From aa2cca99cedea1aed9153fa5366b03cf080be26d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henning=20Schulze=20Ei=C3=9Fing?= <h_schu55@uni-muenster.de>
Date: Thu, 21 Mar 2024 09:45:20 -0500
Subject: [PATCH 1/5] Add draft for PMT dark count simulation

---
 fuse/context.py                               |   1 +
 .../detector_physics/s1_photon_propagation.py |   2 +-
 .../detector_physics/s2_photon_propagation.py |   2 +-
 fuse/plugins/pmt_and_daq/__init__.py          |   3 +
 fuse/plugins/pmt_and_daq/dark_counts.py       | 213 ++++++++++++++++++
 fuse/plugins/pmt_and_daq/photon_summary.py    |   2 +-
 fuse/plugins/pmt_and_daq/pmt_afterpulses.py   |   2 +-
 fuse/plugins/truth_information/peak_truth.py  |   4 +-
 .../truth_information/records_truth.py        |   5 +-
 9 files changed, 228 insertions(+), 6 deletions(-)
 create mode 100644 fuse/plugins/pmt_and_daq/dark_counts.py

diff --git a/fuse/context.py b/fuse/context.py
index 905cc4c8..d9e7c403 100644
--- a/fuse/context.py
+++ b/fuse/context.py
@@ -43,6 +43,7 @@
 # Plugins to simulate PMTs and DAQ
 pmt_and_daq_plugins = [
     fuse.pmt_and_daq.PMTAfterPulses,
+    fuse.pmt_and_daq.DarkCounts,
     fuse.pmt_and_daq.PhotonSummary,
     fuse.pmt_and_daq.PulseWindow,
     fuse.pmt_and_daq.PMTResponseAndDAQ,
diff --git a/fuse/plugins/detector_physics/s1_photon_propagation.py b/fuse/plugins/detector_physics/s1_photon_propagation.py
index 2b43272c..b6e0231e 100644
--- a/fuse/plugins/detector_physics/s1_photon_propagation.py
+++ b/fuse/plugins/detector_physics/s1_photon_propagation.py
@@ -45,7 +45,7 @@ class S1PhotonPropagationBase(FuseBasePlugin):
         (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
         (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
         (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-        (("Type of the photon. S1 (1), S2 (2) or PMT AP (0)", "photon_type"), np.int8),
+        (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
     ]
     dtype = dtype + strax.time_fields
 
diff --git a/fuse/plugins/detector_physics/s2_photon_propagation.py b/fuse/plugins/detector_physics/s2_photon_propagation.py
index 70c79941..73480b11 100644
--- a/fuse/plugins/detector_physics/s2_photon_propagation.py
+++ b/fuse/plugins/detector_physics/s2_photon_propagation.py
@@ -52,7 +52,7 @@ class S2PhotonPropagationBase(FuseBaseDownChunkingPlugin):
         (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
         (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
         (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-        (("Type of the photon. S1 (1), S2 (2) or PMT AP (0)", "photon_type"), np.int8),
+        (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
     ]
     dtype = dtype + strax.time_fields
 
diff --git a/fuse/plugins/pmt_and_daq/__init__.py b/fuse/plugins/pmt_and_daq/__init__.py
index 0aa69962..c4e34a64 100644
--- a/fuse/plugins/pmt_and_daq/__init__.py
+++ b/fuse/plugins/pmt_and_daq/__init__.py
@@ -9,3 +9,6 @@
 
 from . import photon_pulses
 from .photon_pulses import *
+
+from . import dark_counts
+from .dark_counts import *
diff --git a/fuse/plugins/pmt_and_daq/dark_counts.py b/fuse/plugins/pmt_and_daq/dark_counts.py
new file mode 100644
index 00000000..56f21b3d
--- /dev/null
+++ b/fuse/plugins/pmt_and_daq/dark_counts.py
@@ -0,0 +1,213 @@
+import strax
+import straxen
+import logging
+import numpy as np
+
+from ...plugin import FuseBasePlugin
+from ...common import pmt_gains, build_photon_propagation_output
+from ...common import (
+    init_spe_scaling_factor_distributions,
+    photon_gain_calculation,
+)
+
+export, __all__ = strax.exporter()
+
+logging.basicConfig(handlers=[logging.StreamHandler()])
+log = logging.getLogger("fuse.pmt_and_daq.dark_counts")
+
+@export
+class DarkCounts(FuseBasePlugin):
+    """Plugin to simulate dark counts in a window around the physics interaction"""
+
+    __version__ = "0.0.1"
+
+    depends_on = "microphysics_summary"
+    provides = "dark_count_photons"
+    data_kind = "dark_count_photons"
+
+    save_when = strax.SaveWhen.TARGET
+
+    dtype = [
+        (("PMT channel of the photon", "channel"), np.int16),
+        (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
+        (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
+        (("ID of the cluster creating the photon", "cluster_id"), np.int32),
+        (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
+    ]
+    dtype = dtype + strax.time_fields
+
+    # Config options
+
+    enable_dark_counts = straxen.URLConfig(
+        default=False,
+        type=bool,
+        track=True,
+        help="Decide if you want to to enable dark count simulation",
+    )
+
+    # Get this value from a database. For now lets just set it to 50 Hz per PMT
+    dark_count_rate = straxen.URLConfig(
+        default=50 * 494,
+        type=(int, float),
+        track=True,
+        help="Rate of dark counts in Hz combined for all PMTs",
+    )
+
+    dark_count_left_window = straxen.URLConfig(
+        default=2e6,
+        type=int,
+        track=True,
+        help="Left window of the dark count simulation",
+    )
+
+    dark_count_right_window = straxen.URLConfig(
+        default=2e6,
+        type=int,
+        track=True,
+        help="Right window of the dark count simulation",
+    )
+
+    #Add a default pointing to the database
+    dark_count_probability_per_pmt = straxen.URLConfig(
+        track=True,
+        help="Probability of dark counts per PMT",
+    )
+
+    # reconsider this one for dark counts....
+    p_double_pe_emision = straxen.URLConfig(
+        default="take://resource://"
+        "SIMULATION_CONFIG_FILE.json?&fmt=json"
+        "&take=p_double_pe_emision",
+        type=(int, float),
+        cache=True,
+        help="Probability of double photo-electron emission",
+    )
+
+    pmt_circuit_load_resistor = straxen.URLConfig(
+        default="take://resource://"
+        "SIMULATION_CONFIG_FILE.json?&fmt=json"
+        "&take=pmt_circuit_load_resistor",
+        type=(int, float),
+        cache=True,
+        help="PMT circuit load resistor [kg m^2/(s^3 A)]",
+    )
+
+    digitizer_bits = straxen.URLConfig(
+        default="take://resource://SIMULATION_CONFIG_FILE.json?&fmt=json&take=digitizer_bits",
+        type=(int, float),
+        cache=True,
+        help="Number of bits of the digitizer boards",
+    )
+
+    digitizer_voltage_range = straxen.URLConfig(
+        default="take://resource://"
+        "SIMULATION_CONFIG_FILE.json?&fmt=json"
+        "&take=digitizer_voltage_range",
+        type=(int, float),
+        cache=True,
+        help="Voltage range of the digitizer boards [V]",
+    )
+
+    gain_model_mc = straxen.URLConfig(
+        default="cmt://to_pe_model?version=ONLINE&run_id=plugin.run_id",
+        infer_type=False,
+        help="PMT gain model",
+    )
+
+    photon_area_distribution = straxen.URLConfig(
+        default="simple_load://resource://simulation_config://"
+        "SIMULATION_CONFIG_FILE.json?"
+        "&key=photon_area_distribution"
+        "&fmt=csv",
+        cache=True,
+        help="Photon area distribution",
+    )
+
+    n_tpc_pmts = straxen.URLConfig(
+        type=int,
+        help="Number of PMTs in the TPC",
+    )
+
+    def setup(self):
+        super().setup()
+
+        # self.dark_count_probability_per_pmt = np.ones(494) / 494 # uniform distribution
+
+        self.gains = pmt_gains(
+            self.gain_model_mc,
+            digitizer_voltage_range=self.digitizer_voltage_range,
+            digitizer_bits=self.digitizer_bits,
+            pmt_circuit_load_resistor=self.pmt_circuit_load_resistor,
+        )
+
+        self.pmt_mask = np.array(self.gains) > 0  # Converted from to pe (from cmt by default)
+        self.turned_off_pmts = np.nonzero(np.array(self.gains) == 0)[0]
+
+        self.spe_scaling_factor_distributions = init_spe_scaling_factor_distributions(
+            self.photon_area_distribution
+        )
+
+    def compute(self, interactions_in_roi, start, end):
+        if not self.enable_dark_counts or (len(interactions_in_roi) == 0):
+            return np.zeros(0, dtype=self.dtype)
+
+        single_simulation_window = np.zeros(len(interactions_in_roi), dtype=strax.interval_dtype)
+        #single_simulation_window["length"] = (self.dark_count_left_window + self.dark_count_right_window)
+        single_simulation_window["time"] = interactions_in_roi["time"]
+        single_simulation_window["dt"] = np.ones(len(interactions_in_roi)) #length will give time in ns
+
+
+        simulation_windows = strax.concat_overlapping_hits(
+            single_simulation_window,
+            extensions=(self.dark_count_left_window, self.dark_count_right_window), 
+            pmt_channels=(0, self.n_tpc_pmts),
+            start = start,
+            end = end
+            )
+
+        #simulation_windows["time"] -= np.int64(left_window)
+
+        # Get the number of dark counts in the simulation window
+        expected_dark_counts_in_simulation_window = simulation_windows["length"].astype(np.int64) * self.dark_count_rate/1e9
+        dark_counts_in_simulation_window =self.rng.poisson(expected_dark_counts_in_simulation_window)
+        
+        dark_count_times = get_random_times(simulation_windows["length"], dark_counts_in_simulation_window, self.rng)
+        dark_count_times += np.repeat(simulation_windows["time"], dark_counts_in_simulation_window)
+
+        # Do we need to add the transit time spread here??
+        # I guess no as we just distribute the dark counts randomly in time and it will not make any difference
+
+
+        # distribute the dark counts to the PMTs
+        dark_count_channels = self.rng.choice(self.n_tpc_pmts, len(dark_count_times), p=self.dark_count_probability_per_pmt)
+
+
+        # We for sure need to update the inputs for this step
+        photon_gains, photon_is_dpe = photon_gain_calculation(
+            _photon_channels=dark_count_channels,
+            p_double_pe_emision=self.p_double_pe_emision,
+            gains=self.gains,
+            spe_scaling_factor_distributions=self.spe_scaling_factor_distributions,
+            rng=self.rng,
+            )
+        photon_is_dpe = False
+
+        # now build the output
+        result = build_photon_propagation_output(
+            dtype=self.dtype,
+            _photon_timings=dark_count_times,
+            _photon_channels=dark_count_channels,
+            _photon_gains=photon_gains,
+            _photon_is_dpe=photon_is_dpe,
+            _cluster_id=0, #rethink this part...
+            photon_type=3,
+        )
+
+        return result
+
+#For sure this can be done more efficiently 
+def get_random_times(interval_length, number_of_entries, rng):
+    times = []
+    for max_time, n in zip(interval_length, number_of_entries):
+        times.append(rng.uniform(0, max_time, n))
+    return np.concatenate(times)
\ No newline at end of file
diff --git a/fuse/plugins/pmt_and_daq/photon_summary.py b/fuse/plugins/pmt_and_daq/photon_summary.py
index 0f1b5f87..0f1bfc86 100644
--- a/fuse/plugins/pmt_and_daq/photon_summary.py
+++ b/fuse/plugins/pmt_and_daq/photon_summary.py
@@ -10,7 +10,7 @@ class PhotonSummary(VerticalMergerPlugin):
     """Plugin that concatenates propagated photons for S1, S2 and PMT
     afterpulses."""
 
-    depends_on = ("propagated_s2_photons", "propagated_s1_photons", "pmt_afterpulses")
+    depends_on = ("propagated_s2_photons", "propagated_s1_photons", "pmt_afterpulses", "dark_count_photons")
 
     provides = "photon_summary"
     data_kind = "propagated_photons"
diff --git a/fuse/plugins/pmt_and_daq/pmt_afterpulses.py b/fuse/plugins/pmt_and_daq/pmt_afterpulses.py
index 4affb54b..f1a00757 100644
--- a/fuse/plugins/pmt_and_daq/pmt_afterpulses.py
+++ b/fuse/plugins/pmt_and_daq/pmt_afterpulses.py
@@ -35,7 +35,7 @@ class PMTAfterPulses(FuseBasePlugin):
         (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
         (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
         (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-        (("Type of the photon. S1 (1), S2 (2) or PMT AP (0)", "photon_type"), np.int8),
+        (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
     ]
     dtype = dtype + strax.time_fields
 
diff --git a/fuse/plugins/truth_information/peak_truth.py b/fuse/plugins/truth_information/peak_truth.py
index 3cd4e86e..5d87d9f5 100644
--- a/fuse/plugins/truth_information/peak_truth.py
+++ b/fuse/plugins/truth_information/peak_truth.py
@@ -9,7 +9,7 @@
 
 @export
 class PeakTruth(strax.OverlapWindowPlugin):
-    __version__ = "0.0.3"
+    __version__ = "0.0.4"
 
     depends_on = (
         "photon_summary",
@@ -26,6 +26,7 @@ class PeakTruth(strax.OverlapWindowPlugin):
         ("s1_photons_in_peak", np.int32),
         ("s2_photons_in_peak", np.int32),
         ("ap_photons_in_peak", np.int32),
+        ("dark_count_photons_in_peak", np.int32),
         ("raw_area_truth", np.float32),
         ("observable_energy_truth", np.float32),
         ("number_of_contributing_clusters_s1", np.int16),
@@ -113,6 +114,7 @@ def compute(self, interactions_in_roi, propagated_photons, peaks):
             "s1": 1,
             "s2": 2,
             "ap": 0,
+            "dark_count": 3,
         }
 
         for i in range(n_peaks):
diff --git a/fuse/plugins/truth_information/records_truth.py b/fuse/plugins/truth_information/records_truth.py
index 2f57debd..43075f7c 100644
--- a/fuse/plugins/truth_information/records_truth.py
+++ b/fuse/plugins/truth_information/records_truth.py
@@ -12,7 +12,7 @@
 class RecordsTruth(strax.Plugin):
     """Plugin that computes the truth information for raw_records."""
 
-    __version__ = "0.0.1"
+    __version__ = "0.0.2"
 
     depends_on = ("raw_records", "photon_summary")
     provides = "records_truth"
@@ -21,6 +21,7 @@ class RecordsTruth(strax.Plugin):
         (("Number of S1 photons in record", "s1_photons_in_record"), np.int32),
         (("Number of S2 photons in record", "s2_photons_in_record"), np.int32),
         (("Number of AP photons in record", "ap_photons_in_record"), np.int32),
+        (("Number of dark counts in record", "dark_count_photons_in_record"), np.int32),
         (("Sum of the photon gains", "raw_area"), np.float32),
     ]
 
@@ -97,6 +98,7 @@ def compute(self, raw_records, propagated_photons):
             result["s1_photons_in_record"][result_mask] = result_buffer["s1_photons_in_record"]
             result["s2_photons_in_record"][result_mask] = result_buffer["s2_photons_in_record"]
             result["ap_photons_in_record"][result_mask] = result_buffer["ap_photons_in_record"]
+            result["dark_count_photons_in_record"][result_mask] = result_buffer["dark_count_photons_in_record"]
 
         return result
 
@@ -109,6 +111,7 @@ def fill_result_buffer(list_input, result_buffer):
         result_buffer["s1_photons_in_record"][i] = np.sum(photons["photon_type"] == 1)
         result_buffer["s2_photons_in_record"][i] = np.sum(photons["photon_type"] == 2)
         result_buffer["ap_photons_in_record"][i] = np.sum(photons["photon_type"] == 0)
+        result_buffer["dark_count_photons_in_record"][i] = np.sum(photons["photon_type"] == 3)
 
 
 def split_photons_by_channel(propagated_photons):

From 0e4166b16d41fdfc143b1a0addea5a92b01f6f3b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 21 Mar 2024 14:47:07 +0000
Subject: [PATCH 2/5] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../detector_physics/s1_photon_propagation.py |  5 +-
 .../detector_physics/s2_photon_propagation.py |  5 +-
 fuse/plugins/pmt_and_daq/dark_counts.py       | 57 ++++++++++++-------
 fuse/plugins/pmt_and_daq/photon_summary.py    |  7 ++-
 fuse/plugins/pmt_and_daq/pmt_afterpulses.py   |  5 +-
 .../truth_information/records_truth.py        |  4 +-
 6 files changed, 56 insertions(+), 27 deletions(-)

diff --git a/fuse/plugins/detector_physics/s1_photon_propagation.py b/fuse/plugins/detector_physics/s1_photon_propagation.py
index b6e0231e..56fe8bc6 100644
--- a/fuse/plugins/detector_physics/s1_photon_propagation.py
+++ b/fuse/plugins/detector_physics/s1_photon_propagation.py
@@ -45,7 +45,10 @@ class S1PhotonPropagationBase(FuseBasePlugin):
         (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
         (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
         (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-        (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
+        (
+            ("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"),
+            np.int8,
+        ),
     ]
     dtype = dtype + strax.time_fields
 
diff --git a/fuse/plugins/detector_physics/s2_photon_propagation.py b/fuse/plugins/detector_physics/s2_photon_propagation.py
index 73480b11..19d0156c 100644
--- a/fuse/plugins/detector_physics/s2_photon_propagation.py
+++ b/fuse/plugins/detector_physics/s2_photon_propagation.py
@@ -52,7 +52,10 @@ class S2PhotonPropagationBase(FuseBaseDownChunkingPlugin):
         (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
         (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
         (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-        (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
+        (
+            ("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"),
+            np.int8,
+        ),
     ]
     dtype = dtype + strax.time_fields
 
diff --git a/fuse/plugins/pmt_and_daq/dark_counts.py b/fuse/plugins/pmt_and_daq/dark_counts.py
index 56f21b3d..14a59e34 100644
--- a/fuse/plugins/pmt_and_daq/dark_counts.py
+++ b/fuse/plugins/pmt_and_daq/dark_counts.py
@@ -15,9 +15,11 @@
 logging.basicConfig(handlers=[logging.StreamHandler()])
 log = logging.getLogger("fuse.pmt_and_daq.dark_counts")
 
+
 @export
 class DarkCounts(FuseBasePlugin):
-    """Plugin to simulate dark counts in a window around the physics interaction"""
+    """Plugin to simulate dark counts in a window around the physics
+    interaction."""
 
     __version__ = "0.0.1"
 
@@ -32,7 +34,10 @@ class DarkCounts(FuseBasePlugin):
         (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
         (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
         (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-        (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
+        (
+            ("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"),
+            np.int8,
+        ),
     ]
     dtype = dtype + strax.time_fields
 
@@ -67,7 +72,7 @@ class DarkCounts(FuseBasePlugin):
         help="Right window of the dark count simulation",
     )
 
-    #Add a default pointing to the database
+    # Add a default pointing to the database
     dark_count_probability_per_pmt = straxen.URLConfig(
         track=True,
         help="Probability of dark counts per PMT",
@@ -152,35 +157,42 @@ def compute(self, interactions_in_roi, start, end):
             return np.zeros(0, dtype=self.dtype)
 
         single_simulation_window = np.zeros(len(interactions_in_roi), dtype=strax.interval_dtype)
-        #single_simulation_window["length"] = (self.dark_count_left_window + self.dark_count_right_window)
+        # single_simulation_window["length"] = (self.dark_count_left_window + self.dark_count_right_window)
         single_simulation_window["time"] = interactions_in_roi["time"]
-        single_simulation_window["dt"] = np.ones(len(interactions_in_roi)) #length will give time in ns
-
+        single_simulation_window["dt"] = np.ones(
+            len(interactions_in_roi)
+        )  # length will give time in ns
 
         simulation_windows = strax.concat_overlapping_hits(
             single_simulation_window,
-            extensions=(self.dark_count_left_window, self.dark_count_right_window), 
+            extensions=(self.dark_count_left_window, self.dark_count_right_window),
             pmt_channels=(0, self.n_tpc_pmts),
-            start = start,
-            end = end
-            )
+            start=start,
+            end=end,
+        )
 
-        #simulation_windows["time"] -= np.int64(left_window)
+        # simulation_windows["time"] -= np.int64(left_window)
 
         # Get the number of dark counts in the simulation window
-        expected_dark_counts_in_simulation_window = simulation_windows["length"].astype(np.int64) * self.dark_count_rate/1e9
-        dark_counts_in_simulation_window =self.rng.poisson(expected_dark_counts_in_simulation_window)
-        
-        dark_count_times = get_random_times(simulation_windows["length"], dark_counts_in_simulation_window, self.rng)
+        expected_dark_counts_in_simulation_window = (
+            simulation_windows["length"].astype(np.int64) * self.dark_count_rate / 1e9
+        )
+        dark_counts_in_simulation_window = self.rng.poisson(
+            expected_dark_counts_in_simulation_window
+        )
+
+        dark_count_times = get_random_times(
+            simulation_windows["length"], dark_counts_in_simulation_window, self.rng
+        )
         dark_count_times += np.repeat(simulation_windows["time"], dark_counts_in_simulation_window)
 
         # Do we need to add the transit time spread here??
         # I guess no as we just distribute the dark counts randomly in time and it will not make any difference
 
-
         # distribute the dark counts to the PMTs
-        dark_count_channels = self.rng.choice(self.n_tpc_pmts, len(dark_count_times), p=self.dark_count_probability_per_pmt)
-
+        dark_count_channels = self.rng.choice(
+            self.n_tpc_pmts, len(dark_count_times), p=self.dark_count_probability_per_pmt
+        )
 
         # We for sure need to update the inputs for this step
         photon_gains, photon_is_dpe = photon_gain_calculation(
@@ -189,7 +201,7 @@ def compute(self, interactions_in_roi, start, end):
             gains=self.gains,
             spe_scaling_factor_distributions=self.spe_scaling_factor_distributions,
             rng=self.rng,
-            )
+        )
         photon_is_dpe = False
 
         # now build the output
@@ -199,15 +211,16 @@ def compute(self, interactions_in_roi, start, end):
             _photon_channels=dark_count_channels,
             _photon_gains=photon_gains,
             _photon_is_dpe=photon_is_dpe,
-            _cluster_id=0, #rethink this part...
+            _cluster_id=0,  # rethink this part...
             photon_type=3,
         )
 
         return result
 
-#For sure this can be done more efficiently 
+
+# For sure this can be done more efficiently
 def get_random_times(interval_length, number_of_entries, rng):
     times = []
     for max_time, n in zip(interval_length, number_of_entries):
         times.append(rng.uniform(0, max_time, n))
-    return np.concatenate(times)
\ No newline at end of file
+    return np.concatenate(times)
diff --git a/fuse/plugins/pmt_and_daq/photon_summary.py b/fuse/plugins/pmt_and_daq/photon_summary.py
index 0f1bfc86..1bf83587 100644
--- a/fuse/plugins/pmt_and_daq/photon_summary.py
+++ b/fuse/plugins/pmt_and_daq/photon_summary.py
@@ -10,7 +10,12 @@ class PhotonSummary(VerticalMergerPlugin):
     """Plugin that concatenates propagated photons for S1, S2 and PMT
     afterpulses."""
 
-    depends_on = ("propagated_s2_photons", "propagated_s1_photons", "pmt_afterpulses", "dark_count_photons")
+    depends_on = (
+        "propagated_s2_photons",
+        "propagated_s1_photons",
+        "pmt_afterpulses",
+        "dark_count_photons",
+    )
 
     provides = "photon_summary"
     data_kind = "propagated_photons"
diff --git a/fuse/plugins/pmt_and_daq/pmt_afterpulses.py b/fuse/plugins/pmt_and_daq/pmt_afterpulses.py
index f1a00757..a2c3d633 100644
--- a/fuse/plugins/pmt_and_daq/pmt_afterpulses.py
+++ b/fuse/plugins/pmt_and_daq/pmt_afterpulses.py
@@ -35,7 +35,10 @@ class PMTAfterPulses(FuseBasePlugin):
         (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
         (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
         (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-        (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
+        (
+            ("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"),
+            np.int8,
+        ),
     ]
     dtype = dtype + strax.time_fields
 
diff --git a/fuse/plugins/truth_information/records_truth.py b/fuse/plugins/truth_information/records_truth.py
index 43075f7c..a78c62be 100644
--- a/fuse/plugins/truth_information/records_truth.py
+++ b/fuse/plugins/truth_information/records_truth.py
@@ -98,7 +98,9 @@ def compute(self, raw_records, propagated_photons):
             result["s1_photons_in_record"][result_mask] = result_buffer["s1_photons_in_record"]
             result["s2_photons_in_record"][result_mask] = result_buffer["s2_photons_in_record"]
             result["ap_photons_in_record"][result_mask] = result_buffer["ap_photons_in_record"]
-            result["dark_count_photons_in_record"][result_mask] = result_buffer["dark_count_photons_in_record"]
+            result["dark_count_photons_in_record"][result_mask] = result_buffer[
+                "dark_count_photons_in_record"
+            ]
 
         return result
 

From a2620557367cdf17b8d5e69aecee40d551004d92 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henning=20Schulze=20Ei=C3=9Fing?= <h_schu55@uni-muenster.de>
Date: Thu, 21 Mar 2024 16:53:52 +0100
Subject: [PATCH 3/5] Cleanup

---
 fuse/plugins/pmt_and_daq/dark_counts.py | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/fuse/plugins/pmt_and_daq/dark_counts.py b/fuse/plugins/pmt_and_daq/dark_counts.py
index 14a59e34..f2ae4373 100644
--- a/fuse/plugins/pmt_and_daq/dark_counts.py
+++ b/fuse/plugins/pmt_and_daq/dark_counts.py
@@ -157,11 +157,8 @@ def compute(self, interactions_in_roi, start, end):
             return np.zeros(0, dtype=self.dtype)
 
         single_simulation_window = np.zeros(len(interactions_in_roi), dtype=strax.interval_dtype)
-        # single_simulation_window["length"] = (self.dark_count_left_window + self.dark_count_right_window)
         single_simulation_window["time"] = interactions_in_roi["time"]
-        single_simulation_window["dt"] = np.ones(
-            len(interactions_in_roi)
-        )  # length will give time in ns
+        single_simulation_window["dt"] = np.ones(len(interactions_in_roi))
 
         simulation_windows = strax.concat_overlapping_hits(
             single_simulation_window,
@@ -171,8 +168,6 @@ def compute(self, interactions_in_roi, start, end):
             end=end,
         )
 
-        # simulation_windows["time"] -= np.int64(left_window)
-
         # Get the number of dark counts in the simulation window
         expected_dark_counts_in_simulation_window = (
             simulation_windows["length"].astype(np.int64) * self.dark_count_rate / 1e9
@@ -186,9 +181,6 @@ def compute(self, interactions_in_roi, start, end):
         )
         dark_count_times += np.repeat(simulation_windows["time"], dark_counts_in_simulation_window)
 
-        # Do we need to add the transit time spread here??
-        # I guess no as we just distribute the dark counts randomly in time and it will not make any difference
-
         # distribute the dark counts to the PMTs
         dark_count_channels = self.rng.choice(
             self.n_tpc_pmts, len(dark_count_times), p=self.dark_count_probability_per_pmt

From 2bbcda3595e7c6ce39050d0d55288b9be91de2e1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henning=20Schulze=20Ei=C3=9Fing?= <h_schu55@uni-muenster.de>
Date: Mon, 25 Mar 2024 07:49:55 -0500
Subject: [PATCH 4/5] Make dark_count_probability_per_pmt optional

---
 fuse/plugins/pmt_and_daq/dark_counts.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/fuse/plugins/pmt_and_daq/dark_counts.py b/fuse/plugins/pmt_and_daq/dark_counts.py
index f2ae4373..ee95ced8 100644
--- a/fuse/plugins/pmt_and_daq/dark_counts.py
+++ b/fuse/plugins/pmt_and_daq/dark_counts.py
@@ -74,6 +74,7 @@ class DarkCounts(FuseBasePlugin):
 
     # Add a default pointing to the database
     dark_count_probability_per_pmt = straxen.URLConfig(
+        default=None,
         track=True,
         help="Probability of dark counts per PMT",
     )
@@ -136,8 +137,6 @@ class DarkCounts(FuseBasePlugin):
     def setup(self):
         super().setup()
 
-        # self.dark_count_probability_per_pmt = np.ones(494) / 494 # uniform distribution
-
         self.gains = pmt_gains(
             self.gain_model_mc,
             digitizer_voltage_range=self.digitizer_voltage_range,
@@ -182,9 +181,13 @@ def compute(self, interactions_in_roi, start, end):
         dark_count_times += np.repeat(simulation_windows["time"], dark_counts_in_simulation_window)
 
         # distribute the dark counts to the PMTs
-        dark_count_channels = self.rng.choice(
-            self.n_tpc_pmts, len(dark_count_times), p=self.dark_count_probability_per_pmt
-        )
+        if self.dark_count_probability_per_pmt is None:
+            log.warning("No dark count probability per PMT provided. Using uniform distribution.")
+            dark_count_channels = self.rng.choice(self.n_tpc_pmts, len(dark_count_times))
+        else:
+            dark_count_channels = self.rng.choice(
+                self.n_tpc_pmts, len(dark_count_times), p=self.dark_count_probability_per_pmt
+            )
 
         # We for sure need to update the inputs for this step
         photon_gains, photon_is_dpe = photon_gain_calculation(

From d49e69397ea14bcd039766f03b39d2a1a27db502 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henning=20Schulze=20Ei=C3=9Fing?= <h_schu55@uni-muenster.de>
Date: Fri, 19 Apr 2024 14:05:42 +0200
Subject: [PATCH 5/5] Update DarkCounts dtype

---
 fuse/dtypes.py                          |  2 +-
 fuse/plugins/pmt_and_daq/dark_counts.py | 13 ++-----------
 2 files changed, 3 insertions(+), 12 deletions(-)

diff --git a/fuse/dtypes.py b/fuse/dtypes.py
index 65acfafd..058bcef4 100644
--- a/fuse/dtypes.py
+++ b/fuse/dtypes.py
@@ -74,5 +74,5 @@
     (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
     (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
     (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-    (("Type of the photon. S1 (1), S2 (2) or PMT AP (0)", "photon_type"), np.int8),
+    (("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"), np.int8),
 ]
diff --git a/fuse/plugins/pmt_and_daq/dark_counts.py b/fuse/plugins/pmt_and_daq/dark_counts.py
index ee95ced8..62ae9142 100644
--- a/fuse/plugins/pmt_and_daq/dark_counts.py
+++ b/fuse/plugins/pmt_and_daq/dark_counts.py
@@ -4,6 +4,7 @@
 import numpy as np
 
 from ...plugin import FuseBasePlugin
+from ...dtypes import propagated_photons_fields
 from ...common import pmt_gains, build_photon_propagation_output
 from ...common import (
     init_spe_scaling_factor_distributions,
@@ -29,17 +30,7 @@ class DarkCounts(FuseBasePlugin):
 
     save_when = strax.SaveWhen.TARGET
 
-    dtype = [
-        (("PMT channel of the photon", "channel"), np.int16),
-        (("Photon creates a double photo-electron emission", "dpe"), np.bool_),
-        (("Sampled PMT gain for the photon", "photon_gain"), np.int32),
-        (("ID of the cluster creating the photon", "cluster_id"), np.int32),
-        (
-            ("Type of the photon. S1 (1), S2 (2), PMT AP (0) or dark count (3)", "photon_type"),
-            np.int8,
-        ),
-    ]
-    dtype = dtype + strax.time_fields
+    dtype = propagated_photons_fields + strax.time_fields
 
     # Config options