Make more plugins optionally built

src/plugins/Analysis/SConscript

@@ -7,23 +7,25 @@ Import('*')
 subdirs = ['ReactionFilter', 'b1pi_hists', 'ReactionEfficiency']
 subdirs.extend(['DAQTree', 'DAQTreeBCAL'])
 subdirs.extend(['monitoring_hists'])
-subdirs.extend(['p2pi_hists','p3pi_hists','p4pi_hists','p2k_hists'])
-subdirs.extend(['p2gamma_hists','ppi0gamma_hists','p2pi0_hists'])
-subdirs.extend(['npp_hists','cpp_hists'])
+subdirs.extend(['p2pi_hists','p3pi_hists','ppi0gamma_hists'])
 subdirs.extend(['fcal_charged','TPOL_tree','mcthrown_tree'])
-subdirs.extend(['trackeff_hists','imaging'])
-subdirs.extend(['pid_dirc','truth_dirc', 'lut_dirc', 'dirc_hists', 'dirc_reactions', 'dirc_tree', 'TRD_hists'])
-subdirs.extend(['B3pi_eff_missgamma','B3pi_eff_misspip','B3pi_eff_misspim','B3pi_eff_missprot', 'mcthrown_hists'])
-subdirs.extend(['compton'])
-subdirs.extend(['src-ct'])
+subdirs.extend(['trackeff_hists','imaging','dirc_reactions','TRD_hists'])
 SConscript(dirs=subdirs, exports='env osname', duplicate=0)
 
 
 # Optional targets
-optdirs = ['phys_tree', 'pedestals','bcal_calib','bcal_calib_cosmic_cdc', 'CPPMVAtree']
-
-optdirs.extend(['acceptance_hists', 'mcthrown_hists', 'cdc_hists', 'fcal_hists'])
-optdirs.extend(['dc_alignment','p2pi_trees','Z2pi_trees','ccal_hits','ccal_display','fcal_led','F250_mode10_pedestal','Z2pi0_trees'])
-
+optdirs = ['pedestals','bcal_calib','bcal_calib_cosmic_cdc', 'CPPMVAtree']
+
+optdirs.extend(['mcthrown_hists', 'cdc_hists', 'fcal_hists'])
+optdirs.extend(['p4pi_hists','p2k_hists','p2gamma_hists','p2pi0_hists'])
+optdirs.extend(['B3pi_eff_missgamma','B3pi_eff_misspip','B3pi_eff_misspim','B3pi_eff_missprot'])
+subdirs.extend(['pid_dirc','truth_dirc', 'lut_dirc', 'dirc_hists', 'dirc_tree'])
+optdirs.extend(['dc_alignment','p2pi_trees','fcal_led','F250_mode10_pedestal'])
+optdirs.extend(['npp_hists','cpp_hists'])
+optdirs.extend(['Z2pi0_trees','Z2pi_trees','ccal_hits','ccal_display'])
+optdirs.extend(['compton','src-ct'])
+
+optdirs.extend(['retired'])
+
 sbms.OptionallyBuild(env, optdirs)
 

src/plugins/Calibration/SConscript

@@ -5,8 +5,11 @@ Import('*')
 
 # update this when plugins are added
 
-subdirs = ['BCAL_SiPM_saturation','BCAL_attenlength_gainratio','BCAL_gainmatrix','BCAL_point_time','BCAL_point_calib','BCAL_saturation','BCAL_TDC_Timing','CDC_amp','HLDetectorTiming','TAGH_timewalk','CDC_TimeToDistance','PS_timing','PSC_TW','PS_E_calib','st_tw_corr_auto','ST_Propagation_Time','ST_Tresolution','TAGM_TW','TOF_calib','FCALLEDTree','FCAL_LED_shifts','FCAL_TimingOffsets_Primex']
+subdirs = ['BCAL_attenlength_gainratio','BCAL_gainmatrix','BCAL_TDC_Timing','CDC_amp','HLDetectorTiming','TAGH_timewalk','CDC_TimeToDistance','PS_timing','PSC_TW','PS_E_calib','st_tw_corr_auto','ST_Propagation_Time','ST_Tresolution','TAGM_TW','TOF_calib','FCALLEDTree','FCAL_TimingOffsets_Primex']
 
 SConscript(dirs=subdirs, exports='env osname', duplicate=0)
 
-sbms.OptionallyBuild(env, ['FCALgains','FCALpedestals','FCALpulsepeak','FCAL_TimingOffsets','FCAL_Pi0HFA','FCAL_Pi0TOF'])
+optdirs = ['FCALpedestals','FCALpulsepeak','FCAL_TimingOffsets','FCAL_Pi0TOF']
+optdirs.extend(['BCAL_saturation','BCAL_SiPM_saturation','FCAL_LED_shifts'])
+
+sbms.OptionallyBuild(env, optdirs)

src/plugins/SConscript

@@ -5,6 +5,8 @@ Import('*')
 
 Import('env osname')
 
-subdirs = ['Analysis', 'Utilities', 'monitoring', 'Calibration', 'include', 'Alignment']
+subdirs = ['Analysis', 'Utilities', 'monitoring', 'Calibration', 'include']
+sbms.OptionallyBuild(env, ['Alignment'])
+
 SConscript(dirs=subdirs, exports='env osname', duplicate=0)
 

src/plugins/Utilities/SConscript

@@ -5,14 +5,18 @@ Import('*')
 
 # Default targets (always built)
 subdirs = ['danarest', 'evio_writer', 'evio-hddm']
-subdirs.extend(['2trackskim', 'pi0bcalskim', 'pi0fcalskim', 'twogamma_fcal_skim', 'run_summary', 'track_skimmer', 'trackeff_missing','ps_skim', 'trigger_skims', 'bigevents_skim', 'coherent_peak_skim','exclusivepi0skim','randomtrigger_skim','pi0fcaltofskim','single_neutral_skim','compton_neutral_skim','eta2g_primexd_skim','eta6g_primexd_skim','etapi0_primexd_skim', 'cdcbcal_skim', 'cdc_goodtrack_skim'])
-
-subdirs.extend(['Pi0Finder', 'EventTagPi0','es_test','omega_skim','cal_high_energy_skim', 'syncskim', 'dedx_tree', 'phi_skim', 'npp_skim', 'cpp_skim'])
+subdirs.extend(['pi0bcalskim', 'trackeff_missing','ps_skim', 'trigger_skims', 'exclusivepi0skim', 'randomtrigger_skim', 'pi0fcaltofskim' ])
+subdirs.extend(['omega_skim', 'syncskim'])
 
 SConscript(dirs=subdirs, exports='env osname', duplicate=0)
 
 # Optional targets
-optdirs = ['danahddm', 'dumpcandidates', 'dumpthrowns', 'l3bdt']
-optdirs.extend(['merge_rawevents', 'syncskim', 'DAQ', 'TTab', 'rawevent'])
+optdirs = [ '2trackskim', 'bigevents_skim', 'coherent_peak_skim' , 'twogamma_fcal_skim' ]
+optdirs.extend(['pi0fcalskim', 'single_neutral_skim','compton_neutral_skim' ])
+optdirs.extend(['eta2g_primexd_skim','eta6g_primexd_skim','etapi0_primexd_skim' ])
+optdirs.extend(['cdcbcal_skim', 'cdc_goodtrack_skim'])
+optdirs.extend(['run_summary', 'track_skimmer' ])
+optdirs.extend(['merge_rawevents', 'syncskim'])
+optdirs.extend(['Pi0Finder', 'EventTagPi0','cal_high_energy_skim', 'phi_skim', 'npp_skim', 'cpp_skim'])  
 optdirs.extend(['cdc_amp_t','cdc_echo','cdc_emu','cdc_scan', 'fmwpc_scan', 'epem_ml_skim'])
 sbms.OptionallyBuild(env, optdirs)

src/plugins/Utilities/retired/dedx_tree/JEventProcessor_dedx_tree.cc

@@ -0,0 +1,199 @@
+// $Id$
+//
+//    File: JEventProcessor_dedx_tree.cc
+// Created: Wed Aug 28 14:48:25 EDT 2019
+// Creator: njarvis (on Linux albert.phys.cmu.edu 3.10.0-693.5.2.el7.x86_64 x86_64)
+//
+
+#include "JEventProcessor_dedx_tree.h"
+
+
+// Routine used to create our JEventProcessor
+#include <JANA/JApplication.h>
+#include <JANA/JFactory.h>
+
+extern "C"{
+void InitPlugin(JApplication *app){
+	InitJANAPlugin(app);
+	app->Add(new JEventProcessor_dedx_tree());
+}
+} // "C"
+
+//define static local variable //declared in header file
+thread_local DTreeFillData JEventProcessor_dedx_tree::dTreeFillData;
+
+//------------------
+// JEventProcessor_dedx_tree (Constructor)
+//------------------
+JEventProcessor_dedx_tree::JEventProcessor_dedx_tree()
+{
+	SetTypeName("JEventProcessor_dedx_tree");
+}
+
+//------------------
+// ~JEventProcessor_dedx_tree (Destructor)
+//------------------
+JEventProcessor_dedx_tree::~JEventProcessor_dedx_tree()
+{
+
+}
+
+//------------------
+// init
+//------------------
+void JEventProcessor_dedx_tree::Init()
+{
+	// This is called once at program startup. 
+
+    //TTREE INTERFACE
+    //MUST DELETE WHEN FINISHED: OR ELSE DATA WON'T BE SAVED!!!
+    dTreeInterface = DTreeInterface::Create_DTreeInterface("dedx_tree", "dedx_tree.root");
+
+    //TTREE BRANCHES
+    DTreeBranchRegister locTreeBranchRegister;
+
+    locTreeBranchRegister.Register_Single<ULong64_t>("eventnumber"); 
+    locTreeBranchRegister.Register_Single<UInt_t>("ctracks"); 
+
+    locTreeBranchRegister.Register_Single<UInt_t>("ndedxhits"); 
+
+    locTreeBranchRegister.Register_Single<Double_t>("x"); 
+    locTreeBranchRegister.Register_Single<Double_t>("y"); 
+    locTreeBranchRegister.Register_Single<Double_t>("z"); 
+    locTreeBranchRegister.Register_Single<Double_t>("r");
+
+    locTreeBranchRegister.Register_Single<Double_t>("phi");   
+    locTreeBranchRegister.Register_Single<Double_t>("theta"); 
+
+    locTreeBranchRegister.Register_Single<Int_t>("charge"); 
+    locTreeBranchRegister.Register_Single<Double_t>("p"); 
+    locTreeBranchRegister.Register_Single<Double_t>("dedx"); 
+    locTreeBranchRegister.Register_Single<Double_t>("dedx_int"); 
+    locTreeBranchRegister.Register_Single<Double_t>("dedx_corr");
+    locTreeBranchRegister.Register_Single<Double_t>("dedx_int_corr");
+
+    //REGISTER BRANCHES
+    dTreeInterface->Create_Branches(locTreeBranchRegister);
+}
+
+//------------------
+// brun
+//------------------
+void JEventProcessor_dedx_tree::BeginRun(const std::shared_ptr<const JEvent> &event)
+{
+	// This is called whenever the run number changes
+}
+
+//------------------
+// evnt
+//------------------
+void JEventProcessor_dedx_tree::Process(const std::shared_ptr<const JEvent> &event)
+{
+	// This is called for every event. Use of common resources like writing
+	// to a file or filling a histogram should be mutex protected. Using
+	// event->Get(...) to get reconstructed objects (and thereby activating the
+	// reconstruction algorithm) should be done outside of any mutex lock
+	// since multiple threads may call this method at the same time.
+	// Here's an example:
+	//
+	// vector<const MyDataClass*> mydataclasses;
+	// event->Get(mydataclasses);
+	//
+	// japp->RootFillLock(this);
+	//  ... fill historgrams or trees ...
+	// japp->RootFillUnLock(this);
+
+  auto eventnumber = event->GetEventNumber();
+
+  // select events with physics events, i.e., not LED and other front panel triggers
+  const DTrigger* locTrigger = NULL; 
+  event->GetSingle(locTrigger);
+  if(locTrigger->Get_L1FrontPanelTriggerBits() != 0) return;
+
+  const DVertex* locVertex  = NULL;
+  event->GetSingle(locVertex);
+  double z = locVertex->dSpacetimeVertex.Z();
+  if ((z < 45.0) || (z > 85.0)) return;
+
+  double x = locVertex->dSpacetimeVertex.X();
+  double y = locVertex->dSpacetimeVertex.Y();
+  double r = sqrt (x*x + y*y);
+
+
+  vector<const DChargedTrack*> ctracks;
+  event->Get(ctracks);
+
+  if ((int)ctracks.size() ==0) return;
+
+  dTreeFillData.Fill_Single<ULong64_t>("eventnumber",(ULong64_t)eventnumber);
+
+  dTreeFillData.Fill_Single<UInt_t>("ctracks",(UInt_t)ctracks.size()); 
+
+
+  for (uint32_t i=0; i<ctracks.size(); i++) {
+
+    const DChargedTrackHypothesis *hyp=ctracks[i]->Get_BestFOM();
+
+    if (hyp != NULL) {  
+
+      const DTrackTimeBased *track = hyp->Get_TrackTimeBased();
+
+      int nhits = (int)track->dNumHitsUsedFordEdx_CDC; 
+
+      if (nhits==0) continue;
+
+      dTreeFillData.Fill_Single<UInt_t>("ndedxhits",(UInt_t)nhits); 
+
+      double charge = track->charge();
+      DVector3 mom = track->momentum();
+      double p = mom.Mag();
+
+      double theta_degrees = mom.Theta() * 180.0/3.14159;
+      double phi_degrees = mom.Phi() * 180.0/3.14159;
+
+      double dedx = 1.0e6*track->ddEdx_CDC_amp;
+      double dedxfromintegral = 1.0e6*track->ddEdx_CDC;
+      double dedx_corr = 1.0e6*hyp->Get_dEdx_CDC_amp();
+      double dedxfromintegral_corr = 1.0e6*hyp->Get_dEdx_CDC_int();
+
+      dTreeFillData.Fill_Single<Double_t>("x",x); 
+      dTreeFillData.Fill_Single<Double_t>("y",y); 
+      dTreeFillData.Fill_Single<Double_t>("z",z); 
+      dTreeFillData.Fill_Single<Double_t>("r",r); 
+      dTreeFillData.Fill_Single<Double_t>("phi",phi_degrees);   
+      dTreeFillData.Fill_Single<Double_t>("theta",theta_degrees); 
+
+      dTreeFillData.Fill_Single<Int_t>("charge",(Int_t)charge); 
+      dTreeFillData.Fill_Single<Double_t>("p",p); 
+      dTreeFillData.Fill_Single<Double_t>("dedx",dedx); 
+      dTreeFillData.Fill_Single<Double_t>("dedx_int",dedxfromintegral); 
+      dTreeFillData.Fill_Single<Double_t>("dedx_corr",dedx_corr);
+      dTreeFillData.Fill_Single<Double_t>("dedx_int_corr",dedxfromintegral_corr);
+
+       //FILL TTREE
+       dTreeInterface->Fill(dTreeFillData);
+    }
+
+  }
+}
+
+//------------------
+// erun
+//------------------
+void JEventProcessor_dedx_tree::EndRun()
+{
+	// This is called whenever the run number changes, before it is
+	// changed to give you a chance to clean up before processing
+	// events from the next run number.
+}
+
+//------------------
+// fini
+//------------------
+void JEventProcessor_dedx_tree::Finish()
+{
+	// Called before program exit after event processing is finished.
+
+        delete dTreeInterface; //saves trees to file, closes file
+}
+

src/plugins/Utilities/retired/dedx_tree/JEventProcessor_dedx_tree.h

@@ -0,0 +1,49 @@
+// $Id$
+//
+//    File: JEventProcessor_dedx_tree.h
+// Created: Wed Aug 28 14:48:25 EDT 2019
+// Creator: njarvis (on Linux albert.phys.cmu.edu 3.10.0-693.5.2.el7.x86_64 x86_64)
+//
+
+#ifndef _JEventProcessor_dedx_tree_
+#define _JEventProcessor_dedx_tree_
+
+#include <JANA/JEventProcessor.h>
+#include <JANA/Services/JLockService.h>
+
+#include "TRIGGER/DTrigger.h"
+#include "TRACKING/DTrackTimeBased.h"
+#include "PID/DVertex.h"
+#include "PID/DChargedTrack.h"
+#include "PID/DChargedTrackHypothesis.h"
+
+#include "ANALYSIS/DTreeInterface.h"
+
+#include <vector>
+
+
+class JEventProcessor_dedx_tree:public JEventProcessor{
+	public:
+		JEventProcessor_dedx_tree();
+		~JEventProcessor_dedx_tree();
+
+	private:
+		void Init() override;
+		void BeginRun(const std::shared_ptr<const JEvent>& event) override;
+		void Process(const std::shared_ptr<const JEvent>& event) override;
+		void EndRun() override;
+		void Finish() override;
+
+                //TREE
+                DTreeInterface* dTreeInterface;
+
+                //thread_local: Each thread has its own object: no lock needed
+                //important: manages it's own data internally: don't want to call new/delete every event!
+
+                static thread_local DTreeFillData dTreeFillData;
+
+
+};
+
+#endif // _JEventProcessor_dedx_tree_
+

src/plugins/Utilities/retired/dedx_tree/README.md

@@ -0,0 +1,53 @@
+# CDC dE/dx correction procedure for variation with theta
+
+The first iteration of this process is documented in [GlueX-doc-4693](https://halldweb.jlab.org/doc-private/DocDB/ShowDocument?docid=4693).
+The scripts are stored in the subdirectory scripts.
+The correction matrix is loaded into the CCDB table /CDC/dedx\_theta.
+
+## Prerequisites: 
+* 300+ evio files processed with the dedx\_tree plugin, with dE/dx truncation and the dE/dx correction switched off ( -PPID:CDC_CORRECT_DEDX_THETA=0 and -PPID:CDC_TRUNCATE_DEDX=0 ) 
+
+* Simulated data processed similarly. 
+
+
+## Process overview:
+
+1. makebinnedhistos.C - create many histograms of dedx vs p, for 1 degree bins in theta
+
+2. fitbinnedhistoslg.C - find the peak position for the proton and pion bands in each (p, theta) bin, using theta-specific functions to define the fit regions
+
+3. makesimsinglebinnedhistos.C - as (1), with simulated data
+
+4. fitbinnedhistoslg.C - as (2) with simulated data
+
+5. makescalefactors.C - calculate the scale factors to match the real data to the simulated data
+
+6. extendscalefactors.C - extrapolate the scale factors to populate the edges of a rectangular space in (dedx, theta)  (root -b -q dedx_correction_factors.root extendscalefactors.C)
+
+7. smooth_histo.C - run a smoothing algorithm over the scale factors and write the matrix of scale factors into a text file which can be used in the reconstruction code. (root extended_dedx_correction_factors.root smooth_histo.C)
+
+8. checkmatrix.C - use the matrix contained in the text file to correct the data in the root trees and create a set of corrected binned histograms, which can be fitted as before to verify that the correction process produced acceptable results. 
+
+
+## Plotting scripts
+* drawdedxcuts.C - plots functions on top of specified dEdx vs p histogram from histogram file
+* drawalldedxcuts.C - loops through all histograms in histo file, saves 2x2 canvases of dedx functions over data
+* plotdata.C - reads in fitresults.root or fittedsimresults.root, plots coloured bands of dedx peak position for one particle type 
+* plotf.C - reads in dedx_correction_factors.root, plots coloured bands of correction factors for one particle type
+* plotfdedx.C - reads in dedx_correction_factors.root, plots dedx vs theta for the data used for the correction factors
+* plot_cf_vs_dedx.C - reads in dedx_correction_factors.root, makes plots cf vs theta for 5 degree steps in theta
+* dots.C - reads in dedx_correction_factors.root - makes a selection of plots of cf, dedx, theta including a 3D dot plot
+* drawsurf2.C - use this with the tree file open, works with dedx_correction_factors.root or extended_dedx_correction_factors.root  - draws surfaces, dots and surface+dots
+
+
+## Other scripts
+* make_histo_into_text_file.C - writes the histogram into a text file without smoothing
+
+
+
+A quick 3D plot of plot correction factors vs dedx, theta in colour scale can be made from the open root tree using 
+```sh
+t->Draw("f:dedx:theta:f","","cont4 col")
+```
+
+