diff options
Diffstat (limited to 'pyspike/python_backend.py')
| -rw-r--r-- | pyspike/python_backend.py | 72 |
1 files changed, 36 insertions, 36 deletions
diff --git a/pyspike/python_backend.py b/pyspike/python_backend.py index e5b74e9..cf1a92f 100644 --- a/pyspike/python_backend.py +++ b/pyspike/python_backend.py @@ -1,6 +1,6 @@ """ python_backend.py -Collection of python functions that can be used instead of the cython +Collection of python functions that can be used instead of the cython implementation. Copyright 2014, Mario Mulansky <mario.mulansky@gmx.net> @@ -21,18 +21,18 @@ def isi_distance_python(s1, s2): """ Plain Python implementation of the isi distance. """ # compute the interspike interval - nu1 = s1[1:]-s1[:-1] - nu2 = s2[1:]-s2[:-1] - + nu1 = s1[1:] - s1[:-1] + nu2 = s2[1:] - s2[:-1] + # compute the isi-distance - spike_events = np.empty(len(nu1)+len(nu2)) + spike_events = np.empty(len(nu1) + len(nu2)) spike_events[0] = s1[0] # the values have one entry less - the number of intervals between events - isi_values = np.empty(len(spike_events)-1) + isi_values = np.empty(len(spike_events) - 1) # add the distance of the first events # isi_values[0] = nu1[0]/nu2[0] - 1.0 if nu1[0] <= nu2[0] \ # else 1.0 - nu2[0]/nu1[0] - isi_values[0] = (nu1[0]-nu2[0])/max(nu1[0],nu2[0]) + isi_values[0] = (nu1[0] - nu2[0]) / max(nu1[0], nu2[0]) index1 = 0 index2 = 0 index = 1 @@ -49,28 +49,28 @@ def isi_distance_python(s1, s2): if index2 >= len(nu2): break spike_events[index] = s2[index2] - else: # s1[index1+1] == s2[index2+1] + else: # s1[index1 + 1] == s2[index2 + 1] index1 += 1 index2 += 1 if (index1 >= len(nu1)) or (index2 >= len(nu2)): break spike_events[index] = s1[index1] # compute the corresponding isi-distance - isi_values[index] = (nu1[index1]-nu2[index2]) / \ - max(nu1[index1], nu2[index2]) + isi_values[index] = (nu1[index1] - nu2[index2]) / \ + max(nu1[index1], nu2[index2]) index += 1 # the last event is the interval end spike_events[index] = s1[-1] - # use only the data added above + # use only the data added above # could be less than original length due to equal spike times - return PieceWiseConstFunc(spike_events[:index+1], isi_values[:index]) + return PieceWiseConstFunc(spike_events[:index + 1], isi_values[:index]) ############################################################ # get_min_dist ############################################################ def get_min_dist(spike_time, spike_train, start_index=0): - """ Returns the minimal distance |spike_time - spike_train[i]| + """ Returns the minimal distance |spike_time - spike_train[i]| with i>=start_index. """ d = abs(spike_time - spike_train[start_index]) @@ -99,18 +99,18 @@ def spike_distance_python(spikes1, spikes2): - PieceWiseLinFunc describing the spike-distance. """ # check for auxiliary spikes - first and last spikes should be identical - assert spikes1[0]==spikes2[0], \ + assert spikes1[0] == spikes2[0], \ "Given spike trains seems not to have auxiliary spikes!" - assert spikes1[-1]==spikes2[-1], \ + assert spikes1[-1] == spikes2[-1], \ "Given spike trains seems not to have auxiliary spikes!" # shorter variables t1 = spikes1 t2 = spikes2 - spike_events = np.empty(len(t1)+len(t2)-2) + spike_events = np.empty(len(t1) + len(t2) - 2) spike_events[0] = t1[0] - y_starts = np.empty(len(spike_events)-1) - y_ends = np.empty(len(spike_events)-1) + y_starts = np.empty(len(spike_events) - 1) + y_ends = np.empty(len(spike_events) - 1) index1 = 0 index2 = 0 @@ -133,9 +133,10 @@ def spike_distance_python(spikes1, spikes2): break spike_events[index] = t1[index1] # first calculate the previous interval end value - dt_p1 = dt_f1 # the previous time now was the following time before + dt_p1 = dt_f1 # the previous time was the following time before s1 = dt_p1 - s2 = (dt_p2*(t2[index2+1]-t1[index1]) + dt_f2*(t1[index1]-t2[index2])) / isi2 + s2 = (dt_p2*(t2[index2+1]-t1[index1]) + + dt_f2*(t1[index1]-t2[index2])) / isi2 y_ends[index-1] = (s1*isi2 + s2*isi1) / ((isi1+isi2)**2/2) # now the next interval start value dt_f1 = get_min_dist(t1[index1+1], t2, index2) @@ -148,8 +149,9 @@ def spike_distance_python(spikes1, spikes2): break spike_events[index] = t2[index2] # first calculate the previous interval end value - dt_p2 = dt_f2 # the previous time now was the following time before - s1 = (dt_p1*(t1[index1+1]-t2[index2]) + dt_f1*(t2[index2]-t1[index1])) / isi1 + dt_p2 = dt_f2 # the previous time was the following time before + s1 = (dt_p1*(t1[index1+1]-t2[index2]) + + dt_f1*(t2[index2]-t1[index1])) / isi1 s2 = dt_p2 y_ends[index-1] = (s1*isi2 + s2*isi1) / ((isi1+isi2)**2/2) # now the next interval start value @@ -158,7 +160,7 @@ def spike_distance_python(spikes1, spikes2): isi2 = t2[index2+1]-t2[index2] # s2 is the same as above, thus we can compute y2 immediately y_starts[index] = (s1*isi2 + s2*isi1) / ((isi1+isi2)**2/2) - else: # t1[index1+1] == t2[index2+1] - generate only one event + else: # t1[index1+1] == t2[index2+1] - generate only one event index1 += 1 index2 += 1 if (index1+1 >= len(t1)) or (index2+1 >= len(t2)): @@ -183,9 +185,9 @@ def spike_distance_python(spikes1, spikes2): s1 = dt_p1*(t1[-1]-t1[-2])/isi1 s2 = dt_p2*(t2[-1]-t2[-2])/isi2 y_ends[index-1] = (s1*isi2 + s2*isi1) / ((isi1+isi2)**2/2) - # use only the data added above + # use only the data added above # could be less than original length due to equal spike times - return PieceWiseLinFunc(spike_events[:index+1], + return PieceWiseLinFunc(spike_events[:index+1], y_starts[:index], y_ends[:index]) @@ -209,7 +211,7 @@ def add_piece_wise_const_python(x1, y1, x2, y2): elif x1[index1+1] > x2[index2+1]: index2 += 1 x_new[index] = x2[index2] - else: # x1[index1+1] == x2[index2+1]: + else: # x1[index1+1] == x2[index2+1]: index1 += 1 index2 += 1 x_new[index] = x1[index1] @@ -217,15 +219,13 @@ def add_piece_wise_const_python(x1, y1, x2, y2): # one array reached the end -> copy the contents of the other to the end if index1+1 < len(y1): x_new[index+1:index+1+len(x1)-index1-1] = x1[index1+1:] - y_new[index+1:index+1+len(y1)-index1-1] = y1[index1+1:] + \ - y2[-1] + y_new[index+1:index+1+len(y1)-index1-1] = y1[index1+1:] + y2[-1] index += len(x1)-index1-2 elif index2+1 < len(y2): x_new[index+1:index+1+len(x2)-index2-1] = x2[index2+1:] - y_new[index+1:index+1+len(y2)-index2-1] = y2[index2+1:] + \ - y1[-1] + y_new[index+1:index+1+len(y2)-index2-1] = y2[index2+1:] + y1[-1] index += len(x2)-index2-2 - else: # both arrays reached the end simultaneously + else: # both arrays reached the end simultaneously # only the last x-value missing x_new[index+1] = x1[-1] # the last value is again the end of the interval @@ -244,9 +244,9 @@ def add_piece_wise_lin_python(x1, y11, y12, x2, y21, y22): y2_new = np.empty_like(y1_new) x_new[0] = x1[0] y1_new[0] = y11[0] + y21[0] - index1 = 0 # index for self - index2 = 0 # index for f - index = 0 # index for new + index1 = 0 # index for self + index2 = 0 # index for f + index = 0 # index for new while (index1+1 < len(y11)) and (index2+1 < len(y21)): # print(index1+1, x1[index1+1], self.y[index1+1], x_new[index]) if x1[index1+1] < x2[index2+1]: @@ -272,7 +272,7 @@ def add_piece_wise_lin_python(x1, y11, y12, x2, y21, y22): x_new[index] = x2[index2] # and the starting value for the next interval y1_new[index] = y21[index2] + y - else: # x1[index1+1] == x2[index2+1]: + else: # x1[index1+1] == x2[index2+1]: y2_new[index] = y12[index1] + y22[index2] index1 += 1 index2 += 1 @@ -297,7 +297,7 @@ def add_piece_wise_lin_python(x1, y11, y12, x2, y21, y22): y1_new[index+1:index+1+len(y21)-index2-1] = y21[index2+1:] + y y2_new[index:index+len(y22)-index2-1] = y22[index2:-1] + y index += len(x2)-index2-2 - else: # both arrays reached the end simultaneously + else: # both arrays reached the end simultaneously # only the last x-value missing x_new[index+1] = x1[-1] # finally, the end value for the last interval |