def test_with_mask_groups(self):
nbins = 100
nsets = 10
data = numpy.random.normal(size=(nsets, nbins))
mask = numpy.random.randint(2, size=data.shape).astype(numpy.uint8)
rate_stats1 = StreamingStats1D(nbins)
for di, d in enumerate(data[:(nbins / 2)]):
rate_stats1.update(d, mask[di])
rate_stats2 = StreamingStats1D(nbins)
for di, d in enumerate(data[(nbins / 2):]):
rate_stats2.update(d, mask[di])
rate_stats3 = rate_stats1 + rate_stats2
rate_stats1 += rate_stats2
data_masked = numpy.ma.array(data, mask=mask)
assert numpy.allclose(rate_stats1.mean,
data_masked.mean(axis=0).filled(fill_value=0.0))
assert numpy.allclose(rate_stats1.var,
data_masked.var(axis=0).filled(fill_value=0.0))
assert numpy.allclose(rate_stats3.mean,
data_masked.mean(axis=0).filled(fill_value=0.0))
assert numpy.allclose(rate_stats3.var,
data_masked.var(axis=0).filled(fill_value=0.0))
def test_nomask(self):
nbins = 100
nsets = 10
data = numpy.random.normal(size=(nsets, nbins))
mask = numpy.zeros((nbins,), numpy.uint8)
rate_stats = StreamingStats1D(nbins)
for d in data:
rate_stats.update(d, mask)
assert numpy.allclose(rate_stats.mean, data.mean(axis=0))
assert numpy.allclose(rate_stats.var, data.var(axis=0,))
def test_nomask_groups(self):
nbins = 100
nsets = 10
data = numpy.random.normal(size=(nsets, nbins))
mask = numpy.zeros((nbins,), numpy.uint8)
rate_stats1 = StreamingStats1D(nbins)
for d in data[:(nbins/2)]:
rate_stats1.update(d, mask)
rate_stats2 = StreamingStats1D(nbins)
for d in data[(nbins/2):]:
rate_stats2.update(d, mask)
rate_stats3 = rate_stats1 + rate_stats2
rate_stats1 += rate_stats2
assert numpy.allclose(rate_stats1.mean, data.mean(axis=0))
assert numpy.allclose(rate_stats1.var, data.var(axis=0,))
assert numpy.allclose(rate_stats3.mean, data.mean(axis=0))
assert numpy.allclose(rate_stats3.var, data.var(axis=0,))
def calculate(self, iter_start=None, iter_stop=None, n_blocks=1, queue_size=1):
'''Read the HDF5 file and collect flux matrices and population vectors
for each bin for each iteration in the range [iter_start, iter_stop). Break
the calculation into n_blocks blocks. If the calculation is broken up into
more than one block, queue_size specifies the maxmimum number of tasks in
the work queue.'''
iter_start = iter_start or 1
iter_stop = iter_stop or self.data_manager.current_iteration
itercount = iter_stop - iter_start
block_size = max(1, itercount // n_blocks)
nbins = self.bin_mapper.nbins
if n_blocks == 1:
flux_stats_t, rate_stats_t, population_stats_t = process_iter_chunk(self.bin_mapper, range(iter_start, iter_stop))
flux_stats = tuple2stats(flux_stats_t)
rate_stats = tuple2stats(rate_stats_t)
population_stats = tuple2stats(population_stats_t)
else:
flux_stats = StreamingStats2D((nbins, nbins))
rate_stats = StreamingStats2D((nbins, nbins))
population_stats = StreamingStats1D(nbins)
task_generator = self.task_generator(iter_start, iter_stop, block_size)
for future in self.work_manager.submit_as_completed(task_generator, queue_size):
chunk_flux_stats_t, chunk_rate_stats_t, chunk_pop_stats_t = future.get_result()
chunk_flux_stats = tuple2stats(chunk_flux_stats_t)
chunk_rate_stats = tuple2stats(chunk_rate_stats_t)
chunk_pop_stats = tuple2stats(chunk_pop_stats_t)
# Update statistics with chunked subsets
flux_stats += chunk_flux_stats
rate_stats += chunk_rate_stats
population_stats += chunk_pop_stats
self.average_flux = flux_stats.mean
self.stderr_flux = numpy.nan_to_num(numpy.sqrt(flux_stats.var) / flux_stats.n)
self.average_populations = population_stats.mean
self.stderr_populations = numpy.nan_to_num(numpy.sqrt(population_stats.var) / population_stats.n)
self.average_rate = rate_stats.mean
self.stderr_rate = numpy.nan_to_num(numpy.sqrt(rate_stats.var) / rate_stats.n)
assert ~numpy.any(numpy.isinf(self.stderr_flux))
assert ~numpy.any(numpy.isinf(self.stderr_rate))
assert ~numpy.any(numpy.isinf(self.stderr_populations))
def tuple2stats(stat_tuple):
ndims = stat_tuple.M1.ndim
assert ndims == 1 or ndims == 2
if ndims == 2:
stats = StreamingStats2D(stat_tuple.M1.shape)
elif ndims == 1:
stats = StreamingStats1D(stat_tuple.M1.shape[0])
else:
raise ValueError
stats.M1 = stat_tuple.M1
stats.M2 = stat_tuple.M2
stats.n = stat_tuple.n
return stats
def test_tuple2stats1D(self):
StreamingStatsTuple = namedtuple('StreamingStatsTuple', ['M1', 'M2', 'n'])
nbins = 100
nsets = 10
data = numpy.random.normal(size=(nsets, nbins))
mask = numpy.zeros((nbins,), numpy.uint8)
rate_stats = StreamingStats1D(nbins)
for d in data:
rate_stats.update(d, mask)
c_rate_stats = StreamingStatsTuple(rate_stats.M1, rate_stats.M2, rate_stats.n)
rate_stats2 = tuple2stats(c_rate_stats)
assert numpy.allclose(rate_stats.M1, rate_stats2.M1)
assert numpy.allclose(rate_stats.M2, rate_stats2.M2)
assert numpy.allclose(rate_stats.n, rate_stats2.n)
assert numpy.allclose(rate_stats.mean, rate_stats2.mean)
assert numpy.allclose(rate_stats.var, rate_stats2.var)
def process_iter_chunk(bin_mapper, iter_indices, iter_data=None):
'''Calculate the flux matrices and populations of a set of iterations specified
by iter_indices. Optionally provide the necessary arrays to perform the calculation
in iter_data. Otherwise get data from the data_manager directly.
'''
data_manager = westpa.rc.get_data_manager()
system = westpa.rc.get_system_driver()
itercount = len(iter_indices)
nbins = bin_mapper.nbins
flux_stats = StreamingStats2D((nbins, nbins))
rate_stats = StreamingStats2D((nbins, nbins))
pop_stats = StreamingStats1D(nbins)
nomask1d = numpy.zeros((nbins, ), numpy.uint8)
nomask2d = numpy.zeros((nbins, nbins), numpy.uint8)
rate_mask = numpy.zeros((nbins, nbins), numpy.uint8)
flux_matrix = numpy.zeros((nbins, nbins), numpy.float64)
rate_matrix = numpy.zeros((nbins, nbins), numpy.float64)
population_vector = numpy.zeros((nbins, ), numpy.float64)
pcoord_len = system.pcoord_len
assign = bin_mapper.assign
for iiter, n_iter in enumerate(iter_indices):
flux_matrix.fill(0.0)
population_vector.fill(0.0)
if iter_data:
iter_group_name = 'iter_{:0{prec}d}'.format(
int(n_iter), prec=data_manager.iter_prec)
iter_group = iter_data[iter_group_name]
else:
iter_group = data_manager.get_iter_group(n_iter)
# first, account for the flux due to recycling
# we access the hdf5 file directly to avoid nearly 50% overhead of creating a ton of
# tiny newweightentry objects
try:
nwgroup = iter_group['new_weights']
except KeyError:
# no new weight data
pass
else:
if iter_data:
index = None
weights = nwgroup['weight']
prev_init_pcoords = nwgroup['prev_init_pcoord']
new_init_pcoords = nwgroup['new_init_pcoord']
else:
index = nwgroup['index'][...]
weights = index['weight']
prev_init_pcoords = nwgroup['prev_init_pcoord'][...]
new_init_pcoords = nwgroup['new_init_pcoord'][...]
prev_init_assignments = assign(prev_init_pcoords)
new_init_assignments = assign(new_init_pcoords)
flux_assign(weights, prev_init_assignments, new_init_assignments,
flux_matrix)
#for (weight,i,j) in izip (weights, prev_init_assignments, new_init_assignments):
# flux_matrices[iiter,i,j] += weight
del index
del prev_init_pcoords, new_init_pcoords, prev_init_assignments, new_init_assignments, weights
#iter_group = data_manager.get_iter_group(n_iter)
if iter_data:
weights = iter_group['weight']
initial_pcoords = iter_group['initial_pcoords']
final_pcoords = iter_group['final_pcoords']
else:
weights = iter_group['seg_index']['weight']
initial_pcoords = iter_group['pcoord'][:, 0]
final_pcoords = iter_group['pcoord'][:, pcoord_len - 1]
initial_assignments = assign(initial_pcoords)
final_assignments = assign(final_pcoords)
flux_assign(weights, initial_assignments, final_assignments,
flux_matrix)
pop_assign(weights, initial_assignments, population_vector)
flux_stats.update(flux_matrix, nomask2d)
pop_stats.update(population_vector, nomask1d)
calc_rates(flux_matrix, population_vector, rate_matrix, rate_mask)
rate_stats.update(rate_matrix, rate_mask)
del weights
del initial_assignments, final_assignments
del initial_pcoords, final_pcoords
del iter_group
# Create namedtuple proxies for the cython StreamingStats objects
# since the typed memoryviews class variables do not seem to return
# cleanly from the zmq workers
c_flux_stats = StreamingStatsTuple(flux_stats.M1, flux_stats.M2,
flux_stats.n)
c_rate_stats = StreamingStatsTuple(rate_stats.M1, rate_stats.M2,
rate_stats.n)
c_pop_stats = StreamingStatsTuple(pop_stats.M1, pop_stats.M2, pop_stats.n)
return c_flux_stats, c_rate_stats, c_pop_stats