How to set the settings
=======================

A lot of features in efel can have their behaviour changed with
settings, in order to be more customisable, depending on the traces and
the need of the user. Here, we are going to see how to change the
settings with an exmaple, and where to find the list of all the settings
in efel with their default values.

For this example, we are going to use a trace of a cell model with a bAP
(backpropagating action potential) stimulus, recorded in the dendrite.

.. code:: ipython3

    import efel
    
    import numpy
    import json
    
    %matplotlib notebook
    %matplotlib inline
    from matplotlib import pyplot as plt
    plt.rcParams['figure.figsize'] = 10, 10
    
    test_url = '../../tests/testdata/allfeatures/testbap2data.txt'
    test_data = numpy.loadtxt(test_url)
    time = test_data[:,0]
    voltage = test_data[:, 1]

We can now plot this data

.. code:: ipython3

    plt.rcParams['figure.figsize'] = 10, 10
    
    fig1, ax1 = plt.subplots(1)
    ax1.plot(time, voltage)
    ax1.set_xlabel('Time (ms)')
    ax1.set_ylabel('Membrane voltage (mV)');



.. image:: settings_notebook_files/settings_notebook_4_0.png


Now, let us extract the peak time. We expect one value shortly after 300
ms.

.. code:: ipython3

    stim_start = 295
    stim_end = 500
    trace = {'T': time, 'V': voltage, 'stim_start': [stim_start], 'stim_end': [stim_end]}
    
    feature_values = efel.get_feature_values([trace], ['peak_time'])[0]
    print(f'Spike detection threshold is {efel.get_settings().Threshold} mV.')
    print(feature_values)


.. parsed-literal::

    Spike detection threshold is -20.0 mV.
    {'peak_time': None}


.. parsed-literal::

    /path/to/efel/pyfeatures/cppfeature_access.py:14: RuntimeWarning: Error while calculating peak_time, An error occurred while computing the feature, feature is not found. Voltage never goes below or above threshold in spike detection.
      warnings.warn(


We can see that we don’t have any value returned. The reason is that, by
default, eFEL looks for spikes that go above -20 mV. This is fine for
most cells when recorded in the soma, but here, we are recording a spike
in the dendrite after a soma stimulus. This spike has a smaller
amplitude than the one in the soma, and is thus below the
spike-detecting threshold.

This can be solved by modifying the settings, using the easy to use
set_setting function! By simply modifying the default threshold value of
-20 to a lower value, e.g. -30, the spike gets detected!

.. code:: ipython3

    efel.api.set_setting('Threshold', -30.)
    
    feature_values = efel.get_feature_values([trace], ['peak_time'])[0]
    print(feature_values)


.. parsed-literal::

    {'peak_time': array([304.])}


If you want to see the current settings, you can do so by using the
get_settings function:

.. code:: ipython3

    print(efel.get_settings())


.. parsed-literal::

    Threshold: -30.0
    DerivativeThreshold: 10.0
    DownDerivativeThreshold: -12.0
    dependencyfile_path: /path/to/efel/DependencyV5.txt
    spike_skipf: 0.1
    max_spike_skip: 2
    interp_step: 0.1
    burst_factor: 1.5
    strict_burst_factor: 2.0
    voltage_base_start_perc: 0.9
    voltage_base_end_perc: 1.0
    current_base_start_perc: 0.9
    current_base_end_perc: 1.0
    rise_start_perc: 0.0
    rise_end_perc: 1.0
    initial_perc: 0.1
    min_spike_height: 20.0
    strict_stiminterval: False
    initburst_freq_threshold: 50
    initburst_sahp_start: 5
    initburst_sahp_end: 100
    DerivativeWindow: 3
    voltage_base_mode: mean
    current_base_mode: mean
    precision_threshold: 1e-10
    sahp_start: 5.0
    ignore_first_ISI: True
    impedance_max_freq: 50.0
    AP_phaseslope_range: 2
    inactivation_tc_end_skip: 10


You can reset the settings to their default value at any time using the
reset() function. It is good practice to use it whenever you want to
change the settings, in order to be sure that previously set settings
are not interfering with your new settings.

.. code:: ipython3

    efel.reset()

The settings can also be passed down to efel by passing them through the
trace dictionary, inside a list:

.. code:: ipython3

    trace['Threshold'] = [-30.]
    feature_values = efel.get_feature_values([trace], ['peak_time'])[0]
    print(feature_values)


.. parsed-literal::

    {'peak_time': array([304.])}


The complete list of settings and their default value can be found in
the documentation of `the Settings class
here <https://efel.readthedocs.io/en/latest/_autosummary/efel.settings.html#efel.settings.Settings>`__