Run neutrino filter from XML files.

analysis/scripts/config.sh

@@ -0,0 +1,12 @@
+xml=$1
+output=$2
+start=$4
+end=$5
+cutset=$6
+mode=$7
+
+export ALIBUILD_WORK_DIR=/afs/cern.ch/user/s/schuetha/work/public/data_work_flow/sw
+source /cvmfs/sndlhc.cern.ch/SNDLHC-2025/Jan30/setUp.sh
+eval `alienv -a slc9_x86-64 load --no-refresh sndsw/master-local1`
+echo "Finished setting up SNDSW env"
+export EOSSHIP=root://eosuser.cern.ch

analysis/scripts/count_the_run.py

@@ -0,0 +1,72 @@
+import argparse
+import xml.etree.ElementTree as ET
+
+def count_runs(xml_file, min_events, outfile):
+    tree = ET.parse(xml_file)
+    root = tree.getroot()
+
+    runs_selected = []
+    n = 0
+
+    # Find all <run> anywhere under the root
+    for run in root.findall(".//run"):
+        run_number = run.findtext("run_number")
+        n_events_text = run.findtext("n_events", "0")
+
+        # Skip if missing run_number
+        if run_number is None:
+            continue
+
+        try:
+            n_events = int(n_events_text)
+
+        except ValueError:
+            # Bad number in XML – skip this run
+            continue
+
+        n += 1
+
+        if n_events >= min_events:
+            runs_selected.append(run_number)
+
+    floor    = n // min_events
+    mod      = n %  min_events
+
+    with open(outfile, "w") as f:
+        for rn in range(1, floor + 1 if mod == 0 else floor + 2):
+            if rn == 1:
+                f.write(f"{rn}\t{rn*min_events-1}\n")
+
+            if (rn)*min_events - 1 >= n and mod != 0:
+                f.write(f"{(rn - 1)*min_events}\t{n}\n")
+                break
+
+            elif rn > 1 and rn <= floor + 1 and mod != 0:
+                f.write(f"{(rn-1)*min_events}\t{rn*min_events-1}\n")
+
+            elif rn > 1 and rn <= floor + 1 and mod == 0:
+                f.write(f"{(rn-1)*min_events}\t{rn*min_events}\n")
+
+    return len(runs_selected)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Select runs from an XML runlist based on minimum number of events."
+    )
+    parser.add_argument(
+        "-xml", "--xml_file", required=True,
+        help="Path to the XML runlist file."
+    )
+    parser.add_argument(
+        "-n", "--min-events", dest="min_events", type=int, default=0,
+        help="number of event per job."
+    )
+    parser.add_argument(
+        "-o", "--output", default="se.txt",
+        help="Output text file with selected run_numbers (default: se.txt)."
+    )
+
+    args = parser.parse_args()
+
+    n_selected = count_runs(args.xml_file, args.min_events, args.output)
+    print(f"Total runs selected: {n_selected}")

analysis/scripts/run_neutrino_filter_xml.sh

@@ -0,0 +1,85 @@
+#!/bin/bash
+set -o errexit -o pipefail -o noclobber
+source $3/config.sh "$@"
+set -o nounset
+
+# Iterate through every <run> automatically
+echo "Reading the XML file: $xml"
+for run in $(xmllint --xpath 'count(/runlist/runs/run)' "${xml}"); do :; done  # pre-check count
+
+mode_list=(STAGE1 RECO STAGE2)
+
+if [[ ! ${mode_list[@]} =~ $mode ]]
+then
+    echo Mode $mode not available. It must be one of "${mode_list[*]}"
+    echo Exitting.
+    exit
+fi
+
+for i in $(seq $start $end) 
+do
+    run_number=$(xmllint --xpath "string(/runlist/runs/run[$i]/run_number)" "${xml}")
+    start_year=$(xmllint --xpath "string(/runlist/runs/run[$i]/start)" "${xml}")
+    year=${start_year:0:4}
+    end=$(xmllint --xpath "string(/runlist/runs/run[$i]/end)" "${xml}")
+    n_events=$(xmllint --xpath "string(/runlist/runs/run[$i]/n_events)" "${xml}")
+    n_files=$(xmllint --xpath "string(/runlist/runs/run[$i]/n_files)" "${xml}")
+    n_files=$((n_files-1))  # to make the seq 0 based
+    path=$(xmllint --xpath "string(/runlist/runs/run[$i]/path)" "${xml}")
+
+    if [ "$mode" == "STAGE1" ] 
+    then
+        for j in $(seq 0 "$n_files")
+        do
+            if [ -f "${output}/${run_number}/${mode}/filtered_MC_00${run_number}_${j}.root" ]
+            then
+                echo "File ${output}/${run_number}/${mode}/filtered_MC_00${run_number}_${j}.root exists. Skipping."
+                continue
+	        fi
+            js=$(printf "%03d" $((j)))
+            neutrinoFilterGoldenSample ${path}/sndsw_raw-0${js}.root filtered_MC_00${run_number}_${j}.root ${cutset}
+            mkdir -p ${output}/${run_number}/${mode}/
+            xrdcp -f ./filtered_MC_00${run_number}_${j}.root ${output}/${run_number}/${mode}/
+            rm -f ./filtered_MC_00${run_number}_${j}.root
+        done
+
+    elif [ "$mode" == "RECO" ] 
+    then
+        geo_file=$( root -l -b -q -e '.L sndGeometryGetter.cxx+' -e "std::string csv=std::string(gSystem->Getenv(\"SNDSW_ROOT\"))+\"/analysis/tools/geo_paths.csv\"; \
+                    std::cout << snd::analysis_tools::GetGeoPath(csv, ${run_number}) << std::endl;" | tail -n 1 )
+        for j in $(seq 0 "$n_files")
+        do
+            if [ -f "${output}/${run_number}/${mode}/filtered_MC_00${run_number}_${j}__muonReco.root" ]
+            then
+                echo "File ${output}/${run_number}/${mode}/filtered_MC_00${run_number}_${j}.root exists. Skipping."
+                continue
+            fi
+            python3 $SNDSW_ROOT/shipLHC/run_muonRecoSND.py -f ${output}/${run_number}/STAGE1/filtered_MC_00${run_number}_${j}.root -g ${geo_file} -c passing_mu_DS -sc 1 -s ./ -hf linearSlopeIntercept -o
+            mkdir -p ${output}/${run_number}/${mode}/
+            xrdcp -f ./filtered_MC_00${run_number}_${j}__muonReco.root ${output}/${run_number}/${mode}/
+            rm -f ./filtered_MC_00${run_number}_${j}__muonReco.root
+        done
+
+    elif [ "$mode" == "STAGE2" ] 
+    then
+        geo_file=$( root -l -b -q -e '.L sndGeometryGetter.cxx+' -e "std::string csv=std::string(gSystem->Getenv(\"SNDSW_ROOT\"))+\"/analysis/tools/geo_paths.csv\"; \
+                    std::cout << snd::analysis_tools::GetGeoPath(csv, ${run_number}) << std::endl;" | tail -n 1 )
+        for j in $(seq 0 "$n_files")
+        do
+            if [ -f "${output}/${run_number}/${mode}/filtered_MC_00${run_number}_${j}_stage2_noscifi2.root" ]
+            then
+                echo "File "${output}/${run_number}/${mode}/filtered_MC_00${run_number}_${j}_stage2_noscifi2.root" exists. Skipping."
+                continue
+            fi
+            python3 ${SNDSW_ROOT}/analysis/neutrinoFilterGoldenSample_stage2.py -f ${output}/${run_number}/STAGE1/filtered_MC_00${run_number}_${j}.root -t ${output}/${run_number}/RECO/filtered_MC_00${run_number}_${j}__muonReco.root -o filtered_MC_00${run_number}_${j}_stage2_noscifi2.root -g ${geo_file};
+            mkdir -p ${output}/${run_number}/${mode}/
+            xrdcp -f ./filtered_MC_00${run_number}_${j}_stage2_noscifi2.root ${output}/${run_number}/${mode}/
+            rm -f ./filtered_MC_00${run_number}_${j}_stage2_noscifi2.root
+        done
+
+    else
+        echo "Mode $mode not recognized. Exitting."
+        exit
+    fi
+    echo "Finished processing run number $run_number"
+done

analysis/scripts/run_neutrino_xml_all_stage.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+set -o errexit -o pipefail -o noclobber
+source $3/config.sh "$@"
+set -o nounset
+
+# Iterate through every <run> automatically
+echo "Reading the XML file: $xml"
+for run in $(xmllint --xpath 'count(/runlist/runs/run)' "${xml}"); do :; done  # pre-check count
+
+
+for i in $(seq $start $end) 
+do
+    run_number=$(xmllint --xpath "string(/runlist/runs/run[$i]/run_number)" "${xml}")
+    start_year=$(xmllint --xpath "string(/runlist/runs/run[$i]/start)" "${xml}")
+    year=${start_year:0:4}
+    end=$(xmllint --xpath "string(/runlist/runs/run[$i]/end)" "${xml}")
+    n_events=$(xmllint --xpath "string(/runlist/runs/run[$i]/n_events)" "${xml}")
+    n_files=$(xmllint --xpath "string(/runlist/runs/run[$i]/n_files)" "${xml}")
+    n_files=$((n_files-1))  # to make the seq 0 based
+    path=$(xmllint --xpath "string(/runlist/runs/run[$i]/path)" "${xml}")
+    geo_file=$( root -l -b -q -e '.L sndGeometryGetter.cxx+' -e "std::string csv=std::string(gSystem->Getenv(\"SNDSW_ROOT\"))+\"/analysis/tools/geo_paths.csv\"; \
+                std::cout << snd::analysis_tools::GetGeoPath(csv, ${run_number}) << std::endl;" | tail -n 1 )
+
+    for j in $(seq 0 "$n_files")
+    do
+        js=$(printf "%03d" $((j)))
+        neutrinoFilterGoldenSample ${path}/sndsw_raw-0${js}.root filtered_MC_00${run_number}_${j}.root ${cutset}
+        python3 $SNDSW_ROOT/shipLHC/run_muonRecoSND.py -f filtered_MC_00${run_number}_${j}.root -g ${geo_file} -c passing_mu_DS -sc 1 -s ./ -hf linearSlopeIntercept -o
+        python3 ${SNDSW_ROOT}/analysis/neutrinoFilterGoldenSample_stage2.py -f ${run_number}/filtered_MC_00${run_number}_${j}.root -t filtered_MC_00${run_number}_${j}__muonReco.root -o filtered_MC_00${run_number}_${j}_stage2_noscifi2.root -g ${geo_file}; 
+    done
+
+    mkdir -p ${output}/${run_number}/
+    xrdcp -f ./filtered_MC_00${run_number}_*.root ${output}/${run_number}/
+    xrdcp -f ./filtered_MC_00${run_number}_*__muonReco.root ${output}/${run_number}/
+    xrdcp -f ./filtered_MC_00${run_number}_*_stage2_noscifi2.root ${output}/${run_number}/
+    rm -f ./filtered_MC_00${run_number}_*.root
+    rm -f ./filtered_MC_00${run_number}_*__muonReco.root
+    rm -f ./filtered_MC_00${run_number}_*_stage2_noscifi2.root
+    echo "Finished processing run number $run_number"
+done