def test_spike_empty():
st1 = SpikeTrain([], edges=(0.0, 1.0))
st2 = SpikeTrain([], edges=(0.0, 1.0))
d = spk.spike_distance(st1, st2)
assert_allclose(d, 0.0)
prof = spk.spike_profile(st1, st2)
assert_allclose(d, prof.avrg())
assert_array_equal(prof.x, [0.0, 1.0])
assert_array_equal(prof.y1, [
0.0,
])
assert_array_equal(prof.y2, [
0.0,
])
st1 = SpikeTrain([], edges=(0.0, 1.0))
st2 = SpikeTrain([
0.4,
], edges=(0.0, 1.0))
d = spk.spike_distance(st1, st2)
d_expect = 2 * 0.4 * 0.4 * 1.0 / (0.4 + 1.0)**2 + 2 * 0.6 * 0.4 * 1.0 / (
0.6 + 1.0)**2
assert_almost_equal(d, d_expect, decimal=15)
prof = spk.spike_profile(st1, st2)
assert_allclose(d, prof.avrg())
assert_array_equal(prof.x, [0.0, 0.4, 1.0])
assert_array_almost_equal(
prof.y1,
[2 * 0.4 * 1.0 / (0.4 + 1.0)**2, 2 * 0.4 * 1.0 / (0.6 + 1.0)**2],
decimal=15)
assert_array_almost_equal(
prof.y2,
[2 * 0.4 * 1.0 / (0.4 + 1.0)**2, 2 * 0.4 * 1.0 / (0.6 + 1.0)**2],
decimal=15)
st1 = SpikeTrain([
0.6,
], edges=(0.0, 1.0))
st2 = SpikeTrain([
0.4,
], edges=(0.0, 1.0))
d = spk.spike_distance(st1, st2)
s1 = np.array([0.2, 0.2, 0.2, 0.2])
s2 = np.array([0.2, 0.2, 0.2, 0.2])
isi1 = np.array([0.6, 0.6, 0.4])
isi2 = np.array([0.4, 0.6, 0.6])
expected_y1 = (s1[:-1] * isi2 + s2[:-1] * isi1) / (0.5 * (isi1 + isi2)**2)
expected_y2 = (s1[1:] * isi2 + s2[1:] * isi1) / (0.5 * (isi1 + isi2)**2)
expected_times = np.array([0.0, 0.4, 0.6, 1.0])
expected_spike_val = sum((expected_times[1:] - expected_times[:-1]) *
(expected_y1 + expected_y2) / 2)
expected_spike_val /= (expected_times[-1] - expected_times[0])
assert_almost_equal(d, expected_spike_val, decimal=15)
prof = spk.spike_profile(st1, st2)
assert_allclose(d, prof.avrg())
assert_array_almost_equal(prof.x, [0.0, 0.4, 0.6, 1.0], decimal=15)
assert_array_almost_equal(prof.y1, expected_y1, decimal=15)
assert_array_almost_equal(prof.y2, expected_y2, decimal=15)
def test_spike_empty():
st1 = SpikeTrain([], edges=(0.0, 1.0))
st2 = SpikeTrain([], edges=(0.0, 1.0))
d = spk.spike_distance(st1, st2)
assert_equal(d, 0.0)
prof = spk.spike_profile(st1, st2)
assert_equal(d, prof.avrg())
assert_array_equal(prof.x, [0.0, 1.0])
assert_array_equal(prof.y1, [0.0, ])
assert_array_equal(prof.y2, [0.0, ])
st1 = SpikeTrain([], edges=(0.0, 1.0))
st2 = SpikeTrain([0.4, ], edges=(0.0, 1.0))
d = spk.spike_distance(st1, st2)
assert_almost_equal(d, 0.4*0.4*1.0/(0.4+1.0)**2 + 0.6*0.4*1.0/(0.6+1.0)**2,
decimal=15)
prof = spk.spike_profile(st1, st2)
assert_equal(d, prof.avrg())
assert_array_equal(prof.x, [0.0, 0.4, 1.0])
assert_array_almost_equal(prof.y1, [0.0, 2*0.4*1.0/(0.6+1.0)**2],
decimal=15)
assert_array_almost_equal(prof.y2, [2*0.4*1.0/(0.4+1.0)**2, 0.0],
decimal=15)
st1 = SpikeTrain([0.6, ], edges=(0.0, 1.0))
st2 = SpikeTrain([0.4, ], edges=(0.0, 1.0))
d = spk.spike_distance(st1, st2)
s1 = np.array([0.0, 0.4*0.2/0.6, 0.2, 0.0])
s2 = np.array([0.0, 0.2, 0.2*0.4/0.6, 0.0])
isi1 = np.array([0.6, 0.6, 0.4])
isi2 = np.array([0.4, 0.6, 0.6])
expected_y1 = (s1[:-1]*isi2+s2[:-1]*isi1) / (0.5*(isi1+isi2)**2)
expected_y2 = (s1[1:]*isi2+s2[1:]*isi1) / (0.5*(isi1+isi2)**2)
expected_times = np.array([0.0, 0.4, 0.6, 1.0])
expected_spike_val = sum((expected_times[1:] - expected_times[:-1]) *
(expected_y1+expected_y2)/2)
expected_spike_val /= (expected_times[-1]-expected_times[0])
assert_almost_equal(d, expected_spike_val, decimal=15)
prof = spk.spike_profile(st1, st2)
assert_equal(d, prof.avrg())
assert_array_almost_equal(prof.x, [0.0, 0.4, 0.6, 1.0], decimal=15)
assert_array_almost_equal(prof.y1, expected_y1, decimal=15)
assert_array_almost_equal(prof.y2, expected_y2, decimal=15)
def test_regression_spiky():
# standard example
st1 = SpikeTrain(np.arange(100, 1201, 100), 1300)
st2 = SpikeTrain(np.arange(100, 1201, 110), 1300)
isi_dist = spk.isi_distance(st1, st2)
assert_almost_equal(isi_dist, 9.0909090909090939e-02, decimal=15)
isi_profile = spk.isi_profile(st1, st2)
assert_equal(isi_profile.y, 0.1 / 1.1 * np.ones_like(isi_profile.y))
spike_dist = spk.spike_distance(st1, st2)
assert_equal(spike_dist, 0.211058782487353908)
spike_sync = spk.spike_sync(st1, st2)
assert_equal(spike_sync, 8.6956521739130432e-01)
# multivariate check
spike_trains = spk.load_spike_trains_from_txt(
os.path.join(TEST_PATH, "PySpike_testdata.txt"), (0.0, 4000.0))
isi_dist = spk.isi_distance_multi(spike_trains)
# get the full precision from SPIKY
assert_almost_equal(isi_dist, 0.17051816816999129656, decimal=15)
spike_profile = spk.spike_profile_multi(spike_trains)
assert_equal(len(spike_profile.y1) + len(spike_profile.y2), 1252)
spike_dist = spk.spike_distance_multi(spike_trains)
# get the full precision from SPIKY
assert_almost_equal(spike_dist, 0.25188056475463755, decimal=15)
spike_sync = spk.spike_sync_multi(spike_trains)
# get the full precision from SPIKY
assert_equal(spike_sync, 0.7183531505298066)
# Eero's edge correction example
st1 = SpikeTrain([0.5, 1.5, 2.5], 6.0)
st2 = SpikeTrain([3.5, 4.5, 5.5], 6.0)
f = spk.spike_profile(st1, st2)
expected_times = np.array([0.0, 0.5, 1.5, 2.5, 3.5, 4.5, 5.5, 6.0])
y_all = np.array([
0.271604938271605, 0.271604938271605, 0.271604938271605,
0.617283950617284, 0.617283950617284, 0.444444444444444,
0.285714285714286, 0.285714285714286, 0.444444444444444,
0.617283950617284, 0.617283950617284, 0.271604938271605,
0.271604938271605, 0.271604938271605
])
expected_y1 = y_all[::2]
expected_y2 = y_all[1::2]
assert_equal(f.x, expected_times)
assert_array_almost_equal(f.y1, expected_y1, decimal=14)
assert_array_almost_equal(f.y2, expected_y2, decimal=14)
def get_data():
print 'Starting analysis of spike times per cell: ' + str(label_network)
sync_data = [[[[] for i in range(2)] for x in range(len(gids))]
for p in range(len(stats))]
spktsRange = [
spkt for spkt in spkts if timeRange[0] <= spkt <= timeRange[1]
]
for i, stat in enumerate(stats):
for ii, subset in enumerate(gids):
spkmat = [
pyspike.SpikeTrain([
spkt for spkind, spkt in zip(spkinds, spkts)
if (spkind == gid and spkt in spktsRange)
], timeRange) for gid in set(subset)
]
if stat == 'spike_sync_profile':
print str(stat) + ", subset: " + str(
ii) + ", number of trains: " + str(len(spkmat))
syncMat1 = pyspike.spike_sync_profile(spkmat)
x, y = syncMat1.get_plottable_data()
sync_data[i][ii][0] = x
sync_data[i][ii][1] = y
elif stat == 'spike_profile':
print str(stat) + ", subset: " + str(
ii) + ", number of trains: " + str(len(spkmat))
syncMat2 = pyspike.spike_profile(spkmat)
x, y = syncMat2.get_plottable_data()
sync_data[i][ii][0] = x
sync_data[i][ii][1] = y
elif stat == 'isi_profile':
print str(stat) + ", subset: " + str(
ii) + ", number of trains: " + str(len(spkmat))
syncMat3 = pyspike.isi_profile(spkmat)
x, y = syncMat3.get_plottable_data()
sync_data[i][ii][0] = x
sync_data[i][ii][1] = y
f = spk.isi_profile(spike_trains[0], spike_trains[1])
print("ISI-distance: %.8f" % f.avrg())
isi1 = f.avrg(interval=(0, 1000))
isi2 = f.avrg(interval=(1000, 2000))
isi3 = f.avrg(interval=[(0, 1000), (2000, 3000)])
isi4 = f.avrg(interval=[(1000, 2000), (3000, 4000)])
print("ISI-distance (0-1000): %.8f" % isi1)
print("ISI-distance (1000-2000): %.8f" % isi2)
print("ISI-distance (0-1000) and (2000-3000): %.8f" % isi3)
print("ISI-distance (1000-2000) and (3000-4000): %.8f" % isi4)
print()
f = spk.spike_profile(spike_trains[0], spike_trains[1])
print("SPIKE-distance: %.8f" % f.avrg())
spike1 = f.avrg(interval=(0, 1000))
spike2 = f.avrg(interval=(1000, 2000))
spike3 = f.avrg(interval=[(0, 1000), (2000, 3000)])
spike4 = f.avrg(interval=[(1000, 2000), (3000, 4000)])
print("SPIKE-distance (0-1000): %.8f" % spike1)
print("SPIKE-distance (1000-2000): %.8f" % spike2)
print("SPIKE-distance (0-1000) and (2000-3000): %.8f" % spike3)
print("SPIKE-distance (1000-2000) and (3000-4000): %.8f" % spike4)
print()
f = spk.spike_sync_profile(spike_trains[0], spike_trains[1])
t_start = time.clock()
# load the data
time_loading = time.clock()
spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt",
edges=(0, 4000))
t_loading = time.clock()
print("Number of spike trains: %d" % len(spike_trains))
num_of_spikes = sum([len(spike_trains[i]) for i in range(len(spike_trains))])
print("Number of spikes: %d" % num_of_spikes)
# calculate the multivariate spike distance
f = spk.spike_profile(spike_trains)
t_spike = time.clock()
# print the average
avrg = f.avrg()
print("Spike distance from average: %.8f" % avrg)
t_avrg = time.clock()
# compute average distance directly, should give the same result as above
spike_dist = spk.spike_distance(spike_trains)
print("Spike distance directly: %.8f" % spike_dist)
t_dist = time.clock()
spike_trains = spk.load_spike_trains_from_txt("../test/SPIKE_Sync_Test.txt",
edges=(0, 4000))
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.x)
print(f.y)
print(f.mp)
print("Average:", f.avrg())
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.figure()
plt.subplot(211)
f = spk.spike_sync_profile_multi(spike_trains)
x, y = f.get_plottable_data()
plt.plot(x, y, '-b', alpha=0.7, label="SPIKE-Sync profile")
import pyspike as spk
spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt",
edges=(0, 4000))
# plot the spike times
for (i, spike_train) in enumerate(spike_trains):
# print np.asarray(spike_train)
plt.scatter(spike_train, i * np.ones_like(spike_train), marker='|')
plt.savefig('fig/plot0.png')
# profile of the first two spike trains
f = spk.isi_profile(spike_trains, indices=[0, 1])
x, y = f.get_plottable_data()
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())
plt.legend(loc="upper left")
plt.savefig('fig/plot1.png')
# plt.show()
def test_spike():
# generate two spike trains:
t1 = SpikeTrain([0.0, 2.0, 5.0, 8.0], 10.0)
t2 = SpikeTrain([0.0, 1.0, 5.0, 9.0], 10.0)
expected_times = np.array([0.0, 1.0, 2.0, 5.0, 8.0, 9.0, 10.0])
f = spk.spike_profile(t1, t2)
assert_equal(f.x, expected_times)
# from SPIKY:
y_all = np.array([
0.000000000000000000, 0.555555555555555580, 0.222222222222222210,
0.305555555555555580, 0.255102040816326536, 0.000000000000000000,
0.000000000000000000, 0.255102040816326536, 0.255102040816326536,
0.285714285714285698, 0.285714285714285698, 0.285714285714285698
])
#assert_array_almost_equal(f.y1, y_all[::2])
assert_array_almost_equal(f.y2, y_all[1::2])
assert_almost_equal(f.avrg(), 0.186309523809523814, decimal=15)
assert_equal(spk.spike_distance(t1, t2), f.avrg())
t1 = SpikeTrain([0.2, 0.4, 0.6, 0.7], 1.0)
t2 = SpikeTrain([0.3, 0.45, 0.8, 0.9, 0.95], 1.0)
# pen&paper calculation of the spike distance
expected_times = [0.0, 0.2, 0.3, 0.4, 0.45, 0.6, 0.7, 0.8, 0.9, 0.95, 1.0]
s1 = np.array([
0.1, 0.1, (0.1 * 0.1 + 0.05 * 0.1) / 0.2, 0.05,
(0.05 * 0.15 * 2) / 0.2, 0.15, 0.1, (0.1 * 0.1 + 0.1 * 0.2) / 0.3,
(0.1 * 0.2 + 0.1 * 0.1) / 0.3, (0.1 * 0.05 + 0.1 * 0.25) / 0.3, 0.1
])
s2 = np.array([
0.1, (0.1 * 0.2 + 0.1 * 0.1) / 0.3, 0.1, (0.1 * 0.05 * 2) / .15, 0.05,
(0.05 * 0.2 + 0.1 * 0.15) / 0.35, (0.05 * 0.1 + 0.1 * 0.25) / 0.35,
0.1, 0.1, 0.05, 0.05
])
isi1 = np.array([0.2, 0.2, 0.2, 0.2, 0.2, 0.1, 0.3, 0.3, 0.3, 0.3])
isi2 = np.array([0.3, 0.3, 0.15, 0.15, 0.35, 0.35, 0.35, 0.1, 0.05, 0.05])
expected_y1 = (s1[:-1] * isi2 + s2[:-1] * isi1) / (0.5 * (isi1 + isi2)**2)
expected_y2 = (s1[1:] * isi2 + s2[1:] * isi1) / (0.5 * (isi1 + isi2)**2)
expected_times = np.array(expected_times)
expected_y1 = np.array(expected_y1)
expected_y2 = np.array(expected_y2)
expected_spike_val = sum((expected_times[1:] - expected_times[:-1]) *
(expected_y1 + expected_y2) / 2)
expected_spike_val /= (expected_times[-1] - expected_times[0])
print("SPIKE value:", expected_spike_val)
f = spk.spike_profile(t1, t2)
assert_equal(f.x, expected_times)
assert_array_almost_equal(f.y1, expected_y1, decimal=15)
assert_array_almost_equal(f.y2, expected_y2, decimal=15)
assert_almost_equal(f.avrg(), expected_spike_val, decimal=15)
assert_almost_equal(spk.spike_distance(t1, t2),
expected_spike_val,
decimal=15)
# check with some equal spike times
t1 = SpikeTrain([0.2, 0.4, 0.6], [0.0, 1.0])
t2 = SpikeTrain([0.1, 0.4, 0.5, 0.6], [0.0, 1.0])
expected_times = [0.0, 0.1, 0.2, 0.4, 0.5, 0.6, 1.0]
# due to the edge correction in the beginning, s1 and s2 are different
# for left and right values
s1_r = np.array(
[0.1, (0.1 * 0.1 + 0.1 * 0.1) / 0.2, 0.1, 0.0, 0.0, 0.0, 0.0])
s1_l = np.array(
[0.1, (0.1 * 0.1 + 0.1 * 0.1) / 0.2, 0.1, 0.0, 0.0, 0.0, 0.0])
# s2_r = np.array([0.1*0.1/0.3, 0.1*0.3/0.3, 0.1*0.2/0.3,
# 0.0, 0.1, 0.0, 0.0])
# s2_l = np.array([0.1*0.1/0.3, 0.1*0.1/0.3, 0.1*0.2/0.3, 0.0,
# 0.1, 0.0, 0.0])
# eero's edge correction:
s2_r = np.array(
[0.1, 0.1 * 0.3 / 0.3, 0.1 * 0.2 / 0.3, 0.0, 0.1, 0.0, 0.0])
s2_l = np.array(
[0.1, 0.1 * 0.3 / 0.3, 0.1 * 0.2 / 0.3, 0.0, 0.1, 0.0, 0.0])
isi1 = np.array([0.2, 0.2, 0.2, 0.2, 0.2, 0.4])
isi2 = np.array([0.3, 0.3, 0.3, 0.1, 0.1, 0.4])
expected_y1 = (s1_r[:-1] * isi2 + s2_r[:-1] * isi1) / (0.5 *
(isi1 + isi2)**2)
expected_y2 = (s1_l[1:] * isi2 + s2_l[1:] * isi1) / (0.5 *
(isi1 + isi2)**2)
expected_times = np.array(expected_times)
expected_y1 = np.array(expected_y1)
expected_y2 = np.array(expected_y2)
expected_spike_val = sum((expected_times[1:] - expected_times[:-1]) *
(expected_y1 + expected_y2) / 2)
expected_spike_val /= (expected_times[-1] - expected_times[0])
f = spk.spike_profile(t1, t2)
assert_equal(f.x, expected_times)
assert_array_almost_equal(f.y1, expected_y1, decimal=14)
assert_array_almost_equal(f.y2, expected_y2, decimal=14)
assert_almost_equal(f.avrg(), expected_spike_val, decimal=16)
assert_almost_equal(spk.spike_distance(t1, t2),
expected_spike_val,
decimal=16)
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()
#Grab all the spike times and neurons indices from the "SpikeMonitor" objects
poiSpikeTimes = numpy.asarray(PoiMonitor.t)
poiSpikeNeuro = numpy.asarray(PoiMonitor.i)
neuSpikeTimes = numpy.asarray(NeuMonitor1.t)
#Make a list where we will put the set of "SpikeTrain" objects
spikiTimesObjList = []
#Fill the list with spike trains for each neuron in the simulation
for i in numpy.unique(poiSpikeNeuro):
inds = numpy.argwhere(poiSpikeNeuro==i) #FInd tthe spike-times that correspond to neuron i
inds = inds[:,0] #the variable "inds" is a 2D array, I just want a 1D array to give to the "SpikeTrain" class.
spikiTimesObjList.append(spk.SpikeTrain(poiSpikeTimes[inds], edges=(0., 1.), is_sorted=True)) #Append the spikiTimesObjList with a "SpikeTrain" object
#Make a "spike_profile", which essentially is a simultaneous comparison of all the spike trains together simutaneously
spike_profile = spk.spike_profile(spikiTimesObjList)
#Make a "isi_profile", which essentially is a simultaneous comparison of all the spike trains together simutaneously
isi_profile = spk.isi_profile(spikiTimesObjList)
#Make a "spike_sync_profile", which essentially is a simultaneous comparison of all the spike trains together simutaneously
sync_profile = spk.spike_sync_profile(spikiTimesObjList)
#Now I want to pring out want these profiles that have just been created look like.
plt.figure(1)
x, y = spike_profile.get_plottable_data()
plt.plot(x, y, '--k')
plt.figure(2)
x, y = isi_profile.get_plottable_data()
plt.plot(x,y, '--k')
plt.figure(3)
import pyspike as spk
spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt",
edges=(0, 4000))
# plot the spike times
for (i, spike_train) in enumerate(spike_trains):
plt.scatter(spike_train, i*np.ones_like(spike_train), marker='|')
# profile of the first two spike trains
f = spk.isi_profile(spike_trains, indices=[0, 1])
x, y = f.get_plottable_data()
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())
plt.legend(loc="upper left")
plt.show()
def get_spike_distance(spike_train_1, spike_train_2):
return spk.spike_profile(spike_train_1, spike_train_2).avrg()
def test_spike():
# generate two spike trains:
t1 = SpikeTrain([0.0, 2.0, 5.0, 8.0], 10.0)
t2 = SpikeTrain([0.0, 1.0, 5.0, 9.0], 10.0)
expected_times = np.array([0.0, 1.0, 2.0, 5.0, 8.0, 9.0, 10.0])
f = spk.spike_profile(t1, t2)
assert_equal(f.x, expected_times)
assert_almost_equal(f.avrg(), 1.6624149659863946e-01, decimal=15)
assert_almost_equal(f.y2[-1], 0.1394558, decimal=6)
t1 = SpikeTrain([0.2, 0.4, 0.6, 0.7], 1.0)
t2 = SpikeTrain([0.3, 0.45, 0.8, 0.9, 0.95], 1.0)
# pen&paper calculation of the spike distance
expected_times = [0.0, 0.2, 0.3, 0.4, 0.45, 0.6, 0.7, 0.8, 0.9, 0.95, 1.0]
s1 = np.array([0.1, 0.1, (0.1*0.1+0.05*0.1)/0.2, 0.05, (0.05*0.15 * 2)/0.2,
0.15, 0.1, (0.1*0.1+0.1*0.2)/0.3, (0.1*0.2+0.1*0.1)/0.3,
(0.1*0.05+0.1*0.25)/0.3, 0.1])
s2 = np.array([0.1, (0.1*0.2+0.1*0.1)/0.3, 0.1, (0.1*0.05 * 2)/.15, 0.05,
(0.05*0.2+0.1*0.15)/0.35, (0.05*0.1+0.1*0.25)/0.35,
0.1, 0.1, 0.05, 0.05])
isi1 = np.array([0.2, 0.2, 0.2, 0.2, 0.2, 0.1, 0.3, 0.3, 0.3, 0.3])
isi2 = np.array([0.3, 0.3, 0.15, 0.15, 0.35, 0.35, 0.35, 0.1, 0.05, 0.05])
expected_y1 = (s1[:-1]*isi2+s2[:-1]*isi1) / (0.5*(isi1+isi2)**2)
expected_y2 = (s1[1:]*isi2+s2[1:]*isi1) / (0.5*(isi1+isi2)**2)
expected_times = np.array(expected_times)
expected_y1 = np.array(expected_y1)
expected_y2 = np.array(expected_y2)
expected_spike_val = sum((expected_times[1:] - expected_times[:-1]) *
(expected_y1+expected_y2)/2)
expected_spike_val /= (expected_times[-1]-expected_times[0])
f = spk.spike_profile(t1, t2)
assert_equal(f.x, expected_times)
assert_array_almost_equal(f.y1, expected_y1, decimal=15)
assert_array_almost_equal(f.y2, expected_y2, decimal=15)
assert_almost_equal(f.avrg(), expected_spike_val, decimal=15)
assert_almost_equal(spk.spike_distance(t1, t2), expected_spike_val,
decimal=15)
# check with some equal spike times
t1 = SpikeTrain([0.2, 0.4, 0.6], [0.0, 1.0])
t2 = SpikeTrain([0.1, 0.4, 0.5, 0.6], [0.0, 1.0])
expected_times = [0.0, 0.1, 0.2, 0.4, 0.5, 0.6, 1.0]
# due to the edge correction in the beginning, s1 and s2 are different
# for left and right values
s1_r = np.array([0.1, (0.1*0.1+0.1*0.1)/0.2, 0.1, 0.0, 0.0, 0.0, 0.0])
s1_l = np.array([0.1, (0.1*0.1+0.1*0.1)/0.2, 0.1, 0.0, 0.0, 0.0, 0.0])
s2_r = np.array([0.1*0.1/0.3, 0.1*0.3/0.3, 0.1*0.2/0.3,
0.0, 0.1, 0.0, 0.0])
s2_l = np.array([0.1*0.1/0.3, 0.1*0.1/0.3, 0.1*0.2/0.3, 0.0,
0.1, 0.0, 0.0])
isi1 = np.array([0.2, 0.2, 0.2, 0.2, 0.2, 0.4])
isi2 = np.array([0.3, 0.3, 0.3, 0.1, 0.1, 0.4])
expected_y1 = (s1_r[:-1]*isi2+s2_r[:-1]*isi1) / (0.5*(isi1+isi2)**2)
expected_y2 = (s1_l[1:]*isi2+s2_l[1:]*isi1) / (0.5*(isi1+isi2)**2)
expected_times = np.array(expected_times)
expected_y1 = np.array(expected_y1)
expected_y2 = np.array(expected_y2)
expected_spike_val = sum((expected_times[1:] - expected_times[:-1]) *
(expected_y1+expected_y2)/2)
expected_spike_val /= (expected_times[-1]-expected_times[0])
f = spk.spike_profile(t1, t2)
assert_equal(f.x, expected_times)
assert_array_almost_equal(f.y1, expected_y1, decimal=14)
assert_array_almost_equal(f.y2, expected_y2, decimal=14)
assert_almost_equal(f.avrg(), expected_spike_val, decimal=16)
assert_almost_equal(spk.spike_distance(t1, t2), expected_spike_val,
decimal=16)
t_start = time.clock()
# load the data
time_loading = time.clock()
spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt",
edges=(0, 4000))
t_loading = time.clock()
print("Number of spike trains: %d" % len(spike_trains))
num_of_spikes = sum([len(spike_trains[i])
for i in range(len(spike_trains))])
print("Number of spikes: %d" % num_of_spikes)
# calculate the multivariate spike distance
f = spk.spike_profile(spike_trains)
t_spike = time.clock()
# print the average
avrg = f.avrg()
print("Spike distance from average: %.8f" % avrg)
t_avrg = time.clock()
# compute average distance directly, should give the same result as above
spike_dist = spk.spike_distance(spike_trains)
print("Spike distance directly: %.8f" % spike_dist)
t_dist = time.clock()
b = spk.SpikeTrain(a, [0, 10], is_sorted=False)
print b.spikes
spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt",
edges=(0, 4000))
# compute the two spike trains and multivariate ISI profile
f = spk.isi_profile(spike_trains[0], spike_trains[1])
f = spk.isi_profile(spike_trains)
# t = [900, 1100, 2000, 3100]
# print("ISI value at t =", t, ":", f(t))
# print("Average ISI distance:", f.avrg())
# compute the two spike trains and multivariate SPIKE profile
f = spk.spike_profile(spike_trains[0], spike_trains[1])
f = spk.spike_profile(spike_trains)
# t = [900, 1100, 2000, 3100]
# print("Multivariate SPIKE value at t =", t, ":", f(t))
# print("Average multivariate SPIKE distance:", f.avrg())
# plot the spike times
for (i, spike_train) in enumerate(spike_trains):
plt.scatter(spike_train, i * np.ones_like(spike_train), marker='|')
# print np.asarray(spike_train)
# profile of the first two spike trains
f = spk.isi_profile(spike_trains, indices=[0, 1])
x, y = f.get_plottable_data()
# x = f.x
