added spike sync matrix

4 files changed, 68 insertions, 19 deletions

diff --git a/pyspike/__init__.py b/pyspike/__init__.py
index 1b18569..55687e6 100644
--- a/pyspike/__init__.py
+++ b/pyspike/__init__.py
@@ -10,9 +10,9 @@ from function import PieceWiseConstFunc, PieceWiseLinFunc, \
     DiscreteFunction, average_profile
 from distances import isi_profile, isi_distance, \
     spike_profile, spike_distance, \
-    spike_sync_profile, spike_sync_distance, \
+    spike_sync_profile, spike_sync, \
     isi_profile_multi, isi_distance_multi, isi_distance_matrix, \
     spike_profile_multi, spike_distance_multi, spike_distance_matrix, \
-    spike_sync_profile_multi
+    spike_sync_profile_multi, spike_sync_multi, spike_sync_matrix
 from spikes import add_auxiliary_spikes, load_spike_trains_from_txt, \
     spike_train_from_string, merge_spike_trains, generate_poisson_spikes
diff --git a/pyspike/distances.py b/pyspike/distances.py
index 0f0efa9..8a14a8d 100644
--- a/pyspike/distances.py
+++ b/pyspike/distances.py
@@ -152,10 +152,10 @@ Falling back to slow python backend.")
 
 
 ############################################################
-# spike_sync_distance
+# spike_sync
 ############################################################
-def spike_sync_distance(spikes1, spikes2):
-    return spike_sync_profile(spikes1, spikes2).avrg()
+def spike_sync(spikes1, spikes2, interval=None):
+    return spike_sync_profile(spikes1, spikes2).avrg(interval)
 
 
 ############################################################
@@ -314,6 +314,28 @@ def spike_profile_multi(spike_trains, indices=None):
 
 
 ############################################################
+# spike_distance_multi
+############################################################
+def spike_distance_multi(spike_trains, indices=None, interval=None):
+    """ Computes the multi-variate spike distance for a set of spike trains.
+    That is the time average of the multi-variate spike profile:
+    S_{spike} = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{spike}^{i, j} dt
+    where the sum goes over all pairs <i,j>
+
+    :param spike_trains: list of spike trains
+    :param indices: list of indices defining which spike trains to use,
+                    if None all given spike trains are used (default=None)
+    :type indices: list or None
+    :param interval: averaging interval given as a pair of floats, if None
+                     the average over the whole function is computed.
+    :type interval: Pair of floats or None.
+    :returns: The averaged spike distance S.
+    :rtype: double
+    """
+    return spike_profile_multi(spike_trains, indices).avrg(interval)
+
+
+############################################################
 # spike_profile_multi
 ############################################################
 def spike_sync_profile_multi(spike_trains, indices=None):
@@ -341,11 +363,9 @@ def spike_sync_profile_multi(spike_trains, indices=None):
 ############################################################
 # spike_distance_multi
 ############################################################
-def spike_distance_multi(spike_trains, indices=None, interval=None):
-    """ Computes the multi-variate spike distance for a set of spike trains.
-    That is the time average of the multi-variate spike profile:
-    S_{spike} = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{spike}^{i, j} dt
-    where the sum goes over all pairs <i,j>
+def spike_sync_multi(spike_trains, indices=None, interval=None):
+    """ Computes the multi-variate spike synchronization value for a set of
+    spike trains.
 
     :param spike_trains: list of spike trains
     :param indices: list of indices defining which spike trains to use,
@@ -354,10 +374,10 @@ def spike_distance_multi(spike_trains, indices=None, interval=None):
     :param interval: averaging interval given as a pair of floats, if None
                      the average over the whole function is computed.
     :type interval: Pair of floats or None.
-    :returns: The averaged spike distance S.
+    :returns: The averaged spike synchronization value SYNC.
     :rtype: double
     """
-    return spike_profile_multi(spike_trains, indices).avrg(interval)
+    return spike_sync_profile_multi(spike_trains, indices).avrg(interval)
 
 
 ############################################################
@@ -433,3 +453,25 @@ def spike_distance_matrix(spike_trains, indices=None, interval=None):
     """
     return _generic_distance_matrix(spike_trains, spike_distance,
                                     indices, interval)
+
+
+############################################################
+# spike_sync_matrix
+############################################################
+def spike_sync_matrix(spike_trains, indices=None, interval=None):
+    """ Computes the time averaged spike-synchronization value of all pairs of
+    spike-trains.
+
+    :param spike_trains: list of spike trains
+    :param indices: list of indices defining which spike trains to use,
+                    if None all given spike trains are used (default=None)
+    :type indices: list or None
+    :param interval: averaging interval given as a pair of floats, if None
+                     the average over the whole function is computed.
+    :type interval: Pair of floats or None.
+    :returns: 2D array with the pair wise time spike synchronization values
+              :math:`SYNC_{ij}`
+    :rtype: np.array
+    """
+    return _generic_distance_matrix(spike_trains, spike_sync,
+                                    indices, interval)
diff --git a/pyspike/function.py b/pyspike/function.py
index 62b0e2c..e0dadf6 100644
--- a/pyspike/function.py
+++ b/pyspike/function.py
@@ -429,6 +429,7 @@ class DiscreteFunction(object):
         """
 
         def get_indices(ival):
+            """ Retuns the indeces surrounding the given interval"""
             start_ind = np.searchsorted(self.x, ival[0], side='right')
             end_ind = np.searchsorted(self.x, ival[1], side='left')
             assert start_ind > 0 and end_ind < len(self.x), \
diff --git a/test/test_distance.py b/test/test_distance.py
index 6bdb049..2650313 100644
--- a/test/test_distance.py
+++ b/test/test_distance.py
@@ -135,22 +135,22 @@ def test_spike_sync():
     spikes2 = np.array([2.1])
     spikes1 = spk.add_auxiliary_spikes(spikes1, 4.0)
     spikes2 = spk.add_auxiliary_spikes(spikes2, 4.0)
-    assert_almost_equal(spk.spike_sync_distance(spikes1, spikes2),
+    assert_almost_equal(spk.spike_sync(spikes1, spikes2),
                         0.5, decimal=16)
 
     spikes2 = np.array([3.1])
     spikes2 = spk.add_auxiliary_spikes(spikes2, 4.0)
-    assert_almost_equal(spk.spike_sync_distance(spikes1, spikes2),
+    assert_almost_equal(spk.spike_sync(spikes1, spikes2),
                         0.5, decimal=16)
 
     spikes2 = np.array([1.1])
     spikes2 = spk.add_auxiliary_spikes(spikes2, 4.0)
-    assert_almost_equal(spk.spike_sync_distance(spikes1, spikes2),
+    assert_almost_equal(spk.spike_sync(spikes1, spikes2),
                         0.5, decimal=16)
 
     spikes2 = np.array([0.9])
     spikes2 = spk.add_auxiliary_spikes(spikes2, 4.0)
-    assert_almost_equal(spk.spike_sync_distance(spikes1, spikes2),
+    assert_almost_equal(spk.spike_sync(spikes1, spikes2),
                         0.5, decimal=16)
 
 
@@ -207,11 +207,11 @@ def test_multi_spike_sync():
     spikes1 = spk.add_auxiliary_spikes(spikes1, 1000)
     spikes2 = spk.add_auxiliary_spikes(spikes2, 1000)
     spikes3 = spk.add_auxiliary_spikes(spikes3, 1000)
-    assert_almost_equal(spk.spike_sync_distance(spikes1, spikes2),
+    assert_almost_equal(spk.spike_sync(spikes1, spikes2),
                         0.5, decimal=15)
-    assert_almost_equal(spk.spike_sync_distance(spikes1, spikes3),
+    assert_almost_equal(spk.spike_sync(spikes1, spikes3),
                         0.5, decimal=15)
-    assert_almost_equal(spk.spike_sync_distance(spikes2, spikes3),
+    assert_almost_equal(spk.spike_sync(spikes2, spikes3),
                         0.5, decimal=15)
 
     f = spk.spike_sync_profile_multi([spikes1, spikes2, spikes3])
@@ -220,6 +220,8 @@ def test_multi_spike_sync():
     #            (np.sum(f1.mp[1:-1])+np.sum(f2.mp[1:-1])+np.sum(f3.mp[1:-1]))
     expected = 0.5
     assert_almost_equal(f.avrg(), expected, decimal=15)
+    assert_almost_equal(spk.spike_sync_multi([spikes1, spikes2, spikes3]),
+                        expected, decimal=15)
 
     # multivariate regression test
     spike_trains = spk.load_spike_trains_from_txt("test/SPIKE_Sync_Test.txt",
@@ -267,6 +269,10 @@ def test_spike_matrix():
     check_dist_matrix(spk.spike_distance, spk.spike_distance_matrix)
 
 
+def test_spike_sync_matrix():
+    check_dist_matrix(spk.spike_sync, spk.spike_sync_matrix)
+
+
 def test_regression_spiky():
     spike_trains = spk.load_spike_trains_from_txt("test/PySpike_testdata.txt",
                                                   (0.0, 4000.0))