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outcomelist.py
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outcomelist.py
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#!/usr/bin/python
# author: Rodney Summerscales
"""
Create list of outcomes and their values for a summary
"""
import xmlutil
import irstats
import templates
import htmlutil
class OutcomeList:
""" Maintain list of outcomes measured in an abstract along with the
summary statistics. """
outcomeTemplates = None # list of outcome templates for the abstract
primaryOutcomes = None
secondaryOutcomes = None
abstract = None
nTrueOutcomes = 0
def __init__(self, abstract, useAnnotated=False, useTrialReports=True):
""" create a list of outcomes measured and their statistics given
an abstact object. """
self.primaryOutcomes = []
self.secondaryOutcomes = []
self.nTrueOutcomes = 0
if useAnnotated == True:
self.outcomeTemplates = abstract.annotatedEntities.getList('outcome')
else:
self.outcomeTemplates = abstract.entities.getList('outcome')
for outcome in self.outcomeTemplates:
if outcome.isPrimary():
self.primaryOutcomes.append(outcome)
else:
self.secondaryOutcomes.append(outcome)
self.abstract = abstract
def computeStatistics(self, errorOut):
""" Count RPF statistics for each unique OUTCOME entity
statOut = file stream for RPF stats for all parts of summarization system
errorOut = file stream for TPs, FPs, FNs
return hash of IRstats, one for each mention type, keyed by mention type
"""
aOutcomeTemplates = self.abstract.annotatedEntities.getList('outcome')
self.nTrueOutcomes = len(aOutcomeTemplates)
errorOut.write('outcome:\n')
stats = {}
stats['outcome'] = templates.countMatches(aOutcomeTemplates, self.outcomeTemplates, errorOut)
errorOut.write('primary outcome:\n')
primaryOutcomeStats = irstats.IRstats()
for oTemplate in self.outcomeTemplates:
if oTemplate.isPrimary():
if oTemplate.matchedTemplate != None and oTemplate.matchedTemplate.isPrimary(useAnnotated=True):
primaryOutcomeStats.incTP()
errorOut.write(' +TP: %s is PRIMARY OUTCOME\n' % oTemplate.name)
oTemplate.primaryOutcomeEvaluation.markCorrect()
else:
primaryOutcomeStats.incFP()
errorOut.write(' -FP: %s is NOT known to be PRIMARY OUTCOME\n' % oTemplate.name)
print self.abstract.id, oTemplate.name, 'is not a primary outcome'
oTemplate.primaryOutcomeEvaluation.markIncorrect()
for oTemplate in aOutcomeTemplates:
if oTemplate.isPrimary(useAnnotated=True) and oTemplate.matchedTemplate != None \
and oTemplate.matchedTemplate.isPrimary() == False:
primaryOutcomeStats.incFN()
errorOut.write(' -FN: %s SHOULD BE PRIMARY OUTCOME\n' \
% oTemplate.matchedTemplate.name)
stats['primary outcome'] = primaryOutcomeStats
return stats
def createGroupNode(self, doc, groupTemplate, idPrefix):
"""
Return XML node containing information for a Group element
"""
groupNode = doc.createElement('Group')
groupNode.setAttribute('Id', idPrefix+groupTemplate.id)
return groupNode
def getGroupXML(self, doc, omTemplate, idPrefix):
""" return XML node containing outcome results for group.
omTemplate = outcome measurement template containing outcome info for
the group"""
groupNode = self.createGroupNode(doc, omTemplate.getGroup(), idPrefix)
bad = omTemplate.getOutcomes()
if bad >= 0:
badNode = xmlutil.createNodeWithTextChild(doc, 'Bad', str(bad))
groupNode.appendChild(badNode)
size = omTemplate.getGroupSize()
if size > 0:
gsNode = xmlutil.createNodeWithTextChild(doc, 'GroupSize', str(size))
groupNode.appendChild(gsNode)
er = omTemplate.eventRateString()
if len(er) > 0:
er = omTemplate.eventRateString()
erNode = xmlutil.createNodeWithTextChild(doc, 'EventRate', er)
groupNode.appendChild(erNode)
scoreNode = xmlutil.createNodeWithTextChild(doc, 'Score',
str(omTemplate.getConfidence()))
groupNode.appendChild(scoreNode)
return groupNode
def getOutcomeXML(self, doc, oTemplate, idPrefix):
""" write given outcome template to XML file stream """
outcomeNode = doc.createElement('Outcome')
if oTemplate.isPrimary():
oType = 'primary'
else:
oType = 'unknown'
poNode = xmlutil.createNodeWithTextChild(doc, 'Type', oType)
id = idPrefix+oTemplate.id+'oType'
poNode.setAttribute('Id', id)
oTemplate.primaryOutcomeEvaluation.id = id
outcomeNode.appendChild(poNode)
id = idPrefix+oTemplate.id
outcomeNode.setAttribute('Id', id)
oTemplate.evaluation.id = id
nameNode = xmlutil.createNodeWithTextChild(doc, 'Name', oTemplate.getCanonicalName())
# setUMLSAttribute(nameNode, oTemplate)
outcomeNode.appendChild(nameNode)
# write Cost values
cvCount = 0
for cvTemplate in oTemplate.costValues:
cvNode = doc.createElement('CostValue')
outcomeNode.appendChild(cvNode)
id = idPrefix + oTemplate.id + 'cv' + str(cvCount)
cvNode.setAttribute('id', id)
cvCount += 1
if cvTemplate.group.name is not None:
cvNode.appendChild(self.createGroupNode(doc, cvTemplate.group, idPrefix))
valueNode = xmlutil.createNodeWithTextChild(doc, 'Value', cvTemplate.token.text)
valueNode.setAttribute('units', cvTemplate.token.getUnits())
cvNode.appendChild(valueNode)
# write ARR/NNT
epCount = 0
for ssTemplate in oTemplate.summaryStats:
epNode = doc.createElement('Endpoint')
id = idPrefix+oTemplate.id+'ep'+str(epCount)
ssTemplate.evaluation.id = id
epNode.setAttribute('id', id)
epCount += 1
outcomeNode.appendChild(epNode)
epNode.appendChild(self.getGroupXML(doc, ssTemplate.lessEffective, idPrefix))
epNode.appendChild(self.getGroupXML(doc, ssTemplate.moreEffective, idPrefix))
if ssTemplate.time != None:
tNode = xmlutil.createNodeWithTextChild(doc, 'time', ssTemplate.time.name)
if len(ssTemplate.time.units) > 0:
tNode.setAttribute('units', ssTemplate.time.units)
if ssTemplate.time.value > 0:
tNode.setAttribute('value', str(ssTemplate.time.value))
epNode.appendChild(tNode)
ssNode = doc.createElement('SummaryStatistics')
epNode.appendChild(ssNode)
sNode = doc.createElement('Statistic')
sNode.setAttribute('Worse', idPrefix+ssTemplate.lessEffective.getGroup().id)
sNode.setAttribute('Better', idPrefix+ssTemplate.moreEffective.getGroup().id)
ssNode.appendChild(sNode)
arNode = doc.createElement('AbsoluteRisk')
sNode.appendChild(arNode)
arNode.setAttribute('Type', ssTemplate.riskType())
vNode = xmlutil.createNodeWithTextChild(doc, 'Value', ssTemplate.arrString())
arNode.appendChild(vNode)
if ssTemplate.hasConfidenceIntervals():
iNode = doc.createElement('Interval')
iNode.setAttribute('lower', ssTemplate.arrLowerBound())
iNode.setAttribute('upper', ssTemplate.arrUpperBound())
arNode.appendChild(iNode)
if ssTemplate.infiniteNumberNeeded() == False:
nnNode = doc.createElement('NumberNeeded')
sNode.appendChild(nnNode)
nnNode.setAttribute('Type', ssTemplate.numberNeededType())
vNode = xmlutil.createNodeWithTextChild(doc, 'Value', ssTemplate.nntString())
nnNode.appendChild(vNode)
if ssTemplate.hasConfidenceIntervals():
iNode = doc.createElement('Interval')
iNode.setAttribute('lower', ssTemplate.nntLowerBound())
iNode.setAttribute('upper', ssTemplate.nntUpperBound())
nnNode.appendChild(iNode)
# for omTemplate in oTemplate.unusedNumbers:
# epNode = doc.createElement('Endpoint')
# epNode.setAttribute('id', idPrefix+oTemplate.id+'ep'+str(epCount))
# epCount += 1
# outcomeNode.appendChild(epNode)
# if omTemplate.getGroup() != None:
# if omTemplate.getTime() != None:
# tNode = xmlutil.createNodeWithTextChild(doc, 'time', omTemplate.getTime().name)
# if len(omTemplate.getTime().units) > 0:
# tNode.setAttribute('units', omTemplate.getTime().units)
# if omTemplate.getTime().value > 0:
# tNode.setAttribute('value', str(omTemplate.getTime().value))
#
# epNode.appendChild(tNode)
# outcomeNode.appendChild(epNode)
# epNode.appendChild(self.getGroupXML(doc, omTemplate, idPrefix))
return outcomeNode
def getXML(self, doc, idPrefix):
""" return an xml node that contains information about the outcomes
measured in the study. """
if len(self.outcomeTemplates) == 0:
return None
outcomeListNode = doc.createElement('Outcomes')
for oTemplate in self.primaryOutcomes:
outcomeNode = self.getOutcomeXML(doc, oTemplate, idPrefix)
outcomeListNode.appendChild(outcomeNode)
for oTemplate in self.secondaryOutcomes:
outcomeNode = self.getOutcomeXML(doc, oTemplate, idPrefix)
outcomeListNode.appendChild(outcomeNode)
return outcomeListNode
def writeOutcomeHTML(self, oTemplate, out, showError):
""" write a given outcome to HTML stream """
out.write('<li>'+oTemplate.getCanonicalName()+'<ul>\n')
for cvTemplate in oTemplate.costValues:
out.write('<li>')
if cvTemplate.group.name is None:
groupName = 'unknown'
else:
groupName = cvTemplate.group.name
htmlutil.HTMLWriteText(out, groupName+': ', 'blue', bold=True)
out.write(cvTemplate.valueString())
out.write('</li>')
for ssTemplate in oTemplate.summaryStats:
if ssTemplate.correctlyMatched == True or showError == False:
color = 'black'
else:
color = 'red'
out.write(' <span style=\"color:'+color+'\">')
if ssTemplate.time != None:
time = '('+ssTemplate.time.name+')'
else:
time = ''
out.write('<li>Endpoint '+time+'<ul>')
out.write('<li> More effective: '+ ssTemplate.moreEffective.getGroup().name + ': ' )
out.write(ssTemplate.moreEffective.statisticString())
out.write('</li>')
out.write('<li> Less effective: '+ ssTemplate.lessEffective.getGroup().name+': ')
out.write(ssTemplate.lessEffective.statisticString())
out.write('</li>')
rLabel = ssTemplate.riskType()
nnLabel = ssTemplate.numberNeededType()
out.write('<li>'+rLabel+ ': ' + ssTemplate.arrString())
if ssTemplate.hasConfidenceIntervals():
out.write(', 95% confidence interval ['+ssTemplate.arrLowerBound())
out.write(',' + ssTemplate.arrUpperBound() + ']')
if ssTemplate.infiniteNumberNeeded() == False:
out.write('</li><li>'+nnLabel+ ': ' + ssTemplate.nntString())
if ssTemplate.hasConfidenceIntervals():
out.write(', 95% confidence interval ['+ ssTemplate.nntLowerBound())
out.write(ssTemplate.nntUpperBound()+']')
out.write('</li></ul></li>')
out.write('</span>')
for omTemplate in oTemplate.unusedNumbers:
if omTemplate.getGroup() != None:
if omTemplate.getTime() != None:
time = ' ('+omTemplate.getTime().name+')'
else:
time = ''
out.write('<li>Endpoint '+time+'<ul>')
out.write('<li>'+ omTemplate.getGroup().name + ': ' )
out.write(omTemplate.statisticString())
out.write('</ul></li>')
out.write('</ul></li>\n')
def writeHTML(self, out, showError):
""" write outcome list information to given output stream in html format. """
out.write('<h3>Outcomes</h3>\n')
# out.write('<b>Primary Outcomes:</b>')
out.write('<ul>\n')
for oTemplate in self.primaryOutcomes:
self.writeOutcomeHTML(oTemplate, out, showError)
out.write('</ul>\n')
# out.write('<b>Secondary Outcomes:</b>')
out.write('<ul>\n')
for oTemplate in self.secondaryOutcomes:
self.writeOutcomeHTML(oTemplate, out, showError)
out.write('</ul>\n')