def autoAnalysis(kwik_fullpath):
model = KwikModel(kwik_fullpath)
kwikPath,kwikFile = os.path.split(kwik_fullpath)
allsamples = []
allspikes = []
for j in model.channel_groups: # for statement walks through different channel_groups (i.e., those on different shanks)
model.channel_group = j
samples = model.spike_samples
spikes = model.spike_clusters
for i,n in enumerate(spikes):
allsamples.append(samples[i])
allspikes.append(spikes[i])
alltimes = np.array(allsamples)/model.sample_rate
allspikes = np.array(allspikes)
#plt.figure(figsize=(15,5))
#plt.plot(alltimes, allspikes, '|',mew=.5,color=[.5,.5,.5])
#plt.savefig(kwikPath+'\\allSpikes.png')
[di, ai] = liic.load_intan_input_channels()
intan_trigger = di['0'][:]
intan_camera = di['1'][:]
intan_transitions = np.where(intan_trigger[:-1] != intan_trigger[1:])[0]
adjustmentAmount = (intan_transitions[0])
[matlab_trigger, matlab_triggerCMD, matlab_brush] = loadMatlabFile(adjustmentAmount)
plt.figure(figsize=(15,10))
plt.subplot(211)
plt.plot(alltimes, allspikes, '|',color =[.5,.5,.5],markersize=5,mew=.4)
plt.ylabel('unit')
topxlim = plt.xlim()
plt.xlim(topxlim)
plt.subplot(212)
plt.plot(np.arange(0,len(matlab_brush)/20000,1/20000),matlab_brush,color = [.5,.5,.5],linewidth=.5)
plt.savefig(kwikPath+'\\brushSpikes.png')
