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)
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')