def generate_prediction(self, model):
model.inject_square_current(observation['current'])
spike_train = model.get_spike_train()
if len(spike_train) >= 3:
cv(spike_train)*pq.dimensionless
#isis = isi(spike_train)
#cv_old = np.std(isis) / np.mean(isis)
else:
cv = None
return {'cv':cv}
def generate_prediction(self, model):
model.inject_square_current(observation['current'])
spike_train = model.get_spike_train()
if len(spike_train) >= 3:
cv(spike_train) * pq.dimensionless
#isis = isi(spike_train)
#cv_old = np.std(isis) / np.mean(isis)
else:
cv = None
return {'cv': cv}
def generate_prediction(self, model, **kwargs):
isi_var = self.get_prediction(model)
if isi_var is None:
if kwargs:
self.params.update(kwargs)
if 'variation_measure' not in self.params:
self.params.update(variation_measure='lv')
spiketrains = model.produce_spiketrains(**self.params)
isi_list = [isi(st) for st in spiketrains]
if self.params['variation_measure'] == 'lv':
isi_var = []
for intervals in isi_list:
if intervals.size > 2:
isi_var.append(lv(intervals))
elif self.params['variation_measure'] == 'cv':
isi_var = []
for intervals in isi_list:
if intervals.size > 2:
isi_var.append(cv(intervals))
elif self.params['variation_measure'] == 'isi':
isi_var = [
float(item) for sublist in isi_list for item in sublist
]
else:
raise ValueError('Variation measure not known.')
self.set_prediction(model, isi_var)
return isi_var
def spike_statistics(idx, row):
from elephant.statistics import mean_firing_rate, cv, isi
from elephant.conversion import BinnedSpikeTrain
from elephant.spike_train_correlation import corrcoef
print(idx)
results = {}
# read spike trains from file
io = get_io(row["output_file"])
data_block = io.read()[0]
spiketrains = data_block.segments[0].spiketrains
# calculate mean firing rate
results["spike_counts"] = sum(st.size for st in spiketrains)
rates = [mean_firing_rate(st) for st in spiketrains]
results["firing_rate"] = Quantity(rates, units=rates[0].units).rescale("1/s").mean()
# calculate coefficient of variation of the inter-spike interval
cvs = [cv(isi(st)) for st in spiketrains if st.size > 1]
if len(cvs) > 0:
results["cv_isi"] = sum(cvs)/len(cvs)
else:
results["cv_isi"] = 0
# calculate global cross-correlation
#cc_matrix = corrcoef(BinnedSpikeTrain(spiketrains, binsize=5*ms))
#results["cc_min"] = cc_matrix.min()
#results["cc_max"] = cc_matrix.max()
#results["cc_mean"] = cc_matrix.mean()
io.close()
return results
def generate_prediction(self, model):
model.inject_square_current(self.run_params['current'])
spike_train = model.get_spike_train()
if len(spike_train) >= 3:
value = cv(spike_train)*pq.dimensionless
else:
value = None
return {'cv': value}
def generate_prediction(self, model=None):
st = model.get_spike_train()
if len(st) >= 3:
value = abs(cv(st))*pq.dimensionless
else:
value = None
prediction = {'cv': value}
return prediction
def generate_prediction(self, model = None):
st = model.get_spike_train()
#prediction = abs(cv(st))
if len(st) >= 3:
value = abs(cv(st))*pq.dimensionless
else:
value = None
prediction = {'cv':value}
return prediction
def calc_cv_isi_hist(spike_times, spike_ids, num, duration, bin_x=None):
# Loop through neurons
cv_isi = []
for n in range(num):
# Get mask of spikes from this neuron and use to extract their times
mask = (spike_ids == n)
neuron_spike_times = spike_times[mask]
# If this neuron spiked more than once i.e. it is possible to calculate ISI!
if len(neuron_spike_times) > 1:
cv_isi.append(cv(isi(neuron_spike_times)))
return calc_histogram(cv_isi, 0.04, bin_x)
def calculate_neuron_cov(col, num_mins_per_bin, total_time):
num_bins = np.int(total_time / num_mins_per_bin)
col_bins = np.array_split(col, num_bins)
cv_isis = pd.Series(np.zeros(num_bins))
for ind, col_bin in enumerate(col_bins):
spike_times = pd.to_numeric(col_bin[col_bin.notnull()].index.values)
try:
spike_train = SpikeTrain(times=spike_times,
t_stop=spike_times[-1],
units=ns)
plt.tight_layout()
cv_isi = cv(isi(spike_train))
except IndexError:
cv_isi = np.nan
cv_isis[ind] = cv_isi
return cv_isis
# In[6]:
dir(ass)
# In[40]:
#dir(spike_trains)
#len(spike_trains)
from elephant.statistics import cv
import matplotlib.pyplot as plt
hist_cv = []
import numpy as np
for i in spike_trains:
cva = cv(i)
if np.isnan(cva):
hist_cv.append(0)
else:
hist_cv.append(cva)
# print(cv(i))
x_axis = [i for i in range(0, len(hist_cv))]
plt.bar(x_axis, hist_cv)
plt.show()
plt.hist(hist_cv)
#dir(elephant)
#plt.
# In[46]:
for i, spiketrain in enumerate(snglnrn_spikes_neo):
t = spiketrain.rescale(q.ms)
plt.plot(t, i * np.ones_like(t), 'k.', markersize=2)
plt.axis('tight')
plt.xlim(0, runtime)
plt.xlabel('Time (ms)', fontsize=16)
plt.ylabel('Spike Train Index', fontsize=16)
plt.gca().tick_params(axis='both', which='major', labelsize=14)
plt.savefig('decorr_rasterplot_w{}_k{}.png'.format(w, numInhPerNeuron))
'''
# calculate ISIs and coefficient of variation (CV)
isi_list = [np.nanmean(isi(spiketrain)) for spiketrain in snglnrn_spikes_neo]
rate_list = [(np.size(spiketrain) / runtime * 1e3) for spiketrain in snglnrn_spikes]
cv_list = [cv(isi(spiketrain)) for spiketrain in snglnrn_spikes_neo]
train = BinnedSpikeTrain(snglnrn_spikes_neo, binsize=5 * q.ms)
cc_matrix = corrcoef(train, binary=False)
# Matrix zwischenspeichern
#np.savetxt('cc_matrix.txt', cc_matrix)
#print(np.shape(cc_matrix)) # (192, 192)
#print(cc_matrix)
#plt.plot(cc_matrix)
# Hauptdiagonale entfernen
for i in range(192):
cc_matrix[i][i] = np.nan
def test_cv_isi_regular_array_is_zero(self):
st = self.test_array_regular
targ = 0.0
res = es.cv(es.isi(st))
self.assertEqual(res, targ)
def test_cv_isi_regular_spiketrain_is_zero(self):
st = neo.SpikeTrain(self.test_array_regular, units='ms', t_stop=10.0)
targ = 0.0
res = es.cv(es.isi(st))
self.assertEqual(res, targ)
def test_cv_isi_regular_spiketrain_is_zero(self):
st = neo.SpikeTrain(self.test_array_regular, units='ms', t_stop=10.0)
targ = 0.0
res = es.cv(es.isi(st))
self.assertEqual(res, targ)
mean_rate = np.divide(rate, (max_ms - min_ms) / 1000.0, dtype=float)
print("Mean firing rate: %fHz" % np.average(mean_rate))
# Sort spikes by id
neuron_spikes = spikes.groupby("id")
# Loop through neurons
cv_isi = []
for n in range(num_excitatory):
try:
# Get this neuron's spike times
neuron_spike_times = neuron_spikes.get_group(n)["time"].values
# If this neuron spiked more than once i.e. it is possible to calculate ISI!
if len(neuron_spike_times) > 1:
cv_isi.append(cv(isi(neuron_spike_times)))
except KeyError:
pass
print("Mean CV ISI: %f" % np.average(cv_isi))
# Pick 1000 neurons
binned_spike_times = None
for i, n in enumerate(np.random.choice(num_excitatory, 1000, replace=False)):
# Get this neuron's spike times
neuron_spike_times = neuron_spikes.get_group(n)["time"].values
# Bin spike times
neuron_binned_spike_times, _ = np.histogram(neuron_spike_times,
bins=np.arange(
min_ms, max_ms, 3))
sta_i_df = None
sta_ind = None
sta_avg = None
plt.legend()
#plt.show()
plt.savefig(item+'_sta_meansubtracted.png',dpi=600,format='png')
#%% ISI and CV isi, has problem when there are no spikes at all.
os.chdir('/home/ngg1/[email protected]/Data_Urban/NEURON/Analysis/'
'AlmogAndKorngreen2014/ModCell_5_thrdsafe/summary')
from elephant.statistics import isi, cv
cvdf = pd.Series()
for item in g_list:
for key in channels[item]:
isi_list = [isi(spiketrain) for spiketrain in channels[item][key]['spikeTimes500']]
cv_list = [cv(isi_list[i]) for i in range(len(isi_list))]
channels[item][key]['isi'] = isi_list
channels[item][key]['CVisi'] = np.mean(cv_list)
cv_mean = pd.Series(np.mean(cv_list))
cvdf = pd.concat([cvdf,cv_mean])
stats3df = pd.concat([statsdf2,cvdf],axis=1)
stats3df = stats3df.rename(columns = {0:'CV ISI'})
stats3df.to_csv('wns_delta_stats3.csv',float_format='%10.4f',index=False,header=True)
#%% plot cv isi as function of delta conductance
os.chdir('/home/ngg1/[email protected]/Data_Urban/NEURON/Analysis/'
'AlmogAndKorngreen2014/ModCell_5_thrdsafe/figures')
plt.figure()
plt.xlabel('Global Channel Conductance Factor')
plt.ylabel('CV ISI')
for item in g_list:
raster_list.append(t)
plt.plot(t, (i + 1) * np.ones_like(t), 'k.', markersize=2)
plt.axis('tight')
plt.xlim(0, 3100)
plt.xlabel('Time (ms)', fontsize=16)
plt.ylim(0, 51)
plt.ylabel('Trial Number', fontsize=16)
plt.gca().tick_params(axis='both', which='major', labelsize=14)
plt.show()
#%%
#CV isi NEVER CONVERTED FOR MULTIPLE FILES###
from elephant.statistics import isi, cv
isi_list = [isi(spiketrain) for spiketrain in st_list]
cv_list = [cv(item) for item in isi_list]
plt.figure()
plt.hist(cv_list)
plt.xlabel('CV', fontsize=16)
plt.ylabel('count', fontsize=16)
plt.show()
plt.figure()
plt.plot(cv_list)
#%%
"""
28Sep2017
NOTE: Work on conversion of discrete spike time lists to binary spike counts.
Use this conversion for PSTH and for spike-time correlations.
"""
##ADDED bstc_df to cut the first 500 ms of data out for correlations
###conversion of discrete spike times to binary counts
def main(p,file,save_path):
pre = 10*pq.ms
post = 10*pq.ms
fid = PIO(file)
blk = fid.read_block()
FR,ISI,contact_trains = get_contact_sliced_trains(blk,pre=pre,post=post)
binsize = 2*pq.ms
for unit in blk.channel_indexes[-1].units:
root = blk.annotations['ratnum'] + blk.annotations['whisker'] + 'c{}'.format(unit.name[-1])
trains = contact_trains[unit.name]
all_isi = np.array([])
CV_array = np.array([])
LV_array = np.array([])
for interval in ISI[unit.name]:
all_isi = np.concatenate([all_isi,interval])
if np.all(np.isfinite(interval)):
CV_array = np.concatenate([CV_array,[cv(interval)]])
LV_array = np.concatenate([LV_array,[lv(interval)]])
all_isi = all_isi * interval.units
CV_array = CV_array
CV = np.mean(CV_array)
LV = np.mean(LV_array)
## calculate data for PSTH
b,durations = get_binary_trains(contact_trains[unit.name])
b_times = np.where(b)[1] * pq.ms#interval.units
b_times-=pre
PSTH,t_edges = np.histogram(b_times,bins=np.arange(-np.array(pre),np.max(durations)+np.array(post),float(binsize)))
plt.bar(t_edges[:-1],
PSTH.astype('f8')/len(durations)/binsize*1000,
width=float(binsize),
align='edge',
alpha=0.8
)
ax = plt.gca()
thresh = 500 * pq.ms
ax.set_xlim(-15, thresh.__int__())
ax.set_xlabel('Time after contact (ms)')
ax.set_ylabel('Spikes per second')
ax.set_title('PSTH for: {}'.format(root))
plt.savefig(os.path.join(save_path,root+'_PSTH.svg'))
plt.close('all')
# ============================================
# PLOT ISIs
plt.figure()
thresh = 100 * pq.ms
if len(all_isi[np.logical_and(np.isfinite(all_isi), all_isi < thresh)])==0:
return
ax = sns.distplot(all_isi[np.logical_and(np.isfinite(all_isi), all_isi < thresh)],
bins=np.arange(0,100,1),
kde_kws={'color':'k','lw':3,'alpha':0.5,'label':'KDE'})
ax.set_xlabel('ISI '+all_isi.dimensionality.latex)
ax.set_ylabel('Percentage of all ISIs')
a_inset = plt.axes([.55, .5, .2, .2], facecolor='w')
a_inset.grid(color='k',linestyle=':',alpha=0.4)
a_inset.axvline(CV,color='k',lw=0.5)
a_inset.set_title('CV = {:0.2f}\nLV = {:0.2f}'.format(CV,LV))
a_inset.set_xlabel('CV')
a_inset.set_ylabel('# of Contacts')
sns.distplot(CV_array,color='g',kde=False)
ax.set_title('ISI distribution for {}'.format(root))
plt.savefig(os.path.join(save_path, root + '_ISI.svg'))
plt.close('all')
def get_CV(spike_train):
from elephant.statistics import cv
return cv(get_ISI(spike_train))
def iter_plot0(md):
import seaborn as sns
import pickle
with open('cell_indexs.p', 'rb') as f:
returned_list = pickle.load(f)
index_exc = returned_list[0]
index_inh = returned_list[1]
index, mdf1 = md
#wgf = {0.025:None,0.05:None,0.125:None,0.25:None,0.3:None,0.4:None,0.5:None,1.0:None,1.5:None,2.0:None,2.5:None,3.0:None}
wgf = {
0.0025: None,
0.0125: None,
0.025: None,
0.05: None,
0.125: None,
0.25: None,
0.3: None,
0.4: None,
0.5: None,
1.0: None,
1.5: None,
2.0: None,
2.5: None,
3.0: None
}
weight_gain_factors = {k: v for k, v in enumerate(wgf.keys())}
print(len(weight_gain_factors))
print(weight_gain_factors.keys())
#weight_gain_factors = {0:0.5,1:1.0,2:1.5,3:2.0,4:2.5,5:3}
#weight_gain_factors = {:None,1.0:None,1.5:None,2.0:None,2.5:None}
k = weight_gain_factors[index]
#print(len(mdf1.segments),'length of block')
ass = mdf1.analogsignals[0]
time_points = ass.times
avg = np.mean(ass, axis=0) # Average over signals of Segment
#maxx = np.max(ass, axis=0) # Average over signals of Segment
std = np.std(ass, axis=0) # Average over signals of Segment
#avg_minus =
plt.figure()
plt.plot([i for i in range(0, len(avg))], avg)
plt.plot([i for i in range(0, len(std))], std)
plt.title("Mean and Standard Dev of $V_{m}$ amplitude per neuron ")
plt.xlabel('time $(ms)$')
plt.xlabel('Voltage $(mV)$')
plt.savefig(str(index) + 'prs.png')
vm_spiking = []
vm_not_spiking = []
spike_trains = []
binary_trains = []
max_spikes = 0
vms = np.array(mdf1.analogsignals[0].as_array().T)
#print(data)
#for i,vm in enumerate(data):
cnt = 0
for spiketrain in mdf1.spiketrains:
#spiketrain = mdf1.spiketrains[index]
y = np.ones_like(spiketrain) * spiketrain.annotations['source_id']
#import sklearn
#sklearn.decomposition.NMF(y)
# argument edges is the time interval you want to be considered.
pspikes = pyspike.SpikeTrain(spiketrain, edges=(0, len(ass)))
spike_trains.append(pspikes)
if len(spiketrain) > max_spikes:
max_spikes = len(spiketrain)
if np.max(ass[spiketrain.annotations['source_id']]) > 0.0:
vm_spiking.append(vms[spiketrain.annotations['source_id']])
else:
vm_not_spiking.append(vms[spiketrain.annotations['source_id']])
cnt += 1
for spiketrain in mdf1.spiketrains:
x = conv.BinnedSpikeTrain(spiketrain,
binsize=1 * pq.ms,
t_start=0 * pq.s)
binary_trains.append(x)
end_floor = np.floor(float(mdf1.t_stop))
dt = float(mdf1.t_stop) % end_floor
mdf1.t_start
#v = mdf1.take_slice_of_analogsignalarray_by_unit()
t_axis = np.arange(float(mdf1.t_start), float(mdf1.t_stop), dt)
plt.figure()
plt.clf()
plt.figure()
plt.clf()
cleaned = []
data = np.array(mdf1.analogsignals[0].as_array().T)
#print(data)
for i, vm in enumerate(data):
if np.max(vm) > 900.0 or np.min(vm) < -900.0:
pass
else:
plt.plot(ass.times, vm) #,label='neuron identifier '+str(i)))
cleaned.append(vm)
#vm = s#.as_array()[:,i]
assert len(cleaned) < len(ass)
print(len(cleaned))
plt.title('neuron $V_{m}$')
#plt.legend(loc="upper left")
plt.savefig(str('weight_') + str(k) + 'analogsignals' + '.png')
plt.xlabel('Time $(ms)$')
plt.ylabel('Voltage $(mV)$')
plt.close()
#pass
plt.figure()
plt.clf()
plt.title('Single Neuron $V_{m}$ trace')
plt.plot(ass.times[0:int(len(ass.times) / 10)],
vm_not_spiking[index_exc[0]][0:int(len(ass.times) / 10)])
plt.xlabel('$ms$')
plt.ylabel('$mV$')
plt.xlabel('Time $(ms)$')
plt.ylabel('Voltage $(mV)$')
plt.savefig(str('weight_') + str(k) + 'eespecific_analogsignals' + '.png')
plt.close()
plt.figure()
plt.clf()
plt.title('Single Neuron $V_{m}$ trace')
plt.plot(ass.times[0:int(len(ass.times) / 10)],
vm_not_spiking[index_inh[0]][0:int(len(ass.times) / 10)])
plt.xlabel('$ms$')
plt.ylabel('$mV$')
plt.savefig(str('weight_') + str(k) + 'inhibitory_analogsignals' + '.png')
plt.close()
cvs = [0 for i in range(0, len(spike_trains))]
cvsd = {}
cvs = []
cvsi = []
rates = [] # firing rates per cell. in spikes a second.
for i, j in enumerate(spike_trains):
rates.append(float(len(j) / 2.0))
cva = cv(j)
if np.isnan(cva) or cva == 0:
pass
#cvs[i] = 0
#cvsd[i] = 0
else:
pass
#cvs[i] = cva
#cvsd[i] = cva
cvs.append(cva)
#import pickle
#with open(str('weight_')+str(k)+'coefficients_of_variation.p','wb') as f:
# pickle.dump([cvs,cvsd],f)
import numpy
a = numpy.asarray(cvs)
numpy.savetxt('pickles/' + str('weight_') + str(k) +
'coefficients_of_variation.csv',
a,
delimiter=",")
import numpy
a = numpy.asarray(rates)
numpy.savetxt('pickles/' + str('weight_') + str(k) + 'firing_of_rate.csv',
a,
delimiter=",")
cvs = [i for i in cvs if i != 0]
cells = [i for i in range(0, len(cvs))]
plt.clf()
fig, axes = plt.subplots()
axes.set_title('Coefficient of Variation Versus Neuron')
axes.set_xlabel('Neuron number')
axes.set_ylabel('CV estimate')
mcv = np.mean(cvs)
#plt.scatter(cells,cvs)
cvs = np.array(cvs)
plt.scatter(index_inh, cvs[index_inh], label="inhibitory cells")
plt.scatter(index_exc, cvs[index_exc], label="excitatory cells")
plt.legend(loc="upper left")
fig.tight_layout()
plt.savefig(str('weight_') + str(k) + 'cvs_mean_' + str(mcv) + '.png')
plt.close()
plt.clf()
#frequencies, power = elephant.spectral.welch_psd(ass)
#mfreq = frequencies[np.where(power==np.max(power))[0][0]]
#fig, axes = plt.subplots()
axes.set_title('Firing Rate Versus Neuron Number at mean f=' +
str(np.mean(rates)) + str('(Spike Per Second)'))
axes.set_xlabel('Neuron number')
axes.set_ylabel('Spikes per second')
rates = np.array(rates)
plt.scatter(index_inh, rates[index_inh], label="inhibitory cells")
plt.scatter(index_exc, rates[index_exc], label="excitatory cells")
plt.legend(loc="upper left")
fig.tight_layout()
plt.savefig(str('firing_rates_per_cell_') + str(k) + str(mcv) + '.png')
plt.close()
'''
import pandas as pd
d = {'coefficent_of_variation': cvs, 'cells': cells}
df = pd.DataFrame(data=d)
ax = sns.regplot(x='cells', y='coefficent_of_variation', data=df)#, fit_reg=False)
plt.savefig(str('weight_')+str(k)+'cvs_regexp_'+str(mcv)+'.png');
plt.close()
'''
spike_trains = []
ass = mdf1.analogsignals[0]
tstop = mdf1.t_stop
np.max(ass.times) == mdf1.t_stop
#assert tstop == 2000
tstop = 2000
vm_spiking = []
for spiketrain in mdf1.spiketrains:
vm_spiking.append(
mdf1.analogsignals[0][spiketrain.annotations['source_id']])
y = np.ones_like(spiketrain) * spiketrain.annotations['source_id']
# argument edges is the time interval you want to be considered.
pspikes = pyspike.SpikeTrain(spiketrain, edges=(0, tstop))
spike_trains.append(pspikes)
# plot the spike times
plt.clf()
for (i, spike_train) in enumerate(spike_trains):
plt.scatter(spike_train, i * np.ones_like(spike_train), marker='.')
plt.xlabel('Time (ms)')
plt.ylabel('Cell identifier')
plt.title('Raster Plot for weight strength:' + str(k))
plt.savefig(str('weight_') + str(k) + 'raster_plot' + '.png')
plt.close()
f = spk.isi_profile(spike_trains, indices=[0, 1])
x, y = f.get_plottable_data()
#text_file.close()
text_file = open(str('weight_') + str(index) + 'net_out.txt', 'w')
plt.figure()
plt.plot(x, np.abs(y), '--k', label="ISI-profile")
print("ISI-distance: %.8f" % f.avrg())
f = spk.spike_profile(spike_trains, indices=[0, 1])
x, y = f.get_plottable_data()
plt.plot(x, y, '-b', label="SPIKE-profile")
#print("SPIKE-distance: %.8f" % f.avrg())
string_to_write = str("ISI-distance:") + str(f.avrg()) + str("\n\n")
plt.title(string_to_write)
plt.xlabel('Time $(ms)$')
plt.ylabel('ISI distance')
plt.legend(loc="upper left")
plt.savefig(str('weight_') + str(k) + 'ISI_distance_bivariate' + '.png')
plt.close()
text_file.write(string_to_write)
#text_file.write("SPIKE-distance: %.8f" % f.avrg())
#text_file.write("\n\n")
plt.figure()
f = spk.spike_sync_profile(spike_trains[0], spike_trains[1])
x, y = f.get_plottable_data()
plt.plot(x, y, '--ok', label="SPIKE-SYNC profile")
print(f, f.avrg())
print("Average:" + str(f.avrg()))
#print(len(f.avrg()),f.avrg())
string_to_write = str("instantaneous synchrony:") + str(
f.avrg()) + 'weight: ' + str(index)
plt.title(string_to_write)
plt.xlabel('Time $(ms)$')
plt.ylabel('instantaneous synchrony')
text_file.write(string_to_write)
#text_file.write(list())
f = spk.spike_profile(spike_trains[0], spike_trains[1])
x, y = f.get_plottable_data()
plt.plot(x, y, '-b', label="SPIKE-profile")
plt.axis([0, 4000, -0.1, 1.1])
plt.legend(loc="center right")
plt.clf()
plt.figure()
plt.subplot(211)
f = spk.spike_sync_profile(spike_trains)
x, y = f.get_plottable_data()
plt.plot(x, y, '-b', alpha=0.7, label="SPIKE-Sync profile")
x1, y1 = f.get_plottable_data(averaging_window_size=50)
plt.plot(x1, y1, '-k', lw=2.5, label="averaged SPIKE-Sync profile")
plt.subplot(212)
f_psth = spk.psth(spike_trains, bin_size=50.0)
x, y = f_psth.get_plottable_data()
plt.plot(x, y, '-k', alpha=1.0, label="PSTH")
plt.savefig(str('weight_') + str(k) + 'multivariate_PSTH' + '.png')
plt.close()
plt.xlabel('Time $(ms)$')
plt.ylabel('Spikes per bin')
plt.clf()
plt.figure()
f_psth = spk.psth(spike_trains, bin_size=50.0)
x, y = f_psth.get_plottable_data()
plt.plot(x, y, '-k', alpha=1.0, label="PSTH")
plt.savefig(str('weight_') + str(k) + 'exclusively_PSTH' + '.png')
plt.close()
plt.figure()
isi_distance = spk.isi_distance_matrix(spike_trains)
plt.imshow(isi_distance, interpolation='none')
plt.title('Pairwise ISI distance, T=0-2000')
plt.xlabel('post-synaptic neuron number')
plt.ylabel('pre-synaptic neuron number')
plt.title("ISI-distance")
plt.savefig(str('weight_') + str(k) + 'ISI_distance' + '.png')
plt.close()
#plt.show()
plt.figure()
plt.clf()
import seaborn as sns
sns.set()
sns.clustermap(isi_distance) #,vmin=-,vmax=1);
plt.savefig(str('weight_') + str(k) + 'cluster_isi_distance' + '.png')
plt.close()
plt.figure()
spike_distance = spk.spike_distance_matrix(spike_trains,
interval=(0, float(tstop)))
import pickle
with open('spike_distance_matrix.p', 'wb') as f:
pickle.dump(spike_distance, f)
plt.imshow(spike_distance, interpolation='none')
plt.title("Pairwise SPIKE-distance, T=0-2000")
plt.xlabel('post-synaptic neuron number')
plt.ylabel('pre-synaptic neuron number')
plt.savefig(str('weight_') + str(k) + 'spike_distance_matrix' + '.png')
plt.close()
plt.figure()
plt.clf()
sns.set()
sns.clustermap(spike_distance)
plt.savefig(str('weight_') + str(k) + 'cluster_spike_distance' + '.png')
plt.close()
plt.figure()
spike_sync = spk.spike_sync_matrix(spike_trains,
interval=(0, float(tstop)))
plt.imshow(spike_sync, interpolation='none')
plt.title('Pairwise Spike Synchony, T=0-2000')
plt.xlabel('post-synaptic neuron number')
plt.ylabel('pre-synaptic neuron number')
import numpy
a = numpy.asarray(spike_sync)
numpy.savetxt("spike_sync_matrix.csv", a, delimiter=",")
plt.figure()
plt.clf()
sns.clustermap(spike_sync)
plt.savefig(
str('weight_') + str(k) + 'cluster_spike_sync_distance' + '.png')
plt.close()
plt.hist(hist_isi, bins=100)
plt.xlim((0, 20))
if plot_isi_scattergram:
plt.figure("ISI scattergram {}".format(ear_index))
# plt.ylabel("ISI + 1 (ms)")
# plt.xlabel("ISI (ms)")
sr = math.sqrt(len(neuron_list))
num_cols = np.ceil(sr)
num_rows = np.ceil(len(neuron_list) / num_cols)
plt.subplot(num_rows, num_cols, i + 1)
plt.plot(isi_n[0], isi_n[1], '.')
plt.ylim((0, 30))
plt.xlim((0, 30))
if plot_isi_cv:
plt.figure("CV {}".format(ear_index))
cvs = [cv(interval) for interval in t_isi if len(interval) > 0]
plt.subplot(len(neuron_list), 1, i + 1)
plt.hist(cvs) #,bins=100)
plt.xlim((0, 2))
# plt.ylim((0,100))
if plot_moc:
plt.figure("moc ear {} test {}".format(ear_index, test_index))
n_channels = len(moc_att[ear_index])
# a = np.sum(moc_att[ear_index][::n_channels/10],axis=0)
# a = moc_att[ear_index][n_channels/2]
# plt.plot(a)
# print "ear {} zero moc spikes {}".format(ear_index,len(np.where(a<1)[0]))
for i, moc in enumerate(moc_att[ear_index][::n_channels / 10]):
# for i,moc in enumerate(moc_att[ear_index][::1]):
# for i,moc in enumerate([moc_att[ear_index][n_channels/20]]):
def compute_cv(a, v_ext, g):
from elephant.statistics import isi, cv
times = read_file(a, v_ext, g)
cv_list = [cv(isi(spiketrain)) for spiketrain in times.values()]
return np.nanmean(cv_list)
def test_cv_isi_regular_array_is_zero(self):
st = self.test_array_regular
targ = 0.0
res = es.cv(es.isi(st))
self.assertEqual(res, targ)
os.chdir('Analysis/PSTH') # /PSTH')
plt.savefig('Noise_PSTH_' + file_name + '.png', bbox_inches='tight')
plt.close()
os.chdir('../..')
print 'PSTH for ' + file_name + 'saved'
#%% CV-ISI
"""
The below calculates CV-ISI from only the latter 2.5 s current step, output = half_mean_CV
Method = drop values from neospiketrain_list that occur before 1000 ms, then calculating ISI and CV from that
"""
from elephant.statistics import isi, cv
half_isi_list = [isi(spiketrain) for spiketrain in half_spiketime_list]
half_cv_list = [cv(item) for item in half_isi_list]
half_isi_list = [
isis for i, isis in enumerate(half_isi_list) if i not in depolarized_sweeps
]
#excluding depolarized sweeps - can't use del_half_spiketime_list bc
#need to sort by current injection later
for item in exclude:
half_cv_list[item] = np.nan
half_mean_CV = np.nanmean(half_cv_list)
#%% Plot ISI histogram for second 1.5 s half of sweep