def test_replace_with_union(self):
i = P.closed(0, 1) | P.open(2, 3)
assert i.replace() == i
assert i.replace(P.OPEN, -1, 4, P.OPEN) == P.openclosed(-1, 1) | P.open(2, 4)
assert i.replace(lower=2) == P.closedopen(2, 3)
assert i.replace(upper=1) == P.closedopen(0, 1)
assert i.replace(lower=5) == P.empty()
assert i.replace(upper=-5) == P.empty()
assert i.replace(left=lambda v: ~v, lower=lambda v: v - 1, upper=lambda v: v + 1, right=lambda v: ~v) == P.openclosed(-1, 1) | P.openclosed(2, 4)
def test_parameters(self):
i1, i2, i3, i4 = P.closed(0, 1), P.openclosed(0, 1), P.closedopen(0, 1), P.open(0, 1)
params = {
'disj': ' or ',
'sep': '-',
'left_open': '<!',
'left_closed': '<',
'right_open': '!>',
'right_closed': '>',
'conv': lambda s: '"{}"'.format(s),
'pinf': '+oo',
'ninf': '-oo',
}
assert P.to_string(i1, **params) == '<"0"-"1">'
assert P.to_string(i2, **params) == '<!"0"-"1">'
assert P.to_string(i3, **params) == '<"0"-"1"!>'
assert P.to_string(i4, **params) == '<!"0"-"1"!>'
assert P.to_string(P.empty(), **params) == '<!!>'
assert P.to_string(P.singleton(1), **params) == '<"1">'
assert P.to_string(P.openclosed(-P.inf, 1), **params) == '<!-oo-"1">'
assert P.to_string(P.closedopen(1, P.inf), **params) == '<"1"-+oo!>'
assert P.to_string(P.closed(0, 1) | P.closed(2, 3), **params) == '<"0"-"1"> or <"2"-"3">'
def test_parameters(self):
i1, i2, i3, i4 = '<"0"-"1">', '<!"0"-"1">', '<"0"-"1"!>', '<!"0"-"1"!>'
params = {
'conv': lambda s: int(s[1:-1]),
'disj': ' or ',
'sep': '-',
'left_open': '<!',
'left_closed': '<',
'right_open': '!>',
'right_closed': '>',
'pinf': r'\+oo',
'ninf': '-oo',
}
assert P.from_string(i1, **params) == P.closed(0, 1)
assert P.from_string(i2, **params) == P.openclosed(0, 1)
assert P.from_string(i3, **params) == P.closedopen(0, 1)
assert P.from_string(i4, **params) == P.open(0, 1)
assert P.from_string('<!!>', **params) == P.empty()
assert P.from_string('<"1">', **params) == P.singleton(1)
assert P.from_string('<!-oo-"1">', **params) == P.openclosed(-P.inf, 1)
assert P.from_string('<"1"-+oo!>', **params) == P.closedopen(1, P.inf)
assert P.from_string('<"0"-"1"> or <"2"-"3">', **params) == P.closed(0, 1) | P.closed(2, 3)
def parse_or_empty(parser, text, verbose=False):
try:
return parser.parse(text)
except Exception as e:
if verbose:
print('E:', text, str(e))
return I.empty()
def _to_p_intervals(intervals):
"""
Converts a `TimeInterval` instance or a list to an `Interval` list
(portion library objects).
This is usually done to merge and simplify the elements of the list.
Parameters
----------
intervals : TimeInterval or list[TimeInterval]
List of intervals
Returns
-------
`Interval` object with the list of time intervals
"""
# Fill the `Interval` list and merge as necessary
p_intervals = p.empty()
if isinstance(intervals, list):
for interval in intervals:
# make sure interval is not None
if interval:
p_intervals = p_intervals.union(interval.p_interval)
else:
# intervals object is a single TimeInterval
p_intervals = intervals.p_interval
return p_intervals
def test_is_empty(self):
assert P.openclosed(1, 1).empty
assert P.closedopen(1, 1).empty
assert P.open(1, 1).empty
assert not P.closed(1, 1).empty
assert P.Interval().empty
assert P.empty().empty
def delays(values: ClockValuation, constraint: ClockConstraint) -> Interval:
"""Compute the allowable delay with the given clock valuations and constraints
.. todo::
Write the LaTeX version of the function.
Parameters
----------
values :
A mapping from `Clock` to the valuation of the clock.
constraint :
A clock constrain.
Returns
-------
:
An interval that represents the set of possible delays that satisfy the
given clock constraint.
"""
if isinstance(constraint, bool):
constraint = Boolean(constraint)
if isinstance(constraint, Boolean):
if constraint.value:
return P.closed(0, P.inf)
return P.empty()
if isinstance(constraint, SingletonConstraint):
v_c = values[constraint.clock]
n: int = constraint.rhs
if constraint.op == ComparisonOp.GE:
return P.closed(n - v_c, P.inf)
if constraint.op == ComparisonOp.GT:
return P.open(n - v_c, P.inf)
if constraint.op == ComparisonOp.LE:
return P.closed(0, n - v_c)
if constraint.op == ComparisonOp.LT:
return P.closedopen(0, n - v_c)
if isinstance(constraint, And):
return delays(values, constraint.args[0]) & delays(values, constraint.args[1])
if isinstance(constraint, DiagonalConstraint):
v_c1 = values[constraint.lhs.clock1]
v_c2 = values[constraint.lhs.clock2]
op_fn = constraint.op.to_op()
if op_fn(v_c1 - v_c2, n):
return P.closed(0, P.inf)
return P.empty()
raise TypeError("Unsupported ClockConstraint type: {}".format(type(constraint)))
def _reassemble(self, ctr):
if 'deliver' not in ctr.actions:
return
if not (ctr.bundle.primary.bundle_flags & PrimaryBlock.Flag.IS_FRAGMENT):
return
final_ident = ctr.bundle_ident()[:3]
frag_offset = ctr.bundle.primary.fragment_offset
total_length = ctr.bundle.primary.total_app_data_len
reassm = self._reassembly.get(final_ident, None)
if reassm is None:
reassm = Reassembly(
ident=final_ident,
total_length=total_length,
total_valid=portion.closedopen(0, total_length),
valid=portion.empty(),
data=bytearray(total_length)
)
self._reassembly[final_ident] = reassm
else:
if reassm.total_length != total_length:
LOGGER.warning('Mismatch in fragment-bundle total application data length')
if frag_offset == 0:
reassm.first_frag = ctr.bundle
# Inject the new fragment
payload_data = ctr.block_num(1).getfieldval('btsd')
end_ix = frag_offset + len(payload_data)
reassm.data[frag_offset:end_ix] = payload_data
reassm.valid |= portion.closedopen(frag_offset, end_ix)
if reassm.valid == reassm.total_valid:
del self._reassembly[final_ident]
LOGGER.info('Finished reassembly of %s size %d', final_ident, reassm.total_length)
# Synthesize original bundle
rctr = BundleContainer()
rctr.bundle.primary = reassm.first_frag.primary.copy()
rctr.bundle.primary.bundle_flags &= ~PrimaryBlock.Flag.IS_FRAGMENT
rctr.bundle.primary.crc_type = AbstractBlock.CrcType.NONE
rctr.bundle.primary.crc_value = None
LOGGER.debug('Copying %d first-fragment blocks', len(reassm.first_frag.blocks))
for blk in reassm.first_frag.blocks:
rctr.bundle.blocks.append(blk.copy())
rctr.reload()
pyld_blk = rctr.block_num(Bundle.BLOCK_NUM_PAYLOAD)
pyld_blk.setfieldval('btsd', reassm.data)
pyld_blk.crc_type = AbstractBlock.CrcType.NONE
pyld_blk.crc_value = None
glib.idle_add(self._agent.recv_bundle, rctr)
ctr.actions.clear()
return True
def test_creation(self):
assert P.Interval() == P.empty()
assert P.Interval(P.closed(0, 1)) == P.closed(0, 1)
assert P.Interval(P.closed(0, 1)) == P.closed(0, 1)
assert P.Interval(P.closed(0, 1), P.closed(2, 3)) == P.closed(0, 1) | P.closed(2, 3)
assert P.Interval(P.closed(0, 1) | P.closed(2, 3)) == P.closed(0, 1) | P.closed(2, 3)
with pytest.raises(TypeError):
P.Interval(1)
def test_empty(self):
assert P.empty() == P.Interval.from_atomic(P.OPEN, P.inf, -P.inf, P.open)
assert P.closed(3, -3) == P.empty()
assert P.openclosed(0, 0) == P.empty()
assert P.closedopen(0, 0) == P.empty()
assert P.open(0, 0) == P.empty()
assert P.closed(0, 0) != P.empty()
assert P.singleton(P.inf) == P.empty()
assert P.singleton(-P.inf) == P.empty()
def choose_action(self, i_ph):
# Activation rule
not_covered = P.closed(lower=0, upper=1)
# not_covered = P.closed(lower=0.01, upper=self.sigma_square)
# scale = not_covered.upper - not_covered.lower
for arm in self.active_arms:
# confidence_radius = scale * self.confidence_radius(i_ph, i)
confidence_radius = self.confidence_radius(i_ph, arm)
confidence_interval = P.closed(arm.norm_value - confidence_radius,
arm.norm_value + confidence_radius)
not_covered = not_covered - confidence_interval
if debug:
print(
f"arm: {arm.index}, value: {arm.value}, i_ph: {i_ph}, pulled_arms: {arm.pulled}"
)
print(
f"not_covered: {not_covered}, confidence_radius: {confidence_radius}"
)
if not_covered != P.empty():
rans = []
height = 0
heights = []
for i in not_covered:
rans.append(np.random.uniform(i.lower, i.upper))
height += i.upper - i.lower
heights.append(i.upper - i.lower)
ran_n = np.random.uniform(0, height)
j = 0
ran = 0
for i in range(len(heights)):
if j < ran_n < j + heights[i]:
ran = rans[i]
j += heights[i]
if debug_pricing:
ran = 0.1
new_arm = Arm(len(self.active_arms),
ran * (self.sigma_square - lower) + lower, ran)
self.active_arms.append(new_arm)
# self.pulled_arms.append(0)
# self.avg_rewards.append(0)
# Selection rule
max_index = float('-inf')
max_index_arm = None
for arm in self.active_arms:
confidence_radius = self.confidence_radius(i_ph, arm)
index = arm.avg_learning_reward + 2 * confidence_radius
if index > max_index:
max_index = index
max_index_arm = arm
action = max_index_arm.value
self.current_arm = max_index_arm
# self.current_action = action
# action = action * (self.sigma_square - lower) + lower
return action
def get(self, request, *args, **kwargs):
context = self.get_context_data(**kwargs)
dim = (24 - self.start_hour) * self.splits
m = np.zeros((7, dim))
for day in range(7):
time = P.empty()
tt = TeacherTime.objects.filter(teacher=request.user, day=day)
for t in tt:
time = time|P.closed(tools.to_min(t.start_time), tools.to_min(t.end_time))
print(time)
if time != P.empty():
for t in range(dim):
if P.closed(t*self.step+self.start_hour*60, (t+1)*self.step+self.start_hour*60) in time:
m[day, t] = 1
print(m.shape)
context["freetime"] = m.tolist()
return render(request, self.template_name, context)
def test_hash_with_hashable(self):
assert hash(P.closed(0, 1)) is not None
assert hash(P.closed(0, 1)) != hash(P.closed(1, 2))
assert hash(P.openclosed(-P.inf, 0)) is not None
assert hash(P.closedopen(0, P.inf)) is not None
assert hash(P.empty()) is not None
assert hash(P.closed(0, 1) | P.closed(3, 4)) is not None
assert hash(P.closed(0, 1) | P.closed(3, 4)) != hash(P.closed(0, 1))
assert hash(P.closed(0, 1) | P.closed(3, 4)) != hash(P.closed(3, 4))
def test_empty(self):
assert P.empty().adjacent(P.closed(0, 2))
assert P.empty().adjacent(P.empty())
assert P.closed(0, 2).adjacent(P.empty())
assert not P.empty().adjacent(P.closed(0, 1) | P.closed(2, 3))
assert not (P.closed(0, 1) | P.closed(2, 3)).adjacent(P.empty())
def test_replace_with_empty(self):
assert P.empty().replace(left=P.CLOSED, right=P.CLOSED) == P.empty()
assert P.empty().replace(lower=1, upper=2) == P.open(1, 2)
assert P.empty().replace(lower=lambda v: 1,
upper=lambda v: 2) == P.empty()
assert P.empty().replace(lower=lambda v: 1,
upper=lambda v: 2,
ignore_inf=False) == P.open(1, 2)
def get_free_teacher_time(teacher, day, raw=True):
tt = list(TeacherTime.objects.filter(day=day,
teacher=teacher).order_by("start_time").values_list("start_time", "end_time"))
t = P.empty()
for start_time, end_time in tt:
print(start_time)
t = t | P.closed(to_min(start_time), to_min(end_time))
ls = list(Lesson.objects.filter(teacher=teacher, day=day, active__gt=0).values_list("start_time", "end_time"))
for start_time, end_time in ls:
t = t - P.closed(to_min(start_time), to_min(end_time))
return list(t)
def post(self, request, *args, **kwargs):
step = self.step
start_hour = self.start_hour
TeacherTime.objects.filter(teacher=request.user).delete()
for day in range(7):
times = P.empty()
for time in range((24-self.start_hour)*self.step):
if request.POST.get("{}_{}".format(day, time), False):
times = times|P.closed(time, time+1)
if times!=P.empty():
for time in list(times):
print(time.lower, time.upper)
start_time = tools.to_time(time.lower, step, duration=start_hour*60)
end_time = tools.to_time(time.upper, step, duration=start_hour*60)
print(start_time, end_time)
tt = TeacherTime(teacher=request.user, day=day, start_time = start_time, end_time = end_time)
tt.save()
#duration = request.POST["day_{}".format(day)]
#LessonBook(day=day, duration=duration, user_id=request.user, )
return redirect(reverse('lms:choose_day'))
def choose_action(self, episode):
if episode == 1:
i_ph = 1
else:
i_ph = math.ceil(math.log2(episode))
if self.i_ph != i_ph:
self.active_arms = []
self.pulled_arms = []
self.avg_rewards = []
self.i_ph = i_ph
# Activation rule
not_covered = self.action_space
for arm in self.active_arms:
arm.confidence_radius = math.sqrt((8 * i_ph)/(1 + arm.pulled))
confidence_interval = P.closed(arm.value - arm.confidence_radius,
arm.value + arm.confidence_radius)
not_covered = not_covered - confidence_interval
if not_covered != P.empty():
rans = []
height = 0
heights = []
for i in not_covered:
rans.append(np.random.uniform(i.lower, i.upper))
height += i.upper - i.lower
heights.append(i.upper - i.lower)
ran_n = np.random.uniform(0, height)
j = 0
ran = 0
for i in range(len(heights)):
if j < ran_n < j + heights[i]:
ran = rans[i]
j += heights[i]
new_arm = Arm(len(self.active_arms), ran)
self.active_arms.append(new_arm)
# Selection rule
max_index = float('-inf')
max_index_arm = None
for arm in self.active_arms:
confidence_radius = arm.confidence_radius
index = arm.avg_reward + 2 * confidence_radius
if index > max_index:
max_index = index
max_index_arm = arm
self.current_arm = max_index_arm
return max_index_arm.value
def get_visits(self):
""" Method get visits for days from database and prepare time intervals """
first_day = datetime.combine(self.days[0], time.min)
last_day = datetime.combine(self.days[-1], time.max)
intervals = portion.empty()
visits = Visit.objects.filter(
~Q(is_confirmed=True, is_available=False)
& (Q(user=self.user, start__range=[first_day, last_day])
| Q(user=self.user, end__range=[first_day, last_day])))
for visit in visits:
intervals |= portion.closedopen(visit.start, visit.end)
return visits, intervals
def get_time_off_interval(self):
""" Method get visits for days from database and prepare time intervals """
first_day = datetime.combine(self.days[0], time.min)
last_day = datetime.combine(self.days[-1], time.max)
intervals = portion.empty()
times_off = TimeOff.objects.filter(
Q(user=self.user, start__range=[first_day, last_day])
| Q(user=self.user, end__range=[first_day, last_day]))
for time_off in times_off:
intervals |= portion.closedopen(time_off.start, time_off.end)
return intervals
def test_bounds_on_empty(self):
i = P.empty()
assert i.left == P.OPEN
assert i.right == P.OPEN
assert i.lower == P.inf
assert i.upper == -P.inf
i = P.openclosed(10, -10)
assert i.left == P.OPEN
assert i.right == P.OPEN
assert i.lower == P.inf
assert i.upper == -P.inf
i = P.open(0, 1) | P.closed(3, 4)
assert i.left == P.OPEN
assert i.right == P.CLOSED
assert i.lower == 0
assert i.upper == 4
class TestIntervalDifference:
@pytest.mark.parametrize('i', [
P.closed(0, 1),
P.open(0, 1),
P.openclosed(0, 1),
P.closedopen(0, 1),
P.empty(),
P.singleton(0)
])
def test_with_itself(self, i):
assert i - i == P.empty()
def test_with_disjoint(self):
assert P.closed(0, 1) - P.closed(2, 3) == P.closed(0, 1)
assert P.closed(0, 4) - P.empty() == P.closed(0, 4)
assert P.empty() - P.closed(0, 4) == P.empty()
def test_with_smaller(self):
assert P.closed(0, 4) - P.closed(2, 3) == P.closedopen(
0, 2) | P.openclosed(3, 4)
assert P.closed(1, 4) - P.closed(1, 3) == P.openclosed(3, 4)
assert P.closed(1, 4) - P.closed(2, 4) == P.closedopen(1, 2)
assert P.closed(0, 4) - P.open(1, 2) == P.closed(0, 1) | P.closed(2, 4)
assert P.closed(0, 2) - P.open(0, 2) == P.singleton(0) | P.singleton(2)
def test_with_larger(self):
assert P.closed(0, 2) - P.closed(0, 4) == P.empty()
assert P.closed(0, 2) - P.closed(-2, 2) == P.empty()
assert P.closed(0, 2) - P.closed(-2, 4) == P.empty()
assert P.open(0, 2) - P.closed(0, 2) == P.empty()
def test_with_overlap(self):
assert P.closed(0, 2) - P.closed(1, 3) == P.closedopen(0, 1)
assert P.closed(0, 2) - P.open(1, 3) == P.closed(0, 1)
assert P.closed(0, 2) - P.closed(-2, 1) == P.openclosed(1, 2)
assert P.closed(0, 2) - P.open(-2, 1) == P.closed(1, 2)
def test_proxy_method(self):
i1, i2 = P.closed(0, 1), P.closed(2, 3)
assert i1 - i2 == i1.difference(i2)
def test_with_invalid_type(self):
with pytest.raises(TypeError):
P.closed(0, 1) - 1
def get_stereotype_ratio(self):
'''
Calculate stereotype ratio for the underlying ReferencedSequence.
Stereotype ratio is the fraction of sequence elements presented as
entries of some repetitive pattern. E.g., consider the following case:
`seq` = [a, b (->1), c (->0), d]. Element 'b' is included into pattern
referring to 'b' elem, and 'c' is the part of pattern referring to 'a'.
Thus, 'a', 'b' and 'c' relate to some patterns while 'd' does not.
So, ratio here is 3/4.
'''
refs = self.content['refs']
patterned_area = P.empty()
for i in range(len(refs)):
for ref in refs[i]:
patterned_area |= P.closed(*sorted([i, ref]))
indices = list(P.iterate(patterned_area, step=1))
return len(indices) / len(refs)
def create_interval_dict_linear_time(gene, isoform_interval_dict):
interval_set = set(isoform_interval_dict.keys())
d = P.IntervalDict()
union = P.empty()
for transcript, inter in isoform_interval_dict.items():
union = union | inter
power_set_coords_dict = {}
for p in P.iterate(union, step=1):
s = list()
for transcript, inter in isoform_interval_dict.items():
if p in inter:
s.append(transcript)
s = repr(s)
if s in power_set_coords_dict:
power_set_coords_dict[s].append(p)
else:
power_set_coords_dict[s] = [p]
for s, coords in power_set_coords_dict.items():
d[interval(intervals_extract(coords))] = set(eval(s))
return gene, d
def get_work_time_interval(self):
intervals = portion.empty()
holidays_work = UserSettings.objects.get(user=self.user).holidays
for day in self.days:
if not self.is_holiday(day) or holidays_work:
day_number = day.weekday()
work_time = WorkTime.objects.filter(user=self.user,
day_of_week=day_number)
if work_time:
for work_hours in work_time:
day_datetime = datetime.combine(day, time.min)
work_hours.start = day_datetime + work_hours.start
work_hours.end = day_datetime + work_hours.end
intervals |= portion.closedopen(
work_hours.start, work_hours.end)
return intervals
def get(self, request, *args, **kwargs):
context = self.get_context_data(**kwargs)
teacher = User.objects.get(id=self.kwargs['id'])
t_all = []
week = ["Пн", "Вт", "Ср", "Чт", "Пт", "Cб", "Вс"]
my_week = []
for day in range(7):
t = tools.get_free_teacher_time(teacher, day)
if t[0]!=P.empty():
t_all.append([tools.min_to_time(el.lower), tools.min_to_time(el.upper)] for el in t)
my_week.append((day, week[day]))
else:
t_all.append(())
context["times"] = t_all
context["week"] = my_week
context["teacher"] = teacher
return render(request, self.template_name, context)
def get_time_steps(self):
""" Method return list of quarters of hours to display in schedule. """
times = []
if self.time_range == 'full':
times.append(timedelta(seconds=0))
times.append(timedelta(hours=24))
else:
for day in self.days[1:-1]:
datetime_day = datetime.combine(day, time.min)
day_interval = portion.closedopen(
datetime_day, datetime_day + timedelta(days=1))
on_intervals = day_interval & self.work_interval - self.time_off_interval
if on_intervals != portion.empty():
for on_interval in on_intervals:
times.append(on_interval.lower -
datetime.combine(day, time.min))
times.append(on_interval.upper -
datetime.combine(day, time.min))
if self.time_range == 'extra':
for visit in self.visits:
if visit.start in day_interval:
times.append(visit.start - datetime_day)
if visit.end in day_interval:
times.append(visit.end - datetime_day)
if times:
start_time = min(times)
end_time = max(times)
else:
start_time = timedelta(hours=8)
end_time = timedelta(hours=16)
time_steps = self.generate_time_steps(start_time, end_time)
return time_steps, start_time, end_time
def get_visits_per_day(self):
visits_per_days = []
for day in self.days[1:-1]:
visits_per_day = []
dt_day = datetime.combine(day, time.min)
day_interval = portion.closedopen(dt_day + self.start_day,
dt_day + self.end_day)
for visit in self.visits:
visit_interval = portion.closedopen(visit.start,
visit.end) & day_interval
if visit_interval != portion.empty():
day_visit = deepcopy(visit)
day_visit.start = visit_interval.lower
day_visit.end = visit_interval.upper
visits_per_day.append(day_visit)
visits_per_days.append(visits_per_day)
return visits_per_days
def get_portions_from_intervals(intervals: List[int]) -> portion.interval.Interval:
p = portion.empty()
for x in range(len(intervals) // 2):
p |= portion.closed(*(intervals[x * 2:x * 2 + 2]))
return p
default=1,
help='Number of threads')
args = parser.parse_args()
gtffile = args.gtf
dbfile = args.db
jsonfile = args.json
threads = int(args.threads)
print('Creating gtf database, this will take some time...')
db = gffutils.create_db(gtffile, dbfile)
isoform_interval_dict = {}
for gene in db.features_of_type('gene'):
g_id = gene['gene_id'][0]
isoform_interval_dict[g_id] = {}
for transcript in db.children(gene, featuretype='transcript'):
t_id = transcript['transcript_id'][0]
isoform_interval_dict[g_id][t_id] = P.empty()
for exon in db.children(transcript, featuretype='exon'):
isoform_interval_dict[g_id][
t_id] = isoform_interval_dict[g_id][t_id] | P.closed(
exon.start, exon.end)
print('Extracting unque isoform intervals')
res = Parallel(n_jobs=threads, verbose=3, backend='loky')(
delayed(create_interval_dict_linear_time)(gene, transcript_intervals)
for gene, transcript_intervals in isoform_interval_dict.items())
isoform_unique_intervals = {k: v for k, v in res}
isoform_unique_intervals_for_json_dump = {
gene: {P.to_string(k): ','.join(v)
for k, v in d.items()}
for gene, d in isoform_unique_intervals.items()
}
print('Writing unique isoform intervals to json file {}'.format(jsonfile))