def test_regression_15_isi():
# load spike trains
spike_trains = spk.load_spike_trains_from_txt(TEST_DATA, edges=[0, 4000])
N = len(spike_trains)
dist_mat = spk.isi_distance_matrix(spike_trains)
assert_equal(dist_mat.shape, (N, N))
ind = np.arange(N // 2)
dist_mat = spk.isi_distance_matrix(spike_trains, ind)
assert_equal(dist_mat.shape, (N // 2, N // 2))
ind = np.arange(N // 2, N)
dist_mat = spk.isi_distance_matrix(spike_trains, ind)
assert_equal(dist_mat.shape, (N // 2, N // 2))
def multiprocessFunctions(analysis):
if analysis == 'isi_distance':
#print ('isi distance')
print("ISI distance calcualtion started!!!")
plt.figure()
isi_distance = spk.isi_distance_matrix(spike_trains, interval=None)
isi_distance[isi_distance > 1] = 1
print(isi_distance)
np.save("isi_distance", isi_distance)
np.savetxt("isi_distance.csv", isi_distance, delimiter=",")
isi_distance = spk.isi_distance_matrix(spike_trains,
interval=(0, 5000))
isi_distance[isi_distance > 1] = 1
print(isi_distance)
np.save("isi_distance", isi_distance)
plt.imshow(isi_distance, clim=(0.0, 1.0), interpolation='nearest')
plt.colorbar()
plt.title("ISI-distance(0-100ms)")
print('----------Took %s seconds for isi distance-----' %
(time.time() - start_time))
plt.show()
elif analysis == 'spike_distance':
#print ('spike distance')
plt.figure()
spike_distance = spk.spike_distance_matrix(spike_trains,
interval=(0, 100))
spike_distance[spike_distance > 1] = 1
np.save("spike_distance", spike_distance)
plt.imshow(spike_distance, clim=(0.0, 1.0), interpolation='nearest')
plt.colorbar()
plt.title("SPIKE-distance(0-100ms)")
print('----------Took %s seconds for spike distance-----' %
(time.time() - start_time))
plt.show()
elif analysis == 'spike_sync':
#print ('spike sync')
plt.figure()
spike_sync = spk.spike_sync_matrix(spike_trains, interval=(3300, 3500))
plt.imshow(spike_sync, interpolation='none')
plt.colorbar()
plt.title("SPIKE-Sync")
print('----------Took %s seconds for spike_sync-----' %
(time.time() - start_time))
plt.show()
else:
pass
def get_matrix(select='subset',
min_spike_number=0,
save=None,
analysis=['SPIKE-Sync'],
network=[0]):
import pyspike
load_data(network)
getmat = {}
empty_dict_array = {}
no_empty_dict_array = {}
spkts = {}
spkinds = {}
spktsRange = {}
spkt_train = {}
spike_sync = {}
for f, p in enumerate(data_files):
if f in network:
spkts[f] = d[p]['simData']['spkt'] #list
spkinds[f] = d[p]['simData']['spkid'] #list
print 'Starting analysis of spike times per ' + str(
select) + ': ' + str(p)
for t, y in enumerate(timeRange):
spktsRange = [
spkt for spkt in spkts[f]
if timeRange[t][0] <= spkt <= timeRange[t][1]
]
spkt_train[str(f) + str(t)] = []
if select == 'subset':
print 'Time Range: ' + str(y)
empty_array = np.zeros(
((len(net_labels) * 2), (len(net_labels) * 2)))
no_empty_array = np.zeros(
((len(net_labels) * 2), (len(net_labels) * 2)))
array_ii = np.zeros(
((len(net_labels) * 2), (len(net_labels) * 2)))
empty_gids = []
gids_included = []
for k, v in enumerate(gids):
train = []
for i, gid in enumerate(v):
for spkind, spkt in zip(spkinds[f], spkts[f]):
if (spkind == gid and spkt in spktsRange):
train.append(spkt)
spkt_train[str(f) + str(t)].append(
pyspike.SpikeTrain(train, timeRange[t]))
if len(train) < min_spike_number:
empty_gids.append(k)
else:
gids_included.append(k)
for i in range(len(spkt_train[str(f) + str(t)])):
if i in gids_included:
for k, v in enumerate(gids_included):
no_empty_array[i][v] = 1.0
for l in range(len(array_ii)):
array_ii[l][l] = 1.0
no_empty_dict_array[str(f) + str(t)] = no_empty_array
elif select == 'cell':
print 'Time Range: ' + str(y)
empty_array = np.zeros(
((len(net_labels) * 80), (len(net_labels) * 80)))
no_empty_array = np.zeros(
((len(net_labels) * 80), (len(net_labels) * 80)))
empty_gids = []
spkmat2 = []
gids_included = []
#sync = np.zeros(((len(net_labels)*80),(len(net_labels)*80)))
for ii, subset in enumerate(gids):
spkmat = [
pyspike.SpikeTrain([
spkt
for spkind, spkt in zip(spkinds[f], spkts[f])
if (spkind == gid and spkt in spktsRange)
], timeRange[t]) for gid in set(subset)
]
spkt_train[str(f) + str(t)].extend(spkmat)
for gid in set(subset):
list_spkt = [
spkt
for spkind, spkt in zip(spkinds[f], spkts[f])
if (spkind == gid and spkt in spktsRange)
]
if len(list_spkt) < min_spike_number:
empty_gids.append(gid)
else:
spkmat2.append(
pyspike.SpikeTrain(list_spkt,
timeRange[t]))
gids_included.append(gid)
pos_labels.append(len(gids_included))
#print gids_included
empty_gids[:] = [x - 200 for x in empty_gids]
gids_included[:] = [x - 200 for x in gids_included]
#print empty_gids
for i in range(len(spkt_train[str(f) + str(t)])):
if i in empty_gids:
for k, v in enumerate(empty_gids):
empty_array[i][v] = 1.0
for i in range(len(spkt_train[str(f) + str(t)])):
if i in gids_included:
for k, v in enumerate(gids_included):
no_empty_array[i][v] = 1.0
#print empty_array
empty_dict_array[str(f) + str(t)] = empty_array
no_empty_dict_array[str(f) + str(t)] = no_empty_array
#print spkt_train
for l, mat in enumerate(mats):
#spike_sync
if (mat == 'ISI-distance' and mat in analysis):
print str(mat) + ", number of trains: " + str(
len(spkt_train[str(f) + str(t)]))
isi_distance = pyspike.isi_distance_matrix(
spkt_train[str(f) + str(t)])
getmat[str(f) + str(t) + str(l)] = isi_distance
elif (mat in analysis and mat == 'SPIKE-distance'):
print str(mat) + ", number of trains: " + str(
len(spkt_train[str(f) + str(t)]))
spike_distance = pyspike.spike_distance_matrix(
spkt_train[str(f) + str(t)])
getmat[str(f) + str(t) + str(l)] = spike_distance
elif (mat in analysis and mat == 'SPIKE-Sync'):
print str(mat) + ", number of trains: " + str(
len(spkt_train[str(f) + str(t)]))
spike_sync[str(f) +
str(t)] = pyspike.spike_sync_matrix(
spkt_train[str(f) + str(t)])
#if select == 'subset':
getmat[str(f) + str(t) + str(l)] = (
spike_sync[str(f) + str(t)] *
no_empty_dict_array[str(f) + str(t)]) + array_ii
#elif select == 'cell':
#getmat[str(f)+str(t)+str(l)] = spike_sync[str(f)+str(t)] * no_empty_dict_array[str(f)+str(t)]
empty_array = np.zeros(
((len(net_labels) * 80), (len(net_labels) * 80)))
else:
pass
if save == True:
with open(str(path) + 'data1.pkl', 'wb') as output:
pickle.dump(getmat, output)
return getmat
print 'finished getting data for matrix plotting'
Distributed under the BSD License
"""
# from __future__ import print_function
import matplotlib.pyplot as plt
import pyspike as spk
import numpy as np
# first load the data, interval ending time = 4000, start=0 (default)
spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt", 4000)
print(len(spike_trains))
plt.figure()
isi_distance = spk.isi_distance_matrix(spike_trains)
plt.imshow(isi_distance, interpolation='none')
plt.title("ISI-distance")
plt.savefig("fig/ISI-distance")
plt.close()
plt.figure()
spike_distance = spk.spike_distance_matrix(spike_trains, interval=(0, 1000))
plt.imshow(spike_distance, interpolation='none')
plt.title("SPIKE-distance, T=0-1000")
plt.savefig("fig/SPIKE-distance,T=0-1000")
plt.close()
plt.figure()
spike_sync = spk.spike_sync_matrix(spike_trains, interval=(2000, 4000))
plt.imshow(spike_sync, interpolation='none')
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()
"""
from __future__ import print_function
import matplotlib.pyplot as plt
import pyspike as spk
# first load the data, interval ending time = 4000, start=0 (default)
spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt", 4000)
print(len(spike_trains))
plt.figure()
isi_distance = spk.isi_distance_matrix(spike_trains)
plt.imshow(isi_distance, interpolation='none')
plt.title("ISI-distance")
plt.figure()
spike_distance = spk.spike_distance_matrix(spike_trains, interval=(0, 1000))
plt.imshow(spike_distance, interpolation='none')
plt.title("SPIKE-distance, T=0-1000")
plt.figure()
spike_sync = spk.spike_sync_matrix(spike_trains, interval=(2000, 4000))
plt.imshow(spike_sync, interpolation='none')
plt.title("SPIKE-Sync, T=2000-4000")
plt.show()
