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feat: qtl xcharge for charge and clock analyses
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‎bin/qtl‎

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@@ -18,6 +18,7 @@ usage() {
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physics Generate and analyze physics QA timelines (Step 2)
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error Scan for errors in Slurm logs (for Step 1)
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reheat Reproduce a data file, e.g., to rerun postprocessing
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xcharge Cross check and analyze FC charge
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xtrain Cross check run list from trains and DSTs
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OPTIONS: Each command has its own set of options; run a command with no
@@ -42,6 +43,7 @@ case $cmd in
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ph*) exec $TIMELINESRC/bin/qtl-physics "$@" ;;
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er*) exec $TIMELINESRC/bin/qtl-error "$@" ;;
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re*) exec $TIMELINESRC/bin/qtl-reheat "$@" ;;
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xc*) exec $TIMELINESRC/bin/qtl-xcharge "$@" ;;
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xt*) exec $TIMELINESRC/bin/qtl-xtrain "$@" ;;
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-v|--version)
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echo $(mvn -q help:evaluate -Dexpression=project.version -DforceStdout -f $TIMELINESRC/pom.xml || echo "UNKNOWN")

‎bin/qtl-xcharge‎

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#!/usr/bin/env bash
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set -euo pipefail
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source $(dirname $0)/../libexec/environ.sh
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# constants ############################################################
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# methods: name -> description
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declare -A METHODS=(
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[charge]="run charge analysis (from Bhawani)"
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[clock]="plot the clock vs timestamp"
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)
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########################################################################
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# usage
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suffix=''
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sep="================================================================"
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usage() {
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echo """
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Take a closer look at the FC charge
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NOTE: chefs should not typically need to run this
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$sep
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USAGE: qtl xcharge [OPTIONS]
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$sep
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REQUIRED OPTIONS:
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-i [INPUT_FILE] input HIPO file
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-o [OUTPUT_DIR] output directory
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-m [METHOD] which analysis method, one of:
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$(for key in "${!METHODS[@]}"; do printf "%24s %-11s %-s\n" "" "$key" "${METHODS[$key]}"; done)
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OPTIONAL OPTIONS:
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-s [SUFFIX] a suffix to append to output files
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default: $suffix
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""" >&2
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}
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if [ $# -lt 1 ]; then
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usage
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exit 101
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fi
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# parse options
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inputFile=""
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outputDir=""
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mtd=""
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while getopts "i:o:m:s:h-:" opt; do
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case $opt in
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i) inputFile=$OPTARG ;;
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o) outputDir=$OPTARG ;;
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m)
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[ -z "${METHODS[$OPTARG]-}" ] && printError "unknown command '$OPTARG'" && exit 100
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mtd=$OPTARG
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;;
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s) suffix=$OPTARG ;;
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h)
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usage
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exit 101
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;;
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*) exit 100 ;;
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esac
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done
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# check arguments
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[ -z "$inputFile" ] && printError "missing input directory argument" && exit 100
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[ -z "$outputDir" ] && printError "missing output directory argument" && exit 100
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[ -z "$mtd" ] && printError "missing method argument" && exit 100
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# make output directory
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mkdir -p $outputDir
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# run the script
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case $mtd in
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charge)
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$TIMELINESRC/qa-physics/charge_analysis/analyze_charge.py $inputFile $outputDir $suffix
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;;
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clock)
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$TIMELINESRC/libexec/run-groovy-timeline.sh $TIMELINESRC/qa-physics/charge_analysis/analyze_clock.groovy $inputFile $outputDir $suffix
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root -b -q $TIMELINESRC/qa-physics/charge_analysis/plot_clock.C'("'$outputDir'", "'$suffix'")'
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;;
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*)
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echo "ERROR: unknown method '$mtd'" >&2
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exit 100
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;;
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esac
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echo "Done, see files in '$outputDir' with suffix '$suffix'"

‎qa-physics/charge_analysis/README.md‎

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@@ -1,18 +1,13 @@
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These scripts are called by `qtl xcharge`
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# Charge Analysis
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From Bhawani Singh
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`./analyze.py` Produces PNG files comparing the DAQ-gated FC charge determined from
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`./analyze_charge.py` Produces PNG files comparing the DAQ-gated FC charge determined from
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- the `RUN::scaler` bank directly
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- the livetime and ungated charge, by multiplication
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### Example
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Suppose we have reheated (`qtl reheat`) a skim file on `/cache` and
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stored it at `/volatile/reheat/`. To compare results:
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```bash
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./analyze.py /cache/...../skim.hipo before_reheat
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./analyze.py /volatile/reheat/skim.hipo after_reheat
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ls -t *.png
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```
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# Clock analysis
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- `analyze_clock.groovy`: gets the clock for each timestamp
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- `plot_clock.C`: plots the clock vs. timestamp

qa-physics/charge_analysis/analyze.py renamed to qa-physics/charge_analysis/analyze_charge.py

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def main():
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if len(sys.argv) != 3:
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if len(sys.argv) != 4:
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print(f'''
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USAGE: {sys.argv[0]} [INPUT_HIPO_FILE] [OUTPUT_FILE_SUFFIX]
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USAGE: {sys.argv[0]} [INPUT_HIPO_FILE] [OUTPUT_DIR] [OUTPUT_FILE_SUFFIX]
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INPUT_HIPO_FILE input HIPO file
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OUTPUT_FILE_SUFFIX append this string to the output
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file name; useful if you are comparing
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output files before and after reheating
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''')
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exit(2)
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hipo_file = sys.argv[1]
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output_suffix = sys.argv[2]
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hipo_file = sys.argv[1]
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output_dir = sys.argv[2]
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output_suffix = sys.argv[3]
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hipo_prefix = os.getenv('HIPO')
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if hipo_prefix == None:
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ax.tick_params(axis='both', labelsize=9)
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fig1.tight_layout(rect=[0, 0.03, 1, 0.95])
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fig1.savefig(f'fcup_vs_timestamp_{run_number}_{output_suffix}.png', bbox_inches='tight', dpi=300)
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fig1.savefig(f'{output_dir}/fcup_vs_timestamp_{run_number}_{output_suffix}.png', bbox_inches='tight', dpi=300)
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plt.close(fig1)
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# ---------- Compute Chunked FCUP Gated with neighbor handling ----------
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chunk_size = 2000
@@ -296,7 +297,7 @@ def main():
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ax_ltdist.tick_params(axis='both', labelsize=10)
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fig2.tight_layout(rect=[0, 0.03, 1, 0.95])
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fig2.savefig(f'chunked_fcupgated_comparison_{run_number}_{output_suffix}.png', bbox_inches='tight', dpi=300)
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fig2.savefig(f'{output_dir}/chunked_fcupgated_comparison_{run_number}_{output_suffix}.png', bbox_inches='tight', dpi=300)
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plt.close(fig2)
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‎qa-physics/charge_analysis/analyze_clock.groovy‎

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import org.jlab.detector.scalers.DaqScalers;
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import org.jlab.detector.scalers.DaqScalersSequence;
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import org.jlab.detector.calib.utils.ConstantsManager;
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import org.jlab.jnp.hipo4.io.HipoReader;
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import org.jlab.jnp.hipo4.data.Event;
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import org.jlab.jnp.hipo4.data.Bank;
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import org.jlab.jnp.hipo4.data.SchemaFactory;
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import java.util.List;
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import java.util.ArrayList;
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if(args.length<3) {
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System.err.println """
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USAGE: groovy ${this.class.getSimpleName()}.groovy [HIPO file] [output directory] [suffix]
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"""
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System.exit(101)
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}
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def in_file = args[0]
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def out_dir = args[1]
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def suffix = args[2]
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List<String> filenames = new ArrayList<>();
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filenames.add(in_file);
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ConstantsManager consts = new ConstantsManager();
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consts.init("/runcontrol/fcup","/runcontrol/slm","/runcontrol/helicity","/daq/config/scalers/dsc1","/runcontrol/hwp");
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DaqScalersSequence seq = DaqScalersSequence.rebuildSequence(1, consts, filenames);
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// seq.fixClockRollover();
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def out_file_name = "${out_dir}/clock_${suffix}.dat";
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def out_file = new File(out_file_name);
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def out_file_writer = out_file.newWriter(false);
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out_file_writer << [ "timestamp/L", "clock_gated/L", "clock_ungated/L" ].join(':') << '\n';
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for(String filename : filenames) {
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HipoReader reader = new HipoReader();
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reader.setTags(1);
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reader.open(filename);
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SchemaFactory schema = reader.getSchemaFactory();
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while(reader.hasNext()) {
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Bank rcfgBank = new Bank(schema.getSchema("RUN::config"));
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Event event = new Event();
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reader.nextEvent(event);
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event.read(rcfgBank);
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long timestamp = -1;
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if (rcfgBank.getRows()>0)
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timestamp = rcfgBank.getLong("timestamp",0);
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DaqScalers ds=seq.get(timestamp);
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if (ds!=null) {
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out_file_writer << [ds.getTimestamp(), ds.dsc2.gatedClock, ds.dsc2.clock].join(' ') << '\n';
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}
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}
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reader.close();
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}
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out_file_writer.flush();
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out_file_writer.close();
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System.out.println("WROTE $out_file_name");

‎qa-physics/charge_analysis/plot_clock.C‎

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void plot_clock(TString out_dir, TString suffix) {
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TString basename = out_dir + "/clock_" + suffix;
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TFile* o = new TFile(basename+".root", "RECREATE");
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TTree* tr = new TTree("tr", "tr");
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tr->ReadFile(basename+".dat");
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tr->Write();
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o->Close();
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std::cout << "WROTE " << basename << ".root\n";
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std::cout << "Recommended plot commands:" << std::endl;
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std::cout << " tr->Draw(\"clock_ungated:timestamp\")" << std::endl;
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std::cout << " tr->Draw(\"clock_gated:timestamp\")" << std::endl;
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}

‎qadb/notes/rga_sp18.md‎

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@@ -80,16 +80,15 @@ bin/qtl reheat -m rollover -c 13.3.0 -d rga_sp18_6.4GeV_outbending_lo_nSidis -o
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bin/qtl reheat -m rollover -c 13.3.0 -d rga_sp18_6.4GeV_inbending_lo_nSidis -o /volatile/clas12/users/$LOGNAME/reheat/rga_sp18_6.4GeV_inbending_lo_nSidis -i /cache/clas12/rg-a/production/recon/spring2018/6.42gev/torus-0.75/pass1/dst/train/nSidis
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```
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3. check the results on some runs; see [`qa-physics/charge_analysis/README.md`](/qa-physics/charge_analysis/README.md); for example:
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3. check the results on some runs; for example:
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```bash
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cd qa-physics/charge_analysis
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# before reheat
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for f in /cache/clas12/rg-a/production/recon/spring2018/6.42gev/torus+1/pass1/dst/train/nSidis/*.hipo; do ./analyze.py $f original; done
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for f in /cache/clas12/rg-a/production/recon/spring2018/6.42gev/torus+1/pass1/dst/train/nSidis/*.hipo; do bin/qtl xcharge -m charge -i $f -o test_charge -s original; done
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# after reheat
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for f in ~/v/reheat/rga_sp18_6.4GeV_outbending_nSidis/*.hipo; do ./analyze.py $f reheated; done
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for f in ~/v/reheat/rga_sp18_6.4GeV_outbending_nSidis/*.hipo; do bin/qtl xcharge -m charge -i $f -o test_charge -s original; done
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```
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then see files in `test_charge/`.
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## Run monitoring
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