feat: Adds alt bayes solver with monte carlo sampler

deepdog/__init__.py

@@ -1,6 +1,7 @@
 import logging
 from deepdog.meta import __version__
 from deepdog.bayes_run import BayesRun
+from deepdog.alt_bayes_run import AltBayesRun
 from deepdog.diagnostic import Diagnostic
 
 
@@ -8,7 +9,7 @@ def get_version():
 	return __version__
 
 
-__all__ = ["get_version", "BayesRun", "Diagnostic"]
+__all__ = ["get_version", "BayesRun", "AltBayesRun", "Diagnostic"]
 
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

deepdog/alt_bayes_run.py

@@ -0,0 +1,124 @@
+import pdme.model
+import pdme.measurement.oscillating_dipole
+import pdme.util.fast_v_calc
+from typing import Sequence, Tuple, List
+import datetime
+import csv
+import logging
+import numpy
+
+
+# TODO: remove hardcode
+COST_THRESHOLD = 1e-10
+
+
+# TODO: It's garbage to have this here duplicated from pdme.
+DotInput = Tuple[numpy.typing.ArrayLike, float]
+
+
+_logger = logging.getLogger(__name__)
+
+
+class AltBayesRun():
+	'''
+	A single Bayes run for a given set of dots.
+
+	Parameters
+	----------
+	dot_inputs : Sequence[DotInput]
+		The dot inputs for this bayes run.
+	discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
+		The models to evaluate.
+	actual_model_discretisation : pdme.model.Discretisation
+		The discretisation for the model which is actually correct.
+	filename_slug : str
+		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, low_error: float = 0.9, high_error: float = 1.1, monte_carlo_count: int = 10000, max_frequency: float = 20, end_threshold: float = None) -> None:
+		self.dot_inputs = dot_inputs
+		self.dot_inputs_array = pdme.measurement.oscillating_dipole.dot_inputs_to_array(dot_inputs)
+		self.discretisations = [disc for (_, disc) in discretisations_with_names]
+		self.model_names = [name for (name, _) in discretisations_with_names]
+		self.actual_model = actual_model
+		self.model_count = len(self.discretisations)
+		self.monte_carlo_count = monte_carlo_count
+		self.run_count = run_count
+		self.low_error = low_error
+		self.high_error = high_error
+		self.csv_fields = ["dipole_moment", "dipole_location", "dipole_frequency"]
+		self.compensate_zeros = True
+		for name in self.model_names:
+			self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
+
+		self.probabilities = [1 / self.model_count] * self.model_count
+
+		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
+		self.filename = f"{timestamp}-{filename_slug}.altbayes.csv"
+		self.max_frequency = max_frequency
+
+		if end_threshold is not None:
+			if 0 < end_threshold < 1:
+				self.end_threshold: float = end_threshold
+				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}")
+
+	def go(self) -> None:
+		with open(self.filename, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writeheader()
+
+		for run in range(1, self.run_count + 1):
+
+			rng = numpy.random.default_rng()
+			frequency = rng.uniform(1, self.max_frequency)
+
+			# 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.oscillating_dipole.dot_range_measurements_low_high_arrays(dots)
+			_logger.info(f"Going to work on dipole at {actual_dipoles.dipoles}")
+
+			results = []
+			_logger.debug("Going to iterate over discretisations now")
+			for disc_count, discretisation in enumerate(self.discretisations):
+				_logger.debug(f"Doing discretisation #{disc_count}")
+				sample_dipoles = discretisation.get_model().get_n_single_dipoles(self.monte_carlo_count, self.max_frequency)
+				vals = pdme.util.fast_v_calc.fast_vs_for_dipoles(self.dot_inputs_array, sample_dipoles)
+				results.append(numpy.count_nonzero(pdme.util.fast_v_calc.between(vals, lows, highs)))
+
+			_logger.debug("Done, constructing output now")
+			row = {
+				"dipole_moment": actual_dipoles.dipoles[0].p,
+				"dipole_location": actual_dipoles.dipoles[0].s,
+				"dipole_frequency": actual_dipoles.dipoles[0].w
+			}
+			successes: List[float] = []
+			counts: List[int] = []
+			for model_index, (name, result) in enumerate(zip(self.model_names, results)):
+
+				row[f"{name}_success"] = result
+				row[f"{name}_count"] = self.monte_carlo_count
+				successes.append(max(result, 0.5))
+				counts.append(self.monte_carlo_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)]
+			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.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}")
+					break

poetry.lock

@@ -304,7 +304,7 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
 [[package]]
 name = "pdme"
-version = "0.5.3"
+version = "0.5.4"
 description = "Python dipole model evaluator"
 category = "main"
 optional = false
@@ -697,7 +697,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8,<3.10"
-content-hash = "9ab90751e7341b5d3bf97445385aee4201807ffddc9ead94a9e2244ac797f85d"
+content-hash = "ba794e6f69d42e44e2b1abc40731fd78d2f417cdc9be12d6e752dbcfa95adaad"
 
 [metadata.files]
 atomicwrites = [
@@ -952,8 +952,8 @@ packaging = [
     {file = "packaging-21.3.tar.gz", hash = "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb"},
 ]
 pdme = [
-    {file = "pdme-0.5.3-py3-none-any.whl", hash = "sha256:91f2340e392159b688f3dd56a43be2093e9acdd573d1614aa8937316155552fd"},
+    {file = "pdme-0.5.4-py3-none-any.whl", hash = "sha256:90ba75efbec04f5a505c9c5228824538510149e218372e758c15150d5967d92b"},
-    {file = "pdme-0.5.3.tar.gz", hash = "sha256:ccb7e173849a6650f79767f4fc1b74ff820d22f5d8c0937c9ffb0d818fc4f147"},
+    {file = "pdme-0.5.4.tar.gz", hash = "sha256:82bff2ccc8f38996c23b43ab7d7dc80d87a6b340492f368861e7748105b50174"},
 ]
 pkginfo = [
     {file = "pkginfo-1.8.2-py2.py3-none-any.whl", hash = "sha256:c24c487c6a7f72c66e816ab1796b96ac6c3d14d49338293d2141664330b55ffc"},

pyproject.toml

@@ -6,7 +6,7 @@ authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
 
 [tool.poetry.dependencies]
 python = "^3.8,<3.10"
-pdme = "^0.5.3"
+pdme = "^0.5.4"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6"