A web-based plot tool to visualize Earth core flows
Project description
webgeodyn is a web-based plot tool to visualize Earth core flows and scalar fields at the Core Mantle Boundary (CMB). It consists in a Tornado web server, that can be started locally, that provides a set of visualisation tools on a variety of data formats.
Installation
Requirements
The installation of webgeodyn requires Python 3 to be installed.
The other dependencies will be automatically installed by the next step but are listed here for the sake of completeness:
numpy
scipy (version > 1.1)
h5py
tornado
cdflib
astropy
Installing the package
webgeodyn can be installed
from pip:
pip3 install webgeodyn [--user]
Put the --user
flag if you are not installing in a virtual environment.
from the git repository :
Clone first the webgeodyn repository
git clone https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/webgeodyn.git
Then install the package:
cd webgeodyn
python3 setup.py install [--user]
Again, put the --user
flag if needed.
Whatever the method used, you can test if the install succeed by importing webgeodyn in Python3:
python3 -c "import webgeodyn; print(webgeodyn.__version__)"
This command should return the installed version.
Running the example
You can give a first try at starting the web server by running the example:
python3 webgeodyn/example.py
or in the Python console:
>>> import webgeodyn.example
>>> webgeodyn.example.run()
This starts the server locally and should open your browser and display a page resembling the one at https://geodyn.univ-grenoble-alpes.fr/. If not, try to type http://localhost:8080
in your browser.
You can try the different visualisations tools provided on the loaded example model (CHAOS-7).
Note that this example will also try to load the result from the latest pygeodyn (geomagnetic data assimilation Python package also developed in our group) computation (if present in ~/pygeodyn_results/Current_computation/).
Running the server with your data
The server can be used to visualise any data of supported format. For that, it is necessary to follow the template of example.py:
First, load the data under the form of Model objects, of a given name and format, in a Models dictionary.
Then, the server must be started with the loaded Models.
This is shown in details below:
# 0.Import the necessary submodules
import webgeodyn.server
import webgeodyn.models
# 1.Initialising the Models dictionary
models = webgeodyn.models.Models()
# 2.Loading your data in the Models dictionary
# Syntax: models.loadModel('/path/to/the/model/directory', "Name of the model", "Format of the model")
# Example for pygeodyn:
models.loadModel('pygeodyn_results/Current_computation', 'Current pygeodyn computation', 'pygeodyn_hdf5')
# Several models can be loaded at once. Example for CHAOS:
models.loadModel('webgeodyn/webgeodyn/example_data/CHAOS-7', 'CHAOS-7.13', 'CHAOS')
# 3.Start the server with the loaded Models
webgeodyn.server.startServer(models,{})
By copying this code in a Python file of your own, you should be able to use the visualisation tools on data of supported formats.
The format of the models, that define the format of the files to read, are the modules of webgeodyn.inout. Here are some dataFormat examples:
archomag: to read COVARCH et COVLAKE files
chaos: to read CHAOS splines files
covobs: to read COVOBS realisations files in the spherical harmonics basis
covobs_splines: to read COVOBS realisations files filled with splines coefficients
enscore: to read files generated using [GBF15]-
pygeodyn_asc: for files in the old ASCII format used in pygeodyn
pygeodyn_hdf5: to read HDF5 files generated by pygeodyn
A list of the formats can be displayed by running:
>>> import webgeodyn.inout
>>> print(webgeodyn.inout._formats)
If you need the support of a new format of file, you can follow the templates given in the documentation of webgeodyn.inout to implement your own loading function. Otherwise, you can contact us using the information given below.
Developer documentation
Documentation of the submodules of the package are available online.
If Sphinx is installed and the files were cloned from the repository, it is possible to generate the documentation locally using:
cd doc && ./make_all_doc.sh
The documentation will then be available in HTML format at doc/html/index.html.
Conditions of use
The work is licensed under the GNU GPLv3.
Git repository
The source code is stored on a Git repository (https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/webgeodyn) which can also be used to give feedbacks through Issues.
References
Gillet, N., Barrois, O. & Finlay, C. C. Stochastic forecasting of the geomagnetic field from the COV-OBS.x1 geomagnetic field model, and candidate models for IGRF-12. Earth, Planets and Space 67, (2015). doi:10.1186/s40623-015-0225-z
Barrois, O., N. Gillet, and J. Aubert. “Contributions to the geomagnetic secular variation from a reanalysis of core surface dynamics.” Geophysical Journal International 211.1 (2017): 50-68.
Barrois, O., Hammer, M. D., Finlay, C. C., Martin, Y. & Gillet, N. Assimilation of ground and satellite magnetic measurements: inference of core surface magnetic and velocity field changes. Geophysical Journal International (2018). doi:10.1093/gji/ggy297
Contact information
For scientific inquiries, contact Nicolas Gillet. For technical problems, contact Francois Dallasta and/or Franck Thollard.
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