feat(qa): support for charge studies and reheat idempotence

bin/qtl-reheat

@@ -16,6 +16,10 @@ declare -A REHEAT_METHODS=(
 
 # default options
 dataset=train
+declare -A modes
+for key in submit; do
+  modes[$key]=false
+done
 
 # usage
 sep="================================================================"
@@ -37,6 +41,8 @@ $(for key in "${!REHEAT_METHODS[@]}"; do printf "%24s %-11s %-s\n" "" "$key" "${
   OPTIONAL OPTIONS:
      -d [DATASET]      unique name for this dataset
                        default: $dataset
+     --submit          submit the slurm jobs, rather than just
+                       printing the \`sbatch\` command
   """ >&2
 }
 if [ $# -lt 1 ]; then
@@ -48,7 +54,7 @@ fi
 inputDir=""
 outputDir=""
 cmd=""
-while getopts "i:o:c:d:h" opt; do
+while getopts "i:o:c:d:h-:" opt; do
   case $opt in
     i) inputDir=$OPTARG ;;
     o) outputDir=$OPTARG ;;
@@ -61,6 +67,12 @@ while getopts "i:o:c:d:h" opt; do
       usage
       exit 101
       ;;
+    -)
+      for key in "${!modes[@]}"; do
+        [ "$key" == "$OPTARG" ] && modes[$OPTARG]=true && break
+      done
+      [ -z "${modes[$OPTARG]-}" ] && printError "unknown option --$OPTARG" && exit 100
+      ;;
     *) exit 100 ;;
   esac
 done
@@ -159,6 +171,12 @@ EOF
 echo """
 SLURM SCRIPT: $slurmScript
 JOB LIST:     $jobList
-Now submitting!
 """
-sbatch $slurmScript
+if ${modes['submit']}; then
+  echo "Now submitting!"
+  sbatch $slurmScript
+else
+  echo """Run this command to submit:
+  sbatch $slurmScript
+  """
+fi

qa-physics/charge_analysis/.gitignore

@@ -0,0 +1,2 @@
+__pycache__
+*.png

qa-physics/charge_analysis/README.md

@@ -0,0 +1,10 @@
+# Charge Analysis
+
+From Bhawani Singh
+
+```bash
+./analyze HIPO_FILE
+```
+Produces PNG files comparing the DAQ-gated FC charge determined from
+- directly from the `RUN::scaler` bank
+- from the livetime and ungated charge, by multiplication

qa-physics/charge_analysis/analyze.py

@@ -0,0 +1,277 @@
+#!/usr/bin/env python3
+##################################################################################
+# ADAPTED FROM BHAWANI SINGH's ORIGINAL SCRIPT:
+#   /w/hallb-scshelf2102/clas12/singh/Softwares/QADB_studies/python/main2.py
+##################################################################################
+import numpy as np
+import os
+import sys
+import logging
+from glob import glob
+import matplotlib.pyplot as plt
+import hipolib
+
+# Configure logging
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(levelname)s - %(message)s'
+)
+logger = logging.getLogger(__name__)
+
+# plt.style.use('seaborn-darkgrid')
+
+def main():
+
+    if len(sys.argv) != 2:
+        print(f'USAGE: {sys.argv[0]} [HIPO_FILE]')
+        exit(2)
+    hipo_file = sys.argv[1]
+
+    hipo_prefix = os.getenv('HIPO')
+    if hipo_prefix == None:
+        raise ValueError("HIPO env var not set")
+
+    logger.info(f"Processing file: {hipo_file}")
+
+    reader = hipolib.hreader(f'{hipo_prefix}/lib')
+    reader.open_with_tag(hipo_file, 1)  # filter by tag at open time
+    reader.define('RUN::config')
+    reader.define('RUN::scaler')
+
+    timestamps, fcups, fcupgateds, live_times = [], [], [], []
+
+    counter = 0
+    while reader.next():
+        if counter % 10000 == 0 and counter > 0:
+            logger.info(f'Processing event # {counter}')
+        counter += 1
+
+        if reader.getSize('RUN::config') == 0 or reader.getSize('RUN::scaler') == 0:
+            # logger.warning(f"Skipping empty bank at event {counter}")
+            continue
+
+        timestamp = reader.getEntry('RUN::config', 'timestamp')
+        fcup = reader.getEntry('RUN::scaler', 'fcup')
+        fcupgated = reader.getEntry('RUN::scaler', 'fcupgated')
+        live_time = reader.getEntry('RUN::scaler', 'livetime')
+
+        timestamps.append(timestamp[0])
+        fcups.append(fcup[0])
+        fcupgateds.append(fcupgated[0])
+        live_times.append(live_time[0])
+
+    logger.info(f"Processed {counter} events.")
+
+    # Sort data by timestamps
+    sorted_data = sorted(zip(timestamps, fcups, fcupgateds, live_times))
+    if not sorted_data:
+        raise ValueError("No data to plot.")
+
+    timestamps, fcups, fcupgateds, live_times = zip(*sorted_data)
+
+    timestamps = np.array(timestamps)
+    fcups = np.array(fcups)
+    fcupgateds = np.array(fcupgateds)
+    live_times = np.array(live_times)
+
+    run_number = 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)
+
+    plots1 = [
+        (axs1[0, 0], fcups, 'FCUP', 'FCUP vs Timestamp', 'darkgreen', 'line'),
+        (axs1[0, 1], fcupgateds, 'FCUP Gated', 'FCUP Gated vs Timestamp', 'darkorange', 'line'),
+        (axs1[1, 0], live_times, 'Live Time', 'Live Time vs Timestamp', 'purple', 'scatter'),
+        (axs1[1, 1], fcups * live_times, 'FCUP × Live Time', 'FCUP × Live Time vs Timestamp', 'steelblue', 'line'),
+    ]
+
+    for ax, data, label, title, color, style in plots1:
+        if style == 'line':
+            ax.plot(timestamps, data, label=label, color=color, linewidth=1.5)
+        elif style == 'scatter':
+            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_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'fcup_vs_timestamp_{run_number}.png', bbox_inches='tight', dpi=300)
+    plt.close(fig1)
+    # ---------- Compute Chunked FCUP Gated with neighbor handling ----------
+    chunk_size = 2000
+    num_chunks = len(timestamps) // chunk_size
+
+    chunk_caseA, chunk_caseB, chunk_caseC, chunk_default = [], [], [], []
+    cum_caseA, cum_caseB, cum_caseC, cum_default = [], [], [], []
+    chunk_indices, skipped_counts = [], []
+
+    runA, runB, runC, runDef = 0, 0, 0, 0
+    total_skipped = 0
+
+    corrected_livetimes_A = []
+    corrected_livetimes_B = []
+    corrected_livetimes_C = []
+
+    for i in range(num_chunks):
+        start = i * chunk_size
+        end = start + chunk_size
+        if end >= len(fcups):
+            break
+
+        # use np.diff for correct increments
+        fcup_diff = np.diff(fcups[start:end])
+        fcupgated_diff = np.diff(fcupgateds[start:end])
+        live_sub = live_times[start+1:end]
+
+        sumA, sumB, sumC, sumDef = 0, 0, 0, 0
+        skipped_in_chunk = 0
+
+        for j, lt in enumerate(live_sub):
+            if lt > 0:
+                # Case A
+                sumA += lt * fcup_diff[j]
+                corrected_livetimes_A.append(lt)
+                # Case B
+                sumB += lt * fcup_diff[j]
+                corrected_livetimes_B.append(lt)
+                # Case C
+                sumC += lt * fcup_diff[j]
+                corrected_livetimes_C.append(lt)
+                # Default
+                sumDef += fcupgated_diff[j]
+            else:
+                # ----- Case A/B nearest-neighbor substitution -----
+                idx_candidates = []
+                if j - 1 >= 0 and live_sub[j - 1] > 0:
+                    idx_candidates.append(j - 1)
+                if j + 1 < len(live_sub) and live_sub[j + 1] > 0:
+                    idx_candidates.append(j + 1)
+
+                if idx_candidates:
+                    nn = min(
+                        idx_candidates,
+                        key=lambda k: abs(timestamps[start + 1 + k] - timestamps[start + 1 + j])
+                    )
+                    lt_nn = live_sub[nn]
+
+                    # Case A
+                    sumA += lt_nn * fcup_diff[j]
+                    corrected_livetimes_A.append(lt_nn)
+
+                    # Case B
+                    sumB += lt_nn * fcupgated_diff[nn]
+                    corrected_livetimes_B.append(lt_nn)
+
+                    # Default
+                    sumDef += fcupgated_diff[j]
+                else:
+                    skipped_in_chunk += 1
+                    total_skipped += 1
+                    logger.warning(
+                        f"No valid positive LT neighbor at chunk {i}, local index {j}, "
+                        f"timestamp {timestamps[start+1+j]}"
+                    )
+
+                # ----- Case C: mean of ±20 neighbors -----
+                window = 10
+                idx_range = range(max(0, j - window), min(len(live_sub), j + window + 1))
+                neigh_lts = [live_sub[k] for k in idx_range if live_sub[k] > 0]
+                if neigh_lts:
+                    lt_mean = np.mean(neigh_lts)
+                    sumC += lt_mean * fcup_diff[j]
+                    corrected_livetimes_C.append(lt_mean)
+
+        runA += sumA
+        runB += sumB
+        runC += sumC
+        runDef += sumDef
+
+        chunk_caseA.append(sumA)
+        chunk_caseB.append(sumB)
+        chunk_caseC.append(sumC)
+        chunk_default.append(sumDef)
+        cum_caseA.append(runA)
+        cum_caseB.append(runB)
+        cum_caseC.append(runC)
+        cum_default.append(runDef)
+        chunk_indices.append(i)
+        skipped_counts.append(skipped_in_chunk)
+
+    logger.info(f"Computed chunked FCUP Gated values with neighbor handling (Cases A, B, C).")
+    logger.info(f"Total skipped events (no valid LT neighbor): {total_skipped}")
+
+    # ---------- Plot 2: Chunked FCUP Gated + Ratios + Skips + LT Distribution ----------
+    fig2, (ax_top, ax_mid, ax_bottom, ax_ltdist) = plt.subplots(
+        4, 1, figsize=(12, 14), sharex=False,
+        gridspec_kw={'height_ratios': [3, 1, 1, 2]}
+    )
+    fig2.suptitle(f'Run {run_number} - Chunked FCUP Gated (Neighbor Handling)', 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.set_ylabel('Cumulative Σ', fontsize=11)
+    ax_top.grid(True, linestyle='--', alpha=0.6)
+    ax_top.legend(fontsize=10)
+    ax_top.tick_params(axis='both', labelsize=10)
+
+    # Middle: ratios wrt default
+    ratioA = np.divide(cum_caseA, cum_default, out=np.full_like(cum_caseA, np.nan, dtype=float), where=np.array(cum_default) != 0)
+    #ratioB = np.divide(cum_caseB, cum_default, out=np.full_like(cum_caseB, np.nan, dtype=float), where=np.array(cum_default) != 0)
+    ratioC = np.divide(cum_caseC, cum_default, out=np.full_like(cum_caseC, 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.axhline(1.0, color='black', linestyle='--', linewidth=1)
+    ax_mid.set_ylabel('Ratio', fontsize=11)
+    ax_mid.grid(True, linestyle='--', alpha=0.6)
+    ax_mid.legend(fontsize=10)
+    ax_mid.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_ylabel('# Skipped', fontsize=11)
+    ax_bottom.grid(True, linestyle='--', alpha=0.6)
+    ax_bottom.tick_params(axis='both', labelsize=10)
+
+    # Bottom-2: livetime distributions
+    bins = 100
+    mean_raw, sigma_raw = np.mean(live_times), np.std(live_times)
+    mean_A, sigma_A = np.mean(corrected_livetimes_A), np.std(corrected_livetimes_A)
+    mean_B, sigma_B = np.mean(corrected_livetimes_B), np.std(corrected_livetimes_B)
+    mean_C, sigma_C = np.mean(corrected_livetimes_C), np.std(corrected_livetimes_C)
+
+    ax_ltdist.hist(live_times, bins=bins, alpha=0.4,
+                   label=f'Raw LT (μ={mean_raw:.3f}, σ={sigma_raw:.3f})', color='purple')
+    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')
+
+    ax_ltdist.set_xlabel('Live Time', fontsize=11)
+    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'chunked_fcupgated_comparison_{run_number}.png', bbox_inches='tight', dpi=300)
+    plt.close(fig2)
+
+
+if __name__ == "__main__":
+    main()
+    logger.info("HipoReader example completed.")