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authorMario Mulansky <mario.mulansky@gmx.net>2016-03-09 12:30:35 +0100
committerMario Mulansky <mario.mulansky@gmx.net>2016-03-09 12:30:35 +0100
commitee0e980b72c299eed12b7a3afc542fc470dd6d98 (patch)
tree6d63e2fe7bf9805ab6358e31bd0a641d58e40c87
parent9f00431282ef2aae4b98a7a05fe5aa83b0e59673 (diff)
updated examples to use new unified interface
removed all occasions of *multi functions from examples as they are considered deprecated now. Uses unified interface everywhere.
-rw-r--r--examples/averages.py2
-rw-r--r--examples/merge.py6
-rw-r--r--examples/multivariate.py4
-rw-r--r--examples/performance.py27
-rw-r--r--examples/plot.py5
-rw-r--r--examples/profiles.py4
-rw-r--r--examples/spike_sync.py2
7 files changed, 27 insertions, 23 deletions
diff --git a/examples/averages.py b/examples/averages.py
index c3e81e2..8b405d0 100644
--- a/examples/averages.py
+++ b/examples/averages.py
@@ -12,7 +12,7 @@ from __future__ import print_function
import pyspike as spk
spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt",
- time_interval=(0, 4000))
+ edges=(0, 4000))
f = spk.isi_profile(spike_trains[0], spike_trains[1])
diff --git a/examples/merge.py b/examples/merge.py
index 2ea96ea..b4437a3 100644
--- a/examples/merge.py
+++ b/examples/merge.py
@@ -21,9 +21,9 @@ merged_spike_train = spk.merge_spike_trains([spike_trains[0], spike_trains[1]])
print(merged_spike_train.spikes)
-plt.plot(spike_trains[0].spikes, np.ones_like(spike_trains[0].spikes), 'o')
-plt.plot(spike_trains[1].spikes, np.ones_like(spike_trains[1].spikes), 'x')
+plt.plot(spike_trains[0], np.ones_like(spike_trains[0]), 'o')
+plt.plot(spike_trains[1], np.ones_like(spike_trains[1]), 'x')
plt.plot(merged_spike_train.spikes,
- 2*np.ones_like(merged_spike_train.spikes), 'o')
+ 2*np.ones_like(merged_spike_train), 'o')
plt.show()
diff --git a/examples/multivariate.py b/examples/multivariate.py
index 93f8516..e9579a5 100644
--- a/examples/multivariate.py
+++ b/examples/multivariate.py
@@ -28,7 +28,7 @@ num_of_spikes = sum([len(spike_trains[i])
print("Number of spikes: %d" % num_of_spikes)
# calculate the multivariate spike distance
-f = spk.spike_profile_multi(spike_trains)
+f = spk.spike_profile(spike_trains)
t_spike = time.clock()
@@ -39,7 +39,7 @@ 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_multi(spike_trains)
+spike_dist = spk.spike_distance(spike_trains)
print("Spike distance directly: %.8f" % spike_dist)
t_dist = time.clock()
diff --git a/examples/performance.py b/examples/performance.py
index ec6c830..30691f8 100644
--- a/examples/performance.py
+++ b/examples/performance.py
@@ -31,38 +31,41 @@ for i in range(M):
t_end = datetime.now()
runtime = (t_end-t_start).total_seconds()
+sort_by = 'tottime'
+# sort_by = 'cumtime'
+
print("Spike generation runtime: %.3fs" % runtime)
print()
print("================ ISI COMPUTATIONS ================")
print(" MULTIVARIATE DISTANCE")
-cProfile.run('spk.isi_distance_multi(spike_trains)', 'performance.stat')
+cProfile.run('spk.isi_distance(spike_trains)', 'performance.stat')
p = pstats.Stats('performance.stat')
-p.strip_dirs().sort_stats('tottime').print_stats(5)
+p.strip_dirs().sort_stats(sort_by).print_stats(5)
print(" MULTIVARIATE PROFILE")
-cProfile.run('spk.isi_profile_multi(spike_trains)', 'performance.stat')
+cProfile.run('spk.isi_profile(spike_trains)', 'performance.stat')
p = pstats.Stats('performance.stat')
-p.strip_dirs().sort_stats('tottime').print_stats(5)
+p.strip_dirs().sort_stats(sort_by).print_stats(5)
print("================ SPIKE COMPUTATIONS ================")
print(" MULTIVARIATE DISTANCE")
-cProfile.run('spk.spike_distance_multi(spike_trains)', 'performance.stat')
+cProfile.run('spk.spike_distance(spike_trains)', 'performance.stat')
p = pstats.Stats('performance.stat')
-p.strip_dirs().sort_stats('tottime').print_stats(5)
+p.strip_dirs().sort_stats(sort_by).print_stats(5)
print(" MULTIVARIATE PROFILE")
-cProfile.run('spk.spike_profile_multi(spike_trains)', 'performance.stat')
+cProfile.run('spk.spike_profile(spike_trains)', 'performance.stat')
p = pstats.Stats('performance.stat')
-p.strip_dirs().sort_stats('tottime').print_stats(5)
+p.strip_dirs().sort_stats(sort_by).print_stats(5)
print("================ SPIKE-SYNC COMPUTATIONS ================")
print(" MULTIVARIATE DISTANCE")
-cProfile.run('spk.spike_sync_multi(spike_trains)', 'performance.stat')
+cProfile.run('spk.spike_sync(spike_trains)', 'performance.stat')
p = pstats.Stats('performance.stat')
-p.strip_dirs().sort_stats('tottime').print_stats(5)
+p.strip_dirs().sort_stats(sort_by).print_stats(5)
print(" MULTIVARIATE PROFILE")
-cProfile.run('spk.spike_sync_profile_multi(spike_trains)', 'performance.stat')
+cProfile.run('spk.spike_sync_profile(spike_trains)', 'performance.stat')
p = pstats.Stats('performance.stat')
-p.strip_dirs().sort_stats('tottime').print_stats(5)
+p.strip_dirs().sort_stats(sort_by).print_stats(5)
diff --git a/examples/plot.py b/examples/plot.py
index 1922939..a0e04da 100644
--- a/examples/plot.py
+++ b/examples/plot.py
@@ -24,7 +24,8 @@ spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt",
for (i, spike_train) in enumerate(spike_trains):
plt.scatter(spike_train, i*np.ones_like(spike_train), marker='|')
-f = spk.isi_profile(spike_trains[0], spike_trains[1])
+# profile of the first two spike trains
+f = spk.isi_profile(spike_trains, indices=[0, 1])
x, y = f.get_plottable_data()
plt.figure()
@@ -32,7 +33,7 @@ plt.plot(x, np.abs(y), '--k', label="ISI-profile")
print("ISI-distance: %.8f" % f.avrg())
-f = spk.spike_profile(spike_trains[0], spike_trains[1])
+f = spk.spike_profile(spike_trains, indices=[0, 1])
x, y = f.get_plottable_data()
plt.plot(x, y, '-b', label="SPIKE-profile")
diff --git a/examples/profiles.py b/examples/profiles.py
index 05494bd..8412ffb 100644
--- a/examples/profiles.py
+++ b/examples/profiles.py
@@ -29,7 +29,7 @@ print("Average ISI distance:", f.avrg())
print()
# compute the multivariate ISI profile
-f = spk.isi_profile_multi(spike_trains)
+f = spk.isi_profile(spike_trains)
t = 1200
print("Multivariate ISI value at t =", t, ":", f(t))
@@ -56,7 +56,7 @@ print("Average SPIKE distance:", f.avrg())
print()
# compute the multivariate SPIKE profile
-f = spk.spike_profile_multi(spike_trains)
+f = spk.spike_profile(spike_trains)
# SPIKE values at certain points
t = 1200
diff --git a/examples/spike_sync.py b/examples/spike_sync.py
index 37dbff4..13ca0ce 100644
--- a/examples/spike_sync.py
+++ b/examples/spike_sync.py
@@ -31,7 +31,7 @@ plt.figure()
plt.subplot(211)
-f = spk.spike_sync_profile_multi(spike_trains)
+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")