def evidence(self, model, useMaximumApproximation):
evidences = sequitur_.EvidenceStore()
evidences.setSequenceModel(model)
if useMaximumApproximation:
accumulator = sequitur_.ViterbiAccumulator()
else:
accumulator = sequitur_.Accumulator()
accumulator.setTarget(evidences)
logLik = 0.0
for eg in self.graphs(model):
logLik += accumulator.accumulate(eg, 1.0)
misc.reportMemoryUsage()
return evidences, logLik
def evidence(self, model, useMaximumApproximation):
evidences = sequitur_.EvidenceStore()
evidences.setSequenceModel(model)
if useMaximumApproximation:
accumulator = sequitur_.ViterbiAccumulator()
else:
accumulator = sequitur_.Accumulator()
accumulator.setTarget(evidences)
logLik = 0.0
for eg in self.graphs(model):
logLik += accumulator.accumulate(eg, 1.0)
misc.reportMemoryUsage()
return evidences, logLik
def run(self, context):
lastCheckpoint = misc.cputime()
shouldStop = False
while not shouldStop:
if context.iteration >= self.maxIterations:
print >> context.log, 'maximum number of iterations reached.'
break
print >> context.log, 'iteration: %s' % context.iteration
try:
shouldStop = self.iterate(context)
except:
import traceback
traceback.print_exc()
print >> context.log, 'iteration failed.'
break
if ((self.checkpointInterval) and
(misc.cputime() > lastCheckpoint + self.checkpointInterval)):
self.checkpoint(context)
lastCheckpoint = misc.cputime()
context.iteration += 1
misc.reportMemoryUsage()
print >> context.log
context.log.flush()
def run(self, context):
lastCheckpoint = misc.cputime()
shouldStop = False
while not shouldStop:
if context.iteration >= self.maxIterations:
print >> context.log, 'maximum number of iterations reached.'
break
print >> context.log, 'iteration: %s' % context.iteration
try:
shouldStop = self.iterate(context)
except Exception:
import traceback
traceback.print_exc()
print >> context.log, 'iteration failed.'
break
if ((self.checkpointInterval) and
(misc.cputime() > lastCheckpoint + self.checkpointInterval)):
self.checkpoint(context)
lastCheckpoint = misc.cputime()
context.iteration += 1
misc.reportMemoryUsage()
print >> context.log
context.log.flush()