def writeRKProbTraj(fh, trajs, probabilities, config):
"""writes time, distance, kappa and the total probability in an opened file handle"""
if config:
startclip = config.get("Photon Flooding", "startclip")
endclip = config.get("Photon Flooding", "endclip")
else:
startclip = 0
endclip = 0
keys = trajs.keys()
keys.sort()
for key in keys:
fh.write("# starting traj %s\n" % key)
classprob = getTrajClassProbability(trajs[key], probabilities)
nrtrajs = getClassTrajCount(trajs[key]["species"], trajs)
trajlen = trajs[key]["length"] - startclip - endclip
probprefact = classprob / nrtrajs / trajlen
if not trajs[key].has_key("photons"):
trajs[key]["photons"] = numpy.ones(len(trajs[key]["t"]))
trajs[key]["photons"] = trajs[key]["photons"] * probprefact
arr = numpy.array((trajs[key]["t"], trajs[key]["R"], trajs[key]["k2"], trajs[key]["photons"]))
if endclip == 0:
numpy.savetxt(fh, arr.T[startclip:, :])
else:
numpy.savetxt(fh, arr.T[startclip:-endclip, :])
print key, "written with traj %s probability with length %d, clipping %d and %d frames at beginning and end." % (probprefact, trajs[key]["length"], startclip, endclip)
def writeRKProbTraj(fh, trajs, probabilities, config):
"""writes time, distance, kappa and the total probability in an opened file handle"""
if config:
startclip = config.get("Photon Flooding", "startclip")
endclip = config.get("Photon Flooding", "endclip")
else:
startclip = 0
endclip = 0
keys = trajs.keys()
keys.sort()
for key in keys:
fh.write("# starting traj %s\n" % key)
classprob = getTrajClassProbability(trajs[key], probabilities)
nrtrajs = getClassTrajCount(trajs[key]["species"], trajs)
trajlen = trajs[key]["length"] - startclip - endclip
probprefact = classprob / nrtrajs / trajlen
if not trajs[key].has_key("photons"):
trajs[key]["photons"] = numpy.ones(len(trajs[key]["t"]))
trajs[key]["photons"] = trajs[key]["photons"] * probprefact
arr = numpy.array((trajs[key]["t"], trajs[key]["R"], trajs[key]["k2"],
trajs[key]["photons"]))
if endclip == 0:
numpy.savetxt(fh, arr.T[startclip:, :])
else:
numpy.savetxt(fh, arr.T[startclip:-endclip, :])
print key, "written with traj %s probability with length %d, clipping %d and %d frames at beginning and end." % (
probprefact, trajs[key]["length"], startclip, endclip)
def normalizeTrajProbForSpecies(trajs, probs):
for trajkey in trajs:
traj = trajs[trajkey]
if not traj.has_key("l"):
continue
print "Correcting trajectory", trajkey, "for class probability in 4th column."
prb = getTrajClassProbability(traj, probs)
traj["l"] *= prb
def normalizeTrajProbForSpecies(trajs, probs):
for trajkey in trajs:
traj = trajs[trajkey]
if not traj.has_key("l"):
continue
print "Correcting trajectory", trajkey, "for class probability in 4th column."
prb = getTrajClassProbability(traj, probs)
traj["l"] *= prb