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Examples
========

Below is a gallery of examples



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Examples: Grid handling
-----------------------




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    <div class="sphx-glr-thumbcontainer" tooltip="Grids for CRTomo can be created in multiple ways. We now support two ways:">

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  .. image:: /_examples/00_grids/images/thumb/sphx_glr_plot_grid1_thumb.png
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  :ref:`sphx_glr__examples_00_grids_plot_grid1.py`

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      <div class="sphx-glr-thumbnail-title">Creating and handling meshes</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="It is possible to use Inkscape to define some of the internal structure of a FE mesh. This can be used to:">

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  .. image:: /_examples/00_grids/images/thumb/sphx_glr_plot_triag_with_internal_structure_inkscape_thumb.png
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  :ref:`sphx_glr__examples_00_grids_plot_triag_with_internal_structure_inkscape.py`

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      <div class="sphx-glr-thumbnail-title">Using Inkscape to define internal structure</div>
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Examples: Forward Modelling
---------------------------




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    <div class="sphx-glr-thumbcontainer" tooltip="Sensitivity distributions can be easily plotted using the tdMan class:">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_00_sensitivity_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_00_sensitivity.py`

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      <div class="sphx-glr-thumbnail-title">Plotting sensitivities</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="A subsurface model is basically an array of the same length as the number of model cells in the finite-element mesh. We refer to such an array as a parameter set (or parset), and the numeric (integer) id that refers to such as parset in the parameter manager as a pid. For DC forward modeling you only need one resistivity model (with M resistivity values for the M model cells), while for complex resistivity modeling you need a resistivity and a phase array.">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_01_modifying_models_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_01_modifying_models.py`

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      <div class="sphx-glr-thumbnail-title">Modify a subsurface model</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Generate Gaussian Models">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_02_anomalies_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_02_anomalies.py`

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      <div class="sphx-glr-thumbnail-title">Generate Gaussian Models</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="CRMod can return the potential distribution associated with the current electrode locations of each registered quadrupole. We can retrieve those potentials using the tdMan object and plot them. The current distribution can then be computed TODO">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_03_potentials_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_03_potentials.py`

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      <div class="sphx-glr-thumbnail-title">Plot a potential distribution</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The eit manager can be used to easily create forward models using different parameterizations.">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_04_gen_seit_model_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_04_gen_seit_model.py`

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      <div class="sphx-glr-thumbnail-title">Generating sEIT forward models</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Generating sEIT forward models using a mask and a lookup table">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_05_seit_fwd_lookup_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_05_seit_fwd_lookup.py`

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      <div class="sphx-glr-thumbnail-title">Generating sEIT forward models using a mask and a lookup table</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="A 2D space, time and frequency data set is generated for testing purposes in reda.">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_06_synthetic_4d_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_06_synthetic_4d.py`

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      <div class="sphx-glr-thumbnail-title">Generating a 4D synthetic data set with noise.</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Test plotting forward models for different mesh boundaries.">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_07_fwd_model_plotting_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_07_fwd_model_plotting.py`

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      <div class="sphx-glr-thumbnail-title">Plot forward models</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Segmenting sensitivity distributions">

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  .. image:: /_examples/01_modelling/images/thumb/sphx_glr_plot_08_sensitivity_thresholding_thumb.png
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  :ref:`sphx_glr__examples_01_modelling_plot_08_sensitivity_thresholding.py`

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      <div class="sphx-glr-thumbnail-title">Segmenting sensitivity distributions</div>
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Examples: Single-frequency inversion
------------------------------------




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    <div class="sphx-glr-thumbcontainer" tooltip="This example discusses details of settings various settings for modeling or inversion using the single-frequency tdManager">

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  .. image:: /_examples/02_simple_inversion/images/thumb/sphx_glr_plot_01_inversion_settings_thumb.png
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  :ref:`sphx_glr__examples_02_simple_inversion_plot_01_inversion_settings.py`

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      <div class="sphx-glr-thumbnail-title">Setting modeling and inversion settings</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="CRTomo implements a last-square inversion with regularization based on the Thikonov appraoch. Herey a cost function is minimized, consisting of a data misfit \Psi_d and a model misfit \Psi_m. Both terms are weighted against each other using a regularization parameter $\lambda$.">

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  .. image:: /_examples/02_simple_inversion/images/thumb/sphx_glr_plot_02_data_errors_thumb.png
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  :ref:`sphx_glr__examples_02_simple_inversion_plot_02_data_errors.py`

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      <div class="sphx-glr-thumbnail-title">Data error handling in CRTomo</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Especially for synthetic modeling/inversion studies it is important to add data noise to the data.">

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  .. image:: /_examples/02_simple_inversion/images/thumb/sphx_glr_plot_03_adding_data_noise_thumb.png
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  :ref:`sphx_glr__examples_02_simple_inversion_plot_03_adding_data_noise.py`

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      <div class="sphx-glr-thumbnail-title">Adding data noise to measurements</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Full processing of one frequency of one timestep of the data from Weigand and Kemna 2017 (Biogeosciences).">

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  .. image:: /_examples/02_simple_inversion/images/thumb/sphx_glr_plot_05_single_freq_inversion_CR_thumb.png
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  :ref:`sphx_glr__examples_02_simple_inversion_plot_05_single_freq_inversion_CR.py`

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      <div class="sphx-glr-thumbnail-title">A single-frequency inversion (CR container)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Full processing of one frequency of one timestep of the data from Weigand and Kemna 2017 (Biogeosciences).">

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  .. image:: /_examples/02_simple_inversion/images/thumb/sphx_glr_plot_06_single_freq_inversion_sEIT_thumb.png
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  :ref:`sphx_glr__examples_02_simple_inversion_plot_06_single_freq_inversion_sEIT.py`

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      <div class="sphx-glr-thumbnail-title">A single-frequency inversion (sEIT container)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example aims to provide a full discussion of a single-frequency complex resistivity simulation study. A simulation study usually consists of the following steps:">

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  .. image:: /_examples/02_simple_inversion/images/thumb/sphx_glr_plot_07_synthetic_modinv_study_thumb.png
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  :ref:`sphx_glr__examples_02_simple_inversion_plot_07_synthetic_modinv_study.py`

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      <div class="sphx-glr-thumbnail-title">Single frequency synthetic study</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="In principle an individual data error can be assigned to each data point. However, since data errors are not easily determined in geoelectrical applications, it is common to employ various data error models that exploit empirically observed relationships between the data errors and the measurements themselves.">

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  .. image:: /_examples/02_simple_inversion/images/thumb/sphx_glr_plot_09_individual_errors_thumb.png
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  :ref:`sphx_glr__examples_02_simple_inversion_plot_09_individual_errors.py`

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      <div class="sphx-glr-thumbnail-title">Using individual data errors in CRTomo</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Generating regularization decouplins">

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  .. image:: /_examples/02_simple_inversion/images/thumb/sphx_glr_plot_10_generating_decouplings_thumb.png
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  :ref:`sphx_glr__examples_02_simple_inversion_plot_10_generating_decouplings.py`

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      <div class="sphx-glr-thumbnail-title">Generating regularization decouplins</div>
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Examples: Postprocessing of inversion results
---------------------------------------------




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    <div class="sphx-glr-thumbcontainer" tooltip="One of the purposes of the tdManager is to provide an easy interface to analyze inversion results. Inversion results can either be directly generated using the crtomo.tdMan.invert function, or by loading from an already-finished inversion directory (the tomodir).">

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  .. image:: /_examples/03_inversion_postprocessing/images/thumb/sphx_glr_plot_01_tdm_basics_thumb.png
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  :ref:`sphx_glr__examples_03_inversion_postprocessing_plot_01_tdm_basics.py`

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      <div class="sphx-glr-thumbnail-title">Using the tdManager to investigate inversion results</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Plot inversion results from a tomodir">

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  .. image:: /_examples/03_inversion_postprocessing/images/thumb/sphx_glr_plot_02_inversion_results_thumb.png
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  :ref:`sphx_glr__examples_03_inversion_postprocessing_plot_02_inversion_results.py`

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      <div class="sphx-glr-thumbnail-title">Plot inversion results from a tomodir</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Analyzing data response of inversion result">

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  .. image:: /_examples/03_inversion_postprocessing/images/thumb/sphx_glr_plot_03_seit_forward_responses_thumb.png
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  :ref:`sphx_glr__examples_03_inversion_postprocessing_plot_03_seit_forward_responses.py`

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      <div class="sphx-glr-thumbnail-title">Analyzing data response of inversion result</div>
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Examples: sEIT import and inversions
------------------------------------




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    <div class="sphx-glr-thumbcontainer" tooltip="Full processing of one timestep of the data from Weigand and Kemna 2017 (Biogeosciences).">

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  .. image:: /_examples/04_full_dataprocessing/images/thumb/sphx_glr_plot_sEIT_import_inversion_thumb.png
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  :ref:`sphx_glr__examples_04_full_dataprocessing_plot_sEIT_import_inversion.py`

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      <div class="sphx-glr-thumbnail-title">Full sEIT data processing example</div>
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Calculating correction factors
------------------------------




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    <div class="sphx-glr-thumbcontainer" tooltip="Calculation factors used to correct rhizotron tank measurements for analysis with the 2D CRTomo branch, as described in Weigand and Kemna 2017 (Biogeosciences).">

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  .. image:: /_examples/05_correction_factors/images/thumb/sphx_glr_plot_calculate_correction_factors_thumb.png
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  :ref:`sphx_glr__examples_05_correction_factors_plot_calculate_correction_factors.py`

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      <div class="sphx-glr-thumbnail-title">Calculating 2D correction factors</div>
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Examples: Field data processing
-------------------------------




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    <div class="sphx-glr-thumbcontainer" tooltip="    This example is work in progress!!!">

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  .. image:: /_examples/06_field_data_processing/images/thumb/sphx_glr_plot_01_field_data_syscal_thumb.png
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  :ref:`sphx_glr__examples_06_field_data_processing_plot_01_field_data_syscal.py`

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      <div class="sphx-glr-thumbnail-title">Example for processing field data from Sycal</div>
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.. toctree::
   :hidden:
   :includehidden:


   /_examples/00_grids/index.rst
   /_examples/01_modelling/index.rst
   /_examples/02_simple_inversion/index.rst
   /_examples/03_inversion_postprocessing/index.rst
   /_examples/04_full_dataprocessing/index.rst
   /_examples/05_correction_factors/index.rst
   /_examples/06_field_data_processing/index.rst



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