1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
|
# 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 __future__ import absolute_import
import pyspike
from pyspike import PieceWiseLinFunc
from pyspike.generic import _generic_profile_multi, _generic_distance_multi, \
_generic_distance_matrix
############################################################
# spike_profile
############################################################
def spike_profile(*args, **kwargs):
""" Computes the spike-distance profile :math:`S(t)` of the given
spike trains. Returns the profile as a PieceWiseConstLin object. The
SPIKE-values are defined positive :math:`S(t)>=0`.
Valid call structures::
spike_profile(st1, st2) # returns the bi-variate profile
spike_profile(st1, st2, st3) # multi-variate profile of 3 spike trains
spike_trains = [st1, st2, st3, st4] # list of spike trains
spike_profile(spike_trains) # profile of the list of spike trains
spike_profile(spike_trains, indices=[0, 1]) # use only the spike trains
# given by the indices
The multivariate spike-distance profile is defined as the average of all
pairs of spike-trains:
.. math:: <S(t)> = \\frac{2}{N(N-1)} \\sum_{<i,j>} S^{i, j}`,
where the sum goes over all pairs <i,j>
:returns: The spike-distance profile :math:`S(t)`
:rtype: :class:`.PieceWiseConstLin`
"""
if len(args) == 1:
return spike_profile_multi(args[0], **kwargs)
elif len(args) == 2:
return spike_profile_bi(args[0], args[1])
else:
return spike_profile_multi(args)
############################################################
# spike_profile_bi
############################################################
def spike_profile_bi(spike_train1, spike_train2):
""" Specific function to compute a bivariate SPIKE-profile. This is a
deprecated function and should not be called directly. Use
:func:`.spike_profile` to compute SPIKE-profiles.
:param spike_train1: First spike train.
:type spike_train1: :class:`.SpikeTrain`
:param spike_train2: Second spike train.
: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
assert spike_train1.t_start == spike_train2.t_start, \
"Given spike trains are not defined on the same interval!"
assert spike_train1.t_end == spike_train2.t_end, \
"Given spike trains are not defined on the same interval!"
# cython implementation
try:
from .cython.cython_profiles import spike_profile_cython \
as spike_profile_impl
except ImportError:
if not(pyspike.disable_backend_warning):
print("Warning: spike_profile_cython not found. Make sure that \
PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \
Falling back to slow python backend.")
# use python backend
from .cython.python_backend import spike_distance_python \
as spike_profile_impl
times, y_starts, y_ends = spike_profile_impl(
spike_train1.get_spikes_non_empty(),
spike_train2.get_spikes_non_empty(),
spike_train1.t_start, spike_train1.t_end)
return PieceWiseLinFunc(times, y_starts, y_ends)
############################################################
# spike_profile_multi
############################################################
def spike_profile_multi(spike_trains, indices=None):
""" Specific function to compute a multivariate SPIKE-profile. This is a
deprecated function and should not be called directly. Use
:func:`.spike_profile` to compute SPIKE-profiles.
: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>(t)`
:rtype: :class:`.PieceWiseLinFunc`
"""
average_dist, M = _generic_profile_multi(spike_trains, spike_profile_bi,
indices)
average_dist.mul_scalar(1.0/M) # normalize
return average_dist
############################################################
# spike_distance
############################################################
def spike_distance(*args, **kwargs):
""" Computes the SPIKE-distance :math:`D_S` of the given spike trains. The
spike-distance is the integral over the spike distance profile
:math:`D(t)`:
.. math:: D_S = \\int_{T_0}^{T_1} S(t) dt.
Valid call structures::
spike_distance(st1, st2) # returns the bi-variate distance
spike_distance(st1, st2, st3) # multi-variate distance of 3 spike trains
spike_trains = [st1, st2, st3, st4] # list of spike trains
spike_distance(spike_trains) # distance of the list of spike trains
spike_distance(spike_trains, indices=[0, 1]) # use only the spike trains
# given by the indices
In the multivariate case, the spike distance is given as the integral over
the multivariate profile, that is the average profile of all spike train
pairs:
.. math:: D_S = \\int_0^T \\frac{2}{N(N-1)} \\sum_{<i,j>}
S^{i, j} dt
:returns: The spike-distance :math:`D_S`.
:rtype: double
"""
if len(args) == 1:
return spike_distance_multi(args[0], **kwargs)
elif len(args) == 2:
return spike_distance_bi(args[0], args[1], **kwargs)
else:
return spike_distance_multi(args, **kwargs)
############################################################
# spike_distance_bi
############################################################
def spike_distance_bi(spike_train1, spike_train2, interval=None):
""" Specific function to compute a bivariate SPIKE-distance. This is a
deprecated function and should not be called directly. Use
:func:`.spike_distance` to compute SPIKE-distances.
:param spike_train1: First spike train.
:type spike_train1: :class:`.SpikeTrain`
:param spike_train2: Second spike train.
: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 spike-distance.
:rtype: double
"""
if interval is None:
# distance over the whole interval is requested: use specific function
# for optimal performance
try:
from .cython.cython_distances import spike_distance_cython \
as spike_distance_impl
return spike_distance_impl(spike_train1.get_spikes_non_empty(),
spike_train2.get_spikes_non_empty(),
spike_train1.t_start,
spike_train1.t_end)
except ImportError:
# Cython backend not available: fall back to average profile
return spike_profile_bi(spike_train1, spike_train2).avrg(interval)
else:
# some specific interval is provided: compute the whole profile
return spike_profile_bi(spike_train1, spike_train2).avrg(interval)
############################################################
# spike_distance_multi
############################################################
def spike_distance_multi(spike_trains, indices=None, interval=None):
""" Specific function to compute a multivariate SPIKE-distance. This is a
deprecated function and should not be called directly. Use
:func:`.spike_distance` to compute SPIKE-distances.
: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 multi-variate spike distance :math:`D_S`.
:rtype: double
"""
return _generic_distance_multi(spike_trains, spike_distance_bi, indices,
interval)
############################################################
# spike_distance_matrix
############################################################
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:`.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: 2D array with the pair wise time average spike distances
:math:`D_S^{ij}`
:rtype: np.array
"""
return _generic_distance_matrix(spike_trains, spike_distance_bi,
indices, interval)
|
