Example #1
0
def make_raster(spikedata, experiment, prestim, poststim, dest):
	# get number of units, number of stims
	cells = btsf.get_cluids(spikedata)
	stim_names = btsf.get_stim_names(spikedata)
	for stimn in stim_names:
		ntrials = btsf.get_num_trials(spikedata, stimn)

		for cluid in cells:
			cellstimdata = btsf.find_spikes_by_stim_name(btsf.find_spikes_by_cluid(spikedata, cluid), stimn)
			cell_clugroup = btsf.get_clugroups(cellstimdata)
			raster = plt.figure()

			for trialnum in range(ntrials):
				spikes_to_plot = btsf.find_spikes_by_stim_trial(cellstimdata, stimn, trialnum)
				[stim_start_samps, stim_end_samps] = btsf.get_stim_times(cellstimdata, stimn, trialnum)
				stim_start = (stim_start_samps - stim_start_samps)/info['fs']
				stim_end = (stim_end_samps - stim_start_samps)/info['fs']
				nspikes = btsf.get_num_spikes(spikes_to_plot)
				spiketimes = btsf.get_spike_times_seconds_stim_aligned(spikes_to_plot)
				ylimits = [trialnum, trialnum+1]

				for j in range(nspikes):
					ydata = ylimits
					xdata = [spiketimes[j], spiketimes[j]]
					plt.plot(xdata, ydata, 'b')

				stim_start_x = [stim_start, stim_start]
				stim_end_x = [stim_end, stim_end]
				stim_start_y = [0, ntrials]
				stim_end_y = [0, ntrials]

				plt.plot(stim_start_x, stim_start_y, 'r')
				plt.plot(stim_end_x, stim_end_y, 'r')
				plt.title("Bird: " + experiment['name'] + " Cell: " + str(cluid) + " Type: " + str(cell_clugroup) + " Stim: " + stimn)
				plt.xlabel('Time (s)')
				plt.ylabel('Trial')
				plt.xlim(-1.0*prestim, poststim + stim_end)
				plt.ylim(0, ntrials) 
				save_raster(raster, dest, experiment['name'], cluid, stimn)
Example #2
0
def make_cell_groups(spikedata, win_dt, win_n, prestim_dt, fs, clu_group, destdir):
	stim_names = spf.get_stim_names(spikedata)
	for stim in stim_names:
		ntrials = spf.get_num_trials(spikedata, stim)
		for trial in range(ntrials):
			debug_print('make_cell_groups: Stim %s, Trial %s...\n' % (stim, trial))
			stim_period_vert_list = set()
			prestim_vert_list = set()

			debug_print('- Extracting spikes\n')
			stimtimes = spf.get_stim_times(spikedata, stim, trial)
			trialdata = spf.find_spikes_by_stim_trial(spikedata, stim, trial)
			prestimwin = [stimtimes[0] - 2.0, stimtimes[0]]

			debug_print('- Creating Windows\n')
			# Subdivide a given time period into windows
			prestim_cg_win_list = win_subdivide(prestimwin, win_n, win_dt, fs)
			stim_cg_win_list = win_subdivide(stimtimes, win_n, win_dt, fs)

			debug_print('- Extracting stim period cell groups\n')
			for winl, winh in stim_cg_win_list:
				# debug_print('WinL: %s 	WinH: %s\n' % (winl, winh))
				# Get cell groups
				cgs = spf.get_cluster_group(trialdata, winl, winh)
				#debug_print(str(cgs) + '\n')
				# Convert to tuple and add to the vertex set list. 
				stim_period_vert_list.add(tuple(cgs))
				#debug_print('Vert list size: %s\n' % len(stim_period_vert_list))
			
			debug_print('- Extracting prestim period cell groups\n')
			for winl, winh in prestim_cg_win_list:
				cgs = spf.get_cluster_group(trialdata, winl, winh)
				prestim_vert_list.add(tuple(cgs))

			debug_print('- Writing perseus input files\n')	
			write_vert_list_to_perseus(stim_period_vert_list, destdir, stim, trial, bird, clu_group)
			write_vert_list_to_perseus(prestim_vert_list, destdir, 'pretrial'+stim, trial, bird, clu_group)
			debug_print('DONE\n')