diff --git a/code/test.py b/code/test.py index a0eddc9..32b704e 100644 --- a/code/test.py +++ b/code/test.py @@ -1,4 +1,3 @@ - import glob import pathlib import numpy as np @@ -42,7 +41,6 @@ def power_spectrum(rate, dt): freq, power = welch(rate, fs = 1/dt, nperseg = 2**16, noverlap = 2**15) return freq, power - def extract_stim_data(stimulus): ''' extracts all necessary metadata for each stimulus @@ -72,110 +70,6 @@ def extract_stim_data(stimulus): stim_freq = stim.metadata[stim.name]['Frequency'][0][0] return amplitude, df, eodf, stim_freq - - -#find example data -datafolder = "../data" - -example_file = datafolder + "/" + "2024-10-16-ad-invivo-1.nix" - -#load dataset -dataset = rlx.Dataset(example_file) -# find all sams -sams = dataset.repro_runs('SAM') -sam = sams[2] # our example sam -potential,time = sam.trace_data("V-1") #membrane potential -spike_times, _ = sam.trace_data('Spikes-1') #spike times -df = sam.metadata['RePro-Info']['settings']['deltaf'][0][0] #find df in metadata -amp = sam.metadata['RePro-Info']['settings']['contrast'][0][0] * 100 #find amplitude in metadata - -#figure for a quick plot -fig = plt.figure(figsize = (5, 2.5)) -ax = fig.add_subplot() -ax.plot(time[time < 0.1], potential[time < 0.1]) # plot the membrane potential in 0.1s -ax.scatter(spike_times[spike_times < 0.1], - np.ones_like(spike_times[spike_times < 0.1]) * np.max(potential)) #plot teh spike times on top -plt.show() -plt.close() -# get all the stimuli -stims = sam.stimuli -# empty list for the spike times -spikes = [] -#spikes2 = np.array(range(len(stims))) -# loop over the stimuli -for stim in stims: - # get the spike times - spike, _ = stim.trace_data('Spikes-1') - # append the first 100ms to spikes - spikes.append(spike[spike < 0.1]) - # get stimulus duration - duration = stim.duration - ti = stim.trace_info("V-1") - dt = ti.sampling_interval # get the stimulus interval - bin_spikes = binary_spikes(spike, duration, dt) #binarize the spike_times - print(len(bin_spikes)) - pot,tim= stim.trace_data("V-1") #membrane potential - rate = firing_rate(bin_spikes, dt = dt) - print(np.mean(rate)) - fig, [ax1, ax2] = plt.subplots(1, 2,layout = 'constrained') - ax1.plot(tim,rate) - ax1.set_ylim(0,600) - ax1.set_xlim(0, 0.04) - freq, power = power_spectrum(rate, dt) - ax2.plot(freq,power) - ax2.set_xlim(0,1000) - -# make an eventplot -fig = plt.figure(figsize = (5, 3), layout = 'constrained') -ax = fig.add_subplot() -ax.eventplot(spikes, linelength = 0.8) -ax.set_xlabel('time [ms]') -ax.set_ylabel('loop no.') -<<<<<<< HEAD -======= -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 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 firing_rate(binary_spikes, dt = 0.000025, box_width = 0.01): - 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(rate, dt): - freq, power = welch(rate, fs = 1/dt, nperseg = 2**16, noverlap = 2**15) - return freq, power - #find example data datafolder = "../data" @@ -233,4 +127,3 @@ ax = fig.add_subplot() ax.eventplot(spikes, linelength = 0.8) ax.set_xlabel('time [ms]') ax.set_ylabel('loop no.') -plt.show() \ No newline at end of file