Microcircuit. 
PLOS Computational Biology 12, 1-34 (2016).
"""

import plot_helpers
import meanfield.circuit as circuit
import numpy as np
import h5py_wrapper.wrapper as h5

fix_path = 'integration/data/'

if __name__ == '__main__':
    filename = fix_path + 'Bos2016_data.h5'

    # Original parameters extracted from the data + modification
    circ_params_with_modifications = plot_helpers.get_parameter_microcircuit()

    circ = circuit.Circuit('microcircuit',
                           circ_params_with_modifications,
                           analysis_type='dynamical',
                           fmax=500.0,
                           from_file=False)

    power_spectra_freqs, power_spectra = circ.create_power_spectra()

    exemplary_frequency_idx = 20
    omega = circ.omegas[exemplary_frequency_idx]
    print(omega)
    H = circ.ana.create_H(omega)
    MH = circ.ana.create_MH(omega)
    delay_dist = circ.ana.create_delay_dist_matrix(omega)
Exemple #2
0
import numpy as np
import matplotlib.pyplot as plt
import read_sim as rs
import plot_helpers as ph
import h5py_wrapper.wrapper as h5
import meanfield.circuit as circuit

ph.set_fig_defaults()
circuit_params = ph.get_parameter_microcircuit()


def get_sensitivity_measure(calcAna, calcAnaAll, mode='gamma', eig_index=None):
    print 'Calculate sensitivity measure.'
    if calcAna or calcAnaAll:
        if mode == 'gamma' or mode == 'low':
            fmax = 100.0
        elif mode == 'high_gamma':
            fmax = 400.0
        circ = circuit.Circuit('microcircuit',
                               circuit_params,
                               fmax=fmax,
                               from_file=not calcAnaAll)
        freqs, eigs = circ.create_eigenvalue_spectra('MH')
        if mode == 'gamma':
            fmax = freqs[np.argmin(abs(eigs[eig_index] - 1))]
            Z = circ.get_sensitivity_measure(fmax)
            eigc = eigs[eig_index][np.argmin(abs(eigs[eig_index] - 1))]
        elif mode == 'high_gamma':
            eigs = eigs[eig_index][np.where(freqs > 150.)]
            freqs = freqs[np.where(freqs > 150.)]
            fmax = freqs[np.argmin(abs(eigs - 1.0))]
Options:
  -h --help     Show this screen.
  --version     Show version.
"""

import plot_helpers
import meanfield.circuit as circuit
from docopt import docopt
import sys

if __name__ == '__main__':
    arguments = docopt(__doc__, version='0.1')
    filename = arguments['<filename>']

    # New parameters used for Fig. 1
    circ_params_new = plot_helpers.get_parameter_microcircuit()

    # Original parameters extracted from the data
    circ = circuit.Circuit('microcircuit', analysis_type=None)
    circ_params_old = circ.params

    file = open(filename, 'w')
    sys.stdout = file

    for attribute in circ_params_new.keys():
        print(attribute)
        print('old/original:')
        print(circ_params_old[attribute])
        print('new:')
        print(circ_params_new[attribute])
        print('\n')