warp” method, which is the algorithm used in previous versions of PaleoGIS.  In PaleoGIS for ArcGIS 10.3 and 10.3.1 the pixel method is used for raster reconstructions.

For all 4.2 versions except the versions for ArcGIS  10.3 and 10.3.1, the raster reconstruction method can be selected in the Misc. Settings tab in the PaleoGIS Configuration window. The pixel method is the default method.

Pixel Method (recommended method)

This method resamples the raster and converts it to a point feature class and then reconstructs the points to the selected age.  Once the reconstruction is complete, the points are converted back to a raster, which is the reconstruction output.   Before the input raster is initially converted to a point feature class, the user is allowed to selected the resampled cell area as a percentage (from <1% to 100%) of the original cell area, where a higher percentage will given higher resolution results, while a lower percentage will improve reconstruction performance.

Currently, only one raster can be reconstructed at a time using this method, but a single raster can be reconstructed at the same time as any number of vector layers.

To reconstruct a raster using the pixel method, add the raster to the present day map and make sure its visibility is turned on.  Next select or enter a reconstruction age in the PaleoGIS: Basic Functions toolbar and then click the Go button.  This window will open:

The Post-process raster option uses an interpolation algorithm to eliminate null values in the reconstructed raster.  This option produces more aesthetically pleasing results, but it also increases the reconstruction time.

The resampled raster resolution will be automatically set to a recommended level, but if a different resolution is desired, use the slider to increase or decrease the percentage.  Alternatively, you can enter a numeric percent value in the text box to the right of the slider.  The estimated reconstruction time and the resampled cell size will be displayed in the area below the slider.  Note that there will not be a time estimate provided the first time a raster reconstruction is run after PaleoGIS is installed.  

Once you have the resampled resolution selected, click the Continue button to start the reconstruction.

Once the reconstruction is complete, the Use resampled raster from cache option will be enabled for subsequent reconstructions of the raster that was just reconstructed.  This option reduces reconstruction time because it reuses the present day point feature class that was created for the previous reconstruction.

Warp Method

This raster reconstruction method “cookie cuts” the raster into fragments and then “warps” the fragments into their reconstructed positions.  The reconstructed fragments are then mosaiced back into a single reconstructed raster.  Multiple rasters can be reconstructed at one time using this method, although reconstructing more than one or two at a time, especially if they are large rasters, is not recommended.  The warp method requires the ArcGIS Spatial Analyst extension to be turned on and licensed.

To reconstruct a raster using the warp method, add the raster to the present day map and make sure its visibility is turned on.  Next select or enter a reconstruction age in the PaleoGIS: Basic Functions toolbar and then click the Go button to start the reconstruction.  

If desired, before starting the reconstruction the raster can be pre-cookie cut using the Preprocess Raster context menu command.  In addition, the raster fragments can be preserved in the cache by selecting the Cache raster fragments option in the Advanced Settings tab in the Configuration window.  Selecting the Cache raster fragments option can significantly lower the reconstruction time for subsequent reconstructions of the same raster.

Set Fixed Plate Tool

The Set Fixed Plate tool is used to set the reconstruction reference frame to a selected plate.  The effect is that the selected reference plate will not move from its present day position (i.e., it will be “fixed” in place) while all other plates will move relative to the selected plate’s position.

1. Select the polygon plate model layer in the Table of Contents.

2. Click on the  Set Fixed Plate tool  and then click on the desired plate to be fixed.

3. The selected plate will flash and a message indicating the fixed plate ID number will appear in the lower left corner of the ArcMap window.

Note:  At any time you can find out which plate is fixed (if any), by hovering the mouse cursor over the Set Fixed Plate tool button, which will display a tooltip showing the current reference plate.

Clear Fixed Plate Tool

Resets the reference frame to the default value.

1. Click on the Clear Fixed Plate tool .  The map reference frame will revert back to the “spin axis” of the model, which is the default reference frame.

2. You will notice a message in the lower left corner of the ArcMap window confirming that the map reference frame has been set back to 0000 (the spin axis).

Animation Tool

The Animation tool creates animations of plate movement over time by performing reconstructions at specified time intervals over a specified time range, and then exporting the reconstructions as a series of JPEG or GIF images.  Note that all numeric ages must be entered as millions of years ago (Ma), e.g. 1 = 1 million years ago.

1. Starting with a present-day map, click on the Animation tool  and the Animation window will display (see image below).

2. In the Start Age field, either enter the numeric animation start age or click on the dropdown menu and select the starting time period.

3. In the End Age field, either enter the numeric animation end age or click on the dropdown menu and select the ending time period.

4. If you are using a plate model that contains time slices and you want to included the time slices in your animation, select the Include time slice layers in animation option.  If the plate model does not contain time slices, selecting this option will have no effect on the animation.

5. In the Step Interval field, either enter an interval or click to the desired interval using the up/down arrows.

6. If desired, change the animation output folder name in the Animation Name field.  The default output path for the animation folder is the PaleoGIS scratch directory, but this can be changed by clicking on the ellipses button to the right of the Path field, and then browsing to the new output location.

7. The Output Format option determines the image file format that is will be used for the output reconstructions. If the GIF option is chosen, once the animation is completed you will have the option of saving it as an animated GIF file.

8. The View animation when complete option automatically opens the Animation Viewer window when when the animation is finished processing.  The Remove data frames from TOC option automatically removes each reconstruction data frame from the Table of Contents when the next animation reconstruction data frame is created.  If this option is not selected, all of the reconstruction data frames for the animation will remain in the Table of Contents.  Note: By default, these options will be automatically selected. To deselect, click in the checkbox to remove the checkmark.

9. Each output image file in the specified output folder will be numbered starting with the value in the File Counter Start text box.  Enter the desired start number if a value other than 0000 (the default) is required.  This numbering allows the animation output frames to be easily imported and animated in third party image editing programs like Blender.

10. Click Start.  The animation reconstructions will begin.  

11. When all of the animation reconstructions are done, if the View animation when complete option is selected, the animation will open in the Animation Viewer window (see below).  

12. Previously created animations can be viewed at anytime by clicking on the View Existing Animation button and navigating to the desired animation output folder in the browse window that opens.  Select the desired folder and click OK.  The animation will then open in the Animation Viewer window.

13. Click Play to run the animation. Click Stop to stop the animation.  The Close button closes the Animation Viewer window and the Full Size button makes the window twice as large.

14. There are a number of options available on this window to change the animation speed, direction and looping.  Clicking the up/down arrows in the Frame box allows you to manually step through the animation frames.

15. If you selected GIF as the output format for the animation, one of the available controls will be a Save to Animated GIF button.  Clicking this button will save the animation as an animated GIF at a specified location.  The saved animated GIF will have the same properties (i.e, speed, direction, looping) as the animation in the Animation Viewer window.

Quick Spin Tool

The Quick Spin tool changes the map projection to "The World From Space", and then re-centers the map to a specified point.

1. Click on the Quick Spin tool .  The map projection will change to “The World From Space”.

2. Click on the desired point on the map and the map will re-center itself on the selected point.

3. To revert back to the map’s previous projection, click on another tool (such as the ArcMap Select Elements tool) in order to deselect the Quick Spin tool, and then re-click on the Quick Spin tool button.  

Note:  The “The World From Space” projection has become slower with every release of ArcMap since 9.0. Please be aware that it may take a long time for the map to redraw in this projection.

Configuration Window

To open the PaleoGIS Configuration window, click on the Configuration button .  The options and settings on the various tabs in the Configuration window allow you to customize PaleoGIS operation to best suit the analysis being performed.  Common configuration changes include:

1. Changing the currently loaded plate model.

2. Adding plate models to PaleoGIS.

3. Changing timescale sorting or switching to an alternate timescale.

4. Changing the content of the reconstruction map labels.

Basic Configuration Options

The Basic Options tab provides the plate model and timescale options described below, plus several self-explanatory options for configuring plate model and timescale information displayed in the reconstruction map labels.

Loading a Plate Model

1. Select the desired model from the Select Model dropdown menu.

2. Click the Load Selected Plate Model button.  

3. The selected model will be loaded into memory and a new data frame containing the model’s plate polygons, and possibly some supporting data, will be added to top of the ArcMap table of contents.  The name of the new data frame will be the name of the plate model that was just loaded.  All other data frames that existed before loading the model will remain in the map - they will just be moved below the new data frame. No data frames or data will be removed from the map.

Adding (Registering) a Plate Model in PaleoGIS

Plate models can be added to PaleoGIS using the following procedure:

1. Click on the Register Model button and the following window will display:

2. Click on the browse button  and then navigate to and select the plate model database.  The file name will end with a .mdb (Microsoft Access database) extension.

3. Click the Open button in the browse window.

4. The Model Settings Table text box will usually be automatically filled in with a table name.  If, however, this box is enabled as a dropdown menu, you must select the appropriate model settings table from the menu.  You may need to contact the plate model vendor for this information.

5. Enter a model name or accept the default in the Model Name text box.

6. If you want to model to load immediately after clicking OK, leave the Load model after registering box checked, otherwise, uncheck this option.

7. Click OK.

8. The model will now be added to the plate models that are available in the Select Model menu, and if the Load model after registering option was selected, the newly added model will load immediately.

Removing (Unregistering) a Plate Model from PaleoGIS

1. Be sure that the plate model you wish to remove is not the currently load plate model.  If it is, load a different plate model before proceeding.

2. Select the plate model to be removed in Select Model dropdown menu.

3. Click on the Unregister Model button, and click the Yes button in response to the message that appears.

Timescale Options

1. To switch to a non-default timescale, check the Do age conversion checkbox and select the desired timescale from the dropdown menu below the checkbox. This will cause PaleoGIS to convert ages from the selected timescale to the equivalent age in the loaded model’s default timescale.

2. To change the age sorting in the PaleoGIS: Basic Functions toolbar’s Age menu, select the desired Timescale Age Sorting option - either Alphabetical or Chronological.

Configuration Database Location

Gives the path to the Access database that contains all PaleoGIS application settings.

Advanced Configuration Options

The Advanced Options tab provides a number options that will be of use to power users, including the ability to choose the cache type that is used by PaleoGIS.

Advanced Options

1. Skip repairing features - Improves reconstruction performance by skipping the repair of any invalid features that might be created as a result of the intersection process between the plate model "cookie cutter" layer and user data layers.

2. Ignore assigned ages - Causes reconstructions and animations to ignore the “appearance” and “disappearance” fields in the plate model and user data layers. This means that regardless of the reconstruction age, all plate model polygons and all user data features that intersect a plate model polygon will be reconstructed and displayed during reconstructions and animations.

3. Ignore children – Removes the linkage between a parent plate and its children when making changes to the parent plate's poles of rotation using the Drag and Drop, Spin and Drop and Enter Pole tools on the Plate Model Tools toolbar.

4. Add unique ID to cache – Adds a “PaleoUniqueId” field to the attribute tables of all layers when they are copied to the cache, which is automatically populated with a unique ID number for each feature in the cached layer.  This field is then persisted to reconstructed and animated layers, where it can be used to trace the lineage of a reconstructed feature back to the present day.

5. Cache raster fragments (warp raster method only - not available for ArcGIS 10.3 and 10.3.1) – Improves performance when doing multiple warp reconstructions using the same raster.  When this option is selected, the plate model intersection with the raster is only performed during the first reconstruction, and the results of the intersection (the raster fragments) are saved in the cache for use during subsequent reconstructions.

Type of Cache

This option (not available in ArcGIS 10.3 and 10.3.1) allows you to change the type of data cache used by PaleoGIS.  It also determines the output format for reconstruction results within the scratch directory or when saving reconstructions.  The cache choices are File Geodatabase and Personal Geodatabase.  It is recommended to use the File Geodatabase option, which is the default cache type.  In ArcGIS 10.3 and 10.3.1, the cache is a File Geodatabase.

Miscellaneous Settings

Scratch and Cache Paths

The scratch path gives the location for the “scratch directory”, which is the output location for reconstruction results when using the File or Personal Geodatabase cache types.  The cache path shows the location and name of the PaleoGIS data cache when using the Personal or File Geodatabase cache types.

For both of these settings, browse to the desired folder location in the navigation window that appears when the setting button (Change Scratch Path or Change Cache Path) is clicked.  Note that PaleoGIS will automatically add the cache name (cache.gdb or cache.mdb) to the end of the cache path.

Licensing

Keep the ByPass Expect100Continue Header option checked unless your IT person instructs you to do otherwise.

Raster Reconstruction Method

This option (not available in ArcGIS 10.3 and 10.3.1) allows you select which method of reconstruction will be used by PaleoGIS when reconstructing rasters.  In ArcGIS 10.3 and 10.3.1, the pixel method is used for raster reconstructions.

Pixel (default method) - Converts the raster to a point feature class and then reconstructs this feature class to the selected age.  The reconstructed feature class is then converted back to a raster.

Warp - “Cookie cuts” the raster into fragments and then “warps” the fragments into their reconstructed positions.  The reconstructed fragments are then mosaiced back into a single reconstructed raster.

Time Slice Layers

The Enable time slice layers option enables Time Slice Viewer functionality if the currently loaded plate model contains time slice layers.  If the model contains time slices, the Time slice path will be the path to directory where the time slice layers are located.  However, it is possible for this path to be empty even if the model contains time slices.  Time Slice Viewer operation is discussed in a later section.

Application Settings

PaleoGIS is highly configurable, and configuration changes can be made through the table on the Application Settings tab.  After making changes to the table, click the Save Updates button to save the changes to the PaleoGIS setting file (PaleoGIS_Settings.mdb).  Application setting changes can also be made directly in PaleoGIS_Settings.mdb using Microsoft Access.  For a complete list and description of all the available PaleoGIS application settings, refer to the PaleoGIS Application Settings section of this manual.

Model Settings

The Model Settings tab provides access to the settings for the currently loaded plate model.  Detailed information about these settings can be found in the PaleoGIS Plate Modeler Manual.

Models

The Models tab provides a list of registered plate models and their source locations.

Timescales

The Timescales tab provides a list of the alternate timescales available with PaleoGIS and their source locations.  

PaleoGIS: Plate Model Tools Toolbar

 Genealogist Tool: Used to view the sub-plates (i.e. child plates) for a specified plate within a reconstruction data frame.

 Pole Finder Tool:  Displays the latitude, longitude, and angle of rotation for the pole that was used to rotate a selected plate within a reconstruction data frame.

 Spin and Drop Tool:  Allows the user to rotate a selected plate into a new position.

 Drag and Drop Tool:  Allows the user to drag a selected plate to a new position. 

 Enter Pole Tool:  Allows the user to enter a new total finite or stage pole for a plate.

 Undo Move Tool:  Allows the user to undo the last plate movement made using the Spin and Drop, Drag and Drop and Enter Pole tools.  

 Redo Move Tool:  After using the Undo Move tool, the user can use this tool to redo the last move.  

 Pole Saver Tool:  Allows the user to save poles of rotation for plates that have been moved.

 Pole Set Maintenance Tool:  Allows the user to save, move, delete, and edit plate rotation data within the currently loaded plate model.  

 Time Slice Manager Tool:  Facilitates time slice incorporation into plate models by allowing the user to make changes directly to the time slice table (TIMESLICE_LAYERS) in the plate model geodatabase, save time slice symbology inside of the geodatabase and view previously saved symbology.

 Plate Model Symbology Tool:  Allows the user to save display layer symbology inside of the plate model geodatabase and to view or delete symbology that was previously saved in the geodatabase.

Important:  The POLE_SOURCE_1 table as specified in the Model Settings is the master pole rotation table for the currently loaded model.  It is best to not make changes to this table, but instead to add another POLE_SOURCE table (e.g., POLE_SOURCE_2) to the model to hold pole changes.  This will keep your original rotation table in its original state in case you need to revert to those poles.  Another “safety” option to consider before editing the model is to make a copy of the entire plate model file as a backup in case your changes don’t go as planned.

Note: A reconstruction must first be performed in order for most of the tools on the PaleoGIS: Plate Model Tools toolbar to be enabled.

Genealogist Tool

The Genealogist tool is used to view the sub-plates (i.e. child plates) for a specified plate within a reconstruction data frame.

1. Run a reconstruction to the desired age.

2. Click on the plate polygon layer in the Table of Contents to select it (it will be highlighted in blue).

3. Click on the Genealogist tool  and then click on the plate of interest in the map.

Note:  If you click on overlapping plates resulting in multiple selections, the window below will display.  In this case, select the desired plate from the dropdown list.

4. Every plate that is a child of the selected plate will be selected (see below), and each of these plates will be labeled with a number.  The number indicates each plates generation – 0 is the selected plate (the parent), 1 is a child, 2 is a grandchild, and so on.

Tip: When using the Genealogist tool you can clear the graphics created by the tool by holding down Ctrl + Shift and clicking the map. You can also clear selected features by holding down Ctrl and clicking the map.

Pole Finder Tool

The Pole Finder tool is used to display the latitude, longitude, and angle of rotation for the total finite absolute pole that was used to rotate a selected plate within a reconstruction data frame.

1. Run a reconstruction to the desired age.

2. Click on the plate polygon layer in the Table of Contents to select it (it will be highlighted in blue).

3. Click on the Pole Finder tool  and then click on the plate of interest in the map.

Note:  If you click on overlapping plates resulting in multiple selections, the window below will display.  In this case, select the desired plate from the dropdown list.

4. The pole information information for the plate will display as follows:

Spin and Drop Tool

The Spin and Drop tool is used to rotate a selected plate into a new position.

1. Run a reconstruction to the desired age.

2. If there is more than one layer in the map, make the plate polygon layer the only selectable layer.
4. Using the Select Features tool , click on the plate to be moved.  When a single plate has been selected, the Spin and Drop tool will be enabled.  The tool will not be enabled if multiple plates are selected.

5. After the plate has been selected, click on the Spin and Drop tool and click on the three points that construct a “pole of rotation” for that plate.  The second point will be the axis about which the spin will occur.  Note that this “pole of rotation” is merely a graphical tool that allows you to move the selected plate to a new position.  This is not the pole that will move the plate during reconstructions - the “real” pole that will be added to the rotation table is automatically calculated by PaleoGIS based on the location of the plate after it has been moved to its final position during the plate editing session.

After clicking on the third point, the selected plate and any of its children will automatically move to the new position:

Note:  If you don’t wish for child plates of the selected plate to move during this operation, select the Ignore children option on the Advance Options tab in the Configuration window.

6. Save the changes using the Pole Saver Tool.

Drag and Drop Tool

The Drag and Drop tool is used to linearly offset the position of a selected plate to a new position.

1. Run a reconstruction to the desired age.

2. If there is more than one layer in the map, make the plate polygon layer the only selectable layer.

3. Using the Select Features tool , click on the plate to be moved.  When a single plate has been selected, the Drag and Drop tool will be enabled.  The tool will not be enabled if multiple plates are selected.

4. After the plate has been selected, click on the Drag and Drop tool and then click on the starting point and followed by the ending point representing the distance and direction of the drag:

5. After clicking on the ending point, the selected plate and any of its children will automatically move to the new position:

Note:  If you don’t wish for child plates of the selected plate to move during this operation, select the Ignore children option on the Advance Options tab in the Configuration window.

6. Save the changes using the Pole Saver Tool.

Enter Pole Tool

The Enter Pole tool allows the user to manually add pole values to a specific plate in the currently loaded plate model. This is useful for implementing precise pole values that have been calculated or obtained from published sources.

The Enter Pole tool accepts total finite poles and stage poles.  In order for an entered pole to be correctly interpreted by PaleoGIS, the map reference frame must set to the reference frame that was used to calculate the pole value.  In addition, this reference frame needs to correspond to the parent plate of the selected plate.  For example, for a total finite relative pole for 50 Ma for S.America moving relative to Africa (i.e. the pole reference frame), the model to be modified should have Africa as the parent plate for S.America during the applicable geologic age, and Africa should be selected as the reference frame for the reconstruction.

1. Set the map to the correct reference frame using the Set Fixed Plate tool.

2. Run a reconstruction to the appropriate age for the pole being entered.

3. Using the Select Features tool , click on the plate of interest.  When a single plate has been selected, the Enter Pole tool will be enabled.  The tool will not be enabled if multiple plates are selected.

4. Click on the Enter Pole tool  and the following window will display:

5. The pole values that are initially in the New Pole fields represent the total finite absolute pole that was used to move the selected plate to its current position.  

Note:  The Map Reference Frame and the Parent Plate values must be the same for correct implementation of the entered pole.  If these values are different, re-run the reconstruction with the map in the appropriate reference frame before continuing.

6. Enter the Latitude, Longitude, Angle for the new pole in the appropriate New Pole fields.

7. Select the Pole Type: Total Finite or Stage.

8. Click Continue. The plate will move to the position determined by the new pole.

Note:  If you don’t wish for child plates of the selected plate to move during this operation, select the Ignore children option on the Advance Options tab in the Configuration window.

9. Save the new pole using the Pole Saver Tool.

Pole Saver Tool

The Pole Saver tool is used to save new poles of rotations that have either been calculated by PaleoGIS for plates moved using the Spin and Drop and Drag and Drop tools or that have been manually entered using the Enter Pole tool.

1. After a plate has been moved to the desired position or new poles have been entered for a plate, click on the Pole Saver tool and the following window will open:

2. You will see the entry for the newly calculated or entered pole.  To make changes, click inside the field and enter the new information.

3. To delete a row, select the row by clicking in the far right column and press the “Delete” key on your keyboard.  Note that edits and deletes cannot be undone.

4. To save the new pole, click Save and then click Close to exit the window.  If you want to discard the new pole without saving, click Close without first clicking Save.

Note: If you want the ability to make pole changes to multiple plates before saving, change the Application Setting EDIT_SKIP_PLATE_LIST value to FALSE (the default setting is TRUE).  Then when the Pole Saver tool is clicked, the window below will open with a list off all the plates that have pole changes:

Click to highlight a plate to be edited or saved and click the Edit/Save Pole button.  The Pole Saver Edit Window will open.  Edit and/or save the pole as described starting in step 1 above.  Repeat this process for the other plates in the Poles to Save window.

Pole Set Maintenance Tool

The Pole Set Maintenance tool allows the user to save, move, delete, and edit plate rotation data within the currently loaded plate model.

1. Click on the Pole Set Maintenance tooland the following window will display:

2. For the Move and Delete operations refer to the instructions in the specific section in this window.  The Move and Delete operations cannot be undone after clicking the Move or Delete buttons (mistakes must be fixed manually using the Edit function), so use caution when using these tools.  

3. To use the Edit function, select the rotation table to be edited from the dropdown menu and then click the Edit button.  The the Pole Saver Edit Window will open containing the selected rotation table.  Make changes manually to the table.  These changes can be undone by clicking the Undo/Refresh button before the Save button is clicked, but once Save has been clicked, mistakes must be fixed manually.

Time Slice Manager Tool  

The Time Slice Manager tool facilitates time slice incorporation into plate models by allowing the user to make changes directly to the time slice table (TIMESLICE_LAYERS) in the plate model geodatabase, save time slice symbology inside of the geodatabase and view previously saved symbology.

Note:  To save time slice symbology to the plate model geodatabase, the time slice feature class must be contained in the plate model geodatabase.

1. Click on the Time Slice Manager tool  and the following window will display:

2. Click on the browse button  and then navigate to and select the target plate model geodatabase in the Select a Geodatabase window that opens.  The file name will end with a .mdb (Microsoft Access database) extension.  

3. Once a plate model geodatabase has been selected, the other buttons in the window will be enabled, and any existing time slices in the TIMESLICE_LAYERS table will be shown in the Time Slice Table section in the window:

4. If the plate model geodatabase does not already contain a TIMESLICE_LAYERS table, the table will be automatically created within the geodatabase when the geodatabase is opened in Step 2 above.

5. Time slice layers that currently have symbology saved in the plate model geodatabase will have a .lyr icon () in the LAYER column in the table.

6. Follow the instructions in the Time Slice Manager window for saving and viewing time slice symbology and for making edits/deletions in the table.

Plate Model Symbology Tool 

The Plate Model Symbology tool allows the user to save display layer symbology (i.e., .lyr file) inside of the plate model geodatabase and to view or delete symbology that was previously saved in the geodatabase.  This tool improves upon the Database layers application that previously had to be downloaded and added to the ArcMap in order to save symbology in a geodatabase.

Note:  To save display layer symbology to the plate model geodatabase, the display layer feature class must be contained in the plate model geodatabase.

1. Click on the Plate Model Symbology tool  and the following window will display:

2. Click on the browse button  and then navigate to and select the target plate model geodatabase in the Select a Geodatabase window that opens.  The file name will end with a .mdb (Microsoft Access database) extension.  

3. Click the Add button in the Select a Geodatabase window.

4. Once a plate model geodatabase has been selected, the other buttons in the window will be enabled, and any plate model layers that currently have symbology saved in the geodatabase will be listed in the table in the View or Delete Symbology section:

Saving Symbology to the Plate Model Geodatabase

1. Add the feature class to be symbolized to the map.  The feature class must be contained in the plate model geodatabase; however, it does not matter whether or not the feature class currently has symbology.  

2. Change the symbology as desired.  Once you have finished, click on the layer in the Table of Contents, and then click the Save Symbology button.

3. You will receive a warning message that the change you are about to make cannot be undone (you will get this message even if there is no existing symbology in the geodatabase for the feature class).  Click OK to continue saving the symbology, and the save will be finalized.

Viewing or Deleting Existing Plate Model Symbology

1. Select a layer to be viewed by clicking on the corresponding row in the table, and then click Add to Map to load the symbolized layer into the map.

2. Select a layer to be deleted by clicking on the corresponding row in the table, and then click  Delete.  This will delete the symbology (.lyr file), but it will not delete the actual display layer feature class from the geodatabase.

PaleoGIS Analysis Toolbar

The PaleoGIS Analysis Toolbar provides access to the following analysis tools:

• Azimuth & Rate vs. Time:  Graphically shows the speed and direction of movement for a single point on a single plate over a specified time range.

• Instantaneous Motion: Draws a grid of arrows on a reconstructed map to show the

speed and direction of motion for all plates at that time.

• Point Path Visualization:  Draws a path on the map showing the movement of a single point on a single plate over a specified time range.  The width of the path indicates the speed of the point at different times.

• Paleo Calculator: This tool provides an array of useful tools that perform calculations commonly used by power users (pole addition, point rotation, great circle distance calculation, and pole position calculation).

• Paleo Data Converter:  Provides tools to convert between commonly used plate model data formats.

• PaleoClimate:  PaleoClimate is a fast-cycle parametric global climate modeling tool which is licensed separately from PaleoGIS.  PaleoClimate will only launch from the PaleoGIS Analysis Toolbar if you have purchased a license for this product.

Note: Custom proprietary analysis tools can be added to this toolbar for additional functionality. Please contact The Rothwell Group, L. P. for details.

Azimuth & Rate vs. Time

This tool operates on present day maps (not on reconstructed maps).

The Azimuth & Rate vs. Time analysis graphically shows the speed and direction of movement for a single point on a single plate over a specified time range at specified step intervals.  The position, azimuth and speed of the point is calculated for each step interval from present to past.

Changes in azimuth or rate can indicate times when a major tectonic event has occurred.  This tool is can also be useful for plate modelers because the analysis can highlight rapid changes in azimuth and/or unreasonable rates of plate motion which may indicate errors in the plate model.

1. Starting in a present-day map, click on the plate polygon layer in the Table of Contents to highlight it and then use the ArcMap Select Features tool to select the plate be analyzed.

2. Click on the PaleoGIS:  Analysis Tools toolbar dropdown menu and select Azimuth & Rate vs. Time.

3. Click Go and the following window will appear:

4. The Latitude of Feature Center and Longitude of Feature Center fields are by default populated with the coordinates for the centroid of the selected plate; however, you can manually change these values to the coordinates for any point of interest on the plate.  The analysis will show the movement of the point indicated by these coordinates.

5. The Plate ID of Feature for the selected plate and the selected Reference Plate (if there is one) will be indicated in the respective fields.  

6. Enter the desired Start Age (Ma) and End Age (Ma) values.

7. In the Step Interval field, enter the interval in millions of years for the analysis steps.

8. The Calculate using half rates option can be used to show the speed and direction of movement of the point of interest relative to a mid-ocean spreading ridge, rather than relative to the earth’s spin axis or another plate.  For proper use of this option, the reference plate should first be set (using the Set Fixed Plate tool), to be the plate that is moving in the opposite direction from the spreading ridge relative to the plate selected for this analysis.  For example, if the point being analysed is in S. America, then to use Calculate using half rates to show the movement of the point relative to the Mid-Atlantic Ridge, Africa should be set as the reference plate since S. America is moving away from the spreading ridge at half the rate that it is moving away from Africa.

9. The Show results table when finished option opens a table when the analysis is done that gives the starting/end latitude and longitude, direction and rate of motion for each interval in the analysis.  This table can be easily exported for later use (select Export... from the Table Options menu in the upper left-hand corner of the table).

10. Click Continue.

11. The analysis will be processed and the results will be displayed as follows:

12. To print the results, click Print.

13. To exit, click Close.

Instantaneous Motion

This tool operates on the last reconstructed map (not on the present day map or previously run reconstructions).

This tool draws a regularly-spaced grid of arrows on a reconstructed map to show the speed and direction of motion for the location under each arrow at that time.  This tool operates by generating a grid of points with user-defined spacing (default = 4 degrees) and assigning the points to the plates in their present day locations.  The points are then reconstructed to the time of the reconstructed map, followed by a reconstruction to a slightly older time based upon a user-defined age delta (default = 100,000 years). The positions of the points from the two reconstructions are then compared and the results are used to create a map layer of arrows that indicate the direction and relative speed of movement of each point at that moment in time.

This analysis can be used to illustrate the "instantaneous" stresses affecting the plates. By comparing the motion between plates, the relative plate interactions can be inferred (colliding, diverging, translation, trans-tension, and/or transpression).

1. Perform a reconstruction to the desired age.  This tool will not work on the present day map.

2. Click on the Analysis Toolbar dropdown menu and select Instantaneous Motion. Click Go and the following window will open:

3. If you want a Grid increment that is different than the default, type it in or use the up/down arrows to enter a new grid spacing.

4. If you want a Delta to add to reconstruction age that is different than the default, type it in or use the up/down arrows to enter the new delta. 

5. In the Whole Map or AOI (Area of Interest) section, select either Whole Map or AOI as the area for the analysis to evaluate.  If AOI is select, only the currently visible area of the map will be evaluated, i.e., if you are zoomed-in to a region on the map, only that region will be considered in the analysis.  This can speed up processing if you are using a very detailed plate model, but you are only interested in the results for a small area.

6. Click Calculate.

7. The analysis will be processed and the results added to the map as a point layer with each point symbolized as an arrow (see image below).  The direction of each arrow indicates that point’s direction of motion at the time of the reconstruction, and the size of the arrow shows its speed. The calculated speed in (cm/yr) is shown above each arrow on the map.

8. The legend in the Table of Contents for the resulting point layer shows the speed ranges indicated by the arrow sizes:

Point Path Visualization

This tool operates on present day maps (not on reconstructed maps).

This tool operates much the same as the Azimuth and Rate vs. Time tool, where the direction and rate of motion for a single point is calculated back through time. However, instead of creating a set of graphs, a line is added to the map showing the path of the point over the specified time period, and the width of the path indicates the speed of the point at different times.  The starting point of the line is the present day location of the point and the end of the line is its position at the oldest analysis step.  

This analysis is useful for the same reasons as the Azimuth and Rate vs. Time tool, but it provides a different way to view and understand the data.

1. Starting in a present-day map, click on the plate polygon layer in the Table of Contents to highlight it and then use the ArcMap Select Features tool to select the plate be analyzed.

2. Click on the Analysis Toolbar dropdown menu and select Point Path Visualization.

3. Click Go and the following window will appear:

4. The Latitude of Feature Center and Longitude of Feature Center fields are by default populated with the coordinates for the centroid of the selected plate; however, you can manually change these values to the coordinates for any point of interest on the plate.  The analysis will show the movement of the point indicated by these coordinates.

5. The Plate ID of Feature for the selected plate and the selected Reference Plate (if there is one) will be indicated in the respective fields.  

6. Enter the desired Start Age (Ma) and End Age (Ma) values.

7. In the Step Interval field, enter the interval in millions of years for the analysis steps.

8. The Calculate using half rates option can be used to show the speed and direction of movement of the point of interest relative to a mid-ocean spreading ridge, rather than relative to the earth’s spin axis or another plate.  For proper use of this option, the reference plate should first be set (using the Fixed Plate Tool), to be the plate that is moving in the opposite direction from the spreading ridge relative to the plate selected for this analysis.  For example, if the point being analysed is in S. America, then to use Calculate using half rates to show the movement of the point relative to the Mid-Atlantic Ridge, Africa should be set as the reference plate since S. America is moving away from the spreading ridge at half the rate that it is moving away from Africa.

9. The Show results table when finished option opens a table when the analysis is done that gives the starting/end latitude and longitude, direction and rate of motion for each interval in the analysis.  This table can be easily exported for later use (select Export... from the Table Options menu in the upper left-hand corner of the table).

10. Click Continue.

11. The analysis will be processed and the results will be displayed as a line layer on the map where the line thickness represents that speed at which the plate was moving at various times, and the numbers represent ages in millions of years (Ma):

12. The legend in the Table of Contents for the resulting line layer shows the speeds indicated by the line thickness:

Paleo Calculator

The Paleo Calculator provides four tools to perform calculations commonly used by power users: pole addition, point rotation, pole position, and  great circle distance.  Click on the PaleoGIS: Analysis Toolbar dropdown menu and select Paleo Calculator.  Click Go and the window shown below will display.  To use any of the tools, enter the required values in each white text field for the tool, and then click the Calculate button.  The results will be displayed in the gray text box for the tool being used.

PaleoGIS Data Frame Context Menu

 Save Reconstruction Tool: Allows the user save all the data layers shown in a reconstruction to a new directory for permanent storage.  Until this is done, the layers are stored in the scratch directory and risk being deleted.  The data is saved in a geodatabase along with layer files that will render the data with the symbology was assigned to it in the reconstruction.  

 Export to ArcGlobe Tool: Exports an entire data frame to ArcGlobe, assuming that ArcGlobe is installed.  Once the data is exported, ArcGlobe will open and show the data and will allow manipulation.

 Refresh Cache Tool:  Refreshes the cached data for all the layers in the present day map (the top data frame).  This operation copies all the data layers to the cache and then intersects (“cookie cuts”) the copied data with the plate model polygon layer.  When edits are made to data in the present day map, the edits will not be automatically updated in the cached data; therefore, it is important to refresh that data in the cache to make sure the cache is up-to-date.  

 Empty Scratch Directory Tool:  Clears all temporary data out of the scratch directory so that the directory does not grow too large.  It is important to first run the “Save Reconstruction Tool” to save any reconstructions that need to be preserved.  Note: this is a “blanket” delete – EVERYTHING in the scratch directory will be deleted, even non-PaleoGIS-related files.

 Validate All Layers Tool:  Validates all the layers in a data frame to make sure they are compatible with PaleoGIS by checking that the data is in a PaleoGIS supported format and that they do not contain malformed geometries.

Detailed information for using each tool is given below.

Save Reconstruction

This function allows a user to save all the data layers shown in a reconstruction to a new directory for permanent storage.  Until this is done the layers will be stored in the scratch directory and risk being deleted if the scratch directory is emptied.  After clicking Save Reconstruction the data is saved in a geodatabase along with layer files that will render the data with the symbology that was assigned to it in the reconstruction.  

1. Right-click on the reconstructed data frame that you wish to save in the Table of Contents to access the PaleoGIS context menu and select Save Reconstruction.

2. The following window will appear:

3. Browse to the desired location in the dialog box.  You can also create a new directory using the Make New Folder button.

4. If desired, change the default “File name” for the saved reconstruction.

5. Click OK.  The reconstruction data and layer files will be saved in the specified location.  

6. When the save process is complete, a message with the output location will be displayed:

7. The output folder will contain a folder of layer files which link to the saved data contained an geodatabase in the same folder.  These layers files can be added to a map at any time in the future to view the reconstruction results.  The type of geodatabase containing the saved data will be the same type as selected for the cache (either file or personal).  

Export to ArcGlobe

This function exports an entire reconstruction data frame to ArcGlobe, assuming that ArcGlobe is installed.  Once the data is exported, ArcGlobe will open and show the data.

1. Right-click on any reconstructed data frame in the Table of Contents to access the PaleoGIS context menu and select Export to ArcGlobe.

2. The status of this process will show in the ArcMap status bar in the bottom left corner of the ArcMap window.

3. When complete, ArcGlobe will appear with the layers loaded:

Note: For the best results, make the following changes to your ArcGlobe application before using the Export to ArcGlobe tool:

1. At the top of the ArcGlobe window select Customize > ArcGlobe Options:

2. In the window that opens, go to the Messages tab and make sure the Use wizard when adding a new layer option is NOT selected:

Refresh Cache

This tool refreshes the cached data for all the layers in the present day map (the top data frame) by copying all the data layers to the cache and then intersecting (“cookie cutting”) the copied data with the plate model polygon layer.  

When you edit layers in the present day map, the edits will not be automatically updated in the cached data; therefore, it is important to refresh the cache after making edits to make sure that the cache is up-to-date, otherwise the edits will not appear in your reconstructions.  Normally, PaleoGIS manages the cache automatically, but in the case of attribute and feature edits it does not.

1. Right-click on the present day (topmost) data frame in the Table of Contents to access the PaleoGIS context menu and select Refresh Cache .

2. PaleoGIS will copy all visible data layers in the present day data frame to the cache and then intersect (“cookie cut”) the cached data with the plate model polygon layer.

Empty Scratch Directory

This tool clears all temporary data out of the scratch directory so that the directory does not grow too large.  It will also delete any reconstructed data frames in your current MXD.  Therefore is important to use the Save Reconstruction  tool to save any reconstructed data frames in your map that you wish to preserve before emptying the scratch directory.  

Note: this is a “blanket” delete – EVERYTHING in the scratch directory will be deleted, even non-PaleoGIS-related files.  If there are any locked files, they will be left untouched until the next time this command is run.

1. Right-click on any data frame in the Table of Contents to access the PaleoGIS context menu and select Empty Scratch Directory .

2. The following warning will appear.  Click Yes to proceed.

3. When the process is complete, this message will appear:

Validate All Layers

This tool validates all the layers in a data frame to make sure they are compatible with PaleoGIS by checking that the data is in a PaleoGIS supported format and that they do not contain malformed geometries.

1. Right-click on the data frame to be validated in the Table of Contents to access the PaleoGIS context menu and select Validate All Layers .

2. PaleoGIS will begin validating the layers in the data frame and window containing a status bar will be shown.

3. When complete, a Layer Validation Results window will display (see image below).   It will contain the result of the validation for each layer in the data frame.  Any problems will be noted here.

4. If the validation windows says that a layer is not in a PaleoGIS supported format, you can create a copy of the data in a supported format (shapefile or a featureclass in a Personal or File Geodatabase) by right-clicking on the layer in the Table of Contents and then choosing the Data > Export Data option.  You can then add the exported data to the map.

5. If the validation window says that there are malformed geometries, run the Repair Layer tool on the specified layer(s). This tool calls the ESRI Repair tool and should fix any problems with the data layer.

PaleoGIS Layer Context Menu

 Refresh Cache for Single Layer: Refreshes the cached data for a single layer.  When a layer is edited, the edits will not be automatically updated in the cached data; therefore, it is important to refresh that data in the cache to make sure the cache is up-to-date.  

 Un-Reconstruct Tool: Allows the user to add point, line, or polygon data layers to a reconstructed map and then do a “reverse” reconstruction on the data, moving the features to their present-day coordinates. 

 Validate Layer Tool: Validates a single layer to make sure it is compatible with PaleoGIS by checking that the data is in a PaleoGIS supported format and that it does not contain malformed geometries.

 Repair Layer Tool:  This tool will attempt to fix any geometry errors (i.e. null geometry, crossover polygons, etc.) so the layer will work within PaleoGIS.  

 Preprocess Raster Tool (not available in ArcGIS 10.3 and 10.3.1): Allows the user to pre-“cookie cut” a single raster layer prior to doing a reconstruction or animation when using the warp method for raster reconstructions.

Detailed information for using each tool is given below.

Refresh Cache for Single Layer

Refreshes the cached data for a single layer.  When a layer is edited, the edits will not be automatically updated in the cached data; therefore, it is important to refresh that data in the cache to make sure the cache is up-to-date, otherwise the edits will not appear in your reconstructions.  Normally, PaleoGIS manages the cache automatically, but in the case of attribute and feature edits it does not.

1. Right-click on the layer to be refreshed in the Table of Contents to access the PaleoGIS context menu and select Refresh Cache for Single Layer .

2. PaleoGIS will copy the selected layer into the cache.

Un-Reconstruct

Allows the user to add point, line, polygon and raster data layers to a reconstructed map and then do a “reverse” reconstruction on the data, moving the features to their present day coordinates.

1. Run a reconstruction to the age of interest.

2. Add the data layer that you want to un-reconstruct to the reconstructed data frame.  This data can be existing data that corresponds to the reconstruction age, or it can be a new layer that you might have created based on reconstructed features in the reconstructed map.  There is no need to add any special attributes (such as appearance, disappearance, or plate code) to the data layers that are to be un-reconstructed, as these will be added automatically during the un-reconstruct process.  

3. In the Table of Contents, right click on the layer to be un-reconstructed to access the PaleoGIS context menu and select Un-Reconstruct .

4. PaleoGIS will do the processing required to intersect the data with the reconstructed plate model, and then move the data to its present day position.

5. When complete, the new layer will be added to the present day (topmost) data frame where it will be given its original name with “_0” appended to it.

6. In order to view the un-reconstructed data, you must activate the “Present Day” (topmost) layer.

Note: It is also possible to add features directly to a reconstructed layer in the reconstructed map, and then un-reconstructed the edited layer.  However, since the reconstructed layer will already contain plate code, appearance, disappearance columns that were added during the original reconstruction, you must manually add these attribute values for the newly added features in order for them to to properly un-reconstruct.

Un-Reconstruct Example:

The figure below shows 3 layers that have been added to a reconstruction – a point layer with 3 points, a line layer with 2 lines, and a polygon layer with 1 polygon.

The present day un-reconstruction for the 3 layers shown above looks like this:

Validate Layer 

Validates a single layer to make sure it is compatible with PaleoGIS by checking that the data is in a PaleoGIS supported format and that it does not contain malformed geometries.

1. Right click on the layer to be validated in the Table of Contents to access the PaleoGIS context menu and select Validate Layer .

2. PaleoGIS will begin validating the selected layer and window containing a status bar will be shown.

3. When complete, a Layer Validation Results window will display (see image below).   Any problems with the validated layer will be noted here.

4. If the validation windows says that the layer is not in a PaleoGIS supported format, you can create a copy of the data in a supported format (shapefile or a featureclass in a Personal or File Geodatabase) by right-clicking on the layer in the Table of Contents and then choosing the Data > Export Data option.  You can then add the exported data to the map.

5. If the validation window says that there are malformed geometries, run the Repair Layer tool on the specified layer. This tool calls the ESRI Repair tool and should fix any problems with the data layer.  

Repair Layer

This tool will attempt to fix any geometry errors (i.e. null geometry, crossover polygons, etc.) in a single layer so that the layer will work within PaleoGIS.

Note that the Repair Layer tool will change your data when making the repairs, so you should first make a backup copy of the data before running this tool.

1. Right-click on the layer to be repaired in the Table of Contents to access the PaleoGIS context menu and select Repair Layer .

2. The selected layer will be repaired using the ESRI Repair Geometry ArcToolbox tool.  If there are any problems, they will be reported.

3. The layer will be moved to the top of the data frame when the repair process is complete, and a window showing the results of the repair operation will be displayed.

Preprocess Raster (warp raster method only)

This function allows the user to preprocess a single raster layer prior to doing a reconstruction or animation.  This function is not available in ArcGIS 10.3 and 10.3.1 because the warp raster reconstruction method is not used in these versions.

Raster layers (imagery data) can be reconstructed in PaleoGIS but they use more system resources and take more time to reconstruct. The first and most time consuming step in this process involves “cookie cutting” the raster into numerous fragments based on the borders of the loaded published plate model. The fragments are then placed in the PaleoGIS cache so they can be used by the reconstruction and animation tools.

Using this tool will perform just the “cooking cutting” step and the fragments will be maintained in the cache as long as the Cache raster fragments option is checked in the Configuration window. This allows the preprocessed raster to be used in any number of reconstructions and animations without repeating the time-consuming “cookie cutting” process.

Time Slice Viewer

Certain plate models will now include pre-reconstructed data layers call “time slices” that can add valuable information to your reconstructions or improve reconstruction speed.  The Time Slice Viewer automatically adds these time slices to reconstructions if they are available for the reconstruction age.  The time slices may contain supplemental data or they can be pre-reconstructed plate model display layers that were included to improve processing speed by eliminating the need to reconstruct all of the model’s display layers.

To enable Time Slice Viewer functionality, check the Enable time slice layers option in the Misc. Settings tab in the Configuration window:

Note that if the currently loaded plate model doesn’t contain time slices, then selecting this option will have no effect on PaleoGIS operation.  If the model contains time slices, the Time slice path on the Misc. Settings tab will be the path to directory where the time slice layers are located.  However, it is possible for this path to be empty even if the model contains time slices.  

When the Time Slice Viewer is enabled ages that have corresponding time slices in the model will be bolded and labeled “(Time slice)” in the Age dropdown menu on the PaleoGIS: Basic Functions toolbar:

In the example above, reconstructions to the Zanclean, Lutetian, Ypresian or Hauterivian ages will cause time slice layers to be automatically added to the reconstruction map.  The time slices will be added to the reconstructions if any of these ages are selected from the dropdown menu or if a numeric age that corresponds to one of these geologic ages is entered in the Age box.

When creating animations with a model that contains time slices, by default the time slices will not be included in the animation.  However, if you would like for them to be included, check the Include time slice layers in animations option on the Animation window.  Note that this option will not be available unless the Enable time slice layers option is checked in the Configuration window.

Time Slice Viewer functionality is only available when using the default timescale for the currently loaded plate model.  If you choose to convert to an alternate timescale on the Basic Options tab in the Configuration window, the Time Slice Viewer functionality will be turned off even if the Enable time slice layers option is checked.

Using PaleoGIS with a Proxy Server

For PaleoGIS licensing to operate correctly, PaleoGIS must be able to contact the The Rothwell Group’s license server via the internet.  If your company is using a proxy server, you will need to configure PaleoGIS to insure that it can access the internet through the proxy server firewall.

In the Applications Settings tab in the Configuration window, change the value for the PROXY_SERVER_SETTINGS_SHOW setting to TRUE, then click the Save Updates button at the bottom of the table.

Go to the Misc. Settings tab in the Configuration window.  A section titled Proxy Server Information will now be present at the bottom of the page (see image below).  Contact your IT person for the information required to fill in the spaces in this area.  Note that, if necessary, the Username and Password spaces can be left empty.  Once you have filled in the appropriate information, click the Save Proxy Server Settings button.  You are now ready to use PaleoGIS.

PaleoGIS Application Settings

This section documents the configuration settings included in PaleoGIS. PaleoGIS is highly configurable in ways other than the default configuration. Below is a table of all the settings that can be found in the specified tables of the PaleoGIS Settings File (PaleoGIS_Setting.mdb file).  Many of these settings can be set and saved to the PaleoGIS Settings File through the PaleoGIS Configuration window.

T_PaleoGIS_Settings Table

T_PaleoGIS_Timescales Table

Australian Geological Survey, 1995

i.e. Provider=Microsoft.Jet.OLEDB.4.0;Data Source=$PGD$;User Id=admin;Password=;|AGSO95|OLDER|YOUNGER|NAME                                                                              

Berggeren, 2005
i.e. Provider=Microsoft.Jet.OLEDB.4.0;Data Source=$PGD$;User Id=admin;Password=;|BERGGERE|OLDER|YOUNGER|NAME                                                                            

DNAG 1999
i.e. Provider=Microsoft.Jet.OLEDB.4.0;Data Source=$PGD$;User Id=admin;Password=;|DNAG99|OLDER|YOUNGER|NAME

Kent & Gradstein 1986 (DNAG 1986)
i.e. Provider=Microsoft.Jet.OLEDB.4.0;Data Source=$PGD$;User Id=admin;Password=;|DNAG86|OLDER|YOUNGER|NAME

T_PaleoGIS_Models Table

ScoteseDemoModelv2d3
i.e. Provider=Microsoft.Jet.OLEDB.4.0;Data Source=ScoteseDemoModelv2d3.mdb;User Id=admin;Password=;|T_Model_Settings

UTIG_demo
i.e. Provider=Microsoft.Jet.OLEDB.4.0;Data Source=UTIG_demo.mdb;User Id=admin;Password=;|T_Model_Settings

PaleoGIS Metadata Keywords

PaleoGIS can be instructed to perform certain specialized functions on a specific layer based on certain keywords in that layer’s ArcGIS metadata.  This capability is primary intended to be used by plate modelers to add custom functionality their plate models.  The available metadata keywords and their functions are described in the table below.  To add any of these capabilities to a layer, the keyword must be included in the the “Purpose” field in the layer’s metadata.  There can be any other text in the “Purpose” field, so this does not preclude using the “Purpose” field as it was intended, but the PaleoGIS keyword must be on a line by itself within the “Purpose” field.

Due to metadata changes made by ESRI starting in ArcMap 10.0, in order to access the metadata “Purpose” field, you must download and install the FGDC Metadata Editor add-in in ArcCatalog.  From this add-in you can open a layer’s FGDC compliant metadata which contains the “Purpose” field. Entering the PaleoGIS keywords using ESRI’s standard metadata interface will NOT write the keywords to the correct location in the metadata, and therefore the keywords will not be recognized by PaleoGIS.  Conversely, keywords entered into the “Purpose” field using the FGDC Metadata Editor will not be visible in via the standard metadata interface even though they will still be available for use by PaleoGIS.

Command Line Tool and Batch Scripting With PaleoGIS

The PaleoGIS suite of tools also offers a command line that enables some of the most commonly used functions that can be carried out in the PaleoGIS GUI in ArcMap. There are also some utility functions that only make sense in a batch scripting environment. This functionality is available to you via the PaleoGISExternal.exe program, a simple DOS executable can be found in the installation directory of PaleoGIS. This program has no GUI - all of its functionality is accessed via options on the DOS command line. Various options have various numbers of optional parameters that must also be provided via the command line. The program will provide various status messages as it progresses, and will write error and warning messages to the usual PaleoGIS logging folder.

The advantage of a command line tool is that it can be scripted with DOS scripting tools, and set to run jobs in a batch-oriented way. These scripts can be written once, then run many times, at regular or irregular intervals, and they will produce the same results repeatedly.  

Below is a list of the existing command line options that are available to you.

Location:

C:\Program Files\<EIMT or Rothwell>\PaleoGIS\PaleoGISExternal.exe

Basic Format:

…/PaleoGISExternal.exe /<Command> <Argument1> <Argument2> ... <ArgumentN>

Making Batch Reconstructions:

To use PaleoGISExternal.exe to make batch reconstructions, there are 4 to 5 commands you need to know.  They must be called at specific times, and in a specific order for them to work correctly.

Speeding up reconstructions using a “flat” rotation table:

One way to speed up the reconstruction process (both interactive and batch) is to do all the pole calculations ahead of time, store them as a “flat” rotation table, and then read them from storage instead of recalculating them.  PaleoGISExternal.exe offers two related tools for doing the pole “pre-calculation”.

Reconstruction Script:

The best way to use this executable to perform batch reconstructions is to use the batch scripting capability that is built into DOS for handling command line programs like PaleoGISExternal.exe.  Some DOS scripting experience is definitely required to do this correctly and successfully.  To help accelerate the learning process, a sample batch script has been included below, with annotations to explain what each step means: annotations start with >>> and are in green bold font..  You will need to modify some of the parameters in the batch file to get this to work - simply cut and paste this text to a file on the disk, and edit it there.  You will have to delete all the annotations.

After making your edits and saving the batch script file, open a DOS window, change to the directory where you stored the batch file, and run it like this (but all on one line):

batch_reconstruction.bat

"<path to PaleoGISExternal.exe>"

"<source path with featureclass name>"

"<featureclass name>"

"<age of reconstruction>"

"<path of reconstruction file geodatabase to be created>"

"<Path to published model to use>"

"<name of setup table in published plate model>"

Example:

batch_reconstruction.bat         

"C:\Program Files\Rothwell\PaleoGIS\PaleoGISExternal.exe"                 

"C:\Temp\Reconstructions.gdb\cities"

"cities"

"30"

"C:\Temp\Reconstructions.gdb"

 "C:\Plate Models\UTPlates\Demo\2009_06_24\UTIG_demo.mdb"

 "T_Model_Settings"

>>> <<<<<<<<<<<<<<<<<<START OF BATCH RECONSTRUCTION SCRIPT>>>>>>>>>>>>>>>>

echo off

>>> Turns off extraneous messages to the DOS Window

REM

>>> Any line that starts with REM is a “Remark”, and will be ignored by DOS
REM %1% (first argument) - path to PaleoGISExternal.exe
REM %2% (second agrument) - source path with featureclass name

REM         ie. (c:\xxx\MyShape.shp  or c:\xxx\MyPGDB.mdb\fc_name)
REM %3% (third agrument) - featureclass name to use in cache
REM %4% (fourth agrument) - Age of reconstruction
REM %5% (fifth agrument) - path of reconstruction File Geodatabase to be created
REM %6% (sixth agrument) - Path to published model to use
REM %7% (seventh agrument) - Name of setup table in published plate model

REM

REM To do the reconstruction, you must call PaleoGISExternal.exe 4 times for each layer -

REM once to create the reconstruction mdb/xml, once to copy the layer to the cache, once to copy workspace

REM structure to recon mdb, and once to actually do the reconstructing

REM

REM If you have more than one layer to reconstruct to the same time, you can repeat the last 3 steps as many REM times as needed

REM

REM step 0: Save the arguments to this bast as local variables

REM

>>> Previous 18 line are simple documentation

set EXE=%1%

set SOURCE=%2%

set FC=%3%

set AGE=%4%

set RECONMDB=%5%

set MODELMDB=%6%

set MODELTABLE=%7%

set MODELNAME=BatchModel

set CACHE=%temp%\pgiscache.gdb

>>> Previous 9 line grab variables from the command line you provided, and makes local variables

>>> from them. We will later refer to this local variables as %EXE%, %SOURCE%, and so on.  These

>>> variables are provided once on the command line, then used in various combinations by all the

>>> steps in the process.  This step is required because as soon as another program runs, %1%,

>>> %2%, %3% are wiped out, so we need to preserve them

echo cleaning up some old files, if they are there (may produce file-not-found errors, which is ok)

>>> This is a message that the user will see

DEL /f /s /q %RECONMDB%

del /f /s /q %CACHE%

>>>Previous 2 lines will clean up old files, if present.  If not present, these command will throw an

>>> error but it is safe to ignore it

echo start reconstructing %SOURCE% to %RECONMDB%

>>> another user message

REM Step 1: Create the reconstruction MDB/XML

echo Creating reconstruction MDB/XML as %RECONMDB%

>>>Another user message

%EXE% /setup_for_reconstruction %MODELNAME% %MODELMDB% %MODELTABLE% %RECONMDB% %AGE% %CACHE%

>>> This step calls the first required option of the PaleoGISExternal.exe, using the local variables

>>> we recently saved.

REM Step 2: Cache the layer they want to reconstruct

echo Copying %SOURCE% to %FC%

>>>Another user message

%EXE% /copytocache_vector %SOURCE% %FC% "" %CACHE% %MODELNAME% %MODELMDB% %MODELTABLE%

>>Do the next step.

REM Step 3: Copy the workspace structure of the layer to reconstruct (no data)

echo Copying workspace structure for %FC% to %RECONMDB%

>>>Another user message

%EXE% /copy_workspace_structure %CACHE% %RECONMDB% %FC%

>>> Do the third step

REM Step 4: Do the actual reconstructing

echo Doing reconstruction of %FC% to %RECONMDB% for age = %AGE%

>>>Another user message

%EXE% /reconstruct_vector %FC% %RECONMDB% 1

>>> Do the final step.

echo done reconstructing %SOURCE% to %RECONMDB%

>>>Another user message
echo on

>>>Turn echo back on, since we turned it off last time.

>>> <<<<<<<<<<<<<<<<<<END OF BATCH RECONSTRUCTION SCRIPT>>>>>>>>>>>>>>>>

It is very common that users wish to make multiple calls to the external program in a loop.  DOS offers the “FOR” command that allows looping.  Type “FOR /?” at the DOS command for more information.

Product Support

The Rothwell Group, L. P. provides PaleoGIS product support for all users. For any questions concerning PaleoGIS, please contact us:

www.paleogis.com/support

support@rothwellgroup.com 

Appendix A:  ArcMap Skills

ArcMap Table of Contents

The ArcMap Table of Contents is the column of layers listed on the left side of the ArcMap main window.

In the above example, there are two data frames with three layers each.  “EarthByte_demo” is active, as indicated by the heading in bold.

Activating a Data Frame

1. Click to highlight the data frame heading and then right-click on the mouse.  The following menu will display.

2. Select Activate.  The data frame and its layers will then be activated.
3. You can also quickly activate data frames in ArcMap by holding down the ALT key and then left clicking on the data frame you wish to activate.

Setting Layer Properties in ArcMap

Setting Layer Visibility

In order for the PaleoGIS to work, one or more layers will need to be visible within the data frame. To change the visibility of a layer either check (visible) or uncheck (not visible) the check box to the left of the layer name in the Table of Contents.

Setting Display Units for a Layer

Note:  The default Unit of Measure for all layers in an ArcMap project is set to Degrees, Minutes, and Seconds.  

1. Select the data frame heading and right-click the mouse.  The following menu will display.

2. Select Properties and the Data Frame Properties window will display.

3. Select the General tab.
4. Under the Units section, click on the Display dropdown menu and select the desired Unit of Measurement in which the layer will be displayed.
5. Click OK.

Setting Selectable Layers

1. In the ArcMap Table of Contents, right click the layer that you want to limit selections to and select  Selection > Make This The Only Selectable Layer as show below:

Select Feature

To select a feature in a layer, click on the Select Features tool  in the ArcMap toolbar, then click on the feature to be selected.  By default, the selected feature will be highlighted in light blue.

Selecting more than one Feature in a Layer

1. While holding down the Shift key, use the Select Features tool to select the desired features.

OR

2. Using the Select Features tool, click and drag a box around the desired features.  When using this method, features that fall partially or wholly inside the box will be selected. Features will be selected from all of the currently selected layers.

Note:  To de-select the features, from the ArcMap toolbar click Selection > Clear Selected Features.

Note:  There are various other ways of selecting features in ArcMap, including selecting a feature by using shapes, finds, records, or a query.  For more information, go to the ArcMap help topic Selecting Features in a Layer.

Selecting Only One Feature in a Layer with Stacked Polygons

The PaleoGIS tools will require that only ONE feature is selected.  If multiple polygons are stacked in a layer, they will ALL be selected with the Select Features tool.  When this happens, a warning that more than one feature is selected will display.  In this case, use the attribute table to select the one desired feature.

1. Use the Select Features tool  to select the desired feature, then right-click on the layer in the table of contents.  The following menu will display.

2. Select Open Attribute Table and the attribute table for the selected layer will display as follows.

 Note:  The selected features will be highlighted.

3. Click on the Show selected records button  at the bottom of the table.  Now only the selected features will be shown in the table.
4. Click to highlight the desired feature from the table.  Only that feature will be selected in the layer.
5. Close the table.