pynoddy
What is pynoddy
pynoddy is a python package to write, change, and analyse kinematic geological modelling simulations. It provides methods to define, load, modify, and safe kinematic models for simulation with Noddy. In addition, the package contains an extensive range for postprocessing of results. One main aspect of pynoddy is that it enables the encapsulation of full scientific kinematic modelling experiments for full reproducibility of results.
What is Noddy?
Noddy itself is a kinematic modelling program written by Mark Jessell [1][2] to simulate the effect of subsequent geological events (folding, unconformities, faulting, etc.) on a primary sedimentary pile. A typical example would be:
- Create a sedimentary pile with defined thicknesses for multiple formations
- Add a folding event (for example simple sinoidal folding, but complex methods are possible!)
- Add an unconformity and, above it, a new stratigraphy
- Finally, add a sequence of late faults affecting the entire system.
The result could look something like this:
Noddy has been used to generate models for teaching and interpretation purposes, but also
for scientific studies (e.g. [3]).
Installation
Installation of the pynoddy package
A successful installation of pynoddy requires two steps:
- An installation of the python modules in the package
pynoddy - The existance of an executable
Noddy(.exe)program
Installation of the first part is straight-forward:
For the best (and most complete) installation, we suggest to clone the pynoddy
repository on:
https://github.com/flohorovicic/pynoddy
To install pynoddy simply run:
python setup.py install
.. Note:
sufficient privileges are required (i.e. run in sudo with MacOSX/ Linux and set permissions on Windows)
The pynoddy packages themselves can also be installed directly from the Python Package Index (pypi.org) via pip:
pip install pynoddy
A Windows installer is also available on the Pypi page:
https://pypi.python.org/pypi/pynoddy/
Installation of Noddy
Noddy is a command line program, written in C, that performs the kinematic simulation itself. The program compilation is platform dependent, and therefore several ways for installation are possible (see below information for specific platforms).
Using a pre-compiled version of Noddy
The easy way to obtain a executable version of Noddy is simply
to download the appropriate version for your operating
system. Currently, these executables versions are also stored on
github (check the up-to-date online documentation if this should not
anymore be the case) in the directory:
https://github.com/flohorovicic/pynoddy/tree/master/noddyapp
Furthermore, the executables for Windows are also available for download on the webpage:
http://www.tectonique.net/pynoddy
Download the appropriate app, rename it to noddy or
noddy.exe and place it into a folder that is in
your local environment path variable. If you are not sure if a folder
is in the PATH or would like to add new one, see
below for more information.
Compiling Noddy from source files (recommended installation)
The source code for the executable Noddy is located in the repository
directory noddy. In order to perform the
installation, a gcc compiler is required. This compiler
should be available on Linux and MacOSX operating systems. On Windows,
one possibility is to install MinGW. Otherwise, the code requires no
specific libraries.
Note for MacOSX users: some header files have to be adapted to avoid conflicts with local libraries. The required adaptations are executed when running the script:
> adjust_for_MacOSX.sh
The compilation is then performed (in a Linux, MacOSX, or Windows MinGW terminal) with the command:
> compile.sh
Compilation usually produces multiple warnings, but should otherwise proceed successfully.
Placing the executable noddy in the Path
For the most general installation, the executable of Noddy
should be placed in a folder that can be located from any terminal
application in the system. This (usually) means that the folder with
the executable has to be in the PATH environment
variable. On Linux and MacOSX, a path can simply be added by:
> export PATH="path/to/executable/:\$PATH"
Note that this command should be placed into your .bash_profile file to ensure that the path is added whenever you start a new Python script.
On windows, adding a folder to the local environment variable
Path is usually done through the System Control Panel
(Start - Settings - Control Panel - System). in Advanced mode, open
the Environment Variables sub-menu, and find the variable Path. Click
to edit the variable, and add the location of your folder to this path.
Noddy executable and GUI for Windows
The original graphical user interface for Noddy and the compiled
executable program for Windows can be obtained from:
This site also contains the source code, as well as extensive documentation and tutorial material concerning the original implementation of the software, as well as more technical details on the modelling method itself.
Testing the installation
Testing noddy
Simply test the installation by running the generated (or downloaded)
executable in a terminal window (on Windows: cmd):
> noddy
or (depending on your compilation or naming convention):
> noddy.exe
Which should produce the general output:
Arguments <historyfile> <outputfile> <calc_mode>:
BLOCK
GEOPHYSICS
SURFACES
BLOCK_GEOPHYS
BLOCK_SURFACES
TOPOLOGY
ANOM_FROM_BLOCK
ALL
Note: if the executable is correctly placed in a folder which is
recognised by the (Environment) path variable, then you should be able
to run Noddy from any directory. If this is not the case,
please check if it is correctly placed in the path (see above).
Testing pynoddy
The pynoddy package contains a set of tests which can be
executed in the standard Python testing environment. If you cloned or
downloaded the repository, then these tests can directly be performed
through the setup script:
> python setup.py test
Of specific relevance is the test that determines if the
noddy(.exe) executable is correctly accessible from
pynoddy. If this is the case, then the
compute_model test should return:
test_compute_model (test.TestHistory) ... ok}
If this test is not ok, then please check carefully the installation
of the noddy(.exe) executable.
If all tests are successful, you are ready to go!
How to get started
Tutorial Jupyter notebooks
The best way to get started with pynoddy is to have a look at the IPython notebooks
in pynoddy/docs/notebooks. The numbered notebooks are those that are part of the
documentation, and a good point to get started.
The notebooks require an installed Jupyter notebook. More information here:
The notebook can be installed via pip or conda.
The Atlas of Strutural Geophysics
The Atlas of Structural Geophysics contains a collection of structural models, together with their expression as geophysical potential fields (gravity and magnetics), with a focus on guiding the interpretation of observed features in potential-field maps.
The atlas is currently available on:
The structural models are
created with Noddy and the history files can be downloaded from the
atlas. Models from this Atlas can directly be loaded with pynoddy. See example notebooks and documentation for more details.
Documentation
An updated version of the documentation is available within the pynoddy repository (pynoddy/docs).
In addition, an online html version of the documentation is also hosted on readthedocs:
http://pynoddy.readthedocs.org
Technical Notes
Dependencies
pynoddy depends on several standard Python packages that should be shipped with any standard distribution (and are easy to install, otherwise):
- numpy
- matplotlib
- pickle
The uncertainty analysis, quantification, and visualisation methods based on information theory are implemented in the python package pygeoinfo. This package is available on github and part of the python package index. It is automatically installed with the setup script provided with this package.
In addition, to export model results for full 3-D visualisation with VTK, the pyevtk package is used, available on bitbucket:
https://bitbucket.org/pauloh/pyevtk/src/9c19e3a54d1e?at=v0.1.0
The package is automatically downloaded and installed when running python setup.py install.
3-D Visualisation
At this stage, we do not supply methods for 3-D visualisation in python (although this may change in the future). However, we provide methods to export results into a VTK format. Exported files can then be viewed with the highly functional VTK viewers, and several free options are available, for example:
License
pynoddy is free software (see license file included in the repository). Please attribute the work when you use it and cite the publication if you use it in a scientific context - feel free to change and adapt it otherwise!
References
[1] Mark W. Jessell. Noddy, an interactive map creation package. Unpublished MSc Thesis, University of London. 1981.
[2] Mark W. Jessell, Rick K. Valenta, Structural geophysics: Integrated structural and geophysical modelling, In: Declan G. De Paor, Editor(s), Computer Methods in the Geosciences, Pergamon, 1996, Volume 15, Pages 303-324, ISSN 1874-561X, ISBN 9780080424309, http://dx.doi.org/10.1016/S1874-561X(96)80027-7.
[3] Armit, R. J., Betts, P. G., Schaefer, B. F., & Ailleres, L. (2012). Constraints on long-lived Mesoproterozoic and Palaeozoic deformational events and crustal architecture in the northern Mount Painter Province, Australia. Gondwana Research, 22(1), 207–226. http://doi.org/10.1016/j.gr.2011.11.003