from stimuli.AbstractStimulus import AbstractStimulus from models.AbstractModel import AbstractModel import numpy as np class LIFACModel(AbstractModel): # all times in milliseconds KEYS = ["mem_res", "mem_tau", "v_base", "v_zero", "threshold", "step_size", "delta_a", "tau_a"] VALUES = [100 * 1000000, 0.1 * 200, 0, 0, 10, 0.01, 1, 20] # membrane time constant tau = mem_cap*mem_res def __init__(self, params: dict = None): super().__init__(params) self.voltage_trace = [] self.adaption_trace = [] self.spiketimes = [] self.stimulus = None # self.frequency_trace = [] def simulate(self, stimulus: AbstractStimulus, total_time_s): self.stimulus = stimulus output_voltage = [] adaption = [] spiketimes = [] current_v = self.parameters["v_zero"] current_a = 0 for time_point in np.arange(0, total_time_s*1000, self.parameters["step_size"]): v_next = self._calculate_voltage_step(current_v, stimulus.value_at_time_in_ms(time_point) - current_a) a_next = self._calculate_adaption_step(current_a) if v_next > self.parameters["threshold"]: v_next = self.parameters["v_base"] spiketimes.append(time_point/1000) a_next += self.parameters["delta_a"] output_voltage.append(v_next) adaption.append(a_next) current_v = v_next current_a = a_next self.voltage_trace = output_voltage self.adaption_trace = adaption self.spiketimes = spiketimes return output_voltage, spiketimes def _calculate_voltage_step(self, current_v, input_v): v_base = self.parameters["v_base"] step_size = self.parameters["step_size"] # mem_res = self.parameters["mem_res"] mem_tau = self.parameters["mem_tau"] return current_v + (step_size * (v_base - current_v + input_v)) / mem_tau def _calculate_adaption_step(self, current_a): step_size = self.parameters["step_size"] return current_a + (step_size * (-current_a)) / self.parameters["tau_a"] def set_parameters(self, params): self._test_given_parameters(params) for k in params.keys(): self.parameters[k] = params[k] for i in range(len(self.KEYS)): if self.KEYS[i] not in self.parameters.keys(): self.parameters[self.KEYS[i]] = self.VALUES[i] def get_parameters(self): return self.parameters def set_variable(self, key, value): if key not in self.KEYS: raise ValueError("Given key is unknown!\n" "Please check spelling and refer to list LIFAC.KEYS.") self.parameters[key] = value def _set_default_parameters(self): for i in range(len(self.KEYS)): self.parameters[self.KEYS[i]] = self.VALUES[i] def _test_given_parameters(self, params): for k in params.keys(): if k not in self.KEYS: err_msg = "Unknown key in the given parameters:" + str(k) raise ValueError(err_msg) def min_stimulus_strength_to_spike(self): return self.parameters["threshold"] - self.parameters["v_base"] def get_sampling_interval(self): return self.parameters["step_size"] def get_frequency(self): # TODO also change simulates_frequency() if any calculation is added! raise NotImplementedError("No calculation implemented yet for the frequency.") def get_spiketimes(self): return self.spiketimes def get_voltage_trace(self): return self.voltage_trace def get_adaption_trace(self): return self.adaption_trace def simulates_frequency(self) -> bool: return False def simulates_spiketimes(self) -> bool: return True def simulates_voltage_trace(self) -> bool: return True def get_recording_times(self): # [delay, stimulus_start, stimulus_duration, time_to_end] self.stimulus = AbstractStimulus() delay = 0 start = self.stimulus.get_stimulus_start_s() duration = self.stimulus.get_stimulus_duration_s() total_time = len(self.voltage_trace) / self.parameters["step_size"] return [delay, start, duration, total_time]