Merge branch 'development' into unix-time

baltzell · web-flow · commit c3db6b46c68e · 2026-05-22T22:41:28.000-04:00
diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Reader.java b/common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Reader.java
@@ -12,7 +12,7 @@
 import org.json.JSONObject;
 
 /**
- * Just reads EVIO or HIPO, and passes it along.
+ * Just reads EVIO or HIPO and passes it along.
  * 
  * @author baltzell
  */
diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Writer.java b/common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Writer.java
@@ -22,13 +22,12 @@
 import org.json.JSONObject;
 
 /**
- * Combined with DecoderReader, a port of the standard "decoder" to CLARA.
- *
+ * 
  * 1. Copies certain banks on-the-fly to new tag-1 events
- * 2. Caches helicity states and scaler readouts, for later use in post-processing
- * 3. Writes the helicity sequence to HEL::flip banks in new tag-1 events
- * 4. Adds .hipo to the output filename, if necessary
- * 5. Runs post-processing, writing tag-1 information to all events 
+ * 2. Caches helicity states, scaler readouts, and unix time
+ * 3. Writes HEL::flip, RUN/HEL::scaler, and RUN::unix to new tag-1 events
+ * 4. Runs post-processing, writing tag-1 information to all events 
+ * 5. Adds .hipo to the output filename, if necessary
  *
  * @author baltzell
  */
diff --git a/common-tools/clara-io/src/main/java/org/jlab/io/clara/DecoderReader.java b/common-tools/clara-io/src/main/java/org/jlab/io/clara/DecoderReader.java
@@ -14,11 +14,7 @@
 import org.json.JSONObject;
 
 /**
- * Combined with Clas12Writer, a port of the standard "decoder" to CLARA.
- * 
- * 1. Convert EVIO to HIPO
- * 2. CCDB translation tables, c/s/c -> s/l/c/o
- * 3. Pulse extraction, e.g., Mode-1 FADC250
+ * The CLAS decoder.  Requires EVIO input.
  * 
  * @author baltzell
  */
diff --git a/common-tools/clas-utils/src/main/java/org/jlab/utils/options/OptionValue.java b/common-tools/clas-utils/src/main/java/org/jlab/utils/options/OptionValue.java
@@ -55,6 +55,6 @@ public boolean parse(List<String> arguments){
     }
 
     public boolean isDefault() {
-        return this.optionValue == null || this.optionValue.equals(this.optionDefault);
+        return this.optionValue==null || this.optionValue.equals(this.optionDefault);
     }
 }
diff --git a/etc/bankdefs/hipo4/rich.json b/etc/bankdefs/hipo4/rich.json
@@ -238,6 +238,8 @@
             {"name":"time",           "type":"F", "info":"Hit time" },
             {"name":"rawtime",        "type":"F", "info":"Hit rawtime" },
             {"name":"duration",       "type":"S", "info":"Hit duration" },
+            {"name":"mchi2",          "type":"F", "info":"Track-cluster matching chi2 (if any)"},
+            {"name":"msize",          "type":"S", "info":"Cluster size"},
             {"name":"status",         "type":"S", "info":"Hit status" },
             {"name":"used",           "type":"B", "info":"eligible for PID in time (1=yes, 0=no) angle (10=yes, 0=no) hypo (100=by other) or cluster (2)"},
             {"name":"emilay",         "type":"B", "info":"aerogel layer of photon emission"},
diff --git a/etc/services/data-ai-2026.yaml b/etc/services/data-ai-2026.yaml
@@ -1,11 +1,13 @@
 io-services:
   reader:
-    class: org.jlab.io.clara.HipoToHipoReader
-    name: HipoToHipoReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
-    class: org.jlab.io.clara.HipoToHipoWriter
-    name: HipoToHipoWriter
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.clas.swimtools.MagFieldsEngine
     name: MAGFIELDS
   - class: org.jlab.rec.ft.cal.FTCALEngine
diff --git a/etc/services/data-ai-uber.yml b/etc/services/data-ai-uber.yml
@@ -14,12 +14,14 @@ configuration:
       run: "19000"
 io-services:
   reader:
-    class: org.jlab.io.clara.DecoderReader
-    name: DecoderReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
     class: org.jlab.io.clara.Clas12Writer
     name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.service.uber.Uber$First
     name: 1ST
   - class: org.jlab.service.uber.Uber$ForwardTagger
diff --git a/etc/services/data-ai.yaml b/etc/services/data-ai.yaml
@@ -1,11 +1,13 @@
 io-services:
   reader:
-    class: org.jlab.io.clara.HipoToHipoReader
-    name: HipoToHipoReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
-    class: org.jlab.io.clara.HipoToHipoWriter
-    name: HipoToHipoWriter
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.clas.swimtools.MagFieldsEngine
     name: MAGFIELDS
   - class: org.jlab.rec.ft.cal.FTCALEngine
diff --git a/etc/services/data-aicv-uber.yml b/etc/services/data-aicv-uber.yml
@@ -14,12 +14,14 @@ configuration:
       run: "19000"
 io-services:
   reader:
-    class: org.jlab.io.clara.DecoderReader
-    name: DecoderReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
     class: org.jlab.io.clara.Clas12Writer
     name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.service.uber.Uber$First
     name: 1ST
   - class: org.jlab.service.uber.Uber$ForwardTagger
diff --git a/etc/services/data-aicv.yaml b/etc/services/data-aicv.yaml
@@ -1,11 +1,13 @@
 io-services:
   reader:
-    class: org.jlab.io.clara.HipoToHipoReader
-    name: HipoToHipoReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
-    class: org.jlab.io.clara.HipoToHipoWriter
-    name: HipoToHipoWriter
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.clas.swimtools.MagFieldsEngine
     name: MAGFIELDS
   - class: org.jlab.rec.ft.cal.FTCALEngine
diff --git a/etc/services/data-cv-uber.yml b/etc/services/data-cv-uber.yml
@@ -12,12 +12,14 @@ configuration:
       run: "19000"
 io-services:
   reader:
-    class: org.jlab.io.clara.DecoderReader
-    name: DecoderReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
     class: org.jlab.io.clara.Clas12Writer
     name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.service.uber.Uber$First
     name: 1ST
   - class: org.jlab.service.uber.Uber$ForwardTagger
diff --git a/etc/services/data-cv.yaml b/etc/services/data-cv.yaml
@@ -1,11 +1,13 @@
 io-services:
   reader:
-    class: org.jlab.io.clara.HipoToHipoReader
-    name: HipoToHipoReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
-    class: org.jlab.io.clara.HipoToHipoWriter
-    name: HipoToHipoWriter
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.clas.swimtools.MagFieldsEngine
     name: MAGFIELDS
   - class: org.jlab.rec.ft.cal.FTCALEngine
diff --git a/etc/services/dcalign.yaml b/etc/services/dcalign.yaml
@@ -1,11 +1,13 @@
 io-services:
   reader:
-    class: org.jlab.io.clara.HipoToHipoReader
-    name: HipoToHipoReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
-    class: org.jlab.io.clara.HipoToHipoWriter
-    name: HipoToHipoWriter
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.clas.swimtools.MagFieldsEngine
     name: MAGFIELDS
   - class: org.jlab.rec.ft.cal.FTCALEngine
diff --git a/etc/services/denoise.yaml b/etc/services/denoise.yaml
@@ -1,11 +1,13 @@
 io-services:
   reader:
-    class: org.jlab.io.clara.HipoToHipoReader
-    name: HipoToHipoReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
-    class: org.jlab.io.clara.HipoToHipoWriter
-    name: HipoToHipoWriter
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.clas.swimtools.MagFieldsEngine
     name: MAGFIELDS
   - class: org.jlab.rec.ft.cal.FTCALEngine
diff --git a/etc/services/eb.yaml b/etc/services/eb.yaml
@@ -1,11 +1,13 @@
 io-services:
   reader:
-    class: org.jlab.io.clara.HipoToHipoReader
-    name: HipoToHipoReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
-    class: org.jlab.io.clara.HipoToHipoWriter
-    name: HipoToHipoWriter
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.service.eb.EBTBEngine
     name: EBTB
 configuration:
diff --git a/etc/services/kpp.yaml b/etc/services/kpp.yaml
@@ -1,11 +1,13 @@
 io-services:
   reader:
-    class: org.jlab.io.clara.HipoToHipoReader
-    name: HipoToHipoReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
-    class: org.jlab.io.clara.HipoToHipoWriter
-    name: HipoToHipoWriter
+    class: org.jlab.io.clara.Clas12Writer
+    name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.clas.swimtools.MagFieldsEngine
     name: MAGFIELDS
   - class: org.jlab.rec.ft.cal.FTCALEngine
diff --git a/etc/services/rgd-clarode.yml b/etc/services/rgd-clarode.yml
@@ -19,8 +19,8 @@ configuration:
       outputBankPrefix: "HB"
 io-services:
   reader:
-    class: org.jlab.io.clara.EvioToEvioReader
-    name: EvioReader
+    class: org.jlab.io.clara.Clas12Reader
+    name: Clas12Reader
   writer:
     class: org.jlab.io.clara.Clas12Writer
     name: Clas12Writer
diff --git a/etc/services/rgl-clarode.yml b/etc/services/rgl-clarode.yml
@@ -6,6 +6,8 @@ io-services:
     class: org.jlab.io.clara.Clas12Writer
     name: Clas12Writer
 services:
+  - class: org.jlab.clas.reco.DecoderEngine
+    name: DECO
   - class: org.jlab.clas.swimtools.MagFieldsEngine
     name: MAGFIELDS
   - class: org.jlab.rec.ft.cal.FTCALEngine
diff --git a/reconstruction/calib/src/main/java/org/jlab/calibration/detectors/RICHBankBuilder.java b/reconstruction/calib/src/main/java/org/jlab/calibration/detectors/RICHBankBuilder.java
@@ -35,6 +35,7 @@ public DataBank buildCalibBank(DataEvent event) {
         DataBank part = event.getBank("REC::Particle");
         DataBank rich = event.getBank("RICH::Particle");        
         DataBank hits = event.getBank("RICH::Hit");
+        DataBank clus = event.getBank("RICH::Cluster");
         DataBank phos = event.getBank("RICH::Photon");
             
         List<Integer> goodPhotons = new ArrayList<>();
@@ -45,9 +46,12 @@ public DataBank buildCalibBank(DataEvent event) {
         }
 
         Map<Integer,Integer> part2Rich = new HashMap<>();
+        Map<Integer,Integer> clus2Rich = new HashMap<>();
         for(int i=0; i<rich.rows(); i++) {
             int pindex = rich.getByte("pindex", i);
+            int hindex = rich.getShort("hindex", i);
             part2Rich.put(pindex, i);
+            clus2Rich.put(hindex, i);
         }
         
         List<Integer> goodClusters = new ArrayList<>();
@@ -99,6 +103,7 @@ public DataBank buildCalibBank(DataEvent event) {
                 row++;
             }
             for(int i : goodClusters) {
+                int cluster = hits.getShort("cluster", i);
                 calib.setShort("hindex",       row, (short) i);
                 calib.setByte( "sector",       row, (byte) hits.getShort("sector", i));
                 calib.setShort("pmt",          row, hits.getShort("pmt", i));
@@ -111,6 +116,14 @@ public DataBank buildCalibBank(DataEvent event) {
                 calib.setFloat("time",         row, hits.getFloat("time", i));
                 calib.setFloat("rawtime",      row, hits.getFloat("rawtime", i));
                 calib.setShort("duration",     row, hits.getShort("duration", i));
+                if(clus2Rich.containsKey(cluster-1)) {
+                    int rindex  = clus2Rich.get(cluster-1);
+                    calib.setByte("pindex",    row, rich.getByte("pindex", rindex));
+                    calib.setFloat("mchi2",    row, rich.getFloat("mchi2", rindex));
+                    calib.setShort("msize",    row, clus.getShort("size", cluster-1));
+                }
+                else
+                    calib.setByte("pindex",    row, (byte) -1);
                 row++;
             }
             return calib;

Original file line number	Diff line number	Diff line change
`@@ -12,7 +12,7 @@`
`12`	`12`	`import org.json.JSONObject;`
`13`	`13`
`14`	`14`	`/**`
`15`		`- * Just reads EVIO or HIPO, and passes it along.`
	`15`	`+ * Just reads EVIO or HIPO and passes it along.`
`16`	`16`	`*`
`17`	`17`	`* @author baltzell`
`18`	`18`	`*/`
Original file line number	Diff line number	Diff line change
`@@ -55,6 +55,6 @@ public boolean parse(List<String> arguments){`
`55`	`55`	`}`
`56`	`56`
`57`	`57`	`public boolean isDefault() {`
`58`		`- return this.optionValue == null \|\| this.optionValue.equals(this.optionDefault);`
	`58`	`+ return this.optionValue==null \|\| this.optionValue.equals(this.optionDefault);`
`59`	`59`	`}`
`60`	`60`	`}`