def makeStat(seed,
rate=None,
minRate=None,
maxRate=None,
N=None,
prior=None,
cert=None,
likelihoodObj=None,
dagObj=None,
counts=None):
if rate is None:
if minRate is None:
minRate = 0.0
if maxRate is None:
maxRate = 1.0
rate = random.uniform(minRate, maxRate)
if N is None:
N = random.randint(2, maxLen)
if prior is None:
prior = [1 / float(N) for i in range(N)]
if cert is None:
db = random.uniform(3, 6)
cert = 1.0 - pow(0.5, db)
if dagObj is None:
dagObj = dag.listDagObj
tester = detect(N, rate, dagObj, dagObj is likelihoods.multiRateCalc)
finder = BBChop.BBChop(prior, cert, tester, likelihoodObj, dagObj)
loc = tester.loc
if counts is not None:
finder.restoreCheckpoint(prior, copy.copy(counts))
key = (rate, loc, N, cert, counts[-1][0], counts[-1][1],
likelihoodObj.name().strip(), seed)
if statDb.has_key(key):
(tests, guess, right) = statDb.get(key)
sys.stdout.write('.')
sys.stdout.flush()
else:
guess = finder.search()
right = (loc == guess)
tests = tester.tests
sys.stdout.write('#')
sys.stdout.flush()
statDb.add(key, (tests, guess, right))
return (rate, loc, N, cert, tests, guess, right, likelihoodObj.name(),
counts[-1])
def makeStat(seed,rate=None,minRate=None,maxRate=None,N=None,prior=None,cert=None,likelihoodObj=None,dagObj=None,counts=None):
if rate is None:
if minRate is None:
minRate=0.0
if maxRate is None:
maxRate=1.0
rate=random.uniform(minRate,maxRate)
if N is None:
N=random.randint(2,maxLen)
if prior is None:
prior=[ 1/float(N) for i in range(N)]
if cert is None:
db=random.uniform(3,6)
cert=1.0-pow(0.5,db)
if dagObj is None:
dagObj=dag.listDagObj
tester=detect(N,rate,dagObj,dagObj is likelihoods.multiRateCalc)
finder=BBChop.BBChop(prior,cert,tester,likelihoodObj,dagObj)
loc=tester.loc
if counts is not None:
finder.restoreCheckpoint(prior,copy.copy(counts))
key=(rate,loc,N,cert,counts[-1][0],counts[-1][1],likelihoodObj.name().strip(),seed)
if statDb.has_key(key):
(tests,guess,right)=statDb.get(key)
sys.stdout.write('.')
sys.stdout.flush()
else:
guess=finder.search()
right=(loc==guess)
tests=tester.tests
sys.stdout.write('#')
sys.stdout.flush()
statDb.add(key,(tests,guess,right))
return (rate,loc,N,cert,tests,guess,right,likelihoodObj.name(),counts[-1])
def testChop(likelihoodObj, randomDag, falseNeg, multi):
tests = 0
right = 0
wrong = []
totalLooks = 0.0
for k in range(trials):
random.seed(k + 1)
dagObj = testCases.testDag(N, randomDag)
if falseNeg:
rate = random.random()
else:
rate = 1
tester = detect(N, rate, dagObj, multi)
finder = BBChop.BBChop(prior, cert, tester, likelihoodObj, dagObj)
loc = tester.loc
guess = finder.search()
totalLooks += finder.total
tests += tester.tests
if loc == guess:
right = right + 1
else:
wrong.append(guess)
# if((k+1)%10 == 0):
print "test ", k, " right%=", 100.0 * right / (k + 1), "right=", loc == guess, "totallooks=", totalLooks / (
k + 1
), "looks=", finder.total, "rate=", rate
# if((k+1)%100 ==0):
# tester.printLocs()
print "right:", right, " out of", trials, tests / trials
return (float(right) / trials) < cert
def testChop(likelihoodObj, randomDag, falseNeg, multi):
tests = 0
right = 0
wrong = []
totalLooks = 0.0
for k in range(trials):
random.seed(k + 1)
dagObj = testCases.testDag(N, randomDag)
if falseNeg:
rate = random.random()
else:
rate = 1
tester = detect(N, rate, dagObj, multi)
finder = BBChop.BBChop(prior, cert, tester, likelihoodObj, dagObj)
loc = tester.loc
guess = finder.search()
totalLooks += finder.total
tests += tester.tests
if (loc == guess):
right = right + 1
else:
wrong.append(guess)
#if((k+1)%10 == 0):
print "test ", k, " right%=", 100.0 * right / (
k + 1), "right=", loc == guess, "totallooks=", totalLooks / (
k + 1), "looks=", finder.total, "rate=", rate
#if((k+1)%100 ==0):
# tester.printLocs()
print "right:", right, " out of", trials, tests / trials
return (float(right) / trials) < cert
self.value = value
isGit = os.environ["TEST_SEARCHER"] == "git"
print isGit
try:
ancestryFilename = os.environ["TEST_ANCESTRY"]
testDir = os.environ["TEST_DIR"]
loc = int(os.environ["TEST_LOC"])
f = file(ancestryFilename, "r")
(identifiers, parents) = dagRead.read(f)
f.close()
N = len(parents)
thisDag = dag.dag(parents, N)
t = testDetector.detect(N, 1.0, thisDag, False, loc)
numbers = {}
for i in range(len(identifiers)):
numbers[identifiers[i]] = i
if isGit:
os.system("git rev-parse HEAD >$TEST_DIR/__head__")
where = open(testDir + "/__head__", "r").readline().strip()
where = numbers[where]
else:
where = sys.argv[1]
where = numbers[where]
os.system("echo 'foo' >>$TEST_DIR/tries")
self.value = value
isGit = os.environ['TEST_SEARCHER']=='git'
print isGit
try:
ancestryFilename=os.environ['TEST_ANCESTRY']
testDir = os.environ["TEST_DIR"]
loc=int(os.environ['TEST_LOC'])
f=file(ancestryFilename,"r")
(identifiers,parents)=dagRead.read(f)
f.close()
N=len(parents)
thisDag=dag.dag(parents,N)
t=testDetector.detect(N,1.0,thisDag,False,loc)
numbers={}
for i in range(len(identifiers)):
numbers[identifiers[i]]=i
if isGit:
os.system("git rev-parse HEAD >$TEST_DIR/__head__")
where=open(testDir+"/__head__","r").readline().strip()
where=numbers[where]
else:
where = sys.argv[1]
where=numbers[where]
os.system("echo 'foo' >>$TEST_DIR/tries")