performance improvement for spike sync

Additional cython implementation for overall spike sync values. It is not
necessary to compute the profile anymore if only the spike sync value is
required. 3x performance gain.

1 files changed, 40 insertions, 6 deletions

diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py
index 107734d..40d98d2 100644
--- a/pyspike/spike_sync.py
+++ b/pyspike/spike_sync.py
@@ -58,6 +58,40 @@ Falling back to slow python backend.")
 
 
 ############################################################
+# _spike_sync_values
+############################################################
+def _spike_sync_values(spike_train1, spike_train2, interval, max_tau):
+    """" Internal function. Computes the summed coincidences and multiplicity
+    for spike synchronization of the two given spike trains.
+
+    Do not call this function directly, use `spike_sync` or `spike_sync_multi`
+    instead.
+    """
+    if interval is None:
+        # distance over the whole interval is requested: use specific function
+        # for optimal performance
+        try:
+            from cython.cython_distances import coincidence_value_cython \
+                as coincidence_value_impl
+            if max_tau is None:
+                max_tau = 0.0
+            c, mp = coincidence_value_impl(spike_train1.spikes,
+                                           spike_train2.spikes,
+                                           spike_train1.t_start,
+                                           spike_train1.t_end,
+                                           max_tau)
+            return c, mp
+        except ImportError:
+            # Cython backend not available: fall back to profile averaging
+            return spike_sync_profile(spike_train1, spike_train2,
+                                      max_tau).integral(interval)
+    else:
+        # some specific interval is provided: use profile
+        return spike_sync_profile(spike_train1, spike_train2,
+                                  max_tau).integral(interval)
+
+
+############################################################
 # spike_sync
 ############################################################
 def spike_sync(spike_train1, spike_train2, interval=None, max_tau=None):
@@ -80,8 +114,8 @@ def spike_sync(spike_train1, spike_train2, interval=None, max_tau=None):
     :rtype: `double`
 
     """
-    return spike_sync_profile(spike_train1, spike_train2,
-                              max_tau).avrg(interval)
+    c, mp = _spike_sync_values(spike_train1, spike_train2, interval, max_tau)
+    return 1.0*c/mp
 
 
 ############################################################
@@ -144,10 +178,10 @@ def spike_sync_multi(spike_trains, indices=None, interval=None, max_tau=None):
     coincidence = 0.0
     mp = 0.0
     for (i, j) in pairs:
-        profile = spike_sync_profile(spike_trains[i], spike_trains[j])
-        summed_vals = profile.integral(interval)
-        coincidence += summed_vals[0]
-        mp += summed_vals[1]
+        c, m = _spike_sync_values(spike_trains[i], spike_trains[j],
+                                  interval, max_tau)
+        coincidence += c
+        mp += m
 
     return coincidence/mp