Merge pull request #300 from JeffersonLab/develop

Merge the current develop back into the master branch

.gitignore

@@ -59,3 +59,6 @@ z_*
 
 # setup files
 SetupFiles/SET_ME_UP.*
+
+# Max burst indices
+Parity/prminput/max_burst_index.*

Analysis/prminput/EpicsTable.5275-.map

@@ -349,11 +349,19 @@ FB_C:BPM:N6:pos_asym.VALB	slow_controls_data		float		!
 FB_C:BPM:N7:pos_asym.VALA	slow_controls_data		float		! 
 FB_C:BPM:N7:pos_asym.VALB	slow_controls_data		float		! 
 CTD673				slow_controls_data		float		! 
+!!!
+RTPPITA1CNT	slow_controls_data		float		! 
+RTPPITA2CNT	slow_controls_data		float		! 
+RTPQWP1CNT	slow_controls_data		float		! 
+RTPQWP2CNT	slow_controls_data		float		! 
+RTPAPOSUCNT	slow_controls_data		float		! 
+RTPAPOSVCNT	slow_controls_data		float		! 
+RTPDPOSUCNT	slow_controls_data		float		! 
+RTPDPOSVCNT	slow_controls_data		float		!
+!!!
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !  Composite slow control variables
 !    These are variables for which there is not an actual EPICS variable,
 !    but a value is generated internally by the QwEPICSEvent class.
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 WienMode        	slow_controls_data	String	 !  This will indicate the spin direction in the hall as defined by the Wien setting + precession
-RTPAPOSUCNT	slow_controls_data		float		! 
-RTPAPOSVCNT	slow_controls_data		float		! 

Analysis/prminput/EpicsTable.map

@@ -41,8 +41,10 @@ IBC3H00CRCUR4			slow_controls_data		float		! Beam Current (Hall C), Hall C Curre
 IGL1I00OD16_16			slow_controls_data		string		! another HWP, INSERTABLE waveplate
 IGL1I00DIOFLRD			slow_controls_data		float		! Fake Half-Wave Plate (8960=OUT)
 APEXPOS				slow_controls_data		float		! Target encoder position
-pcrex90BDSPOS.VAL  slow_controls_data		float		! Target encoder position
-pcrex90BDS_PullString.VAL  slow_controls_data		float		! Target encoder position
+pcrex90BDSPOS.VAL               slow_controls_data		float		! PREX/CREX Production Target encoder position
+pcrex90_PullString.VAL          slow_controls_data		float		! PREX/CREX Production Target encoder position
+pcrex45BDSPOS.VAL               slow_controls_data		float		! PREX/CREX Optics Target encoder position
+pcrex45_PullString.VAL          slow_controls_data		float		! PREX/CREX Optics Target encoder position
 HALLA:dpp			slow_controls_data		float		! Tiefenbach 6GeV orbit correction (dpp), Hall A momentum orbit correction (dpp)
 INJ:p				slow_controls_data		float		! Injector Measured Energy
 ARC1:p				slow_controls_data		float		! 
@@ -67,6 +69,7 @@ EHAR_B_IXPEAK			slow_controls_data		float		! Fast Raster-B Ix
 EHAR_B_IYPEAK			slow_controls_data		float		! Fast Raster-B Iy
 halla_MeV			slow_controls_data		float		! Hall A energy  (halla_MeV), Tiefenbach energy
 hallc_MeV			slow_controls_data		float		! Hall C energy  (hallc_MeV) 
+MQ171LM                         slow_controls_data              float           ! Left Arm Q1 readback current
 HacL_Q1_P0rb			slow_controls_data		float		! Left Arm Q1 momentum  
 HacL_Q1_LS450:FLD_DATA		slow_controls_data		float		! Left Arm Q1 gauss meter
 HacL_Q2_HP3458A:IOUT		slow_controls_data		float		! Left Arm Q2 power supply current
@@ -92,6 +95,8 @@ HacR_Q3_P0rb			slow_controls_data		float		! Right Arm Q3 momentum
 HacR_Q3_LS450:FLD_DATA		slow_controls_data		float		! Right Arm Q3 gauss meter 
 HacR_VMIC1182:0_Ch26		slow_controls_data		string		! Right Arm Q3 power supply polarity 
 HacR_D_LS450:FLD_DATA		slow_controls_data		float		! Right Arm B Field Hall Probe (D-G)
+MSUPERBIGBITEreadcalc           slow_controls_data              float           ! Septum current 1
+hesDipole_current               slow_controls_data              float           ! Septum current 2
 HrsH_VDC_rCURTop		slow_controls_data		float		! Left Arm Top VDC Current 
 HrsH_VDC_rCURBot		slow_controls_data		float		! Left Arm Bottom VDC Current 
 HrsH_VDC_rHVTop			slow_controls_data		float		! Left Arm Top VDC voltage
@@ -349,11 +354,19 @@ FB_C:BPM:N6:pos_asym.VALB	slow_controls_data		float		!
 FB_C:BPM:N7:pos_asym.VALA	slow_controls_data		float		! 
 FB_C:BPM:N7:pos_asym.VALB	slow_controls_data		float		! 
 CTD673				slow_controls_data		float		! 
+!!!
+RTPPITA1CNT	slow_controls_data		float		! 
+RTPPITA2CNT	slow_controls_data		float		! 
+RTPQWP1CNT	slow_controls_data		float		! 
+RTPQWP2CNT	slow_controls_data		float		! 
+RTPAPOSUCNT	slow_controls_data		float		! 
+RTPAPOSVCNT	slow_controls_data		float		! 
+RTPDPOSUCNT	slow_controls_data		float		! 
+RTPDPOSVCNT	slow_controls_data		float		!
+!!!
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !  Composite slow control variables
 !    These are variables for which there is not an actual EPICS variable,
 !    but a value is generated internally by the QwEPICSEvent class.
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 WienMode        	slow_controls_data	String	 !  This will indicate the spin direction in the hall as defined by the Wien setting + precession
-RTPAPOSUCNT	slow_controls_data		float		! 
-RTPAPOSVCNT	slow_controls_data		float		! 

Analysis/src/QwEPICSEvent.cc

@@ -1344,16 +1344,27 @@ void QwEPICSEvent::WriteEPICSStringValues()
 
 Int_t QwEPICSEvent::DetermineIHWPPolarity() const{
   Int_t ihwppolarity = 0;
-  if (GetDataString("IGL1I00DI24_24M")=="OUT"
-      || GetDataString("IGL1I00DI24_24M")=="1"){
+  if (GetDataString("IGL1I00OD16_16")=="OUT"
+      || GetDataString("IGL1I00OD16_16")=="0"){
     ihwppolarity = 1;
-  } else if (GetDataString("IGL1I00DI24_24M")=="IN"
-	     || GetDataString("IGL1I00DI24_24M")=="0"){
+  } else if (GetDataString("IGL1I00OD16_16")=="IN"
+       || GetDataString("IGL1I00OD16_16")=="1"){
     ihwppolarity = -1;
   } else {
     QwWarning << "IHWP state is not well defined: '"
-	      << GetDataString("IGL1I00DI24_24M") << "'"
-	      << QwLog::endl;
+        << GetDataString("IGL1I00OD16_16") << "'"
+        << QwLog::endl;
+    if (GetDataString("IGL1I00DI24_24M")=="OUT"
+        || GetDataString("IGL1I00DI24_24M")=="1"){
+      ihwppolarity = 1;
+    } else if (GetDataString("IGL1I00DI24_24M")=="IN"
+        || GetDataString("IGL1I00DI24_24M")=="0"){
+      ihwppolarity = -1;
+    } else {
+      QwWarning << "IHWP state is not well defined: '"
+        << GetDataString("IGL1I00DI24_24M") << "'"
+        << QwLog::endl;
+    }
   }
   QwDebug << "QwEPICSEvent::DetermineIHWPPolarity: "
 	  << "raw IHWP polarity is: "

Analysis/src/QwParameterFile.cc

@@ -864,7 +864,7 @@ std::pair<int,int> QwParameterFile::ParseIntRange(const std::string& separatorch
     QwError << "The first value must not be negative!" << QwLog::endl;
     return std::pair<int,int>(INT_MAX,INT_MAX);
   } else if (mypair.first > mypair.second){
-    QwError << "The first value must not be larger than the second value"
+    QwError << "The first value ("<< mypair.first<< ") must not be larger than the second value (" << mypair.second <<")"
 	    << QwLog::endl;
     return std::pair<int,int>(INT_MAX,INT_MAX);
   }

Parity/include/QwBlinder.h

@@ -244,7 +244,12 @@ class QwBlinder {
     void SetWienState(EQwWienMode wienmode);
     void SetIHWPPolarity(Int_t ihwppolarity);
 
-    Bool_t fUseCREXPositions;
+    //  Target position look-up index for PREX/CREX.
+    //  Index value of -1 is for the PREX positons
+    //  CREX index values in date order go from "min" to "Max" and must correspond to cases in the QwBlinder::Update(const QwEPICSEvent& epics) function.
+    Int_t  fCREXTargetIndex;
+    Int_t  kCREXTgtIndexMin = 1;
+    Int_t  kCREXTgtIndexMax = 2;
 
     Double_t fBeamCurrentThreshold;
     Bool_t fBeamIsPresent;

Parity/include/QwHelicityPattern.h

@@ -9,6 +9,8 @@
 
 // System headers
 #include <vector>
+#include <iostream>
+#include <fstream>
 
 // ROOT headers
 #include <TTree.h>
@@ -61,9 +63,29 @@ class QwHelicityPattern {
 
   Bool_t IsCompletePattern() const;
 
+  void PrintIndexMapFile(Int_t runNum){
+    if ( fPrintIndexFile && (fGoodPatterns < fBurstMinGoodPatterns) ) {
+      // Print a text map file to max_burst_index.####.conf
+      Int_t maxBurst = 0;
+      if (fBurstCounter==0) {
+        // It's a single burst run anyway
+        maxBurst = 0;
+      }
+      else {
+        // It's a multi burst run and we want to merge the final two bursts
+        maxBurst = fBurstCounter-1;
+      }
+      QwWarning << "Printing max_burst_index." << runNum << ".conf file with " << maxBurst << " max burst number" << QwLog::endl;
+      std::ofstream output;
+      output.open(Form("max_burst_index.%d.conf",runNum));
+      output<< "max-burst-index=" << maxBurst << std::endl; // Print the current index before incrementing further, this will be the max index and the next pass will overflow this one instead of having another
+      output.close();
+    }
+  }
+
   Bool_t IsEndOfBurst(){
-    //  Is this the end of a burst?
-    return (fBurstLength > 0 && fGoodPatterns >= fBurstLength);
+    //  Is this the end of a burst? And is this not the final burst?
+    return (( fBurstLength > 0 && fGoodPatterns >= fBurstLength ) && ( fBurstCounter<fMaxBurstIndex ));
   }
 
   void  CalculateAsymmetry();
@@ -168,7 +190,12 @@ class QwHelicityPattern {
   };
 
   Bool_t HasBurstData(){return fGoodPatterns>0;};
-  void  IncrementBurstCounter(){fBurstCounter++;}
+  void  IncrementBurstCounter(){
+    if (fBurstCounter < fMaxBurstIndex) {
+      fBurstCounter++;
+    }
+    // Else we just park here and don't try to increment any more. This is a parameter from command line or map file
+  }
   Short_t GetBurstCounter() const {return fBurstCounter;}
   void  ClearEventData();
 
@@ -211,6 +238,9 @@ class QwHelicityPattern {
 
   // Burst sum/difference of the yield and asymmetry
   Int_t fBurstLength;
+  Int_t fMaxBurstIndex;
+  Bool_t fPrintIndexFile;
+  Int_t fBurstMinGoodPatterns;
   Int_t fGoodPatterns;
   Short_t fBurstCounter;
   Bool_t fEnableBurstSum;

Parity/main/QwParity.cc

@@ -99,11 +99,12 @@ Int_t main(Int_t argc, Char_t* argv[])
   //  QwPromptSummary promptsummary;
 
   ///  Start loop over all runs
+  Int_t run_number = 0;
   while (eventbuffer.OpenNextStream() == CODA_OK) {
 
     ///  Begin processing for the first run
 
-    Int_t run_number = eventbuffer.GetRunNumber();
+    run_number = eventbuffer.GetRunNumber();
     TString run_label = eventbuffer.GetRunLabel();
 
     ///  Set the current event number for parameter file lookup
@@ -460,6 +461,7 @@ Int_t main(Int_t argc, Char_t* argv[])
 
       // Fill data handler tree branches
       datahandlerarray_burst.FillTreeBranches(burstrootfile);
+      patternsum_per_burst.PrintIndexMapFile(run_number);
     }
 
     //  Perform actions at the end of the event loop on the

Parity/prminput/0.5pass.conf

@@ -0,0 +1,4 @@
+disable-trees         = 1
+disable-histos        = 1
+print-burst-index-map = 1
+min-burstlength       = 9000

Parity/prminput/2pass.conf

@@ -0,0 +1 @@
+add-config = max_burst_index.conf

Parity/prminput/blinder.3433.map

@@ -0,0 +1,18 @@
+# Blinder parameter
+
+# strategy = Disabled | Additive | Multiplicative | AdditiveMultiplicative (case insensitive)
+strategy = additive
+
+# seed = unquoted string without starting or ending spaces
+seed = Roadkill stew sounds mighty good right NOW. --- Unspecified collaborator
+
+# max_asymmetry = positive float in ppm such that additive blinding asymmetry is between 0 +/- (this value)
+max_asymmetry = 0.150
+
+# max_factor = positive float fraction such that multiplicative blinding asymmetry is between 1 +/- (this value)
+max_factor = 0.0
+
+######  Super dangerous options... to be ONLY used when no other solution can work. 
+######  Do not just copy these elsewhere
+force-target-type    = target-blindable
+force-spin-direction = spin-forward

Parity/prminput/blinder.3571.map

@@ -0,0 +1,18 @@
+# Blinder parameter
+
+# strategy = Disabled | Additive | Multiplicative | AdditiveMultiplicative (case insensitive)
+strategy = additive
+
+# seed = unquoted string without starting or ending spaces
+seed = Roadkill stew sounds mighty good right NOW. --- Unspecified collaborator
+
+# max_asymmetry = positive float in ppm such that additive blinding asymmetry is between 0 +/- (this value)
+max_asymmetry = 0.150
+
+# max_factor = positive float fraction such that multiplicative blinding asymmetry is between 1 +/- (this value)
+max_factor = 0.0
+
+######  Super dangerous options... to be ONLY used when no other solution can work. 
+######  Do not just copy these elsewhere
+force-target-type    = target-blindable
+force-spin-direction = spin-forward

Parity/prminput/blinder.5104-5274.map

@@ -12,4 +12,4 @@ max_asymmetry = 0.900
 # max_factor = positive float fraction such that multiplicative blinding asymmetry is between 1 +/- (this value)
 max_factor = 0.0
 
-use_crex_target_position = true
+crex_target_index = 1

Parity/prminput/blinder.5275-.map → Parity/prminput/blinder.5275-5857.map

@@ -12,4 +12,4 @@ max_asymmetry = 0.900
 # max_factor = positive float fraction such that multiplicative blinding asymmetry is between 1 +/- (this value)
 max_factor = 0.0
 
-use_crex_target_position = true
+crex_target_index = 1

Parity/prminput/blinder.5858-.map

@@ -0,0 +1,15 @@
+# Blinder parameter
+
+# strategy = Disabled | Additive | Multiplicative | AdditiveMultiplicative (case insensitive)
+strategy = additive
+
+# seed = unquoted string without starting or ending spaces
+  seed = It is a capital mistake to theorize before one has data. Insensibly one begins to twist facts to suit theories, instead of theories to suit facts.---A Scandal in Bohemia, Arthur Conan Doyle.
+
+# max_asymmetry = positive float in ppm such that additive blinding asymmetry is between 0 +/- (this value)
+max_asymmetry = 0.900
+
+# max_factor = positive float fraction such that multiplicative blinding asymmetry is between 1 +/- (this value)
+max_factor = 0.0
+
+crex_target_index = 2

Parity/prminput/eventNumberCut.6852.conf

@@ -0,0 +1,3 @@
+# Cuts to keep only evnts with Ca-48 target in position  
+event=20000:
+blinder.force-target-blindable=1

Parity/prminput/prexCH_beamline.2721-.map

@@ -54,10 +54,10 @@ sample_size=4084
     VQWK, 4, 1,  bpmstripline,  BPM1xm
     VQWK, 4, 2,  bpmstripline,  BPM1yp 
     VQWK, 4, 3,  bpmstripline,  BPM1ym
-    VQWK, 4, 4,  bpmstripline,  BPM8xp
-    VQWK, 4, 5,  bpmstripline,  BPM8xm
-    VQWK, 4, 6,  bpmstripline,  BPM8yp
-    VQWK, 4, 7,  bpmstripline,  BPM8ym
+    VQWK, 4, 4,  bpmstripline,  BPM8yp
+    VQWK, 4, 5,  bpmstripline,  BPM8ym
+    VQWK, 4, 6,  bpmstripline,  BPM8xp
+    VQWK, 4, 7,  bpmstripline,  BPM8xm
 
 !ADC5
     VQWK, 5, 0,  bcm,  ch_tsettle
@@ -90,6 +90,11 @@ sample_size=4084
     VQWK, 7, 6,  bpmstripline,  BPM4ecYM
     VQWK, 7, 7,  bpmstripline,  BPM4ecYP
 
+begin=combinedbcm
+name=bcm_target
+  bcm_an_us, bcm, 2.0
+  bcm_an_ds, bcm, 1.0
+end=combinedbcm
 
 !! bank=0x2 
 !!
@@ -115,4 +120,4 @@ sample_size=4084
 
 [PUBLISH]
 ! new.tree.variable.name, analysis.class, old.tree.variable.name, element.to.store
-  q_targ, bcm, bcm_an_ds3, c
+  q_targ, combinedbcm, bcm_target, c

Parity/prminput/prexCH_beamline.2844-.map

@@ -54,10 +54,10 @@ sample_size=4084
     VQWK, 4, 1,  bpmstripline,  BPM1xm
     VQWK, 4, 2,  bpmstripline,  BPM1yp 
     VQWK, 4, 3,  bpmstripline,  BPM1ym
-    VQWK, 4, 4,  bpmstripline,  BPM8xp
-    VQWK, 4, 5,  bpmstripline,  BPM8xm
-    VQWK, 4, 6,  bpmstripline,  BPM8yp
-    VQWK, 4, 7,  bpmstripline,  BPM8ym
+    VQWK, 4, 4,  bpmstripline,  BPM8yp
+    VQWK, 4, 5,  bpmstripline,  BPM8ym
+    VQWK, 4, 6,  bpmstripline,  BPM8xp
+    VQWK, 4, 7,  bpmstripline,  BPM8xm
 
 !ADC5
     VQWK, 5, 0,  bcm,  ch_tsettle
@@ -90,6 +90,11 @@ sample_size=4084
     VQWK, 7, 6,  bpmstripline,  BPM4ecYM
     VQWK, 7, 7,  bpmstripline,  BPM4ecYP
 
+begin=combinedbcm
+name=bcm_target
+  bcm_an_us, bcm, 2.0
+  bcm_an_ds, bcm, 1.0
+end=combinedbcm
 
 !! bank=0x2 
 !!
@@ -115,4 +120,4 @@ sample_size=4084
 
 [PUBLISH]
 ! new.tree.variable.name, analysis.class, old.tree.variable.name, element.to.store
-  q_targ, bcm, bcm_an_ds3, c
+  q_targ, combinedbcm, bcm_target, c