81 lines
3.6 KiB
Python
81 lines
3.6 KiB
Python
# ---------------------------------------------------------------------------------------------------------------------
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# Name: Firing Rate and Fourier Script (moving comb repro)
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# Purpose: Takes nixio spike data from moving comb repro and plots firing rate and power spectrum density graph
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# Usage: python3 analysis_graphs.py average
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# Author: Carolin Sachgau, University of Tuebingen
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# Created: 20/09/2018
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# ---------------------------------------------------------------------------------------------------------------------
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import matplotlib.pyplot as plt
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from IPython import embed
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import sys
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from icr_analysis import *
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from open_nixio_new import *
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# Parameters
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sampling_rate = 20000
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sigma = 0.01 # for Gaussian
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delay = 1.5 # delay in seconds after comb reaches one end, before commencing movement again
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cell_name = sys.argv[1].split('/')[-2]
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# Open Nixio File
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curr_comb, intervals_dict = open_nixio_new(sys.argv[1], sys.argv[2])
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# Kernel Density estimator: gaussian fit
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t = np.arange(-sigma*4, sigma*4, 1/sampling_rate)
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fxn = np.exp(-0.5*(t/sigma)**2) / np.sqrt(2*np.pi) / sigma # gaussian function
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if sys.argv[2] == 'average':
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for (speed, direct, comb) in intervals_dict:
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for trial in intervals_dict[(speed, direct, comb)]:
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spike_train = trial[1]
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pos = trial[0]
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avg_convolve_spikes = gaussian_convolve(spike_train, fxn, sampling_rate)
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p, freq, std_four, mn_four = fourier_psd(avg_convolve_spikes, sampling_rate)
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# Graphing
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fig, (ax1, ax2) = plt.subplots(nrows=2, ncols=1)
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# Firing Rate Graph
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firing_times = np.arange(0, len(avg_convolve_spikes))
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ax1.plot((firing_times / sampling_rate), avg_convolve_spikes)
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ax1.set_title('Firing Rate of trial ' + str((speed, direct)) + ' comb = ' + str(comb) + '\n')
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ax1.set_xlabel('Time (s)')
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ax1.set_ylabel('Firing rate (Hz)')
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# Fourier Graph
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ax2.semilogy(freq[freq < 400], p[freq < 400])
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ax2.axhline(y=(mn_four+std_four), xmin=0, xmax=1, linestyle='--', color='red')
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plt.tight_layout()
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plt.savefig(('avg_' + '_' + str(cell_name) + '_' + str(speed) + '_' + str(comb)
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+ '_' + str(direct) + '.png'))
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plt.close(fig)
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elif sys.argv[2] == 'nonaverage':
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for (repro, speed, direct, pos, comb) in intervals_dict:
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spike_train = intervals_dict[speed, direct, pos, comb]
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avg_convolve_spikes = gaussian_convolve(spike_train, fxn, sampling_rate)
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p, freq, std_four, mn_four = fourier_psd(avg_convolve_spikes, sampling_rate)
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# Graphing
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fig, (ax1, ax2) = plt.subplots(nrows=2, ncols=1)
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# Firing Rate Graph
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firing_times = np.arange(0, len(avg_convolve_spikes))
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ax1.plot((firing_times / sampling_rate), avg_convolve_spikes)
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ax1.set_title('Firing Rate of trial ' + str((speed, pos)) + ' comb = ' + str(comb) + '\n')
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ax1.set_xlabel('Time (s)')
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ax1.set_ylabel('Firing rate (Hz)')
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# Fourier Graph
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ax2.semilogy(freq[freq < 200], p[freq < 200])
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ax2.axhline(y=(mn_four+std_four), xmin=0, xmax=1, linestyle='--', color='red')
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# ax2.axvline(x=max_four,linestyle='--', color='green')
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plt.savefig(('nonavg_' + str(repro) +'_' + str(cell_name) + '_' + str(speed) + '_' + str(pos)
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+ '_' + str(comb) + '_' + str(direct) + '.png'))
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plt.close(fig)
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# ---------------------------------------------------------------------------------------------------------------------
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