def test_MergeOverlapping(self):
int1 = interval('[1,5]')
int2 = interval('[2,6)')
int3 = interval('(8,10]')
int4 = interval('[8,18]')
intlist = [int1, int2, int3, int4]
self.assertEqual(str(mergeOverlapping(intlist)),'[[1,6), [8,18]]')
def test_sqrt2(self):
import math
f, p = lambda x: x**2 - 2, lambda x: 2 * x
u, v = 6369051672525772 * 2.0 ** -52, 6369051672525773 * 2.0 ** -52
s = interval[u, v]
assert v == math.sqrt(2)
assert s == interval[0.1, 5].newton(f, p)
assert s == interval[0, 2].newton(f, p)
assert s == interval[-1, 10].newton(f, p)
assert interval() == interval[2, 5].newton(f, p)
assert -s == interval[-5, 0].newton(f, p)
assert -s | s == interval[-5, +5].newton(f, p)
# Failure to converge in only three iterations:
messages = []
assert interval() == interval[0, 2].newton(
f, p, maxiter=3,
tracer_cb = lambda tag, interval: messages.append((tag, interval)))
assert messages == [
('branch' , interval[0.0, 2.0]),
('step' , interval[1.25, 2.0]),
('step' , interval[1.36875, 1.46484375]),
('step' , interval[1.4141253188320488, 1.4143005729166669]),
('abandon', interval[1.4141253188320488, 1.4143005729166669])
]
def main_function():
ListOfIntervals = list()
while len(ListOfIntervals)==0:
try:
InputIntervals = raw_input("List of intervals?:")
if InputIntervals == "quit":
break
temp = (re.compile('(\(|\[)(-?\d+),(-?\d+)(\)|\])')).findall(InputIntervals)
InputIntervals = temp
for i in temp:
ListOfIntervals.append(interval.interval(i))
if len(ListOfIntervals)==0:
print("Bad input. Please try again with the proper input format")
except Exception as ErrorMessage:
print ErrorMessage
while True:
NewInt = raw_input("another interval?")
if InputIntervals == "quit" or "Quit":
break
try:
ListOfIntervals = interval.interval.insert(ListofIntervals,interval.interval(NewInt))
print ListOfIntervals
except Exception and ErrorMessage:
print ErrorMessage
def test_mergeIntervals(self):
self.assertEqual(str(interval.mergeIntervals("[1,5]", "[2,6)")), '[1, 6)')
self.assertEqual(str(interval.mergeIntervals("(8,10]", "[8,18]")), '[8, 18]')
self.assertEqual(str(interval.mergeIntervals("(0,3]", "[2,5)")), '(0, 5)')
self.assertRaises(ValueError, interval.mergeIntervals, interval.interval('[1,2]'), interval.interval('[3,4)'))
self.assertRaises(ValueError, interval.mergeIntervals, interval.interval('[1,2]'), interval.interval('(0,1)'))
def main():
interval_list = raw_input('List of intervals?')
split_intlist=interval_list.split(", ")
result = [interval(i) for i in split_intlist]
try:
split_intlist=interval_list.split(", ")
result = [interval(i) for i in split_intlist] #list holds for the interval objects
except ValueError:
print('Invalid interval')
except IndexError:
print('Invalid interval')
while True:
input_str = raw_input('Interval?').lower()
if input_str == 'quit':
exit('End')
try:
newint = interval(input_str)
result=insert(result,newint)
str_re = [str(i) for i in result]
join_str = ', '.join(str_re)
print (join_str)
except ValueError:
print('Invalid interval')
def test_mergeIntervals_4(self):
int1 = interval('[5,8)')
int2 = interval('(8,10]')
with self.assertRaises(ValueError) as cm:
mergeIntervals(int1,int2)
thisexception = cm.exception
self.assertEquals(str(thisexception), "Invalid input: disjoint intervals")
def setUp(self):
self.interval1 = interval('[1,2]')
self.interval2 = interval('[3,4]')
self.interval3 = interval('[1,4]')
self.interval4 = interval('(5,10]')
self.list = [self.interval1, self.interval2, self.interval4]
def testCalculateSlicesBeginningAndEnd(self):
"one interval at the beginning and one at the end"
secs = np.arange(10)
inter = interval([0,3]) | interval([8,9])
slices = ObsFile.calculateSlices(inter, secs)
new = ObsFile.repackArray(secs, slices)
self.assertTrue(npEquals(new, np.array([4,5,6,7])))
def test_insert(self):
int1 = interval('[2,6)')
int2 = interval('(4,7]')
int3 = interval('[9,12)')
intervals = [int1,int2,int3]
newint = interval('(11,16)')
self.assertEqual(str(insert(intervals,newint)),"[[2,7], [9,16)]")
def add_conservation_features(self):
'''
will go through the wiggle track and make features of type conservation
for intronic regions where conservation is higher than it should be for
introns and is at least 6 bp wide
'''
tr = self.wigs['MamConserv']
feature_locs = []
idx = 0
for scores in score.sliding_window(self.wigs['MamConserv'], 6, step=1):
loc = (idx, idx + 6)
if sum(scores) / 6 > cfg.MAM_CONSERV_MIN_WINDOW_SCORE:
feature_locs.append(loc)
idx += 1
consol_flocs = interval.union([interval(*feature_locs)])
#remove exons and splice signals:
consol_flocs = consol_flocs & \
interval(self.get_exon_and_signal_pos()).invert()
for cfloc in consol_flocs:
sta = int(cfloc[0])
end = int(cfloc[1])
if end - sta < 6: continue
fscore = sum(tr[slice(sta, end)]) / (end - sta)
self.features.append(make_seq_feature(sta, end, 'MamConserv',
{'label' : ['MamConserv', ],
'evidence' : str(fscore)}))
def test_inverse(self):
self.assertEqual(interval[0.5, 1], interval[1, 2].inverse())
self.assertEqual(interval[-1, -0.5],(-interval[1, 2]).inverse())
self.assertEqual(interval([-fpu.infinity, -1], [0.5, +fpu.infinity]), interval[-1,2].inverse())
self.assertEqual(interval(-fpu.infinity, [1, +fpu.infinity]), interval[0,1].inverse())
self.assertEqual(interval([-fpu.infinity, -2.0], [0.0, fpu.infinity]),
interval([-0.5, 0.5], [0.2, fpu.infinity]).inverse())
def test_sqrt(self):
f, p = lambda x: x**2 - 2, lambda x: 2 * x
self.assertEqual(imath.sqrt(2), interval[1.4142135623730949, 1.4142135623730951])
self.assertEqual(imath.sqrt(4), interval[2])
self.assertEqual(imath.sqrt(interval[-3, -1]), interval())
self.assertEqual(imath.sqrt(interval[-1, 4]), interval([0.0, 2]))
self.assertEqual(imath.sqrt(interval([-3.14, 2], [4,9], [25, 64])), interval([0, 1.4142135623730951], [2, 3], [5, 8]))
def test_mergeIntervals_4(self):
a = interval.interval('[1,2)')
b = interval.interval('(2,4]')
with self.assertRaises(ValueError) as cm:
interval.mergeIntervals(a,b)
the_exception = cm.exception
self.assertEquals(str(the_exception), 'Disjoint intervals!')
def main():
while True:
try:
list_of_intervals = input("List of intervals? ")
if list_of_intervals == 'quit':
print ('')
sys.exit(1)
list_of_intervals = interval.mergeOverlapping(list_of_intervals)
break
except KeyboardInterrupt:
sys.exit(1)
except Exception:
print ('Invalid list of intervals')
pass
while True:
try:
interv = input('Interval? ')
if interv == 'quit':
print ('')
break
else:
interval(interv)
list_of_intervals = interval.insert(list_of_intervals, interv)
print (list_of_intervals)
except KeyboardInterrupt:
sys.exit(1)
except:
print ('Invalid interval')
def test_insert2(self):
ints = [interval(i) for i in ['(1,10)','[2,13)', '[3,5]', '[14,16]']]
newint = interval('[17,18]')
inserted = insert(ints, newint)
self.assertEqual(len(inserted), 2)
self.assertEqual(inserted[0].intervallist, [2,12])
self.assertEqual(inserted[1].intervallist, [14,18])
def test_isOverlapping(self):
int1 = interval('[1,6)')
int2 = interval('(4,7]')
int3 = interval('[1,4)')
int4 = interval('(4,7]')
self.assertTrue(isOverlapping(int1, int2))
self.assertFalse(isOverlapping(int3, int4))
def test_sum(self):
assert interval[-fpu.infinity, +fpu.infinity] == interval[-fpu.infinity] + interval[fpu.infinity]
assert interval[4, 6] == interval[1, 2] + interval[3, 4]
assert interval[3, fpu.infinity] == interval[1, fpu.infinity] + interval[2]
assert interval[-fpu.infinity, +fpu.infinity] == interval[-fpu.infinity, -1] + interval[2, +fpu.infinity]
assert interval[-fpu.infinity, +fpu.infinity] == interval[-fpu.infinity] + interval[8, +fpu.infinity]
assert interval([1, 2], [10, fpu.infinity]) + interval([1, 9], [-2, -1]) == interval([-1, 1], [2, fpu.infinity])
assert interval[1, 9] + interval([1, 2], [10, fpu.infinity]) == interval[2, fpu.infinity]
def test_insert_3(self):
a = ['[1,3]', '[6,9]']
lst = []
for item in a:
lst.append(interval.interval(item))
b = interval.interval('[4,5]')
c = interval.insert(lst, b)
self.assertEqual(str(c), '[[1,9]]')
def test_insert_2(self):
a = ['[1,2]', '(3,5)', '[6,7)', '(8,10]', '[12,16]']
lst = []
for item in a:
lst.append(interval.interval(item))
b = interval.interval('[4,9]')
c = interval.insert(lst, b)
self.assertEqual(str(c), '[[1,2], (3,10], [12,16]]')
def test_insert_4(self):
a = ['[1,2)', '(2,9]']
lst = []
for item in a:
lst.append(interval.interval(item))
b = interval.interval('(3,10]')
c = interval.insert(lst, b)
self.assertEqual(str(c), '[[1,2), (2,10]]')
def test_dennis_schnabel(self):
def f(x):
return (((x - 12) * x + 47 ) * x - 60 )* x
def p(x):
return ((4 * x - 12*3) * x + 47*2) * x - 60
self.assertApproximate(interval[-100, 100].newton(f, p), interval(0, 3, 4, 5), 43)
self.assertApproximate(interval[-100, 100].newton(lambda x: f(x) + 24, p), interval(0.888305779071752, 1), 59)
self.assertApproximate(interval[-100, 100].newton(lambda x: f(x) + 24.1, p), interval(), 0)
def test_sum(self):
self.assertEqual(interval[-fpu.infinity, +fpu.infinity], interval[-fpu.infinity] + interval[fpu.infinity])
self.assertEqual(interval[4, 6], interval[1, 2] + interval[3, 4])
self.assertEqual(interval[3, fpu.infinity], interval[1, fpu.infinity] + interval[2])
self.assertEqual(interval[-fpu.infinity, +fpu.infinity], interval[-fpu.infinity, -1] + interval[2, +fpu.infinity])
self.assertEqual(interval[-fpu.infinity, +fpu.infinity], interval[-fpu.infinity] + interval[8, +fpu.infinity])
self.assertEqual(interval([1, 2], [10, fpu.infinity]) + interval([1,9],[-2,-1]), interval([-1, 1], [2, fpu.infinity]))
self.assertEqual(interval[1, 9] + interval([1, 2], [10, fpu.infinity]), interval[2, fpu.infinity])
def setUp(self):
print 'Test whether two intervals can merge'
#interval1 and interval2 can be merged, and interval3 and interval4 cannot be merged.
self.interval1 = interval('(1,4)')
self.interval2 = interval('[1,3]')
self.interval3 = interval('(3,8)')
self.interval4 = interval('(-3,2]')
self.interval = None
def test_mergeIntervals(self):
i = interval()
int1 = interval('[',1,5,']')
int2 = interval('[',2,6,']')
int3 = interval('[',1,6,']')
self.assertEqual(i.mergeIntervals(int1, int2).bra1, int3.bra1)
self.assertEqual(i.mergeIntervals(int1, int2).bra2, int3.bra2)
self.assertEqual(i.mergeIntervals(int1, int2).start, int3.start)
self.assertEqual(i.mergeIntervals(int1, int2).end, int3.end)
def test_mergeIntervals(self):
int1 = interval('[2,6)')
int2 = interval('(4,7]')
intm1 = mergeIntervals(int1,int2)
int3 = interval('[5,11]')
int4 = interval('[12,14]')
intm2 = mergeIntervals(int3,int4)
self.assertEqual(str(intm1), '[2,7]')
self.assertEqual(str(intm2), '[5,14]')
def get_features(self, query, meta=False, aggregate=False, correct=None):
'''
returns an iterator on features given a certain query, a meta feature,
a sequence motif type object, or a type string.
'''
#special cases for 'donor_intron' and 'acceptor_intron'
if query == 'donor_intron':
return ifilter(lambda f: len(self) in interval(f.extract_pos()),
self.get_features('intron'))
if query == 'acceptor_intron':
return ifilter(lambda f: 0 in interval(f.extract_pos()),
self.get_features('intron'))
#if aggregate flag, then get all motif types that have that agg string
if aggregate:
query = ifilter(lambda m: 'aggregate' in m.attribs and \
m.attribs['aggregate'] == query, \
motif.motif_types.values())
#if correct flag, then get all motif types that have the 'correct splice
# signal' string
if correct is True:
is_correct_fxn = \
lambda f: 'function' in f.qualifiers and \
'correct splice signal' in f.qualifiers['function']
return ifilter(is_correct_fxn, \
self.get_features(query, \
meta=meta, \
aggregate=aggregate))
if correct is False:
not_correct_fxn = \
lambda f: 'function' not in f.qualifiers or \
'correct splice signal' not in f.qualifiers['function']
return ifilter(not_correct_fxn, \
self.get_features(query, \
meta=meta, \
aggregate=aggregate))
sametype = lambda f, q: (f.type == q) or ('seq_motif_type' in f.qualifiers \
and f.qualifiers['seq_motif_type'] == q)
if not isinstance(query, str) and isinstance(query, collections.Iterable):
recurse_this = lambda q: self.get_features(q, meta, aggregate, correct)
iter = chain.from_iterable(map(recurse_this, query))
elif isinstance(query, str):
iter = ifilter(lambda f: sametype(f, query), self.features)
elif isinstance(query, motif.SeqMotifType):
iter = ifilter(lambda f: sametype(f, query.type), self.features)
elif isinstance(query, SeqFeature) and query.qualifiers['meta'] == True:
iter = self._consolidated[f.qualifiers['seq_motif_type']][query]
else:
raise GetFeaturesQueryUnknownType
return ifilter(lambda f: meta is f.is_meta(), iter)
def __init__(self, a = interval([0, 0]), b = interval([0, 0])): self.a = a self.b = b self.real_max = max(max(self.a)) self.real_min = min(min(self.a)) self.im_max = max(max(self.b)) self.im_min = min(min(self.b))
def test_width(self):
assert helpers.ulpwidth(interval[3] ** -1) == [1]
assert [1, 1, 1] == helpers.ulpwidth(interval(
[9007199254740991 * 2.0 ** -51, 4503599627370496 * 2.0 ** -50],
[9007199254740991 * 2.0 ** -49, 16],
[-16, -9007199254740991 * 2.0 ** -49]))
assert helpers.ulpwidth(interval([5249383869325653 * 2.0 ** -51, 5249383869325655 * 2.0 ** -51])) == [2]
assert helpers.ulpwidth(interval[123.34]) == [0]
assert helpers.ulpwidth(interval[fpu.infinity]) == [0]
assert helpers.ulpwidth(interval[2, fpu.infinity]) == [fpu.infinity]
def test_width(self):
self.assertEqual(helpers.ulpwidth(interval[3]**-1), [1])
self.assertEqual(helpers.ulpwidth(interval([9007199254740991 * 2.0 ** -51, 4503599627370496 * 2.0 ** -50],
[9007199254740991 * 2.0 ** -49, 16],
[-16, -9007199254740991 * 2.0 ** -49],
)),[1, 1, 1])
self.assertEqual(helpers.ulpwidth(interval([5249383869325653 * 2.0 ** -51, 5249383869325655 * 2.0 ** -51])),[2])
self.assertEqual(helpers.ulpwidth(interval[123.34]), [0])
self.assertEqual(helpers.ulpwidth(interval[fpu.infinity]), [0])
self.assertEqual(helpers.ulpwidth(interval[2, fpu.infinity]), [fpu.infinity])
def invert(self):
'''
separates all the components and takes the intersection of their individual
inverses
'''
ivls = []
inverse_func = lambda cmp: interval([-inf, cmp[0][0]], [cmp[0][1], inf])
inverses = map(inverse_func, self.components)
return reduce(lambda x, y: x & y, inverses, interval((-inf, inf)))
def test_invalidInterval(self):
invalidintervallist = ['(1,6]]', '((4,7)', 'foo', '{1,2]']
for invalidinterval in invalidintervallist:
with self.assertRaises(IntervalInputException):
self.interval = interval(invalidinterval)
def __bwd_propag(self, n_id, box):
n = self.dag[n_id]
fwd = self.__fwd
bwd = self.__bwd
rec = self.__bwd_propag
if n[0] == '+':
bwd[n[1]] = bwd[n_id] - fwd[n[2]]
rec(n[1], box)
bwd[n[2]] = bwd[n_id] - fwd[n[1]]
rec(n[2], box)
elif n[0] == '-':
bwd[n[1]] = bwd[n_id] + fwd[n[2]]
rec(n[1], box)
bwd[n[2]] = fwd[n[1]] - bwd[n_id]
rec(n[2], box)
elif n[0] == '*':
bwd[n[1]] = bwd[n_id] / fwd[n[2]]
rec(n[1], box)
bwd[n[2]] = bwd[n_id] / fwd[n[1]]
rec(n[2], box)
elif n[0] == '/':
bwd[n[1]] = bwd[n_id] * fwd[n[2]]
rec(n[1], box)
bwd[n[2]] = fwd[n[1]] / bwd[n_id]
rec(n[2], box)
elif n[0] == '^':
i = self.dag[n[2]][1]
if i % 2 == 0:
p = root(bwd[n_id], i)
pp = p & fwd[n[1]]
np = (-p) & fwd[n[1]]
if is_empty(pp) or is_empty(np):
bwd[n[1]] = interval()
else:
bwd[n[1]] = interval.hull([pp, np])
else:
bwd[n[1]] = root(bwd[n_id], i)
rec(n[1], box)
elif n[0] == 'sqrt':
if is_empty(bwd[n_id]) or bwd[n_id][0].sup < 0:
bwd[n[1]] = interval()
elif bwd[n_id][0].inf < 0:
i = interval([0, bwd[n_id][0].sup])
bwd[n[1]] &= i * i
else:
bwd[n[1]] &= bwd[n_id] * bwd[n_id]
assert (not is_empty(bwd[n[1]]))
# TODO
#elif n[0] == 'sin':
elif n[0] == 'C':
bwd[n_id] &= n[1]
elif n[0] == 'V':
box[n[1]] &= bwd[n_id]
else:
print('unsupported node: ' + str(n))
assert (False)
from interval import interval, inf, imath
f = open("day_16.txt")
#f = open("test.txt")
departure = interval()
non_departure = interval()
my_ticket = ""
overall_rules = interval()
rows = {}
while True:
l = f.readline()
if not l.rstrip():
break
row = l.rstrip().split(':')
intervals = row[1].split(' or ')
rule_ivls = interval()
for inter in intervals:
interval_str = inter.split('-')
rule_ivls = rule_ivls | interval[int(interval_str[0]),
int(interval_str[1])]
overall_rules = overall_rules | rule_ivls
rows[row[0]] = rule_ivls
print(overall_rules)
rules_len = len(rows)
while True:
l = f.readline().rstrip()
if not l:
def test_get_junctions(self):
chrom = 'chr1'
gtf_donors = {'chr1': {1, 2, 3}}
gtf_acceptors = {'chr1': {1, 2, 3}}
values = [
[interval([4300.0, 4349.0]),
interval([4000.0, 4099.0])], # + chim
[interval([4000.0, 4099.0]),
interval([4300.0, 4349.0])], # - non-chim
[interval([3050.0, 3149.0]),
interval([4000.0, 4099.0])], # + non-chim
[interval([4000.0, 4099.0]),
interval([3050.0, 3149.0])], # - chim
[
interval([74598831.0, 74598855.0]),
interval([74601450.0, 74601467.0]), # + 1324
interval([74600055.0, 74600075.0]),
interval([74603869.0, 74603880.0])
],
]
chains = [
'+',
'-',
'+',
'-',
'+',
]
exp_lists = [
[{
'n_junctions': 1,
'chrom': 'chr1',
'chain': '+',
'donor': str(4350),
'annot_donor': 0,
'acceptor': str(3999),
'annot_acceptor': 0,
'chimeric': True
}],
[{
'n_junctions': 1,
'chrom': 'chr1',
'chain': '-',
'donor': str(4299),
'annot_donor': 0,
'acceptor': str(4100),
'annot_acceptor': 0,
'chimeric': False
}],
[{
'n_junctions': 1,
'chrom': 'chr1',
'chain': '+',
'donor': str(3150),
'annot_donor': 0,
'acceptor': str(3999),
'annot_acceptor': 0,
'chimeric': False
}],
[{
'n_junctions': 1,
'chrom': 'chr1',
'chain': '-',
'donor': str(3049),
'annot_donor': 0,
'acceptor': str(4100),
'annot_acceptor': 0,
'chimeric': True
}],
[
{
'n_junctions': 3,
'chrom': 'chr1',
'chain': '+',
'donor': str(74598856),
'annot_donor': 0,
'acceptor': str(74601449),
'annot_acceptor': 0,
'chimeric': False
},
{
'n_junctions': 3,
'chrom': 'chr1',
'chain': '+',
'donor': str(74601468),
'annot_donor': 0,
'acceptor': str(74600054),
'annot_acceptor': 0,
'chimeric': True
},
{
'n_junctions': 3,
'chrom': 'chr1',
'chain': '+',
'donor': str(74600076),
'annot_donor': 0,
'acceptor': str(74603868),
'annot_acceptor': 0,
'chimeric': False
},
],
]
for i, value in enumerate(values):
res_list = ptes.get_junctions(chrom, chains[i], value, gtf_donors,
gtf_acceptors)
self.assertListEqual(exp_lists[i], res_list)
def get_sin_cos_table(max_theta, min_theta, max_theta_dot, min_theta_dot,
action):
assert min_theta <= max_theta, f"min_theta = {min_theta},max_theta={max_theta}"
assert min_theta_dot <= max_theta_dot, f"min_theta_dot = {min_theta_dot},max_theta_dot={max_theta_dot}"
step_theta = 0.1
step_theta_dot = 0.1
# min_theta = max(min_theta, -math.pi / 2)
# max_theta = min(max_theta, math.pi / 2)
split_theta1 = np.arange(min(min_theta, 0), min(max_theta, 0),
step_theta)
split_theta2 = np.arange(max(min_theta, 0), max(max_theta, 0),
step_theta)
split_theta = np.concatenate([split_theta1, split_theta2])
split_theta_dot1 = np.arange(min(min_theta_dot, 0),
min(max_theta_dot, 0), step_theta)
split_theta_dot2 = np.arange(max(min_theta_dot, 0),
max(max_theta_dot, 0), step_theta)
split_theta_dot = np.concatenate([split_theta_dot1, split_theta_dot2])
if len(split_theta_dot) == 0:
split_theta_dot = np.array([max_theta_dot])
if len(split_theta) == 0:
split_theta = np.array([max_theta])
env = MonitoredPendulum(None)
force = 0
if action == 1:
force = -env.max_torque
elif action == 2:
force = env.max_torque
else:
force = 0
split = []
for t_dot in split_theta_dot:
for theta in split_theta:
lb_theta_dot = t_dot
ub_theta_dot = min(t_dot + step_theta_dot, max_theta_dot)
lb = theta
ub = min(theta + step_theta, max_theta)
split.append((interval([lb_theta_dot,
ub_theta_dot]), interval([lb, ub])))
sin_cos_table = []
while (len(split)):
theta_dot, theta = split.pop()
# dynamics
newthdot = theta_dot + (-3 * env.g /
(2 * env.l) * imath.sin(theta + np.pi) +
3. / (env.m * env.l**2) * force) * env.dt
newth = theta + newthdot * env.dt
newthdot = interval([
np.clip(newthdot[0].inf, -env.max_speed, env.max_speed),
np.clip(newthdot[0].sup, -env.max_speed, env.max_speed)
])
if newth[0].sup > np.pi:
if newth[0].inf >= np.pi: # both over the limit, just make a single interval
sin_cos_table.append(
(theta, theta_dot,
PendulumExperiment.interval_normalise_theta_interval(
newth), interval(newthdot)))
else: # only the upper bound is over the limit, make 2 intervals
newth2 = interval([newth[0].inf, np.pi])
sin_cos_table.append(
(theta, theta_dot, newth2, interval(newthdot)))
normalised2 = PendulumExperiment.normalise_theta_value(
newth[0].sup)
newth3 = interval([-np.pi, normalised2])
sin_cos_table.append(
(theta, theta_dot, newth3, interval(newthdot)))
continue
elif newth[0].inf < -np.pi:
if newth[0].sup <= -np.pi: # both over the limit, just make a single interval
sin_cos_table.append(
(theta, theta_dot,
PendulumExperiment.interval_normalise_theta_interval(
newth), interval(newthdot)))
else: # only the lower bound is over the limit, make 2 intervals
normalise_theta2 = PendulumExperiment.normalise_theta_value(
newth[0].inf)
newth2 = interval([np.pi, normalise_theta2])
sin_cos_table.append(
(theta, theta_dot, newth2, interval(newthdot)))
newth3 = interval([-np.pi, newth[0].sup])
sin_cos_table.append(
(theta, theta_dot, newth3, interval(newthdot)))
continue
else:
sin_cos_table.append(
(theta, theta_dot, newth, interval(newthdot)))
return sin_cos_table
def test_format(self):
for x in interval[1], interval[1, 2], interval([1, 2], [3, 4]), interval[2, 2.0000000000000004]:
assert x == eval(repr(x))
x = interval([1, 2])
assert str(x) == repr(x)
def test_inverse(self):
assert interval[0.5, 1] == interval[1, 2].inverse()
assert interval[-1, -0.5] == (-interval[1, 2]).inverse()
assert interval([-fpu.infinity, -1], [0.5, +fpu.infinity]) == interval[-1, 2].inverse()
assert interval(-fpu.infinity, [1, +fpu.infinity]) == interval[0, 1].inverse()
assert interval([-fpu.infinity, -2.0], [0.0, fpu.infinity]) == interval([-0.5, 0.5], [0.2, fpu.infinity]).inverse()
def test_count_relative_position(self):
interval_lists = [
[interval([-10, 10]), interval([1.0, 100.0])],
[interval([-10, 1]), interval([1.0, 100.0])],
[interval([10, 20]), interval([1.0, 100.0])],
[interval([90, 99]), interval([1.0, 100.0])],
[interval([90, 100]), interval([1.0, 100.0])],
[interval([20, 10]), interval([1.0, 100.0])],
[interval([90, 199]), interval([1.0, 100.0])],
[interval([200, 1000]),
interval([1.0, 100.0])],
[interval([150, 200]),
interval([1.0, 100.0])],
]
for i, tuple in enumerate(interval_lists):
res_int = ptes.count_relative_position(feature=tuple[0],
container=tuple[1])
print res_int
def test_get_read_interval(self):
cigars = [
'20M30S',
'30S20M',
'30S20M30S',
'20M2I20M',
'20M2D20M',
'20M32N20M',
'20S20M32N20M',
'20S20M32N20M1000p76M',
]
leftpos = 100
exp_read_dicts = [
OrderedDict([
('M1', interval([100.0, 119.0])),
]),
OrderedDict([
('M1', interval([100.0, 119.0])),
]),
OrderedDict([
('M1', interval([100.0, 119.0])),
]),
OrderedDict([('M1', interval([100.0, 119.0])),
('M2', interval([120.0, 139.0]))]),
OrderedDict([('M1', interval([100.0, 119.0])),
('D1', interval([120.0, 121.0])),
('M2', interval([122.0, 141.0]))]),
OrderedDict([('M1', interval([100.0, 119.0])),
('N1', interval([120.0, 151.0])),
('M2', interval([152.0, 171.0]))]),
OrderedDict([('M1', interval([100.0, 119.0])),
('N1', interval([120.0, 151.0])),
('M2', interval([152.0, 171.0]))]),
OrderedDict([('M1', interval([100.0, 119.0])),
('N1', interval([120.0, 151.0])),
('M2', interval([152.0, 171.0])),
('p1', interval([172.0, 1171.0])),
('M3', interval([1172.0, 1247.0]))]),
]
res_read_dicts = [
ptes.get_read_interval(cigar=cigar, leftpos=leftpos, output='dict')
for cigar in cigars
]
for i in range(len(exp_read_dicts)):
self.assertEqual(exp_read_dicts[i], res_read_dicts[i])
def test_split_by_p(self):
read_dicts = [
OrderedDict([('M1', interval([100.0, 119.0])),
('N1', interval([120.0, 151.0])),
('M2', interval([152.0, 171.0])),
('p1', interval([172.0, 1171.0])),
('M3', interval([1172.0, 1247.0]))]),
]
results = [
ptes.split_by_p(read_dict=read_dict)
for read_dict in self.input_read_dicts
]
exp_results = [
[
OrderedDict([('M1', interval([100.0, 119.0])),
('N1', interval([120.0, 151.0])),
('M2', interval([152.0, 171.0]))]),
OrderedDict([('M3', interval([1172.0, 1247.0]))])
],
[
OrderedDict([('M1', interval([100.0, 119.0])),
('N1', interval([120.0, 151.0])),
('M2', interval([152.0, 171.0]))]),
OrderedDict([('M3', interval([1248.0, 1260.0]))])
],
[
OrderedDict([('M1', interval([100.0, 119.0])),
('N1', interval([120.0, 151.0])),
('M2', interval([152.0, 171.0]))]),
OrderedDict([('M3', interval([1248.0, 1260.0]))])
],
]
for i in range(len(read_dicts)):
self.assertEqual(exp_results[i], results[i])
def test_insert(self):
ints = [interval(i) for i in ['(1,10)', '[2,13)', '[3,5]', '[14,16]']]
newint = interval('[13,14]')
self.assertEqual(insert(ints, newint)[0].intervallist, [2, 16])
def test_mergeOverlapping2(self):
ints = [interval(i) for i in ['(1,10)', '[2,13)', '[3,5]', '[14,16]']]
a = mergeOverlapping(ints)
self.assertEqual(len(a), 2)
self.assertEqual(a[0].intervallist, [2, 12])
self.assertEqual(a[1].intervallist, [14, 16])
def test_nan_constructor(self):
assert interval[2, fpu.nan] == ((-fpu.infinity, fpu.infinity),)
assert interval[2, fpu.nan] == ((-fpu.infinity, fpu.infinity),)
assert interval(2, fpu.nan, 9) == ((-fpu.infinity, fpu.infinity),)
def test_union(self):
assert interval([1, 6], 9) == interval([1, 3], [4, 6]) | interval([2, 5], 9)
assert interval[1, 2] | 2.1 == interval([1, 2], 2.1)
assert 2.1 | interval[1, 2] == interval([1, 2], 2.1)
self.assertRaises(TypeError, lambda: interval[1, 2] | 1j)
def interval_normalise_theta_interval(theta):
result = interval([
PendulumExperiment.normalise_theta_value(theta[0].inf),
PendulumExperiment.normalise_theta_value(theta[0].sup)
])
return result
def test_abs(self):
assert interval([0, 3]) == abs(interval[-3, 2])
assert interval([1, 6], 9) == abs(interval([-9], [-5, -2], [1, 3], [4, 6]))
assert interval([1, 6], 9) == abs(interval([9], [2, 5], [-3, -1], [-6, -4]))
def test_hull(self):
assert interval([1, 9]) == interval.hull((interval([1, 3], [4, 6]), interval([2, 5], 9)))
def verify_in(x, y):
assert x in y
assert x & y == interval(x)
def filter_short_intvls(intvls, min_len):
"""Filter out intervals in <intvls> shorter than <min_len>.
<intvls> must consist of INTEGER intervals with inclusive boundaries.
"""
return interval(*[i for i in intvls if intvl_len(i) >= min_len])
def test_extrema(self):
assert interval(1, [2, 3], 4).extrema == interval(1, 2, 3, 4)
print('trying case 1|567 ...')
ctr = 0
while not case_queue.empty() and curr_depth < MAX_DEPTH:
(M,Mdenom, N,Ndenom, A1,A1denom, A6,A6denom, depth) = case_queue.get()
if depth != curr_depth:
curr_depth = depth
curr_size = next_size
ctr += curr_size
next_size = 0
print('\ton depth =', curr_depth, '...', 'size =', curr_size, '...', 'so far', ctr, '...')
mu = interval[M, M+1] / interval(Mdenom)
nu = interval[N, N+1] / interval(Ndenom)
a1 = interval[A1, A1+1] / interval(A1denom)
a6 = interval[A6, A6+1] / interval(A6denom)
if is_feasible(mu, nu, a1, a6):
next_size += 2
if depth % 4 == 0:
case_queue.put( (M,Mdenom, N,Ndenom, 2*A1, 2*A1denom, A6, A6denom, depth+1) )
case_queue.put( (M,Mdenom, N,Ndenom, 2*A1+1, 2*A1denom, A6, A6denom, depth+1) )
if depth % 4 == 1:
case_queue.put( (M,Mdenom, N,Ndenom, A1, A1denom, 2*A6, 2*A6denom, depth+1) )
case_queue.put( (M,Mdenom, N,Ndenom, A1, A1denom, 2*A6+1, 2*A6denom, depth+1) )
def test_midpoint(self):
assert interval[0, 4].midpoint == interval[2]
assert interval(-1, 1, 4) == interval(-1, [0, 2], [3, 5]).midpoint
time = time.rename("t")
size = (len(time), len(S))
columns = np.arange(0, len(S))
s_values = pd.DataFrame(np.zeros(size), index=time, columns=columns)
s_epsilon = pd.DataFrame(np.zeros(size), index=time, columns=columns)
s_error = pd.DataFrame(np.zeros(size), index=time, columns=columns)
print("\n\nMonitor ...")
window = deque(maxlen=5)
for index, row in data.iterrows():
timestamp = row['t_clock']
# move values (as intervals) from row to itoms
for name in itoms.keys():
v = row[name]
e = epsilon[name]
itoms[name].v = interval([v - e, v + e])
itoms[name].t = timestamp
# transform
outputs = bring_to_common_domain(S, itoms)
# intervals to compare
values = [output.v for output in outputs.values()]
# each value is only a single interval (otherwise take the hull first)
for v in values:
assert len(v) == 1
# log
s_epsilon.at[timestamp, :] = [(v[0][1] - v[0][0]) / 2 for v in values]
s_values.at[timestamp, :] = [v.midpoint[0][0] for v in values]
# compare
error = faulty(values)
if args.median:
window.append(error)
def test_opts(self):
self.assertRaises(TypeError, lambda: interval(0, 1).newton(None, None, nonexisting=True))
def test_sort_by_xq(self):
interval_lists = [
[(0, interval([4300.0, 4349.0])),
(1, interval([4000.0, 4099.0]))], # + chim
[(0, interval([4300.0, 4349.0])),
(1, interval([4000.0, 4099.0]))], # - non-chim
[(0, interval([3050.0, 3149.0])),
(1, interval([4000.0, 4099.0]))], # + non-chim
[(0, interval([3050.0, 3149.0])),
(1, interval([4000.0, 4099.0]))], # - chim
]
chains = [
'+',
'-',
'+',
'-',
]
exp_lists = [
[interval([4300.0, 4349.0]),
interval([4000.0, 4099.0])],
[interval([4000.0, 4099.0]),
interval([4300.0, 4349.0])],
[interval([3050.0, 3149.0]),
interval([4000.0, 4099.0])],
[interval([4000.0, 4099.0]),
interval([3050.0, 3149.0])],
]
for i, tuple in enumerate(interval_lists):
res_list = ptes.sort_by_xq(tuple, chains[i])
self.assertEqual(exp_lists[i], res_list)
def test_cubic(self):
assert interval[-2, 2].newton(lambda x: x ** 3 - x, lambda x: 3 * x ** 2 - 1) == interval(-1, 0, 1)
assert interval[-5, 5].newton(lambda x: x ** 3 + x - 10, lambda x: 3 * x ** 2 + 1) == interval[2]
assert interval[-5, 5].newton(lambda x: x ** 3 + x - 15, lambda x: 3 * x ** 2 + 1) == interval[5249383869325653 * 2.0 ** -51, 5249383869325655 * 2.0 ** -51]
def get_intrinsic_frames(self):
int_steps = self.env.intrinsic_timesteps
one_min_frames = 60 * self.video_fps * self.frame_freq
return interval([0, one_min_frames],
[int_steps / 2, int_steps / 2 + one_min_frames],
[int_steps - one_min_frames, int_steps])
def modify_parser(subparsers):
import argparse
from interval import interval
subparser = subparsers.add_parser('simple')
subparser_preprocess = subparser.add_argument_group(
'data preprocessing options')
subparser_preprocess.add_argument('--unit_norm', action='store_true')
subparser_preprocess.add_argument('--triangle',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--label_corruption',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--label_corruption_valid',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--label_unshifted_percentile',
type=interval(float),
default=100.0)
subparser_preprocess.add_argument('--gaussian_X',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--zero_Y',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--huge_Y',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--huge_X',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--tiny_X',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--ones', type=interval(int), default=0)
subparser_preprocess.add_argument('--max_Y', type=interval(int), default=0)
subparser_preprocess.add_argument('--pad_dim',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--pad_dim_numbad',
type=interval(int),
default=0)
subparser_preprocess.add_argument('--parallel', type=int, default=10)
subparser_preprocess.add_argument('--prefetch', type=int, default=1000)
def test_interval(self):
self.assertEqual(interval('(1,10)').intervallist, [2, 9])
self.assertEqual(interval('[7,20]').intervallist, [7, 20])
self.assertEqual(interval('(-1,4)').intervallist, [0, 3])
self.assertRaises(ValueError, interval, '(0,-10)') #Exception test
def test_failing_constructor(self):
self.assertRaises(interval.ComponentError, lambda: interval[1, [2, 3]])
self.assertRaises(interval.ComponentError, lambda: interval[1, 2, 3])
self.assertRaises(interval.ComponentError, lambda: interval(0, [1, 2, 3]))
self.assertRaises(interval.ComponentError, lambda: interval(0, [1, [2, 3]]))
self.assertRaises(interval.ComponentError, lambda: interval['a', 1])