def __init__(self): """ Initialise the structural information, coupling function, and monitors. """ # Initialise some Monitors with period in physical time raw = monitors.Raw() gavg = monitors.GlobalAverage(period=2 ** -2) subsamp = monitors.SubSample(period=2 ** -2) tavg = monitors.TemporalAverage(period=2 ** -2) # DON'T load a projection because it'll make this behave like it # has a surface and do very, very bad things eeg = monitors.EEG(sensors=SensorsEEG(load_file="eeg_brainstorm_65.txt"), period=2 ** -2) eeg2 = monitors.EEG(sensors=SensorsEEG(load_file="eeg_brainstorm_65.txt"), period=2 ** -2, reference='Fp2') # EEG with a reference electrode meg = monitors.MEG(sensors=SensorsMEG(load_file='meg_brainstorm_276.txt'), period=2 ** -2) self.monitors = (raw, gavg, subsamp, tavg, eeg, eeg2, meg) self.method = None self.sim = None
def __init__(self): """ Initialise the structural information, coupling function, and monitors. """ # Initialise some Monitors with period in physical time raw = monitors.Raw() gavg = monitors.GlobalAverage(period=2**-2) subsamp = monitors.SubSample(period=2**-2) tavg = monitors.TemporalAverage(period=2**-2) eeg = monitors.EEG.from_file() eeg.period = 2**-2 eeg2 = monitors.EEG.from_file() eeg2.period = 2**-2 eeg2.reference = 'Fp2' # EEG with a reference electrode meg = monitors.MEG.from_file() meg.period = 2**-2 self.monitors = (raw, gavg, subsamp, tavg, eeg, eeg2, meg) self.method = None self.sim = None self.stim_nodes = numpy.r_[10, 20] self.stim_value = 3.0
def __init__(self): """ Initialise the structural information, coupling function, and monitors. """ #Initialise some Monitors with period in physical time raw = monitors.Raw() gavg = monitors.GlobalAverage(period=2**-2) subsamp = monitors.SubSample(period=2**-2) tavg = monitors.TemporalAverage(period=2**-2) #spheeg = monitors.SphericalEEG(sensors=sens_eeg, period=2 ** -2) #sphmeg = monitors.SphericalMEG(sensors=sens_meg, period=2 ** -2) # TODO test all monitors self.monitors = (raw, gavg, subsamp, tavg) self.method = None self.sim = None
def __init__(self): """ Initialise the structural information, coupling function, and monitors. """ # Initialise some Monitors with period in physical time raw = monitors.Raw() gavg = monitors.GlobalAverage(period=2 ** -2) subsamp = monitors.SubSample(period=2 ** -2) tavg = monitors.TemporalAverage(period=2 ** -2) eeg = monitors.EEG(load_default=True, period=2 ** -2) eeg2 = monitors.EEG(load_default=True, period=2 ** -2, reference='Fp2') # EEG with a reference electrode meg = monitors.MEG(load_default=True, period=2 ** -2) self.monitors = (raw, gavg, subsamp, tavg, eeg, eeg2, meg) self.method = None self.sim = None
def test_monitor_subsample(self): monitor = monitors.SubSample() assert monitor.period == self.default_period
### empfc_path="/Users/jzimmermann/Documents/AD/Data/" + subject_id + "_FC.mat") sub_sim = Subject_Simulation( subject=sub ) # creating an instance of class Subject_Simulation = creating a new simulation sim_results = [ ] # will hold a list of all the dictionaries, each dictionary represents one param combo and results # for (K11, K12, K21) in product(K11range, K12range, K21range): for (linear_coupling, conduction_speed) in product(linear_coupling_range, conduction_speed_range): # PE with SubSample: what_to_watch = monitors.SubSample( period=period_length_subsample, variables_of_interest=variables_of_interest) sim_result = sub_sim.prepare_and_run( what_to_watch=what_to_watch, linear_coupling=linear_coupling.item(), conduction_speed=conduction_speed.item(), K11=K11, K12=K12, K21=K21, simulation_length=simulation_length_PE, period_length=period_length_subsample) # PE with BOLD: # what_to_watch = monitors.Bold(period=period_length_bold, hrf_kernel=equations.MixtureOfGammas(), variables_of_interest = variables_of_interest) # Set hemodynamic response function (hrf) to gamma kernal rather than the voltera kernal # sim_result = sub_sim.prepare_and_run(what_to_watch = what_to_watch, linear_coupling=linear_coupling.item(), conduction_speed=conduction_speed.item(), K11=K11, K12=K12, K21=K21, simulation_length=simulation_length_PE, period_length=period_length_bold)
def test_monitor_subsample(self): monitor = monitors.SubSample() self.assertEqual(monitor.period, self.default_period)