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.
The repository is subdivided into different directories containing a number of different Python scripts:
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,
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).
formatting directory contains two main scripts to reformat, convert and clean up rotation files, in particular the new
rotconv.pyconverts and formats standard
*.rotfiles to the new-ish
*.grotrotation file format which GPlates can read and has a richer and structured set of metadata. It is also able to convert
*.dbffiles which are the default format when exporting from PaleoGIS(r) to the new
rotconvwill report statics such as the number of plates, plate acronyms, plate names, zero rotations, future rotations. A (evolving) documentation is available here
grotcat.pyallows 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 provide a time-independent visual guidance.
graticules subdirectory contains a script to generate graticule lines for reconstructions.
The graticule is generated as reconstructable feature which can be cookie-cut.
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
mkdirto 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.
See wiki for requirements
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.
Copyright (c) Christian Heine, 2013-2021
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