299 lines
9.3 KiB
Python
299 lines
9.3 KiB
Python
import numpy as np
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import matplotlib.pyplot as plt
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import pyrelacs.DataLoader as dl
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import os
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import helperFunctions as hf
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from IPython import embed
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from scipy.optimize import curve_fit
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import warnings
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SAMPLING_INTERVAL = 1/20000
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STIMULUS_START = 0
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STIMULUS_DURATION = 0.400
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PRE_DURATION = 0.250
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TOTAL_DURATION = 1.25
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def main():
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for folder in hf.get_subfolder_paths("data/"):
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filepath = folder + "/fispikes1.dat"
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set_savepath("figures/" + folder.split('/')[1] + "/")
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print("Folder:", folder)
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if not os.path.exists(get_savepath()):
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os.makedirs(get_savepath())
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spiketimes = []
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intensities = []
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index = -1
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for metadata, key, data in dl.iload(filepath):
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# embed()
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if len(metadata) != 0:
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metadata_index = 0
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if '----- Control --------------------------------------------------------' in metadata[0].keys():
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metadata_index = 1
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print(metadata)
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i = float(metadata[metadata_index]['intensity'][:-2])
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intensities.append(i)
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spiketimes.append([])
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index += 1
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spiketimes[index].append(data[:, 0]/1000)
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intensities, spiketimes = hf.merge_similar_intensities(intensities, spiketimes)
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# Sort the lists so that intensities are increasing
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x = [list(x) for x in zip(*sorted(zip(intensities, spiketimes), key=lambda pair: pair[0]))]
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intensities = x[0]
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spiketimes = x[1]
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mean_frequencies = calculate_mean_frequencies(intensities, spiketimes)
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popt, pcov = fit_exponential(intensities, mean_frequencies)
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plot_frequency_curve(intensities, mean_frequencies)
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f_baseline = calculate_f_baseline(mean_frequencies)
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f_infinity = calculate_f_infinity(mean_frequencies)
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f_zero = calculate_f_zero(mean_frequencies)
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# plot_fi_curve(intensities, f_baseline, f_zero, f_infinity)
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# TODO !!
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def fit_exponential(intensities, mean_frequencies):
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start_idx = int((PRE_DURATION + STIMULUS_START+0.005) / SAMPLING_INTERVAL)
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end_idx = int((PRE_DURATION + STIMULUS_START + 0.1) / SAMPLING_INTERVAL)
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time_constants = []
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#print(start_idx, end_idx)
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popts = []
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pcovs = []
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for i in range(len(mean_frequencies)):
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freq = mean_frequencies[i]
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y_values = freq[start_idx:end_idx+1]
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x_values = np.arange(start_idx*SAMPLING_INTERVAL, end_idx*SAMPLING_INTERVAL, SAMPLING_INTERVAL)
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try:
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popt, pcov = curve_fit(exponential_function, x_values, y_values, p0=(1/(np.power(1, 10)), .5, 50, 180), maxfev=10000)
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except RuntimeError:
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print("RuntimeError happened in fit_exponential.")
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continue
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#print(popt)
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#print(pcov)
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#print()
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popts.append(popt)
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pcovs.append(pcov)
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plt.plot(np.arange(-PRE_DURATION, TOTAL_DURATION, SAMPLING_INTERVAL), freq)
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plt.plot(x_values-PRE_DURATION, [exponential_function(x, popt[0], popt[1], popt[2], popt[3]) for x in x_values])
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# plt.show()
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save_path = get_savepath() + "exponential_fits/"
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if not os.path.exists(save_path):
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os.makedirs(save_path)
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plt.savefig(save_path + "fit_intensity:" + str(round(intensities[i], 4)) + ".png")
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plt.close()
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return popts, pcovs
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def calculate_mean_frequency(freqs):
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mean_freq = [sum(e) / len(e) for e in zip(*freqs)]
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return mean_freq
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def gaussian_kernel(sigma, dt):
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x = np.arange(-4. * sigma, 4. * sigma, dt)
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y = np.exp(-0.5 * (x / sigma) ** 2) / np.sqrt(2. * np.pi) / sigma
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return y
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def calculate_kernel_frequency(spiketimes, time, sampling_interval):
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sp = spiketimes
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t = time # Probably goes from -200ms to some amount of ms in the positive ~1200?
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dt = sampling_interval
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kernel_width = 0.01 # kernel width is a time in seconds how sharp the frequency should be counted
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binary = np.zeros(t.shape)
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spike_indices = ((sp - t[0]) / dt).astype(int)
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binary[spike_indices[(spike_indices >= 0) & (spike_indices < len(binary))]] = 1
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g = gaussian_kernel(kernel_width, dt)
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rate = np.convolve(binary, g, mode='same')
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return rate
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def calculate_isi_frequency(spiketimes, time):
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first_isi = spiketimes[0] - (-PRE_DURATION) # diff to the start at 0
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last_isi = TOTAL_DURATION - spiketimes[-1] # diff from the last spike to the end of time :D
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isis = [first_isi]
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isis.extend(np.diff(spiketimes))
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isis.append(last_isi)
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if np.isnan(first_isi):
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print(spiketimes[:10])
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print(isis[0:10])
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quit()
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rate = []
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for isi in isis:
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if isi == 0:
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print("probably a problem")
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isi = 0.0000000001
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freq = 1/isi
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frequency_step = int(round(isi*(1/SAMPLING_INTERVAL)))*[freq]
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rate.extend(frequency_step)
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#plt.plot((np.arange(len(rate))-PRE_DURATION)/(1/SAMPLING_INTERVAL), rate)
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#plt.plot([sum(isis[:i+1]) for i in range(len(isis))], [200 for i in isis], 'o')
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#plt.plot(time, [100 for t in time])
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#plt.show()
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if len(rate) != len(time):
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if "12-13-af" in get_savepath():
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warnings.warn("preStimulus duration > 0 still not supported")
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return [1]*len(time)
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else:
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print(len(rate), len(time), len(rate) - len(time))
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print(rate)
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print(isis)
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print("Quitting because time and rate aren't the same length")
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quit()
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return rate
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def calculate_mean_frequencies(intensities, spiketimes):
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time = np.arange(-PRE_DURATION, TOTAL_DURATION, SAMPLING_INTERVAL)
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mean_frequencies = []
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for i in range(len(intensities)):
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freqs = []
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for spikes in spiketimes[i]:
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if len(spikes) < 2:
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continue
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freq = calculate_isi_frequency(spikes, time)
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freqs.append(freq)
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mf = calculate_mean_frequency(freqs)
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mean_frequencies.append(mf)
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return mean_frequencies
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def calculate_f_baseline(mean_frequencies):
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buffer_time = 0.05
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start_idx = int(0.05/SAMPLING_INTERVAL)
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end_idx = int((PRE_DURATION - STIMULUS_START - buffer_time)/SAMPLING_INTERVAL)
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f_zeros = []
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for freq in mean_frequencies:
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f_0 = np.mean(freq[start_idx:end_idx])
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f_zeros.append(f_0)
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return f_zeros
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def calculate_f_infinity(mean_frequencies):
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buffer_time = 0.05
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start_idx = int((PRE_DURATION + STIMULUS_START + STIMULUS_DURATION - 0.15 - buffer_time) / SAMPLING_INTERVAL)
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end_idx = int((PRE_DURATION + STIMULUS_START + STIMULUS_DURATION - buffer_time) / SAMPLING_INTERVAL)
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f_infinity = []
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for freq in mean_frequencies:
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f_inf = np.mean(freq[start_idx:end_idx])
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f_infinity.append(f_inf)
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return f_infinity
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def calculate_f_zero(mean_frequencies):
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buffer_time = 0.1
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start_idx = int((PRE_DURATION + STIMULUS_START - buffer_time) / SAMPLING_INTERVAL)
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end_idx = int((PRE_DURATION + STIMULUS_START + buffer_time) / SAMPLING_INTERVAL)
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f_peaks = []
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for freq in mean_frequencies:
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fp = np.mean(freq[start_idx-500:start_idx])
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for i in range(start_idx+1, end_idx):
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if abs(freq[i] - freq[start_idx]) > abs(fp - freq[start_idx]):
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fp = freq[i]
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f_peaks.append(fp)
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return f_peaks
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def plot_fi_curve(intensities, f_baseline, f_zero, f_infinity):
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plt.plot(intensities, f_baseline, label="f_baseline")
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plt.plot(intensities, f_zero, 'o', label="f_zero")
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plt.plot(intensities, f_infinity, label="f_infinity")
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max_f0 = float(max(f_zero))
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mean_int = float(np.mean(intensities))
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start_k = float(((f_zero[-1] - f_zero[0]) / (intensities[-1] - intensities[0])*4)/f_zero[-1])
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popt, pcov = curve_fit(fill_boltzmann, intensities, f_zero, p0=(max_f0, start_k, mean_int), maxfev=10000)
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print(popt)
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min_x = min(intensities)
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max_x = max(intensities)
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step = (max_x - min_x) / 5000
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x_values_boltzmann_fit = np.arange(min_x, max_x, step)
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plt.plot(x_values_boltzmann_fit, [fill_boltzmann(i, popt[0], popt[1], popt[2]) for i in x_values_boltzmann_fit], label='fit')
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plt.title("FI-Curve")
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plt.ylabel("Frequency in Hz")
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plt.xlabel("Intensity in mV")
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plt.legend()
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# plt.show()
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plt.savefig(get_savepath() + "fi_curve.png")
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plt.close()
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def plot_frequency_curve(intensities, mean_frequencies):
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colors = ["red", "green", "blue", "violet", "orange", "grey"]
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time = np.arange(-PRE_DURATION, TOTAL_DURATION, SAMPLING_INTERVAL)
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for i in range(len(intensities)):
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plt.plot(time, mean_frequencies[i], color=colors[i % 6], label=str(intensities[i]))
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plt.plot((0, 0), (0, 500), color="black")
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plt.plot((0.4, 0.4), (0, 500), color="black")
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plt.legend()
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plt.xlabel("Time in seconds")
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plt.ylabel("Frequency in Hz")
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plt.title("Frequency curve")
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plt.savefig(get_savepath() + "mean_frequency_curves.png")
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plt.close()
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def exponential_function(x, a, b, c, d):
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return a*np.exp(-c*(x-b))+d
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def upper_boltzmann(x, f_max, k, x_zero):
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return f_max * np.clip((2 / (1+np.power(np.e, -k*(x - x_zero)))) - 1, 0, None)
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def fill_boltzmann(x, f_max, k, x_zero):
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return f_max * (1 / (1 + np.power(np.e, -k * (x - x_zero))))
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SAVEPATH = ""
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def get_savepath():
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global SAVEPATH
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return SAVEPATH
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def set_savepath(new_path):
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global SAVEPATH
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SAVEPATH = new_path
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if __name__ == '__main__':
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main()
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