def analyzePEReport(self, report, mode, modFilters = None ):
"""given an individual radiology report, creates a pyConTextSql
object that contains the context markup
report: a text string containing the radiology reports
mode: ???
modFilters: """
context = self.context.get(mode)
targets = self.targets.get(mode)
modifiers = self.modifiers.get(mode)
if modFilters == None :
modFilters = ['indication','pseudoneg','probable_negated_existence',
'definite_negated_existence', 'probable_existence',
'definite_existence', 'historical']
context.reset()
terms = itemData.itemData(targets)
sentences = helpers.sentenceSplitter(report)
count = 0
for s in sentences:
context.setTxt(s)
if( modifiers ):
context.markModifiers(modifiers)
context.markTargets(terms)
context.pruneMarks()
context.dropMarks('Exclusion')
context.applyModifiers()
context.commit()
count += 1
model = pycontextSql()
model.populate(context,modFilters)
return model
def analyzePEReport(self, report, mode, modFilters=None):
"""given an individual radiology report, creates a pyConTextSql
object that contains the context markup
report: a text string containing the radiology reports
mode: ???
modFilters: """
context = self.context.get(mode)
targets = self.targets.get(mode)
modifiers = self.modifiers.get(mode)
if modFilters == None:
modFilters = [
'indication', 'pseudoneg', 'probable_negated_existence',
'definite_negated_existence', 'probable_existence',
'definite_existence', 'historical'
]
context.reset()
terms = itemData.itemData(targets)
sentences = helpers.sentenceSplitter(report)
count = 0
for s in sentences:
context.setTxt(s)
if (modifiers):
context.markModifiers(modifiers)
context.markTargets(terms)
context.pruneMarks()
context.dropMarks('Exclusion')
context.applyModifiers()
context.commit()
count += 1
model = pycontextSql()
model.populate(context, modFilters)
return model
def analyzePEReport(self, report, mode, modFilters=None):
"""given an individual radiology report, creates a pyConTextSql
object that contains the context markup
report: a text string containing the radiology reports
mode: ???
modFilters: """
try:
fo = open("pedoc%d_%s.txt" % (self.currentCase, mode), "w")
context = self.context.get(mode)
targets = self.targets.get(mode)
modifiers = self.modifiers.get(mode)
if modFilters == None:
modFilters = [
'indication', 'pseudoneg', 'probable_negated_existence',
'definite_negated_existence', 'probable_existence',
'definite_existence', 'historical'
]
context.reset()
terms = itemData.itemData(targets)
sentences = helpers.sentenceSplitter(report)
count = 0
for s in sentences:
context.setTxt(s)
if (modifiers):
context.markModifiers(modifiers)
context.markTargets(terms)
fo.write("Original markup\n%s\n" % context.__str__())
context.pruneMarks()
fo.write("Pruned markup\n%s\n" % context.__str__())
context.dropMarks('Exclusion')
fo.write("Post Exclusion\n%s\n" % context.__str__())
context.applyModifiers()
fo.write("Post modifiers\n%s\n" % context.__str__())
fo.write("*" * 42 + "\n")
pnxobj = pnx.pyConTextGraph(context)
pnxobj.drawGraph("pedoc%d_%s_%s" %
(self.currentCase,
context.getCurrentSentenceNumber(), mode),
format="png")
#print context
context.commit()
count += 1
model = pycontextSql(db=self.dbn)
model.populate(context, modFilters)
fo.close()
return model
except Exception, error:
print "failed in analyzePEReport", error
def analyzePEReport(self, report, mode, modFilters = None ):
"""given an individual radiology report, creates a pyConTextSql
object that contains the context markup
report: a text string containing the radiology reports
mode: ???
modFilters: """
try:
fo = open("pedoc%d_%s.txt"%(self.currentCase, mode),"w")
context = self.context.get(mode)
targets = self.targets.get(mode)
modifiers = self.modifiers.get(mode)
if modFilters == None :
modFilters = ['indication','pseudoneg','probable_negated_existence','definite_negated_existence', 'probable_existence', 'definite_existence', 'historical']
context.reset()
terms = itemData.itemData(targets)
sentences = helpers.sentenceSplitter(report)
count = 0
for s in sentences:
context.setTxt(s)
if( modifiers ):
context.markModifiers(modifiers)
context.markTargets(terms)
fo.write("Original markup\n%s\n"%context.__str__())
context.pruneMarks()
fo.write("Pruned markup\n%s\n"%context.__str__())
context.dropMarks('Exclusion')
fo.write("Post Exclusion\n%s\n"%context.__str__())
context.applyModifiers()
fo.write("Post modifiers\n%s\n"%context.__str__())
fo.write("*"*42+"\n")
pnxobj = pnx.pyConTextGraph(context)
pnxobj.drawGraph("pedoc%d_%s_%s"%(self.currentCase,context.getCurrentSentenceNumber(),mode), format="png")
#print context
context.commit()
count += 1
model = pycontextSql(db=self.dbn)
model.populate(context,modFilters)
fo.close()
return model
except Exception, error:
print "failed in analyzePEReport", error
