def query_pos_t1_given_pos_t0(j, index, evidence, twoD, scen):
EVDs = ast.literal_eval(evidence)
#init PyDC
pydc = PyDC(DIR_PATH + scen + IN_NAME)
totDX, totstdDX, totDY, totstdDY = [], [], [], []
for i, EVD in enumerate(EVDs):
evd, param = EVD
W, I = param
if twoD:
avgDX, stdDX = query_displX(pydc, evd, W, I)
avgDY, stdDY = query_displY(pydc, evd, W, I)
totDX += avgDX
totstdDX += stdDX
totDY += avgDY
totstdDY += stdDY
else:
avgDX, stdDX = query_displX(pydc, evd, W, I)
totDX += avgDX
totstdDX += stdDX
#terminate PyDC
pydc.terminate()
if twoD:
with open(OUT_PATH + scen + OUT_NAME % (str(j), index), 'wb') as f:
pickle.dump([(totDX, totstdDX)] + [(totDY, totstdDY)], f)
else:
with open(OUT_PATH + scen + OUT_NAME % (str(j), index), 'wb') as f:
pickle.dump((totDX, totstdDX), f)
def query_action_given_pos_t0_and_pos_t1(j,index, evidence,twoD):
EVDs = ast.literal_eval(evidence)
#init PyDC
pydc = PyDC(DIR_PATH + IN_NAME)
for i, EVD in enumerate(EVDs):
evd, rng = EVD
if i == 0:
totDX, totstdDX = query_displX(pydc,evd,rng)
totDX, totstdDX = reshape(totDX), reshape(totstdDX)
if twoD:
totDY, totstdDY = query_displY(pydc,evd,rng)
totDY, totstdDY = reshape(totDY), reshape(totstdDY)
else:
avgDX, stdDX = query_displX(pydc,evd,rng)
avgDX, stdDX = reshape(avgDX), reshape(stdDX)
totDX = np.append(totDX,avgDX, axis=0)
totstdDX = np.append(totstdDX,stdDX, axis=0)
if twoD:
avgDY, stdDY = query_displY(pydc,evd,rng)
avgDY, stdDY = reshape(avgDY), reshape(stdDY)
totDY = np.append(totDY, avgDY, axis=0)
totstdDY = np.append(totstdDY, stdDY, axis=0)
#terminate PyDC
pydc.terminate()
if twoD:
with open(OUT_PATH + OUT_NAME % (str(j),index),'wb') as f:
pickle.dump([(totDX,totstdDX)] + [(totDY,totstdDY)], f)
else:
with open(OUT_PATH + OUT_NAME % (str(j),index),'wb') as f:
pickle.dump((totDX,totstdDX), f)
from yapWrapper import PyDC
## After executing from command line : $ python setup.py build_ext --inplace
BIGNUM = 1000000
obj = PyDC('/testHepatitis.pl')
query = 'age(447,5.0)'
query = 'requsite(' + query + ',ProbEvidence,Intervention).'
obj.requisiteEvidence(query, BIGNUM)
print obj.probEvidence
print obj.intervention
obj.terminate()
def consultWithTwoFiles(self, yapFileName1, yapFileName2, numOfSamples):
self.yapObject = PyDC(yapFileName1, yapFileName2)
self.yapFileName.append(yapFileName1)
self.yapFileName.append(yapFileName2)
self.numOfSamples = numOfSamples
def consultWithOneFile(self, yapFileName):
self.yapObject = PyDC(yapFileName)
self.yapFileName.append(yapFileName)
class YapPrologInterface(object):
def __init__(self, randomVariableName=[]):
logging.basicConfig(
level=logging.INFO,
filename="dcProbLogs",
filemode="w",
format="%(asctime)-15s %(levelname)-8s %(message)s")
self.yapPrologInterface_logger = logging.getLogger(
'YapPrologInterface Logger :')
yapPrologInterface_logger_handler = logging.FileHandler("dcProbLogs",
mode="w")
yapPrologInterface_logger_handler.setFormatter(
logging.Formatter("%(asctime)-15s %(levelname)-8s %(message)s"))
yapPrologInterface_logger_handler.setLevel(logging.INFO)
self.yapPrologInterface_logger.addHandler(
yapPrologInterface_logger_handler)
self.translator = TranslateToDC()
self.numOfSamples = 0
self.yapObject = None
self.yapFileName = []
if randomVariableName != []:
self.setRandomVariablePredicates(randomVariableName)
def setRandomVariablePredicates(self, name):
self.translator.setRandomVariablePredicates(name)
def consultWithOneFile(self, yapFileName):
self.yapObject = PyDC(yapFileName)
self.yapFileName.append(yapFileName)
def consultWithTwoFiles(self, yapFileName1, yapFileName2, numOfSamples):
self.yapObject = PyDC(yapFileName1, yapFileName2)
self.yapFileName.append(yapFileName1)
self.yapFileName.append(yapFileName2)
self.numOfSamples = numOfSamples
def setNumOfSamples(self, num):
self.numOfSamples = num
def query(self, numOfSamples, query, evidence):
probability = self.yapObject.query(numOfSamples, query, evidence)
return probability
def terminate(self):
self.yapObject.terminate()
def executeQuery(self, queryStr):
success = self.yapObject.execute(queryStr)
return success
def sample(self, numOfSamples, query, evidence, variable):
return self.yapObject.sample(numOfSamples, query, evidence, variable,
BIGNUM)
def prologQuery(self, query):
st = self.yapObject.prologQuery(VARIABLE_NUMBER, query, BIGNUM)
return st
def queryWithSamples(self, numOfSamples, query, evidence, variable):
self.yapObject.queryWithSamples(numOfSamples, query, evidence,
variable, FLAG, BIGNUM)
result = dict()
result['probability'] = self.yapObject.prob
result['samples'] = self.yapObject.samples
return result
def requisiteEvidence(self, query):
query = 'requsite(' + query + ',ProbEvidence,Intervention).'
self.yapObject.requisiteEvidence(query, BIGNUM)
result = dict()
result['ProbEvidence'] = self.convertStringReprOfListToList2(
self.yapObject.probEvidence)
result['Intervention'] = self.convertStringReprOfListToList2(
self.yapObject.intervention)
return result
def simpleQuery(self, query):
query = query.replace(' ', '')
listOfVars = re.findall('\((.*)\)', query)[0]
listOfVars = listOfVars.split(',')
result = self.listQuery(query, listOfVars)
keys = result.keys()
akey = keys[0]
avalue = result[akey]
res = []
for i in range(0, len(avalue)):
tempres = {}
for key in keys:
tempres[key] = result[key][i]
res.append(tempres)
return res
## Merge this with listQuery function
def listQueryPatch(self, query, listOfVars):
result = {}
for var in listOfVars:
result[var] = []
stringOfVars = '['
lenOfListOfVars = len(listOfVars)
for i in range(0, lenOfListOfVars):
if i == lenOfListOfVars - 1:
stringOfVars += listOfVars[i] + ']'
else:
stringOfVars += listOfVars[i] + ','
if query[-1] == '.':
query = query[:-1]
query = 'findall(' + stringOfVars + ',' + '(' + query + '),FINDALL).'
response = self.prologQuery(query)
response = response[1:-1]
response = self.convertStringReprOfListToList(response)
for i in range(0, len(listOfVars)):
result[listOfVars[i]] = response[i]
s = 'Query: ', query, ' Response ' + str(result)
logging.info(s)
return result
def listQuery(self, query, listOfVars):
result = {}
for var in listOfVars:
result[var] = []
stringOfVars = '['
lenOfListOfVars = len(listOfVars)
for i in range(0, lenOfListOfVars):
if i == lenOfListOfVars - 1:
stringOfVars += listOfVars[i] + ']'
else:
stringOfVars += listOfVars[i] + ','
if query[-1] == '.':
query = query[:-1]
query = 'findall(' + stringOfVars + ',' + '(' + query + '),FINDALL).'
response = self.prologQuery(query)
response = self.convertStringReprOfListToList(response)
for ele in response:
for i in range(0, len(listOfVars)):
a = result[listOfVars[i]]
a.append(ele[i])
s = 'Query: ', query, ' Response ' + str(result)
logging.info(s)
return result
def convertStringReprOfListToList2(self, inp):
openBrackets = ['[', '(', '{']
closeBrackets = [']', ')', '}']
insideBracketCounter = 0
inp = inp.replace(' ', '')
inp = list(inp)
for i in range(0, len(inp)):
if inp[i] in openBrackets:
insideBracketCounter += 1
elif inp[i] in closeBrackets:
insideBracketCounter -= 1
else:
pass
if inp[i] == ',' and insideBracketCounter == 1:
inp[i] = ';'
elif inp[i] == ',' and insideBracketCounter == 2:
pass
else:
pass
inp = ''.join(inp)
inp = inp[1:]
inp = inp[:-1]
out = []
if inp == '':
return out
inp = inp.split(';')
out = inp
return out
def convertStringReprOfListToList(self, inp):
openBrackets = ['[', '(', '{']
closeBrackets = [']', ')', '}']
insideBracketCounter = 0
inp = inp.replace(' ', '')
inp = list(inp)
for i in range(0, len(inp)):
if inp[i] in openBrackets:
insideBracketCounter += 1
elif inp[i] in closeBrackets:
insideBracketCounter -= 1
else:
pass
if inp[i] == ',' and insideBracketCounter == 1:
inp[i] = ';'
elif inp[i] == ',' and insideBracketCounter == 2:
inp[i] = ':'
else:
pass
inp = ''.join(inp)
inp = inp[1:]
inp = inp[:-1]
out = []
if inp == '':
return out
inp = inp.split(';')
for i in range(0, len(inp)):
inp[i] = inp[i][1:]
inp[i] = inp[i][:-1]
inp[i] = inp[i].split(':')
for i in range(0, len(inp)):
tempOutput = []
for j in range(0, len(inp[i])):
if ('[' in inp[i][j]):
tempLiteralList = []
tempLiteral = inp[i][j]
tempLiteral = tempLiteral[1:]
tempLiteral = tempLiteral[:-1]
tempLiteral = tempLiteral.split(',')
for k in range(0, len(tempLiteral)):
st = self.returnLiteral(tempLiteral[k])
if st == '':
pass
else:
tempLiteralList.append(st)
tempLiteral = tempLiteralList
tempOutput.append(tempLiteral)
else:
tempLiteral = self.returnLiteral(inp[i][j])
tempOutput.append(tempLiteral)
out.append(tempOutput)
return out
def returnLiteral(self, inp):
out = inp
try:
out = ast.literal_eval(inp)
except Exception:
pass
return out
def getProbabilityOfQuery(self, query, body, listOfSubstitutionVars):
result = self.listQuery(query, listOfSubstitutionVars)
keys = result.keys()
akey = keys[0]
avalue = result[akey]
response = []
for i in range(0, len(avalue)):
tempres = {}
for key in keys:
tempres[key] = result[key][i]
response.append(tempres)
prob = []
for ele in response:
subs = {}
for var in listOfSubstitutionVars:
if var in ele.keys():
subs[var] = ele[var]
dcQuery = self.generateDCQuery(body, subs)
p = self.query(self.numOfSamples, "(" + dcQuery + ")", "")
s = str(p) + ' ' + dcQuery
self.yapPrologInterface_logger.info(s)
prob.append(p)
return prob
def getSamplesAndProbabilityOfQuery(self, query, body,
listOfSubstitutionVars,
listOfContinuousVars):
stringOfContVars = '['
lenOfListOfContVars = len(listOfContinuousVars)
for i in range(0, lenOfListOfContVars):
if i == lenOfListOfContVars - 1:
stringOfContVars += listOfContinuousVars[i] + ']'
else:
stringOfContVars += listOfContinuousVars[i] + ','
result = self.listQuery(query, listOfSubstitutionVars)
keys = result.keys()
akey = keys[0]
avalue = result[akey]
response = []
for i in range(0, len(avalue)):
tempres = {}
for key in keys:
tempres[key] = result[key][i]
response.append(tempres)
prob = []
for ele in response:
subs = {}
for var in listOfSubstitutionVars:
if var in ele.keys():
subs[var] = ele[var]
dcQuery = self.generateDCQuery(body, subs)
probAndSamples = self.queryWithSamples(self.numOfSamples,
"(" + dcQuery + ")", "",
stringOfContVars)
samples = probAndSamples['samples']
probability = probAndSamples['probability']
listSamples = self.convertStringReprOfListToList(samples)
acceptedSamples = []
sumW1 = 0
for i in range(0, len(listSamples)):
if listSamples[i][2] == 0:
pass
else:
acceptedSamples.append(listSamples[i])
sumW1 += listSamples[i][1]
for i in range(0, len(acceptedSamples)):
p = (acceptedSamples[i][1] * acceptedSamples[i][2]) / sumW1
acceptedSamples[i].append(p)
s = str(probability) + ' ' + dcQuery + ' ' + str(acceptedSamples)
self.yapPrologInterface_logger.info(s)
prob.append(acceptedSamples)
return prob
def generateDCQuery(self, query, subs):
query = query.replace('\\\\+', '\\+')
query = query.replace(' ', '')
for key in subs.keys():
keyStr = '(' + key + ')'
valStr = '(' + str(subs[key]) + ')'
query = query.replace(keyStr, valStr)
keyStr = ',' + key + ')'
valStr = ',' + str(subs[key]) + ')'
query = query.replace(keyStr, valStr)
keyStr = ',' + key + ','
valStr = ',' + str(subs[key]) + ','
query = query.replace(keyStr, valStr)
keyStr = '(' + key + ','
valStr = '(' + str(subs[key]) + ','
query = query.replace(keyStr, valStr)
query = self.translator.convertDCPredicates(query, 'body')
return query
def getProlog(self):
return self.yapObject
class YapInterface(object):
def __init__(self):
self.numOfSamples = 0
self.yapObject = None
self.yapFileName = []
def consultWithOneFile(self, yapFileName):
self.yapObject = PyDC(yapFileName)
self.yapFileName.append(yapFileName)
def setNumOfSamples(self, num):
self.numOfSamples = num
def executeQuery(self, queryStr):
success = self.yapObject.execute(queryStr)
return success
def queryWithSamples(self, numOfSamples, query, evidence, variable):
self.yapObject.queryWithSamples(numOfSamples, query, evidence,
variable, FLAG, BIGNUM)
result = dict()
result['probability'] = self.yapObject.prob
result['samples'] = self.yapObject.samples
return result
def requisiteEvidence(self, query_null, query_X):
query = 'requsite(' + query_null + ',ProbEvidence,Intervention,' + query_X + ').'
self.yapObject.requisiteEvidence(query, BIGNUM)
result = dict()
result['ProbEvidence'] = self.convertStringReprOfListToList2(
self.yapObject.probEvidence)
result['Intervention'] = self.convertStringReprOfListToList2(
self.yapObject.intervention)
return result
def convertStringReprOfListToList(self, inp):
openBrackets = ['[', '(', '{']
closeBrackets = [']', ')', '}']
insideBracketCounter = 0
inp = inp.replace(' ', '')
inp = list(inp)
for i in range(0, len(inp)):
if inp[i] in openBrackets:
insideBracketCounter += 1
elif inp[i] in closeBrackets:
insideBracketCounter -= 1
else:
pass
if inp[i] == ',' and insideBracketCounter == 1:
inp[i] = ';'
elif inp[i] == ',' and insideBracketCounter == 2:
inp[i] = ':'
else:
pass
inp = ''.join(inp)
inp = inp[1:]
inp = inp[:-1]
out = []
if inp == '':
return out
inp = inp.split(';')
for i in range(0, len(inp)):
inp[i] = inp[i][1:]
inp[i] = inp[i][:-1]
inp[i] = inp[i].split(':')
for i in range(0, len(inp)):
tempOutput = []
for j in range(0, len(inp[i])):
if ('[' in inp[i][j]):
tempLiteralList = []
tempLiteral = inp[i][j]
tempLiteral = tempLiteral[1:]
tempLiteral = tempLiteral[:-1]
tempLiteral = tempLiteral.split(',')
for k in range(0, len(tempLiteral)):
st = self.returnLiteral(tempLiteral[k])
if st == '':
pass
else:
tempLiteralList.append(st)
tempLiteral = tempLiteralList
tempOutput.append(tempLiteral)
else:
tempLiteral = self.returnLiteral(inp[i][j])
tempOutput.append(tempLiteral)
out.append(tempOutput)
return out
def returnLiteral(self, inp):
out = inp
try:
out = ast.literal_eval(inp)
except Exception:
pass
return out
def convertStringReprOfListToList2(self, inp):
openBrackets = ['[', '(', '{']
closeBrackets = [']', ')', '}']
insideBracketCounter = 0
inp = inp.replace(' ', '')
inp = list(inp)
for i in range(0, len(inp)):
if inp[i] in openBrackets:
insideBracketCounter += 1
elif inp[i] in closeBrackets:
insideBracketCounter -= 1
else:
pass
if inp[i] == ',' and insideBracketCounter == 1:
inp[i] = ';'
elif inp[i] == ',' and insideBracketCounter == 2:
pass
else:
pass
inp = ''.join(inp)
inp = inp[1:]
inp = inp[:-1]
out = []
if inp == '':
return out
inp = inp.split(';')
out = inp
return out