Merge lp:~m-a-uchida/maus/GlobalDevelopment into lp:maus/merge

[Adam Dobbs]

[lp:~m-a-uchida/maus/GlobalDevelopment]

1201. By Adam Dobbs on 2017-05-11

Merge: global recon updates

=== removed file 'bin/Global/SampleDataCards/datacard_mu_plus_batch.py'
--- bin/Global/SampleDataCards/datacard_mu_plus_batch.py	2017-01-18 14:20:43 +0000
+++ bin/Global/SampleDataCards/datacard_mu_plus_batch.py	1970-01-01 00:00:00 +0000
@@ -1,104 +0,0 @@
-"""
-Datacard to run with simulation of 200MeV/c muons
-"""
-# pylint: disable=C0103, W0611
-
-import os
-job_number = int(os.getenv("LSB_JOBINDEX", 100))
-input_root_file_name = "200MeV_mu_plus_hypothesis_Global_Recon" + \
-    str(job_number) + ".root"
-output_root_file_name = "200MeV_mu_plus_hypothesis_Global_Recon" + \
-    str(job_number) + ".root"
-output_json_file_name = "200MeV_mu_plus_hypothesis_Global_Recon" + \
-    str(job_number) + ".json"
-output_json_file_type = "text"
-input_json_file_name = "200MeV_mu_plus_hypothesis_Global_Recon" + \
-    str(job_number) + ".json"
-Ntuples_filename = "ntuples" + str(job_number) + ".root"
-efficiency_filename = "efficiency" + str(job_number) + ".csv"
-# Used by MapPyRemoveTracks.
-keep_only_muon_tracks = False
-
-# Used by MapCppSimulation
-keep_tracks = True # set to true to keep start and end point of every track
-keep_steps = False # set to true to keep start and end point of every track and
-                   # every step point
-simulation_geometry_filename = \
-  '%s/files/geometry/download/run7469/ParentGeometryFile.dat' \
-  % os.environ.get("MAUS_ROOT_DIR")
-reconstruction_geometry_filename = \
-  '%s/files/geometry/download/run7469/ParentGeometryFile.dat' \
-  % os.environ.get("MAUS_ROOT_DIR")
-maximum_number_of_steps = 100000000
-simulation_reference_particle = {
-    "position":{"x":0.0, "y":-0.0, "z":5200.0}, # 5200
-    "momentum":{"x":0.0, "y":0.0, "z":1.0},
-    "particle_id":-13, "energy":244.3, "time":0.0, "random_seed":job_number
-}
-
-#266.2 muon -13, 281.4 pion 211, 244.3 positron -11
-
-muon_half_life = 1.e24
-# used by InputPySpillGenerator to determine the number of empty spills that
-# will be generated by the simulation
-spill_generator_number_of_spills = 1000
-# used by MapPyBeamMaker to generate input particle data
-# This is a sample beam distribution based on guesses by Chris Rogers of what
-# an optimised beam might look like
-beam = {
-    "particle_generator":"counter", # routine for generating empty primaries
-    "random_seed":job_number, # random seed for beam generation; controls also
-                              # how the MC seeds are generated
-    "definitions":[
-    {
-       "reference":simulation_reference_particle, # reference particle
-       "random_seed_algorithm":"incrementing_random", # algorithm for seeding MC
-       "n_particles_per_spill":1, # probability of generating a particle
-       "transverse":{
-          "transverse_mode":"twiss",
-          "beta_x":1000.,
-          "alpha_x":0.,
-          "emittance_x":6.0, # 4d emittance
-          #~ "emittance_x":0.0001,
-          "beta_y":8000.,
-          "alpha_y":0.5,
-          "emittance_y":6.0,
-          #~ "emittance_y":0.0001,
-          },
-       #~ "transverse":{
-          #~ "transverse_mode":"constant_solenoid", # transverse distribution
-                                        #matched to constant solenoid field
-          #~ "emittance_4d":1., # 4d emittance
-          #~ "normalised_angular_momentum":0.1, # angular momentum from diffuser
-          #~ "bz":4.e-3 # magnetic field strength for angular p calculation
-       #~ },
-       "longitudinal":{"longitudinal_mode":"sawtooth_time",
-                   "momentum_variable":"p",
-                   "sigma_p":25., # RMS total momentum
-                   "t_start":-1.e6, # start time of sawtooth
-                   "t_end":+1.e6}, # end time of sawtooth
-       "coupling":{"coupling_mode":"none"} # no dispersion
-    }]
-}
-
-particle_decay = True
-physics_processes = "standard"
-#~ physics_processes = "mean_energy_loss"
-TOF_calib_by = "date"
-TOF_calib_date_from = "2013-10-01 00:00:00"
-#~ header_and_footer_mode = "dont_append"
-verbose_level = 0
-track_matching_pid_hypothesis = "kMuPlus"
-track_matching_energy_loss = True
-track_matching_tolerances = {
-  "TOF0t":2.0,
-  "TOF1x":50.0,
-  "TOF1y":50.0,
-  "TOF2x":50.0,
-  "TOF2y":50.0,
-  "KLy":42.0,
-  "EMRx":1.5, # Multiplier for standard tolerance which is recon error*sqrt(12)
-  "EMRy":1.5,
-  "TOF12maxSpeed":1.0, # fraction of c between TOFs for through matching
-  "TOF12minSpeed":0.5,
-}

=== removed file 'bin/Global/SampleDataCards/datacard_mu_plus_through_tracks.py'
--- bin/Global/SampleDataCards/datacard_mu_plus_through_tracks.py	2016-12-06 12:47:51 +0000
+++ bin/Global/SampleDataCards/datacard_mu_plus_through_tracks.py	1970-01-01 00:00:00 +0000
@@ -1,65 +0,0 @@
-"""
-Datacard to run with simulation of 200MeV/c muons
-"""
-# pylint: disable=C0103, W0611
-
-import os
-job_number = int(os.getenv("LSB_JOBINDEX", 10))
-
-output_json_file_name = "200MeV_mu_plus_through" + str(job_number) + ".json"
-output_json_file_type = "text"
-efficiency_filename = "efficiency" + str(job_number) + ".csv"
-# Used by MapPyRemoveTracks.
-keep_only_muon_tracks = False
-
-# Used by MapCppSimulation
-keep_tracks = True # set to true to keep start and end point of every track
-keep_steps = False # set to true to keep start and end point of every track and
-                   # every step point
-simulation_geometry_filename = "Stage4_NoField.dat"
-maximum_number_of_steps = 10000
-simulation_reference_particle = {
-    "position":{"x":0.0, "y":-0.0, "z":10500.0},
-    "momentum":{"x":0.0, "y":0.0, "z":1.0},
-    "particle_id":-13, "energy":266.0, "time":0.0, "random_seed":job_number
-}
-
-muon_half_life = 1.e24
-# used by InputPySpillGenerator to determine the number of empty spills that
-# will be generated by the simulation
-spill_generator_number_of_spills = 100
-# used by MapPyBeamMaker to generate input particle data
-# This is a sample beam distribution based on guesses by Chris Rogers of what
-# an optimised beam might look like
-beam = {
-    "particle_generator":"counter", # routine for generating empty primaries
-    "random_seed":job_number, # random seed for beam generation; controls also
-                              # how the MC seeds are generated
-    "definitions":[
-    {
-       "reference":simulation_reference_particle, # reference particle
-       "random_seed_algorithm":"incrementing_random", # algorithm for seeding MC
-       "n_particles_per_spill":1, # probability of generating a particle
-       "transverse":{
-          "transverse_mode":"twiss",
-          "beta_x":8000.,
-          "alpha_x":1.,
-          "emittance_x":3.0, # 4d emittance
-          "beta_y":8000.,
-          "alpha_y":1.0,
-          "emittance_y":3.0,
-          },
-       "longitudinal":{"longitudinal_mode":"sawtooth_time",
-                   "momentum_variable":"p",
-                   "sigma_p":25., # RMS total momentum
-                   "t_start":-1.e6, # start time of sawtooth
-                   "t_end":+1.e6}, # end time of sawtooth
-       "coupling":{"coupling_mode":"none"} # no dispersion
-    }]
-}
-
-particle_decay = True
-physics_processes = "mean_energy_loss"
-TOF_calib_by = "date"
-TOF_calib_date_from = "2013-10-01 00:00:00"
-SciFiPRHelicalOn = False

=== modified file 'bin/Global/pid_example_datacard.py'
--- bin/Global/pid_example_datacard.py	2016-12-06 12:47:51 +0000
+++ bin/Global/pid_example_datacard.py	2017-05-11 16:29:09 +0000
@@ -19,7 +19,7 @@
 input_root_file_name = "maus_output.root"
 
 # Output root file with track pid information included
-output_root_file_name = "output_Global_PID.json"
+output_root_file_name = "output_Global_PID.root"
 
 # Path to PDF file. The one currently listed (on 16/02/2016) is outdated
 # and will be replaced, and this card updated.
@@ -60,11 +60,10 @@
 # competing pid hypotheses before they are selected as the correct hypothesis
 pid_confidence_level = 10
 
-# PID track selection- select which tracks from TrackMatching to perform PID on.
-# Can perform PID on all tracks by setting to "all", or on all downstream tracks
-# (set to "DS"), all upstream (set to "US"), through tracks (set to "Through"),
-# or the upstream or downstream components of the throught track (set to
-# "Through_US" or "Through_DS" respectively). Or a combination of the above can
-# be used, entered as a space separated list,
-# e.g. "Through Through_US Through_DS"
-pid_track_selection = "Through"
+# PID track selection- select which tracks from TrackMatching to perform PID on. 
+# Can perform PID on all tracks by setting to "all" which will give you PID'd 
+# through and unmatched US and DS tracks, 
+# on "through" tracks only (constituent tracks will be PID'd, so this excludes orphans) 
+# with through or on all upstream and downstream tracks (ignoring whether tracks have 
+# been through-matched) with "us\_and\_ds"
+pid_track_selection = "all"

=== modified file 'bin/Global/process_datacard.py'
--- bin/Global/process_datacard.py	2017-02-17 14:32:36 +0000
+++ bin/Global/process_datacard.py	2017-05-11 16:29:09 +0000
@@ -43,14 +43,14 @@
 # When editing, keep in mind the fundamental limit imposed by detector
 # resolution.
 track_matching_tolerances = {
-  "TOF0t":2.0,
-  "TOF1x":40.0,
-  "TOF1y":40.0,
-  "TOF2x":40.0,
-  "TOF2y":40.0,
-  "KLy":32.0, # KL only reconstructs y position
-  "EMRx":40.0, # Multiplier for the standard tolerance which is the
-  "EMRy":40.0, # reconstructed error*sqrt(12)
+  "TOF0t":2.0, #ns between actual and expected TOF0-1 Delta t
+  "TOF1x":60.0,
+  "TOF1y":60.0,
+  "TOF2x":50.0,
+  "TOF2y":50.0,
+  "KLy":50.0, # KL only reconstructs y position
+  "EMRx":75.0, # Multiplier for the standard tolerance which is the
+  "EMRy":75.0, # reconstructed error*sqrt(12)
   "TOF12maxSpeed":1.0, # fraction of c to calculate travel time between TOFs
   "TOF12minSpeed":0.5, # for through matching
 }

=== modified file 'doc/workbook/MausWorkBook.tex'
--- doc/workbook/MausWorkBook.tex	2017-02-14 10:26:17 +0000
+++ doc/workbook/MausWorkBook.tex	2017-05-11 16:29:09 +0000
@@ -546,7 +546,9 @@
 \item{set \texttt{input\_root\_file\_name to trackmatched\_data.root}.}
 \item{change \texttt{PID\_PDFs\_file} to point to \texttt{single\_PDF\_filename.root} from above.}
 \item{\texttt{pid\_config}, \texttt{pid\_beam\_setting} and \texttt{pid\_beamline\_polarity} must also be set (to match those set when the PDFs were made).}
+\item{Set \texttt{pid\_track\_selection} to select which tracks from TrackMatching to perform PID on. Can perform PID on all tracks by setting to ``all'' which will give you PID'd Through and unmatched US and DS tracks, on through tracks only (constituent tracks will be PID'd, so this excludes orphans) with ``through'' or on all upstream and downstream tracks (ignoring whether tracks have been through-matched) with "us\_and\_ds"}
 \end{enumerate}
+
 \item At the command line, run:
 \begin{lstlisting}
 python GlobalPID.py --configuration_file edited_pid_example_datacard.py

=== modified file 'src/common_py/ConfigurationDefaults.py'
--- src/common_py/ConfigurationDefaults.py	2017-05-02 16:26:10 +0000
+++ src/common_py/ConfigurationDefaults.py	2017-05-11 16:29:09 +0000
@@ -796,7 +796,7 @@
 # PID track selection- select which tracks from TrackMatching to perform PID on. Can perform PID on all tracks by
 # setting to "all", on through tracks only (constituent tracks will be PID'd, so this excludes orphans) with
 # "through" or on all upstream and downstream tracks (ignoring whether tracks have been through-matched) with
-# "constituents"
+# "us_and_ds"
 pid_track_selection = "all"
 
 # Determines for which pid hypotheses track matching should be attempted. Default is "all"
@@ -810,13 +810,13 @@
 # so a multiplier is used.
 track_matching_tolerances = {
   "TOF0t":2.0, # ns between actual and expected TOF0-1 Delta t
-  "TOF1x":40.0,
-  "TOF1y":40.0,
-  "TOF2x":40.0,
-  "TOF2y":40.0,
-  "KLy":32.0,
-  "EMRx":40.0, # Multiplier for the standard tolerance which is the reconstructed error*sqrt(12)
-  "EMRy":40.0,
+  "TOF1x":60.0,
+  "TOF1y":60.0,
+  "TOF2x":50.0,
+  "TOF2y":50.0,
+  "KLy":50.0,
+  "EMRx":75.0, # Multiplier for the standard tolerance which is the reconstructed error*sqrt(12)
+  "EMRy":75.0,
   "TOF12maxSpeed":1.0, # fraction of c to calculate travel time between TOFs for through matching
   "TOF12minSpeed":0.5,
 }

=== modified file 'src/map/MapCppGlobalPID/MapCppGlobalPID.cc'
--- src/map/MapCppGlobalPID/MapCppGlobalPID.cc	2017-02-16 17:44:47 +0000
+++ src/map/MapCppGlobalPID/MapCppGlobalPID.cc	2017-05-11 16:29:09 +0000
@@ -140,7 +140,7 @@
     _pid_track_selection = _configJSON["pid_track_selection"].asString();
 
     if (_pid_track_selection != "all" and _pid_track_selection != "through"
-                                      and _pid_track_selection != "constituents") {
+                                      and _pid_track_selection != "us_and_ds") {
       throw MAUS::Exceptions::Exception(Exceptions::recoverable,
           "Invalid pid_track_selection set in configuration", "MapCppGlobalPID::birth");
     }
@@ -316,8 +316,16 @@
       if (!global_event) {
         continue;
       }
-      // Regardless of whether we PID through tracks or not, we first have to PID the constituents
-      if (_pid_track_selection == "all" or _pid_track_selection == "constituents") {
+
+      // For comissioning, we ignore pid_track_selection as PIDing us_and_ds doesn't make sense
+      // due to cross-channel PID variables
+      if (_pid_config == "commissioning") {
+        PerformPID(global_event->GetThroughPrimaryChains(), global_event);
+        continue;
+      }
+
+      // Regardless of whether we PID through tracks or not, we first have to PID the us_and_ds
+      if (_pid_track_selection == "all" or _pid_track_selection == "us_and_ds") {
         PerformPID(global_event->GetNonThroughPrimaryChains(), global_event);
       } else if (_pid_track_selection == "through") {
         PerformPID(global_event->GetUSPrimaryChains(), global_event);
@@ -427,7 +435,7 @@
     std::vector<const MAUS::DataStructure::Global::Track*> constituent_tracks =
         through_track->GetConstituentTracks();
     // Make sure that we have an intact through-constituent set. There should be exactly two
-    // constituents and the through track should have all the detectors the constituents have
+    // us_and_ds and the through track should have all the detectors the us_and_ds have
     // with no overlaps
     if (!(constituent_tracks.size() == 2 and
         (constituent_tracks.at(0)->get_detectorpoints() +
@@ -441,7 +449,7 @@
         constituent_tracks.at(1)->get_pid_logL_values();
     if (!(pairs_0.size() == 3 and pairs_1.size() == 3)) {
       Squeak::mout(Squeak::error) << "Through PID failed due to incorrect number of PIDLogLPairs "
-                                  << "in constituents. MapCppGlobalPID::ThroughPID()" << std::endl;
+                                  << "in us_and_ds. MapCppGlobalPID::ThroughPID()" << std::endl;
       return;
     }
     // Assemble all logL pairs into a single vector so we can iterate over it