Commit 71a53b5e authored by Stefan Mauerberger's avatar Stefan Mauerberger
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Link FieldTools

parent d9c0f088
...@@ -20,9 +20,9 @@ You should have received a copy of the GNU General Public License ...@@ -20,9 +20,9 @@ You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>. along with this program. If not, see <https://www.gnu.org/licenses/>.
# Citation # Citation
> Schanner, Maximilian Arthus and Mauerberger, Stefan (2019) > Schanner, Maximilian Arthus and Mauerberger, Stefan (2019)
> CORBASS: CORrelation Based Archeomagnetic SnapShot model. V. 1.0. > CORBASS: CORrelation Based Archeomagnetic SnapShot model. V. 1.0.
> GFZ Data Services. http://doi.org/10.5880/GFZ.2.3.2019.008 > GFZ Data Services. http://doi.org/10.5880/GFZ.2.3.2019.008
[![DOI](https://img.shields.io/badge/DOI-10.5880%2FGFZ.2.3.2019.008-blue.svg)](http://doi.org/10.5880/GFZ.2.3.2019.008) [![DOI](https://img.shields.io/badge/DOI-10.5880%2FGFZ.2.3.2019.008-blue.svg)](http://doi.org/10.5880/GFZ.2.3.2019.008)
...@@ -38,8 +38,8 @@ graph LR; ...@@ -38,8 +38,8 @@ graph LR;
ParameterFile-->Exploration-->Integration-->Evaluation; ParameterFile-->Exploration-->Integration-->Evaluation;
``` ```
`CORBASS` uses parameter files, which include among other things a link to `CORBASS` uses parameter files, which include among other things a link to
datasets, in a format similar to the [GEOMAGIA](http://geomagia.gfz-potsdam.de/) datasets, in a format similar to the [GEOMAGIA](http://geomagia.gfz-potsdam.de/)
output. Thus a first step is to create such a file for your data. You can find output. Thus a first step is to create such a file for your data. You can find
an [example](examples/Example_Parfile.py) an [example](examples/Example_Parfile.py)
in the [*examples* section]. in the [*examples* section].
...@@ -47,7 +47,7 @@ in the [*examples* section]. ...@@ -47,7 +47,7 @@ in the [*examples* section].
Once you have a parameter file, the recommended way to run `CORBASS` is to use Once you have a parameter file, the recommended way to run `CORBASS` is to use
```console ```console
(CORBASS)$ python run.py <path/to/parfile.py> (CORBASS)$ python run.py <path/to/parfile.py>
``` ```
This way the `CORBASS` posterior model coefficients, the NEZ- and DIF-field models This way the `CORBASS` posterior model coefficients, the NEZ- and DIF-field models
...@@ -55,7 +55,7 @@ and down component and intensity at the CMB are calculated and provided as `.txt ...@@ -55,7 +55,7 @@ and down component and intensity at the CMB are calculated and provided as `.txt
files. The output location is specified in the parameter file. files. The output location is specified in the parameter file.
Under the hood, `CORBASS` first explores the model parameter space by using the Under the hood, `CORBASS` first explores the model parameter space by using the
`exploration` module. This way the region of interest, i.e. where the `exploration` module. This way the region of interest, i.e. where the
probability mass is concentrated, is found and can be accessed by the probability mass is concentrated, is found and can be accessed by the
`integration` module. The output can then be used to calculate further results, `integration` module. The output can then be used to calculate further results,
using the `evaluation` module. using the `evaluation` module.
...@@ -66,14 +66,14 @@ each module in the [*examples* section]. ...@@ -66,14 +66,14 @@ each module in the [*examples* section].
[*examples* section]: examples [*examples* section]: examples
# Installation # Installation
0. Clone the repository 0. Clone the repository
```console ```console
$ git clone https://gitext.gfz-potsdam.de/arthus/corbass.git $ git clone https://gitext.gfz-potsdam.de/arthus/corbass.git
``` ```
In the following `<corbass>` refers to the path you cloned the `CORBASS` repository into. In the following `<corbass>` refers to the path you cloned the `CORBASS` repository into.
1. Download and install [Miniconda](https://conda.io/miniconda.html) for Python 3. 1. Download and install [Miniconda](https://conda.io/miniconda.html) for Python 3.
By default, the installation directory `<conda>` is `~/miniconda3/`. By default, the installation directory `<conda>` is `~/miniconda3/`.
If you let conda modify your `bash.rc`, `<conda>/bin/conda` may be replaced by If you let conda modify your `bash.rc`, `<conda>/bin/conda` may be replaced by
`conda`. `conda`.
...@@ -99,7 +99,7 @@ each module in the [*examples* section]. ...@@ -99,7 +99,7 @@ each module in the [*examples* section].
$ source <conda>/bin/activate CORBASS $ source <conda>/bin/activate CORBASS
``` ```
Careful with tcshell, you have to use activate.csh. Careful with tcshell, you have to use activate.csh.
When you are done, deactivate the environment by When you are done, deactivate the environment by
```console ```console
(CORBASS)$ conda deactivate (CORBASS)$ conda deactivate
...@@ -116,44 +116,44 @@ each module in the [*examples* section]. ...@@ -116,44 +116,44 @@ each module in the [*examples* section].
$ <conda>/bin/conda env update -f corbass.yml $ <conda>/bin/conda env update -f corbass.yml
``` ```
[FieldTools]: https://gitup.uni-potsdam.de/matusche/fieldtools [FieldTools]: https://doi.org/10.5880/fidgeo.2019.033
# Contact # Contact
* [Maximilian Schanner](mailto:arthus@gfz-potsdam.de) * [Maximilian Schanner](mailto:arthus@gfz-potsdam.de)
Helmholtz Centre Potsdam German Research Centre for Geoscienes GFZ Helmholtz Centre Potsdam German Research Centre for Geoscienes GFZ
Section 2.3: Geomagnetism Section 2.3: Geomagnetism
Telegrafenberg Telegrafenberg
14473 Potsdam, Germany 14473 Potsdam, Germany
* [Stefan Mauerberger](mailto:mauerber@uni-potsdam.de) * [Stefan Mauerberger](mailto:mauerber@uni-potsdam.de)
Institut of mathematics Institut of mathematics
University of Potsdam University of Potsdam
Campus Golm, Haus 9 Campus Golm, Haus 9
Karl-Liebknecht-Str. 24-25 Karl-Liebknecht-Str. 24-25
14476 Potsdam OT Golm, Germany 14476 Potsdam OT Golm, Germany
# References # References
`CORBASS` uses `numpy`, `scipy`, `pandas`, `matplotlib` and `cartopy`: `CORBASS` uses `numpy`, `scipy`, `pandas`, `matplotlib` and `cartopy`:
[\[scipy\]](https://www.scipy.org/) Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, [\[scipy\]](https://www.scipy.org/) Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland,
Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson,
Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett, Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett,
Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson, Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson,
Eric Jones, Robert Kern, Eric Larson, CJ Carey, İlhan Polat, Yu Feng, Eric Jones, Robert Kern, Eric Larson, CJ Carey, İlhan Polat, Yu Feng,
Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman, Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman,
Ian Henriksen, E.A. Quintero, Charles R Harris, Anne M. Archibald, Ian Henriksen, E.A. Quintero, Charles R Harris, Anne M. Archibald,
Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt, Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt,
and SciPy 1.0 Contributors (2020) and SciPy 1.0 Contributors (2020)
"SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python". "SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python".
Nature Methods, in press. Nature Methods, in press.
[\[pandas\]](https://pandas.pydata.org/) Wes McKinney (2010) [\[pandas\]](https://pandas.pydata.org/) Wes McKinney (2010)
"Data structures for statistical computing in python", "Data structures for statistical computing in python",
Proceedings of the 9th Python in Science Conference, Volume 445 Proceedings of the 9th Python in Science Conference, Volume 445
[\[matplotlib\]](https://matplotlib.org/) J. D. Hunter (2007) [\[matplotlib\]](https://matplotlib.org/) J. D. Hunter (2007)
"Matplotlib: A 2D Graphics Environment", "Matplotlib: A 2D Graphics Environment",
Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95 Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95
[\[cartopy\]](https://scitools.org.uk/cartopy) Met Office (2015) [\[cartopy\]](https://scitools.org.uk/cartopy) Met Office (2015)
"Cartopy: a cartographic python library with a Matplotlib interface" "Cartopy: a cartographic python library with a Matplotlib interface"
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