Merge remote-tracking branch 'origin/main' into rgk-pass2

Author: c-dilks

.github/workflows/ci.yml

@@ -95,7 +95,7 @@ jobs:
           key: validation_files_lfs_${{ matrix.type }}
           path: validation_files.tar.zst
       - name: download timeline build
-        uses: actions/download-artifact@v7
+        uses: actions/download-artifact@v8
         with:
           name: build_timeline
       - name: untar
@@ -141,7 +141,7 @@ jobs:
           key: validation_files_lfs_${{ matrix.type }}
           path: validation_files.tar.zst
       - name: download timeline build
-        uses: actions/download-artifact@v7
+        uses: actions/download-artifact@v8
         with:
           name: build_timeline
       - name: untar
@@ -174,13 +174,13 @@ jobs:
     steps:
       - uses: actions/checkout@v6
       - name: download outfiles
-        uses: actions/download-artifact@v7
+        uses: actions/download-artifact@v8
         with:
           pattern: outfiles_*
           merge-multiple: true
           path: outfiles
       - name: download timeline build
-        uses: actions/download-artifact@v7
+        uses: actions/download-artifact@v8
         with:
           name: build_timeline
       - name: untar

bin/qtl-histogram

@@ -8,6 +8,7 @@ source $(dirname $0)/../libexec/environ.sh
 # constants ############################################################
 # slurm settings
 SLURM_MEMORY=2000 # must be more than max heap size in $TIMELINE_JAVA_OPTS
+SLURM_DISK=32M
 SLURM_TIME=10:00:00
 SLURM_LOG=/farm_out/%u/%x-%A_%a
 ########################################################################
@@ -489,6 +490,7 @@ for key in ${jobkeys[@]}; do
 #SBATCH --account=clas12
 
 #SBATCH --mem-per-cpu=$SLURM_MEMORY
+#SBATCH --gres=disk:$SLURM_DISK
 #SBATCH --time=$SLURM_TIME
 
 #SBATCH --array=1-$(cat $joblist | wc -l)

bin/qtl-reheat

@@ -6,6 +6,7 @@ source $(dirname $0)/../libexec/environ.sh
 # constants ############################################################
 # slurm settings
 SLURM_MEMORY=2000 # must be more than max heap size `java` calls
+SLURM_DISK=32M
 SLURM_TIME=12:00:00
 SLURM_LOG=/farm_out/%u/%x-%A_%a
 # reheating methods: name -> description
@@ -16,7 +17,9 @@ declare -A REHEAT_METHODS=(
 
 # default options
 dataset=train
-coatjava_version=13.3.0 # the first version with rollover correction, used for RG-A Spring 2018 reheating
+coatjava_version=13.8.0 # 13.3.0: first version with rollover correction, used for RG-A Spring 2018 reheating
+                        # 13.8.0: fix: avoid call to method that recalibrates already-calibrated dsc2
+                        #         https://github.com/JeffersonLab/coatjava/pull/1153
 declare -A modes
 for key in submit; do
   modes[$key]=false
@@ -187,6 +190,7 @@ cat > $slurmScript << EOF
 #SBATCH --partition=production
 #SBATCH --account=clas12
 #SBATCH --mem-per-cpu=$SLURM_MEMORY
+#SBATCH --gres=disk:$SLURM_DISK
 #SBATCH --time=$SLURM_TIME
 #SBATCH --array=1-$(cat $jobList | wc -l)
 #SBATCH --ntasks=1

pom.xml

@@ -4,7 +4,7 @@
 
   <groupId>org.jlab.clas.timeline</groupId>
   <artifactId>clas12-timeline</artifactId>
-  <version>4.0.2</version>
+  <version>4.0.4</version>
   <name>clas12-timeline</name>
   <url>http://www.github.com/JeffersonLab/clas12-timeline</url>
 
@@ -35,21 +35,21 @@
     <dependency>
       <groupId>org.jlab.coat</groupId>
       <artifactId>coat-libs</artifactId>
-      <version>13.6.0</version>
+      <version>13.8.0</version>
       <type>jar</type>
     </dependency>
     <!-- https://mvnrepository.com/artifact/org.apache.groovy/groovy-all -->
     <dependency>
       <groupId>org.apache.groovy</groupId>
       <artifactId>groovy-all</artifactId>
-      <version>5.0.4</version>
+      <version>5.0.5</version>
       <type>pom</type>
     </dependency>
     <!-- https://mvnrepository.com/artifact/org.apache.groovy/groovy-dateutil -->
     <dependency>
       <groupId>org.apache.groovy</groupId>
       <artifactId>groovy-dateutil</artifactId>
-      <version>5.0.4</version>
+      <version>5.0.5</version>
     </dependency>
     <!-- https://mvnrepository.com/artifact/org.codehaus.gpars/gpars -->
     <dependency>
@@ -82,7 +82,7 @@
           <dependency>
             <groupId>org.codehaus.groovy</groupId>
             <artifactId>groovy-eclipse-batch</artifactId>
-            <version>5.0.4-02</version> <!-- NOTE: if no release notes, try commit history of https://github.com/groovy/groovy-eclipse -->
+            <version>5.0.5-01</version> <!-- NOTE: if no release notes, try commit history of https://github.com/groovy/groovy-eclipse -->
           </dependency>
         </dependencies>
       </plugin>

qa-physics/charge_analysis/analyze_charge.py

@@ -82,12 +82,12 @@ def main():
     fcupgateds = np.array(fcupgateds)
     live_times = np.array(live_times)
 
-    run_number = os.path.splitext(os.path.basename(hipo_file))[0]
+    file_basename = os.path.splitext(os.path.basename(hipo_file))[0]
 
     # ---------- Plot 1: Per-event data ----------
     # ---------- Plot 1: Per-event data ----------
     fig1, axs1 = plt.subplots(2, 2, figsize=(14, 8))
-    fig1.suptitle(f'Run {run_number} - Event-Level Detector Data', fontsize=16)
+    fig1.suptitle(f'{file_basename}', fontsize=16)
 
     plots1 = [
         (axs1[0, 0], fcups, 'FCUP', 'FCUP vs Timestamp', 'darkgreen', 'line'),
@@ -103,18 +103,19 @@ def main():
             ax.scatter(timestamps, data, label=label, color=color, s=10, alpha=0.7)
 
         ax.set_title(title, fontsize=12)
-        ax.set_xlabel('Timestamp', fontsize=10)
+        ax.set_xlabel('Timestamp', fontsize=10, loc='center')
         ax.set_ylabel(label, fontsize=10)
         ax.legend(fontsize=9)
         ax.grid(True, linestyle='--', alpha=0.6)
         ax.tick_params(axis='both', labelsize=9)
 
     fig1.tight_layout(rect=[0, 0.03, 1, 0.95])
-    fig1.savefig(f'{output_dir}/fcup_vs_timestamp_{run_number}_{output_suffix}.png', bbox_inches='tight', dpi=300)
+    fig1.savefig(f'{output_dir}/fcup_vs_timestamp_{file_basename}_{output_suffix}.png', bbox_inches='tight', dpi=300)
     plt.close(fig1)
     # ---------- Compute Chunked FCUP Gated with neighbor handling ----------
-    chunk_size = 2000
+    chunk_size = 100
     num_chunks = len(timestamps) // chunk_size
+    xlabel     = f'Bin num. (size={chunk_size} scalers)'
 
 
     chunk_caseA, chunk_caseB, chunk_caseC, chunk_default, chunk_default_ungated = [], [], [], [], []
@@ -229,15 +230,16 @@ def main():
         5, 1, figsize=(12, 17), sharex=False,
         gridspec_kw={'height_ratios': [3, 1, 1, 1, 2]}
     )
-    fig2.suptitle(f'Run {run_number} - Chunked FCUP Gated (Neighbor Handling)', fontsize=16)
+    fig2.suptitle(f'{file_basename}', fontsize=16)
 
     # Top: cumulative sums
-    ax_top.plot(chunk_indices, cum_caseA, label='Cumulative Case A (LT_nn × FCUPungated)', color='darkred', marker='o')
-    #ax_top.plot(chunk_indices, cum_caseB, label='Cumulative Case B (LT_nn × FCUPungated_nn)', color='darkgreen', marker='s')
-    ax_top.plot(chunk_indices, cum_caseC, label='Cumulative Case C (20-NN mean × FCUPungated)', color='darkorange', marker='d')
-    ax_top.plot(chunk_indices, cum_default, label='Cumulative Default (FCUPgated)', color='blue', marker='^')
-    ax_top.plot(chunk_indices, cum_default_ungated, label='Cumulative Default Ungated (FCUPungated)', color='teal', marker='x',linestyle='--')
+    ax_top.plot(chunk_indices, cum_default_ungated, label='U: ungated FC charge', color='black',       marker='o', markersize=4, linestyle='--')
+    ax_top.plot(chunk_indices, cum_default,         label='G: gated FC charge',   color='red',         marker='^', markersize=4)
+    ax_top.plot(chunk_indices, cum_caseA,           label='G\': LiveTime × U',    color='deepskyblue', marker='x', markersize=4, linestyle='--')
+    # ax_top.plot(chunk_indices, cum_caseB, label='Cumulative Case B (LT_nn × FCUPungated_nn)', color='darkgreen',  marker='s', markersize=4)
+    # ax_top.plot(chunk_indices, cum_caseC, label='Cumulative Case C (20-NN mean × U)',         color='darkorange', marker='d', markersize=4)
     ax_top.set_ylabel('Cumulative Σ', fontsize=11)
+    ax_top.set_xlabel(xlabel, fontsize=11, loc='right')
     ax_top.grid(True, linestyle='--', alpha=0.6)
     ax_top.legend(fontsize=10)
     ax_top.tick_params(axis='both', labelsize=10)
@@ -248,28 +250,30 @@ def main():
     ratioC = np.divide(cum_caseC, cum_default, out=np.full_like(cum_caseC, np.nan, dtype=float), where=np.array(cum_default) != 0)
     ratioDefUng = np.divide(cum_default_ungated, cum_default, out=np.full_like(cum_default_ungated, np.nan, dtype=float), where=np.array(cum_default) != 0)
 
-    ax_mid.plot(chunk_indices, ratioA, label='Case A / Default', color='darkred', marker='o')
-    #ax_mid.plot(chunk_indices, ratioB, label='Case B / Default', color='darkgreen', marker='s')
-    ax_mid.plot(chunk_indices, ratioC, label='Case C / Default', color='darkorange', marker='d')
-    ax_mid.plot(chunk_indices, ratioDefUng, label='Default FCUP Ungated / Default FCUP gated', color='teal', marker='x',linestyle='--')
+    ax_mid.plot(chunk_indices, ratioA, label='G\' / G', color='magenta', marker='x', markersize=4, linestyle='--')
+    #ax_mid.plot(chunk_indices, ratioB, label='Case B / G', color='darkgreen', marker='s', markersize=4)
+    # ax_mid.plot(chunk_indices, ratioC, label='Case C / G', color='darkorange', marker='d', markersize=4)
+    # ax_mid.plot(chunk_indices, ratioDefUng, label='U / G', color='teal', marker='x', markersize=4, linestyle='--')
     ax_mid.axhline(1.0, color='black', linestyle='--', linewidth=1)
     ax_mid.set_ylabel('Ratio', fontsize=11)
+    ax_mid.set_xlabel(xlabel, fontsize=11, loc='right')
     ax_mid.grid(True, linestyle='--', alpha=0.6)
     ax_mid.legend(fontsize=10)
     ax_mid.tick_params(axis='both', labelsize=10)
 
     # Gated / Ungated ratio panel
     ratio_gated_ung = np.divide(cum_default, cum_default_ungated, out=np.full_like(cum_default, np.nan, dtype=float), where=np.array(cum_default_ungated) != 0)
-    ax_gatedrat.plot(chunk_indices, ratio_gated_ung, label='FCUPgated / FCUPungated', color='navy', marker='o')
+    ax_gatedrat.plot(chunk_indices, ratio_gated_ung, label='G / U', color='orange', marker='o', markersize=4)
     ax_gatedrat.axhline(1.0, color='black', linestyle='--', linewidth=1)
     ax_gatedrat.set_ylabel('Gated / Ungated', fontsize=11)
+    ax_gatedrat.set_xlabel(xlabel, fontsize=11, loc='right')
     ax_gatedrat.grid(True, linestyle='--', alpha=0.6)
     ax_gatedrat.legend(fontsize=10)
     ax_gatedrat.tick_params(axis='both', labelsize=10)
 
     # Bottom-1: skipped events count
     ax_bottom.bar(chunk_indices, skipped_counts, color='gray', alpha=0.7)
-    ax_bottom.set_xlabel(f'Chunk Index (Each = {chunk_size} events)', fontsize=11)
+    ax_bottom.set_xlabel(xlabel, fontsize=11, loc='right')
     ax_bottom.set_ylabel('# Skipped', fontsize=11)
     ax_bottom.grid(True, linestyle='--', alpha=0.6)
     ax_bottom.tick_params(axis='both', labelsize=10)
@@ -286,20 +290,23 @@ def main():
     ax_ltdist.hist(corrected_livetimes_A, bins=bins, alpha=0.4,
                    label=f'Case A LT (μ={mean_A:.3f}, σ={sigma_A:.3f})', color='red')
     #ax_ltdist.hist(corrected_livetimes_B, bins=bins, alpha=0.4,
-     #              label=f'Case B LT (μ={mean_B:.3f}, σ={sigma_B:.3f})', color='green')
-    ax_ltdist.hist(corrected_livetimes_C, bins=bins, alpha=0.4,
-                   label=f'Case C LT (μ={mean_C:.3f}, σ={sigma_C:.3f})', color='orange')
+    #               label=f'Case B LT (μ={mean_B:.3f}, σ={sigma_B:.3f})', color='green')
+    # ax_ltdist.hist(corrected_livetimes_C, bins=bins, alpha=0.4,
+    #                label=f'Case C LT (μ={mean_C:.3f}, σ={sigma_C:.3f})', color='orange')
 
-    ax_ltdist.set_xlabel('Live Time', fontsize=11)
+    ax_ltdist.set_xlabel('Live Time', fontsize=11, loc='right')
     ax_ltdist.set_ylabel('Counts', fontsize=11)
     ax_ltdist.legend(fontsize=9)
     ax_ltdist.grid(True, linestyle='--', alpha=0.6)
     ax_ltdist.tick_params(axis='both', labelsize=10)
 
     fig2.tight_layout(rect=[0, 0.03, 1, 0.95])
-    fig2.savefig(f'{output_dir}/chunked_fcupgated_comparison_{run_number}_{output_suffix}.png', bbox_inches='tight', dpi=300)
+    fig2.savefig(f'{output_dir}/chunked_fcupgated_comparison_{file_basename}_{output_suffix}.png', bbox_inches='tight', dpi=300)
     plt.close(fig2)
 
+    print(f'TOTAL UNGATED CHARGE = {fcups[-1]-fcups[0]}')
+    print(f'TOTAL   GATED CHARGE = {fcupgateds[-1]-fcupgateds[0]}')
+
 
 if __name__ == "__main__":
     main()

qa-physics/charge_analysis/analyze_clock.groovy

@@ -7,6 +7,8 @@ import org.jlab.jnp.hipo4.data.Bank;
 import org.jlab.jnp.hipo4.data.SchemaFactory;
 import java.util.List;
 import java.util.ArrayList;
+import java.util.logging.Logger;
+import java.util.logging.Level;
 
 if(args.length<4) {
   System.err.println """
@@ -22,6 +24,7 @@ def rollover = args[3] == '1'
 List<String> filenames = new ArrayList<>();
 filenames.add(in_file);
 
+Logger.getLogger("org.jlab.detector.scalers.DaqScalersSequence").setLevel(Level.INFO);
 ConstantsManager consts = new ConstantsManager();
 consts.init("/runcontrol/fcup","/runcontrol/slm","/runcontrol/helicity","/daq/config/scalers/dsc1","/runcontrol/hwp");
 DaqScalersSequence seq = DaqScalersSequence.rebuildSequence(1, consts, filenames);

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

@@ -20,11 +20,13 @@ def has_data = new AtomicBoolean(false)
     (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){
+        if (h1.getBinContent(h1.getMaximumBin()) > 3 && h1.getEntries()>10){
           data[run].put(String.format('atof_time_%02d', component),  h1)
-          def f1 = ALERTFitter.atof_time_fitter(h1,component)
+          double fit_min = h1.getXaxis().getBinCenter(1)
+          double fit_max = h1.getXaxis().getBinCenter(h1.getXaxis().getNBins())
+          def f1 = ALERTFitter.atof_time_fitter(h1, component, fit_min, fit_max)
           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('peak_location_atof_time_%02d', component),  f1.getParameter(1))
           data[run].put(String.format('sigma_atof_time_%02d', component),  f1.getParameter(2).abs())
           has_data.set(true)
         }

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

@@ -0,0 +1,75 @@
+package org.jlab.clas.timeline.analysis
+import java.util.concurrent.ConcurrentHashMap
+import java.util.concurrent.atomic.AtomicBoolean
+import org.jlab.groot.data.TDirectory
+import org.jlab.groot.data.GraphErrors
+import org.jlab.clas.timeline.fitter.ALERTFitter
+
+class alert_atof_time_sl {
+
+  def data = new ConcurrentHashMap()
+  def has_data = new AtomicBoolean(false)
+  int sector
+  int layer
+
+  alert_atof_time_sl(int sector, int layer) {
+    this.sector = sector
+    this.layer  = layer
+  }
+
+  def getName() {
+    return String.format("%s_sector%02d_layer%d", this.class.simpleName, sector, layer)
+  }
+
+  def processRun(dir, run) {
+    data[run] = [run:run]
+    (0..<11).each { component ->
+      def h1 = dir.getObject(String.format('/ALERT/ATOF_Time_sector%02d_layer%02d_component%02d', sector, layer, component))
+      if (h1 != null) {
+        if (h1.getBinContent(h1.getMaximumBin()) > 3 && h1.getEntries() > 10) {
+          def name = String.format('atof_time_sl_s%02d_l%d_c%02d', sector, layer, component)
+          data[run].put(name, h1)
+          double fit_min = h1.getXaxis().getBinCenter(1)
+          double fit_max = h1.getXaxis().getBinCenter(h1.getXaxis().getNBins())
+          def f1 = ALERTFitter.atof_time_fitter(h1, component, fit_min, fit_max)
+          data[run].put('fit_' + name, f1)
+          data[run].put('peak_location_' + name, f1.getParameter(1))
+          data[run].put('sigma_' + name, f1.getParameter(2).abs())
+          has_data.set(true)
+        }
+      }
+    }
+  }
+
+  def write() {
+    if (!has_data.get()) {
+      System.err.println "WARNING: no data for this timeline, not producing"
+      return
+    }
+    ['peak_location', 'sigma'].each { variable ->
+      TDirectory out = new TDirectory()
+      out.mkdir('/timelines')
+      (0..<11).each { component ->
+        def name = String.format('atof_time_sl_s%02d_l%d_c%02d', sector, layer, component)
+        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 (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)
+          } 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.cd('/timelines')
+        out.addDataSet(gr)
+      }
+      out.writeFile(String.format('alert_atof_time_sl_%s_sector%02d_layer%d.hipo', variable, sector, layer))
+    }
+  }
+}