def find_data_with_stimulus(filenamelist):
"""Open files passed in `filenamelist` and check for background
and probe stimulus data. The files must be data files, not network
files. Return a list of open file handles of those that are
good"""
files_with_stim = []
files_to_close = []
for filename in filenamelist:
try:
fh = h5.File(filename, 'r')
except IOError:
print filename, 'could not be opened'
continue
try:
bgtimes = analyzer.get_bgtimes(fh)
probetimes = analyzer.get_probetimes(fh)
if (0 in bgtimes.shape) or (0 in probetimes.shape):
files_to_close.append(fh)
else:
files_with_stim.append(fh)
except KeyError:
print filename, 'does not have stimulus data'
files_to_close.append(fh)
for fh in files_to_close:
print 'File without stimulus info:', fh.filename
fh.close()
return files_with_stim
def get_stim_aligned_spike_times(fhandles, cellnames):
"""Collect the spike times for each cell from all the files with
respect to the stimuli.
Parameteres
-----------
fhandles: list
open data file handles.
cellnames: list
list of cell names to be checked.
Returns
-------
A pair containing dicts of list of arrays of spike times following
each stimulus presentation: one for background alone and one for
background + probe. All the spike times are with respect to the
preceding stimulus.
"""
plot = 'all'
bg_spikes = defaultdict(list)
probe_spikes = defaultdict(list)
for fh in fhandles:
stiminfo = dict(fh['runconfig/stimulus'][:])
simtime = float(dict(fh['runconfig/scheduling'])['simtime'])
stim_onset = float(stiminfo['onset'])
interval = float(stiminfo['bg_interval'])
stimwidth = float(stiminfo['pulse_width'])
spike_times = get_spike_times(fh, cellnames)
bgtimes = analyzer.get_bgtimes(fh)
probetimes = analyzer.get_probetimes(fh)
print 'Background times', bgtimes
print 'Probe times', probetimes
bgbins = [(bgtimes[ii], bgtimes[ii]+interval+stimwidth) for ii in range(0, len(bgtimes), 2)]
print bgbins
probebins = [(pt, pt+interval+stimwidth) for pt in probetimes]
print probebins
# Probe stimulus is designed to align with every alternet bg
# stmulus.
cell_no = 1
for cell, spikes in spike_times.items():
bg = [spikes[(spikes >= bin[0]) & (spikes < bin[1])]
for bin in bgbins]
bg_spikes[cell] += bg
probe = [spikes[(spikes >= bin[0]) & (spikes < (bin[1]))]
for bin in probebins]
probe_spikes[cell] += probe
for x in bg:
print 'bg', x
for x in probe:
print 'probe', x
if plot is not None:
x = np.concatenate(bg)
plt.plot(x, np.ones(len(x))*cell_no, 'bx')
x = np.concatenate(probe)
plt.plot(x, np.ones(len(x))*cell_no, 'r+')
if plot == 'each':
plt.title('%s: %s' % (fh.filename, cell))
plt.show()
elif plot == 'all':
cell_no += 1
if plot == 'all':
plt.title(fh.filename)
plt.show()
return (bg_spikes, probe_spikes)