def hungarianAssignment(cases, controls, numberOfControlsPerCase):
selectedControls = list()
convFactor = 100000.00
m = list()
for control in controls:
row = list()
for _ in xrange(numberOfControlsPerCase):
row += [(control.relatedTo.get(case) if (control.relatedTo.has_key(case)) else 0) for case in cases]
m.append(row)
cm = munkres.make_cost_matrix(m, lambda cost: convFactor - cost * convFactor)
matrix = cm
m = Munkres()
indexes = m.compute(matrix)
total = 0
for row, column in indexes:
value = matrix[row][column]
total += value
if value < convFactor:
selectedControls.append(controls[row % len(controls)])
print("\tassignment kic score: %f" % (float(len(indexes) * convFactor - total) / convFactor))
print("\tall kic score: %f" % (kicScore(cases, selectedControls)))
return [person.id for person in selectedControls]
selectedControls = hungarianAssignment(cases, controls,
numberOfControlsPerCase)
else:
print("Have too few good controls - using all of them")
selectedControls = goodControls
#if we don't have enough good controls take all related controls and add
#min resid controls
if (len(selectedControls) < neededControls):
print(
"Number of selected controls (%d) < number of needed controls (%d) - adding min resid controls"
% ((len(selectedControls), neededControls)))
for resid, person in sorted(controlsResidMap.iteritems()):
if ((not manyControls) or (person in goodControls)):
if not (person in selectedControls):
selectedControls.append(person)
if (len(selectedControls) >= neededControls):
break
#print selected controls
print("\nFinal Control Selection (KIC = %f):" %
kicScore(cases, selectedControls))
for person in selectedControls:
print(person.id)
#print("Final KIC score: %d" %kicScore(cases, selectedControls))
print([person.id for person in cases])
print([person.id for person in selectedControls])
return (selectedControls)
def hungarianAssignment(cases, controls, numberOfControlsPerCase):
def main(
numberOfControlsPerCase=2,
KICoutFilepath=currDir + "/KIC_out",
caseFilepath=currDir + "/cases",
contFilepath=currDir + "/controls",
):
print(caseFilepath)
print(numberOfControlsPerCase)
# load cases
caseFile = open(caseFilepath)
next(caseFile)
for caseData in caseFile:
caseData = caseData.strip().split("\t")
caseID = caseData[1]
case = Person(caseID)
people.update({caseID: case})
cases.append(case)
caseFile.close()
neededControls = len(cases) * numberOfControlsPerCase
# load controls
contFile = open(contFilepath)
next(contFile)
for contData in contFile:
contData = contData.strip().split("\t")
contID = contData[1]
contResid = math.fabs(float(contData[-1]))
cont = Person(contID)
people.update({contID: cont})
controls.append(cont)
controlsResidMap.update({contResid: cont})
contFile.close()
if neededControls >= len(controls):
# print(controls)
print("Warning need more controls than available - returning all")
return [person.id for person in controls]
print("%d cases and %d potential controls" % (len(cases), len(controls)))
# load KIC info
KICoutFile = open(KICoutFilepath)
for line in KICoutFile:
lineData = line.strip().split(",")
currPersonID = lineData[1]
if people.has_key(currPersonID):
currPerson = people.get(currPersonID)
relativeID = lineData[2]
if people.has_key(relativeID):
relative = people.get(relativeID)
kc = float(lineData[3])
if kc > 0:
currPerson.putKinship(relative, kc)
count = 0
caseRelCount = dict()
for case in cases:
caseNumRel = case.numRel()
if len(case.kinshipDict) <= 0:
count += 1
if not (caseRelCount.has_key(caseNumRel)):
caseRelCount.update({caseNumRel: 0})
caseRelCount.update({caseNumRel: caseRelCount.get(caseNumRel) + 1})
print("Cases to Number of Related Controls: " + str(caseRelCount))
print("Number of zero-matched cases: %d" % (caseRelCount.get(0)))
goodControls = list()
for person in controls:
for relative in person.relatedTo:
if relative in cases:
goodControls.append(person)
break
print("Number of good controls: %d" % (len(goodControls)))
manyControls = False
if len(goodControls) > neededControls:
manyControls = True
print("Have too many good controls - need to trim down number of controls by modified Hungarian Assignment")
selectedControls = hungarianAssignment(cases, controls, numberOfControlsPerCase)
else:
print("Have too few good controls - using all of them")
selectedControls = goodControls
# if we don't have enough good controls take all related controls and add
# min resid controls
if len(selectedControls) < neededControls:
print(
"Number of selected controls (%d) < number of needed controls (%d) - adding min resid controls"
% ((len(selectedControls), neededControls))
)
for resid, person in sorted(controlsResidMap.iteritems()):
if (not manyControls) or (person in goodControls):
if not (person in selectedControls):
selectedControls.append(person)
if len(selectedControls) >= neededControls:
break
# print selected controls
print("\nFinal Control Selection (KIC = %f):" % kicScore(cases, selectedControls))
for person in selectedControls:
print(person.id)
# print("Final KIC score: %d" %kicScore(cases, selectedControls))
print([person.id for person in cases])
print([person.id for person in selectedControls])
return selectedControls
