©The Rothwell Group, L. P. 2011. All rights reserved.
PaleoGIS™ for ArcGIS™
The Rothwell Group, L. P.
PaleoGIS User’s Manual
Version 4.0
PaleoGIS User’s Manual Version 4.0
Basic Reconstruction Work-flow
Preparing for Reconstructions and/or Animations
Create a Second Data Frame For Holding Your Data
Reconstructing User Data Layers
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 Basic Functions Toolbar
Advanced Configuration Options
PaleoGIS Moving Functions Toolbar
PaleoGIS Data Frame Context Menu
Refresh Cache for Single Layer
Command Line Tool and Batch Scripting With PaleoGIS
PaleoGIS is a comprehensive collection of desktop tools allowing the user to create, display, and manipulate tectonic reconstructions directly from the ArcGIS user interface as an extension.
PaleoGIS allows the user to create a set of reconstructions with data that build upon and extend a default plate tectonic model. This application allows users to incorporate pre-existing data into a reconstruction, in which each reconstruction creates a labeled data frame in ArcGIS and each layer in the data frame can be saved or exported.
This documentation specifically refers to PaleoGIS 4.0 running on ArcGIS 10. If you are using a previous version of ArcGIS some of the content and all of the screenshots specific to ArcGIS functionality may not be accurate for the version you are using.
We can begin by looking at the most common work-flow 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 work-flow for doing this common task is described below. If you are unfamiliar with any ArcGIS terms used in this section, please reference the next section of this document called ArcGIS Skills.
First, make sure to turn on the PaleoGIS extension and at least the PaleoGIS Basic Functions Toolbar as described above in the Introduction to PaleoGIS section. Then open the Configuration window using the Configure Tool. You will see the PaleoGIS Configuration Options window below.
Select the desired plate model from the Select Model dropdown menu and press the Load Selected Plate Model button. The model will now be loaded into memory and the plate polygons will be loaded into the ArcMap table of contents.
You will notice, once you close the configuration window, that the top data frame in the table of contents has been given the name of the plate model that you just loaded. This data frame is the PaleoGIS “present day” (top) data frame because it now contains the present day version of the plate model polygons that you just loaded. Do not insert any other data frames above this one because PaleoGIS always performs reconstructions and animations on this top data frame. PaleoGIS will allow any additional data layers that you add to this present day data frame to be reconstructed as well.
It can be helpful to create a second data frame in the ArcMap table of contents while using PaleoGIS. This new data frame should be inserted below the present day data frame, NOT above it. This data frame can be used as a convenience to hold all the layers you are going to be working with on a regular basis.
To do this click on the Insert > Data Frame menu option as seen below.
Give the new data frame a descriptive name, like “My Data”. After renaming the data frame, use the standard ArcMap Add Data button to add any layers you would like to work with (shapefiles, geodatabase featureclasses, or imagery layers). Now you can simply drag and drop these layers from this new data frame into the top level “present day” data frame in order to perform a reconstruction with these data layers.
It is important to validate any data layers before performing reconstructions on them. This is important because this process will tell you if the layers are 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 seen below.
A window will be displayed showing the results of the validation. This window also contains a few paragraphs with tips for working with data layers in PaleoGIS. Please read these paragraphs carefully.
If the validation windows says that a layer is not a specified format, then you can right-click on that layer and choose the Data > Export Data option. This will allow you to create a copy of the data layer in a supported format. You can export the layer to a shapefile, or a featureclass in a Personal or File Geodatabase, which ever you feel comfortable with.
If the validation routine specifies that there are malformed geometries, then you will want to run the Repair Layer option in the PaleoGIS context menu. This option calls the ESRI Repair tool and should fix any problems with the data layer.
After ensuring that the data layers are valid, you are ready to reconstruct your data. In the Basic Functions Toolbar you can either select a geologic age from the Age drop down or enter an age directly. To execute the reconstruction, select the Go button.
PaleoGIS will display a number of windows as it processes the user data layers and the plate model polygons, and then display these reconstructed layers in a new data frame placed at the bottom of the table of contents.
It may be helpful to explain what PaleoGIS is doing when you press the Go button to do a reconstruction.
First, PaleoGIS compares the list of layers in the present day data frame to the list of layers in the cache file. Layers are added and/or deleted from the cache in order to synchronize the cache with the present day data frame. Regardless of what format the layers are in the present day data frame (SDE, shapefiles, etc.), the layers will be copied to the cache in the same format.
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 currently loaded 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. Now the user data layer is “coded” with the information necessary for PaleoGIS to reconstruct the its features back to a given geologic age.
It is important to understand that PaleoGIS is not directly reconstructing the data layers that are referenced in the present day data frame. PaleoGIS is reconstructing the copy of these layers that have been intersected with the plate model polygons in the cache.
You can perform this “caching” process explicitly by right-clicking on the present day data frame and choosing the the PaleoGIS > Refresh Cache option. 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. It is much more common for an error to occur during the very complex geoprocessing steps needed to copy the data layers to the cache and intersect them. This is why the validation step described above is of great importance.
Finally, if you have validated your data layers and refreshed the cache, you can perform a reconstruction or animation with high confidence that there are no geo-spatial or format issues that could cause errors.
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. 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.
The ArcGIS Table of Contents is the column of layers listed on the left side of the ArcGIS 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 Tools to work, a layer or layers will need to be activated within the data frame.
Note: The default Unit of Measure for all layers in an ArcGIS project is set to Degrees, Minutes, and Seconds.
To select a feature in a layer, click on the Select a Feature Tool in the ArcGIS 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 ArcGIS toolbar click Selection > Clear Selected Features.
Note: This differs from Selecting a Graphic with clicking and dragging the pointer. Only graphics that fall entirely within the box are selected.
Note: There are various other ways of selecting features in ArcGIS, including selecting a feature by using shapes, finds, records, or a query. For more information, go to the ArcGIS 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 Feature 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.
Reconstruction Tool: Sets the desired time of reconstruction.
Fixed Plate Tool: Sets the reference frame for reconstructions.
Clear Fixed Plate Tool: Clears the reference frame.
Animation Tool: Using an entered interval the Animation tool makes a series of reconstructions. Each reconstruction will be saved as an individual file that can be viewed individually or animated.
Quick Spin Tool: Using a specified point on the map, the Quick Spin Tool will re-center the map to the set point and set the project to a "view from space".
Configuration Tool: Is used to configure PaleoGIS.
Help Tool: 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 a plate model reconstruction to the geologic age of interest.
The Fixed Plate Tool is used to set the reference frame to a selected plate for a reconstruction. The effect is that the selected plate will not move from its present day position while everything else will move relative to its fixed position.
The Clear Plate Tool is used to clear the plate that was fixed.
The Animation Command is used to make a series of reconstructions through a specified time period. These reconstructions can then be animated to preview the reconstruction.
Note: 1 = 1 million years
Note: By default, these options will be automatically selected. To deselect, click in the checkbox to remove the checkmark.
The Quick Spin Tool is used to re-center the map on a selected point and resets the projection to a "view from space".
Note: This tool is used for viewing purposes only.
Note: The Project will remain as a "view from space" until the user chooses to change it using the ArcMap tools to change the reconstruction. This projection seems to have become slower with ever release of ArcGIS since 9.0. Please be aware that it can take time for the map to redraw.
PaleoGIS will first need to be configured to the data set being used before any reconstructing is done. These configurations will be saved automatically, so this exercise will only need to be performed once.
To access PaleoGIS Configuration, click on in the Basic Functions Toolbar and the following window will display:
If a published plate is not listed in the dropdown, it can be added to the list of available models.
Click the Advanced Options tab to access this window:
Click the Misc. Setting tab to access this window
This section documents the configuration settings included in PaleoGIS for ArcGIS. PaleoGIS is highly configurable in ways other than the default configuration. For a complete list of all the settings that can be found in the specified tables of the PaleoGIS Settings File (PaleoGIS_Setting.mdb file) please see the PaleoGIS Application Settings section of this documentation.
To access the application settings click the Applications Settings tab in the Configuration window and you will see the following:
PaleoGIS model settings can be accessed from the Model Settings tab in the Configuration window.
PaleoGIS registered models can be accessed from the Models tab in the Configuration window.
PaleoGIS timescales can be accessed from the Timescales tab in the Configuration window.
This tool links to this document on the internet or locally if an internet connection is not found.
Genealogist Tool: Allows the user to view a plate and all of the related plates (i.e. children).
Pole Finder Tool: Displays the latitude, longitude, and angle of rotation for a selected plate. It also displays the plate number, parent plate, map ref plate, and age.
Spin and Drop Tool: Allows the user to spin a selected plate with a three point pole of rotation.
Drag and Drop Tool: Allows the user to drag a selected plate(s) to a specific point.
Undo Last Move Tool: Allows the user to undo the last plate movement they made. There is no limit to the number of times the “undo” command can be issued.
Redo Last Move Tool: After a user has issued the “Undo Last Move” command, this tool allows them to redo that move. The “redo” command is only limited by the number of “undo” commands that have been issued.
Enter Pole Tool: Allows the user to enter new pole coordinates for a plate.
Pole Saver Tool: Allows the user to save poles of rotation for plates that have been moved.
Promotion Tool: Allows the user to save plate rotation data and can be promoted to a Master Table if the additional features of the model turn out to be valuable enough to disseminate widely. It also allows the user to apply other manipulations of pole sets (edit, delete).
Note: A reconstruction must first be done in order for the Plate Moving Functions Toolbar tools to work.
The Genealogist Tool is used to view a plate and all of its related plates (i.e. children) within a reconstruction dataframe.
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 a selected plate.
The Spin and Drop Tool is used to move a selected plate around a pole of rotation.
Note: Only ONE selected feature will activate the Moving Functions Toolbar. If more than one feature is selected, see the section on Select a Feature for selecting one feature with stacked polygons.
The Drag and Drop Tool is used to offset the position of selected plate(s) to a new position.
Note: More than one plate may be selected. If only one polygon needs to be moved, see the section on Select a Feature for selecting one feature with stacked polygons.
The Enter Pole Tool allows the user to enter new pole coordinates to create a new reconstruction.
Note: A reconstruction must first be done in order for the Plate Moving Functions Toolbar tools to work.
Note: Only ONE selected feature will activate the Moving Functions Toolbar. If more than one feature is selected, see the section on Select a Feature for selecting one feature with stacked polygons.
The Pole Saver Tool is used to save poles of rotations after they have been calculated.
Note: Step one will only occur if the Application Setting EDIT_SKIP_PLATE_LIST is set to FALSE. The default setting is TRUE.
The Promotion Tool allows the user to save, move, delete, and edit plate rotation data. This data can be either discarded or moved (promoted) to another sub-table or the Master Table.
Note: The Master Table includes all of the original published rotation data, and should rarely be altered.
The PaleoGIS Analysis Toolbar is used to perform one of three types of analysis on a plate model:
Note: This toolbar can be extended with proprietary analysis tools. Please contact The Rothwell Group, L. P. for details.
Note: A reconstruction must first be done in order for the Plate Moving Functions Toolbar tools to work.
The PaleoGIS Analysis Toolbar is used to perform one of four types of analysis on a plate model:
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. This tool operates on a present day map (not on reconstructed maps). The position, azimuth and speed of the point is calculated for each step interval from present to past.
This type of analysis can be used to spot rapid changes in azimuth and unreasonable movement rates which can indicate errors in the plate model. However, if the changes in azimuth and/or rate are real, these changes can have dramatic effects on basins where the oils are forming, being trapped, etc.
This type of analysis begins on a reconstruction where a user-defined grid interval (normally four degrees) and a user-defined age delta (usually 100,000 years) are entered. A regularly-spaced grid of points at the specified grid intervals is generated where all of the points are assigned to a plate. All of the points are reconstructed to the time of the original reconstruction and then reconstructed again to a slightly older or younger time based upon the entered age delta. The positions of the points are then compared and the results are used to create a map layer in which those points use arrow symbology to indicate the direction and relative speed of movement of each point.
Using this analysis can illustrate the "instantaneous" stress affecting the plates. By comparing the motion between plates, the relative motions can be inferred (colliding, diverging, translation, trans-tension, and/or transpression).
This tool operates much the same as the Azimuth and Rate vs. Time tool, where the position of a single point is calculated back through time and then the direction and rate of motion is calculated. However, instead of creating a set of graphs, a line will be drawn on the map showing the path of the point through time. The thickness of the line is a function of how fast the plate was moving at a given time. The starting point of the line will be the present day location of the point that is entered for the analysis, and the end of the line will be its position at the oldest analysis step. Like the Azimuth and Rate vs. Time tool, this tool operates on a present day map (not on reconstructed maps).
Using this analysis is useful for the same reasons as Azimuth and Rate vs. Time but this provides a different way to view and understand the data.
This tool presents an array of useful tools that make calculations commonly used by power users: pole addition, point rotation, great circle distance calculation, and pole position calculation. Once this tool has been activated, it will stay available. A Power user can activate this tool and drag its window over to a second monitor, where it can stay open and functional, to be called whenever it is needed.
Selecting items on the data frame Context Menu causes PaleoGIS to execute the following actions:
This function allows a user to save all the data layers shown in a reconstruction to a new directory for permanent storage. Until that is done, the layers are only stored in a “scratch directory.” After clicking Save Reconstruction the data is saved in a personal geodatabase along with layer files that will render the data with whatever symbology was assigned to the reconstruction.
This function allows the user to export the entire data frame to ArcGlobe, assuming the user has ArcGlobe installed. Once the data is exported, ArcGlobe will open and show the data.
NOTE: For best results make the following changes to your ArcGlobe application before using the Export to ArcGlobe tool:
In the main menu select Customize > ArcGlobe Options as seen below:
Next go to the Messages tab and make sure the option to “Use wizard when adding a new layer” is NOT selected as seen below:
This tool allows the user to refresh the cached data for all the layers in a data frame. It will copy that data to the cache. When attributes are changed for features in the “Present Day” map (the first data frame), the attributes will not be updated in the cached data; it is important to refresh that data to make sure the cache is up-to-date. Normally, PaleoGIS manages the cache automatically, but in the case of attribute and feature edits it does not.
This tool allows the user to clear 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. It is important to first run the Save Reconstruction tool to save any reconstructions that the user wishes to preserve. 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.
Allows the user to validate all the layers in a data frame to make sure they are compatible with PaleoGIS. Sometimes a user will try to reconstruct data that is improperly formatted or contains malformed geometries. This tool will make sure all layers are usable within PaleoGIS.
Selecting items on the Layer Context Menu causes PaleoGIS to execute the following actions:
This tool allows the user to refresh one layer in a data frame. It will copy that data to the cache. When attributes are changed for features in the “Present Day” map (the first data frame), the attributes will not be updated in the cached data; it is important to refresh that data to make sure the cache is up-to-date. 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, 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.
NOTE: If is also possible to add features directly to a reconstructed layer in the reconstructed map, and then un-reconsructed 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-reconstruct results for the 3 layers shown above looks like this:
Allows the user to validate a single layer in a data frame to make sure it is compatible with PaleoGIS. Sometimes a user will try to reconstruct data that is improperly formatted or contains malformed geometries. This tool will make sure that layer is usable within PaleoGIS.
Allows the user to repair a single layer in a data frame. Sometimes a user will try to reconstruct data that is improperly formatted or contains malformed geometries. This tool will attempt to fix any geometry errors (i.e. null geometry, crossover polygons, etc.) so the layer will work within PaleoGIS.
Allows the user to preprocess a single raster layer prior to doing a reconstruction or animation. 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 parts are then placed in the PaleoGIS cache so they can be used by the reconstruction and animation tools. This tool will perform just this first step and will keep the fragments in the cache as long as the Cache raster fragments option is checked in the configuration window. Once the raster has been “cookie cut” into fragments using this tool, you can do any number of reconstructions and animations without “cookie cutting” it again.
This section documents the configuration settings included in PaleoGIS for ArcGIS. 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. |
APPEND_DISPLAY_LAYERS | No | TRUE | FALSE | When a plate model is loaded from the configuration GUI, by default, the ArcMap Table of Contents will be cleared before loading the plate model. If this value is true, the TOC is not cleared. This value sets the default for the “Don’t remove layers in the table of contents...” option in the Configuration window “Basic 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 it is an empty string, then the cache is virtual (in memory). If it 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. 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. |
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 during drag/drop” option in the Configuration window “Advanced Options” tab. |
DO_MULTI_PROCESS | No | TRUE | FALSE | This option allows PaleoGIS to reconstruct multiple vector layers in parallel by using an external process to reconstruct each featureclass layer in the present day dataframe. This option is only useful if you are working on a multi-CPU computer. Only use this option if the number of layers you wish to reconstruct is not greater than the number of CPUs in the computer. This option is also controlled by the “Advanced Options” tab of the configuration window. Setting this value sets the default value in the GUI. |
DO_TIMESCALE_CONVERSIONS | No | TRUE | FALSE | When a plate model is loaded from the configuration GUI, by default, the ArcMap table of contents will be cleared before loading the plate model. If this is true, the TOC is not cleared. This option is also controlled by the “Basic Options” tab of the configuration window. Setting this value sets the default value in the GUI. |
EDIT_SKIP_PLATE_LIST | No | TRUE | TRUE | When performing plate model pole-of-rotation edits using the Plate Moving Functions 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. |
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_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. |
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. |
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 |
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. |
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. |
VERSION | No | 4.0.4 | 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 Metadata Settings
In several cases, PaleoGIS uses the layer metadata functionality in ArcGIS to change the way a layer is processed. Using this functionality is normally done by people who construct plate models, rather than normal users. PaleoGIS looks for certain keywords in the “Purpose” field o "f a layer’s metadata, and if it is found, processes that layer in a different way. There can be any other text in the “Purpose” field, so this does not preclude using the “Purpose” field as it was intended, but PaleoGIS expects to find it’s keywords somewhere within the field, and expects to find it on a line by itself.
Keyword | Action |
CACHE_IGNORE_DEF_QUERY | Putting this keyword in the metadata causes PaleoGIS to copy the ENTIRE dataset to the cache, rather than just what is visible on the present day map. This is useful when a definition query has been placed on a layer to cause it to just show present day data on the present day map, but the actual data set contains data that is also specific to other times. This option will cause all the data to be stored in the cache, then the automatic “age of appearance / age of disappearance” functionality to operate on the entire data set in the cache, and only the appropriate data will be reconstructed. |
TIME_DEPENDANT_COPY_TABLE_SQL= SQL query (Syntax note: There cannot be a space between ...TABLE_SQL and the equals sign, i.e., the correct syntax is ...TABLE_SQL= , not ...TABLE_SQL =) | Putting this keyword along with an SQL query in a joined table allows “time-dependant joins” to occur. PaleoGIS will preserve feature-to-table joins when it makes reconstructions. This works well with one-to-one joins, but not well for one-to-many joins, where the one-to-many joins are there because of time, and for any one particular time, the one-to-many devolves to a one-to-one join. Think of the stratigraphy in a well - a vertical well is represented by a single point, but a stratigraphy database has many rows related to that one point, and for any one reconstruction time, a maximum of only one row in the stratigraphy table should be related to the well point. By using this keyword/SQL query string pair with the table that joined, the PaleoGIS will use the SQL query to reduce the data that will be joined, usually based on the time of the reconstruction. In order for this to work, the SQL must have a replaceable parameter that will customize the SQL query on the fly. The replaceable keywords are: %AGE%: Age of reconstruction %PM%: Plate Model name %RF%: Reference Frame plate number Example: TIME_DEPENDANT_COPY_TABLE_SQL= StratAge = %AGE% ...for a reconstruction age of 100.5Ma this example will cause the PaleoGIS to pre-filter a joined table by 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). |
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:
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, then just 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 9but 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 settings 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 Rothwell Group, L.P. www.paleogis.com