GeoTrace

GeoTrace is a a QGIS plugin containing some helpful tools for extracting and analysing the orientations of geological structures. It can be used to rapidly digitize structural traces in raster data, estimate their 3D orientations using an associated DEM, and then visualise the results on stereonets and rose diagrams.

The trace extraction method (Trace tab) uses a least-cost path algorithm to "follow" linear features in the raster. This relies on a single-channel cost raster in which the structures of interest are represented by low values, and the background by high values. A variety of functions for quickly calculating such a cost function have been included in the Cost Calculator tab.

Installation

The plugin can be in two ways.

1. The prefered option is to use the QGIS plugin repository as this will retrieve the most recent stable version of the plugin. To do this use the plugin manager in QGIS and select experimental plugins.
2. Clone (or download and unzip) the GeoTrace directory into your QGIS plugin path.
   • On windows, this path will be something like C:/Users/USERNAME/AppData/Roaming/QGIS/QGIS3/profiles/default/python/plugins. Note that you may need to create the plugins folder.
   • On Linux the plugin can be cloned to any directory and then the relevant files are copied to the correct locations using the by running the command 'make deploy'

     Dependencies

     GeoTrace uses Numpy, Matplotlib, mplstereonet and scikit-image. QGis should come bundled with Numpy and Matplotlib.

The other dependencies should be automatically downloaded and installed the first time GeoTrace is run (at least on Windows and Linux). If this automatic install doesn't work then the plugin can be installed in by following the manual install instructions below.

Manual install instructions for MS Windows users

Installing mplstereonet and scikit-image on Windows can be a little tricky, as skimage contains uncompiled c-code. The following instructions should work in most cases however:

1. Open the start menu and search for OSGeo4W Shell. Right-click on it and select Run as administrator. This tool gives you access to the qGIS version of python

2. Check pip (a python package manager) is up to date with the following: python -m pip install --upgrade setuptools

3. Install mplstereonet first, using the following command: python -m pip install mplstereonet

4. Download precompiled 32 or 64 bit (depending on your version of QGIS) python wheels for cython and scikit-image 3.6 (otherwise you need to install a c-compiler) from:

   • http://www.lfd.uci.edu/~gohlke/pythonlibs/#cython (32 Bit: Cython-0.26-cp36-cp36m-win32.whl, 64 Bit: Cython‑0.26.1‑cp36‑cp36m‑win_amd64.whl)
   • http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikit-image (32 Bit: scikit_image-0.13.0-cp36-cp36m-win32.whl, 64 Bit: scikit_image‑0.13.0‑cp36‑cp36m‑win_amd64.whl)

5. Navigate the console to the directory containing these downloaded wheels (e.g. cd C:/SOME_DIRECTORY_NAME/)

6. Install each package using pip: python -m pip install Cython-0.26-cp36-cp36m-win32.whl and python -m pip install scikit_image-0.13.0-cp36-cp36m-win32.whl (n.b. if you downloaded the 64 bit files the filename will change from -win32.whl to -win_amd64.whl)

7. Start/restart QGIS

Assuming these all installed correctly, you should now be set to use the plugin.

Manual install instructions for Linux users

1. Open a terminal window 'ctrl+alt+t'
2. Install mplstereonet first, using the following command: sudo pip install mplstereonet
3. Install scikit-image using the following command: 'sudo pip install scikit-image'
4. Start/restart QGIS

Usage Instructions

On launching QGIS for the first time, the plugin needs to be activated using the QGIS plugin manager (Plugins->Manage and Install Plugins...). Providing the plugin has been installed to the correct directory (see above), GeoTrace should appear in the list of available plugins. Make sure it's checked, and with some luck QGIS won't complain about it (throw errors).

Assuming this worked, a friendly compass icon should appear in the toolbar somewhere. Click this to launch the plugin. A window-pane should then appear, containing plugin GUI. This is organised into 5 tabs, each of which is described below.

Trace tab

The trace tab is used for computer-assisted digitization. Before starting, select:

1. An output layer (polyline .shp file) to write digitized traces to
2. A point layer to store the control points in (optional)
3. A cost layer. This must be a one-channel raster, in which traces will follow low values. (Though the Invert Cost check will make the trace follow high values). Note that the Cost Calculator tab can be used to assist creation of the single-channel cost raster.
4. A DEM layer, used to estimate 3D orientations from the traces (optional)

Once the relevent information has been set, start interpreting by clicking the Start Digitizing button. Left-click adds control points to your trace and Right-Click completes a trace. Hit Backspace to undo.

If a DEM layer has been included (see above), best-fit-planes for each trace will be computed using the trace eigenvectors. It is important to note that this will often produce poor results, especially in flat topography or where the traces have variable orientations. To help identify traces with poor orientation estimates, trace eigenvalues are recorded in the output, along with a "planarity" metric that approaches 1 as as plane orientation becomes well constrained (cf. Thiele et al., 2015). For convenience, orientation estimates are also classified as "Good" (planarity<0.75), "Average" (0.5<planarity<0.75), and "Poor" (planarity<0.5). Also be aware that well-constrained ("Good") orientation estimates sub-parallel to the DEM surface can be produced if the structures being digitised have variable orientations.

Advanced Trace

The Advanced trace tab is used to generate traces from predefined control points. This uses a Cost layer and writes to an Output layer, as above, but rather than requiring manually inserted control points it takes a point feature layer (Control Points) and ID field defining which trace each point belongs to (Unique ID Field), and will then automatically generate traces on clicking Run.

Cost Calculator

This tab wraps a variety of python functions from the scikit-image package for easy generation of cost rasters. Please refer to the scikit-image (http://scikit-image.org/) website for detailed descriptions of each of these functions.

Stereonet

The stereonet tab can be used to plot stereonets of planar orientation estimates (strike/dip or dip/dip direction) created using this plugin, or otherwise. Simply select the layer and associated fields containing the orientation estimates and then use the plotting tools to draw the stereonet.

Rose

This tab works as above, but creates a rose diagram rather than a stereonet.

Licence

GeoTrace is free software licenced under the GNU licence v2

Further Reading and Citation

If you found this tool useful, please cite Thiele et al., 2017. The publication also contains a more detailed description of the methods employed by this plugin.

Thiele, S. T., Grose, L., Samsu, A., Micklethwaite, S., Vollgger, S. A., and Cruden, A. R.: Rapid, semi-automatic fracture and contact mapping for point clouds, images and geophysical data, Solid Earth, 8, 1241-1253, https://doi.org/10.5194/se-8-1241-2017, 2017

For further information on the plane-fitting approach and planarity metric please refer to:

Thiele, S. T., Micklethwaite, S., Bourke, P., Verrall, M., and Kovesi, P.: Insights into the mechanics of en-échelon sigmoidal vein formation using ultra-high resolution photogrammetry and computed tomography, Journal of Structural Geology, 77, 27-44, https://doi.org/10.1016/j.jsg.2015.05.006, 2015

Where the derived orientation estimates are of critical importance, the following will also be a useful reference:

Seers, T. D. and D. Hodgetts., Probabilistic constraints on structural lineament best fit plane precision obtained through numerical analysis Journal of Structural Geology 82: 37-47, https://doi.org/10.1016/j.jsg.2015.11.004 2016