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authorMario Mulansky <mario.mulansky@gmx.net>2015-08-26 18:26:58 +0200
committerMario Mulansky <mario.mulansky@gmx.net>2018-06-02 12:58:46 -0700
commit66bf08417c651d1c0d96cb980571efb2043d7f1a (patch)
tree53b529f2b4cfaf34012ae8755d48129660c12b5d
parent827be39a1646f1e518f7210b8943006f5741144d (diff)
completed python directionality backend
-rw-r--r--pyspike/cython/directionality_python_backend.py57
-rw-r--r--pyspike/spike_directionality.py29
2 files changed, 72 insertions, 14 deletions
diff --git a/pyspike/cython/directionality_python_backend.py b/pyspike/cython/directionality_python_backend.py
index e14238f..c1d820b 100644
--- a/pyspike/cython/directionality_python_backend.py
+++ b/pyspike/cython/directionality_python_backend.py
@@ -15,7 +15,62 @@ import numpy as np
############################################################
# spike_train_order_python
############################################################
-def spike_train_order_python(spikes1, spikes2, t_start, t_end, max_tau):
+def spike_directionality_profile_python(spikes1, spikes2, t_start, t_end,
+ max_tau):
+
+ def get_tau(spikes1, spikes2, i, j, max_tau):
+ m = t_end - t_start # use interval as initial tau
+ if i < len(spikes1)-1 and i > -1:
+ m = min(m, spikes1[i+1]-spikes1[i])
+ if j < len(spikes2)-1 and j > -1:
+ m = min(m, spikes2[j+1]-spikes2[j])
+ if i > 0:
+ m = min(m, spikes1[i]-spikes1[i-1])
+ if j > 0:
+ m = min(m, spikes2[j]-spikes2[j-1])
+ m *= 0.5
+ if max_tau > 0.0:
+ m = min(m, max_tau)
+ return m
+
+ N1 = len(spikes1)
+ N2 = len(spikes2)
+ i = -1
+ j = -1
+ d1 = np.zeros(N1) # directionality values
+ d2 = np.zeros(N2) # directionality values
+ while i + j < N1 + N2 - 2:
+ if (i < N1-1) and (j == N2-1 or spikes1[i+1] < spikes2[j+1]):
+ i += 1
+ tau = get_tau(spikes1, spikes2, i, j, max_tau)
+ if j > -1 and spikes1[i]-spikes2[j] < tau:
+ # coincidence between the current spike and the previous spike
+ # spike in first spike train occurs after second
+ d1[i] = -1
+ d2[j] = +1
+ elif (j < N2-1) and (i == N1-1 or spikes1[i+1] > spikes2[j+1]):
+ j += 1
+ tau = get_tau(spikes1, spikes2, i, j, max_tau)
+ if i > -1 and spikes2[j]-spikes1[i] < tau:
+ # coincidence between the current spike and the previous spike
+ # spike in second spike train occurs after first
+ d1[i] = +1
+ d2[j] = -1
+ else: # spikes1[i+1] = spikes2[j+1]
+ # advance in both spike trains
+ j += 1
+ i += 1
+ d1[i] = 0
+ d2[j] = 0
+
+ return d1, d2
+
+
+############################################################
+# spike_train_order_python
+############################################################
+def spike_train_order_profile_python(spikes1, spikes2, t_start, t_end,
+ max_tau):
def get_tau(spikes1, spikes2, i, j, max_tau):
m = t_end - t_start # use interval as initial tau
diff --git a/pyspike/spike_directionality.py b/pyspike/spike_directionality.py
index f608ecc..cda7fe3 100644
--- a/pyspike/spike_directionality.py
+++ b/pyspike/spike_directionality.py
@@ -33,7 +33,11 @@ def spike_directionality(spike_train1, spike_train2, normalize=True,
max_tau)
c = len(spike_train1.spikes)
except ImportError:
- raise NotImplementedError()
+ d1, x = spike_directionality_profiles([spike_train1, spike_train2],
+ interval=interval,
+ max_tau=max_tau)
+ d = np.sum(d1)
+ c = len(spike_train1.spikes)
if normalize:
return 1.0*d/c
else:
@@ -94,24 +98,23 @@ def spike_directionality_profiles(spike_trains, indices=None,
from cython.cython_directionality import \
spike_directionality_profiles_cython as profile_impl
except ImportError:
- raise NotImplementedError()
-# if not(pyspike.disable_backend_warning):
-# print("Warning: spike_distance_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 coincidence_python \
-# as coincidence_profile_impl
+ if not(pyspike.disable_backend_warning):
+ print("Warning: spike_distance_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.directionality_python_backend import \
+ spike_directionality_profile_python as profile_impl
if max_tau is None:
max_tau = 0.0
for i, j in pairs:
- a1, a2 = profile_impl(spike_trains[i].spikes, spike_trains[j].spikes,
+ d1, d2 = profile_impl(spike_trains[i].spikes, spike_trains[j].spikes,
spike_trains[i].t_start, spike_trains[i].t_end,
max_tau)
- asymmetry_list[i] += a1
- asymmetry_list[j] += a2
+ asymmetry_list[i] += d1
+ asymmetry_list[j] += d2
for a in asymmetry_list:
a /= len(spike_trains)-1
return asymmetry_list
@@ -151,7 +154,7 @@ PySpike is installed by running\n 'python setup.py build_ext --inplace'!\n \
Falling back to slow python backend.")
# use python backend
from cython.directionality_python_backend import \
- spike_train_order_python as spike_train_order_profile_impl
+ spike_train_order_profile_python as spike_train_order_profile_impl
if max_tau is None:
max_tau = 0.0