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#!/usr/bin/python3
################################################################################
#
# This file is part of ghmm (Graph Algorithm Toolbox)
#
# file: HMMEditingContext.py
# author: Janne Grunau
#
# Copyright (C) 2007, Janne Grunau
#
# Contact: schliep@molgen.mpg.de
#
# Information: http://ghmm.org
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Library General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Library General Public License for more details.
#
# You should have received a copy of the GNU Library General Public
# License along with this library; if not, write to the Free
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
################################################################################
import ghmm
import ghmmwrapper
from ObjectHMM import *
class HMMEditingContext(object):
def __init__(self, parameter, mtype=0):
self.modeltype = mtype
# check whether the parameter is an EmissionDomain
if isinstance(parameter, ghmm.EmissionDomain):
if parameter.CDataType == "int":
self.HMM = ObjectHMM(State, Transition, alphabet=parameter, etype=0)
self.modeltype |= ghmmwrapper.kDiscreteHMM
elif parameter.CDataType == "double":
self.HMM = ObjectHMM(State, Transition, emissionClass=ContinuousMixtureDistribution, etype=1)
self.modeltype |= ghmmwrapper.kContinuousHMM
else:
raise ghmm.NoValidCDataType("C data type " + str(parameter.CDataType) + " invalid.")
self.HMM.initHMM(self.modeltype)
# Distribution parameter
elif type(parameter) is type:
self.HMM = ObjectHMM(State, Transition, emissionClass=parameter, etype=1)
self.modeltype |= ghmmwrapper.kContinuousHMM
self.HMM.initHMM(self.modeltype)
# existing hidden markov model
elif isinstance(parameter, ghmm.HMM):
hmm = parameter
self.HMM = ObjectHMM(State, Transition)
if isinstance(hmm, ghmm.DiscreteEmissionHMM):
self.modeltype = hmm.cmodel.model_type
if hmm.cmodel.alphabet is None:
hmm.cmodel.alphabet = self.emissionDomain.toCstruct()
else:
self.modeltype = ghmmwrapper.ContinuousHMM
self.HMM.initHMM(self.modeltype)
self.HMM.buildFromCModel(hmm.cmodel)
# filename
elif isinstance(parameter, str) or isinstance(parameter, str):
self.load(parameter)
else:
raise ghmm.UnknownInputType
def __str__(self):
return str(self.HMM)
## container emulation
def __getitem__(self, key):
if isinstance(key, tuple):
tail,head = [self.getUniqueId(k) for k in key]
return self.HMM.edges[(tail,head)]
elif isinstance(key, int):
return self.HMM.vertices[key]
else:
retlist = [self.HMM.vertices[vid] for vid in self.HMM.name2id[key]]
if len(retlist) == 1:
return retlist[0]
else:
return retlist
def __setitem__(self, key, value):
pass
def __delitem__(self, key):
if isinstance(key, tuple):
tail,head = [self.getUniqueId(k) for k in key]
self.HMM.DeleteEdge(tail, head)
elif isinstance(key, int):
self.deleteState(key)
else:
for vid in self.HMM.name2id[key]:
self.deleteState(vid)
def __len__(self):
return len(self.HMM)
def __contains__(self, key):
if isinstance(key, tuple):
tail,head = [self.getUniqueId(k) for k in key]
return (tail,head) in self.HMM.edges
elif isinstance(key, int):
return key in self.HMM.vertices
else:
return key in self.HMM.name2id
def __iter__(self):
pass
def load(self, filename):
self.HMM = ObjectHMM(State, Transition)
self.HMM.openXML(filename)
self.modeltype = self.HMM.modelType
def save(self, filename):
self.HMM.writeXML(filename)
def finalize(self):
cmodel = self.HMM.finalize()
if (self.modeltype & ghmmwrapper.kContinuousHMM):
return ghmm.ContinuousMixtureHMM(ghmm.Float(),
ghmm.ContinuousMixtureDistribution(ghmm.Float()),
cmodel)
elif ((self.modeltype & ghmmwrapper.kDiscreteHMM)
and not (self.modeltype & ghmmwrapper.kTransitionClasses)
and not (self.modeltype & ghmmwrapper.kPairHMM)):
emission_domain = ghmm.Alphabet([], cmodel.alphabet)
if (self.modeltype & ghmmwrapper.kLabeledStates):
labelDomain = ghmm.LabelDomain([], cmodel.label_alphabet)
return ghmm.StateLabelHMM(emission_domain,
ghmm.DiscreteDistribution(emission_domain),
labelDomain,
cmodel)
else:
return ghmm.DiscreteEmissionHMM(emission_domain,
ghmm.DiscreteDistribution(emission_domain),
cmodel)
def addState(self, emission=None, initial=-1):
vid = self.HMM.AddVertex()
if emission is not None:
self.HMM.vertices[vid].emission = emission
self.HMM.vertices[vid].initial = initial
return vid
def deleteState(self, vid):
self.HMM.DeleteVertex(vid)
def addTransition(self, tail, head, p=-1):
tail = self.getUniqueId(tail)
head = self.getUniqueId(head)
self.HMM.AddEdge(tail, head)
self.HMM.edges[tail,head].SetWeight(p)
def getUniqueId(self, name):
if isinstance(name, str) or isinstance(name, str):
tmp = self.HMM.name2id[name]
if len(tmp) > 1:
raise IdentifierIsAmbigious(name)
else:
return tmp[0]
else:
return name
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