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# pymagglobal
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**python interface for global geomagnetic field models**

[[_TOC_]]
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`pymagglobal` serves the purpose of replacing some Fortran scripts, which are used in the geomagnetism community to evaluate global field models. It can be applied to all cubic-spline based geomagnetic field models stored in the same file format as gufm1 or the CALSxk model series. However, care has to be taken that two header lines of the model files are formatted correctly and the list of spline knot point epochs starts only in line 3. The first header line has to contain start and end epoch of the model as the first two numbers, any further information in that line is ignored. The second header line has to start with three integers, which are the maximum spherical harmonic degree, a dummy that actually is not used, and the number of splines.  
By default, `pymagglobal` includes several models. Use
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```console
$ pymagglobal --list-models
```
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to get a list of these default models or go to [pymagglobal/dat](https://gitext.gfz-potsdam.de/arthus/pymagglobal/-/tree/master/pymagglobal/dat) for further information. Using
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```console
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$ pymagglobal ... <path/to/your_model>
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```
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you can use `pymagglobal` to evaluate your own models, if they come in a similar format. `<path/to/your_model>` specifies the path to your model and is given instead of the name of an included model. You can download additional models [here](ftp://ftp.gfz-potsdam.de/home/mag/arthus/pymagglobal_models/) and use them as above.
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Once installed, `pymagglobal` can be imported and its routines used to access the models from inside your own python code.
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## License
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GNU General Public License, Version 3, 29 June 2007

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Copyright (C) 2020 Helmholtz Centre Potsdam GFZ, German Research Centre for Geosciences, Potsdam, Germany
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pymagglobal is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

pymagglobal is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.

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## Citation
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TODO

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## Documentation
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Check out the extended documention [here](http://arthus.gitext-pages.gfz-potsdam.de/pymagglobal). From the command line, you can use `pymagglobal` to get various results from the models. For example,
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```console
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$ pymagglobal dipole gufm1
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```
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will give a plot of the dipole moment time series for the model gufm1. In general, pymagglobal is called as
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```console
$  pymagglobal command --options model
```
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where `command` specifies the quantity you want to get from `pymagglobal` and `model` is the respective model. You can use 
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```console
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$ pymagglobal command --options <path/to/your_model>
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```
to parse your own model, if it is in a format similar to gufm1. Use
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```console
$ pymagglobal --help
```
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to get further information. Each command has its own help, so you may also use
```console
$ pymagglobal dipole --help
```
to get information on the options for the dipole time series.

When using `python` you can import the pymagglobal package and access the models directly:
```python
import pymagglobal
```
Using the function `file2splines` you can get a spline object, representing the model. For example, to get a spline object for gufm1, use
```python
gufm1_splines = pymagglobal.file2splines(pymagglobal.models['gufm1'])
```
This object can be evaluated to get the coefficients for a specific epoch
```python
gufm1_1600 = gufm1_splines(1600)
```
or passed to other routines in pymagglobal. For example, to get the dipole series from above use
```python
import numpy as np
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times = np.linspace(1590, 1990, 201)
gufm1_dipoles = pymagglobal.dipole_series(times, gufm1_splines)
```
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Additionally, pymagglobal provides a `Model` class, which is set up with a path and a name:
```python
gufm1 = pymagglobal.Model('gufm1', pymagglobal.models['gufm1'])
```
The object now contains several quantities of interest, for example the minimal and maximal time for which the model is valid
```python
>>> gufm1.t_min
1590.0
>>> gufm1.t_max
1990.0
```

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## Installation
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`pymagglobal` is built and installed using [conda](https://www.anaconda.com/).
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0. Clone the repository 
   ```console
    $ git clone https://gitext.gfz-potsdam.de/arthus/pymagglobal.git
   ```
   In the following `<pymagglobal>` refers to the path you cloned the `pymagglobal` repository into.

1. Download and install [Miniconda](https://conda.io/miniconda.html) for Python 3 
   By default, the installation directory `<conda>` is `~/miniconda3/`.  
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   If you do not allow conda to modify your `bash.rc`, `conda` has to be replaced by `<conda>/bin/conda`. This may cause `install.sh` to fail.  
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   You may want to create a fresh environment for pymagglobal. This is done using
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   ```console
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   $ conda create --name Your_Environment
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   ```
   followed by
   ```console
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   $ conda activate Your_Environment
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   ```
   Careful: With tcshell, you have to use activate.csh.
   

2. Install `conda-build`
   ```console
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   $ conda install conda-build
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   ```
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With `conda-build` installed, you may go to `<pymagglobal>` and run 
```console
$ bash install.sh
```
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which will do the next steps for you. If `install.sh` fails or you want to do the steps by hand:
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3. Build [FieldTools]  
   This step will make the pyfield library available via the local conda channel.

   Navigate to `<pymagglobal>` and build [FieldTools]
   ```console
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   $ conda build FieldTools
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   ```

4. Build pymagglobal  
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   Navigate to `<pymagglobal>` and build pymagglobal
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   ```console
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   $ conda build ./
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   ```
5. Install pymagglobal  
   ```console
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   $ conda install pymagglobal -c local
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   ```
   This will make `pymagglobal` available as a python package, i.e. you can use
   ```python
   import pymagglobal
   ```
   as well as register a shell command in your local environmet, so that you can run
   ```console
   $ pymagglobal --help
   ```

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Another way to use `pymagglobal` is via nix-shell. With [nix](https://nixos.org/download.html) installed, simply run
```console
$ nix-shell
```
from within the `pymagglobal` root directory.

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[FieldTools]: http://doi.org/10.5880/fidgeo.2019.033
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## Contact
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* [Maximilian Schanner](mailto:arthus@gfz-potsdam.de)  
Helmholtz Centre Potsdam German Research Centre for Geoscienes GFZ  
Section 2.3: Geomagnetism  
Telegrafenberg  
14473 Potsdam, Germany

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## References
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`pymagglobal` uses `numpy`, `scipy`, `matplotlib`, `cartopy` and `pyfield`:
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[\[scipy\]](https://www.scipy.org/) Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland,  
Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson,   
Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett,  
Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson,   
Eric Jones, Robert Kern, Eric Larson, CJ Carey, İlhan Polat, Yu Feng,  
Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman,  
Ian Henriksen, E.A. Quintero, Charles R Harris, Anne M. Archibald,  
Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt,  
and SciPy 1.0 Contributors (2020)  
"SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python".  
Nature Methods, in press.

[\[matplotlib\]](https://matplotlib.org/)  J. D. Hunter (2007)  
"Matplotlib: A 2D Graphics Environment",  
Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95

[\[cartopy\]](https://scitools.org.uk/cartopy) Met Office (2015)  
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"Cartopy: a cartographic python library with a Matplotlib interface"
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[\[pyfield\]](http://doi.org/10.5880/fidgeo.2019.033) Matuschek, H. and Mauerberger, S. (2019)  
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FieldTools - A toolbox for manipulating vector fields on the sphere  
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GFZ Data Services. 10.5880/fidgeo.2019.033