Merge branch 'main' into yields-no-rf

fuse/plugins/detector_physics/csv_input.py

@@ -1,4 +1,3 @@
-import logging
 from typing import Tuple
 
 import numpy as np
@@ -19,9 +18,6 @@
 export, __all__ = strax.exporter()
 __all__.extend(["microphysics_summary_fields"])
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.csv_input")
-
 
 # In some cases we might want to change dtype of microphysics_summary
 # through microphysics_summary_fields, so do not set microphysics_summary_fields
@@ -90,6 +86,7 @@ def setup(self):
             separation_scale=self.separation_scale,
             n_interactions_per_chunk=self.n_interactions_per_chunk,
             debug=self.debug,
+            log=self.log,
         )
         self.file_reader_iterator = self.file_reader.output_chunk()
 
@@ -136,6 +133,7 @@ def __init__(
         first_chunk_left=1e6,
         last_chunk_length=1e8,
         debug=False,
+        log=None,
     ):
         self.input_file = input_file
         self.rng = random_number_generator
@@ -146,6 +144,7 @@ def __init__(
         self.last_chunk_length = np.int64(last_chunk_length)
         self.first_chunk_left = np.int64(first_chunk_left)
         self.debug = debug
+        self.log = log
 
         # The csv file needs to have these columns:
         _fields = ChunkCsvInput.needed_csv_input_fields()
@@ -167,7 +166,7 @@ def output_chunk(self):
             instructions["time"] = interaction_time + instructions["t"]
         elif self.event_rate == 0:
             instructions["time"] = instructions["t"]
-            log.debug("Using event times from provided input file.")
+            self.log.debug("Using event times from provided input file.")
         else:
             raise ValueError("Source rate cannot be negative!")
 
@@ -193,7 +192,7 @@ def output_chunk(self):
             chunk_bounds = chunk_end + np.int64(self.chunk_delay_fraction * gap_length)
             self.chunk_bounds = np.append(chunk_start[0] - self.first_chunk_left, chunk_bounds)
         else:
-            log.warning("Only one Chunk! Rate too high?")
+            self.log.warning("Only one Chunk! Rate too high?")
             self.chunk_bounds = [
                 chunk_start[0] - self.first_chunk_left,
                 chunk_end[0] + self.last_chunk_length,
@@ -206,15 +205,15 @@ def output_chunk(self):
         ):
             if c_ix == unique_chunk_index_values[-1]:
                 source_done = True
-                log.debug("Build last chunk.")
+                self.log.debug("Build last chunk.")
 
             yield instructions[chunk_idx == c_ix], chunk_left, chunk_right, source_done
 
     def last_chunk_bounds(self):
         return self.chunk_bounds[-1]
 
     def __load_csv_file(self):
-        log.debug("Load detector simulation instructions from a csv file!")
+        self.log.debug("Load detector simulation instructions from a csv file!")
         df = pd.read_csv(self.input_file)
 
         missing_columns = set(self.columns) - set(df.columns)

fuse/plugins/detector_physics/delayed_electrons/delayed_electrons_drift.py

@@ -1,13 +1,9 @@
 import strax
 import straxen
-import logging
 from ..electron_drift import ElectronDrift
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.delayed_electrons.delayed_electrons_drift")
-
 
 @export
 class DelayedElectronsDrift(ElectronDrift):

fuse/plugins/detector_physics/delayed_electrons/delayed_electrons_extraction.py

@@ -1,12 +1,8 @@
 import strax
-import logging
 from ..electron_extraction import ElectronExtraction
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.delayed_electrons.delayed_electrons_extraction")
-
 
 @export
 class DelayedElectronsExtraction(ElectronExtraction):

fuse/plugins/detector_physics/delayed_electrons/delayed_electrons_s1photonhits.py

@@ -1,14 +1,10 @@
 import strax
-import logging
 import numpy as np
 
 from ....plugin import FuseBasePlugin
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.delayed_electrons.delayed_electrons_s1photonhits")
-
 
 @export
 class S1PhotonHitsEmpty(FuseBasePlugin):

fuse/plugins/detector_physics/delayed_electrons/delayed_electrons_secondary_scintillation.py

@@ -1,16 +1,10 @@
 import strax
 import numpy as np
-import logging
 from immutabledict import immutabledict
 from ..secondary_scintillation import SecondaryScintillation
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger(
-    "fuse.detector_physics.delayed_electrons.delayed_electrons_secondary_scintillation"
-)
-
 
 @export
 class DelayedElectronsSecondaryScintillation(SecondaryScintillation):

fuse/plugins/detector_physics/delayed_electrons/delayed_electrons_timing.py

@@ -1,12 +1,8 @@
 import strax
-import logging
 from ..electron_timing import ElectronTiming
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.delayed_electrons.delayed_electrons_timing")
-
 
 @export
 class DelayedElectronsTiming(ElectronTiming):

fuse/plugins/detector_physics/delayed_electrons/photo_ionization_electrons.py

@@ -1,16 +1,12 @@
 import strax
 import straxen
 import numpy as np
-import logging
 from scipy.stats import truncexpon
 
 from ....plugin import FuseBasePlugin
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.delayed_electrons.photo_ionization_electrons")
-
 
 @export
 class PhotoIonizationElectrons(FuseBasePlugin):
@@ -162,7 +158,9 @@ def compute(self, interactions_in_roi, individual_electrons):
         mask = interactions_in_roi["sum_s2_photons"] > 0
 
         if not self.enable_delayed_electrons or (len(interactions_in_roi[mask]) == 0):
-            log.debug("No interactions with S2 photons found or delayed electrons are disabled")
+            self.log.debug(
+                "No interactions with S2 photons found or delayed electrons are disabled"
+            )
             return np.zeros(0, self.dtype)
 
         electrons_per_interaction, unique_cluster_id = group_electrons_by_cluster_id(

fuse/plugins/detector_physics/electron_drift.py

@@ -1,15 +1,11 @@
 import strax
 import straxen
-import logging
 import numpy as np
 
 from ...plugin import FuseBasePlugin
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.electron_drift")
-
 
 @export
 class ElectronDrift(FuseBasePlugin):
@@ -266,7 +262,7 @@ def compute(self, interactions_in_roi):
                 n=n_electron.astype(np.int32), p=electron_lifetime_correction
             )
         else:
-            log.debug("No electron lifetime applied")
+            self.log.debug("No electron lifetime applied")
 
         result = np.zeros(len(interactions_in_roi), dtype=self.dtype)
         result["time"] = interactions_in_roi["time"]

fuse/plugins/detector_physics/electron_extraction.py

@@ -1,5 +1,3 @@
-import logging
-
 import numpy as np
 import strax
 import straxen
@@ -8,9 +6,6 @@
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.electron_extraction")
-
 
 @export
 class ElectronExtraction(FuseBasePlugin):

fuse/plugins/detector_physics/electron_timing.py

@@ -1,15 +1,11 @@
 import strax
 import numpy as np
 import straxen
-import logging
 
 from ...plugin import FuseBasePlugin
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.electron_timing")
-
 
 @export
 class ElectronTiming(FuseBasePlugin):

fuse/plugins/detector_physics/s1_photon_hits.py

@@ -1,6 +1,5 @@
 import strax
 import straxen
-import logging
 
 import numpy as np
 from copy import deepcopy
@@ -10,9 +9,6 @@
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.s1_photon_hits")
-
 
 @export
 class S1PhotonHits(FuseBasePlugin):

fuse/plugins/detector_physics/s1_photon_propagation.py

@@ -1,5 +1,3 @@
-import logging
-
 import numpy as np
 import nestpy
 import strax
@@ -16,9 +14,6 @@
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.s1_photon_propagation")
-
 # Initialize the nestpy random generator
 # The seed will be set in the compute method
 nest_rng = nestpy.RandomGen.rndm()
@@ -137,9 +132,9 @@ def setup(self):
         if self.deterministic_seed or (self.user_defined_random_seed is not None):
             # Dont know but nestpy seems to have a problem with large seeds
             self.short_seed = int(repr(self.seed)[-8:])
-            log.debug(f"Generating nestpy random numbers from seed {self.short_seed}")
+            self.log.debug(f"Generating nestpy random numbers from seed {self.short_seed}")
         else:
-            log.debug("Generating random numbers with seed pulled from OS")
+            self.log.debug("Generating random numbers with seed pulled from OS")
 
         self.gains = pmt_gains(
             self.gain_model_mc,
@@ -338,7 +333,7 @@ class S1PhotonPropagation(S1PhotonPropagationBase):
     def setup(self):
         super().setup()
 
-        log.debug(
+        self.log.debug(
             "Using NEST for scintillation time without set calculator\n"
             "Creating new nestpy calculator"
         )

fuse/plugins/detector_physics/s2_photon_propagation.py

@@ -1,7 +1,6 @@
 import strax
 import straxen
 import numpy as np
-import logging
 
 from numba import njit
 from scipy.stats import skewnorm
@@ -18,9 +17,6 @@
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.s2_photon_propagation")
-
 conversion_to_bar = 1 / constants.elementary_charge / 1e1
 
 
@@ -338,7 +334,9 @@ def compute(self, interactions_in_roi, individual_electrons, start, end):
 
         n_chunks = len(electron_chunks)
         if n_chunks > 1:
-            log.info(f"Chunk size exceeding file size target. Downchunking to {n_chunks} chunks")
+            self.log.info(
+                f"Chunk size exceeding file size target. Downchunking to {n_chunks} chunks"
+            )
 
         last_start = start
         for i, electron_group in enumerate(electron_chunks):
@@ -601,7 +599,7 @@ class S2PhotonPropagation(S2PhotonPropagationBase):
 
     def setup(self):
         super().setup()
-        log.debug(
+        self.log.debug(
             "Using Garfield GasGap luminescence timing and optical propagation "
             f"with plugin version {self.__version__}"
         )
@@ -783,8 +781,8 @@ class S2PhotonPropagationSimple(S2PhotonPropagationBase):
 
     def setup(self):
         super().setup()
-        log.debug("Using simple luminescence timing and optical propagation")
-        log.warn(
+        self.log.debug("Using simple luminescence timing and optical propagation")
+        self.log.warn(
             "This is a legacy option, do you really want to use the simple luminescence model?"
         )
 

fuse/plugins/detector_physics/secondary_scintillation.py

@@ -1,4 +1,3 @@
-import logging
 from immutabledict import immutabledict
 
 import numpy as np
@@ -10,9 +9,6 @@
 
 export, __all__ = strax.exporter()
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.detector_physics.secondary_scintillation")
-
 
 @export
 class SecondaryScintillation(FuseBasePlugin):

fuse/plugins/micro_physics/detector_volumes.py

@@ -1,6 +1,5 @@
 import strax
 import straxen
-import logging
 
 from ...dtypes import (
     primary_positions_fields,
@@ -11,9 +10,6 @@
 from ...volume_plugin import VolumePlugin
 from ...vertical_merger_plugin import VerticalMergerPlugin
 
-logging.basicConfig(handlers=[logging.StreamHandler()])
-log = logging.getLogger("fuse.micro_physics.detector_volumes")
-
 
 class VolumesMerger(VerticalMergerPlugin):
     """Plugin that concatenates the clusters that are in the XENONnT TPC or the