Merge remote-tracking branch 'origin/main' into simplify_source

alea/__init__.py

@@ -4,6 +4,8 @@
 
 from .models import *
 
+from .runner import *
+
 from .utils import *
 
 from .parameters import *

alea/examples/configs/unbinned_wimp_running.yaml

@@ -1,3 +1,4 @@
+statistical_model: alea.models.BlueiceExtendedModel
 statistical_model_config: unbinned_wimp_statistical_model.yaml
 
 poi: wimp_rate_multiplier
@@ -12,8 +13,8 @@ computation:
       }
     parameters_in_common:
       {
-        hypotheses: ["true", "null", "free"],
-        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.hdf5",
+        hypotheses: ["free", "null", "true"],
+        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.h5",
         n_mc: 5000,
         n_batch: 40,
       }
@@ -24,12 +25,12 @@ computation:
     parameters_to_vary: {wimp_mass: [10, 50, 200]}
     parameters_in_common:
       {
-        hypotheses: ["true", "null", "free"],
-        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.hdf5",
+        hypotheses: ["free", "null", "true"],
+        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.h5",
         n_mc: 5000,
         n_batch: 40,
       }
-    limit_threshold: "thresholds.hdf5"
+    limit_threshold: "thresholds.h5"
     toydata_mode: "generate"
     parameters_as_wildcards: ["poi_expectation", "n_mc", "n_batch"]
 
@@ -38,12 +39,12 @@ computation:
     parameters_to_vary: {poi_expectation: [0.], wimp_mass: [10, 50, 200]}
     parameters_in_common:
       {
-        hypotheses: ["true", "null", "free"],
-        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.hdf5",
+        hypotheses: ["free", "null", "true"],
+        output_filename: "toymc_power_wimp_mass_{wimp_mass:d}_poi_expectation_{poi_expectation:.2f}.h5",
         n_mc: 5000,
         n_batch: 40,
         compute_confidence_interval: True,
-        limit_threshold: "thresholds.hdf5",
+        limit_threshold: "thresholds.h5",
       }
     toydata_mode: "generate"
 

alea/examples/configs/unbinned_wimp_statistical_model.yaml

@@ -26,6 +26,9 @@ parameter_definition:
     fit_limits:
       - 0
       - null
+    parameter_interval_bounds:
+      - 0
+      - null
 
   er_rate_multiplier:
     nominal_value: 1.0

alea/model.py

@@ -1,5 +1,6 @@
 import inspect
 import warnings
+from copy import deepcopy
 from typing import Dict, List, Tuple, Callable, Optional
 
 import numpy as np
@@ -10,6 +11,7 @@
 from inference_interface import toydata_to_file
 
 from alea.parameters import Parameters
+from alea.utils import within_limits, clip_limits
 
 
 class StatisticalModel:
@@ -71,6 +73,7 @@ def __init__(
             confidence_level: float = 0.9,
             confidence_interval_kind: str = "central",  # one of central, upper, lower
             confidence_interval_threshold: Callable[[float], float] = None,
+            **kwargs,
         ):
         """Initialize a statistical model"""
         if type(self) == StatisticalModel:
@@ -183,7 +186,8 @@ def store_data(
             data_name_list: Optional[List] = None,
             metadata: Optional[Dict] = None):
         """
-        Store a list of datasets (each on the form of a list of one or more structured arrays)
+        Store a list of datasets.
+        (each on the form of a list of one or more structured arrays or dicts)
         Using inference_interface, but included here to allow over-writing.
         The structure would be: [[datasets1], [datasets2], ..., [datasetsn]],
         where each of datasets is a list of structured arrays.
@@ -198,14 +202,26 @@ def store_data(
             metadata (dict, optional (default=None)): metadata to store with the data.
                 If None, no metadata is stored.
         """
+        if all([isinstance(d, dict) for d in data_list]):
+            _data_list = [list(d.values()) for d in data_list]
+        elif all([isinstance(d, list) for d in data_list]):
+            _data_list = data_list
+        else:
+            raise ValueError(
+                'Unsupported mixed toydata format! '
+                'toydata should be a list of dict or a list of list',)
+
         if data_name_list is None:
             if hasattr(self, "likelihood_names"):
                 data_name_list = self.likelihood_names
             else:
-                data_name_list = ["{:d}".format(i) for i in range(len(data_list[0]))]
+                data_name_list = ["{:d}".format(i) for i in range(len(_data_list[0]))]
 
         kw = {'metadata': metadata} if metadata is not None else dict()
-        toydata_to_file(file_name, data_list, data_name_list, **kw)
+        if len(_data_list[0]) != len(data_name_list):
+            raise ValueError(
+                "The number of data sets and data names must be the same")
+        toydata_to_file(file_name, _data_list, data_name_list, **kw)
 
     def get_expectation_values(self, **parameter_values):
         """
@@ -257,6 +273,7 @@ def cost(args):
             call_kwargs = {}
             for i, k in enumerate(self.parameters.names):
                 call_kwargs[k] = args[i]
+            # for optimization, we want to minimize the negative log-likelihood
             return self.ll(**call_kwargs) * -1
 
         return cost
@@ -338,10 +355,10 @@ def _confidence_interval_checks(
 
         if parameter_interval_bounds is None:
             parameter_interval_bounds = parameter_of_interest.parameter_interval_bounds
-            if parameter_interval_bounds is None:
-                raise ValueError(
-                    "You must set parameter_interval_bounds in the parameter config"
-                    " or when calling confidence_interval")
+        else:
+            value = parameter_interval_bounds
+            parameter_of_interest._check_parameter_interval_bounds(value)
+            parameter_interval_bounds = clip_limits(value)
 
         if parameter_of_interest.ptype == "rate":
             try:
@@ -350,6 +367,7 @@ def _confidence_interval_checks(
                 else:
                     source_name = poi_name
                 mu_parameter = self.get_expectation_values(**kwargs)[source_name]
+                # update parameter_interval_bounds because poi is rate_multiplier
                 parameter_interval_bounds = (
                     parameter_interval_bounds[0] / mu_parameter,
                     parameter_interval_bounds[1] / mu_parameter)
@@ -378,7 +396,9 @@ def confidence_interval(
             parameter_interval_bounds: Tuple[float, float] = None,
             confidence_level: float = None,
             confidence_interval_kind: str = None,
-            **kwargs) -> Tuple[float, float]:
+            best_fit_args: dict = None,
+            confidence_interval_args: dict = None,
+        ) -> Tuple[float, float]:
         """
         Uses self.fit to compute confidence intervals for a certain named parameter.
         If the parameter is a rate parameter, and the model has expectation values implemented,
@@ -401,44 +421,60 @@ def confidence_interval(
                 If None, the default kind of the model is used.
 
         Keyword Args:
-            kwargs: the parameters for get_expectation_values and fit
+            best_fit_args: the parameters to **only** get the global best-fit likelihood
+            confidence_interval_args: the parameters to get the profile-likelihood,
+                also the best-fit parameters of profile-likelihood,
+                parameter_interval_bounds, and confidence interval
         """
+        if best_fit_args is None:
+            best_fit_args = {}
+        if confidence_interval_args is None:
+            confidence_interval_args = {}
         ci_objects = self._confidence_interval_checks(
             poi_name,
             parameter_interval_bounds,
             confidence_level,
             confidence_interval_kind,
-            **kwargs)
+            **confidence_interval_args)
         confidence_interval_kind, confidence_interval_threshold, parameter_interval_bounds = ci_objects
 
-        # find best-fit:
-        best_result, best_ll = self.fit(**kwargs)
+        # best_fit_args only provides the best-fit likelihood
+        _, best_ll = self.fit(**best_fit_args)
+        # the optimization of profile-likelihood under
+        # confidence_interval_args provides the best_parameter
+        best_result, _ = self.fit(**confidence_interval_args)
         best_parameter = best_result[poi_name]
-        mask = (parameter_interval_bounds[0] < best_parameter)
-        mask &= (best_parameter < parameter_interval_bounds[1])
-        assert mask, ("the best-fit is outside your confidence interval"
-            " search limits in parameter_interval_bounds")
-        # log-likelihood - critical value:
+        mask = within_limits(best_parameter, parameter_interval_bounds)
+        if not mask:
+            raise ValueError(
+                f"The best-fit {best_parameter} is outside your confidence interval "
+                f"search limits in parameter_interval_bounds {parameter_interval_bounds}.")
 
         # define intersection between likelihood ratio curve and the critical curve:
-        def t(hypothesis):
+        def t(hypothesis_value):
             # define the intersection
             # between the profile-log-likelihood curve and the rejection threshold
-            kwargs[poi_name] = hypothesis
-            _, ll = self.fit(**kwargs)  # ll is + log-likelihood here
+            _confidence_interval_args = deepcopy(confidence_interval_args)
+            _confidence_interval_args[poi_name] = hypothesis_value
+            _, ll = self.fit(**_confidence_interval_args)  # ll is + log-likelihood here
             ret = 2. * (best_ll - ll)  # likelihood curve "right way up" (smiling)
             # if positive, hypothesis is excluded
-            return ret - confidence_interval_threshold(hypothesis)
+            return ret - confidence_interval_threshold(hypothesis_value)
+
+        t_best_parameter = t(best_parameter)
+
+        if t_best_parameter > 0:
+            warnings.warn(f"CL calculation failed, given fixed parameters {confidence_interval_args}.")
 
-        if confidence_interval_kind in {"upper", "central"}:
+        if confidence_interval_kind in {"upper", "central"} and t_best_parameter < 0:
             if t(parameter_interval_bounds[1]) > 0:
                 ul = brentq(t, best_parameter, parameter_interval_bounds[1])
             else:
                 ul = np.inf
         else:
             ul = np.nan
 
-        if confidence_interval_kind in {"lower", "central"}:
+        if confidence_interval_kind in {"lower", "central"} and t_best_parameter < 0:
             if t(parameter_interval_bounds[0]) > 0:
                 dl = brentq(t, parameter_interval_bounds[0], best_parameter)
             else:

alea/models/blueice_extended_model.py

@@ -38,9 +38,14 @@ class BlueiceExtendedModel(StatisticalModel):
         (assert that all sources have the same analysis_space)
     """
 
-    def __init__(self, parameter_definition: dict, likelihood_config: dict):
-        """Initializes the statistical model."""
-        super().__init__(parameter_definition=parameter_definition)
+    def __init__(self, parameter_definition: dict, likelihood_config: dict, **kwargs):
+        """Initializes the statistical model.
+
+        Args:
+            parameter_definition (dict): A dictionary defining the model parameters.
+            likelihood_config (dict): A dictionary defining the likelihood.
+        """
+        super().__init__(parameter_definition=parameter_definition, **kwargs)
         self._likelihood = self._build_ll_from_config(likelihood_config)
         self.likelihood_names = [t["name"] for t in likelihood_config["likelihood_terms"]]
         self.likelihood_names.append("ancillary_likelihood")
@@ -66,14 +71,23 @@ def data(self) -> dict:
         return super().data
 
     @data.setter
-    def data(self, data: dict):
+    def data(self, data: dict or list):
         """
         Overrides default setter. Will also set the data of the blueice ll.
         Data-sets are expected to be in the form of a list of one
         or more structured arrays representing the data-sets of one or more likelihood terms.
+
+        Args:
+            data (dict or list): Data of the statistical model.
+                If data is a list, it must be a list of length len(self.likelihood_names) + 1.
         """
         # iterate through all likelihood terms and set the science data in the blueice ll
-        # except the generate_values
+        # last entry in data are the generate_values
+        if isinstance(data, list):
+            if len(data) != len(self.likelihood_names) + 1:
+                raise ValueError(
+                    f"Data must be a list of length {len(self.likelihood_names) + 1}")
+            data = dict(zip(self.likelihood_names + ["generate_values"], data))
         for i, (dataset_name, d) in enumerate(data.items()):
             if dataset_name != "generate_values":
                 ll_term = self._likelihood.likelihood_list[i]
@@ -159,7 +173,7 @@ def _build_ll_from_config(self, likelihood_config: dict) -> "LogLikelihoodSum":
             for i, source in enumerate(config["sources"]):
                 parameters_to_ignore: List[str] = [
                     p.name for p in self.parameters if (
-                        p.ptype == "shape") & (p.name not in source["parameters"])]
+                        p.ptype == "shape") and (p.name not in source["parameters"])]
                 # no efficiency affects PDF:
                 parameters_to_ignore += [p.name for p in self.parameters if (p.ptype == "efficiency")]
                 parameters_to_ignore += source.get("extra_dont_hash_settings", [])
@@ -179,6 +193,7 @@ def _build_ll_from_config(self, likelihood_config: dict) -> "LogLikelihoodSum":
                 rate_parameter = rate_parameters[0]
                 if rate_parameter.endswith("_rate_multiplier"):
                     rate_parameter = rate_parameter.replace("_rate_multiplier", "")
+                    # The ancillary term is handled in CustomAncillaryLikelihood
                     ll.add_rate_parameter(rate_parameter, log_prior=None)
                 else:
                     raise NotImplementedError(
@@ -196,6 +211,7 @@ def _build_ll_from_config(self, likelihood_config: dict) -> "LogLikelihoodSum":
                     anchors = self.parameters[p].blueice_anchors
                     if anchors is None:
                         raise ValueError(f"Shape parameter {p} does not have any anchors.")
+                    # The ancillary term is handled in CustomAncillaryLikelihood
                     ll.add_shape_parameter(p, anchors=anchors, log_prior=None)
 
             ll.prepare()
@@ -245,12 +261,20 @@ def _generate_data(self, **generate_values) -> dict:
         data["generate_values"] = dict_to_structured_array(generate_values)
         return data
 
+    def store_data(self, file_name, data_list, data_name_list=None, metadata=None):
+        """
+        Store data in a file.
+        Append the generate_values to the data_name_list.
+        """
+        if data_name_list is None:
+            data_name_list = self.likelihood_names + ["generate_values"]
+        super().store_data(file_name, data_list, data_name_list, metadata)
+
     def _generate_science_data(self, **generate_values) -> dict:
-        """Generate data for all science data terms terms."""
+        """Generate the science data for all likelihood terms except the ancillary likelihood."""
         science_data = [
-            gen.simulate(**generate_values)
-            for gen in self.data_generators]
-        return dict(zip(self.likelihood_names, science_data))
+            gen.simulate(**generate_values) for gen in self.data_generators]
+        return dict(zip(self.likelihood_names[:-1], science_data))
 
     def _generate_ancillary_measurements(self, **generate_values) -> dict:
         """