def gem(query, subject, St0=2, St1=2, E=0.01, symmetric=False, squared=True):
"""GEM local similarity measure"""
# enable openmp support
omp = False
N = lgem.TimeSeries(query)
H = lgem.TimeSeries(subject)
R = lgem.Result()
lgem.match(N, H, R, St0, St1, E, omp, squared)
dist = R[0].penalty
if (symmetric):
R = lgem.Result()
lgem.match(H, N, R, St0, St1, E, omp, squared)
dist = min(dist, R[0].penalty)
return dist
def gem(query, subject, St0=2, St1=2, E=0.01, symmetric=False, squared=True):
"""GEM local similarity measure"""
# enable openmp support
omp = False
N = lgem.TimeSeries(query)
H = lgem.TimeSeries(subject)
R = lgem.Result()
lgem.match(N, H, R, St0, St1, E, omp, squared)
dist = R[0].penalty
if (symmetric):
R = lgem.Result()
lgem.match(H, N, R, St0, St1, E, omp, squared)
dist = min(dist, R[0].penalty)
return dist
H = gem.TimeSeries(S[1000:])
print len(N), len(H)
# matching parameters
St0, St1, E = 2, 2, 0.01
R = gem.Result()
t = time.time()
gemc.cuda_match(N, H, R, St0, St1, E, True)
print "time needed:", time.time(
) - t, "best match:", R[0].penalty, R[0].left, R[0].right
R = gem.Result()
t = time.time()
gem.match(N, H, R, St0, St1, E, True, True)
print "time needed:", time.time(
) - t, "best match:", R[0].penalty, R[0].left, R[0].right
pl.plot(np.array(N) + 1)
pl.plot(H, c="lightgrey")
for item in R[:10]:
L = gem.TimeSeries()
X = gem.TimeCoords()
Y = gem.TimeSeries()
gem.backtrace(N, H, item, L, X, Y, St0, St1, E, False, True)
pl.plot(X, Y, color="r")
pl.plot(X, L, color="b")
N = gem.TimeSeries(S[:1000])
H = gem.TimeSeries(S[1000:])
print len(N), len(H)
# matching parameters
St0, St1, E = 2, 2, 0.01
R = gem.Result()
t=time.time()
gemc.cuda_match(N, H, R, St0, St1, E, True)
print "time needed:", time.time()-t, "best match:", R[0].penalty, R[0].left, R[0].right
R = gem.Result()
t=time.time()
gem.match(N, H, R, St0, St1, E, True, True)
print "time needed:", time.time()-t, "best match:", R[0].penalty, R[0].left, R[0].right
pl.plot(np.array(N) + 1)
pl.plot(H, c = "lightgrey")
for item in R[:10]:
L = gem.TimeSeries()
X = gem.TimeCoords()
Y = gem.TimeSeries()
gem.backtrace(N, H, item, L, X, Y, St0, St1, E, False, True)
pl.plot(X, Y, color="r")
pl.plot(X, L, color="b")