diff --git a/scripts/coyote_protector_xtc_gui_ready_test/bash_launcher.py b/scripts/coyote_protector_xtc_gui_ready_test/bash_launcher.py
new file mode 100644
index 0000000..e4aca2a
--- /dev/null
+++ b/scripts/coyote_protector_xtc_gui_ready_test/bash_launcher.py
@@ -0,0 +1,134 @@
+#!/usr/bin/env python3
+"""
+bash_launcher.py
+Launches routine_detection_v3.sh with specified arguments.
+Can be run from CDS to orchestrate the complete XTC workflow.
+
+USAGE:
+    python bash_launcher.py [OPTIONS]
+    python bash_launcher.py --help
+
+EXAMPLES:
+    # Run with defaults
+    python bash_launcher.py
+
+    # Run with custom parameters
+    python bash_launcher.py --run_number=61 --exp_number=mfx101346325 --max_events=80000
+
+    # Run with specific user
+    python bash_launcher.py --user=pmonteil --run_number=100
+"""
+
+import argparse
+import subprocess
+import sys
+from pathlib import Path
+
+
+def eprint(msg):
+    """Write message to stderr (compatible with older Python)."""
+    sys.stderr.write(str(msg) + "\n")
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Launch coyote XTC detection routine via bash",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog=__doc__
+    )
+
+    parser.add_argument(
+        "--user",
+        default="pmonteil",
+        help="Username for SSH to SDF (default: pmonteil)"
+    )
+    parser.add_argument(
+        "--run_number",
+        type=int,
+        default=61,
+        help="LCLS run number to process (default: 61)"
+    )
+    parser.add_argument(
+        "--exp_number",
+        default="mfx101346325",
+        help="Experiment identifier (default: mfx101346325)"
+    )
+    parser.add_argument(
+        "--save_normalized",
+        type=int,
+        choices=[0, 1],
+        default=1,
+        help="Save normalized images (1=yes, 0=no, default: 1)"
+    )
+    parser.add_argument(
+        "--max_events",
+        type=int,
+        default=10000,
+        help="Maximum events to process (default: 10000)"
+    )
+    parser.add_argument(
+        "--use_normalized",
+        type=int,
+        choices=[0, 1],
+        default=1,
+        help="Use normalized images for inference (1=yes, 0=no, default: 1)"
+    )
+    parser.add_argument(
+        "--dry_run",
+        action="store_true",
+        help="Print command without executing"
+    )
+
+    args = parser.parse_args()
+
+    # Get the script path (should be in same directory)
+    script_path = Path(__file__).parent / "routine_detection_v3.sh"
+
+    if not script_path.exists():
+        eprint("[ERROR] Script not found: {}".format(script_path))
+        sys.exit(1)
+
+    # Build command
+    cmd = [
+        "bash",
+        str(script_path),
+        "--user={}".format(args.user),
+        "RUN_NUMBER={}".format(args.run_number),
+        "EXP_NUMBER={}".format(args.exp_number),
+        "SAVE_NORMALIZED={}".format(args.save_normalized),
+        "MAX_EVENTS={}".format(args.max_events),
+        "USE_NORMALIZED={}".format(args.use_normalized),
+    ]
+
+    print("[INFO] ============================================")
+    print("[INFO] COYOTE XTC DETECTION LAUNCHER")
+    print("[INFO] ============================================")
+    print("[INFO] User: {}".format(args.user))
+    print("[INFO] Run Number: {}".format(args.run_number))
+    print("[INFO] Experiment: {}".format(args.exp_number))
+    print("[INFO] Save Normalized: {}".format(args.save_normalized))
+    print("[INFO] Max Events: {}".format(args.max_events))
+    print("[INFO] Use Normalized: {}".format(args.use_normalized))
+    print("[INFO] ============================================")
+    print()
+
+    print("[INFO] Command: {}".format(" ".join(cmd)))
+    print()
+
+    if args.dry_run:
+        print("[INFO] DRY RUN MODE - Command not executed")
+        return 0
+
+    try:
+        result = subprocess.run(cmd, check=False)
+        return result.returncode
+    except KeyboardInterrupt:
+        eprint("\n[INFO] Interrupted by user")
+        return 130
+    except Exception as e:
+        eprint("[ERROR] Failed to execute command: {}".format(e))
+        return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/scripts/coyote_protector_xtc_gui_ready_test/inference_coyote_xtc.py b/scripts/coyote_protector_xtc_gui_ready_test/inference_coyote_xtc.py
index 1972353..610eda9 100644
--- a/scripts/coyote_protector_xtc_gui_ready_test/inference_coyote_xtc.py
+++ b/scripts/coyote_protector_xtc_gui_ready_test/inference_coyote_xtc.py
@@ -1,18 +1,16 @@
-
-## same as test_xtc/inference_coyote.py but with argument parsing
+#!/usr/bin/env python3
 """
-YOLOv8 Inference Script → CSV (sizes)
+YOLOv8 Inference Script → CSV (sizes) + above-threshold CSV
 ------------------------------------------------------------
 - Runs YOLO inference on a folder of images
 - Computes longest side per detection in px and μm
 - Flags detections larger than a given μm threshold
+- Writes:
+    1) results_csv/measurements_complete.csv  (ALL detections)
+    2) results_csv/measurements_above_threshold.csv (ONLY detections above threshold)
 
 USAGE:
     python inference_coyote_xtc.py <chip_pic_dir>
-
-EDIT THESE BEFORE RUNNING:
- - weights_path: Path to your trained YOLO weights (.pt)
- - px_to_um:     Pixel-to-micron conversion factor for your setup
 """
 
 import os
@@ -37,27 +35,23 @@
 # Paths / parameters
 # -------------------------
 weights_path = (
-    "/sdf/home/p/pmonteil/coyote_protector_test_PL_labeling_tries_v3_run61_mfx101346325_200_random/scripts/runs/detect/train_150epochs_v11_merged/weights/best.pt"
+    "/sdf/home/p/pmonteil/coyote_protector_test_PL_labeling_tries_v3_run61_mfx101346325_200_random/scripts/"
+    "runs/detect/train_150epochs_v11_merged/weights/best.pt"
 )
 
-'''
-weights_path = (
-    "/sdf/home/p/pmonteil/prjlumine22/results/pmonteil/"
-    "coyote_beamtime_19jan/weight_yolov11n_150epochs.pt"
-)
-'''
-
 mag_factor = 5.56     # optical magnification
 px_size = 3.45        # pixel size (μm)
-dowsamp_factor = 2  # if images were downsampled before inference
-px_to_um = px_size*dowsamp_factor / mag_factor
-alert_um = 50.0 #threshold, in μm, above which to flag detections
+dowsamp_factor = 2    # if images were downsampled before inference
+px_to_um = px_size * dowsamp_factor / mag_factor
+alert_um = 50.0       # threshold, in μm, above which to flag detections
 
 # Output CSV directory
-#out_dir = Path("runs/size_measurements")
 out_dir = Path("results_csv")
 out_dir.mkdir(parents=True, exist_ok=True)
-csv_path = out_dir / "measurements.csv"
+
+csv_all_tmp = out_dir / "measurements.csv"
+csv_all_final = out_dir / "measurements_complete.csv"
+csv_above = out_dir / "measurements_above_threshold.csv"
 
 # -------------------------
 # Load model
@@ -74,24 +68,32 @@
 )
 
 # -------------------------
-# Write CSV
+# CSV header
 # -------------------------
-with open(csv_path, "w", newline="") as f:
-    writer = csv.writer(f)
-    writer.writerow([
-        "image",
-        "det_idx",
-        "class_id",
-        "class_name",
-        "confidence",
-        "x_center_px",
-        "y_center_px",
-        "width_px",
-        "height_px",
-        "longest_px",
-        "longest_um",
-        "alert"
-    ])
+header = [
+    "image",
+    "det_idx",
+    "class_id",
+    "class_name",
+    "confidence",
+    "x_center_px",
+    "y_center_px",
+    "width_px",
+    "height_px",
+    "longest_px",
+    "longest_um",
+    "alert"
+]
+
+# -------------------------
+# Write BOTH CSVs
+# -------------------------
+with open(csv_all_tmp, "w", newline="") as f_all, open(csv_above, "w", newline="") as f_above:
+    w_all = csv.writer(f_all)
+    w_above = csv.writer(f_above)
+
+    w_all.writerow(header)
+    w_above.writerow(header)
 
     for r in results:
         img_name = os.path.basename(r.path)
@@ -111,14 +113,16 @@
             cls_name = model.names.get(cls_id, str(cls_id))
             conf = float(confs[i]) if confs.size > i else float("nan")
 
-            alert_flag = "STOP" if longest_um > alert_um else ""
-            if alert_flag:
+            is_above = longest_um > alert_um
+            alert_flag = "STOP" if is_above else ""
+
+            if is_above:
                 print(
                     f"[STOP] {img_name} — det {i+1}: "
                     f"{longest_um:.2f} μm > {alert_um} μm → Stop the beam"
                 )
 
-            writer.writerow([
+            row = [
                 img_name,
                 i + 1,
                 cls_id,
@@ -131,12 +135,21 @@
                 f"{longest_px:.2f}",
                 f"{longest_um:.2f}",
                 alert_flag
-            ])
+            ]
+
+            # Write to "all detections"
+            w_all.writerow(row)
+
+            # Write to "above threshold only"
+            if is_above:
+                w_above.writerow(row)
 
-print(f"\nCSV saved to: {csv_path}")
+print(f"\nCSV (all) saved to: {csv_all_tmp}")
+print(f"CSV (above threshold only) saved to: {csv_above}")
 
-# Rename CSV after completion
-final_csv_path = out_dir / "measurements_complete.csv"
-csv_path.rename(final_csv_path)
+# Rename "all" CSV after completion
+if csv_all_final.exists():
+    csv_all_final.unlink()
+csv_all_tmp.rename(csv_all_final)
 
-print(f"CSV renamed to: {final_csv_path}")
+print(f"CSV (all) renamed to: {csv_all_final}")
diff --git a/scripts/coyote_protector_xtc_gui_ready_test/merge_crystals_data.py b/scripts/coyote_protector_xtc_gui_ready_test/merge_crystals_data.py
index 0bf6cea..342450c 100644
--- a/scripts/coyote_protector_xtc_gui_ready_test/merge_crystals_data.py
+++ b/scripts/coyote_protector_xtc_gui_ready_test/merge_crystals_data.py
@@ -31,7 +31,7 @@
 results_csv_dir = Path(f"run_{run_number}/results_csv")
 results_csv_dir = Path("results_csv")
 event_data_csv = results_csv_dir / "event_data.csv"
-measurements_csv = results_csv_dir / "measurements_complete.csv"
+measurements_csv = results_csv_dir / "measurements_above_threshold.csv"
 
 # Check if files exist
 if not event_data_csv.exists():
diff --git a/scripts/coyote_protector_xtc_gui_ready_test/routine_detection_v3.sh b/scripts/coyote_protector_xtc_gui_ready_test/routine_detection_v3.sh
new file mode 100644
index 0000000..9a0b29c
--- /dev/null
+++ b/scripts/coyote_protector_xtc_gui_ready_test/routine_detection_v3.sh
@@ -0,0 +1,133 @@
+#!/bin/bash
+#
+# routine_detection_v3.sh
+# Orchestrates the XTC export and inference workflow
+# Runs on CDS and launches export_infer_xtc.sh on SDF via SSH
+#
+
+# -------  DEFAULT INPUTS ---------
+USER="pmonteil"
+RUN_NUMBER=61
+EXP_NUMBER="mfx101346325"
+SAVE_NORMALIZED=1
+MAX_EVENTS=10000
+USE_NORMALIZED=1
+# --------------------------------
+
+DEST_HOST="psana.sdf.slac.stanford.edu"
+SDF_BASE="/sdf/home/p/pmonteil/coyote_protector_xtc_gui_ready_test"
+RESULTS_BACK_BASE="/cds/home/p/pmonteil"
+
+# -------  PARSE key=value arguments ---------
+for arg in "$@"; do
+    case $arg in
+        --user=*)
+            USER="${arg#*=}"
+            ;;
+        RUN_NUMBER=*)
+            RUN_NUMBER="${arg#*=}"
+            ;;
+        EXP_NUMBER=*)
+            EXP_NUMBER="${arg#*=}"
+            ;;
+        SAVE_NORMALIZED=*)
+            SAVE_NORMALIZED="${arg#*=}"
+            ;;
+        MAX_EVENTS=*)
+            MAX_EVENTS="${arg#*=}"
+            ;;
+        USE_NORMALIZED=*)
+            USE_NORMALIZED="${arg#*=}"
+            ;;
+        *)
+            echo "[WARN] Unknown argument: $arg"
+            ;;
+    esac
+done
+
+echo "[INFO] =============================================="
+echo "[INFO] COYOTE PROTECTOR XTC DETECTION ROUTINE v3"
+echo "[INFO] =============================================="
+echo "[INFO] User: ${USER}"
+echo "[INFO] SDF Host: ${DEST_HOST}"
+echo "[INFO] SDF Base: ${SDF_BASE}"
+echo "[INFO] Run Number: ${RUN_NUMBER}"
+echo "[INFO] Experiment: ${EXP_NUMBER}"
+echo "[INFO] Save Normalized: ${SAVE_NORMALIZED}"
+echo "[INFO] Max Events: ${MAX_EVENTS}"
+echo "[INFO] Use Normalized for Inference: ${USE_NORMALIZED}"
+echo "[INFO] Results back to: ${RESULTS_BACK_BASE}"
+echo
+
+# ====================================
+# STEP 1: Launch export_infer_xtc.sh on SDF via SSH
+# ====================================
+echo "[STEP 1/3] Launching export_infer_xtc.sh on SDF..."
+
+JOB_ID="$(ssh "${USER}@${DEST_HOST}" "bash -lc '
+  set -euo pipefail
+  cd \"${SDF_BASE}\"
+  jid=\$(sbatch --parsable run_export_infer_xtc.sh RUN_NUMBER=${RUN_NUMBER} EXP_NUMBER=${EXP_NUMBER} SAVE_NORMALIZED=${SAVE_NORMALIZED} MAX_EVENTS=${MAX_EVENTS} USE_NORMALIZED=${USE_NORMALIZED})
+  echo \$jid
+'")"
+
+echo "[INFO] Submitted job on SDF: ${JOB_ID}"
+echo
+
+# ====================================
+# STEP 2: Wait for results on SDF
+# ====================================
+echo "[STEP 2/3] Waiting for merged results on SDF..."
+
+REMOTE_CSV="${SDF_BASE}/run_${RUN_NUMBER}/results_csv/merged_crystals.csv"
+
+max_attempts=360  # 3 hours with 30-second intervals
+attempt=0
+
+while [ $attempt -lt $max_attempts ]; do
+    if ssh "${USER}@${DEST_HOST}" "bash -lc 'test -f \"${REMOTE_CSV}\"'"; then
+        echo "[INFO] Merged CSV detected on SDF."
+        break
+    fi
+    attempt=$((attempt + 1))
+    if [ $((attempt % 4)) -eq 0 ]; then
+        echo "[INFO] Waiting... (attempt $attempt/$max_attempts)"
+    fi
+    sleep 30
+done
+
+if [ $attempt -eq $max_attempts ]; then
+    echo "[ERROR] Timeout waiting for results after 3 hours"
+    exit 1
+fi
+
+echo
+
+# ====================================
+# STEP 3: Copy all results back to CDS
+# ====================================
+echo "[STEP 3/3] Copying results back to CDS..."
+
+RESULTS_DIR="run_${RUN_NUMBER}_results"
+LOCAL_DEST_DIR="${RESULTS_BACK_BASE}/${RESULTS_DIR}"
+mkdir -p "${LOCAL_DEST_DIR}"
+
+echo "[INFO] Copying from: ${DEST_HOST}:${SDF_BASE}/run_${RUN_NUMBER}/results_csv/"
+echo "[INFO] Copying to: ${LOCAL_DEST_DIR}/"
+
+rsync -avr \
+  "${USER}@${DEST_HOST}:${SDF_BASE}/run_${RUN_NUMBER}/results_csv/" \
+  "${LOCAL_DEST_DIR}/"
+
+echo
+echo "[DONE] =============================================="
+echo "[INFO] Complete workflow finished successfully."
+echo "[INFO] Results available at:"
+echo "[INFO]   ${LOCAL_DEST_DIR}/"
+echo "[INFO] =============================================="
+echo "[INFO] Key files:"
+echo "[INFO]   - merged_crystals.csv          (all data merged)"
+echo "[INFO]   - measurements_complete.csv    (all detections)"
+echo "[INFO]   - measurements_above_threshold_complete.csv (above threshold only)"
+echo "[INFO]   - event_data.csv               (trajectory data)"
+echo "[DONE]"
diff --git a/scripts/coyote_protector_xtc_gui_ready_test/run_export_infer_xtc.sh b/scripts/coyote_protector_xtc_gui_ready_test/run_export_infer_xtc.sh
new file mode 100644
index 0000000..b0db199
--- /dev/null
+++ b/scripts/coyote_protector_xtc_gui_ready_test/run_export_infer_xtc.sh
@@ -0,0 +1,114 @@
+#!/bin/bash
+#SBATCH --partition=turing
+#SBATCH --account=lcls:prjlumine22
+#SBATCH --job-name=export_infer_xtc
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --gpus=1
+#SBATCH --time=04:00:00
+#SBATCH --output=logs_export/export_infer_turing_%j.out
+#SBATCH --error=logs_export/export_infer_turing_%j.err
+
+set -euo pipefail
+
+export OMP_PROC_BIND=close
+export OMP_PLACES=cores
+export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK}"
+export MKL_NUM_THREADS="${SLURM_CPUS_PER_TASK}"
+export CUDA_DEVICE_ORDER=PCI_BUS_ID
+
+echo "[SLURM] Host: $(hostname)"
+echo "[SLURM] CUDA_VISIBLE_DEVICES: ${CUDA_VISIBLE_DEVICES:-"(not set)"}"
+echo "[SLURM] Starting job..."
+
+PSCONDA_SH="/sdf/group/lcls/ds/ana/sw/conda2/manage/bin/psconda.sh"
+YOLO_PYTHON="/sdf/data/lcls/ds/prj/prjlumine22/results/coyote_protector/miniconda3_coyote/envs/env_coyote/bin/python"
+
+# -------  DEFAULT INPUTS ---------
+RUN_NUMBER=61
+EXP_NUMBER="mfx101346325"
+SAVE_NORMALIZED=1
+MAX_EVENTS=10000
+USE_NORMALIZED=1
+# --------------------------------
+
+# -------  PARSE key=value arguments ---------
+for arg in "$@"; do
+    case $arg in
+        RUN_NUMBER=*)
+            RUN_NUMBER="${arg#*=}"
+            ;;
+        EXP_NUMBER=*)
+            EXP_NUMBER="${arg#*=}"
+            ;;
+        SAVE_NORMALIZED=*)
+            SAVE_NORMALIZED="${arg#*=}"
+            ;;
+        MAX_EVENTS=*)
+            MAX_EVENTS="${arg#*=}"
+            ;;
+        USE_NORMALIZED=*)
+            USE_NORMALIZED="${arg#*=}"
+            ;;
+        *)
+            echo "[WARN] Unknown argument: $arg"
+            ;;
+    esac
+done
+
+echo "[ARGS] run=${RUN_NUMBER} exp=${EXP_NUMBER} save_norm=${SAVE_NORMALIZED} max_events=${MAX_EVENTS} use_normalized=${USE_NORMALIZED}"
+echo
+
+# ====================================
+# NEW STEP 0: Create run folder and cd into it
+# ====================================
+RUN_DIR="run_${RUN_NUMBER}"
+mkdir -p "${RUN_DIR}"
+cd "${RUN_DIR}"
+
+echo "[STEP 0/3] Created and entered: $(pwd)"
+echo
+
+# ====================================
+# STEP 1: Export XTC Data
+# ====================================
+echo "[STEP 1/3] Running export_xtc_normalized_args.py"
+set +u
+source "${PSCONDA_SH}"
+set -u
+
+# run from parent directory (scripts live one level up)
+python ../export_xtc_normalized_args.py "${RUN_NUMBER}" "${EXP_NUMBER}" "${SAVE_NORMALIZED}" "${MAX_EVENTS}"
+
+echo "[STEP 1/3] Export completed."
+echo
+
+# ====================================
+# STEP 2: Run YOLO Inference
+# ====================================
+echo "[STEP 2/3] Running inference_coyote_xtc.py"
+
+# Determine which image directory to use (now relative to run_${RUN_NUMBER}/)
+if [ "${USE_NORMALIZED}" = "1" ]; then
+    IMAGE_DIR="run_${RUN_NUMBER}_png_norm"
+else
+    IMAGE_DIR="run_${RUN_NUMBER}_png"
+fi
+
+"${YOLO_PYTHON}" ../inference_coyote_xtc.py "${IMAGE_DIR}"
+
+echo "[STEP 2/3] Inference completed."
+echo
+
+# ====================================
+# STEP 3: Merge Results
+# ====================================
+echo "[STEP 3/3] Running merge_crystals_data.py"
+"${YOLO_PYTHON}" ../merge_crystals_data.py "${RUN_NUMBER}"
+
+echo "[STEP 3/3] Merging completed."
+echo
+
+echo "[SLURM] Complete workflow finished successfully."
+echo "Results saved to: ${RUN_DIR}/results_csv/"
diff --git a/scripts/coyote_protector_xtc_gui_ready_test/run_export_xtc.sh b/scripts/coyote_protector_xtc_gui_ready_test/run_export_xtc.sh
new file mode 100644
index 0000000..ed26091
--- /dev/null
+++ b/scripts/coyote_protector_xtc_gui_ready_test/run_export_xtc.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+#SBATCH --partition=turing
+#SBATCH --account=lcls:prjlumine22
+#SBATCH --job-name=export_xtc
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --time=02:00:00
+#SBATCH --output=logs_export/export_turing_%j.out
+#SBATCH --error=logs_export/export_turing_%j.err
+
+set -euo pipefail
+
+export OMP_PROC_BIND=close
+export OMP_PLACES=cores
+export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK}"
+export MKL_NUM_THREADS="${SLURM_CPUS_PER_TASK}"
+
+echo "[SLURM] Host: $(hostname)"
+echo "[SLURM] Starting job..."
+
+PSCONDA_SH="/sdf/group/lcls/ds/ana/sw/conda2/manage/bin/psconda.sh"
+
+# -------  DEFAULT INPUTS ---------
+RUN_NUMBER=61
+EXP_NUMBER="mfx101346325"
+SAVE_NORMALIZED=1
+MAX_EVENTS=10000
+# --------------------------------
+
+# -------  PARSE key=value arguments ---------
+for arg in "$@"; do
+    case $arg in
+        RUN_NUMBER=*)
+            RUN_NUMBER="${arg#*=}"
+            ;;
+        EXP_NUMBER=*)
+            EXP_NUMBER="${arg#*=}"
+            ;;
+        SAVE_NORMALIZED=*)
+            SAVE_NORMALIZED="${arg#*=}"
+            ;;
+        MAX_EVENTS=*)
+            MAX_EVENTS="${arg#*=}"
+            ;;
+        *)
+            echo "[WARN] Unknown argument: $arg"
+            ;;
+    esac
+done
+
+echo "[ARGS] run=${RUN_NUMBER} exp=${EXP_NUMBER} save_norm=${SAVE_NORMALIZED} max_events=${MAX_EVENTS}"
+echo
+
+echo "[STEP 1/1] Running export_xtc_normalized_args.py"
+set +u
+source "${PSCONDA_SH}"
+set -u
+
+python ./export_xtc_normalized_args.py "${RUN_NUMBER}" "${EXP_NUMBER}" "${SAVE_NORMALIZED}" "${MAX_EVENTS}"
+
+echo
+echo "[SLURM] Export completed successfully."
diff --git a/scripts/coyote_protector_xtc_gui_ready_test/run_inference_xtc.sh b/scripts/coyote_protector_xtc_gui_ready_test/run_inference_xtc.sh
new file mode 100644
index 0000000..16e5c8e
--- /dev/null
+++ b/scripts/coyote_protector_xtc_gui_ready_test/run_inference_xtc.sh
@@ -0,0 +1,65 @@
+#!/bin/bash
+#SBATCH --partition=turing
+#SBATCH --account=lcls:prjlumine22
+#SBATCH --job-name=inference_xtc
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --gpus=1
+#SBATCH --time=02:00:00
+#SBATCH --output=logs_export/inference_turing_%j.out
+#SBATCH --error=logs_export/inference_turing_%j.err
+
+set -euo pipefail
+
+export OMP_PROC_BIND=close
+export OMP_PLACES=cores
+export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK}"
+export MKL_NUM_THREADS="${SLURM_CPUS_PER_TASK}"
+export CUDA_DEVICE_ORDER=PCI_BUS_ID
+
+echo "[SLURM] Host: $(hostname)"
+echo "[SLURM] CUDA_VISIBLE_DEVICES: ${CUDA_VISIBLE_DEVICES:-"(not set)"}"
+echo "[SLURM] Starting job..."
+
+YOLO_PYTHON="/sdf/data/lcls/ds/prj/prjlumine22/results/coyote_protector/miniconda3_coyote/envs/env_coyote/bin/python"
+
+# -------  DEFAULT INPUTS ---------
+RUN_NUMBER=61
+USE_NORMALIZED=1
+# --------------------------------
+
+# -------  PARSE key=value arguments ---------
+for arg in "$@"; do
+    case $arg in
+        RUN_NUMBER=*)
+            RUN_NUMBER="${arg#*=}"
+            ;;
+        USE_NORMALIZED=*)
+            USE_NORMALIZED="${arg#*=}"
+            ;;
+        *)
+            echo "[WARN] Unknown argument: $arg"
+            ;;
+    esac
+done
+
+echo "[ARGS] run=${RUN_NUMBER} use_normalized=${USE_NORMALIZED}"
+echo
+
+# Determine which image directory to use
+if [ "${USE_NORMALIZED}" = "1" ]; then
+    IMAGE_DIR="run_${RUN_NUMBER}/run_${RUN_NUMBER}_png_norm"
+else
+    IMAGE_DIR="run_${RUN_NUMBER}/run_${RUN_NUMBER}_png"
+fi
+
+echo "[STEP 1/2] Running inference_coyote_xtc.py"
+"${YOLO_PYTHON}" ./inference_coyote_xtc.py "${IMAGE_DIR}"
+
+echo
+echo "[STEP 2/2] Running merge_crystals_data.py"
+"${YOLO_PYTHON}" ./merge_crystals_data.py "${RUN_NUMBER}"
+
+echo
+echo "[SLURM] Inference and merging completed successfully."