Merge pull request #13 from SpeysideHEP/simplify-update

Missing channel handling in full llhd simplification

.zenodo.json

@@ -1,8 +1,8 @@
 {
     "description": "pyhf plug-in for spey package",
     "license": "MIT",
-    "title": "SpeysideHEP/spey-pyhf: v0.1.5",
-    "version": "v0.1.5",
+    "title": "SpeysideHEP/spey-pyhf: v0.1.6",
+    "version": "v0.1.6",
     "upload_type": "software",
     "creators": [
         {
@@ -29,7 +29,7 @@
         },
         {
             "scheme": "url",
-            "identifier": "https://github.com/SpeysideHEP/spey-pyhf/tree/v0.1.5",
+            "identifier": "https://github.com/SpeysideHEP/spey-pyhf/tree/v0.1.6",
             "relation": "isSupplementTo"
         },
         {

docs/releases/changelog-v0.1.md

@@ -24,6 +24,12 @@
 * Improve undefined channel handling in the patchset
   ([#12](https://github.com/SpeysideHEP/spey-pyhf/pull/12))
 
+* Improve undefined channel handling in the patchset for full likelihood simplification.
+  ([#13](https://github.com/SpeysideHEP/spey-pyhf/pull/13))
+
+* Add modifier check to signal injection.
+  ([#13](https://github.com/SpeysideHEP/spey-pyhf/pull/13))
+
 ## Bug fixes
 
 * Bugfix in `simplify` module, where signal injector was not initiated properly.

setup.py

@@ -30,6 +30,10 @@
     url="https://github.com/SpeysideHEP/spey-pyhf",
     project_urls={
         "Bug Tracker": "https://github.com/SpeysideHEP/spey-pyhf/issues",
+        "Documentation": "https://spey-pyhf.readthedocs.io",
+        "Repository": "https://github.com/SpeysideHEP/spey-pyhf",
+        "Homepage": "https://github.com/SpeysideHEP/spey-pyhf",
+        "Download": f"https://github.com/SpeysideHEP/spey-pyhf/archive/refs/tags/v{version}.tar.gz",
     },
     download_url=f"https://github.com/SpeysideHEP/spey-pyhf/archive/refs/tags/v{version}.tar.gz",
     author="Jack Y. Araz",
@@ -50,8 +54,14 @@
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3",
         "Topic :: Scientific/Engineering :: Physics",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     extras_require={
         "dev": ["pytest>=7.1.2", "pytest-cov>=3.0.0", "twine>=3.7.1", "wheel>=0.37.1"],

src/spey_pyhf/_version.py

@@ -1,3 +1,3 @@
 """Version of the spey - pyhf plugin"""
 
-__version__ = "0.1.5"
+__version__ = "0.1.6"

src/spey_pyhf/helper_functions.py

@@ -9,6 +9,8 @@ def __dir__():
     return __all__
 
 
+# pylint: disable=W1203, W1201, C0103
+
 log = logging.getLogger("Spey")
 
 
@@ -168,6 +170,7 @@ def inject_signal(
         Args:
             channel (``Text``): channel name
             data (``List[float]``): signal yields
+            modifiers (``List[Dict]``): uncertainties. If None, default modifiers will be added.
 
         Raises:
             ``ValueError``: If channel does not exist or number of yields does not match
@@ -184,9 +187,20 @@ def inject_signal(
                 f"{self.bin_map[channel]} expected, {len(data)} received."
             )
 
+        default_modifiers = _default_modifiers(self.poi_name[0][1])
+        if modifiers is not None:
+            for mod in default_modifiers:
+                if mod not in modifiers:
+                    log.warning(
+                        f"Modifier `{mod['name']}` with type `{mod['type']}` is missing"
+                        f" from the input. Adding `{mod['name']}`"
+                    )
+                    log.debug(f"Adding modifier: {mod}")
+                    modifiers.append(mod)
+
         self._signal_dict[channel] = data
         self._signal_modifiers[channel] = (
-            _default_modifiers(self.poi_name[0][1]) if modifiers is None else modifiers
+            default_modifiers if modifiers is None else modifiers
         )
 
     @property
@@ -237,7 +251,7 @@ def reset_signal(self) -> None:
 
     def add_patch(self, signal_patch: List[Dict]) -> None:
         """Inject signal patch"""
-        self._signal_dict, self._to_remove = self.patch_to_map(
+        self._signal_dict, self._signal_modifiers, self._to_remove = self.patch_to_map(
             signal_patch=signal_patch, return_remove_list=True
         )
 
@@ -272,7 +286,10 @@ def remove_list(self) -> List[Text]:
 
     def patch_to_map(
         self, signal_patch: List[Dict], return_remove_list: bool = False
-    ) -> Union[Tuple[Dict[Text, Dict], List[Text]], Dict[Text, Dict]]:
+    ) -> Union[
+        Tuple[Dict[Text, Dict], Dict[Text, Dict], List[Text]],
+        Tuple[Dict[Text, Dict], Dict[Text, Dict]],
+    ]:
         """
         Convert JSONPatch into signal map
 
@@ -288,23 +305,20 @@ def patch_to_map(
                 .. versionadded:: 0.1.5
 
         Returns:
-            ``Tuple[Dict[Text, Dict], List[Text]]`` or ``Dict[Text, Dict]``:
+            ``Tuple[Dict[Text, Dict], Dict[Text, Dict], List[Text]]`` or ``Tuple[Dict[Text, Dict], Dict[Text, Dict]]``:
             signal map including the data and modifiers and the list of channels to be removed.
         """
-        signal_map = {}
-        to_remove = []
+        signal_map, modifier_map, to_remove = {}, {}, []
         for item in signal_patch:
             path = int(item["path"].split("/")[2])
             channel_name = self["channels"][path]["name"]
             if item["op"] == "add":
-                signal_map[channel_name] = {
-                    "data": item["value"]["data"],
-                    "modifiers": item["value"].get(
-                        "modifiers", _default_modifiers(poi_name=self.poi_name[0][1])
-                    ),
-                }
+                signal_map[channel_name] = item["value"]["data"]
+                modifier_map[channel_name] = item["value"].get(
+                    "modifiers", _default_modifiers(poi_name=self.poi_name[0][1])
+                )
             elif item["op"] == "remove":
                 to_remove.append(channel_name)
         if return_remove_list:
-            return signal_map, to_remove
-        return signal_map
+            return signal_map, modifier_map, to_remove
+        return signal_map, modifier_map

src/spey_pyhf/simplify.py

@@ -1,7 +1,9 @@
 """Interface to convert pyhf likelihoods to simplified likelihood framework"""
 import copy
+import logging
 import warnings
-from typing import Callable, List, Optional, Text, Union, Literal
+from contextlib import contextmanager
+from typing import Callable, List, Literal, Optional, Text, Union
 
 import numpy as np
 import spey
@@ -18,6 +20,11 @@ def __dir__():
     return []
 
 
+# pylint: disable=W1203, R0903
+
+log = logging.getLogger("Spey")
+
+
 class ConversionError(Exception):
     """Conversion error class"""
 
@@ -41,6 +48,22 @@ def func(vector: np.ndarray) -> float:
     return func
 
 
+@contextmanager
+def _disable_logging(highest_level: int = logging.CRITICAL):
+    """
+    Temporary disable logging implementation, this should move into Spey
+
+    Args:
+        highest_level (``int``, default ``logging.CRITICAL``): highest level to be set in logging
+    """
+    previous_level = logging.root.manager.disable
+    logging.disable(highest_level)
+    try:
+        yield
+    finally:
+        logging.disable(previous_level)
+
+
 class Simplify(spey.ConverterBase):
     r"""
     An interface to convert pyhf full statistical model prescription into simplified likelihood
@@ -175,9 +198,10 @@ def __call__(
         }[fittype]
 
         interpreter = WorkspaceInterpreter(bkgonly_model)
+        bin_map = interpreter.bin_map
 
         # configure signal patch map with respect to channel names
-        signal_patch_map = interpreter.patch_to_map(signal_patch)
+        signal_patch_map, signal_modifiers_map = interpreter.patch_to_map(signal_patch)
 
         # Prepare a JSON patch to separate control and validation regions
         # These regions are generally marked as CR and VR
@@ -190,25 +214,26 @@ def __call__(
             )
 
         for channel in interpreter.get_channels(control_region_indices):
-            interpreter.inject_signal(
-                channel,
-                [0.0] * len(signal_patch_map[channel]["data"]),
-                signal_patch_map[channel]["modifiers"]
-                if include_modifiers_in_control_model
-                else None,
-            )
+            if channel in signal_patch_map and channel in signal_modifiers_map:
+                interpreter.inject_signal(
+                    channel,
+                    [0.0] * bin_map[channel],
+                    signal_modifiers_map[channel]
+                    if include_modifiers_in_control_model
+                    else None,
+                )
 
         pdf_wrapper = spey.get_backend("pyhf")
-        control_model = pdf_wrapper(
-            background_only_model=bkgonly_model, signal_patch=interpreter.make_patch()
-        )
+        with _disable_logging():
+            control_model = pdf_wrapper(
+                background_only_model=bkgonly_model, signal_patch=interpreter.make_patch()
+            )
 
         # Extract the nuisance parameters that maximises the likelihood at mu=0
         fit_opts = control_model.prepare_for_fit(expected=expected)
         _, fit_param = fit(
             **fit_opts,
             initial_parameters=None,
-            bounds=None,
             fixed_poi_value=0.0,
         )
 
@@ -234,13 +259,33 @@ def __call__(
         )
 
         # Retreive pyhf models and compare parameter maps
-        stat_model_pyhf = statistical_model.backend.model()[1]
+        if include_modifiers_in_control_model:
+            stat_model_pyhf = statistical_model.backend.model()[1]
+        else:
+            # Remove the nuisance parameters from the signal patch
+            # Note that even if the signal yields are zero, nuisance parameters
+            # do contribute to the statistical model and some models may be highly
+            # sensitive to the shape and size of the nuisance parameters.
+            with _disable_logging():
+                tmp_interpreter = copy.deepcopy(interpreter)
+                for channel, data in signal_patch_map.items():
+                    tmp_interpreter.inject_signal(channel=channel, data=data)
+                tmp_model = spey.get_backend("pyhf")(
+                    background_only_model=bkgonly_model,
+                    signal_patch=tmp_interpreter.make_patch(),
+                )
+                stat_model_pyhf = tmp_model.backend.model()[1]
+                del tmp_model, tmp_interpreter
         control_model_pyhf = control_model.backend.model()[1]
         is_nuisance_map_different = (
             stat_model_pyhf.config.par_map != control_model_pyhf.config.par_map
         )
         fit_opts = statistical_model.prepare_for_fit(expected=expected)
         suggested_fixed = fit_opts["model_configuration"].suggested_fixed
+        log.debug(
+            "Number of parameters to be fitted during the scan: "
+            f"{fit_opts['model_configuration'].npar - len(fit_param)}"
+        )
 
         samples = []
         warnings_list = []
@@ -290,7 +335,9 @@ def __call__(
                             _, new_params = fit(
                                 **current_fit_opts,
                                 initial_parameters=init_params.tolist(),
-                                bounds=None,
+                                bounds=current_fit_opts[
+                                    "model_configuration"
+                                ].suggested_bounds,
                             )
                             warnings_list += w
 
@@ -304,13 +351,16 @@ def __call__(
                     # Some of the samples can lead to problems while sampling from a poisson distribution.
                     # e.g. poisson requires positive lambda values to sample from. If sample leads to a negative
                     # lambda value continue sampling to avoid that point.
+                    log.debug("Problem with the sample generation")
+                    log.debug(
+                        f"Nuisance parameters: {current_nui_params if new_params is None else new_params}"
+                    )
                     continue
 
         if len(warnings_list) > 0:
-            warnings.warn(
-                message=f"{len(warnings_list)} warning(s) generated during sampling."
-                " This might be due to edge cases in nuisance parameter sampling.",
-                category=RuntimeWarning,
+            log.warning(
+                f"{len(warnings_list)} warning(s) generated during sampling."
+                " This might be due to edge cases in nuisance parameter sampling."
             )
 
         samples = np.vstack(samples)
@@ -323,9 +373,19 @@ def __call__(
 
         # NOTE: model spec might be modified within the pyhf workspace, thus
         # yields needs to be reordered properly before constructing the simplified likelihood
-        signal_yields = []
+        signal_yields, missing_channels = [], []
         for channel_name in stat_model_pyhf.config.channels:
-            signal_yields += signal_patch_map[channel_name]["data"]
+            try:
+                signal_yields += signal_patch_map[channel_name]
+            except KeyError:
+                missing_channels.append(channel_name)
+                signal_yields += [0.0] * bin_map[channel_name]
+        if len(missing_channels) > 0:
+            log.warning(
+                "Following channels are not in the signal patch,"
+                f" will be set to zero: {', '.join(missing_channels)}"
+            )
+
         # NOTE background yields are first moments in simplified framework not the yield values
         # in the full statistical model!
         background_yields = np.mean(samples, axis=0)