kCSD-python/CSD.py at master · jankmaka/kCSD-python · GitHub

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"""
This script is used to generate Current Source Density Estimates,
And serves as base class for the kCSD method Jan et.al (2012).

This was written by :
Chaitanya Chintaluri,
Laboratory of Neuroinformatics,
Nencki Institute of Exprimental Biology, Warsaw.
"""
import numpy as np

import utility_functions as utils

class CSD(object):
    """CSD - The base class for CSD methods."""
    def __init__(self, ele_pos, pots):
        """Initialize CSD Class.

        Parameters
        ----------
        ele_pos : numpy array
            positions of electrodes
        pots : numpy array
            potentials measured by electrodes

        Returns
        -------
        None
        """
        self.validate(ele_pos, pots)
        self.ele_pos = ele_pos
        self.pots = pots
        self.n_ele = self.ele_pos.shape[0]
        self.n_time = self.pots.shape[1]
        self.dim = self.ele_pos.shape[1]
        self.cv_error = None
        return

    def validate(self, ele_pos, pots):
        """Basic checks to see if inputs are okay

        Parameters
        ----------
        ele_pos : numpy array
            positions of electrodes
        pots : numpy array
            potentials measured by electrodes

        Returns
        -------
        None
        """
        if ele_pos.shape[0] != pots.shape[0]:
            raise Exception("Number of measured potentials is not equal "
                            "to electrode number!")
        if ele_pos.shape[0] < 1+ele_pos.shape[1]: #Dim+1
            raise Exception("Number of electrodes must be at least :",
                            1+ele_pos.shape[1])
        if utils.check_for_duplicated_electrodes(ele_pos) is False:
            raise Exception("Error! Duplicated electrode!")
        return

    def method(self):
        """Place holder for the actual method that computes the CSD.

        Parameters
        ----------
        None

        Returns
        -------
        None
        """
        pass

    def values(self):
        """Place holder for obtaining CSD at the pos_csd locations, it uses the method
        function to obtain the CSD.

        Parameters
        ----------
        None

        Returns
        -------
        None
        """
        pass

    def sanity(self, true_csd, pos_csd):
        """Useful for comparing TrueCSD with reconstructed CSD. Computes, the RMS error
        between the true_csd and the reconstructed csd at pos_csd using the
        method defined.

        Parameters
        ----------

        true_csd : csd values used to generate potentials
        pos_csd : csd estimatation from the method

        Returns
        -------
        RMSE : root mean squared difference
        """
        csd = self.values(pos_csd)
        RMSE = np.sqrt(np.mean(np.square(true_csd - csd)))
        return RMSE

if __name__ == '__main__':
    ele_pos = np.array([[-0.2, -0.2], [0, 0], [0, 1], [1, 0], [1,1], [0.5, 0.5], [1.2, 1.2]])
    pots = np.array([[-1], [-1], [-1], [0], [0], [1], [-1.5]])
    test_class = CSD(ele_pos, pots)