513 lines
22 KiB
Python
513 lines
22 KiB
Python
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from CellData import CellData
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from models.LIFACnoise import LifacNoiseModel
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from stimuli.SinusoidalStepStimulus import SinusoidalStepStimulus
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import numpy as np
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import matplotlib.pyplot as plt
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from warnings import warn
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import functions as fu
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import helperFunctions as hF
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from os.path import join, exists
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import pickle
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from sys import stderr
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class FICurve:
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def __init__(self, stimulus_values, save_dir=None):
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self.save_file_name = "fi_curve_values.pkl"
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self.stimulus_values = stimulus_values
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self.f_baseline_frequencies = []
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self.f_inf_frequencies = []
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self.f_zero_frequencies = []
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# increase, offset
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self.f_inf_fit = []
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# f_max, f_min, k, x_zero
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self.f_zero_fit = []
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if save_dir is None:
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self.initialize()
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else:
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if not self.load_values(save_dir):
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self.initialize()
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self.save_values(save_dir)
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def initialize(self):
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self.calculate_all_frequency_points()
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self.f_inf_fit = hF.fit_clipped_line(self.stimulus_values, self.f_inf_frequencies)
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self.f_zero_fit = hF.fit_boltzmann(self.stimulus_values, self.f_zero_frequencies)
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def calculate_all_frequency_points(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def get_f_baseline_frequencies(self):
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return self.f_baseline_frequencies
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def get_f_inf_frequencies(self):
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return self.f_inf_frequencies
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def get_f_zero_frequencies(self):
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return self.f_zero_frequencies
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def get_f_inf_slope(self):
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if len(self.f_inf_fit) > 0:
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return self.f_inf_fit[0]
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def get_f_zero_fit_slope_at_straight(self):
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fit_vars = self.f_zero_fit
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return fu.full_boltzmann_straight_slope(fit_vars[0], fit_vars[1], fit_vars[2], fit_vars[3])
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def get_f_zero_fit_slope_at_stimulus_value(self, stimulus_value):
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fit_vars = self.f_zero_fit
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return fu.derivative_full_boltzmann(stimulus_value, fit_vars[0], fit_vars[1], fit_vars[2], fit_vars[3])
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def get_f_inf_frequency_at_stimulus_value(self, stimulus_value):
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return fu.clipped_line(stimulus_value, self.f_inf_fit[0], self.f_inf_fit[1])
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def get_f_zero_and_f_inf_intersection(self):
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x_values = np.arange(min(self.stimulus_values), max(self.stimulus_values), 0.0001)
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fit_vars = self.f_zero_fit
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f_zero = fu.full_boltzmann(x_values, fit_vars[0], fit_vars[1], fit_vars[2], fit_vars[3])
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f_inf = fu.clipped_line(x_values, self.f_inf_fit[0], self.f_inf_fit[1])
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intersection_indicies = np.argwhere(np.diff(np.sign(f_zero - f_inf))).flatten()
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# print("fi-curve calc intersection:", intersection_indicies, x_values[intersection_indicies])
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if len(intersection_indicies) > 1:
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f_baseline = np.median(self.f_baseline_frequencies)
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best_dist = np.inf
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best_idx = -1
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for idx in intersection_indicies:
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dist = abs(fu.clipped_line(x_values[idx], self.f_inf_fit[0], self.f_inf_fit[1]) - f_baseline)
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if dist < best_dist:
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best_dist = dist
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best_idx = idx
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return x_values[best_idx]
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elif len(intersection_indicies) == 0:
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raise ValueError("No intersection found!")
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else:
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return x_values[intersection_indicies[0]]
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def get_f_zero_fit_slope_at_f_inf_fit_intersection(self):
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x = self.get_f_zero_and_f_inf_intersection()
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fit_vars = self.f_zero_fit
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return fu.derivative_full_boltzmann(x, fit_vars[0], fit_vars[1], fit_vars[2], fit_vars[3])
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def get_mean_time_and_freq_traces(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def get_time_and_freq_traces(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def get_sampling_interval(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def get_delay(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def get_stimulus_start(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def get_stimulus_end(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def get_stimulus_duration(self):
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return self.get_stimulus_end() - self.get_stimulus_start()
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def plot_mean_frequency_curves(self, save_path=None):
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time_traces, freq_traces = self.get_time_and_freq_traces()
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mean_times, mean_freqs = self.get_mean_time_and_freq_traces()
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for i, sv in enumerate(self.stimulus_values):
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for j in range(len(time_traces[i])):
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plt.plot(time_traces[i][j], freq_traces[i][j], color="gray", alpha=0.8)
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plt.plot(mean_times[i], mean_freqs[i], color="black")
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plt.xlabel("Time [s]")
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plt.ylabel("Frequency [Hz]")
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plt.title("Mean frequency at contrast {:.2f} ({:} trials)".format(sv, len(time_traces[i])))
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if save_path is None:
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plt.show()
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else:
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plt.savefig(save_path + "mean_frequency_contrast_{:.2f}.png".format(sv))
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plt.close()
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def plot_fi_curve(self, save_path=None):
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min_x = min(self.stimulus_values)
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max_x = max(self.stimulus_values)
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step = (max_x - min_x) / 5000
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x_values = np.arange(min_x, max_x, step)
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plt.plot(self.stimulus_values, self.f_baseline_frequencies, color='blue', label='f_base')
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plt.plot(self.stimulus_values, self.f_inf_frequencies, 'o', color='green', label='f_inf')
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plt.plot(x_values, [fu.clipped_line(x, self.f_inf_fit[0], self.f_inf_fit[1]) for x in x_values],
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color='darkgreen', label='f_inf_fit')
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plt.plot(self.stimulus_values, self.f_zero_frequencies, 'o', color='orange', label='f_zero')
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popt = self.f_zero_fit
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plt.plot(x_values, [fu.full_boltzmann(x, popt[0], popt[1], popt[2], popt[3]) for x in x_values],
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color='red', label='f_0_fit')
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plt.legend()
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plt.ylabel("Frequency [Hz]")
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plt.xlabel("Stimulus value")
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if save_path is None:
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plt.show()
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else:
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plt.savefig(save_path + "fi_curve.png")
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plt.close()
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@staticmethod
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def plot_fi_curve_comparision(data_fi_curve, model_fi_curve, save_path=None):
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min_x = min(min(data_fi_curve.stimulus_values), min(model_fi_curve.stimulus_values))
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max_x = max(max(data_fi_curve.stimulus_values), max(model_fi_curve.stimulus_values))
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step = (max_x - min_x) / 5000
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x_values = np.arange(min_x, max_x+step, step)
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fig, axes = plt.subplots(1, 3, sharex="all", sharey='all', figsize=(15, 6))
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# plot baseline
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data_origin = (data_fi_curve, model_fi_curve)
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f_base_color = ("blue", "deepskyblue")
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f_inf_color = ("green", "limegreen")
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f_zero_color = ("red", "orange")
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for i in range(2):
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axes[i].plot(data_origin[i].stimulus_values, data_origin[i].get_f_baseline_frequencies(),
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color=f_base_color[i], label='f_base')
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axes[i].plot(data_origin[i].stimulus_values, data_origin[i].get_f_inf_frequencies(),
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'o', color=f_inf_color[i], label='f_inf')
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y_values = [fu.clipped_line(x, data_origin[i].f_inf_fit[0], data_origin[i].f_inf_fit[1]) for x in x_values]
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axes[i].plot(x_values, y_values, color=f_inf_color[i], label='f_inf_fit')
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axes[i].plot(data_origin[i].stimulus_values, data_origin[i].get_f_zero_frequencies(),
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'o', color=f_zero_color[i], label='f_zero')
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popt = data_origin[i].f_zero_fit
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axes[i].plot(x_values, [fu.full_boltzmann(x, popt[0], popt[1], popt[2], popt[3]) for x in x_values],
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color=f_zero_color[i], label='f_0_fit')
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axes[i].set_xlabel("Stimulus value - contrast")
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axes[i].legend()
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axes[0].set_title("cell")
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axes[0].set_ylabel("Frequency [Hz]")
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axes[1].set_title("model")
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median_baseline = np.median(data_fi_curve.get_f_baseline_frequencies())
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axes[2].plot((min_x, max_x), (median_baseline, median_baseline), color=f_base_color[0], label="cell med base")
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axes[2].plot(model_fi_curve.stimulus_values, model_fi_curve.get_f_baseline_frequencies(),
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'o', color=f_base_color[1], label='model base')
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y_values = [fu.clipped_line(x, data_fi_curve.f_inf_fit[0], data_fi_curve.f_inf_fit[1]) for x in x_values]
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axes[2].plot(x_values, y_values, color=f_inf_color[0], label='f_inf_fit cell')
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axes[2].plot(model_fi_curve.stimulus_values, model_fi_curve.get_f_inf_frequencies(),
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'o', color=f_inf_color[1], label='f_inf model')
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popt = data_fi_curve.f_zero_fit
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axes[2].plot(x_values, [fu.full_boltzmann(x, popt[0], popt[1], popt[2], popt[3]) for x in x_values],
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color=f_zero_color[0], label='f_0_fit cell')
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axes[2].plot(model_fi_curve.stimulus_values, model_fi_curve.get_f_zero_frequencies(),
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'o', color=f_zero_color[1], label='f_zero model')
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axes[2].set_title("cell model comparision")
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axes[2].set_xlabel("Stimulus value - contrast")
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axes[2].legend()
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if save_path is None:
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plt.show()
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else:
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plt.savefig(save_path + "fi_curve_comparision.png")
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plt.close()
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def plot_f_point_detections(self, save_path=None):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def save_values(self, save_directory):
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values = {}
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values["stimulus_values"] = self.stimulus_values
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values["f_baseline_frequencies"] = self.f_baseline_frequencies
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values["f_inf_frequencies"] = self.f_inf_frequencies
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values["f_zero_frequencies"] = self.f_zero_frequencies
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values["f_inf_fit"] = self.f_inf_fit
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values["f_zero_fit"] = self.f_zero_fit
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with open(join(save_directory, self.save_file_name), "wb") as file:
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pickle.dump(values, file)
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print("Fi-Curve: Values saved!")
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def load_values(self, save_directory):
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file_path = join(save_directory, self.save_file_name)
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if not exists(file_path):
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print("Fi-Curve: No file to load")
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return False
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file = open(file_path, "rb")
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values = pickle.load(file)
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if set(values["stimulus_values"]) != set(self.stimulus_values):
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stderr.write("Fi-Curve:load_values() - Given stimulus values are different to the loaded ones!:\n "
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"given: {}\n loaded: {}".format(str(self.stimulus_values), str(values["stimulus_values"])))
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self.stimulus_values = values["stimulus_values"]
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self.f_baseline_frequencies = values["f_baseline_frequencies"]
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self.f_inf_frequencies = values["f_inf_frequencies"]
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self.f_zero_frequencies = values["f_zero_frequencies"]
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self.f_inf_fit = values["f_inf_fit"]
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self.f_zero_fit = values["f_zero_fit"]
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print("Fi-Curve: Values loaded!")
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return True
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class FICurveCellData(FICurve):
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def __init__(self, cell_data: CellData, stimulus_values, save_dir=None):
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self.cell_data = cell_data
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super().__init__(stimulus_values, save_dir)
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def calculate_all_frequency_points(self):
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mean_frequencies = self.cell_data.get_mean_fi_curve_isi_frequencies()
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time_axes = self.cell_data.get_time_axes_fi_curve_mean_frequencies()
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stimulus_start = self.cell_data.get_stimulus_start()
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stimulus_duration = self.cell_data.get_stimulus_duration()
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sampling_interval = self.cell_data.get_sampling_interval()
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if len(mean_frequencies) == 0:
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warn("FICurve:all_calculate_frequency_points(): mean_frequencies is empty.\n"
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"Was all_calculate_mean_isi_frequencies already called?")
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for i in range(len(mean_frequencies)):
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if time_axes[i][0] > self.cell_data.get_stimulus_start():
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raise ValueError("TODO: Deal with to strongly cut frequency traces in cell data! ")
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# self.f_zero_frequencies.append(-1)
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# self.f_baseline_frequencies.append(-1)
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# self.f_inf_frequencies.append(-1)
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# continue
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f_zero = hF.detect_f_zero_in_frequency_trace(time_axes[i], mean_frequencies[i],
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stimulus_start, sampling_interval)
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self.f_zero_frequencies.append(f_zero)
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f_baseline = hF.detect_f_baseline_in_freq_trace(time_axes[i], mean_frequencies[i],
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stimulus_start, sampling_interval)
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self.f_baseline_frequencies.append(f_baseline)
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f_infinity = hF.detect_f_infinity_in_freq_trace(time_axes[i], mean_frequencies[i],
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stimulus_start, stimulus_duration, sampling_interval)
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self.f_inf_frequencies.append(f_infinity)
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def get_mean_time_and_freq_traces(self):
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return self.cell_data.get_time_axes_fi_curve_mean_frequencies(), self.cell_data.get_mean_fi_curve_isi_frequencies()
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def get_time_and_freq_traces(self):
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spiketimes = self.cell_data.get_fi_spiketimes()
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time_traces = []
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freq_traces = []
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for i in range(len(spiketimes)):
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trial_time_traces = []
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trial_freq_traces = []
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for j in range(len(spiketimes[i])):
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time, isi_freq = hF.calculate_time_and_frequency_trace(spiketimes[i][j], self.cell_data.get_sampling_interval())
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trial_freq_traces.append(isi_freq)
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trial_time_traces.append(time)
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time_traces.append(trial_time_traces)
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freq_traces.append(trial_freq_traces)
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return time_traces, freq_traces
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def get_sampling_interval(self):
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return self.cell_data.get_sampling_interval()
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def get_delay(self):
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return self.cell_data.get_delay()
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def get_stimulus_start(self):
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return self.cell_data.get_stimulus_start()
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def get_stimulus_end(self):
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return self.cell_data.get_stimulus_end()
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def get_f_zero_inverse_at_frequency(self, frequency):
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# UNUSED
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b_vars = self.f_zero_fit
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return fu.inverse_full_boltzmann(frequency, b_vars[0], b_vars[1], b_vars[2], b_vars[3])
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def get_f_infinity_frequency_at_stimulus_value(self, stimulus_value):
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# UNUSED
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infty_vars = self.f_inf_fit
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return fu.clipped_line(stimulus_value, infty_vars[0], infty_vars[1])
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def plot_f_point_detections(self, save_path=None):
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mean_frequencies = np.array(self.cell_data.get_mean_fi_curve_isi_frequencies())
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time_axes = self.cell_data.get_time_axes_fi_curve_mean_frequencies()
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sampling_interval = self.cell_data.get_sampling_interval()
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stim_start = self.cell_data.get_stimulus_start()
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stim_duration = self.cell_data.get_stimulus_duration()
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for i, c in enumerate(self.stimulus_values):
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time = time_axes[i]
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frequency = mean_frequencies[i]
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if len(time) == 0 or min(time) > stim_start \
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or max(time) < stim_start + stim_duration:
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continue
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fig, ax = plt.subplots(1, 1, figsize=(8, 8))
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ax.plot(time, frequency)
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start_idx, end_idx = hF.time_window_detect_f_baseline(time[0], stim_start, sampling_interval)
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ax.plot((time[start_idx], time[end_idx]), (self.f_baseline_frequencies[i], self.f_baseline_frequencies[i]),
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label="f_base", color="deepskyblue")
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start_idx, end_idx = hF.time_window_detect_f_infinity(time[0], stim_start, stim_duration,
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sampling_interval)
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ax.plot((time[start_idx], time[end_idx]), (self.f_inf_frequencies[i], self.f_inf_frequencies[i]),
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label="f_inf", color="limegreen")
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start_idx, end_idx = hF.time_window_detect_f_zero(time[0], stim_start, sampling_interval)
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ax.plot((time[start_idx], time[end_idx]), (self.f_zero_frequencies[i], self.f_zero_frequencies[i]),
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label="f_zero", color="orange")
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plt.legend()
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if save_path is not None:
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plt.savefig(save_path + "/detections_contrast_{:.2f}.png".format(c))
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else:
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plt.show()
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plt.close()
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class FICurveModel(FICurve):
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stim_duration = 0.5
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stim_start = 0.5
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total_simulation_time = stim_duration + 2 * stim_start
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def __init__(self, model, stimulus_values, eod_frequency, trials=5):
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self.eod_frequency = eod_frequency
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self.model = model
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self.trials = trials
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self.spiketimes_array = np.zeros((len(stimulus_values), trials), dtype=list)
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self.mean_frequency_traces = []
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self.mean_time_traces = []
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super().__init__(stimulus_values)
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def calculate_all_frequency_points(self):
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sampling_interval = self.model.get_sampling_interval()
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self.f_inf_frequencies = []
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self.f_zero_frequencies = []
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self.f_baseline_frequencies = []
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for i, c in enumerate(self.stimulus_values):
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stimulus = SinusoidalStepStimulus(self.eod_frequency, c, self.stim_start, self.stim_duration)
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frequency_traces = []
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time_traces = []
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for j in range(self.trials):
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_, spiketimes = self.model.simulate_fast(stimulus, self.total_simulation_time)
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self.spiketimes_array[i, j] = spiketimes
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trial_time, trial_frequency = hF.calculate_time_and_frequency_trace(spiketimes, sampling_interval)
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frequency_traces.append(trial_frequency)
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time_traces.append(trial_time)
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|
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time, frequency = hF.calculate_mean_of_frequency_traces(time_traces, frequency_traces, sampling_interval)
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self.mean_frequency_traces.append(frequency)
|
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self.mean_time_traces.append(time)
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|
|
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if len(time) == 0 or min(time) > self.stim_start \
|
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or max(time) < self.stim_start + self.stim_duration:
|
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# print("Too few spikes to calculate f_inf, f_0 and f_base")
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self.f_inf_frequencies.append(0)
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self.f_zero_frequencies.append(0)
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|
self.f_baseline_frequencies.append(0)
|
|
continue
|
|
|
|
f_inf = hF.detect_f_infinity_in_freq_trace(time, frequency, self.stim_start, self.stim_duration, sampling_interval)
|
|
self.f_inf_frequencies.append(f_inf)
|
|
|
|
f_zero = hF.detect_f_zero_in_frequency_trace(time, frequency, self.stim_start, sampling_interval)
|
|
self.f_zero_frequencies.append(f_zero)
|
|
|
|
f_baseline = hF.detect_f_baseline_in_freq_trace(time, frequency, self.stim_start, sampling_interval)
|
|
self.f_baseline_frequencies.append(f_baseline)
|
|
|
|
def get_mean_time_and_freq_traces(self):
|
|
return self.mean_time_traces, self.mean_frequency_traces
|
|
|
|
def get_sampling_interval(self):
|
|
return self.model.get_sampling_interval()
|
|
|
|
def get_delay(self):
|
|
return 0
|
|
|
|
def get_stimulus_start(self):
|
|
return self.stim_start
|
|
|
|
def get_stimulus_end(self):
|
|
return self.stim_start + self.stim_duration
|
|
|
|
def get_time_and_freq_traces(self):
|
|
time_traces = []
|
|
freq_traces = []
|
|
for v in range(len(self.stimulus_values)):
|
|
times_for_value = []
|
|
freqs_for_value = []
|
|
|
|
for s in self.spiketimes_array[v]:
|
|
t, f = hF.calculate_time_and_frequency_trace(s, self.model.get_sampling_interval())
|
|
times_for_value.append(t)
|
|
freqs_for_value.append(f)
|
|
|
|
time_traces.append(times_for_value)
|
|
freq_traces.append(freqs_for_value)
|
|
return time_traces, freq_traces
|
|
|
|
def plot_f_point_detections(self, save_path=None):
|
|
sampling_interval = self.model.get_sampling_interval()
|
|
|
|
for i, c in enumerate(self.stimulus_values):
|
|
time = self.mean_time_traces[i]
|
|
frequency = self.mean_frequency_traces[i]
|
|
|
|
if len(time) == 0 or min(time) > self.stim_start \
|
|
or max(time) < self.stim_start + self.stim_duration:
|
|
continue
|
|
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
|
|
ax.plot(time, frequency)
|
|
start_idx, end_idx = hF.time_window_detect_f_baseline(time[0], self.stim_start, sampling_interval)
|
|
ax.plot((time[start_idx], time[end_idx]), (self.f_baseline_frequencies[i], self.f_baseline_frequencies[i]),
|
|
label="f_base", color="deepskyblue")
|
|
|
|
start_idx, end_idx = hF.time_window_detect_f_infinity(time[0], self.stim_start, self.stim_duration, sampling_interval)
|
|
ax.plot((time[start_idx], time[end_idx]), (self.f_inf_frequencies[i], self.f_inf_frequencies[i]),
|
|
label="f_inf", color="limegreen")
|
|
|
|
start_idx, end_idx = hF.time_window_detect_f_zero(time[0], self.stim_start, sampling_interval)
|
|
ax.plot((time[start_idx], time[end_idx]), (self.f_zero_frequencies[i], self.f_zero_frequencies[i]),
|
|
label="f_zero", color="orange")
|
|
|
|
plt.legend()
|
|
if save_path is not None:
|
|
plt.savefig(save_path + "/detections_contrast_{:.2f}.png".format(c))
|
|
else:
|
|
plt.show()
|
|
|
|
plt.close()
|
|
|
|
|
|
def get_fi_curve_class(data, stimulus_values, eod_freq=None, trials=5, save_dir=None) -> FICurve:
|
|
if isinstance(data, CellData):
|
|
return FICurveCellData(data, stimulus_values, save_dir)
|
|
if isinstance(data, LifacNoiseModel):
|
|
if eod_freq is None:
|
|
raise ValueError("The FiCurveModel needs the eod variable to work")
|
|
return FICurveModel(data, stimulus_values, eod_freq, trials=trials)
|
|
|
|
raise ValueError("Unknown type: Cannot find corresponding Baseline class. Data was type:" + str(type(data)))
|