Add pipeline.sh and fix bugs found in audit

Author: fcladera

pipeline.sh

@@ -0,0 +1,101 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+usage() {
+    echo "Usage: $0 --mission <file.plan> --object <target> [--output-dir <dir>]"
+    echo "       $0 --image <image> --object <target> --scale x1 y1 x2 y2 [--output-dir <dir>]"
+    exit 1
+}
+
+SAM3_WEIGHTS="${SAM3_WEIGHTS:-$HOME/models/sam3}"
+GUROBI_LICENSE="${GUROBI_LICENSE:-$HOME/gurobi.lic}"
+OUTPUT_DIR=""
+MISSION=""
+IMAGE=""
+OBJECT=""
+SCALE_ARGS=""
+
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --mission) MISSION="$2"; shift 2 ;;
+        --image) IMAGE="$2"; shift 2 ;;
+        --object) OBJECT="$2"; shift 2 ;;
+        --output-dir) OUTPUT_DIR="$2"; shift 2 ;;
+        --scale)
+            if [[ $# -lt 5 ]]; then
+                echo "Error: --scale requires 4 numbers (x1 y1 x2 y2)."
+                exit 1
+            fi
+            SCALE_ARGS="--scale $2 $3 $4 $5"; shift 5 ;;
+        *) echo "Unknown option: $1"; usage ;;
+    esac
+done
+
+if [ -z "$OBJECT" ]; then
+    echo "Error: --object is required."
+    usage
+fi
+
+if [ -z "$MISSION" ] && [ -z "$IMAGE" ]; then
+    echo "Error: --mission or --image is required."
+    usage
+fi
+
+if [ ! -d "$SAM3_WEIGHTS" ]; then
+    echo "Error: SAM 3 weights not found at $SAM3_WEIGHTS"
+    echo "Set SAM3_WEIGHTS env var to override."
+    exit 1
+fi
+
+if [ -z "${OPENAI_TOKEN:-}" ]; then
+    echo "Error: OPENAI_TOKEN env var is not set."
+    exit 1
+fi
+
+# Mount the input file
+INPUT_FILE="${MISSION:-$IMAGE}"
+INPUT_BASENAME="$(basename "$INPUT_FILE")"
+INPUT_MOUNT="-v $(realpath "$INPUT_FILE"):/data/input/$INPUT_BASENAME:ro"
+if [ -n "$MISSION" ]; then
+    LAMP_ARGS="--mission /data/input/$INPUT_BASENAME"
+else
+    LAMP_ARGS="--image /data/input/$INPUT_BASENAME"
+fi
+LAMP_ARGS="$LAMP_ARGS --object $OBJECT --generate-waypoints $SCALE_ARGS"
+
+# Output directory
+OUTPUT_MOUNT=""
+COPY_CMD=""
+if [ -n "$OUTPUT_DIR" ]; then
+    mkdir -p "$OUTPUT_DIR"
+    OUTPUT_MOUNT="-v $(realpath "$OUTPUT_DIR"):/data/output"
+    COPY_CMD="cp -r /tmp/LAEP/* /data/output/ 2>/dev/null || true;"
+fi
+
+# Gurobi license (optional but needed for optimizer)
+GUROBI_MOUNT=""
+if [ -f "$GUROBI_LICENSE" ]; then
+    GUROBI_MOUNT="-v $(realpath "$GUROBI_LICENSE"):/opt/gurobi/gurobi.lic:ro"
+else
+    echo "Warning: Gurobi license not found at $GUROBI_LICENSE — optimizer may fail."
+fi
+
+docker run --gpus all --rm \
+    -v "$SAM3_WEIGHTS":/weights \
+    $GUROBI_MOUNT \
+    $INPUT_MOUNT \
+    $OUTPUT_MOUNT \
+    -e OPENAI_TOKEN="$OPENAI_TOKEN" \
+    ${OPENAI_API_BASE:+-e OPENAI_API_BASE="$OPENAI_API_BASE"} \
+    ${OPENAI_MODEL:+-e OPENAI_MODEL="$OPENAI_MODEL"} \
+    lamp bash -c "
+        mkdir -p /tmp/LAEP && \
+        cd /app/scripts && \
+        python3 heat_map_gen.py $LAMP_ARGS && \
+        python3 waypoint_scorer.py && \
+        cd /app/optimization_core/build && \
+        ./main && \
+        echo '[DONE] Pipeline complete.' && \
+        $COPY_CMD
+        echo 'Results in /tmp/LAEP/'
+    "

run.sh

@@ -25,4 +25,6 @@ docker run --gpus all -it --rm \
     -v "$SAM3_WEIGHTS":/weights \
     -v "$GUROBI_LICENSE":/opt/gurobi/gurobi.lic:ro \
     -e OPENAI_TOKEN="$OPENAI_TOKEN" \
+    ${OPENAI_API_BASE:+-e OPENAI_API_BASE="$OPENAI_API_BASE"} \
+    ${OPENAI_MODEL:+-e OPENAI_MODEL="$OPENAI_MODEL"} \
     lamp "$@"

scripts/heat_map_gen.py

@@ -484,7 +484,8 @@ def get_ao_from_mission_file(file_path):
                     full_heatmap_accumulator[y1:y2, x1:x2] -= binary_mask
 
                 successful_generations += 1
-                
+                count_accumulator[y1:y2, x1:x2] += 1.0
+
                 # --- MEMORY CLEANUP ---
                 del result, current_mask, binary_mask
             else:
@@ -494,9 +495,6 @@ def get_ao_from_mission_file(file_path):
             # --- MEMORY CLEANUP ---
             del result
 
-        # Increment the count for every pixel in this window
-        count_accumulator[y1:y2, x1:x2] += 1.0
-        
         # Force Python to collect garbage, then empty the CUDA cache
         gc.collect()
         torch.cuda.empty_cache()

scripts/waypoint_scorer.py

@@ -124,10 +124,10 @@ def load_plan_file(filepath):
 
     except FileNotFoundError:
         print(f"[ERROR] Plan file not found at {filepath}")
-        return None, None, None
+        return None, None, None, None
     except json.JSONDecodeError:
         print(f"[ERROR] Failed to parse {filepath}. Ensure it is valid JSON.")
-        return None, None, None    
+        return None, None, None, None
 
 
 def get_waypoint_scores(waypoint_list, inclusion_polygons, exclusion_polygons, heatmap_path, origin_lat, origin_lon, width_m, height_m, base_wp=None):