diff --git a/code/useful_functions.py b/code/useful_functions.py new file mode 100644 index 0000000..1115ef5 --- /dev/null +++ b/code/useful_functions.py @@ -0,0 +1,173 @@ +import glob +import pathlib +import numpy as np +import matplotlib.pyplot as plt +import rlxnix as rlx +from IPython import embed +from scipy.signal import welch + +def AM(EODf, stimulus): + """ + Calculates the Amplitude Modulation and Nyquist frequency + + Parameters + ---------- + EODf : float or int + The current EODf. + stimulus : float or int + The absolute frequency of the stimulus. + + Returns + ------- + AM : float + The amplitude modulation resulting from the stimulus. + nyquist : float + The maximum frequency possible to resolve with the EODf. + + """ + nyquist = EODf * 0.5 + AM = np.mod(stimulus, nyquist) + return AM, nyquist + +def binary_spikes(spike_times, duration, dt): + """ + Converts the spike times to a binary representations + + Parameters + ---------- + spike_times : np.array + The spike times. + duration : float + The trial duration: + dt : float + The temporal resolution. + + Returns + ------- + binary : np.array + The binary representation of the spike train. + + """ + binary = np.zeros(int(np.round(duration / dt))) #create the binary array with the same length as potential + + spike_indices = np.asarray(np.round(spike_times / dt), dtype = int) # get the indices + binary[spike_indices] = 1 # put the indices into binary + return binary + +def extract_stim_data(stimulus): + ''' + extracts all necessary metadata for each stimulus + + Parameters + ---------- + stimulus : Stimulus object or rlxnix.base.repro module + The stimulus from which the data is needed. + + Returns + ------- + amplitude : float + The relative signal amplitude in percent. + df : float + Distance of the stimulus to the current EODf. + eodf : float + Current EODf. + stim_freq : float + The total stimulus frequency (EODF+df). + amp_mod : float + The current amplitude modulation. + ny_freq : float + The current nyquist frequency. + + ''' + # extract metadata + # the stim.name adjusts the first key as it changes with every stimulus + amplitude = stimulus.metadata[stimulus.name]['Contrast'][0][0] + df = stimulus.metadata[stimulus.name]['DeltaF'][0][0] + eodf = round(stimulus.metadata[stimulus.name]['EODf'][0][0]) + stim_freq = round(stimulus.metadata[stimulus.name]['Frequency'][0][0]) + # calculates the amplitude modulation + amp_mod, ny_freq = AM(eodf, stim_freq) + return amplitude, df, eodf, stim_freq, amp_mod, ny_freq + +def firing_rate(binary_spikes, dt = 0.000025, box_width = 0.01): + ''' + Calculates the firing rate from binary spikes + + Parameters + ---------- + binary_spikes : np.array + The binary representation of the spike train. + dt : float, optional + Time difference between two datapoints. The default is 0.000025. + box_width : float, optional + Time window on which the rate should be computed on. The default is 0.01. + + Returns + ------- + rate : np.array + Array of firing rates. + + ''' + box = np.ones(int(box_width // dt)) + box /= np.sum(box) * dt # normalisierung des box kernels to an integral of one + rate = np.convolve(binary_spikes, box, mode = 'same') + return rate + +def power_spectrum(spike_times, duration, dt): + ''' + Computes a power spectrum based on the spike times + + Parameters + ---------- + spike_times : np.array + The spike times. + duration : float + The trial duration: + dt : float + The temporal resolution. + + Returns + ------- + freq : np.array + All the frequencies of the power spectrum. + power : np.array + Power of the frequencies calculated. + + ''' + # binarizes spikes + binary = binary_spikes(spike_times, duration, dt) + # computes firing rates + rate = firing_rate(binary, dt = dt) + # creates power spectrum + freq, power = welch(rate, fs = 1/dt, nperseg = 2**16, noverlap = 2**15) + return freq, power + +def remove_poor(files): + """ + Removes poor datasets from the set of files for analysis + + Parameters + ---------- + files : list + list of files. + + Returns + ------- + good_files : list + list of files without the ones with the label poor. + + """ + # create list for good files + good_files = [] + # loop over files + for i in range(len(files)): + # print(files[i]) + # load the file (takes some time) + data = rlx.Dataset(files[i]) + # get the quality + quality = str.lower(data.metadata["Recording"]["Recording quality"][0][0]) + # check the quality + if quality != "poor": + # if its good or fair add it to the good files + good_files.append(files[i]) + return good_files \ No newline at end of file