From 5970a9cfdbecc1af232b7ffe485bdc057591a2b8 Mon Sep 17 00:00:00 2001
From: Mario Mulansky <mario.mulansky@gmx.net>
Date: Thu, 16 Oct 2014 14:50:26 +0200
Subject: added spike_matrix, refactoring dist matrix functs

---
 pyspike/__init__.py  |  2 +-
 pyspike/distances.py | 52 +++++++++++++++++++++++++++++++++++++++++++---------
 2 files changed, 44 insertions(+), 10 deletions(-)

(limited to 'pyspike')

diff --git a/pyspike/__init__.py b/pyspike/__init__.py
index 5146507..d2d5b57 100644
--- a/pyspike/__init__.py
+++ b/pyspike/__init__.py
@@ -10,6 +10,6 @@ from function import PieceWiseConstFunc, PieceWiseLinFunc, average_profile
 from distances import isi_profile, isi_distance, \
     spike_profile, spike_distance, \
     isi_profile_multi, isi_distance_multi, isi_distance_matrix, \
-    spike_profile_multi, spike_distance_multi
+    spike_profile_multi, spike_distance_multi, spike_distance_matrix
 from spikes import add_auxiliary_spikes, load_spike_trains_from_txt, \
     spike_train_from_string, merge_spike_trains
diff --git a/pyspike/distances.py b/pyspike/distances.py
index 9056863..7d7044b 100644
--- a/pyspike/distances.py
+++ b/pyspike/distances.py
@@ -99,9 +99,9 @@ def spike_distance(spikes1, spikes2):
 
 
 ############################################################
-# multi_profile
+# generic_profile_multi
 ############################################################
-def multi_profile(spike_trains, pair_distance_func, indices=None):
+def generic_profile_multi(spike_trains, pair_distance_func, indices=None):
     """ Internal implementation detail, don't call this function directly,
     use isi_profile_multi or spike_profile_multi instead.
 
@@ -203,7 +203,7 @@ def isi_profile_multi(spike_trains, indices=None):
     Returns:
     - A PieceWiseConstFunc representing the averaged isi distance S_isi(t)
     """
-    return multi_profile(spike_trains, isi_profile, indices)
+    return generic_profile_multi(spike_trains, isi_profile, indices)
 
 
 ############################################################
@@ -239,7 +239,7 @@ def spike_profile_multi(spike_trains, indices=None):
     Returns:
     - A PieceWiseLinFunc representing the averaged spike distance S(t)
     """
-    return multi_profile(spike_trains, spike_profile, indices)
+    return generic_profile_multi(spike_trains, spike_profile, indices)
 
 
 ############################################################
@@ -261,17 +261,19 @@ def spike_distance_multi(spike_trains, indices=None):
 
 
 ############################################################
-# isi_distance_matrix
+# generic_distance_matrix
 ############################################################
-def isi_distance_matrix(spike_trains, indices=None):
-    """ Computes the average isi-distance of all pairs of spike-trains.
+def generic_distance_matrix(spike_trains, dist_function, indices=None):
+    """ Internal implementation detail. Don't use this function directly.
+    Instead use isi_distance_matrix or spike_distance_matrix.
+    Computes the time averaged distance of all pairs of spike-trains.
     Args:
     - spike_trains: list of spike trains
     - indices: list of indices defining which spike-trains to use
     if None all given spike-trains are used (default=None)
     Return:
     - a 2D array of size len(indices)*len(indices) containing the average
-    pair-wise isi-distance
+    pair-wise distance
     """
     if indices is None:
         indices = np.arange(len(spike_trains))
@@ -284,7 +286,39 @@ def isi_distance_matrix(spike_trains, indices=None):
 
     distance_matrix = np.zeros((len(indices), len(indices)))
     for i, j in pairs:
-        d = isi_distance(spike_trains[i], spike_trains[j])
+        d = dist_function(spike_trains[i], spike_trains[j])
         distance_matrix[i, j] = d
         distance_matrix[j, i] = d
     return distance_matrix
+
+
+############################################################
+# isi_distance_matrix
+############################################################
+def isi_distance_matrix(spike_trains, indices=None):
+    """ Computes the time averaged isi-distance of all pairs of spike-trains.
+    Args:
+    - spike_trains: list of spike trains
+    - indices: list of indices defining which spike-trains to use
+    if None all given spike-trains are used (default=None)
+    Return:
+    - a 2D array of size len(indices)*len(indices) containing the average
+    pair-wise isi-distance
+    """
+    return generic_distance_matrix(spike_trains, isi_distance, indices)
+
+
+############################################################
+# spike_distance_matrix
+############################################################
+def spike_distance_matrix(spike_trains, indices=None):
+    """ Computes the time averaged spike-distance of all pairs of spike-trains.
+    Args:
+    - spike_trains: list of spike trains
+    - indices: list of indices defining which spike-trains to use
+    if None all given spike-trains are used (default=None)
+    Return:
+    - a 2D array of size len(indices)*len(indices) containing the average
+    pair-wise spike-distance
+    """
+    return generic_distance_matrix(spike_trains, spike_distance, indices)
-- 
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