feat: RG-C Su22 manual QA

README.md

@@ -2,10 +2,10 @@
 
 Timeline production for CLAS12. Timelines are deployed to [`clas12mon`](https://clas12mon.jlab.org).
 
-| Table of Contents                                            |                                                     |
-| ---                                                          | ---                                                 |
-| [:star: **Chefs' Documentation** :star:](/doc/chef_guide.md) | Summary documentation for chefs                     |
-| [Setup Guide](/doc/setup.md)                                 | How to compile the timeline code                    |
-| [Detailed Procedure](/doc/procedure.md)                      | Full procedure how to run the timeline code         |
-| [Developers' Notes](/doc/dev_notes.md)                       | Additional notes for developers (_e.g._, flowcharts |
-| [QADB Production](/qa-physics/README.md)                     | Quality Assurance Database (QADB) production guide  |
+| Table of Contents                                            |                                                      |
+| ---                                                          | ---                                                  |
+| [:star: **Chefs' Documentation** :star:](/doc/chef_guide.md) | Summary documentation for chefs                      |
+| [Setup Guide](/doc/setup.md)                                 | How to compile the timeline code                     |
+| [Detailed Procedure](/doc/procedure.md)                      | Full procedure how to run the timeline code          |
+| [Developers' Notes](/doc/dev_notes.md)                       | Additional notes for developers (_e.g._, flowcharts) |
+| [QADB Production](/qa-physics/README.md)                     | Quality Assurance Database (QADB) production guide   |

qa-physics/QA/meld/meld.groovy

@@ -35,7 +35,7 @@ qaTreeNew.each{ runnum, binTree ->
   binTree.each{ binnum, binQAnew ->
     if(debug) println "\nrun=$runnum bin=$binnum"
     qaTreeMelded[runnum][binnum] = [:]
-    
+
     // get QA info from old qaTree
     runQAold = qaTreeOld[runnum]
     if(runQAold!=null) binQAold = qaTreeOld[runnum][binnum]
@@ -62,34 +62,48 @@ qaTreeNew.each{ runnum, binTree ->
 
       // meld new defect bits
       defectListNew.each{ defect ->
-        if(defect==T.bit("TotalOutlier")) meldList << defect
-        if(defect==T.bit("TerminalOutlier")) meldList << defect
-        if(defect==T.bit("MarginalOutlier")) meldList << defect
-        if(defect==T.bit("LowLiveTime")) meldList << defect
+        // meldList << defect
+        if(defect==T.bit("PossiblyNoBeam")) meldList << defect
+        // if(defect==T.bit("TotalOutlier")) meldList << defect
+        // if(defect==T.bit("TerminalOutlier")) meldList << defect
+        // if(defect==T.bit("MarginalOutlier")) meldList << defect
+        // if(defect==T.bit("LowLiveTime")) meldList << defect
       }
 
       // meld old defect bits
       if(binQAold!=null) {
         defectListOld = T.getLeaf(binQAold,['sectorDefects',sector])
         defectListOld.each{ defect ->
-
+
+          if(defect==T.bit("PossiblyNoBeam")) {
+            if(defectListNew.findAll{it==T.bit("PossiblyNoBeam")}.size()==1) {
+              meldList << defect
+              if(comment.contains("manually added")) {
+                deleteComment = true
+              }
+            }
+          }
+          else {
+            meldList << defect
+          }
+
           if(defect==T.bit("SectorLoss")) {
             meldList << defect
             // remove outlier bits
-            meldList.removeAll(T.bit("TotalOutlier"))
-            meldList.removeAll(T.bit("TerminalOutlier"))
-            meldList.removeAll(T.bit("MarginalOutlier"))
+            // meldList.removeAll(T.bit("TotalOutlier"))
+            // meldList.removeAll(T.bit("TerminalOutlier"))
+            // meldList.removeAll(T.bit("MarginalOutlier"))
           }
           if(defect==T.bit("Misc")) {
             if(comment.contains("please delete this comment")) deleteComment=true
             else {
               meldList << defect
               // remove all other bits
-              meldList.removeAll(T.bit("TotalOutlier"))
-              meldList.removeAll(T.bit("TerminalOutlier"))
-              meldList.removeAll(T.bit("MarginalOutlier"))
-              meldList.removeAll(T.bit("SectorLoss"))
-              meldList.removeAll(T.bit("LowLiveTime"))
+              // meldList.removeAll(T.bit("TotalOutlier"))
+              // meldList.removeAll(T.bit("TerminalOutlier"))
+              // meldList.removeAll(T.bit("MarginalOutlier"))
+              // meldList.removeAll(T.bit("SectorLoss"))
+              // meldList.removeAll(T.bit("LowLiveTime"))
             }
           }
         }
@@ -126,4 +140,4 @@ qaTreeNew.each{ runnum, binTree ->
 
 // output melded qaTree.json
 new File("qaTree.json.melded").write(JsonOutput.toJson(qaTreeMelded))
-['new','old','melded'].each{"./prettyPrint.sh $it".execute()}
+['new','old','melded'].each{"./prettyPrint.sh $it".execute().waitFor()}

qa-physics/QA/modifyQaTree.groovy

@@ -11,6 +11,7 @@ usage["setBit"] = "setBit: overwrites stored defectBit(s) with specified bit"
 usage["addBit"] = "addBit: add specified bit to defectBit(s)"
 usage["delBit"] = "delBit: delete specified bit from defectBit(s)"
 usage["sectorLoss"] = "sectorLoss: specify a sector loss"
+usage["noBeam"] = "noBeam: add 'PossiblyNoBeam' bit"
 usage["setComment"] = "setComment: change or delete the comment"
 usage["addComment"] = "addComment: append a comment"
 usage["custom"] = "custom: do a custom action (see code)"
@@ -21,7 +22,7 @@ println("\n\n")
 // check arguments and print usage
 def cmd
 if(args.length>=1) cmd = args[0]
-else { 
+else {
   System.err.println(
   """
   syntax: modify.sh [command] [arguments]\n
@@ -49,7 +50,7 @@ def qaTree = slurper.parse(jsonFile)
 def recomputeDefMask = { runnum,binnum ->
   defList = []
   defMask = 0
-  (1..6).each{ s -> 
+  (1..6).each{ s ->
     qaTree["$runnum"]["$binnum"]["sectorDefects"]["$s"].unique()
     defList +=
       qaTree["$runnum"]["$binnum"]["sectorDefects"]["$s"].collect{it.toInteger()}
@@ -69,15 +70,15 @@ if( cmd=="setBit" || cmd=="addBit" || cmd=="delBit") {
   def rnum,bnumL,bnumR
   def bit
   def secList = []
-  if(args.length>5) {
+  if(args.length>4) {
     bit = args[1].toInteger()
     rnum = args[2].toInteger()
     bnumL = args[3].toInteger()
     bnumR = args[4].toInteger()
-    if(args[5]=="all") secList = (1..6).collect{it}
+    if(args.length<6 || args[5]=="all") secList = (1..6).collect{it}
     else (5..<args.length).each{ secList<<args[it].toInteger() }
 
-    println("run $rnum bins ${bnumL}-"+(bnumR==-1 ? "END" : bnumR) + 
+    println("run $rnum bins ${bnumL}-"+(bnumR==-1 ? "END" : bnumR) +
       " sectors ${secList}: $cmd ${bit}="+T.bitNames[bit])
 
     println("Enter a comment, if you want, otherwise press return")
@@ -90,7 +91,7 @@ if( cmd=="setBit" || cmd=="addBit" || cmd=="delBit") {
       if( qaFnum>=bnumL && ( bnumR==-1 || qaFnum<=bnumR ) ) {
 
         if(cmd=="setBit") {
-          secList.each{ 
+          secList.each{
             qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] = [bit]
           }
         }
@@ -116,7 +117,7 @@ if( cmd=="setBit" || cmd=="addBit" || cmd=="delBit") {
     def helpStr = usage["$cmd"].tokenize(':')[1]
     System.err.println(
     """
-    SYNTAX: ${cmd} [defectBit] [run] [firstBin] [lastBin] [list_of_sectors]
+    SYNTAX: ${cmd} [defectBit] [run] [firstBin] [lastBin] [list_of_sectors (default=all)]
       -$helpStr
       - set [lastBin] to -1 to denote last time bin of run
       - use \"all\" in place of [list_of_sectors] to apply to all sectors
@@ -134,14 +135,14 @@ if( cmd=="setBit" || cmd=="addBit" || cmd=="delBit") {
 else if(cmd=="sectorLoss") {
   def rnum,bnumL,bnumR
   def secList = []
-  if(args.length>4) {
+  if(args.length>3) {
     rnum = args[1].toInteger()
     bnumL = args[2].toInteger()
     bnumR = args[3].toInteger()
-    if(args[4]=="all") secList = (1..6).collect{it}
+    if(args.length<5 || args[4]=="all") secList = (1..6).collect{it}
     else (4..<args.length).each{ secList<<args[it].toInteger() }
 
-    println("run $rnum bins ${bnumL}-"+(bnumR==-1 ? "END" : bnumR) + 
+    println("run $rnum bins ${bnumL}-"+(bnumR==-1 ? "END" : bnumR) +
       " sectors ${secList}: define sector loss")
 
     println("Enter a comment, if you want, otherwise press return")
@@ -152,10 +153,10 @@ else if(cmd=="sectorLoss") {
       def qaFnum = k.toInteger()
       if( qaFnum>=bnumL && ( bnumR==-1 || qaFnum<=bnumR ) ) {
 
-        secList.each{ 
-          qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] -= T.bit("TotalOutlier")
-          qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] -= T.bit("TerminalOutlier")
-          qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] -= T.bit("MarginalOutlier")
+        secList.each{
+          // qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] -= T.bit("TotalOutlier")
+          // qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] -= T.bit("TerminalOutlier")
+          // qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] -= T.bit("MarginalOutlier")
           qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] += T.bit("SectorLoss")
         }
 
@@ -170,7 +171,7 @@ else if(cmd=="sectorLoss") {
     def helpStr = usage["$cmd"].tokenize(':')[1]
     System.err.println(
     """
-    SYNTAX: ${cmd} [run] [firstBin] [lastBin] [list_of_sectors]
+    SYNTAX: ${cmd} [run] [firstBin] [lastBin] [list_of_sectors (default=all)]
       -$helpStr
       - set [lastBin] to -1 to denote last time bin of run
       - use \"all\" in place of [list_of_sectors] to apply to all sectors
@@ -182,6 +183,58 @@ else if(cmd=="sectorLoss") {
   }
 }
 
+else if(cmd=="noBeam") {
+  def rnum,bnumL,bnumR
+  def secList = (1..6).collect{it}
+  if(args.length>3) {
+    rnum = args[1].toInteger()
+    bnumL = args[2].toInteger()
+    bnumR = args[3].toInteger()
+
+    println("run $rnum bins ${bnumL}-"+(bnumR==-1 ? "END" : bnumR) +
+      " sectors ${secList}: add PossiblyNoBeam bit")
+
+    println("Enter an additional comment, if you want, otherwise press return")
+    print("> ")
+    def cmt = System.in.newReader().readLine()
+    cmt = ['manually added PossiblyNoBeam defect bit', cmt].findAll{it.length()>0}.join('; ')
+
+    qaTree["$rnum"].each { k,v ->
+      def qaFnum = k.toInteger()
+      if( qaFnum>=bnumL && ( bnumR==-1 || qaFnum<=bnumR ) ) {
+        secList.each{
+          qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["$it"] += T.bit("PossiblyNoBeam")
+        }
+        recomputeDefMask(rnum,qaFnum)
+        if(cmt.length()>0) {
+          if(!qaTree["$rnum"]["$qaFnum"].containsKey("comment")) {
+            qaTree["$rnum"]["$qaFnum"]["comment"] = cmt
+          }
+          else {
+            if(qaTree["$rnum"]["$qaFnum"]["comment"].length()>0)
+              qaTree["$rnum"]["$qaFnum"]["comment"] += "; "
+            qaTree["$rnum"]["$qaFnum"]["comment"] += cmt
+          }
+        }
+      }
+    }
+
+  }
+  else {
+    def helpStr = usage["$cmd"].tokenize(':')[1]
+    System.err.println(
+    """
+    SYNTAX: ${cmd} [run] [firstBin] [lastBin]
+      -$helpStr
+      - set [lastBin] to -1 to denote last time bin of run
+      - this will set the PossiblyNoBeam bit for specified time bins, and add
+        a comment saying this was done
+      - you will be prompted to enter an additional comment
+    """)
+    System.exit(101)
+  }
+}
+
 else if(cmd=="lossFT") {
   def rnum,bnumL,bnumR
   if(args.length>4) {
@@ -199,9 +252,9 @@ else if(cmd=="lossFT") {
       def qaFnum = k.toInteger()
       if( qaFnum>=bnumL && ( bnumR==-1 || qaFnum<=bnumR ) ) {
 
-        qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["1"] -= T.bit("TotalOutlierFT")
-        qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["1"] -= T.bit("TerminalOutlierFT")
-        qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["1"] -= T.bit("MarginalOutlierFT")
+        // qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["1"] -= T.bit("TotalOutlierFT")
+        // qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["1"] -= T.bit("TerminalOutlierFT")
+        // qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["1"] -= T.bit("MarginalOutlierFT")
         qaTree["$rnum"]["$qaFnum"]["sectorDefects"]["1"] += T.bit("LossFT")
 
         recomputeDefMask(rnum,qaFnum)
@@ -235,9 +288,9 @@ else if( cmd=="addComment" || cmd=="setComment") {
     bnumR = args[3].toInteger()
 
     println("run $rnum bins ${bnumL}-"+(bnumR==-1 ? "END" : bnumR) + ": $cmd")
-    if(cmd=="addComment") 
+    if(cmd=="addComment")
       println("Enter the new comment to be appended")
-    else if(cmd=="setComment") 
+    else if(cmd=="setComment")
       println("Enter the new comment, or leave it blank to delete any stored comment")
     print("> ")
     def cmt = System.in.newReader().readLine()
@@ -254,7 +307,7 @@ else if( cmd=="addComment" || cmd=="setComment") {
             qaTree["$rnum"]["$qaFnum"]["comment"] += cmt
           }
         }
-        else if (cmd=="setComment") 
+        else if (cmd=="setComment")
           qaTree["$rnum"]["$qaFnum"]["comment"] = cmt
       }
     }
@@ -293,7 +346,7 @@ else if( cmd=="custom") {
 
     /* // remove outlier bits and add misc bit, to all sectors
     def secList = (1..6).collect{it}
-    secList.each{ 
+    secList.each{
       qaTree["$rnum"]["$bnum"]["sectorDefects"]["$it"] += T.bit("Misc") // add bit
       //qaTree["$rnum"]["$bnum"]["sectorDefects"]["$it"] = [T.bit("Misc")] // set bit
       qaTree["$rnum"]["$bnum"]["sectorDefects"]["$it"] -= T.bit("TotalOutlier") // delete bit
@@ -329,4 +382,4 @@ else { System.err.println("ERROR: unknown command!"); System.exit(100) }
 
 // update qaTree.json
 new File("qa/qaTree.json").write(JsonOutput.toJson(qaTree))
-"run-groovy parseQaTree.groovy".execute()
+["run-groovy", "parseQaTree.groovy"].execute().waitFor()

qa-physics/QA/parseQaTree.groovy

@@ -8,7 +8,7 @@ Tools T = new Tools()
 
 infile="qa/qaTree.json"
 outfile="qa/qaTree.json.table"
-if(args.size()>=1 && args[0].endsWith(".json")) {
+if(args.size()>=1) {
   infile = args[0]
   outfile = "${infile}.table"
   args = args.minus([args[0]]) // remove json file from args since no longer needed

qa-physics/epochs/epochs.rgc_su22.txt

@@ -0,0 +1,20 @@
+16042 16044 # ET, beam E = 2.2 GeV
+16047 16054 # C
+16066 16078 # NH3
+16089 16090 # ET, beam E = 10.5 GeV
+16096 16134 # C
+16137 16178 # NH3
+16184 16186 # ET
+16188 16191 # Align
+16194 16195 # ET
+16211 16260 # NH3
+16262 16289 # ND3
+16290 16297 # C
+16298 16303 # CH2
+16306 16309 # ET
+16317 16357 # NH3
+16358 16636 # ND3
+16658 16695 # NH3
+16697 16704 # C
+16709 16772 # NH3
+16783 16786 # Align

qa-physics/epochs/epochs.rgc_su22_prescaled.txt

@@ -0,0 +1 @@
+epochs.rgc_su22.txt

qa-physics/epochs/epochs.rgc_su22_sidisdvcs.txt

@@ -0,0 +1 @@
+epochs.rgc_su22.txt