.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "_examples/08_pygimli/plot_00_export_to_pygimli.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download__examples_08_pygimli_plot_00_export_to_pygimli.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr__examples_08_pygimli_plot_00_export_to_pygimli.py:


Exporting to pygimli for ERT inversion
======================================

REDA can also export to pygimli (https://www.pygimli.org/) ert data containers.

.. GENERATED FROM PYTHON SOURCE LINES 10-11

.. code-block:: Python

    # sphinx_gallery_thumbnail_number = 3







.. GENERATED FROM PYTHON SOURCE LINES 12-16

.. code-block:: Python

    import reda
    import pygimli as pg
    from pygimli.physics import ert








.. GENERATED FROM PYTHON SOURCE LINES 17-18

import data into reda, including electrode information

.. GENERATED FROM PYTHON SOURCE LINES 18-27

.. code-block:: Python

    data = reda.ERT()
    data.import_syscal_bin('../01_ERT/data_rodderberg/20140208_01.bin')
    data.import_electrode_positions(
        '../01_ERT/data_rodderberg/electrode_positions.dat',
    )

    # plot the electrode positions
    data.plot_electrode_positions_2d()




.. image-sg:: /_examples/08_pygimli/images/sphx_glr_plot_00_export_to_pygimli_001.png
   :alt: plot 00 export to pygimli
   :srcset: /_examples/08_pygimli/images/sphx_glr_plot_00_export_to_pygimli_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    (<Figure size 629.921x157.48 with 1 Axes>, None)



.. GENERATED FROM PYTHON SOURCE LINES 28-29

compute geometric factors

.. GENERATED FROM PYTHON SOURCE LINES 29-31

.. code-block:: Python

    data.compute_K_numerical(fem_code='pygimli')





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    COMPUTING GEomFacs using PYGimli
    Computing numerical geometric factors using Pyglimi

    array([ -38.52402364, -153.52866075, -378.10597767, ...,  -38.54919138,
           -171.86663742,  -42.25692476], shape=(2816,))



.. GENERATED FROM PYTHON SOURCE LINES 32-33

apply some light filtering

.. GENERATED FROM PYTHON SOURCE LINES 33-35

.. code-block:: Python

    data.filter('rho_a <= 0')





.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    <reda.containers.ERT.ERT object at 0x7f3746700f70>



.. GENERATED FROM PYTHON SOURCE LINES 36-37

plot histograms

.. GENERATED FROM PYTHON SOURCE LINES 37-40

.. code-block:: Python

    with reda.CreateEnterDirectory('output_01_ertinv'):
        data.histogram('r', log10=True, filename='histograms_raw.jpg')




.. image-sg:: /_examples/08_pygimli/images/sphx_glr_plot_00_export_to_pygimli_002.png
   :alt: plot 00 export to pygimli
   :srcset: /_examples/08_pygimli/images/sphx_glr_plot_00_export_to_pygimli_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 41-42

export the data (and electrode positions) into a pygimli data container

.. GENERATED FROM PYTHON SOURCE LINES 42-44

.. code-block:: Python

    pg_scheme = data.export_to_pygimli_scheme()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    WARNING: Implementation and testing still in progress!!!!
    WARNING: Journal and log is not copied!




.. GENERATED FROM PYTHON SOURCE LINES 45-46

set data errors

.. GENERATED FROM PYTHON SOURCE LINES 46-50

.. code-block:: Python

    pg_scheme.estimateError(relativeError=0.01, absoluteUError=7e-5)

    mgr = ert.ERTManager(pg_scheme)








.. GENERATED FROM PYTHON SOURCE LINES 51-62

.. code-block:: Python

    with reda.CreateEnterDirectory('output_01_ertinv'):
        mod = mgr.invert(
            pg_scheme,
            lam=10,
            verbose=True,
            paraDX=0.1,
            paraMaxCellSize=10,
            paraDepth=20,
            quality=33.0
        )





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    fop: <pygimli.physics.ert.ertModelling.ERTModelling object at 0x7f37346c4310>
    Data transformation: Logarithmic LU transform, lower bound 0.0, upper bound 0.0
    Model transformation: Logarithmic transform
    min/max (data): 1.86/2230
    min/max (error): 1%/211%
    min/max (start model): 96.19/96.19
    --------------------------------------------------------------------------------
    inv.iter 0 ... chi² = 6933.37
    --------------------------------------------------------------------------------
    inv.iter 1 ... chi² =  138.92 (dPhi = 97.99%) lam: 10.0
    --------------------------------------------------------------------------------
    inv.iter 2 ... chi² =   18.33 (dPhi = 86.71%) lam: 10.0
    --------------------------------------------------------------------------------
    inv.iter 3 ... chi² =    1.65 (dPhi = 89.64%) lam: 10.0
    --------------------------------------------------------------------------------
    inv.iter 4 ... chi² =    1.44 (dPhi = 11.70%) lam: 10.0
    --------------------------------------------------------------------------------
    inv.iter 5 ... chi² =    1.22 (dPhi = 13.78%) lam: 10.0
    --------------------------------------------------------------------------------
    inv.iter 6 ... chi² =    1.06 (dPhi = 10.34%) lam: 10.0
    --------------------------------------------------------------------------------
    inv.iter 7 ... chi² =    1.06 (dPhi = 0.09%) lam: 10.0
    ################################################################################
    #                Abort criterion reached: dPhi = 0.09 (< 2.0%)                 #
    ################################################################################




.. GENERATED FROM PYTHON SOURCE LINES 63-64

plot the result

.. GENERATED FROM PYTHON SOURCE LINES 64-73

.. code-block:: Python

    with reda.CreateEnterDirectory('output_01_ertinv'):
        ax, cb = mgr.showResult(
            cMap="Spectral_r",
            logScale=False,
        )
        ax.set_title('PyGimli inversion result', loc='left')
        fig = ax.get_figure()
        fig.savefig('pygimli_inversion.jpg', dpi=300)




.. image-sg:: /_examples/08_pygimli/images/sphx_glr_plot_00_export_to_pygimli_003.png
   :alt: PyGimli inversion result
   :srcset: /_examples/08_pygimli/images/sphx_glr_plot_00_export_to_pygimli_003.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 74-77

.. code-block:: Python

    with reda.CreateEnterDirectory('output_01_ertinv'):
        ax, _ = pg.show(mgr.mesh)
        ax.get_figure().savefig('mesh.jpg', dpi=1200)



.. image-sg:: /_examples/08_pygimli/images/sphx_glr_plot_00_export_to_pygimli_004.png
   :alt: plot 00 export to pygimli
   :srcset: /_examples/08_pygimli/images/sphx_glr_plot_00_export_to_pygimli_004.png
   :class: sphx-glr-single-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (2 minutes 16.790 seconds)


.. _sphx_glr_download__examples_08_pygimli_plot_00_export_to_pygimli.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_00_export_to_pygimli.ipynb <plot_00_export_to_pygimli.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_00_export_to_pygimli.py <plot_00_export_to_pygimli.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_00_export_to_pygimli.zip <plot_00_export_to_pygimli.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_