diff --git a/analysis_1.py b/analysis_1.py new file mode 100644 index 0000000..175a862 --- /dev/null +++ b/analysis_1.py @@ -0,0 +1,161 @@ +import rlxnix as rlx +import numpy as np +import matplotlib.pyplot as plt +import os +from scipy.signal import welch + +# close all currently open figures +plt.close('all') + +'''FUNCTIONS''' +def vt_spikes(dataset): + # get sams + sams = dataset.repro_runs('SAM') + sam = sams[2] + + # get potetial over time (vt curve) + potential, time = sam.trace_data('V-1') + + # get spike times + spike_times, _ = sam.trace_data('Spikes-1') + + # plot + fig = plt.figure(figsize=(5, 2.5)) + # alternative to ax = axs[0] + ax = fig.add_subplot() + # plot vt diagram + ax.plot(time[time<0.1], potential[time<0.1]) + # plot spikes into vt diagram, at max V + ax.scatter(spike_times[spike_times<0.1], np.ones_like(spike_times[spike_times<0.1]) * np.max(potential)) + plt.show() + + return sam + +def scatter_plot(sam1): + + ### plot scatter plot for one sam with all 3 stims + # get stim count + stim_count = sam1.stimulus_count + + # create colormap + colors = plt.cm.prism(np.linspace(0, 1, stim_count)) + + # plot + fig = plt.figure() + ax = fig.add_subplot() + + stimuli = [] + for i in range(stim_count): + # get stim i from sam + stim = sam.stimuli[i] + potential_stim, time_stim = stim.trace_data('V-1') + # get spike_times + spike_times_stim, _ = stim.trace_data('Spikes-1') + stimuli.append(spike_times_stim) + + ax.eventplot(stimuli, colors=colors) + ax.set_xlabel('Spike Times [ms]') + ax.set_ylabel('Loop #') + ax.set_yticks(range(stim_count)) + ax.set_title('Spikes of SAM 3') + plt.show() + return stim, stim_count, time_stim + +# create binary array with ones for spike times +def binary_spikes(spike_times, duration , dt): + '''Converts spike times to binary representation + Params + ------ + spike_times: np.array + spike times + duration: float + trial duration + dt: float + temporal resolution + + Returns + -------- + binary: np.array + The binary representation of the spike times + ''' + binary = np.zeros(int(duration//dt)) # // is truncated division, returns number w/o decimals, same as np.round + spike_indices = np.asarray(np.round(spike_times//dt), dtype=int) + binary[spike_indices] = 1 + return binary + +# function to plot psth +def firing_rates(binary_spikes, box_width=0.01, dt=0.000025): + box = np.ones(int(box_width // dt)) + box /= np.sum(box * dt) # normalize box kernel w interal of 1 + rate = np.convolve(binary_spikes, box, mode='same') + return rate + +def power_spectrum(rate, dt): + f, p = welch(rate, fs = 1./dt, nperseg=2**16, noverlap=2**15) + # algorithm makes rounding mistakes, we want to calc many spectra and take mean of those + # nperseg: length of segments in # datapoints + # noverlap: # datapoints that overlap in segments + return f, p + + + +'''IMPORT DATA''' +datafolder = '../data' #./ wo ich gerade bin; ../ eine ebene höher; ../../ zwei ebenen höher + +example_file = os.path.join('..', 'data', '2024-10-16-ac-invivo-1.nix') + +# extract metadata +dataset = rlx.Dataset(example_file) + +### plot +# timeline of whole rec +dataset.plot_timeline() + +# voltage and spikes of current sam +sam = vt_spikes(dataset) + +# spike times of all loops +stim, stim_count, time_stim = scatter_plot(sam) + + +'''POWER SPECTRUM''' +# define variables for binary spikes function +spikes, _ = stim.trace_data('Spikes-1') +ti = stim.trace_info('V-1') +dt = ti.sampling_interval +duration = stim.duration + +### spectrum +# vector with binary values for wholes length of stim +binary = binary_spikes(spikes, duration, dt) + +# calculate firing rate +rate = firing_rates(binary, 0.01, dt) # box width of 10 ms + +# plot psth or whatever +# plt.plot(time_stim, rate) +# plt.show() + +freq, power = power_spectrum(binary, dt) + +# plot power spectrum +fig = plt.figure() +ax = fig.add_subplot() +ax.plot(freq, power) +ax.set_xlabel('Frequency [Hz]') +ax.set_ylabel('Power [1/Hz]') +ax.set_xlim(0, 1000) +plt.show() + +eodf = stim.metadata[stim.name]['EODF'][0][0] +df = stim.metadata['RePro-Info']['settings']['deltaf'][0][0] +stimulus_freq = df + eodf + + +### TODO: + # then loop over sams/dfs, all stims, intensities + # when does stim start in eodf/ at which phase and how does that influence our signal --> alignment problem: egal wenn wir spectren haben + # we want to see peaks at phase locking to own and stim frequency, and at amp modulation frequency + # clean up current code (define variables outside of functions, plot spectrum in function) + # git + # tuning curve over stim intensities or over delta f? \ No newline at end of file