def test_path_hypothesis_checking_online():
# Assume these are the paths we sampled
paths = [
['1', '2', '3', '5'],
['1', '5', '2', '3'],
['5', '2', '3', '4'],
['1', '2', '3', '4'],
['5', '2', '3', '1'],
]
# The formula we are looking for is that 5 is on the path
formula = 'F([5])'
# We set up a hypothesis test for the formula being satisfied on at least
# 50% of the paths
ht = HypothesisTester(0.5, 0.1, 0.1, 0.01)
samples = []
while True:
pc = PathChecker(formula)
path = random.choice(paths)
for idx, node in enumerate(path):
tf = pc.update(node, idx == len(path) - 1)
if tf is not None:
break
print(path, tf)
samples.append(tf)
hyp = ht.test(samples)
if hyp is not None:
break
assert hyp == 0
class RobotPath(object):
def __init__(self):
self.Waypoints = []
self.checker = PathChecker()
def hasPath(self):
return self.Waypoints is not None
def updateWaypoints(self, waypoints_list):
self.Waypoints = waypoints_list
def toShapes(self, robot):
if len(self.Waypoints) > 1:
shapes = []
for i in range(1, len(self.Waypoints)):
# Creating a rectangle with the robot's width between each waypoint
p_w = robot.Position if i == 1 else self.Waypoints[i - 1]
w = self.Waypoints[i]
d = math.sqrt((w.X - p_w.X)**2 + (w.Y - p_w.Y)**2)
pos = Position((w.X + p_w.X) / 2.0, (w.Y + p_w.Y) / 2.0,
angle=math.atan((w.Y - p_w.Y) / (w.X - p_w.X)))
shapes.append(
MapObstacle(pos, Rect(d, robot.Shape.Width),
velocity=None))
# TODO Create a circle at each waypoint position
return shapes
else:
rospy.logerr(
"Path can't create shapes : less than two waypoints in path")
def checkCollisions(self, robot, obstacles):
self.checker.checkCollisions(robot, self.toShapes(), obstacles)
def test_pg_hypothesis_checking_batch():
g_uns = nx.DiGraph()
g_uns.add_edges_from((('A', 'B'), ('A', 'C'), ('C', 'D'), ('B', 'D'),
('D', 'B'), ('D', 'C'), ('B', 'E'), ('C', 'E')))
# For reference, these are the paths in this graph
# [('A', 'B', 'D', 'B', 'E'),
# ('A', 'B', 'D', 'C', 'E'),
# ('A', 'C', 'D', 'B', 'E'),
# ('A', 'C', 'D', 'C', 'E')])
# with 3 of them containing 'B' and one not containing 'B'
source, target, length = ('A', 'E', 4)
pg = PathsGraph.from_graph(g_uns, source, target, length)
# We want to check that B is on the path somewhere
formula = 'F([B])'
# We set up a hypothesis test saying that we want to verify that
# the formula is True with at least 0.2 probability (i.e. the probability
# that a randomly samples path satisfies the formula). We allow
# a Type-I error rate of 0.1 and Type-II error rate of 0.1, and use
# a 0.01 indifference parameter around the value 0.2.
ht = HypothesisTester(0.2, 0.1, 0.1, 0.01)
# We next sample paths one by one until we can decide the hypothesis test
samples = []
while True:
# Sample one path
path = pg.sample_paths(1)[0]
# Verify the path
pc = PathChecker(formula, path)
samples.append(pc.truth)
# Check if the samples so far are sufficient to decide the hypothesis
# and stop sampling if they are
hyp = ht.test(samples)
if hyp is not None:
break
assert hyp == 0
def test_path_checker_online_future():
formula = 'F([5])'
pc = PathChecker(formula)
tf = pc.update('5', False)
assert tf is True, tf
pc = PathChecker(formula)
tf = pc.update('4', False)
assert tf is None, tf
tf = pc.update('5', True)
assert tf is True, tf
def test_path_checker_online_atomic():
formula = '[5]'
pc = PathChecker(formula)
tf = pc.update('5', False)
assert tf is True, tf
pc = PathChecker(formula)
tf = pc.update('4', True)
assert tf is False, tf
def _run_cases(test_cases):
for formula, nodes, tf_expected in test_cases:
pc = PathChecker(formula, nodes)
assert pc.truth == tf_expected, \
'Got unexpected %s for %s with nodes %s' % (pc.truth, formula,
str(nodes))
def test_path_checker_grounded_entity():
pc = PathChecker('F([FPLX:ERK])')
tf = pc.update('FPLX:MEK', True)
assert tf is False, tf
pc = PathChecker('F([FPLX:ERK])')
tf = pc.update('FPLX:ERK', False)
assert tf is True, tf
pc = PathChecker('F([FPLX:])')
tf = pc.update('FPLX:ERK', False)
assert tf is True, tf
pc = PathChecker('F([CATEGORY:kinase])')
tf = pc.update('HGNC:391', True)
assert tf is True, tf
pc = PathChecker('F([CATEGORY:tf])')
tf = pc.update('HGNC:391', True)
assert tf is False, tf
def __init__(self):
self.Waypoints = []
self.checker = PathChecker()