From 2336f1fcf28efeb23e8450f407a008b8032edd5e Mon Sep 17 00:00:00 2001
From: Mario Mulansky <mario.mulansky@gmx.net>
Date: Mon, 27 Apr 2015 18:16:12 +0200
Subject: adjusted PSTH, added to doc index

---
 doc/pyspike.rst        |  8 ++++++++
 examples/spike_sync.py |  2 +-
 pyspike/psth.py        | 39 +++++++++++++++++++++++----------------
 3 files changed, 32 insertions(+), 17 deletions(-)

diff --git a/doc/pyspike.rst b/doc/pyspike.rst
index a6dc1a0..74ab439 100644
--- a/doc/pyspike.rst
+++ b/doc/pyspike.rst
@@ -57,6 +57,14 @@ SPIKE-synchronization
     :undoc-members:
     :show-inheritance:
 
+PSTH
+........................................
+.. automodule:: pyspike.psth
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
 Helper functions
 ........................................
 .. automodule:: pyspike.spikes
diff --git a/examples/spike_sync.py b/examples/spike_sync.py
index 9e81536..37dbff4 100644
--- a/examples/spike_sync.py
+++ b/examples/spike_sync.py
@@ -40,7 +40,7 @@ plt.plot(x1, y1, '-k', lw=2.5, label="averaged SPIKE-Sync profile")
 
 plt.subplot(212)
 
-f_psth = spk.psth(spike_trains, bin_size=5.0)
+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")
 
diff --git a/pyspike/psth.py b/pyspike/psth.py
index 8516460..4027215 100644
--- a/pyspike/psth.py
+++ b/pyspike/psth.py
@@ -1,27 +1,34 @@
-"""
-
-Module containing functions to compute the PSTH profile
-
-Copyright 2015, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-"""
+# Module containing functions to compute the PSTH profile
+# Copyright 2015, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
 import numpy as np
 from pyspike import PieceWiseConstFunc
 
 
-# Computes the Peristimulus time histogram of a set of spike trains
+# Computes the peri-stimulus time histogram of a set of spike trains
 def psth(spike_trains, bin_size):
-
-    bins = int((spike_trains[0][-1] - spike_trains[0][0]) / bin_size)
-
-    N = len(spike_trains)
-    combined_spike_train = spike_trains[0][1:-1]
+    """ Computes the peri-stimulus time histogram of a set of
+    :class:`.SpikeTrain`. The PSTH is simply the histogram of merged spike
+    events. The :code:`bin_size` defines the width of the histogram bins.
+
+    :param spike_trains: list of :class:`.SpikeTrain`
+    :param bin_size: width of the histogram bins.
+    :return: The PSTH as a :class:`.PieceWiseConstFunc`
+    """
+
+    bin_count = int((spike_trains[0].t_end - spike_trains[0].t_start) /
+                    bin_size)
+    bins = np.linspace(spike_trains[0].t_start, spike_trains[0].t_end,
+                       bin_count+1)
+
+    # N = len(spike_trains)
+    combined_spike_train = spike_trains[0].spikes
     for i in xrange(1, len(spike_trains)):
         combined_spike_train = np.append(combined_spike_train,
-                                         spike_trains[i][1:-1])
+                                         spike_trains[i].spikes)
 
     vals, edges = np.histogram(combined_spike_train, bins, density=False)
+
     bin_size = edges[1]-edges[0]
-    return PieceWiseConstFunc(edges, vals/(N*bin_size))
+    return PieceWiseConstFunc(edges, vals)  # /(N*bin_size))
-- 
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