from models.FirerateModel import FirerateModel from models.LIFACnoise import LifacNoiseModel from stimuli.StepStimulus import StepStimulus from my_util import helperFunctions as hf, functions as fu import numpy as np import matplotlib.pyplot as plt from scipy.optimize import curve_fit def main(): values = [1] # np.arange(5, 40, 1) parameter = "currently not active" for value in values: lifac_model = LifacNoiseModel({"delta_a": 0}) # lifac_model.set_variable(parameter, value) stimulus_strengths = np.arange(50, 60, 1) line_vars = find_fitting_line(lifac_model, stimulus_strengths) relation = find_relation(lifac_model, line_vars, stimulus_strengths, confirm=True) print(parameter, value) print(relation) def find_fitting_line(lifac_model, stimulus_strengths): # Requires a lifac model with adaption delta_a = 0, so just the base is fit frequencies = [] duration = 0.2 for stim_strength in stimulus_strengths: lifac_model.simulate_slow(StepStimulus(0, duration, stim_strength), duration) spiketimes = lifac_model.get_spiketimes() if len(spiketimes) == 0: frequencies.append(0) continue time, freq = hf.calculate_time_and_frequency_trace(spiketimes, lifac_model.get_sampling_interval()) if len(freq) == 0: frequencies.append(0) else: frequencies.append(freq[-1]) popt, pcov = curve_fit(fu.line, stimulus_strengths, frequencies) print("line:", popt) # popt2, pcov = curve_fit(fu.full_boltzmann, stimulus_strengths, frequencies, p0=[700, 0, 5, 25], bounds=([0, 0, -np.inf, -np.inf], [3000, 0.001, np.inf, np.inf])) # print("boltzmann:", popt2) # plt.plot(stimulus_strengths, frequencies) # plt.plot(stimulus_strengths, [fu.line(x, popt[0], popt[1]) for x in stimulus_strengths], '.') # plt.plot(stimulus_strengths, [fu.full_boltzmann(x, popt2[0], popt2[1], popt2[2], popt2[3]) for x in stimulus_strengths], 'o') # plt.show() return popt # , popt2 def find_relation(lifac, line_vars, stimulus_strengths, parameter="", value=0, confirm=False): # boltzmann_vars = [2.00728705e+02, 1.09905953e-12, 1.03639686e-01, 2.55002788e+01] # line_vars = [5.10369405, -29.79774806] # example values for base lifac (15.1.20) and stimulus 20-32 duration = 0.4 lifac_adaption_strength_range = np.arange(0, 0.31, 0.05) firerate_adaption_variables = [] for lifac_adaption_strength in lifac_adaption_strength_range: print(lifac_adaption_strength) lifac.set_variable("delta_a", lifac_adaption_strength) lifac.set_variable("tau_a", 40) adapted_frequencies = [] firerate_adaption_strengths = [] for stim in stimulus_strengths: #print("stim:", stim) stimulus = StepStimulus(0, duration, stim) lifac.simulate_slow(stimulus, duration) spiketimes = lifac.get_spiketimes() time, freq = hf.calculate_time_and_frequency_trace(spiketimes, lifac.get_sampling_interval()) if len(freq) == 0: adapted_frequencies.append(0) goal_adapted_freq = 0 else: adapted_frequencies.append(freq[-1]) goal_adapted_freq = freq[-1] # assume fitted linear firing rate as basis of the fire-rate model: stimulus_strength_after_adaption = fu.inverse_line(goal_adapted_freq, line_vars[0], line_vars[1]) # needed adaption strength adaption_strength = stim - stimulus_strength_after_adaption # adaption variable in model: firerate_adaption = adaption_strength / goal_adapted_freq # test in model if calculated if confirm: test_adaption_strength_in_firerate_model(line_vars, firerate_adaption, stimulus, goal_adapted_freq) firerate_adaption_strengths.append(firerate_adaption) firerate_adaption_variables.append(firerate_adaption_strengths) # plt.plot(stimulus_range, firerate_adaption_strength, label=str(lifac_adaption_strength)) # plt.show() for i in range(len(lifac_adaption_strength_range)): plt.plot([lifac_adaption_strength_range[i]+p*0.001 for p in range(len(stimulus_strengths))], firerate_adaption_variables[i]) mean_firerate_adaption_value = [np.median(strengths) for strengths in firerate_adaption_variables] l_vars, x = curve_fit(fu.line, lifac_adaption_strength_range, mean_firerate_adaption_value) plt.plot(lifac_adaption_strength_range, mean_firerate_adaption_value, label="slope:" + str(round(l_vars[0], 5))) plt.title("Relation of adaption strength variables:\n Colored points values for different stimulus strengths") plt.xlabel("lifac adaption strength: delta_a") plt.ylabel("firerate adaption strength: alpha") plt.legend() if parameter != "": plt.savefig("figures/adaption_relation_" + parameter + "_" + str(value) + ".png") else: plt.savefig("figures/adaption_relation.png") plt.close() popt, pcov = curve_fit(fu.line, lifac_adaption_strength_range, mean_firerate_adaption_value) # print(popt) return popt def test_adaption_strength_in_firerate_model(line_vars, adaption_strength, stimulus, expected_freq): params = {"function_params": line_vars, "adaptation_factor": adaption_strength, "a_tau": 10} model = FirerateModel(params) model.simulate(stimulus, 0.2) freq = model.get_frequency()[-1] diff = expected_freq - freq if diff > 0.00001 * expected_freq: print("expected freq:", expected_freq, "=?=", str(freq), ":", str(diff < 0.00001 * expected_freq)) def test_firerate_model( boltzmann_vars): fr_model = FirerateModel(params={"function_params": boltzmann_vars, "adaptation_factor": 0}) frequencies = [] stim_strengths = np.arange(0, 50, 0.5) duration = 0.5 for stim_strength in stim_strengths: fr_model.simulate(StepStimulus(0, duration, stim_strength), duration) frequencies.append(fr_model.get_frequency()[-1]) plt.plot(stim_strengths, frequencies) plt.plot(np.arange(20, 32, 1), [fu.line(x, 5.10369, -29.7977481) for x in np.arange(20, 32, 1)], 'o') plt.show() if __name__ == '__main__': main()