updated docs

8 files changed, 127 insertions, 129 deletions

diff --git a/pyspike/DiscreteFunc.py b/pyspike/DiscreteFunc.py
index bd13e1f..33b7a81 100644
--- a/pyspike/DiscreteFunc.py
+++ b/pyspike/DiscreteFunc.py
@@ -1,11 +1,7 @@
-"""
-Class representing discrete functions.
+# Class representing discrete functions.
+# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
-Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-
-"""
 from __future__ import print_function
 
 import numpy as np
@@ -174,7 +170,7 @@ class DiscreteFunc(object):
 
     def avrg(self, interval=None):
         """ Computes the average of the interval sequence:
-        :math:`a = 1/N sum f_n` where N is the number of intervals.
+        :math:`a = 1/N \\sum f_n` where N is the number of intervals.
 
         :param interval: averaging interval given as a pair of floats, a
                          sequence of pairs for averaging multiple intervals, or
diff --git a/pyspike/PieceWiseConstFunc.py b/pyspike/PieceWiseConstFunc.py
index dc57ab1..41998ef 100644
--- a/pyspike/PieceWiseConstFunc.py
+++ b/pyspike/PieceWiseConstFunc.py
@@ -1,11 +1,7 @@
-"""
-Class representing piece-wise constant functions.
+# Class representing piece-wise constant functions.
+# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
-Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-
-"""
 from __future__ import print_function
 
 import numpy as np
@@ -103,7 +99,7 @@ class PieceWiseConstFunc(object):
 
     def avrg(self, interval=None):
         """ Computes the average of the piece-wise const function:
-        :math:`a = 1/T int_0^T f(x) dx` where T is the length of the interval.
+        :math:`a = 1/T \int_0^T f(x) dx` where T is the length of the interval.
 
         :param interval: averaging interval given as a pair of floats, a
                          sequence of pairs for averaging multiple intervals, or
diff --git a/pyspike/PieceWiseLinFunc.py b/pyspike/PieceWiseLinFunc.py
index bc0aa2a..f2442be 100644
--- a/pyspike/PieceWiseLinFunc.py
+++ b/pyspike/PieceWiseLinFunc.py
@@ -1,11 +1,7 @@
-"""
-Class representing piece-wise linear functions.
+# Class representing piece-wise linear functions.
+# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
-Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-
-"""
 from __future__ import print_function
 
 import numpy as np
@@ -123,7 +119,7 @@ class PieceWiseLinFunc:
 
     def avrg(self, interval=None):
         """ Computes the average of the piece-wise linear function:
-        :math:`a = 1/T int_0^T f(x) dx` where T is the length of the interval.
+        :math:`a = 1/T \int_0^T f(x) dx` where T is the interval length.
 
         :param interval: averaging interval given as a pair of floats, a
                          sequence of pairs for averaging multiple intervals, or
diff --git a/pyspike/SpikeTrain.py b/pyspike/SpikeTrain.py
index d586fe0..a02b7ab 100644
--- a/pyspike/SpikeTrain.py
+++ b/pyspike/SpikeTrain.py
@@ -1,9 +1,6 @@
-""" Module containing the class representing spike trains for PySpike.
-
-Copyright 2015, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-"""
+# Module containing the class representing spike trains for PySpike.
+# Copyright 2015, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
 import numpy as np
 
@@ -11,15 +8,22 @@ import numpy as np
 class SpikeTrain(object):
     """ Class representing spike trains for the PySpike Module."""
 
-    def __init__(self, spike_times, edges):
-        """ Constructs the SpikeTrain
+    def __init__(self, spike_times, edges, is_sorted=True):
+        """ Constructs the SpikeTrain.
+
         :param spike_times: ordered array of spike times.
         :param edges: The edges of the spike train. Given as a pair of floats
-        (T0, T1) or a single float T1, where then T0=0 is assumed.
+                      (T0, T1) or a single float T1, where then T0=0 is
+                      assumed.
+        :param is_sorted: If `False`, the spike times will sorted by `np.sort`.
+
         """
 
         # TODO: sanity checks
-        self.spikes = np.array(spike_times, dtype=float)
+        if is_sorted:
+            self.spikes = np.array(spike_times, dtype=float)
+        else:
+            self.spikes = np.sort(np.array(spike_times, dtype=float))
 
         try:
             self.t_start = float(edges[0])
@@ -27,3 +31,20 @@ class SpikeTrain(object):
         except:
             self.t_start = 0.0
             self.t_end = float(edges)
+
+    def sort(self):
+        """ Sorts the spike times of this spike train using `np.sort`
+        """
+        self.spikes = np.sort(self.spikes)
+
+    def copy(self):
+        """ Returns a copy of this spike train.
+        Use this function if you want to create a real (deep) copy of this
+        spike train. Simple assignment `t2 = t1` does not create a copy of the
+        spike train data, but a reference as `numpy.array` is used for storing
+        the data.
+
+        :return: :class:`.SpikeTrain` copy of this spike train.
+
+        """
+        return SpikeTrain(self.spikes.copy(), [self.t_start, self.t_end])
diff --git a/pyspike/isi_distance.py b/pyspike/isi_distance.py
index cb8ef54..aeab0df 100644
--- a/pyspike/isi_distance.py
+++ b/pyspike/isi_distance.py
@@ -1,11 +1,6 @@
-"""
-
-Module containing several functions to compute the ISI profiles and distances
-
-Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-"""
+# Module containing several functions to compute the ISI profiles and distances
+# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
 from pyspike import PieceWiseConstFunc
 from pyspike.generic import _generic_profile_multi, _generic_distance_matrix
@@ -15,16 +10,16 @@ from pyspike.generic import _generic_profile_multi, _generic_distance_matrix
 # isi_profile
 ############################################################
 def isi_profile(spike_train1, spike_train2):
-    """ Computes the isi-distance profile :math:`S_{isi}(t)` of the two given
-    spike trains. Retruns the profile as a PieceWiseConstFunc object. The S_isi
-    values are defined positive S_isi(t)>=0.
+    """ Computes the isi-distance profile :math:`I(t)` of the two given
+    spike trains. Retruns the profile as a PieceWiseConstFunc object. The
+    ISI-values are defined positive :math:`I(t)>=0`.
 
     :param spike_train1: First spike train.
-    :type spike_train1: :class:`pyspike.SpikeTrain`
+    :type spike_train1: :class:`.SpikeTrain`
     :param spike_train2: Second spike train.
-    :type spike_train2: :class:`pyspike.SpikeTrain`
-    :returns: The isi-distance profile :math:`S_{isi}(t)`
-    :rtype: :class:`pyspike.function.PieceWiseConstFunc`
+    :type spike_train2: :class:`.SpikeTrain`
+    :returns: The isi-distance profile :math:`I(t)`
+    :rtype: :class:`.PieceWiseConstFunc`
 
     """
     # check whether the spike trains are defined for the same interval
@@ -54,20 +49,20 @@ Falling back to slow python backend.")
 # isi_distance
 ############################################################
 def isi_distance(spike_train1, spike_train2, interval=None):
-    """ Computes the isi-distance I of the given spike trains. The
+    """ Computes the ISI-distance :math:`D_I` of the given spike trains. The
     isi-distance is the integral over the isi distance profile
-    :math:`S_{isi}(t)`:
+    :math:`I(t)`:
 
-    .. math:: I = \int_{T_0}^{T_1} S_{isi}(t) dt.
+    .. math:: D_I = \\int_{T_0}^{T_1} I(t) dt.
 
     :param spike_train1: First spike train.
-    :type spike_train1: :class:`pyspike.SpikeTrain`
+    :type spike_train1: :class:`.SpikeTrain`
     :param spike_train2: Second spike train.
-    :type spike_train2: :class:`pyspike.SpikeTrain`
+    :type spike_train2: :class:`.SpikeTrain`
     :param interval: averaging interval given as a pair of floats (T0, T1),
                      if None the average over the whole function is computed.
     :type interval: Pair of floats or None.
-    :returns: The isi-distance I.
+    :returns: The isi-distance :math:`D_I`.
     :rtype: double
     """
     return isi_profile(spike_train1, spike_train2).avrg(interval)
@@ -79,15 +74,17 @@ def isi_distance(spike_train1, spike_train2, interval=None):
 def isi_profile_multi(spike_trains, indices=None):
     """ computes the multi-variate isi distance profile for a set of spike
     trains. That is the average isi-distance of all pairs of spike-trains:
-    S_isi(t) = 2/((N(N-1)) sum_{<i,j>} S_{isi}^{i,j},
+
+    .. math:: <I(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j},
+
     where the sum goes over all pairs <i,j>
 
-    :param spike_trains: list of :class:`pyspike.SpikeTrain`
+    :param spike_trains: list of :class:`.SpikeTrain`
     :param indices: list of indices defining which spike trains to use,
                     if None all given spike trains are used (default=None)
     :type state: list or None
-    :returns: The averaged isi profile :math:`<S_{isi}>(t)`
-    :rtype: :class:`pyspike.function.PieceWiseConstFunc`
+    :returns: The averaged isi profile :math:`<I(t)>`
+    :rtype: :class:`.PieceWiseConstFunc`
     """
     average_dist, M = _generic_profile_multi(spike_trains, isi_profile,
                                              indices)
@@ -101,16 +98,18 @@ def isi_profile_multi(spike_trains, indices=None):
 def isi_distance_multi(spike_trains, indices=None, interval=None):
     """ computes the multi-variate isi-distance for a set of spike-trains.
     That is the time average of the multi-variate spike profile:
-    I = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{isi}^{i,j},
+
+    .. math:: D_I = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>} I^{i,j},
+
     where the sum goes over all pairs <i,j>
 
-    :param spike_trains: list of spike trains
+    :param spike_trains: list of :class:`.SpikeTrain`
     :param indices: list of indices defining which spike trains to use,
                     if None all given spike trains are used (default=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 time-averaged isi distance :math:`I`
+    :returns: The time-averaged multivariate ISI distance :math:`D_I`
     :rtype: double
     """
     return isi_profile_multi(spike_trains, indices).avrg(interval)
@@ -122,7 +121,7 @@ def isi_distance_multi(spike_trains, indices=None, interval=None):
 def isi_distance_matrix(spike_trains, indices=None, interval=None):
     """ Computes the time averaged isi-distance of all pairs of spike-trains.
 
-    :param spike_trains: list of :class:`pyspike.SpikeTrain`
+    :param spike_trains: list of :class:`.SpikeTrain`
     :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
@@ -130,7 +129,7 @@ def isi_distance_matrix(spike_trains, indices=None, interval=None):
                      the average over the whole function is computed.
     :type interval: Pair of floats or None.
     :returns: 2D array with the pair wise time average isi distances
-              :math:`I_{ij}`
+              :math:`D_{I}^{ij}`
     :rtype: np.array
     """
     return _generic_distance_matrix(spike_trains, isi_distance,
diff --git a/pyspike/spike_distance.py b/pyspike/spike_distance.py
index 8d03d70..cc620d4 100644
--- a/pyspike/spike_distance.py
+++ b/pyspike/spike_distance.py
@@ -1,11 +1,6 @@
-"""
-
-Module containing several functions to compute SPIKE profiles and distances
-
-Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-"""
+# Module containing several functions to compute SPIKE profiles and distances
+# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
 from pyspike import PieceWiseLinFunc
 from pyspike.generic import _generic_profile_multi, _generic_distance_matrix
@@ -15,16 +10,16 @@ from pyspike.generic import _generic_profile_multi, _generic_distance_matrix
 # spike_profile
 ############################################################
 def spike_profile(spike_train1, spike_train2):
-    """ Computes the spike-distance profile S_spike(t) of the two given spike
-    trains. Returns the profile as a PieceWiseLinFunc object. The S_spike
-    values are defined positive S_spike(t)>=0.
+    """ Computes the spike-distance profile :math:`S(t)` of the two given spike
+    trains. Returns the profile as a PieceWiseLinFunc object. The SPIKE-values
+    are defined positive :math:`S(t)>=0`.
 
     :param spike_train1: First spike train.
-    :type spike_train1: :class:`pyspike.SpikeTrain`
+    :type spike_train1: :class:`.SpikeTrain`
     :param spike_train2: Second spike train.
-    :type spike_train2: :class:`pyspike.SpikeTrain`
-    :returns: The spike-distance profile :math:`S_{spike}(t)`.
-    :rtype: :class:`pyspike.function.PieceWiseLinFunc`
+    :type spike_train2: :class:`.SpikeTrain`
+    :returns: The spike-distance profile :math:`S(t)`.
+    :rtype: :class:`.PieceWiseLinFunc`
 
     """
     # check whether the spike trains are defined for the same interval
@@ -56,15 +51,15 @@ Falling back to slow python backend.")
 # spike_distance
 ############################################################
 def spike_distance(spike_train1, spike_train2, interval=None):
-    """ Computes the spike-distance S of the given spike trains. The
-    spike-distance is the integral over the isi distance profile S_spike(t):
+    """ Computes the spike-distance :math:`D_S` of the given spike trains. The
+    spike-distance is the integral over the isi distance profile :math:`S(t)`:
 
-    .. math:: S = \int_{T_0}^{T_1} S_{spike}(t) dt.
+    .. math:: D_S = \int_{T_0}^{T_1} S(t) dt.
 
     :param spike_train1: First spike train.
-    :type spike_train1: :class:`pyspike.SpikeTrain`
+    :type spike_train1: :class:`.SpikeTrain`
     :param spike_train2: Second spike train.
-    :type spike_train2: :class:`pyspike.SpikeTrain`
+    :type spike_train2: :class:`.SpikeTrain`
     :param interval: averaging interval given as a pair of floats (T0, T1),
                      if None the average over the whole function is computed.
     :type interval: Pair of floats or None.
@@ -81,15 +76,17 @@ def spike_distance(spike_train1, spike_train2, interval=None):
 def spike_profile_multi(spike_trains, indices=None):
     """ Computes the multi-variate spike distance profile for a set of spike
     trains. That is the average spike-distance of all pairs of spike-trains:
-    :math:`S_spike(t) = 2/((N(N-1)) sum_{<i,j>} S_{spike}^{i, j}`,
+
+    .. math:: <S(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} S^{i, j}`,
+
     where the sum goes over all pairs <i,j>
 
-    :param spike_trains: list of spike trains
+    :param spike_trains: list of :class:`.SpikeTrain`
     :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
-    :returns: The averaged spike profile :math:`<S_{spike}>(t)`
-    :rtype: :class:`pyspike.function.PieceWiseLinFunc`
+    :returns: The averaged spike profile :math:`<S>(t)`
+    :rtype: :class:`.PieceWiseLinFunc`
 
     """
     average_dist, M = _generic_profile_multi(spike_trains, spike_profile,
@@ -104,17 +101,20 @@ def spike_profile_multi(spike_trains, indices=None):
 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
+
+    .. math::  D_S = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>}
+               S^{i, j} dt
+
     where the sum goes over all pairs <i,j>
 
-    :param spike_trains: list of :class:`pyspike.SpikeTrain`
+    :param spike_trains: list of :class:`.SpikeTrain`
     :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.
+    :returns: The averaged multi-variate spike distance :math:`D_S`.
     :rtype: double
     """
     return spike_profile_multi(spike_trains, indices).avrg(interval)
@@ -126,7 +126,7 @@ def spike_distance_multi(spike_trains, indices=None, interval=None):
 def spike_distance_matrix(spike_trains, indices=None, interval=None):
     """ Computes the time averaged spike-distance of all pairs of spike-trains.
 
-    :param spike_trains: list of :class:`pyspike.SpikeTrain`
+    :param spike_trains: list of :class:`.SpikeTrain`
     :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
@@ -134,7 +134,7 @@ def spike_distance_matrix(spike_trains, indices=None, interval=None):
                      the average over the whole function is computed.
     :type interval: Pair of floats or None.
     :returns: 2D array with the pair wise time average spike distances
-              :math:`S_{ij}`
+              :math:`D_S^{ij}`
     :rtype: np.array
     """
     return _generic_distance_matrix(spike_trains, spike_distance,
diff --git a/pyspike/spike_sync.py b/pyspike/spike_sync.py
index 8ddd32c..9d2e363 100644
--- a/pyspike/spike_sync.py
+++ b/pyspike/spike_sync.py
@@ -1,12 +1,7 @@
-"""
-
-Module containing several functions to compute SPIKE-Synchronization profiles
-and distances
-
-Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-"""
+# Module containing several functions to compute SPIKE-Synchronization profiles
+# and distances
+# Copyright 2014-2015, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
 from functools import partial
 from pyspike import DiscreteFunc
@@ -27,7 +22,7 @@ def spike_sync_profile(spike_train1, spike_train2, max_tau=None):
     :param spike_train2: Second spike train.
     :type spike_train2: :class:`pyspike.SpikeTrain`
     :param max_tau: Maximum coincidence window size. If 0 or `None`, the
-    coincidence window has no upper bound.
+                    coincidence window has no upper bound.
     :returns: The spike-distance profile :math:`S_{sync}(t)`.
     :rtype: :class:`pyspike.function.DiscreteFunction`
 
@@ -77,12 +72,13 @@ def spike_sync(spike_train1, spike_train2, interval=None, max_tau=None):
     :param spike_train2: Second spike train.
     :type spike_train2: :class:`pyspike.SpikeTrain`
     :param interval: averaging interval given as a pair of floats (T0, T1),
-                     if None the average over the whole function is computed.
+                     if `None` the average over the whole function is computed.
     :type interval: Pair of floats or None.
     :param max_tau: Maximum coincidence window size. If 0 or `None`, the
-    coincidence window has no upper bound.
+                    coincidence window has no upper bound.
     :returns: The spike synchronization value.
-    :rtype: double
+    :rtype: `double`
+
     """
     return spike_sync_profile(spike_train1, spike_train2,
                               max_tau).avrg(interval)
@@ -103,7 +99,7 @@ def spike_sync_profile_multi(spike_trains, indices=None, max_tau=None):
                     if None all given spike trains are used (default=None)
     :type indices: list or None
     :param max_tau: Maximum coincidence window size. If 0 or `None`, the
-    coincidence window has no upper bound.
+                    coincidence window has no upper bound.
     :returns: The multi-variate spike sync profile :math:`<S_{sync}>(t)`
     :rtype: :class:`pyspike.function.DiscreteFunction`
 
@@ -130,9 +126,10 @@ def spike_sync_multi(spike_trains, indices=None, interval=None, max_tau=None):
                      the average over the whole function is computed.
     :type interval: Pair of floats or None.
     :param max_tau: Maximum coincidence window size. If 0 or `None`, the
-    coincidence window has no upper bound.
+                    coincidence window has no upper bound.
     :returns: The multi-variate spike synchronization value SYNC.
     :rtype: double
+
     """
     return spike_sync_profile_multi(spike_trains, indices,
                                     max_tau).avrg(interval)
@@ -153,10 +150,11 @@ def spike_sync_matrix(spike_trains, indices=None, interval=None, max_tau=None):
                      the average over the whole function is computed.
     :type interval: Pair of floats or None.
     :param max_tau: Maximum coincidence window size. If 0 or `None`, the
-    coincidence window has no upper bound.
+                    coincidence window has no upper bound.
     :returns: 2D array with the pair wise time spike synchronization values
               :math:`SYNC_{ij}`
     :rtype: np.array
+
     """
     dist_func = partial(spike_sync, max_tau=max_tau)
     return _generic_distance_matrix(spike_trains, dist_func,
diff --git a/pyspike/spikes.py b/pyspike/spikes.py
index 9401b6e..35d8533 100644
--- a/pyspike/spikes.py
+++ b/pyspike/spikes.py
@@ -1,11 +1,6 @@
-""" spikes.py
-
-Module containing several function to load and transform spike trains
-
-Copyright 2014, Mario Mulansky <mario.mulansky@gmx.net>
-
-Distributed under the BSD License
-"""
+# Module containing several function to load and transform spike trains
+# Copyright 2014, Mario Mulansky <mario.mulansky@gmx.net>
+# Distributed under the BSD License
 
 import numpy as np
 from pyspike import SpikeTrain
@@ -15,21 +10,18 @@ from pyspike import SpikeTrain
 # spike_train_from_string
 ############################################################
 def spike_train_from_string(s, edges, sep=' ', is_sorted=False):
-    """ Converts a string of times into a  :class:`pyspike.SpikeTrain`.
+    """ Converts a string of times into a  :class:`.SpikeTrain`.
 
     :param s: the string with (ordered) spike times.
     :param edges: interval defining the edges of the spike train.
-    Given as a pair of floats (T0, T1) or a single float T1, where T0=0 is
-    assumed.
+                  Given as a pair of floats (T0, T1) or a single float T1,
+                  where T0=0 is assumed.
     :param sep: The separator between the time numbers, default=' '.
     :param is_sorted: if True, the spike times are not sorted after loading,
                       if False, spike times are sorted with `np.sort`
-    :returns:  :class:`pyspike.SpikeTrain`
+    :returns: :class:`.SpikeTrain`
     """
-    if not(is_sorted):
-        return SpikeTrain(np.sort(np.fromstring(s, sep=sep)), edges)
-    else:
-        return SpikeTrain(np.fromstring(s, sep=sep), edges)
+    return SpikeTrain(np.fromstring(s, sep=sep), edges, is_sorted)
 
 
 ############################################################
@@ -40,7 +32,7 @@ def load_spike_trains_from_txt(file_name, edges,
     """ Loads a number of spike trains from a text file. Each line of the text
     file should contain one spike train as a sequence of spike times separated
     by `separator`. Empty lines as well as lines starting with `comment` are
-    neglected. The `interval` represents the start and the end of the
+    neglected. The `edges` represents the start and the end of the
     spike trains.
 
     :param file_name: The name of the text file.
@@ -51,7 +43,7 @@ def load_spike_trains_from_txt(file_name, edges,
     :param separator: The character used to seprate the values in the text file
     :param comment: Lines starting with this character are ignored.
     :param sort: If true, the spike times are order via `np.sort`, default=True
-    :returns: list of spike trains
+    :returns: list of :class:`.SpikeTrain`
     """
     spike_trains = []
     spike_file = open(file_name, 'r')
@@ -70,7 +62,7 @@ def load_spike_trains_from_txt(file_name, edges,
 def merge_spike_trains(spike_trains):
     """ Merges a number of spike trains into a single spike train.
 
-    :param spike_trains: list of arrays of spike times
+    :param spike_trains: list of :class:`.SpikeTrain`
     :returns: spike train with the merged spike times
     """
     # get the lengths of the spike trains
@@ -110,7 +102,7 @@ def generate_poisson_spikes(rate, interval):
                      to the spike train at the beginning and end of this
                      interval, if they are not yet present.
     :type interval: pair of doubles or double
-    :returns: Poisson spike train as a :class:`pyspike.SpikeTrain`
+    :returns: Poisson spike train as a :class:`.SpikeTrain`
     """
     try:
         T_start = interval[0]