adapt to new way to calculate freq traces (different start points)
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a.ott
parent
74c9fa55fa
commit
de6c9f0b4d
189
FiCurve.py
189
FiCurve.py
@ -2,6 +2,7 @@
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from CellData import CellData
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import numpy as np
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from scipy.optimize import curve_fit
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from scipy.stats import linregress
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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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@ -33,14 +34,24 @@ class FICurve:
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def all_calculate_frequency_points(self):
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mean_frequencies = self.cell_data.get_mean_isi_frequencies()
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time_axes = self.cell_data.get_time_axes_mean_frequencies()
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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 freq in mean_frequencies:
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self.f_zeros.append(self.__calculate_f_zero__(freq))
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self.f_baselines.append(self.__calculate_f_baseline__(freq))
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self.f_infinities.append(self.__calculate_f_infinity__(freq))
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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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# TODO
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warn("TODO: Deal with to strongly cut frequency traces in cell data! ")
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self.f_zeros.append(-1)
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self.f_baselines.append(-1)
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self.f_infinities.append(-1)
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continue
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self.f_zeros.append(self.__calculate_f_zero__(time_axes[i], mean_frequencies[i]))
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self.f_baselines.append(self.__calculate_f_baseline__(time_axes[i], mean_frequencies[i]))
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self.f_infinities.append(self.__calculate_f_infinity__(time_axes[i], mean_frequencies[i]))
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def fit_line(self):
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popt, pcov = curve_fit(fu.clipped_line, self.stimulus_value, self.f_infinities)
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@ -48,7 +59,7 @@ class FICurve:
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def fit_boltzmann(self):
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max_f0 = float(max(self.f_zeros))
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min_f0 = float(min(self.f_zeros))
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min_f0 = 0.1 # float(min(self.f_zeros))
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mean_int = float(np.mean(self.stimulus_value))
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total_increase = max_f0 - min_f0
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@ -57,78 +68,93 @@ class FICurve:
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popt, pcov = curve_fit(fu.full_boltzmann, self.stimulus_value, self.f_zeros,
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p0=(max_f0, min_f0, start_k, mean_int),
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maxfev=10000, bounds=([0, 0, -np.inf, -np.inf], [3000, 3000, np.inf, np.inf]))
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maxfev=10000, bounds=([0, 0, -np.inf, -np.inf], [5000, 1, np.inf, np.inf]))
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self.boltzmann_fit_vars = popt
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def plot_fi_curve(self, savepath: str = None):
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min_x = min(self.stimulus_value)
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max_x = max(self.stimulus_value)
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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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def __calculate_f_baseline__(self, time, frequency, buffer=0.025):
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plt.plot(self.stimulus_value, self.f_baselines, color='blue', label='f_base')
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stim_start = self.cell_data.get_stimulus_start() - time[0]
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sampling_interval = self.cell_data.get_sampling_interval()
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if stim_start < 0.1:
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warn("FICurve:__calculate_f_baseline__(): Quite short delay at the start.")
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plt.plot(self.stimulus_value, self.f_infinities, 'o', color='lime', label='f_inf')
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plt.plot(x_values, [fu.clipped_line(x, self.f_infinity_fit[0], self.f_infinity_fit[1]) for x in x_values],
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color='darkgreen', label='f_inf_fit')
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start_idx = 0
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end_idx = int((stim_start-buffer)/sampling_interval)
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f_baseline = np.mean(frequency[start_idx:end_idx])
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plt.plot(self.stimulus_value, self.f_zeros, 'o', color='orange', label='f_zero')
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popt = self.boltzmann_fit_vars
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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.plot((start_idx, end_idx), (f_baseline, f_baseline), label="f_baseline")
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return f_baseline
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plt.legend()
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plt.ylabel("Frequency [Hz]")
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if self.using_contrast:
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plt.xlabel("Stimulus contrast")
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else:
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plt.xlabel("Stimulus intensity [mv]")
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if savepath is None:
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plt.show()
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else:
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plt.savefig(savepath + "fi_curve.png")
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plt.close()
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def __calculate_f_zero__(self, time, frequency, peak_buffer_percent=0.05, buffer=0.025):
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def __calculate_f_baseline__(self, frequency, buffer=0.025):
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delay = self.cell_data.get_delay()
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stimulus_start = self.cell_data.get_stimulus_start() - time[0] # time start is generally != 0 and != delay
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sampling_interval = self.cell_data.get_sampling_interval()
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if delay < 0.1:
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warn("FICurve:__calculate_f_baseline__(): Quite short delay at the start.")
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idx_start = int(buffer/sampling_interval)
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idx_end = int((delay-buffer)/sampling_interval)
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return np.mean(frequency[idx_start:idx_end])
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freq_before = frequency[0:int((stimulus_start - buffer) / sampling_interval)]
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min_before = min(freq_before)
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max_before = max(freq_before)
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mean_before = np.mean(freq_before)
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def __calculate_f_zero__(self, frequency, length_of_mean=0.1, buffer=0.025):
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stimulus_start = self.cell_data.get_delay() + self.cell_data.get_stimulus_start()
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sampling_interval = self.cell_data.get_sampling_interval()
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# time where the f-zero is searched in
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start_idx = int((stimulus_start-0.1*buffer) / sampling_interval)
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end_idx = int((stimulus_start + buffer) / sampling_interval)
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start_idx = int((stimulus_start - buffer) / sampling_interval)
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end_idx = int((stimulus_start + buffer*2) / sampling_interval)
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min_during_start_of_stim = min(frequency[start_idx:end_idx])
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max_during_start_of_stim = max(frequency[start_idx:end_idx])
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freq_before = frequency[start_idx-(int(length_of_mean/sampling_interval)):start_idx]
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fb_mean = np.mean(freq_before)
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fb_std = np.std(freq_before)
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if abs(mean_before-min_during_start_of_stim) > abs(max_during_start_of_stim-mean_before):
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f_zero = min_during_start_of_stim
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else:
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f_zero = max_during_start_of_stim
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peak_buffer = (max_before - min_before) * peak_buffer_percent
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if min_before - peak_buffer <= f_zero <= max_before + peak_buffer:
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end_idx = start_idx + int((end_idx-start_idx)/2)
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f_zero = np.mean(frequency[start_idx:end_idx])
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plt.plot(frequency)
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plt.plot((start_idx, end_idx), (f_zero, f_zero), label="f_zero, {:.2f}".format(peak_buffer))
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return f_zero
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# start_idx = int(stimulus_start / sampling_interval)
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# end_idx = int((stimulus_start + buffer*2) / sampling_interval)
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#
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# freq_before = frequency[start_idx-(int(length_of_mean/sampling_interval)):start_idx]
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# fb_mean = np.mean(freq_before)
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# fb_std = np.std(freq_before)
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#
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# peak_frequency = fb_mean
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# count = 0
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# for i in range(start_idx + 1, end_idx):
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# if fb_mean-3*fb_std <= frequency[i] <= fb_mean+3*fb_std:
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# continue
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#
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# if abs(frequency[i] - fb_mean) > abs(peak_frequency - fb_mean):
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# peak_frequency = frequency[i]
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# count += 1
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# return peak_frequency
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def __calculate_f_infinity__(self, time, frequency, length=0.1, buffer=0.025):
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stimulus_end_time = self.cell_data.get_stimulus_start() + self.cell_data.get_stimulus_duration() - time[0]
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peak_frequency = fb_mean
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count = 0
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for i in range(start_idx + 1, end_idx):
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if fb_mean-3*fb_std <= frequency[i] <= fb_mean+3*fb_std:
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continue
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start_idx = int((stimulus_end_time - length - buffer) / self.cell_data.get_sampling_interval())
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end_idx = int((stimulus_end_time - buffer) / self.cell_data.get_sampling_interval())
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if abs(frequency[i] - fb_mean) > abs(peak_frequency - fb_mean):
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peak_frequency = frequency[i]
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count += 1
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x = np.arange(start_idx, end_idx, 1) # time[start_idx:end_idx]
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slope, intercept, r_value, p_value, std_err = linregress(x, frequency[start_idx:end_idx])
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return peak_frequency
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if p_value < 0.0001:
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plt.title("significant slope: {:.2f}, p: {:.5f}, r: {:.5f}".format(slope, p_value, r_value))
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plt.plot(x, [i*slope + intercept for i in x], color="black")
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def __calculate_f_infinity__(self, frequency, length=0.2, buffer=0.025):
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stimulus_end_time = \
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self.cell_data.get_delay() + self.cell_data.get_stimulus_start() + self.cell_data.get_stimulus_duration()
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start_idx = int((stimulus_end_time - length - buffer) / self.cell_data.get_sampling_interval())
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end_idx = int((stimulus_end_time - buffer) / self.cell_data.get_sampling_interval())
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plt.plot((start_idx, end_idx), (np.mean(frequency[start_idx:end_idx]), np.mean(frequency[start_idx:end_idx])), label="f_inf")
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plt.legend()
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plt.show()
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plt.close()
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return np.mean(frequency[start_idx:end_idx])
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@ -150,3 +176,48 @@ class FICurve:
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def get_fi_curve_slope_of_straight(self):
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fit_vars = self.boltzmann_fit_vars
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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 plot_fi_curve(self, savepath: str = None):
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min_x = min(self.stimulus_value)
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max_x = max(self.stimulus_value)
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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_value, self.f_baselines, color='blue', label='f_base')
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plt.plot(self.stimulus_value, self.f_infinities, 'o', color='lime', label='f_inf')
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plt.plot(x_values, [fu.clipped_line(x, self.f_infinity_fit[0], self.f_infinity_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_value, self.f_zeros, 'o', color='orange', label='f_zero')
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popt = self.boltzmann_fit_vars
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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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if self.using_contrast:
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plt.xlabel("Stimulus contrast")
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else:
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plt.xlabel("Stimulus intensity [mv]")
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if savepath is None:
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plt.show()
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else:
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plt.savefig(savepath + "fi_curve.png")
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plt.close()
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def plot_f_point_detections(self):
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mean_frequencies = np.array(self.cell_data.get_mean_isi_frequencies())
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time_axes = self.cell_data.get_time_axes_mean_frequencies()
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for i in range(len(mean_frequencies)):
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fig, axes = plt.subplots(1, 1, sharex="all")
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axes.plot(time_axes[i], mean_frequencies[i], label="voltage")
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axes.plot((time_axes[i][0],time_axes[i][-1]), (self.f_zeros[i], self.f_zeros[i]), label="f_zero")
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axes.plot((time_axes[i][0],time_axes[i][-1]), (self.f_infinities[i], self.f_infinities[i]), '--', label="f_inf")
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axes.plot((time_axes[i][0],time_axes[i][-1]), (self.f_baselines[i], self.f_baselines[i]), label="f_base")
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axes.set_title(str(self.stimulus_value[i]))
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plt.legend()
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plt.show()
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