.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "tutorial-config/eg_04_project_configuration.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        Click :ref:`here <sphx_glr_download_tutorial-config_eg_04_project_configuration.py>`
        to download the full example code

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

.. _sphx_glr_tutorial-config_eg_04_project_configuration.py:


Project configuration
^^^^^^^^^^^^^^^^^^^^^

Alternative configurations can also be used with projects. When using cutom
configurations in the project environment, the name of the configuration is key
as this will determine where any data is saved. The below example shows what
happens when using different configurations with a project.

The dataset in this example has been provided for use by the SAMTEX consortium.
For more information, please refer to [Jones2009]_. Additional details about the
dataset can be found at https://www.mtnet.info/data/kap03/kap03.html.

.. GENERATED FROM PYTHON SOURCE LINES 14-37

.. code-block:: default

    from pathlib import Path
    import seedir as sd
    import plotly
    from resistics.config import Configuration
    import resistics.letsgo as letsgo
    from resistics.time import TimeReaderNumpy, InterpolateNans, RemoveMean, Multiply
    from resistics.decimate import DecimationSetup
    from resistics.window import WindowSetup

    # The first thing to do is define the configuration to use.
    myconfig = letsgo.Configuration(
        name="myconfig",
        time_readers=[TimeReaderNumpy()],
        time_processors=[
            InterpolateNans(),
            RemoveMean(),
            Multiply(multiplier={"Ex": -1, "Ey": -1}),
        ],
        dec_setup=DecimationSetup(n_levels=7, per_level=3),
        win_setup=WindowSetup(min_size=64, min_olap=16),
    )
    myconfig.summary()





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

 Out:

 .. code-block:: none

    {
        'name': 'myconfig',
        'time_readers': [
            {
                'name': 'TimeReaderNumpy',
                'apply_scalings': True,
                'extension': '.npy'
            }
        ],
        'time_processors': [
            {'name': 'InterpolateNans'},
            {'name': 'RemoveMean'},
            {'name': 'Multiply', 'multiplier': {'Ex': -1.0, 'Ey': -1.0}}
        ],
        'dec_setup': {
            'name': 'DecimationSetup',
            'n_levels': 7,
            'per_level': 3,
            'min_samples': 256,
            'div_factor': 2,
            'eval_freqs': None
        },
        'decimator': {
            'name': 'Decimator',
            'resample': True,
            'max_single_factor': 3
        },
        'win_setup': {
            'name': 'WindowSetup',
            'min_size': 64,
            'min_olap': 16,
            'win_factor': 4,
            'olap_proportion': 0.25,
            'min_n_wins': 5,
            'win_sizes': None,
            'olap_sizes': None
        },
        'windower': {'name': 'Windower'},
        'fourier': {
            'name': 'FourierTransform',
            'win_fnc': ['kaiser', 14],
            'detrend': 'linear',
            'workers': -2
        },
        'spectra_processors': [],
        'evals': {'name': 'EvaluationFreqs'},
        'sensor_calibrator': {
            'name': 'SensorCalibrator',
            'chans': None,
            'readers': [
                {
                    'name': 'SensorCalibrationJSON',
                    'extension': '.json',
                    'file_str': 'IC_$sensor$extension'
                }
            ]
        },
        'tf': {
            'name': 'ImpedanceTensor',
            'variation': 'default',
            'out_chans': ['Ex', 'Ey'],
            'in_chans': ['Hx', 'Hy'],
            'cross_chans': ['Hx', 'Hy'],
            'n_out': 2,
            'n_in': 2,
            'n_cross': 2
        },
        'regression_preparer': {'name': 'RegressionPreparerGathered'},
        'solver': {
            'name': 'SolverScikitTheilSen',
            'fit_intercept': False,
            'normalize': False,
            'n_jobs': -2,
            'max_subpopulation': 2000,
            'n_subsamples': None
        }
    }




.. GENERATED FROM PYTHON SOURCE LINES 38-40

Save the configuration to a file. This is to imitate scenarios where users
have an existing configuration file that they want to load in and use.

.. GENERATED FROM PYTHON SOURCE LINES 40-44

.. code-block:: default

    myconfig_path = Path("..", "..", "data", "config", "myconfig.json")
    with myconfig_path.open("w") as f:
        f.write(myconfig.json())








.. GENERATED FROM PYTHON SOURCE LINES 45-47

Let's remind ourselves of the project contents. Note that some
processing with default parameters has already taken place.

.. GENERATED FROM PYTHON SOURCE LINES 47-50

.. code-block:: default

    project_path = Path("..", "..", "data", "project", "kap03")
    sd.seedir(str(project_path), style="emoji")





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

 Out:

 .. code-block:: none

    📁 kap03/
    ├─📁 images/
    ├─📁 time/
    │ ├─📁 kap163/
    │ │ └─📁 meas01/
    │ │   ├─📄 data.npy
    │ │   └─📄 metadata.json
    │ ├─📁 kap160/
    │ │ └─📁 meas01/
    │ │   ├─📄 data.npy
    │ │   └─📄 metadata.json
    │ └─📁 kap172/
    │   └─📁 meas01/
    │     ├─📄 data.npy
    │     └─📄 metadata.json
    ├─📄 resistics.json
    ├─📁 results/
    │ └─📁 kap160/
    │   └─📁 default/
    │     └─📄 0_200000_impedancetensor_default.json
    ├─📁 calibrate/
    ├─📁 evals/
    │ └─📁 kap160/
    │   └─📁 default/
    │     └─📁 meas01/
    │       ├─📄 data.npz
    │       └─📄 metadata.json
    ├─📁 masks/
    ├─📁 spectra/
    └─📁 features/




.. GENERATED FROM PYTHON SOURCE LINES 51-52

Now load our configuration and the project with myconfig.

.. GENERATED FROM PYTHON SOURCE LINES 52-57

.. code-block:: default

    config = Configuration.parse_file(myconfig_path)
    resenv = letsgo.load(project_path, config=config)
    resenv.config.summary()






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

 Out:

 .. code-block:: none

    {
        'name': 'myconfig',
        'time_readers': [
            {
                'name': 'TimeReaderNumpy',
                'apply_scalings': True,
                'extension': '.npy'
            }
        ],
        'time_processors': [
            {'name': 'InterpolateNans'},
            {'name': 'RemoveMean'},
            {'name': 'Multiply', 'multiplier': {'Ex': -1.0, 'Ey': -1.0}}
        ],
        'dec_setup': {
            'name': 'DecimationSetup',
            'n_levels': 7,
            'per_level': 3,
            'min_samples': 256,
            'div_factor': 2,
            'eval_freqs': None
        },
        'decimator': {
            'name': 'Decimator',
            'resample': True,
            'max_single_factor': 3
        },
        'win_setup': {
            'name': 'WindowSetup',
            'min_size': 64,
            'min_olap': 16,
            'win_factor': 4,
            'olap_proportion': 0.25,
            'min_n_wins': 5,
            'win_sizes': None,
            'olap_sizes': None
        },
        'windower': {'name': 'Windower'},
        'fourier': {
            'name': 'FourierTransform',
            'win_fnc': ['kaiser', 14.0],
            'detrend': 'linear',
            'workers': -2
        },
        'spectra_processors': [],
        'evals': {'name': 'EvaluationFreqs'},
        'sensor_calibrator': {
            'name': 'SensorCalibrator',
            'chans': None,
            'readers': [
                {
                    'name': 'SensorCalibrationJSON',
                    'extension': '.json',
                    'file_str': 'IC_$sensor$extension'
                }
            ]
        },
        'tf': {
            'name': 'ImpedanceTensor',
            'variation': 'default',
            'out_chans': ['Ex', 'Ey'],
            'in_chans': ['Hx', 'Hy'],
            'cross_chans': ['Hx', 'Hy'],
            'n_out': 2,
            'n_in': 2,
            'n_cross': 2
        },
        'regression_preparer': {'name': 'RegressionPreparerGathered'},
        'solver': {
            'name': 'SolverScikitTheilSen',
            'fit_intercept': False,
            'normalize': False,
            'n_jobs': -2,
            'max_subpopulation': 2000,
            'n_subsamples': None
        }
    }




.. GENERATED FROM PYTHON SOURCE LINES 58-62

Now calculate the evaluation frequency spectral data and view the directory
structure. This shows how resistics handles saving data for different
configurations. The data is placed in a new folder with the same name as the
the configuration. This is why the configuration name is important.

.. GENERATED FROM PYTHON SOURCE LINES 62-67

.. code-block:: default

    site = resenv.proj["kap160"]
    for meas in site:
        letsgo.process_time_to_evals(resenv, "kap160", meas.name)
    sd.seedir(str(project_path), style="emoji")





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

 Out:

 .. code-block:: none

    📁 kap03/
    ├─📁 images/
    ├─📁 time/
    │ ├─📁 kap163/
    │ │ └─📁 meas01/
    │ │   ├─📄 data.npy
    │ │   └─📄 metadata.json
    │ ├─📁 kap160/
    │ │ └─📁 meas01/
    │ │   ├─📄 data.npy
    │ │   └─📄 metadata.json
    │ └─📁 kap172/
    │   └─📁 meas01/
    │     ├─📄 data.npy
    │     └─📄 metadata.json
    ├─📄 resistics.json
    ├─📁 results/
    │ └─📁 kap160/
    │   └─📁 default/
    │     └─📄 0_200000_impedancetensor_default.json
    ├─📁 calibrate/
    ├─📁 evals/
    │ └─📁 kap160/
    │   ├─📁 default/
    │   │ └─📁 meas01/
    │   │   ├─📄 data.npz
    │   │   └─📄 metadata.json
    │   └─📁 myconfig/
    │     └─📁 meas01/
    │       ├─📄 data.npz
    │       └─📄 metadata.json
    ├─📁 masks/
    ├─📁 spectra/
    └─📁 features/




.. GENERATED FROM PYTHON SOURCE LINES 68-70

Let's calculate the impedance tensor with this configuration. The sampling
frequency to process is 0.2 (Hz)

.. GENERATED FROM PYTHON SOURCE LINES 70-73

.. code-block:: default

    letsgo.process_evals_to_tf(resenv, 0.2, "kap160")
    sd.seedir(str(project_path), style="emoji")





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

 Out:

 .. code-block:: none


      0%|          | 0/21 [00:00<?, ?it/s]
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     19%|#9        | 4/21 [00:00<00:01, 16.99it/s]
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     62%|######1   | 13/21 [00:16<00:03,  2.66it/s]
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     71%|#######1  | 15/21 [00:16<00:01,  3.90it/s]
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     81%|########  | 17/21 [00:16<00:00,  5.35it/s]
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     90%|######### | 19/21 [00:16<00:00,  6.74it/s]
     95%|#########5| 20/21 [00:17<00:00,  7.38it/s]
    100%|##########| 21/21 [00:17<00:00,  7.88it/s]
    100%|##########| 21/21 [00:17<00:00,  1.23it/s]
    📁 kap03/
    ├─📁 images/
    ├─📁 time/
    │ ├─📁 kap163/
    │ │ └─📁 meas01/
    │ │   ├─📄 data.npy
    │ │   └─📄 metadata.json
    │ ├─📁 kap160/
    │ │ └─📁 meas01/
    │ │   ├─📄 data.npy
    │ │   └─📄 metadata.json
    │ └─📁 kap172/
    │   └─📁 meas01/
    │     ├─📄 data.npy
    │     └─📄 metadata.json
    ├─📄 resistics.json
    ├─📁 results/
    │ └─📁 kap160/
    │   ├─📁 default/
    │   │ └─📄 0_200000_impedancetensor_default.json
    │   └─📁 myconfig/
    │     └─📄 0_200000_impedancetensor_default.json
    ├─📁 calibrate/
    ├─📁 evals/
    │ └─📁 kap160/
    │   ├─📁 default/
    │   │ └─📁 meas01/
    │   │   ├─📄 data.npz
    │   │   └─📄 metadata.json
    │   └─📁 myconfig/
    │     └─📁 meas01/
    │       ├─📄 data.npz
    │       └─📄 metadata.json
    ├─📁 masks/
    ├─📁 spectra/
    └─📁 features/




.. GENERATED FROM PYTHON SOURCE LINES 74-75

Finally, let's plot our the impedance tensor for this configuration

.. GENERATED FROM PYTHON SOURCE LINES 75-95

.. code-block:: default

    soln = letsgo.get_solution(
        resenv,
        "kap160",
        resenv.config.name,
        0.2,
        resenv.config.tf.name,
        resenv.config.tf.variation,
    )
    fig = soln.tf.plot(
        soln.freqs,
        soln.components,
        to_plot=["ExHy", "EyHx"],
        x_lim=[1, 5],
        res_lim=[1, 4],
        phs_lim=[0, 100],
        legend="128",
        symbol="circle",
    )
    fig.update_layout(height=900)
    plotly.io.show(fig)



.. raw:: html
    :file: images/sphx_glr_eg_04_project_configuration_001.html






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

   **Total running time of the script:** ( 0 minutes  18.642 seconds)


.. _sphx_glr_download_tutorial-config_eg_04_project_configuration.py:


.. only :: html

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



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

     :download:`Download Python source code: eg_04_project_configuration.py <eg_04_project_configuration.py>`



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

     :download:`Download Jupyter notebook: eg_04_project_configuration.ipynb <eg_04_project_configuration.ipynb>`


.. only:: html

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

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