Embellish some codes (#188)

* Embellish some codes

* Fix bug

* Usually the data_kind is in lower case

docs/source/build_plugin_pages.py

@@ -10,9 +10,9 @@
     tpc_interactions="#F44E43",
     below_cathode_interactions="#F44E43",
     interactions_in_roi="#56C46C",
-    S1_photons="#54E4CF",
-    S2_photons="#54E4CF",
-    AP_photons="#54E4CF",
+    s1_photons="#54E4CF",
+    s2_photons="#54E4CF",
+    ap_photons="#54E4CF",
     propagated_photons="#54E4CF",
     pulse_ids="#54E4CF",
     pulse_windows="#F78C27",

fuse/common.py

@@ -24,11 +24,9 @@ def dynamic_chunking(data, scale, n_min):
         if value <= scale:
             clusters.append(c)
             n_cluster += 1
-
         elif n_cluster + 1 < n_min:
             clusters.append(c)
             n_cluster += 1
-
         elif value > scale:
             c = c + 1
             clusters.append(c)

fuse/plugin.py

@@ -26,12 +26,12 @@ class FuseBasePlugin(strax.Plugin):
     deterministic_seed = straxen.URLConfig(
         default=True,
         type=bool,
-        help="Set the random seed from lineage and run_id, or pull the seed from the OS.",
+        help="Set the random seed from lineage and run_id, or pull the seed from the OS",
     )
 
     user_defined_random_seed = straxen.URLConfig(
         default=None,
-        help="Define the random seed manually. You need to set deterministic_seed to False.",
+        help="Define the random seed manually. You need to set deterministic_seed to False",
     )
 
     def setup(self):

fuse/plugins/detector_physics/csv_input.py

@@ -20,7 +20,7 @@ class ChunkCsvInput(FuseBasePlugin):
     """Plugin which reads a CSV file containing instructions for the detector
     physics simulation and returns the data in chunks."""
 
-    __version__ = "0.2.0"
+    __version__ = "0.2.1"
 
     depends_on: Tuple = tuple()
     provides = "microphysics_summary"
@@ -34,9 +34,9 @@ class ChunkCsvInput(FuseBasePlugin):
         (("x position of the cluster [cm]", "x"), np.float32),
         (("y position of the cluster [cm]", "y"), np.float32),
         (("z position of the cluster [cm]", "z"), np.float32),
-        (("Number of photons at interaction position.", "photons"), np.int32),
-        (("Number of electrons at interaction position.", "electrons"), np.int32),
-        (("Number of excitons at interaction position.", "excitons"), np.int32),
+        (("Number of photons at interaction position", "photons"), np.int32),
+        (("Number of electrons at interaction position", "electrons"), np.int32),
+        (("Number of excitons at interaction position", "excitons"), np.int32),
         (("Electric field value at the cluster position [V/cm]", "e_field"), np.float32),
         (("Energy of the cluster [keV]", "ed"), np.float32),
         (("NEST interaction type", "nestid"), np.int8),
@@ -62,15 +62,15 @@ class ChunkCsvInput(FuseBasePlugin):
     separation_scale = straxen.URLConfig(
         default=1e8,
         type=(int, float),
-        help="separation_scale",
+        help="Start a new chunk when the previous cluster is separated by this time scale",
     )
 
     source_rate = straxen.URLConfig(
         default=1,
         type=(int, float),
-        help="Source rate used to generate event times"
-        "Use a value >0 to generate event times in fuse"
-        "Use source_rate = 0 to use event times from the input file (only for csv input)",
+        help="Source rate used to generate event times. "
+        "Use a value >0 to generate event times in fuse. "
+        "Use source_rate = 0 to use event times from the input file (only for csv input).",
     )
 
     n_interactions_per_chunk = straxen.URLConfig(
@@ -150,9 +150,9 @@ def __init__(
             (("x position of the cluster [cm]", "x"), np.float32),
             (("y position of the cluster [cm]", "y"), np.float32),
             (("z position of the cluster [cm]", "z"), np.float32),
-            (("Number of photons at interaction position.", "photons"), np.int32),
-            (("Number of electrons at interaction position.", "electrons"), np.int32),
-            (("Number of excitons at interaction position.", "excitons"), np.int32),
+            (("Number of photons at interaction position", "photons"), np.int32),
+            (("Number of electrons at interaction position", "electrons"), np.int32),
+            (("Number of excitons at interaction position", "excitons"), np.int32),
             (("Electric field value at the cluster position [V/cm]", "e_field"), np.float32),
             (("Energy of the cluster [keV]", "ed"), np.float32),
             (("NEST interaction type", "nestid"), np.int8),
@@ -225,7 +225,7 @@ 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 to high?")
+            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,

fuse/plugins/detector_physics/electron_timing.py

@@ -20,16 +20,14 @@ class ElectronTiming(FuseBasePlugin):
     extraction.
     """
 
-    __version__ = "0.2.0"
+    __version__ = "0.2.1"
 
-    depends_on = ("drifted_electrons", "extracted_electrons", "microphysics_summary")
+    depends_on = ("microphysics_summary", "drifted_electrons", "extracted_electrons")
     provides = "electron_time"
     data_kind = "individual_electrons"
 
     save_when = strax.SaveWhen.TARGET
 
-    data_kind = "individual_electrons"
-
     dtype = [
         (("x position of the electron [cm]", "x"), np.float32),
         (("y position of the electron [cm]", "y"), np.float32),

fuse/plugins/detector_physics/s1_photon_propagation.py

@@ -32,11 +32,11 @@ class S1PhotonPropagationBase(FuseBasePlugin):
     Note: The timing calculation is defined in the child plugin.
     """
 
-    __version__ = "0.3.0"
+    __version__ = "0.3.1"
 
-    depends_on = ("s1_photons", "microphysics_summary")
+    depends_on = ("microphysics_summary", "s1_photons")
     provides = "propagated_s1_photons"
-    data_kind = "S1_photons"
+    data_kind = "s1_photons"
 
     save_when = strax.SaveWhen.TARGET
 

fuse/plugins/detector_physics/s2_photon_propagation.py

@@ -32,18 +32,18 @@ class S2PhotonPropagationBase(FuseBaseDownChunkingPlugin):
     Note: The timing calculation is defined in the child plugin.
     """
 
-    __version__ = "0.3.2"
+    __version__ = "0.3.3"
 
     depends_on = (
-        "electron_time",
-        "s2_photons",
+        "microphysics_summary",
         "extracted_electrons",
         "drifted_electrons",
         "s2_photons_sum",
-        "microphysics_summary",
+        "electron_time",
+        "s2_photons",
     )
     provides = "propagated_s2_photons"
-    data_kind = "S2_photons"
+    data_kind = "s2_photons"
 
     save_when = strax.SaveWhen.TARGET
 
@@ -318,7 +318,7 @@ def rz_map(z, xy, **kwargs):
 
             self.field_dependencies_map = rz_map
 
-    def compute(self, individual_electrons, interactions_in_roi, start, end):
+    def compute(self, interactions_in_roi, individual_electrons, start, end):
         # Just apply this to clusters with photons
         mask = interactions_in_roi["n_electron_extracted"] > 0
 
@@ -689,14 +689,14 @@ class S2PhotonPropagationSimple(S2PhotonPropagationBase):
         default="take://resource://SIMULATION_CONFIG_FILE.json?&fmt=json&take=pressure",
         type=(int, float),
         cache=True,
-        help="pressure",
+        help="Pressure of liquid xenon [bar/e], while e is the elementary charge",
     )
 
     temperature = straxen.URLConfig(
         default="take://resource://SIMULATION_CONFIG_FILE.json?&fmt=json&take=temperature",
         type=(int, float),
         cache=True,
-        help="temperature",
+        help="Temperature of liquid xenon [K]",
     )
 
     gas_drift_velocity_slope = straxen.URLConfig(
@@ -759,14 +759,14 @@ class S2PhotonPropagationSimple(S2PhotonPropagationBase):
         "&take=gate_to_anode_distance",
         type=(int, float),
         cache=True,
-        help="gate_to_anode_distance",
+        help="Top of gate to bottom of anode (not considering perpendicular wires) [cm]",
     )
 
     anode_voltage = straxen.URLConfig(
         default="take://resource://SIMULATION_CONFIG_FILE.json?&fmt=json&take=anode_voltage",
         type=(int, float),
         cache=True,
-        help="anode_voltage",
+        help="Voltage of anode [V]",
     )
 
     lxe_dielectric_constant = straxen.URLConfig(

fuse/plugins/detector_physics/secondary_scintillation.py

@@ -25,10 +25,10 @@ class SecondaryScintillation(FuseBasePlugin):
     result_name_photons_sum = "s2_photons_sum"
 
     depends_on = (
+        "microphysics_summary",
         "drifted_electrons",
         "extracted_electrons",
         "electron_time",
-        "microphysics_summary",
     )
     provides = (result_name_photons, result_name_photons_sum)
     data_kind = {

fuse/plugins/micro_physics/detector_volumes.py

@@ -41,7 +41,7 @@ class XENONnT_TPC(VolumePlugin):
 
     provides = "tpc_interactions"
     data_kind = "tpc_interactions"
-    __version__ = "0.3.0"
+    __version__ = "0.3.1"
 
     # Can we import this from MergeCluster and just add the needed fields?
     dtype = [
@@ -57,9 +57,9 @@ class XENONnT_TPC(VolumePlugin):
         (("y position of the primary particle [cm]", "y_pri"), np.float32),
         (("z position of the primary particle [cm]", "z_pri"), np.float32),
         (("ID of the cluster", "cluster_id"), np.int32),
-        (("Xenon density at the cluster position.", "xe_density"), np.float32),
-        (("ID of the volume in which the cluster occured.", "vol_id"), np.int8),
-        (("Flag indicating if a cluster can create a S2 signal.", "create_S2"), np.bool_),
+        (("Xenon density at the cluster position", "xe_density"), np.float32),
+        (("ID of the volume in which the cluster occured", "vol_id"), np.int8),
+        (("Flag indicating if a cluster can create a S2 signal", "create_S2"), np.bool_),
     ]
 
     dtype = dtype + strax.time_fields
@@ -126,7 +126,7 @@ class XENONnT_BelowCathode(VolumePlugin):
 
     provides = "below_cathode_interactions"
     data_kind = "below_cathode_interactions"
-    __version__ = "0.3.0"
+    __version__ = "0.3.1"
 
     # Can we import this from MergeCluster and just add the needed fields?
     dtype = [
@@ -142,9 +142,9 @@ class XENONnT_BelowCathode(VolumePlugin):
         (("y position of the primary particle [cm]", "y_pri"), np.float32),
         (("z position of the primary particle [cm]", "z_pri"), np.float32),
         (("ID of the cluster", "cluster_id"), np.int32),
-        (("Xenon density at the cluster position.", "xe_density"), np.float32),
-        (("ID of the volume in which the cluster occured.", "vol_id"), np.int8),
-        (("Flag indicating if a cluster can create a S2 signal.", "create_S2"), np.bool_),
+        (("Xenon density at the cluster position", "xe_density"), np.float32),
+        (("ID of the volume in which the cluster occured", "vol_id"), np.int8),
+        (("Flag indicating if a cluster can create a S2 signal", "create_S2"), np.bool_),
     ]
 
     dtype = dtype + strax.time_fields
@@ -209,7 +209,7 @@ class XENONnT_GasPhase(VolumePlugin):
 
     provides = "gas_phase_interactions"
     data_kind = "gas_phase_interactions"
-    __version__ = "0.3.0"
+    __version__ = "0.3.1"
 
     # Can we import this from MergeCluster and just add the needed fields?
     dtype = [
@@ -225,9 +225,9 @@ class XENONnT_GasPhase(VolumePlugin):
         (("y position of the primary particle [cm]", "y_pri"), np.float32),
         (("z position of the primary particle [cm]", "z_pri"), np.float32),
         (("ID of the cluster", "cluster_id"), np.int32),
-        (("Xenon density at the cluster position.", "xe_density"), np.float32),
-        (("ID of the volume in which the cluster occured.", "vol_id"), np.int8),
-        (("Flag indicating if a cluster can create a S2 signal.", "create_S2"), np.bool_),
+        (("Xenon density at the cluster position", "xe_density"), np.float32),
+        (("ID of the volume in which the cluster occured", "vol_id"), np.int8),
+        (("Flag indicating if a cluster can create a S2 signal", "create_S2"), np.bool_),
     ]
 
     dtype = dtype + strax.time_fields
@@ -237,31 +237,31 @@ class XENONnT_GasPhase(VolumePlugin):
     xenonnt_z_top_pmts = straxen.URLConfig(
         default=7.3936,  # cm
         type=(int, float),
-        help="xenonnt_z_top_pmts",
+        help="Position of the top of gas phase [cm]",
     )
 
     xenonnt_z_lxe = straxen.URLConfig(
         default=0.416,  # cm ... liquid-gas interface
         type=(int, float),
-        help="xenonnt_z_lxe",
+        help="Position of the bottom of gas phase [cm]",
     )
 
     xenonnt_sensitive_volume_radius = straxen.URLConfig(
         default=66.4,  # cm
         type=(int, float),
-        help="xenonnt_sensitive_volume_radius",
+        help="Radius of the XENONnT TPC [cm]",
     )
 
     xenon_density_gas_phase = straxen.URLConfig(
         default=0.0177,
         type=(int, float),
-        help="xenon_density",
+        help="Density of XENON in the gas phase [g/cm3]",
     )
 
     create_S2_xenonnt_gas_phase = straxen.URLConfig(
         default=False,
         type=bool,
-        help="No S2s in gas",
+        help="Whether generate S2s in gas phase",
     )
 
     def compute(self, clustered_interactions):

fuse/plugins/micro_physics/electric_field.py

@@ -18,7 +18,7 @@ class ElectricField(FuseBasePlugin):
 
     __version__ = "0.2.2"
 
-    depends_on = ("interactions_in_roi",)
+    depends_on = "interactions_in_roi"
     provides = "electric_field_values"
     data_kind = "interactions_in_roi"
 

fuse/plugins/micro_physics/input.py

@@ -27,7 +27,7 @@ class ChunkInput(FuseBasePlugin):
     and will create multiple chunks of data if needed.
     """
 
-    __version__ = "0.3.1"
+    __version__ = "0.3.2"
 
     depends_on: Tuple = tuple()
     provides = "geant4_interactions"
@@ -47,9 +47,9 @@ class ChunkInput(FuseBasePlugin):
         (("Geant4 process creating the particle", "creaproc"), "<U25"),
         (("Geant4 process responsible for the energy deposit", "edproc"), "<U25"),
         (("Geant4 event ID", "evtid"), np.int32),
-        (("x position of the primary particle", "x_pri"), np.float32),
-        (("y position of the primary particle", "y_pri"), np.float32),
-        (("z position of the primary particle", "z_pri"), np.float32),
+        (("x position of the primary particle [cm]", "x_pri"), np.float32),
+        (("y position of the primary particle [cm]", "y_pri"), np.float32),
+        (("z position of the primary particle [cm]", "z_pri"), np.float32),
     ]
 
     dtype = dtype + strax.time_fields
@@ -86,7 +86,7 @@ class ChunkInput(FuseBasePlugin):
     cut_delayed = straxen.URLConfig(
         default=9e18,
         type=(int, float),
-        help="All interactions happening after this time (including the event time) will be cut.",
+        help="All interactions happening after this time (including the event time) will be cut",
     )
 
     n_interactions_per_chunk = straxen.URLConfig(
@@ -98,12 +98,12 @@ class ChunkInput(FuseBasePlugin):
     entry_start = straxen.URLConfig(
         default=0,
         type=(int, float),
-        help="Geant4 event to start simulation from.",
+        help="Geant4 event to start simulation from",
     )
 
     entry_stop = straxen.URLConfig(
         default=None,
-        help="Geant4 event to stop simulation at. If None, all events are simulated.",
+        help="Geant4 event to stop simulation at. If None, all events are simulated",
     )
 
     cut_by_eventid = straxen.URLConfig(