README for gptools scripts

This document provides an overview about the gptools (short for "Tools for GPlates") script collection in this Fossil repository.

The purpose of these Python-based routines is to carry out some housekeeping on rotation files (both, the new *.grot format and legacy *.rot formats) as well as for generating other useful datasets such as reconstructable graticules for the free and open source GPlates software for plate kinematic modelling or extracting bibliographic information from rotation files.

See "License" or the below link for a license of the tools in this repository. If you end up using any of the scripts in your publications, please acknowledge the author(s) and the repository URL http://code.paleoearthlabs.org/gptools along with access date/check-in tag/version.

Tools

The repository is subdivided into different directories containing a number of different Python scripts:

• Rotation file formatting
• Reconstructable graticules
• Visualising rotation trees

1. Formatting of rotation files

Metadata is critical for reproducible science through providing a context for models or acquired data. Plate kinematic models usually consist of two key input data - a spatial data set describing the extent and lifespan of tectonic plates and a second dataset describing the plate kinematic framework through a time-dependent, tree-like hierarchical structure of finite rotation sequences. The latter are commonly denoted as rotation files which have been following a standard based on the old PLATES4 software. This standard, however, only specifies the critical input data structure (moving plate ID, age, pole lat, pole lon, angle, fixed plate ID) and that this information is supposed to come in blocks of so-called moving plate rotation sequences with rotations of the same moving plate rotation sequence (MPRS) grouped. A free form comment was allowed to follow the actual rotation data providing knowledge about the author/origin of the data (e.g. citations, a modification date, a short comment on observational constraints).

A number of problems arise with free form comments and unstructured blocks of MPRSs. Firstly, given the rise in popularity of source code management tools such as GIT, SVN or Fossil file structuration and line ordering becomes important for diff operations. Secondly, structuration and standardisation of meta data (comments, citations, key-value pairs) is also required for file comparison. Lastly, metadata fosters and improves reproducibility by providing e.g. citations/DOIs to papers used, comments on observations or changes and allows for easier interchange of model data. The scripts related to rotation file formatting and conversion in this repository help to cast rotation files into the more standardised *.grot format (see supplemental material to Qin et al., 2012 and GROT file format description).

The formatting directory contains two main scripts to reformat, convert and clean up rotation files, in particular the new GPlates *.grot format:

• rotconv.py converts and formats standard *.rot files to the new-ish *.grot rotation file format which GPlates can read and has a richer and structured set of metadata. It is also able to convert *.dbf files which are the default format when exporting from PaleoGIS(r) to the new *.grot format. rotconv will report statics such as the number of plates, plate acronyms, plate names, zero rotations, future rotations. A (evolving) documentation is available here

• grotcat.py allows to concatenate GROT-formatted rotation files.

2. Reconstructable graticules

Plate tectonic reconstructions require to provide a present-day reference for the readers. While country outlines or coastlines are one of the most common features used for such visual guidance, present-day map graticules, rotated back in time and cookie-cut to tectonic block outlines can provide a time-independent visual guidance.

The graticules subdirectory contains a script to generate graticule lines for reconstructions. The graticule is generated as reconstructable feature which can be cookie-cut.

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3. Plotting time-dependent reconstruction tree hierarchies

vis-rot is a Python2 script which was written by James Boyden at the University of Sydney's EarthByte group in 2006 to visualise time-dependent rotation tree hierarchies and released under the GPL v2 license. I have translated it to Python3 syntax using the 2to3 converter.

The script visualises a rotation tree at a specfific time using the dot program of the Graphviz software, which is required to be installed. However, as James points out:

"[...] please note that this program was not written by the authors of the Graphviz package; please do not email them about any problems you may have with this program."

The vis-rot script has a short help menu explaining the usage and can be invoked with vis-rot -h. The source file is accessible here.

./vis-rot.py test.png ../tests/Global_EB_250-0Ma_GK07_Matthews_etal.rot 130 280:714 

generates the graph shown below, with plates between 714 and 280 at 130 Ma coloured:

See the original size image output here.

Requirements/dependencies

See wiki for requirements

Repository use

This repository is hosted using the self-contained Fossil distributed version control software.

• A zip file of the repository content can be downloaded on the Downloads page
• A Forum to discuss the scripts
• An issue tracker to log tickets
• A timeline

Tickets and forum can be used anonymously, however, users can also create an account.

To clone the repository, you have to install Fossil first. The workflow is similar to git, yet you will also have access to the wiki, documentation, and tickets in one go:

• fossil clone https://code.paleoearthlabs.org/gptools/ gptools
• cd/mkdir to the directory which you want to be the root of your directory tree for this repository, then
• fossil open <path>/<to>/<gptools clone>/gptools.fossil

For detailed instructions, please see the Fossil Quick Start guide.

License

Unless otherwise stated the scripts are licensed using the GNU General Public License v3 GPLv3 .

Documentation is relased under a Creative Commons Attribution--ShareAlike 3.0 Unported License.

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Copyright (c) Christian Heine, 2013-2022 PaleoGIS (TM) is a registered trademark of the Rothwell Group L.P.