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This commit is contained in:
Deepak Mallubhotla 2022-04-16 12:55:52 -05:00
parent 492a5e6681
commit f00b29391c
Signed by: deepak
GPG Key ID: BEBAEBF28083E022
6 changed files with 309 additions and 93 deletions

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@ -10,7 +10,13 @@ def get_version():
return __version__
__all__ = ["get_version", "BayesRun", "AltBayesRun", "AltBayesRunSimulPairs", "Diagnostic"]
__all__ = [
"get_version",
"BayesRun",
"AltBayesRun",
"AltBayesRunSimulPairs",
"Diagnostic",
]
logging.getLogger(__name__).addHandler(logging.NullHandler())

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@ -24,47 +24,94 @@ _logger = logging.getLogger(__name__)
def get_a_result(input) -> int:
discretisation, dot_inputs, lows, highs, monte_carlo_count, max_frequency = input
sample_dipoles = discretisation.get_model().get_n_single_dipoles(monte_carlo_count, max_frequency)
sample_dipoles = discretisation.get_model().get_n_single_dipoles(
monte_carlo_count, max_frequency
)
vals = pdme.util.fast_v_calc.fast_vs_for_dipoles(dot_inputs, sample_dipoles)
return numpy.count_nonzero(pdme.util.fast_v_calc.between(vals, lows, highs))
def get_a_result_using_pairs(input) -> int:
discretisation, dot_inputs, pair_inputs, local_lows, local_highs, nonlocal_lows, nonlocal_highs, monte_carlo_count, max_frequency = input
sample_dipoles = discretisation.get_model().get_n_single_dipoles(monte_carlo_count, max_frequency)
(
discretisation,
dot_inputs,
pair_inputs,
local_lows,
local_highs,
nonlocal_lows,
nonlocal_highs,
monte_carlo_count,
max_frequency,
) = input
sample_dipoles = discretisation.get_model().get_n_single_dipoles(
monte_carlo_count, max_frequency
)
local_vals = pdme.util.fast_v_calc.fast_vs_for_dipoles(dot_inputs, sample_dipoles)
local_matches = pdme.util.fast_v_calc.between(local_vals, local_lows, local_highs)
nonlocal_vals = pdme.util.fast_nonlocal_spectrum.fast_s_nonlocal(pair_inputs, sample_dipoles)
nonlocal_matches = pdme.util.fast_v_calc.between(nonlocal_vals, nonlocal_lows, nonlocal_highs)
nonlocal_vals = pdme.util.fast_nonlocal_spectrum.fast_s_nonlocal(
pair_inputs, sample_dipoles
)
nonlocal_matches = pdme.util.fast_v_calc.between(
nonlocal_vals, nonlocal_lows, nonlocal_highs
)
combined_matches = numpy.logical_and(local_matches, nonlocal_matches)
return numpy.count_nonzero(combined_matches)
class AltBayesRun():
'''
class AltBayesRun:
"""
A single Bayes run for a given set of dots.
Parameters
----------
dot_inputs : Sequence[DotInput]
The dot inputs for this bayes run.
The dot inputs for this bayes run.
discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
The models to evaluate.
The models to evaluate.
actual_model_discretisation : pdme.model.Discretisation
The discretisation for the model which is actually correct.
The discretisation for the model which is actually correct.
filename_slug : str
The filename slug to include.
The filename slug to include.
run_count: int
The number of runs to do.
'''
def __init__(self, dot_positions: Sequence[numpy.typing.ArrayLike], frequency_range: Sequence[float], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], actual_model: pdme.model.Model, filename_slug: str, run_count: int = 100, low_error: float = 0.9, high_error: float = 1.1, pairs_high_error=None, pairs_low_error=None, monte_carlo_count: int = 10000, monte_carlo_cycles: int = 10, target_success: int = 100, max_monte_carlo_cycles_steps: int = 10, max_frequency: float = 20, end_threshold: float = None, chunksize: int = CHUNKSIZE, use_pairs: bool = False) -> None:
self.dot_inputs = pdme.inputs.inputs_with_frequency_range(dot_positions, frequency_range)
self.dot_inputs_array = pdme.measurement.input_types.dot_inputs_to_array(self.dot_inputs)
The number of runs to do.
"""
def __init__(
self,
dot_positions: Sequence[numpy.typing.ArrayLike],
frequency_range: Sequence[float],
discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]],
actual_model: pdme.model.Model,
filename_slug: str,
run_count: int = 100,
low_error: float = 0.9,
high_error: float = 1.1,
pairs_high_error=None,
pairs_low_error=None,
monte_carlo_count: int = 10000,
monte_carlo_cycles: int = 10,
target_success: int = 100,
max_monte_carlo_cycles_steps: int = 10,
max_frequency: float = 20,
end_threshold: float = None,
chunksize: int = CHUNKSIZE,
use_pairs: bool = False,
) -> None:
self.dot_inputs = pdme.inputs.inputs_with_frequency_range(
dot_positions, frequency_range
)
self.dot_inputs_array = pdme.measurement.input_types.dot_inputs_to_array(
self.dot_inputs
)
self.use_pairs = use_pairs
self.dot_pair_inputs = pdme.inputs.input_pairs_with_frequency_range(dot_positions, frequency_range)
self.dot_pair_inputs_array = pdme.measurement.input_types.dot_pair_inputs_to_array(self.dot_pair_inputs)
self.dot_pair_inputs = pdme.inputs.input_pairs_with_frequency_range(
dot_positions, frequency_range
)
self.dot_pair_inputs_array = (
pdme.measurement.input_types.dot_pair_inputs_to_array(self.dot_pair_inputs)
)
self.discretisations = [disc for (_, disc) in discretisations_with_names]
self.model_names = [name for (name, _) in discretisations_with_names]
@ -106,7 +153,9 @@ class AltBayesRun():
self.use_end_threshold = True
_logger.info(f"Will abort early, at {self.end_threshold}.")
else:
raise ValueError(f"end_threshold should be between 0 and 1, but is actually {end_threshold}")
raise ValueError(
f"end_threshold should be between 0 and 1, but is actually {end_threshold}"
)
def go(self) -> None:
with open(self.filename, "a", newline="") as outfile:
@ -121,13 +170,31 @@ class AltBayesRun():
# Generate the actual dipoles
actual_dipoles = self.actual_model.get_dipoles(frequency)
dots = actual_dipoles.get_percent_range_dot_measurements(self.dot_inputs, self.low_error, self.high_error)
lows, highs = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(dots)
dots = actual_dipoles.get_percent_range_dot_measurements(
self.dot_inputs, self.low_error, self.high_error
)
(
lows,
highs,
) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
dots
)
pair_lows, pair_highs = (None, None)
if self.use_pairs:
pair_measurements = actual_dipoles.get_percent_range_dot_pair_measurements(self.dot_pair_inputs, self.pairs_low_error, self.pairs_high_error)
pair_lows, pair_highs = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(pair_measurements)
pair_measurements = (
actual_dipoles.get_percent_range_dot_pair_measurements(
self.dot_pair_inputs,
self.pairs_low_error,
self.pairs_high_error,
)
)
(
pair_lows,
pair_highs,
) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
pair_measurements
)
_logger.info(f"Going to work on dipole at {actual_dipoles.dipoles}")
@ -139,18 +206,51 @@ class AltBayesRun():
cycle_count = 0
cycle_success = 0
cycles = 0
while (cycles < self.max_monte_carlo_cycles_steps) and (cycle_success <= self.target_success):
while (cycles < self.max_monte_carlo_cycles_steps) and (
cycle_success <= self.target_success
):
_logger.debug(f"Starting cycle {cycles}")
cycles += 1
current_success = 0
cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
if self.use_pairs:
current_success = sum(
pool.imap_unordered(get_a_result_using_pairs, [(discretisation, self.dot_inputs_array, self.dot_pair_inputs_array, lows, highs, pair_lows, pair_highs, self.monte_carlo_count, self.max_frequency)] * self.monte_carlo_cycles, self.chunksize)
pool.imap_unordered(
get_a_result_using_pairs,
[
(
discretisation,
self.dot_inputs_array,
self.dot_pair_inputs_array,
lows,
highs,
pair_lows,
pair_highs,
self.monte_carlo_count,
self.max_frequency,
)
]
* self.monte_carlo_cycles,
self.chunksize,
)
)
else:
current_success = sum(
pool.imap_unordered(get_a_result, [(discretisation, self.dot_inputs_array, lows, highs, self.monte_carlo_count, self.max_frequency)] * self.monte_carlo_cycles, self.chunksize)
pool.imap_unordered(
get_a_result,
[
(
discretisation,
self.dot_inputs_array,
lows,
highs,
self.monte_carlo_count,
self.max_frequency,
)
]
* self.monte_carlo_cycles,
self.chunksize,
)
)
cycle_success += current_success
@ -160,30 +260,44 @@ class AltBayesRun():
row = {
"dipole_moment": actual_dipoles.dipoles[0].p,
"dipole_location": actual_dipoles.dipoles[0].s,
"dipole_frequency": actual_dipoles.dipoles[0].w
"dipole_frequency": actual_dipoles.dipoles[0].w,
}
successes: List[float] = []
counts: List[int] = []
for model_index, (name, (count, result)) in enumerate(zip(self.model_names, results)):
for model_index, (name, (count, result)) in enumerate(
zip(self.model_names, results)
):
row[f"{name}_success"] = result
row[f"{name}_count"] = count
successes.append(max(result, 0.5))
counts.append(count)
success_weight = sum([(succ / count) * prob for succ, count, prob in zip(successes, counts, self.probabilities)])
new_probabilities = [(succ / count) * old_prob / success_weight for succ, count, old_prob in zip(successes, counts, self.probabilities)]
success_weight = sum(
[
(succ / count) * prob
for succ, count, prob in zip(successes, counts, self.probabilities)
]
)
new_probabilities = [
(succ / count) * old_prob / success_weight
for succ, count, old_prob in zip(successes, counts, self.probabilities)
]
self.probabilities = new_probabilities
for name, probability in zip(self.model_names, self.probabilities):
row[f"{name}_prob"] = probability
_logger.info(row)
with open(self.filename, "a", newline="") as outfile:
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
writer = csv.DictWriter(
outfile, fieldnames=self.csv_fields, dialect="unix"
)
writer.writerow(row)
if self.use_end_threshold:
max_prob = max(self.probabilities)
if max_prob > self.end_threshold:
_logger.info(f"Aborting early, because {max_prob} is greater than {self.end_threshold}")
_logger.info(
f"Aborting early, because {max_prob} is greater than {self.end_threshold}"
)
break

View File

@ -58,15 +58,15 @@ class AltBayesRunSimulPairs:
Parameters
----------
dot_inputs : Sequence[DotInput]
The dot inputs for this bayes run.
The dot inputs for this bayes run.
discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
The models to evaluate.
The models to evaluate.
actual_model_discretisation : pdme.model.Discretisation
The discretisation for the model which is actually correct.
The discretisation for the model which is actually correct.
filename_slug : str
The filename slug to include.
The filename slug to include.
run_count: int
The number of runs to do.
The number of runs to do.
"""
def __init__(
@ -206,26 +206,28 @@ class AltBayesRunSimulPairs:
current_success_no_pairs = 0
cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
current_success_both = numpy.array(sum(
pool.imap_unordered(
get_a_simul_result_using_pairs,
[
(
discretisation,
self.dot_inputs_array,
self.dot_pair_inputs_array,
lows,
highs,
pair_lows,
pair_highs,
self.monte_carlo_count,
self.max_frequency,
)
]
* self.monte_carlo_cycles,
self.chunksize,
current_success_both = numpy.array(
sum(
pool.imap_unordered(
get_a_simul_result_using_pairs,
[
(
discretisation,
self.dot_inputs_array,
self.dot_pair_inputs_array,
lows,
highs,
pair_lows,
pair_highs,
self.monte_carlo_count,
self.max_frequency,
)
]
* self.monte_carlo_cycles,
self.chunksize,
)
)
))
)
current_success_no_pairs = current_success_both[0]
current_success_pairs = current_success_both[1]

View File

@ -20,28 +20,40 @@ DotInput = Tuple[numpy.typing.ArrayLike, float]
_logger = logging.getLogger(__name__)
def get_a_result(discretisation, dots, index) -> Tuple[Tuple[int, ...], scipy.optimize.OptimizeResult]:
def get_a_result(
discretisation, dots, index
) -> Tuple[Tuple[int, ...], scipy.optimize.OptimizeResult]:
return (index, discretisation.solve_for_index(dots, index))
class BayesRun():
'''
class BayesRun:
"""
A single Bayes run for a given set of dots.
Parameters
----------
dot_inputs : Sequence[DotInput]
The dot inputs for this bayes run.
The dot inputs for this bayes run.
discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
The models to evaluate.
The models to evaluate.
actual_model_discretisation : pdme.model.Discretisation
The discretisation for the model which is actually correct.
The discretisation for the model which is actually correct.
filename_slug : str
The filename slug to include.
The filename slug to include.
run_count: int
The number of runs to do.
'''
def __init__(self, dot_inputs: Sequence[DotInput], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], actual_model: pdme.model.Model, filename_slug: str, run_count: int, max_frequency: float = None, end_threshold: float = None) -> None:
The number of runs to do.
"""
def __init__(
self,
dot_inputs: Sequence[DotInput],
discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]],
actual_model: pdme.model.Model,
filename_slug: str,
run_count: int,
max_frequency: float = None,
end_threshold: float = None,
) -> None:
self.dot_inputs = dot_inputs
self.discretisations = [disc for (_, disc) in discretisations_with_names]
self.model_names = [name for (name, _) in discretisations_with_names]
@ -65,7 +77,9 @@ class BayesRun():
self.use_end_threshold = True
_logger.info(f"Will abort early, at {self.end_threshold}.")
else:
raise ValueError(f"end_threshold should be between 0 and 1, but is actually {end_threshold}")
raise ValueError(
f"end_threshold should be between 0 and 1, but is actually {end_threshold}"
)
def go(self) -> None:
with open(self.filename, "a", newline="") as outfile:
@ -87,17 +101,28 @@ class BayesRun():
for disc_count, discretisation in enumerate(self.discretisations):
_logger.debug(f"Doing discretisation #{disc_count}")
with multiprocessing.Pool(multiprocessing.cpu_count() - 1 or 1) as pool:
results.append(pool.starmap(get_a_result, zip(itertools.repeat(discretisation), itertools.repeat(dots), discretisation.all_indices())))
results.append(
pool.starmap(
get_a_result,
zip(
itertools.repeat(discretisation),
itertools.repeat(dots),
discretisation.all_indices(),
),
)
)
_logger.debug("Done, constructing output now")
row = {
"dipole_moment": dipoles.dipoles[0].p,
"dipole_location": dipoles.dipoles[0].s,
"dipole_frequency": dipoles.dipoles[0].w
"dipole_frequency": dipoles.dipoles[0].w,
}
successes: List[float] = []
counts: List[int] = []
for model_index, (name, result) in enumerate(zip(self.model_names, results)):
for model_index, (name, result) in enumerate(
zip(self.model_names, results)
):
count = 0
success = 0
for idx, val in result:
@ -110,19 +135,31 @@ class BayesRun():
successes.append(max(success, 0.5))
counts.append(count)
success_weight = sum([(succ / count) * prob for succ, count, prob in zip(successes, counts, self.probabilities)])
new_probabilities = [(succ / count) * old_prob / success_weight for succ, count, old_prob in zip(successes, counts, self.probabilities)]
success_weight = sum(
[
(succ / count) * prob
for succ, count, prob in zip(successes, counts, self.probabilities)
]
)
new_probabilities = [
(succ / count) * old_prob / success_weight
for succ, count, old_prob in zip(successes, counts, self.probabilities)
]
self.probabilities = new_probabilities
for name, probability in zip(self.model_names, self.probabilities):
row[f"{name}_prob"] = probability
_logger.info(row)
with open(self.filename, "a", newline="") as outfile:
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
writer = csv.DictWriter(
outfile, fieldnames=self.csv_fields, dialect="unix"
)
writer.writerow(row)
if self.use_end_threshold:
max_prob = max(self.probabilities)
if max_prob > self.end_threshold:
_logger.info(f"Aborting early, because {max_prob} is greater than {self.end_threshold}")
_logger.info(
f"Aborting early, because {max_prob} is greater than {self.end_threshold}"
)
break

View File

@ -18,7 +18,7 @@ def get_a_result(discretisation, dots, index):
@dataclass
class SingleDipoleDiagnostic():
class SingleDipoleDiagnostic:
model: str
index: Tuple
bounds: Tuple
@ -43,31 +43,67 @@ class SingleDipoleDiagnostic():
self.w_result = self.result_dipole.w
class Diagnostic():
'''
class Diagnostic:
"""
Represents a diagnostic for a single dipole moment given a set of discretisations.
Parameters
----------
dot_inputs : Sequence[DotInput]
The dot inputs for this diagnostic.
The dot inputs for this diagnostic.
discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
The models to evaluate.
The models to evaluate.
actual_model_discretisation : pdme.model.Discretisation
The discretisation for the model which is actually correct.
The discretisation for the model which is actually correct.
filename_slug : str
The filename slug to include.
The filename slug to include.
run_count: int
The number of runs to do.
'''
def __init__(self, actual_dipole_moment: numpy.ndarray, actual_dipole_position: numpy.ndarray, actual_dipole_frequency: float, dot_inputs: Sequence[DotInput], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], filename_slug: str) -> None:
self.dipoles = OscillatingDipoleArrangement([OscillatingDipole(actual_dipole_moment, actual_dipole_position, actual_dipole_frequency)])
The number of runs to do.
"""
def __init__(
self,
actual_dipole_moment: numpy.ndarray,
actual_dipole_position: numpy.ndarray,
actual_dipole_frequency: float,
dot_inputs: Sequence[DotInput],
discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]],
filename_slug: str,
) -> None:
self.dipoles = OscillatingDipoleArrangement(
[
OscillatingDipole(
actual_dipole_moment,
actual_dipole_position,
actual_dipole_frequency,
)
]
)
self.dots = self.dipoles.get_dot_measurements(dot_inputs)
self.discretisations_with_names = discretisations_with_names
self.model_count = len(self.discretisations_with_names)
self.csv_fields = ["model", "index", "bounds", "p_actual_x", "p_actual_y", "p_actual_z", "s_actual_x", "s_actual_y", "s_actual_z", "w_actual", "success", "p_result_x", "p_result_y", "p_result_z", "s_result_x", "s_result_y", "s_result_z", "w_result"]
self.csv_fields = [
"model",
"index",
"bounds",
"p_actual_x",
"p_actual_y",
"p_actual_z",
"s_actual_x",
"s_actual_y",
"s_actual_z",
"w_actual",
"success",
"p_result_x",
"p_result_y",
"p_result_z",
"s_result_x",
"s_result_y",
"s_result_z",
"w_result",
]
timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
self.filename = f"{timestamp}-{filename_slug}.diag.csv"
@ -75,7 +111,7 @@ class Diagnostic():
def go(self):
with open(self.filename, "a", newline="") as outfile:
# csv fields
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect='unix')
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
writer.writeheader()
for (name, discretisation) in self.discretisations_with_names:
@ -83,17 +119,38 @@ class Diagnostic():
results = []
with multiprocessing.Pool(multiprocessing.cpu_count() - 1 or 1) as pool:
results = pool.starmap(get_a_result, zip(itertools.repeat(discretisation), itertools.repeat(self.dots), discretisation.all_indices()))
results = pool.starmap(
get_a_result,
zip(
itertools.repeat(discretisation),
itertools.repeat(self.dots),
discretisation.all_indices(),
),
)
with open(self.filename, "a", newline='') as outfile:
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect='unix', extrasaction="ignore")
with open(self.filename, "a", newline="") as outfile:
writer = csv.DictWriter(
outfile,
fieldnames=self.csv_fields,
dialect="unix",
extrasaction="ignore",
)
for idx, result in results:
bounds = discretisation.bounds(idx)
actual_success = result.success and result.cost <= 1e-10
diag_row = SingleDipoleDiagnostic(name, idx, bounds, self.dipoles.dipoles[0], discretisation.model.solution_as_dipoles(result.normalised_x)[0], actual_success)
diag_row = SingleDipoleDiagnostic(
name,
idx,
bounds,
self.dipoles.dipoles[0],
discretisation.model.solution_as_dipoles(result.normalised_x)[
0
],
actual_success,
)
row = vars(diag_row)
_logger.debug(f"Writing result {row}")
writer.writerow(row)

View File

@ -1,3 +1,3 @@
from importlib.metadata import version
__version__ = version('deepdog')
__version__ = version("deepdog")