feat: integrate sectors and layers for the ATOF Time

src/main/java/org/jlab/clas/timeline/analysis/alert/alert_atof_time.groovy

@@ -9,41 +9,23 @@ class alert_atof_time {
 
 def data = new ConcurrentHashMap()
 def has_data = new AtomicBoolean(false)
-int sector;
-int min_index;
-int max_index;
-
-  alert_atof_time(int atof_sector){ // atof_sector runs from 0 to 14.
-    this.sector    = atof_sector;
-    this.min_index = 44*(atof_sector); 
-    this.max_index = 44*(atof_sector+1); 
-  }
 
-  def getName() {
-    return "${this.class.simpleName}_${String.format('%02d', sector)}"
-  }
 
   def processRun(dir, run) {
 
     data[run] = [run:run]
     def trigger = dir.getObject('/TRIGGER/bits')
     def reference_trigger_bit = 0
     // data[run].put('bits',  trigger)
-    (min_index..<max_index).collect{index->
-      int atof_sector = index / (11 * 4);
-      assert sector == atof_sector // sanity-check. this should be the same.
-      int layer     = (index % (11 * 4)) / 11;
-      int component = index % 11;
-      def file_index = String.format('sector%02d_layer%d_component%02d', sector, layer, component)
-      def h1 = dir.getObject(String.format('/ALERT/ATOF_Time_%s', file_index))
+    (0..<11).collect{component->
+      def h1 = dir.getObject(String.format('/ALERT/ATOF_Time_component%02d', component))
       if(h1!=null) {
         if (h1.getBinContent(h1.getMaximumBin()) > 30 && h1.getEntries()>300){
-          data[run].put(String.format('atof_time_%s', file_index),  h1)
+          data[run].put(String.format('atof_time_%02d', component),  h1)
           def f1 = ALERTFitter.atof_time_fitter(h1,component)
-          data[run].put(String.format('fit_atof_time_%s', file_index),  f1)
-          data[run].put(String.format('peak_location_atof_time_%s', file_index),  f1.getParameter(1).abs())
-          data[run].put(String.format('sigma_atof_time_%s', file_index),  f1.getParameter(2).abs())
-          data[run].put(String.format('integral_normalized_to_trigger_atof_time_%s', file_index),  Math.sqrt(2*3.141597f) * f1.getParameter(0).abs() * f1.getParameter(2).abs()/trigger.getBinContent(reference_trigger_bit) )
+          data[run].put(String.format('fit_atof_time_%02d', component),  f1)
+          data[run].put(String.format('peak_location_atof_time_%02d', component),  f1.getParameter(1).abs())
+          data[run].put(String.format('sigma_atof_time_%02d', component),  f1.getParameter(2).abs())
           has_data.set(true)
         }
       }
@@ -59,36 +41,31 @@ int max_index;
       return
     }
 
-    ['peak_location', 'sigma', 'integral_normalized_to_trigger'].each{variable->
-      (0..<4).collect{layer->
-        def names = []
-        TDirectory out = new TDirectory()
-        out.mkdir('/timelines')
-        (0..<11).collect{component->
-          def file_index = ''
-           file_index = String.format('sector%02d_layer%d_component%02d', sector, layer, component)
-          names << String.format('atof_time_%s', file_index)
-        }
-        names.each{ name ->
-          def gr = new GraphErrors(name)
-          gr.setTitle(  String.format("ATOF Time %s sector %02d layer %d", variable.replace('_', ' '), sector, layer))
-          gr.setTitleY( String.format("ATOF Time %s sector %02d layer %d (ns)", variable.replace('_', ' '), sector, layer))
-          gr.setTitleX("run number")
-          data.sort{it.key}.each{run,it->
-            out.mkdir('/'+it.run)
-            out.cd('/'+it.run)
-            if (it.containsKey(name)){
-              out.addDataSet(it[name])
-              out.addDataSet(it['fit_'+name])
-              gr.addPoint(it.run, it[variable + '_' + name], 0, 0)
-            }
-            else if (variable=="peak_location") println(String.format("run %d: %s either does not exist or does not have enough statistics.", it.run, name))
+    ['peak_location', 'sigma'].each{variable->
+      TDirectory out = new TDirectory()
+      out.mkdir('/timelines')
+      (0..<11).collect{component->
+        def name = String.format('atof_time_%02d', component)
+
+        def gr = new GraphErrors(name)
+
+        gr.setTitle(  String.format("ATOF Time %s ", variable.replace('_', ' ')))
+        gr.setTitleY( String.format("ATOF Time %s  (ns)", variable.replace('_', ' ')))
+        gr.setTitleX("run number")
+        data.sort{it.key}.each{run,it->
+          out.mkdir('/'+it.run)
+          out.cd('/'+it.run)
+          if (it.containsKey(name)){
+            out.addDataSet(it[name])
+            out.addDataSet(it['fit_'+name])
+            gr.addPoint(it.run, it[variable + '_' + name], 0, 0)
           }
-          out.cd('/timelines')
-          out.addDataSet(gr)
+          else if (variable=="peak_location") println(String.format("run %d: %s either does not exist or does not have enough statistics.", it.run, name))
         }
-        out.writeFile(String.format('alert_atof_time_%s_sector%02d_layer%d.hipo', variable, sector, layer))
+        out.cd('/timelines')
+        out.addDataSet(gr)
       }
+      out.writeFile(String.format('alert_atof_time_%s.hipo', variable))
     }
   }
 }

src/main/java/org/jlab/clas/timeline/histograms/ALERT.java

@@ -57,21 +57,14 @@ public ALERT(int reqrunNum, String reqOutputDir, float reqEb, boolean reqTimeBas
     }
     rf_large_integer = 1000;
 
-    ATOF_Time = new H1F[660];// ATOF Time Histograms
+    ATOF_Time = new H1F[11];// ATOF Time Histograms
 
-    for (int index = 0; index < 660; index++) {
-      int sector    = 0;
-      int layer     = 0;
-      int component = 0;
+    for (int component = 0; component < 11; component++) {
 
-      sector    = index / (11 * 4);
-      layer     = (index % (11 * 4)) / 11;
-      component = index % 11;
-
-      ATOF_Time[index] = new H1F(String.format("ATOF_Time_sector%02d_layer%d_component%02d", sector, layer, component), String.format("ATOF Time sector%02d layer%d component%02d", sector, layer, component), 300, 85, 100);
-      ATOF_Time[index].setTitleX("ATOF Time (ns)");
-      ATOF_Time[index].setTitleY("Counts");
-      ATOF_Time[index].setFillColor(4);
+      ATOF_Time[component] = new H1F(String.format("ATOF_Time_component%02d", component), String.format("ATOF Time component%02d", component), 240, 83, 95);
+      ATOF_Time[component].setTitleX("ATOF Time (ns)");
+      ATOF_Time[component].setTitleY("Counts");
+      ATOF_Time[component].setFillColor(4);
     }
 
     //AHDC ADC Histograms
@@ -154,13 +147,11 @@ public void fillAHDC_hits(DataBank ahdc_hits) {
   public void fillATOF_hits(DataBank atof_hits) {
     int rows = atof_hits.rows();
     for (int loop = 0; loop < rows; loop++) {
-      int sector    = atof_hits.getInt("sector", loop);
-      int layer     = atof_hits.getInt("layer", loop);
+
       int component = atof_hits.getInt("component", loop);
       float time       = atof_hits.getFloat("time", loop);
-      int index     = sector * 44 + layer * 11 + component;
 
-      ATOF_Time[index].fill(time);
+      ATOF_Time[component].fill(time);
 
     }
   }
@@ -231,8 +222,8 @@ public void write() {
     TDirectory dirout = new TDirectory();
     dirout.mkdir("/ALERT/");
     dirout.cd("/ALERT/");
-    for (int index = 0; index < 660; index++) {
-      dirout.addDataSet(ATOF_Time[index]);
+    for (int component = 0; component < 11; component++) {
+      dirout.addDataSet(ATOF_Time[component]);
     }
     for (int index = 0; index < 576; index++) {
       dirout.addDataSet(ADC[index], AHDC_TIME[index]);

src/main/java/org/jlab/clas/timeline/run_analysis.groovy

@@ -9,7 +9,7 @@ def engines = [
     *(1..8).collect {ahdc_layer_number -> new alert_ahdc_adc (ahdc_layer_number) },
     new alert_ahdc_residual(),
     *(1..8).collect {ahdc_layer_number -> new alert_ahdc_time (ahdc_layer_number) },
-    *(0..14).collect {atof_sector -> new alert_atof_time(atof_sector)},
+    new alert_atof_time(),
   ],
   out_BAND: [
     new band_adccor(),