def setup(self):
system = WESTSystem()
system.bin_mapper = RectilinearBinMapper([[0.0, 1.0, 2.0]])
system.bin_target_counts = numpy.array([4, 4])
system.pcoord_len = 2
self.we_driver = WEDriver(system=system)
self.system = system
self._seg_id = 0
def test_merge_by_weight(self):
selected_counts = {0: 0, 1: 0}
alpha = 0.01
nrounds = 1000
from scipy.stats import binom
# lower and upper bounds of 95% CI for selecting the segment with weight 1/3
lb = binom.ppf(alpha / 2.0, nrounds, 1.0 / 3.0)
ub = binom.ppf(1.0 - alpha / 2.0, nrounds, 1.0 / 3.0)
system = WESTSystem()
system.bin_mapper = RectilinearBinMapper([[0.0, 1.0]])
system.bin_target_counts = numpy.array([1])
system.pcoord_len = 2
self.we_driver = WEDriver(system=system)
self.system = system
self._seg_id = 0
segments = [
Segment(n_iter=1,
seg_id=0,
pcoord=numpy.array([[0], [0.25]], dtype=numpy.float32),
weight=1.0 / 3.0),
Segment(n_iter=1,
seg_id=1,
pcoord=numpy.array([[0], [0.75]], dtype=numpy.float32),
weight=2.0 / 3.0)
]
for _iround in xrange(nrounds):
for segment in segments:
segment.endpoint_type = Segment.SEG_ENDPOINT_UNSET
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 1
newseg = self.we_driver.next_iter_binning[0].pop()
assert segments[
newseg.
parent_id].endpoint_type == Segment.SEG_ENDPOINT_CONTINUES
assert segments[
~newseg.parent_id].endpoint_type == Segment.SEG_ENDPOINT_MERGED
selected_counts[newseg.parent_id] += 1
print(selected_counts)
assert lb <= selected_counts[0] <= ub, (
'Incorrect proportion of histories selected.'
'this is expected about {:%} of the time; retry test.'.format(
alpha))
def setup(self):
system = WESTSystem()
system.bin_mapper = RectilinearBinMapper([[0.0, 1.0, 2.0]])
system.bin_target_counts = numpy.array([4,4])
system.pcoord_len = 2
self.we_driver = WEDriver(system=system)
self.system = system
self._seg_id = 0
def test_merge_by_weight(self):
selected_counts = {0: 0, 1: 0}
alpha = 0.01
nrounds = 1000
from scipy.stats import binom
# lower and upper bounds of 95% CI for selecting the segment with weight 1/3
lb = binom.ppf(alpha/2.0, nrounds, 1.0/3.0)
ub = binom.ppf(1.0-alpha/2.0, nrounds, 1.0/3.0)
system = WESTSystem()
system.bin_mapper = RectilinearBinMapper([[0.0, 1.0]])
system.bin_target_counts = numpy.array([1])
system.pcoord_len = 2
self.we_driver = WEDriver(system=system)
self.system = system
self._seg_id = 0
segments = [Segment(n_iter=1, seg_id=0, pcoord=numpy.array([[0],[0.25]], dtype=numpy.float32),weight=1.0/3.0),
Segment(n_iter=1, seg_id=1, pcoord=numpy.array([[0],[0.75]], dtype=numpy.float32),weight=2.0/3.0)]
for _iround in xrange(nrounds):
for segment in segments:
segment.endpoint_type = Segment.SEG_ENDPOINT_UNSET
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 1
newseg = self.we_driver.next_iter_binning[0].pop()
assert segments[newseg.parent_id].endpoint_type == Segment.SEG_ENDPOINT_CONTINUES
assert segments[~newseg.parent_id].endpoint_type == Segment.SEG_ENDPOINT_MERGED
selected_counts[newseg.parent_id] += 1
print(selected_counts)
assert lb <= selected_counts[0] <= ub, ('Incorrect proportion of histories selected.'
'this is expected about {:%} of the time; retry test.'.format(alpha))
class TestWEDriver:
def setup(self):
system = WESTSystem()
system.bin_mapper = RectilinearBinMapper([[0.0, 1.0, 2.0]])
system.bin_target_counts = numpy.array([4, 4])
system.pcoord_len = 2
self.we_driver = WEDriver(system=system)
self.system = system
self._seg_id = 0
def segment(self, init_pcoord, final_pcoord, weight=1.0):
segment = Segment(n_iter=1,
seg_id=self._seg_id,
pcoord=self.system.new_pcoord_array(),
weight=weight)
segment.pcoord[0] = init_pcoord
segment.pcoord[1] = final_pcoord
self._seg_id += 1
return segment
def teardown(self):
self.we_driver.clear()
del self.we_driver
del self.system
del self._seg_id
def test_assign(self):
segments = [
self.segment(0.0, 1.5, weight=0.5),
self.segment(1.5, 0.5, weight=0.5)
]
self.we_driver.new_iteration()
n_recycled = self.we_driver.assign(segments)
assert n_recycled == 0
assert len(self.we_driver.initial_binning[0]) == 1
assert len(self.we_driver.initial_binning[1]) == 1
assert len(self.we_driver.final_binning[0]) == 1
assert len(self.we_driver.final_binning[1]) == 1
assert (self.we_driver.flux_matrix == numpy.array([[0.0, 0.5],
[0.5, 0.0]])).all()
def test_passthrough(self):
segments = ([self.segment(0.0, 1.5, weight=0.125)
for _i in xrange(4)] +
[self.segment(1.5, 0.5, weight=0.125) for _i in xrange(4)])
segs_by_id = {segment.seg_id: segment for segment in segments}
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
out_segs = set()
for bin in self.we_driver.next_iter_binning:
out_segs.update(bin)
assert out_segs == set(self.we_driver.next_iter_segments)
assert abs(
sum(seg.weight
for seg in self.we_driver.next_iter_segments) - 1.0) < 8 * EPS
for segment in self.we_driver.next_iter_segments:
# has n_iter been advanced?
assert segment.n_iter == 2
# is weight correct?
assert segment.weight == 0.125 #rigorous floating point comparison okay here because no math was done
# is parent set correctly?
assert segment.parent_id is not None
# was pcoord set correctly?
assert (segs_by_id[segment.parent_id].pcoord[-1] ==
segment.pcoord[0]).all()
# was status set correctly?
assert segment.status == Segment.SEG_STATUS_PREPARED
# were parent endpoint types set correctly
for segment in segments:
assert segment.endpoint_type == Segment.SEG_ENDPOINT_CONTINUES
def test_split_by_weight(self):
segments = [
self.segment(1.5, 0.5, weight=0.25),
self.segment(0.0, 1.5, weight=0.75)
]
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 4
assert len(self.we_driver.next_iter_binning[1]) == 4
assert abs(
sum(seg.weight for seg in self.we_driver.next_iter_binning[0]) -
0.25) < 4 * EPS
assert abs(
sum(seg.weight for seg in self.we_driver.next_iter_binning[1]) -
0.75) < 4 * EPS
assert numpy.allclose(
[seg.weight for seg in self.we_driver.next_iter_binning[0]],
[0.25 / 4.0 for _i in xrange(4)])
assert numpy.allclose(
[seg.weight for seg in self.we_driver.next_iter_binning[1]],
[0.75 / 4.0 for _i in xrange(4)])
for ibin in xrange(2):
for segment in self.we_driver.next_iter_binning[ibin]:
print(segment)
assert segment.n_iter == 2
assert segment.parent_id is not None
assert segment.parent_id == segments[ibin].seg_id
assert segment.status == Segment.SEG_STATUS_PREPARED
# this test will fail up to alpha of the time
def test_merge_by_weight(self):
selected_counts = {0: 0, 1: 0}
alpha = 0.01
nrounds = 1000
from scipy.stats import binom
# lower and upper bounds of 95% CI for selecting the segment with weight 1/3
lb = binom.ppf(alpha / 2.0, nrounds, 1.0 / 3.0)
ub = binom.ppf(1.0 - alpha / 2.0, nrounds, 1.0 / 3.0)
system = WESTSystem()
system.bin_mapper = RectilinearBinMapper([[0.0, 1.0]])
system.bin_target_counts = numpy.array([1])
system.pcoord_len = 2
self.we_driver = WEDriver(system=system)
self.system = system
self._seg_id = 0
segments = [
Segment(n_iter=1,
seg_id=0,
pcoord=numpy.array([[0], [0.25]], dtype=numpy.float32),
weight=1.0 / 3.0),
Segment(n_iter=1,
seg_id=1,
pcoord=numpy.array([[0], [0.75]], dtype=numpy.float32),
weight=2.0 / 3.0)
]
for _iround in xrange(nrounds):
for segment in segments:
segment.endpoint_type = Segment.SEG_ENDPOINT_UNSET
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 1
newseg = self.we_driver.next_iter_binning[0].pop()
assert segments[
newseg.
parent_id].endpoint_type == Segment.SEG_ENDPOINT_CONTINUES
assert segments[
~newseg.parent_id].endpoint_type == Segment.SEG_ENDPOINT_MERGED
selected_counts[newseg.parent_id] += 1
print(selected_counts)
assert lb <= selected_counts[0] <= ub, (
'Incorrect proportion of histories selected.'
'this is expected about {:%} of the time; retry test.'.format(
alpha))
def test_split_with_adjust(self):
# this is a split followed by merge
self.system.bin_target_counts = numpy.array([5, 5])
segments = [
self.segment(1.5, 0.5, weight=0.125),
self.segment(1.5, 0.5, weight=0.125),
self.segment(0.0, 1.5, weight=0.375),
self.segment(0.0, 1.5, weight=0.375)
]
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 5
assert len(self.we_driver.next_iter_binning[1]) == 5
assert abs(
sum(seg.weight for seg in self.we_driver.next_iter_binning[0]) -
0.25) < 5 * EPS
assert abs(
sum(seg.weight for seg in self.we_driver.next_iter_binning[1]) -
0.75) < 5 * EPS
for ibin in xrange(2):
for segment in self.we_driver.next_iter_binning[ibin]:
print(segment)
assert segment.n_iter == 2
assert segment.parent_id is not None
assert segment.status == Segment.SEG_STATUS_PREPARED
def test_split_with_adjust_istates(self):
# this is a split followed by merge, for segments which are initial states
self.system.bin_target_counts = numpy.array([5, 5])
segments = [
self.segment(1.5, 0.5, weight=0.125),
self.segment(1.5, 0.5, weight=0.125),
self.segment(0.0, 1.5, weight=0.375),
self.segment(0.0, 1.5, weight=0.375)
]
self.we_driver.new_iteration()
self.we_driver._prep_we()
self.we_driver.used_initial_states[-1] = None
self.we_driver.used_initial_states[-2] = None
for ibin, bin in enumerate(self.we_driver.next_iter_binning):
pc = numpy.array([[0.5 + ibin], [0.0]])
for iseg in xrange(6):
segment = Segment(n_iter=1,
seg_id=None,
weight=1.0 / 12.0,
parent_id=-(ibin + 1),
pcoord=pc)
bin.add(segment)
for ibin in xrange(len(self.we_driver.next_iter_binning)):
# This will raise KeyError if initial state tracking is done improperly
self.we_driver._adjust_count(ibin)
assert len(self.we_driver.next_iter_binning[0]) == 5
assert len(self.we_driver.next_iter_binning[1]) == 5
def test_recycle(self):
segments = [
self.segment(0.0, 1.5, weight=0.5),
self.segment(0.0, 0.5, weight=0.5)
]
tstate = TargetState('recycle', [1.5], 0)
istate = InitialState(0, 0, 0, pcoord=[0.0])
self.we_driver.new_iteration(initial_states=[istate],
target_states=[tstate])
n_needed = self.we_driver.assign(segments)
assert n_needed == 0
self.we_driver.construct_next()
n_recycled = len(list(self.we_driver.recycling_segments))
assert n_recycled == 1
assert len(self.we_driver.next_iter_binning[0]) == 4
assert len(self.we_driver.next_iter_binning[1]) == 0
assert abs(
sum(seg.weight for seg in self.we_driver.next_iter_binning[0]) -
1.0) < 4 * EPS
assert numpy.allclose(
[seg.weight for seg in self.we_driver.next_iter_binning[0]],
[0.25 for _i in xrange(4)])
assert segments[0].endpoint_type == Segment.SEG_ENDPOINT_RECYCLED
def test_multiple_merge(self):
# This weight and count combination is known to trigger a split to 51
# followed by a count adjustment to 50 (thanks to Josh Adelman)
segment = self.segment(0.0, 0.5, weight=0.9999999999970001)
# Initial state ID 0
segment.parent_id = -1
segment.wtg_parent_ids = set([-1])
assert segment.initpoint_type == segment.SEG_INITPOINT_NEWTRAJ
self.system.bin_target_counts = numpy.array([50, 50])
self.we_driver.new_iteration()
self.we_driver.assign([segment])
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 50
def check_populate_initial(self, prob, target_counts):
istate = InitialState(0, 0, 0, pcoord=[0.0])
self.system.bin_target_counts = numpy.array(
[target_counts, target_counts])
self.we_driver.populate_initial([istate], [prob], system=self.system)
assert len(self.we_driver.next_iter_binning[0]) == target_counts
@nose.SkipTest
def test_populate_initial(self):
for prob in [0.1, 1.0 / 3.0, 0.9999999999970001, 1.0]:
for tcount in xrange(30, 60):
yield self.check_populate_initial, prob, tcount
class TestWEDriver:
def setup(self):
system = WESTSystem()
system.bin_mapper = RectilinearBinMapper([[0.0, 1.0, 2.0]])
system.bin_target_counts = numpy.array([4,4])
system.pcoord_len = 2
self.we_driver = WEDriver(system=system)
self.system = system
self._seg_id = 0
def segment(self, init_pcoord, final_pcoord, weight=1.0):
segment= Segment(n_iter=1, seg_id=self._seg_id,
pcoord=self.system.new_pcoord_array(),
weight=weight)
segment.pcoord[0] = init_pcoord
segment.pcoord[1] = final_pcoord
self._seg_id += 1
return segment
def teardown(self):
self.we_driver.clear()
del self.we_driver
del self.system
del self._seg_id
def test_assign(self):
segments = [self.segment(0.0, 1.5, weight=0.5),
self.segment(1.5, 0.5, weight=0.5)]
self.we_driver.new_iteration()
n_recycled = self.we_driver.assign(segments)
assert n_recycled == 0
assert len(self.we_driver.initial_binning[0]) == 1
assert len(self.we_driver.initial_binning[1]) == 1
assert len(self.we_driver.final_binning[0]) == 1
assert len(self.we_driver.final_binning[1]) == 1
assert (self.we_driver.flux_matrix == numpy.array([[0.0, 0.5], [0.5,0.0]])).all()
def test_passthrough(self):
segments = ([self.segment(0.0, 1.5, weight=0.125) for _i in xrange(4)]
+[self.segment(1.5, 0.5, weight=0.125) for _i in xrange(4)])
segs_by_id = {segment.seg_id: segment for segment in segments}
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
out_segs = set()
for bin in self.we_driver.next_iter_binning:
out_segs.update(bin)
assert out_segs == set(self.we_driver.next_iter_segments)
assert abs(sum(seg.weight for seg in self.we_driver.next_iter_segments) - 1.0) < 8*EPS
for segment in self.we_driver.next_iter_segments:
# has n_iter been advanced?
assert segment.n_iter == 2
# is weight correct?
assert segment.weight == 0.125 #rigorous floating point comparison okay here because no math was done
# is parent set correctly?
assert segment.parent_id is not None
# was pcoord set correctly?
assert (segs_by_id[segment.parent_id].pcoord[-1] == segment.pcoord[0]).all()
# was status set correctly?
assert segment.status == Segment.SEG_STATUS_PREPARED
# were parent endpoint types set correctly
for segment in segments:
assert segment.endpoint_type == Segment.SEG_ENDPOINT_CONTINUES
def test_split_by_weight(self):
segments = [self.segment(1.5, 0.5, weight=0.25),
self.segment(0.0, 1.5, weight=0.75)]
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 4
assert len(self.we_driver.next_iter_binning[1]) == 4
assert abs(sum(seg.weight for seg in self.we_driver.next_iter_binning[0]) - 0.25) < 4*EPS
assert abs(sum(seg.weight for seg in self.we_driver.next_iter_binning[1]) - 0.75) < 4*EPS
assert numpy.allclose([seg.weight for seg in self.we_driver.next_iter_binning[0]],
[0.25/4.0 for _i in xrange(4)])
assert numpy.allclose([seg.weight for seg in self.we_driver.next_iter_binning[1]],
[0.75/4.0 for _i in xrange(4)])
for ibin in xrange(2):
for segment in self.we_driver.next_iter_binning[ibin]:
print(segment)
assert segment.n_iter == 2
assert segment.parent_id is not None
assert segment.parent_id == segments[ibin].seg_id
assert segment.status == Segment.SEG_STATUS_PREPARED
# this test will fail up to alpha of the time
def test_merge_by_weight(self):
selected_counts = {0: 0, 1: 0}
alpha = 0.01
nrounds = 1000
from scipy.stats import binom
# lower and upper bounds of 95% CI for selecting the segment with weight 1/3
lb = binom.ppf(alpha/2.0, nrounds, 1.0/3.0)
ub = binom.ppf(1.0-alpha/2.0, nrounds, 1.0/3.0)
system = WESTSystem()
system.bin_mapper = RectilinearBinMapper([[0.0, 1.0]])
system.bin_target_counts = numpy.array([1])
system.pcoord_len = 2
self.we_driver = WEDriver(system=system)
self.system = system
self._seg_id = 0
segments = [Segment(n_iter=1, seg_id=0, pcoord=numpy.array([[0],[0.25]], dtype=numpy.float32),weight=1.0/3.0),
Segment(n_iter=1, seg_id=1, pcoord=numpy.array([[0],[0.75]], dtype=numpy.float32),weight=2.0/3.0)]
for _iround in xrange(nrounds):
for segment in segments:
segment.endpoint_type = Segment.SEG_ENDPOINT_UNSET
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 1
newseg = self.we_driver.next_iter_binning[0].pop()
assert segments[newseg.parent_id].endpoint_type == Segment.SEG_ENDPOINT_CONTINUES
assert segments[~newseg.parent_id].endpoint_type == Segment.SEG_ENDPOINT_MERGED
selected_counts[newseg.parent_id] += 1
print(selected_counts)
assert lb <= selected_counts[0] <= ub, ('Incorrect proportion of histories selected.'
'this is expected about {:%} of the time; retry test.'.format(alpha))
def test_split_with_adjust(self):
# this is a split followed by merge
self.system.bin_target_counts = numpy.array([5,5])
segments = [self.segment(1.5, 0.5, weight=0.125), self.segment(1.5, 0.5, weight=0.125),
self.segment(0.0, 1.5, weight=0.375), self.segment(0.0, 1.5, weight=0.375)]
self.we_driver.new_iteration()
self.we_driver.assign(segments)
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 5
assert len(self.we_driver.next_iter_binning[1]) == 5
assert abs(sum(seg.weight for seg in self.we_driver.next_iter_binning[0]) - 0.25) < 5*EPS
assert abs(sum(seg.weight for seg in self.we_driver.next_iter_binning[1]) - 0.75) < 5*EPS
for ibin in xrange(2):
for segment in self.we_driver.next_iter_binning[ibin]:
print(segment)
assert segment.n_iter == 2
assert segment.parent_id is not None
assert segment.status == Segment.SEG_STATUS_PREPARED
def test_split_with_adjust_istates(self):
# this is a split followed by merge, for segments which are initial states
self.system.bin_target_counts = numpy.array([5,5])
segments = [self.segment(1.5, 0.5, weight=0.125), self.segment(1.5, 0.5, weight=0.125),
self.segment(0.0, 1.5, weight=0.375), self.segment(0.0, 1.5, weight=0.375)]
self.we_driver.new_iteration()
self.we_driver._prep_we()
self.we_driver.used_initial_states[-1] = None
self.we_driver.used_initial_states[-2] = None
for ibin,bin in enumerate(self.we_driver.next_iter_binning):
pc = numpy.array([[0.5+ibin],[0.0]])
for iseg in xrange(6):
segment = Segment(n_iter=1, seg_id=None, weight=1.0/12.0,
parent_id=-(ibin+1), pcoord=pc)
bin.add(segment)
for ibin in xrange(len(self.we_driver.next_iter_binning)):
# This will raise KeyError if initial state tracking is done improperly
self.we_driver._adjust_count(ibin)
assert len(self.we_driver.next_iter_binning[0]) == 5
assert len(self.we_driver.next_iter_binning[1]) == 5
def test_recycle(self):
segments = [self.segment(0.0, 1.5, weight=0.5),
self.segment(0.0, 0.5, weight=0.5)]
tstate = TargetState('recycle', [1.5], 0)
istate = InitialState(0, 0, 0, pcoord=[0.0])
self.we_driver.new_iteration(initial_states=[istate], target_states=[tstate])
n_needed = self.we_driver.assign(segments)
assert n_needed == 0
self.we_driver.construct_next()
n_recycled = len(list(self.we_driver.recycling_segments))
assert n_recycled == 1
assert len(self.we_driver.next_iter_binning[0]) == 4
assert len(self.we_driver.next_iter_binning[1]) == 0
assert abs(sum(seg.weight for seg in self.we_driver.next_iter_binning[0]) - 1.0) < 4*EPS
assert numpy.allclose([seg.weight for seg in self.we_driver.next_iter_binning[0]],
[0.25 for _i in xrange(4)])
assert segments[0].endpoint_type == Segment.SEG_ENDPOINT_RECYCLED
def test_multiple_merge(self):
# This weight and count combination is known to trigger a split to 51
# followed by a count adjustment to 50 (thanks to Josh Adelman)
segment = self.segment(0.0, 0.5, weight=0.9999999999970001)
# Initial state ID 0
segment.parent_id = -1
segment.wtg_parent_ids = set([-1])
assert segment.initpoint_type == segment.SEG_INITPOINT_NEWTRAJ
self.system.bin_target_counts = numpy.array([50,50])
self.we_driver.new_iteration()
self.we_driver.assign([segment])
self.we_driver.construct_next()
assert len(self.we_driver.next_iter_binning[0]) == 50
def check_populate_initial(self, prob, target_counts):
istate = InitialState(0, 0, 0, pcoord=[0.0])
self.system.bin_target_counts = numpy.array([target_counts, target_counts])
self.we_driver.populate_initial([istate], [prob], system=self.system)
assert len(self.we_driver.next_iter_binning[0]) == target_counts
@nose.SkipTest
def test_populate_initial(self):
for prob in [0.1, 1.0 / 3.0, 0.9999999999970001, 1.0]:
for tcount in xrange(30, 60):
yield self.check_populate_initial, prob, tcount