def scre_iteration(assignments, K0, lagtime_list, M, X, populations):
KList = []
counts_list = []
for LagTime in lagtime_list:
logger.info("Estimating rates at lagtime %d", LagTime)
K = K0.copy() * float(LagTime)
C0 = MSMLib.GetCountMatrixFromAssignments(assignments,
LagTime=LagTime).toarray()
Counts = C0.sum(1)
Counts /= LagTime
X2 = SCRE.MaximizeRateLikelihood(X, M, populations, C0, K)
K = SCRE.ConstructRateFromParams(X2, M, populations, K)
K /= (LagTime)
KList.append(K)
counts_list.append(Counts)
KList = np.array(KList)
SCRE.PlotRates(KList, lagtime_list, counts_list)
return KList
def interactive_scre(assignments):
Counts = MSMLib.GetCountMatrixFromAssignments(assignments, LagTime=1)
CountsAfterTrimming, Mapping = MSMLib.ErgodicTrim(Counts)
MSMLib.ApplyMappingToAssignments(assignments, Mapping)
ReversibleCounts = MSMLib.EstimateReversibleCountMatrix(
CountsAfterTrimming)
T = MSMLib.EstimateTransitionMatrix(ReversibleCounts).toarray()
populations = np.array(ReversibleCounts.sum(0)).flatten()
populations /= populations.sum()
K0 = SCRE.ConvertTIntoK(T)
M, X = SCRE.get_parameter_mapping(K0)
while len(X) > 0:
lagtime_list = get_lagtimes()
KList = scre_iteration(assignments, K0, lagtime_list, M, X,
populations)
matplotlib.pyplot.show()
if len(X) > 1:
i, j, lagtime = get_input()
SCRE.FixEntry(M, X, populations, K0, i, j, KList[lagtime][i, j])
else:
lagtime = get_lagtime()
return KList[lagtime]
import sys, os
import numpy as np
import scipy.io
from msmbuilder import arglib
from msmbuilder import Serializer
from msmbuilder import MSMLib
Assignments = Serializer.LoadData("%s" % (sys.argv[1]))
NumStates = max(Assignments.flatten()) + 1
LagTime = sys.argv[2]
Counts = MSMLib.GetCountMatrixFromAssignments(Assignments,
NumStates,
LagTime=LagTime,
Slide=True)
scipy.io.mmwrite('%s' % (sys.argv[3]), Counts)
