from DiscreteFrechetDistance import *
# Define two paths:
P = numpy.array([[0.0, 1.0, 1.0], [1.0, 1.0, 1.0], [2.0, 1.0, 1.0],
[3.0, 1.0, 1.0], [4.0, 1.0, 1.0], [5.0, 0.0, 1.0],
[6.0, 1.0, 1.0], [7.0, 1.0, 1.0], [8.0, 1.0, 1.0],
[9.0, 1.0, 1.0]])
Q = numpy.array([[0.0, 2.0, 1.0], [1.0, 2.0, 1.0], [2.0, 2.0, 1.0],
[3.0, 2.0, 1.0], [4.0, 2.0, 1.0], [5.0, 3.0, 1.0],
[6.0, 2.0, 1.0], [7.0, 2.0, 1.0], [8.0, 2.0, 1.0],
[9.0, 2.0, 1.0]])
# Calculate the discrete Frechet distance
FD = DiscreteFrechetDistance(P, Q)
cm = FD.getCouplingMeasure()
# Get the coupling sequence
cm_seq = FD.getCouplingSequence()
# Print the coupling sequence and the distance between points
# Note: points in the sequence are number from 1 to p for path P, and 1 to q for path Q.
print ''
print 'Coupling sequence: '
print ' Path P Path Q Distance '
for i in range(0, len(cm_seq)):
u = P[(cm_seq[i, 0] - 1), :] # minus one because P is indexed from zero
v = Q[(cm_seq[i, 1] - 1), :] # minus one because Q is indexed from zero
dist = numpy.sqrt(numpy.sum((u - v)**2))
print ' %2i %2i %f ' % (cm_seq[i, 0], cm_seq[i, 1], dist)
[1.0, 2.0, 1.0],
[2.0, 2.0, 1.0],
[3.0, 2.0, 1.0],
[4.0, 2.0, 1.0],
[5.0, 3.0, 1.0],
[6.0, 2.0, 1.0],
[7.0, 2.0, 1.0],
[8.0, 2.0, 1.0],
[9.0, 2.0, 1.0]]);
# Calculate the discrete Frechet distance:
# Using DiscreteFrechetDistance class:
t0 = time.time()
FD = DiscreteFrechetDistance(P, Q)
cm1 = FD.getCouplingMeasure()
t = (time.time() - t0)
print ''
print 'Using own function'
print 'Frechet distance = ', cm1
print 'elapsed time = ', t
print '\n'
# Using function from the MDAnalysis library
t0 = time.time()
cm2 = MDAnalysis.analysis.psa.discrete_frechet(P, Q)
t = (time.time() - t0)
print 'Using MDAnalysis library'
print 'Frechet distance = ', cm2
print 'elapsed time = ', t
[8.0, 1.0, 1.0],
[9.0, 1.0, 1.0]]);
Q = numpy.array([[0.0, 2.0, 1.0],
[1.0, 2.0, 1.0],
[2.0, 2.0, 1.0],
[3.0, 2.0, 1.0],
[4.0, 2.0, 1.0],
[5.0, 3.0, 1.0],
[6.0, 2.0, 1.0],
[7.0, 2.0, 1.0],
[8.0, 2.0, 1.0],
[9.0, 2.0, 1.0]]);
# Calculate the discrete Frechet distance
FD = DiscreteFrechetDistance(P, Q)
cm = FD.getCouplingMeasure()
# Get the coupling sequence
cm_seq = FD.getCouplingSequence()
# Print the coupling sequence and the distance between points
# Note: points in the sequence are number from 1 to p for path P, and 1 to q for path Q.
print ''
print 'Coupling sequence: '
print ' Path P Path Q Distance '
for i in range (0, len(cm_seq)):
u = P[(cm_seq[i,0]-1),:] # minus one because P is indexed from zero
v = Q[(cm_seq[i,1]-1),:] # minus one because Q is indexed from zero
dist = numpy.sqrt(numpy.sum((u-v)**2))
print ' %2i %2i %f ' % (cm_seq[i,0], cm_seq[i,1], dist)
