©The Rothwell Group, L. P. 2013. All rights reserved.
PaleoGIS™ for ArcGIS™
The Rothwell Group, L. P.
PaleoGIS User’s Manual
Version 4.2
Table of Contents
Supported Data Types for Use in PaleoGIS
Basic Reconstruction Work-flow
Preparing for Reconstructions and/or Animations
Add User Data to be Reconstructed
PaleoGIS: Basic Functions Toolbar
Advanced Configuration Options
PaleoGIS: Plate Model Tools Toolbar
Saving Symbology to the Plate Model Geodatabase
Viewing or Deleting Existing Plate Model Symbology
PaleoGIS Data Frame Context Menu
Refresh Cache for Single Layer
Preprocess Raster (warp raster reconstruction method only)
Using PaleoGIS with a Proxy Server
Command Line Tool and Batch Scripting With PaleoGIS
Setting Layer Properties in ArcMap
Setting Display Units for a Layer
Selecting more than one Feature in a Layer
Selecting Only One Feature in a Layer with Stacked Polygons
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.
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.
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.
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.
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.
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.
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.
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.
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.
This is the most commonly used tool in PaleoGIS. It is used to perform plate model reconstructions to the geologic age of interest.
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.
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.
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.
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.
Resets the reference frame to the default value.
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.
The Quick Spin tool changes the map projection to "The World From Space", and then re-centers the map to a specified point.
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.
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:
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
Adding (Registering) a Plate Model in PaleoGIS
Plate models can be added to PaleoGIS using the following procedure:
Removing (Unregistering) a Plate Model from PaleoGIS
Timescale Options
Configuration Database Location
Gives the path to the Access database that contains all PaleoGIS application settings.
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
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.
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.
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.
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.
The Models tab provides a list of registered plate models and their source locations.
The Timescales tab provides a list of the alternate timescales available with PaleoGIS and their source locations.
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.
The Genealogist tool is used to view the sub-plates (i.e. child plates) for a specified plate within a reconstruction data frame.
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.
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.
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.
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.
The Spin and Drop tool is used to rotate a selected plate into a new position.
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.
The Drag and Drop tool is used to linearly offset the position of a selected plate to a 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.
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.
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.
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.
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.
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.
The Pole Set Maintenance tool allows the user to save, move, delete, and edit plate rotation data within the currently loaded plate model.
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.
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.
The PaleoGIS Analysis Toolbar provides access to the following analysis tools:
speed and direction of motion for all plates at that time.
Note: Custom proprietary analysis tools can be added to this toolbar for additional functionality. Please contact The Rothwell Group, L. P. for details.
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.
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).
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.
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.
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.
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.
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.
Note: For the best results, make the following changes to your ArcGlobe application before using the Export to ArcGlobe tool:
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.
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.
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.
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.
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.
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.
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:
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.
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.
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.
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.
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.
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.
Setting | Required | Example | Default | Function |
ADD_UNIQUE_ID | No | TRUE | FALSE | Adds a unique numeric ID field called “PaleoUniqueId” to the attribute tables of all vector layers when they are copied to the cache. This field is then persisted to the reconstructed and animated layers. This is useful if you want to trace the lineage of a reconstructed feature back to the present day feature. This value sets the default for the “Add unique ID to cache” option in the Configuration window “Advanced Options” tab. |
ATB_AFTER_FC_RECON | No | ToolboxName|ToolName | “” | If this value is set to valid “Toolbox Name|Tool Name” pair, the PaleoGIS will run that Toolbox tool after each layer in the TOC is reconstructed. That tool can be a out-of-the-box ESRI tool, or a user-created tool. By default, no tool is run. |
ATB_AFTER_RECONSTRUCTION | No | ToolboxName|ToolName | “” | If this value is set to valid “Toolbox Name|Tool Name” pair, the PaleoGIS will run that Toolbox tool after a reconstruction is completed. That tool can be a out-of-the-box ESRI tool, or a user-created tool. By default, no tool is run. |
ATB_APP_STARTUP | No | ToolboxName|ToolName | “” | If this value is set to valid “Toolbox Name|Tool Name” pair, the PaleoGIS will run that Toolbox tool at PaleoGIS extension startup time. That tool can be a out-of-the-box ESRI tool, or a user-created tool. By default, no tool is run. |
ATB_BEFORE_FC_RECON | No | ToolboxName|ToolName | “” | If this value is set to valid “Toolbox Name|Tool Name” pair, the PaleoGIS will run that Toolbox tool before each layer in the TOC is reconstructed. That tool can be a out-of-the-box ESRI tool, or a user-created tool. By default, no tool is run. |
ATB_BEFORE_RECONSTRUCTION | No | ToolboxName|ToolName | “” | If this value is set to valid “Toolbox Name|Tool Name” pair, the PaleoGIS will run that Toolbox tool before a reconstruction is completed. That tool can be a out-of-the-box ESRI tool, or a user-created tool. By default, no tool is run. |
ATB_COOKIE_CUTTER | Yes | Analysis Tools|Intersect | Analysis Tools|Intersect | This value must be set to a valid “Toolbox Name|Tool Name” pair for using to intersect the Display layers with a “cookie cutter” layer. This is an essential part of performing reconstructions. |
ATB_DELETE | Yes | Data Management Tools|Delete | Data Management Tools|Delete | When PaleoGIS needs to delete a featureclass, it calls this toolbox tool. Users can change to a different tool if needed, but this is not advisable. |
ATB_DISSOLVE | Yes | Data Management Tools|Dissolve | Data Management Tools|Dissolve | When PaleoGIS needs to do a dissolve on a featureclass, it calls this toolbox tool. Users can change to a different tool if needed, but this is not advisable. |
ATB_FC_COPY | Yes | Conversion Tools|FeatureClassToFeatureClassas | Conversion Tools|FeatureClassToFeatureClassas | When PaleoGIS needs to do a copy on a featureclass, it calls this toolbox tool. Users can change to a different tool if needed, but this is not advisable. This method of copying is obsolete but still moderately in use. |
ATB_GROUP_FC_COPY | No | Conversion Tools|FeatureClassToGeodatabase | Conversion Tools|FeatureClassToGeodatabase | This method of copying is obsolete in PaleoGIS, but should be left in the table for backwards compatibility. |
ATB_GROUP_RASTER_COPY | No | Conversion Tools|RasterToGeodatabase | Conversion Tools|RasterToGeodatabase | This method of copying is obsolete in PaleoGIS, but should be left in the table for backwards compatibility. |
ATB_MOSAIC | Yes | Data Management Tools|Mosaic | Data Management Tools|Mosaic | This method is used for one step in raster reconstruction. Users can change to a different tool if needed, but this is not advisable. |
ATB_RASTER_COPY | Yes | Data Management Tools|Resample | Data Management Tools|Resample | This method is used for one step in raster reconstruction. Users can change to a different tool if needed, but this is not advisable. |
ATB_RASTER_WARP | Yes | Data Management Tools|Warp | Data Management Tools|Warp | This method is used for one step in raster reconstruction. Users can change to a different tool if needed, but this is not advisable. |
ATB_RENAME | Yes | Data Management Tools|Rename | Data Management Tools|Rename | When PaleoGIS needs to rename a featureclass, it calls this toolbox tool. Users can change to a different tool if needed, but this is not advisable. |
ATB_REPAIR_GEOMETRY | Yes | Data Management Tools|RepairGeometry | Data Management Tools|RepairGeometry | When PaleoGIS needs to repair the geometry of a vector featureclass, it calls this toolbox tool after asigning plate codes. Users can change to a different tool if needed, but this is not advisable. |
ATB_SHOW_TOOLBOX_WINDOW | Yes | FALSE | Required for correctly displaying all ArcToolbox Tools that are run. Do not change. | |
ATB_SHOWPROGRESS | Yes | TRUE | Required for correctly displaying all ArcToolbox Tools that are run. Do not change. | |
ATB_VALIDATE | Yes | FALSE | Required for correctly displaying all ArcToolbox Tools that are run. Do not change. | |
CACHE_PATH | Yes | C:\Temp\PaleoGIS\cache.mdb | %TEMP%\cache.mdb | This value sets the type and path of the cache. If the path ends in .MDB, then it is a personal geodatabase. If it ends in .GDB, then it is a file geodatabase. This value can also be set and saved through the “Misc. Settings” tab in the Configuration window. This value sets the default for this option in the Misc. Settings tab. |
CACHE_RASTER_FRAGMENTS | No | TRUE | FALSE | This option is useful if you plan on doing a lot of raster reconstructions using the warp method. Performance is increased when performing more than one reconstruction or animation using this option. See the detailed description of this tool above in order to understand exactly what this option does. This value sets the default for the “Cache raster fragments” option in the Configuration window “Advanced Options” tab. This setting is obsolete in ArcGIS 10.3 and 10.3.1 but it may still exist in the settings table with no effect on functionality. |
CACHE_ROTATION_TABLES | No | TRUE | FALSE | This option makes a copy of the plate model rotation tables in the local cache so that PaleoGIS will be able to work from the cached copy during reconstructions. This option is useful for increasing performance when the plate model is stored in a remote network location instead of on the local machine. |
CRS_CAN_RECONSTRUCT_0 | No | TRUE | FALSE | No longer in use. |
CRS_IGNORE_AGES | No | TRUE | FALSE | This option makes it such that any reconstructions and animations will ignore the “appearance” and “disappearance” fields in the plate model and any user data layers. This means that regardless of the reconstruction age, all plate model features and all user data features that intersect a plate polygon in the plate model will be reconstructed and displayed in a reconstruction or animation. This value sets the default for the “Ignore assigned ages” option in the Configuration window “Advanced Options” tab. |
CRS_IGNORE_CHILDREN | No | TRUE | FALSE | This option is pertinent when using the Moving Functions Toolbar only. This option removes the linkage between a parent plate and its children when using the Drag and Drop and the Spin and Drop tools. This option does not affect reconstructions and animations. This value sets the default for the “Ignore children” option in the Configuration window “Advanced Options” tab. |
EDIT_SKIP_PLATE_LIST | No | TRUE | TRUE | When performing plate model pole-of-rotation edits using tools from the PaleoGIS: Plate Model Tools toolbar, if this option is set to TRUE, the user must save the edits (using the Pole Saver tool) for a given plate before to poles for another plate can be edited. If this option is set to FALSE, multiple plates can be edited before saving, and then when the Pole Saver tool is clicked. A list of Poles to Save will be displayed, and each edited pole can be saved at that time. |
EXCEPTION_CONTACTINFO | Yes | The Rothwell Group, L.P. at PaleoGIS@RothwellGroup.com | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_DEFAULTDOMAIN | Yes | paleogis.com | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_DISPLAYDIALOG | Yes | TRUE | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_EMAILSCREENSHOT | Yes | FALSE | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_EMAILTO | Yes | paleogis@rothwellgroup.com | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_IGNOREDEBUG | Yes | FALSE | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_KILLAPPONEXCEPTION | Yes | TRUE | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_LOGTOEVENTLOG | Yes | FALSE | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_LOGTOFILE | Yes | TRUE | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_SENDEMAIL | Yes | FALSE | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_SMTPSERVER | Yes | NONE | Set by Rothwell, do not change unless directed by support staff | |
EXCEPTION_TAKESCREENSHOT | Yes | TRUE | Set by Rothwell, do not change unless directed by support staff | |
HELP_PATH | Yes | http://www.paleogis.com/dotnetnuke/UsersManual/tabid/56/Default.aspx | Set by Rothwell, do not change unless directed by support staff | |
HELP_PATH_LOCAL | Yes | PaleoGIS_User_Manual.pdf | PaleoGIS_User_Manual.pdf | Name of the local copy of the User’s Manual installed with PaleoGIS in the PaleoGIS installation folder, usually at C:\Program Files (x86)\Rothwell\PaleoGIS. |
IGNORE_REPAIR_FEATURES | No | FALSE | FALSE | Setting this option to TRUE, can improve 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. This value sets the default for the “Skip repairing features” option in the Configuration window “Advanced Options” tab. |
IN_MEMORY_RASTER | Yes | TRUE | TRUE | Use the pixel raster reconstruction algorithm (true) or the warp raster reconstruction algorithm (false). |
INCLUDE_AGE_IN_MAP_LABEL | No | TRUE | TRUE | When PaleoGIS finishes a reconstruction, it places a multi-part label on the map - this option controls the geologic age (numeric, in Ma) part of the label. This value sets the default for the “Include geological time text in map label” option in the Configuration window “Basic Options” tab. |
INCLUDE_PLATEMODEL_IN_MAP_LABEL | No | TRUE | TRUE | When PaleoGIS finishes a reconstruction, it places a multi-part label on the map - this option controls the plate model part of the label. This value sets the default for the “Include plate model name in the map label...” option in the Configuration window “Basic Options” tab. |
INCLUDE_RELATIVETO_IN_MAP_LABEL | No | TRUE | TRUE | When PaleoGIS finishes a reconstruction, it places a multi-part label on the map - this option controls the “relative to” (if a reference plate has been fixed) part of the label. This value sets the default for the “Include [Relative to...]...” option in the Configuration window “Basic Options” tab. |
INCLUDE_TIMESCALE_IN_MAP_LABEL | No | TRUE | FALSE | When the PaleoGIS finishes, it places a multi-part label on the map - this option controls the geologic age name (e.g., “Berriasian”) part of the label. This value sets the default for the “Include timescale text in map label” option in the Configuration window “Basic Options” tab. |
LAST_USED_MODEL | No | Demo UTIG Plates Model | Demo UTIG Plates Model | Holds the name of the last model used so it can be automatically loaded it in the next PaleoGIS session. |
LAST_USED_REFERENCE_FRAME | No | 0 | 0 | Holds the plate code for the last used reference frame. |
LAST_USED_TIMESCALE | No | DNAG | DNAG | Holds the name of the last used timescale. |
LAST_USED_TIMESCALE_SORT | No | Age | Age | Holds the name of the last used timescale sort method. |
LOG_LEVEL | Yes | INFO, ERROR, or WARN | ERROR | Set by Rothwell, do not change unless directed by support staff |
LOGFILE_PATH | Yes | C:\Temp\PaleoGIS\PaleoGIS_Log.txt | %USERPROFILE%\PaleoGIS_Log.txt | Set by Rothwell, do not change unless directed by support staff |
MAKE_LABEL_EDITABLE | No | True | True | Allows user to move or edit the label that is automatically placed on the map after reconstruction. |
PG_ANALYSIS_1 PG_ANALYSIS_2 PG_ANALYSIS_3 PG_ANALYSIS_X... | Yes | Azimuth & Rate vs. Time|AzimuthAndRateExt.DLL#AzimuthAndRateExt.AzimuthAndRateExt | “” | Set by Rothwell, do not change unless directed by support staff |
PROXY_SERVER_BYPASSEXPECT100 | NO | TRUE | TRUE | This setting is required to be TRUE by most proxy servers for proper connection to the PaleoGIS license server. For more information contact your IT department. This setting sets the default for the “Bypass Expect100Continue header” option in the Configuration window “Misc. Options” tab. This option will only be visible in the “Misc. Settings” tab when the PROXY_SERVER_SETTINGS_SHOW setting is set to TRUE. |
PROXY_SERVER_SETTINGS_SHOW | NO | TRUE | NA | If you are using a concurrent PaleoGIS license and you cannot connect to the PaleoGIS license server because of firewall issues, add this setting to the PaleoGIS Settings File, either directly or by adding it to the table in the Configuration window “Application Settings” tab, and set the value to TRUE. This will make a Proxy Server Information form visible in the Configuration window “Misc. Settings” tab. Fill in your proxy server information in the form to allow PaleoGIS to connect through the firewall. |
RASTER_PIXELPERMINUTE | RASTER_Yes | 20000 | 20000 | The processing rate for the last raster reconstruction. Used for estimating the length of the next raster reconstruction. |
RASTER_PLATECOUNT | Yes | 130 | 130 | The number of plates overlapping the last raster reconstruction. Used for estimating the length of the next raster reconstruction. |
RASTER_POSTPROCPIXELPERMINUTE | Yes | 10000 | 10000 | The processing rate for the last raster reconstruction that had the post processing option enabled. Used for estimating the length of the next raster reconstruction. |
SCRATCH_DIRECTORY | Yes | C:\Temp\PaleoGIS\ | %TEMP%\ | Sets the output directory for all PaleoGIS output files. This value can also be set and saved through the “Misc. Settings” tab in the Configuration window. This value sets the default for this option in the Misc. Settings tab. |
TIMESLICE_ENABLED | Yes | TRUE | Determines if timeslice layers are enabled. | |
VERSION | No | 4.2 | Value depends on the current version. | Set by Rothwell, do not change unless directed by support staff |
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
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 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.
Keyword | Action |
CACHE_IGNORE_DEF_QUERY | This keyword causes PaleoGIS to copy the ENTIRE dataset to the cache, even if only a subset of the data is visible in the present day map due to a definition query. Normal PaleoGIS functionality based on appearance and disappearance ages will then act on the data in the cache causing the appropriate data to be reconstructed for specific ages and appear in the reconstruction results. This feature is useful when the data set contains data for various ages, but it is desirable to only display the present day data on the present day map. In order for this functionality to work correctly, the dataset must contain Appearance and Disappearance columns that are populated to define the existence of the dataset features based on age. |
TIME_DEPENDENT_COPY_TABLE_SQL= SQL query | Putting this keyword along with an SQL query in a joined table allows PaleoGIS to support “time-dependent joins”. PaleoGIS normally preserves feature class-to-table joins during reconstructions, which works well with one-to-one joins, but doesn’t work for one-to-many joins. A common need for one-to-many joins is to represent the evolution of well stratigraphy over time: a vertical well is represented by a single point on the map, but this point can be joined to a stratigraphic database that details the age dependent composition of the well. By using the TIME_DEPENDENT_COPY_TABLE_SQL setting with an appropriate SQL query, PaleoGIS will perform a one-to-many join during reconstructions by joining the well point with the row from the stratigraphic database that corresponds to the reconstruction age. In order for this keyword to work, the SQL must contain a replaceable parameter that will customize the SQL query on the fly. The available replaceable parameters are: %AGE%: Age of reconstruction %PM%: Plate Model name %RF%: Reference Frame plate number Example: TIME_DEPENDENT_COPY_TABLE_SQL= StratAge = %AGE% For a reconstruction age of 100.5Ma this example will cause PaleoGIS to filter a joined table using the query “StratAge = 100.5” These SQL queries can get as complicated as needed in order to produce the required result - they just need to be valid SQL (once the replaceable keyword substitutions have been made). |
TIMESLICE_APPEARANCE | Deprecated. |
TIMESLICE_DISAPPEARANCE | Deprecated. |
TIMESLICE_REFERENCE_FRAME | Deprecated. |
NO_DELETE_AFTER_RECONSTRUCTION | Deprecated. |
NO_CACHE | Deprecated. |
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.
Command | Arguments | Description |
/Setup_For_Reconstruction | "model name" - the name of the plate model. "path to model MDB"- the complete path to the plate model. “Model settings table" - the name of the table in that model MDB that contains the rest of the settings from that model. “Destination geodatabase” - the full path to the reconstruction geodatabase where the reconstructed data will be stored. “Age of reconstruction” - Age of the reconstruction in millions of years, positive is older. “Cache path” - the full path to the cache. | To do a batch reconstruction, you must call this option once for each age you wish to reconstruct. This is normal done once, before any other steps. This option creates the reconctruction MDB, and an XML file containing all the details of the plate model needed by the next step in the process. |
/CopyToCache_Vector | “Layer Path” - Full path of the layer to copy to the cache. Can be shapefile or geodatabase featureclass. In the case of a a layer in a geodatabase, the path is specified as “path to mdb”\”name of layer”. “Name in Cache” - the name the layer will have in the cache. "Query String" - SQL query that allow you to limit the amount of data to be cached based upon an attribute query. Can also be “” to cache all features. “Cache path” - the full path to the cache. | To do a batch reconstruction, you must call this option once for each layer you wish to reconstruct. This option copies your layer into the cache. This step must be carried out after /Setup_for_reconstruction, but before /copy_workspace_structure. |
/Copy_Workspace_Structure | “Cache path” - the full path to the cache. “Destination geodatabase” - the full path to the reconstruction geodatabase where the reconstructed data will be stored. “Layer name” - the name of the layer in the cache whose structure will be copied. {Optional} “New name in Reconstruction MDB” - the name that the layer will have in the reconstruction geodatabase. Default is same name. | To do a batch reconstruction, you must call this option once for each layer you wish to reconstruct. This option copies the structure (attribute table layout) of your layer to the reconstruction MDB, but does not copy the data. That is done in the next step. This step must be carried out after /CopyToCache_Vector, but before /Reconstruct_Vector or /Reconstruct_raster |
/Reconstruct_Vector | “Name of Layer in Cache” - the name of the layer to be reconstructed, as it was stored in the cache. “Reconstruction Geodatabase” - fuull path to the reconstruction geodatabase in which the reconstructed data will be stored. “Process ID” - any user supplied number that will identify the process. {Optional} “New Name in Reconstruction MDB” - the name that the layer will have in the reconstruction geodatabase. Default is same name. | To do a batch reconstruction, you must call this option once for each vector layer you wish to reconstruct. This option reconstructs the actual vector data and copies it to the reconstruction MDB. This step must be carried out after /Copy_Workspace_Structure, but before /AddLayerToMxdAndSymbolize |
/AddLayerToMxdAndSymbolize | “MXD Path” - full path to MXD to be edited. If it does not exist, it is created. “Name of data frame” - name of data frame in MXD to which the layer will be added.If it does not exist, it is created. “Data Path” - full path of the layer to be added. It can be a shapefile, or a featureclass in a geodatabase. In the case of a a layer in a geodatabase, the path is specified as “path to mdb”\”name of layer”. “Layer Name” - Name of layer as it should appear in the TOC. “Layer File” - full path to a layer file that should be used to symbolize data. {Optional} “Group Layer” - If you want to embed the layer in a group layer, specify it with this argument. If the group layer does not exist, it will be created. If you want to embed it further, seperate the group layers with a “\”, like this: GroupLayer\SubGroup\SubSubGroup | This is a optional tool that will open an MXD and add a specified layer to a data frame in it. This is useful for visualizing a layer after reconstruction. |
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”.
Command | Arguments | Description |
/Dump_Flat_rot_header | “path to MDB” - the full path to the MDB that will be updated. “name of the table” - the name of the table to create. | This tool adds a blank, correctly formatted table to an MDB. If it is already there, it will not touch it. |
/Dump_Flat_rot | "model name" - the name of the plate model "path to model MDB"- the complete path to the plate model “Model settings table" - the name of the table in that model MDB that contains the rest of the settings from that model "reference frame plate number" - the plate number for the reference frame you wish to flatten on - almost ALWAYS 0 "Start Age in Ma" - the age in Ma when you want this calculation to start. "End Age in Ma" - the age in Ma when you want this calculation to end. "Increment in Ma" - the increment age in Ma to step between start and end. | This tool stores the “flat” rotation data in the previously created table. The user specifies the destination, the plate model, the reference frame, start age, end age, and the step interval, and this tools calculates all the “flat” poles for ALL the plates in the model. Note that it is possible to specify overlapping time ranges, which would incorrectly store duplicate poles. If this tool is called more than once to write to the same flat rotation table, make sure not to overlap time ranges. |
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.
The Rothwell Group, L. P. provides PaleoGIS product support for all users. For any questions concerning PaleoGIS, please contact us:
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.
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.
Note: The default Unit of Measure for all layers in an ArcMap project is set to Degrees, Minutes, and Seconds.
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.
OR
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.
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.
Note: The selected features will be highlighted.
The Rothwell Group, L.P. www.paleogis.com