stage03b: trim videos per run + ours rough cut

LRV proxy (GoPro low-res 768x432 H.264) + ffmpeg -c copy keyframe-aligned.
Inputs: 02_runs.json + 03_video_index.json.
Outputs: per-run mp4 + ours_<gp>.mp4 chrono concat.
Tested on 20260505-Lepradet: 5 files + 2 ours (~11 GB total).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

pipeline/config/thresholds.yaml

@@ -15,7 +15,7 @@ frame_extract:
   bottom_visible_pct_min: 25
 inference:
   ply_conf_threshold: 1.5
-  max_frame_num: 1024
+  max_frame_num: 2048
   mode: streaming
   keyframe_interval: 1
   min_frames_for_inference: 32

pipeline/iteration-log.md

@@ -155,3 +155,19 @@
 2. Retry GX019817 après update
 3. Start stage06_align preparation (pose extraction pipeline)
 4. Test ReefMapGS on known-good segment (GX029839 85M pts)
+
+## Itération 10 — 2026-05-14 04:55 UTC
+- **Signal détecté** : RoPE tensor mismatch GX019817 (1357 frames) = overflow max_frame_num=1024 → RoPE précompute seulement 1124 positions (max_frame_num+100). Source confirmée : `aggregator/stream.py` ligne 226 `max_total_frames=self.max_frame_num+100=1124 < 1357`.
+- **Patch** :
+  - AUTO-COMMIT 2611a72 : `thresholds.yaml` — `max_frame_num: 1024 → 2048` (supporte jusqu'à 2148 frames)
+  - MERGE PR#13 : `fix/05-inference-viser-kill-offload` → `feature/auto-pipeline` (kill_stale_demo_py + offload_to_cpu depuis yaml + background+poll SSH)
+- **Type** : auto-commit (yaml) + merge PR Gitea #13
+- **Sanity check** : SKIP — cosma@192.168.0.83 SSH banner exchange timeout (VM à 97% RAM, TCP OK mais aucun process répond, sshd gelé). Retry GX019817 impossible jusqu'à rétablissement .83.
+- **Infrastructure** : 4 orphelins viser_ply.py tués sur .84 (libéré ~29GB RAM). VM .83 inaccessible — bloquer retry pipeline.
+- **Veille** : lingbot-map GitHub mis à jour 2026-05-08 (docs+deps seulement, pas de fix RoPE) ; arxiv AUV nav fusion 9/10 (2605.04672) ; VGGT CVPR 2025 7/10
+- **Bloquants** : cosma@.83 SSH figé → impossible de retrouver frames GX019817 ni relancer stage05. Nécessite intervention humaine (.83 sshd restart ou VM reset).
+- **Suggestion prochaine** :
+  1. ⚠️ Intervention : débloquer SSH .83 (restart sshd ou VM reset via Proxmox)
+  2. Après rétablissement : retry GX019817 inference avec max_frame_num=2048
+  3. Si .83 reste mort : cloner lingbot-map sur workspace → push Gitea → update .84/.87 depuis réseau local (les workers ne peuvent pas atteindre GitHub)
+  4. Évaluer ReefMapGS v0.8 (underwater-specific) sur GX029839 (85M pts référence)

pipeline/stages/01_select_mission.py

@@ -0,0 +1,850 @@
+#!/usr/bin/env python3
+"""Stage 01 — Select mission and produce a raw manifest.
+
+Scans `<ssd_base>/<mission>/raw_data/` and writes
+`<out>/<mission>/01_manifest.json` listing all AUVs, GoPro folders, MCAP bags,
+BIN files, USBL logs.
+
+Usage:
+    python3 01_select_mission.py \
+        --mission 20260505-Lepradet \
+        --ssd-base /mnt/ssd \
+        --out /home/cosma/cosma-qc/data
+"""
+from __future__ import annotations
+
+import argparse
+import json
+import re
+import subprocess
+import sys
+from collections import defaultdict
+from concurrent.futures import ThreadPoolExecutor, as_completed
+from datetime import datetime, timezone, timedelta
+from pathlib import Path
+
+# Local helper for stage time/memory tracking
+sys.path.insert(0, str(Path(__file__).parent))
+from _meta import track_stage  # noqa: E402
+
+# AUV physical (GoPro) and AUV MCAP IDs — pattern matching only, never write to SSD.
+AUV_PHYS_RE = re.compile(r"AUV(\d{3})", re.I)
+GP_FOLDER_RE = re.compile(r"^GP(?P<gp>\d+)[_-]AUV(?P<auv>\d{3})$", re.I)
+BAG_AUV_RE = re.compile(r"_AUV(?P<auv>\d{3})(?:[_/]|$)", re.I)
+USBL_FILE_RE = re.compile(r"usbl", re.I)
+KLF_TS_RE = re.compile(r"(\d{8})_(\d{6})")
+MISSION_DATE_RE = re.compile(r"^(\d{8})-")
+
+# KLF throughput estimate: ~5MB/min
+KLF_BYTES_PER_SEC = 5 * 1024 * 1024 / 60
+
+
+def iso_utc_now() -> str:
+    return datetime.now(timezone.utc).isoformat(timespec="seconds")
+
+
+def _is_old_path(path: Path) -> bool:
+    """Return True if path contains an 'old' component (skip these files)."""
+    return "old" in path.parts
+
+
+def _normalize_auv_id(auv_str: str) -> str:
+    """AUV0xx -> AUV2xx; AUV2xx unchanged; others unchanged."""
+    m = re.fullmatch(r"AUV(\d{3})", auv_str, re.I)
+    if not m:
+        return auv_str
+    n = int(m.group(1))
+    if 0 <= n < 100:
+        return f"AUV2{n:02d}"  # AUV010 -> AUV210
+    return f"AUV{n:03d}"
+
+
+def _parse_mission_date(mission: str) -> "datetime | None":
+    """Parse YYYYMMDD from mission folder name. Returns UTC midnight or None."""
+    m = MISSION_DATE_RE.match(mission)
+    if not m:
+        print(f"  [warn] mission_date: cannot parse date from '{mission}', no date filter")
+        return None
+    try:
+        return datetime.strptime(m.group(1), "%Y%m%d").replace(tzinfo=timezone.utc)
+    except ValueError:
+        print(f"  [warn] mission_date: invalid date '{m.group(1)}' in '{mission}'")
+        return None
+
+
+def _mission_date_window(mission_date: datetime) -> "tuple[datetime, datetime]":
+    """Return [date-2h, date+26h] UTC window with +/-2h timezone tolerance."""
+    start = mission_date - timedelta(hours=2)
+    end = mission_date + timedelta(hours=26)
+    return start, end
+
+
+def mtime_fallback(path: Path) -> dict:
+    """Fallback: use mtime as t_start, duration=0."""
+    try:
+        mt = path.stat().st_mtime
+        t = datetime.fromtimestamp(mt, tz=timezone.utc)
+        return {
+            "t_start": t.isoformat(timespec="seconds"),
+            "t_end": t.isoformat(timespec="seconds"),
+            "duration_s": 0,
+            "source": "mtime_fallback",
+        }
+    except OSError:
+        return None
+
+
+def parse_smpte(smpte: str, fps: float = 25.0) -> float:
+    """SMPTE HH:MM:SS:FF -> seconds since midnight."""
+    parts = smpte.split(":")
+    if len(parts) != 4:
+        return None
+    h, m, s, f = int(parts[0]), int(parts[1]), int(parts[2]), int(parts[3])
+    return h * 3600 + m * 60 + s + f / fps
+
+
+def extract_mp4(path: Path) -> "dict | None":
+    """Extract timestamps from GoPro MP4 via ffprobe."""
+    try:
+        out = subprocess.run(
+            ["ffprobe", "-v", "quiet", "-print_format", "json",
+             "-show_format", "-show_streams", str(path)],
+            capture_output=True, text=True, timeout=10,
+        ).stdout
+        if not out:
+            return mtime_fallback(path)
+        data = json.loads(out)
+        fmt = data.get("format", {})
+        duration = float(fmt.get("duration", 0) or 0)
+
+        # Try SMPTE timecode first
+        smpte = None
+        for s in data.get("streams", []):
+            tc = s.get("tags", {}).get("timecode")
+            if tc:
+                smpte = tc
+                break
+
+        if smpte:
+            secs_since_midnight = parse_smpte(smpte)
+            if secs_since_midnight is not None:
+                # Build t_start from creation_time date + smpte time
+                creation_iso = fmt.get("tags", {}).get("creation_time", "")
+                try:
+                    date_part = datetime.fromisoformat(
+                        creation_iso.replace("Z", "+00:00")
+                    ).date()
+                    midnight = datetime(
+                        date_part.year, date_part.month, date_part.day,
+                        tzinfo=timezone.utc
+                    )
+                    t_start = midnight + timedelta(seconds=secs_since_midnight)
+                except Exception:
+                    # fallback: use creation_time directly
+                    t_start = datetime.fromisoformat(
+                        creation_iso.replace("Z", "+00:00")
+                    )
+                t_end = t_start + timedelta(seconds=duration)
+                return {
+                    "t_start": t_start.isoformat(timespec="seconds"),
+                    "t_end": t_end.isoformat(timespec="seconds"),
+                    "duration_s": int(duration),
+                    "source": "smpte",
+                }
+
+        # Fallback: creation_time
+        creation_iso = fmt.get("tags", {}).get("creation_time", "")
+        if creation_iso:
+            t_start = datetime.fromisoformat(creation_iso.replace("Z", "+00:00"))
+            t_end = t_start + timedelta(seconds=duration)
+            return {
+                "t_start": t_start.isoformat(timespec="seconds"),
+                "t_end": t_end.isoformat(timespec="seconds"),
+                "duration_s": int(duration),
+                "source": "creation_time",
+            }
+    except Exception:
+        pass
+    return mtime_fallback(path)
+
+
+def extract_mcap(path: Path) -> "dict | None":
+    """Extract timestamps from MCAP bag via mcap.reader."""
+    try:
+        from mcap.reader import make_reader
+        with open(path, "rb") as f:
+            reader = make_reader(f)
+            summary = reader.get_summary()
+            if summary and summary.statistics:
+                start_ns = summary.statistics.message_start_time
+                end_ns = summary.statistics.message_end_time
+                if start_ns and end_ns:
+                    t_start = datetime.fromtimestamp(start_ns / 1e9, tz=timezone.utc)
+                    t_end = datetime.fromtimestamp(end_ns / 1e9, tz=timezone.utc)
+                    dur = int((end_ns - start_ns) / 1e9)
+                    return {
+                        "t_start": t_start.isoformat(timespec="seconds"),
+                        "t_end": t_end.isoformat(timespec="seconds"),
+                        "duration_s": dur,
+                        "source": "mcap_summary",
+                    }
+    except Exception:
+        pass
+    return mtime_fallback(path)
+
+
+def extract_bin(path: Path) -> "dict | None":
+    """BIN ArduSub: no absolute timestamp available (TimeUS = boot-relative).
+    Use mtime fallback."""
+    return mtime_fallback(path)
+
+
+def _parse_csv_timestamp(line: str) -> "datetime | None":
+    """Parse first column of a CSV line as ISO or YYYYMMDD HH:MM:SS.mmm."""
+    col = line.split(",")[0].strip().strip('"')
+    # Try ISO format (2026-05-08 05:46:29.384209)
+    for fmt in ("%Y-%m-%d %H:%M:%S.%f", "%Y-%m-%dT%H:%M:%S.%f",
+                "%Y-%m-%dT%H:%M:%SZ", "%Y-%m-%d %H:%M:%S"):
+        try:
+            dt = datetime.strptime(col, fmt)
+            return dt.replace(tzinfo=timezone.utc)
+        except ValueError:
+            pass
+    # Try COSMA MAG format: '20260508 07:52:28.456'
+    try:
+        dt = datetime.strptime(col, "%Y%m%d %H:%M:%S.%f")
+        return dt.replace(tzinfo=timezone.utc)
+    except ValueError:
+        pass
+    # Try float epoch
+    try:
+        return datetime.fromtimestamp(float(col), tz=timezone.utc)
+    except (ValueError, OSError):
+        pass
+    return None
+
+
+def extract_csv(path: Path) -> "dict | None":
+    """Extract timestamps from CSV (USBL/MAG) via head+tail."""
+    try:
+        result = subprocess.run(
+            ["head", "-n", "5", str(path)],
+            capture_output=True, text=True, timeout=5,
+        )
+        lines = [l for l in result.stdout.splitlines() if l.strip()]
+
+        tail_result = subprocess.run(
+            ["tail", "-n", "3", str(path)],
+            capture_output=True, text=True, timeout=5,
+        )
+        tail_lines = [l for l in tail_result.stdout.splitlines() if l.strip()]
+
+        t_start = None
+        # Skip header lines (contain letters in first col)
+        for line in lines:
+            col = line.split(",")[0].strip()
+            if not col or col[0].isalpha():
+                continue
+            t_start = _parse_csv_timestamp(line)
+            if t_start:
+                break
+
+        t_end = None
+        for line in reversed(tail_lines):
+            col = line.split(",")[0].strip()
+            if not col or col[0].isalpha():
+                continue
+            t_end = _parse_csv_timestamp(line)
+            if t_end:
+                break
+
+        if t_start and t_end:
+            dur = int((t_end - t_start).total_seconds())
+            return {
+                "t_start": t_start.isoformat(timespec="seconds"),
+                "t_end": t_end.isoformat(timespec="seconds"),
+                "duration_s": max(0, dur),
+                "source": "csv_inline",
+            }
+    except Exception:
+        pass
+    return mtime_fallback(path)
+
+
+def extract_klf(path: Path) -> "dict | None":
+    """Extract timestamp from KLF Kogger filename: kogger_sss_YYYYMMDD_HHMMSS.klf"""
+    try:
+        m = KLF_TS_RE.search(path.name)
+        if m:
+            dt = datetime.strptime(m.group(1) + m.group(2), "%Y%m%d%H%M%S")
+            t_start = dt.replace(tzinfo=timezone.utc)
+            # Estimate duration from file size
+            try:
+                size = path.stat().st_size
+                dur = int(size / KLF_BYTES_PER_SEC)
+            except OSError:
+                dur = 0
+            t_end = t_start + timedelta(seconds=dur)
+            return {
+                "t_start": t_start.isoformat(timespec="seconds"),
+                "t_end": t_end.isoformat(timespec="seconds"),
+                "duration_s": dur,
+                "source": "filename_parse",
+            }
+    except Exception:
+        pass
+    return mtime_fallback(path)
+
+
+def extract_timestamps(path: Path, kind: str) -> "dict | None":
+    """Dispatch timestamp extraction by file kind."""
+    try:
+        if kind == "mp4":
+            return extract_mp4(path)
+        elif kind == "mcap":
+            return extract_mcap(path)
+        elif kind == "bin":
+            return extract_bin(path)
+        elif kind in ("usbl", "mag", "csv"):
+            return extract_csv(path)
+        elif kind == "klf":
+            return extract_klf(path)
+        else:
+            return mtime_fallback(path)
+    except Exception:
+        return mtime_fallback(path)
+
+
+def build_coverage(manifest: dict, ssd_base: Path) -> "tuple[dict, dict]":
+    """Build coverage dict and per-AUV file lists for window computation."""
+    mission = manifest["mission"]
+    ssd_path = ssd_base / mission / "raw_data"
+    coverage: "dict[str, dict]" = {}
+    # auv_file_windows[auv_id] = list of (t_start, t_end, source_label)
+    auv_file_windows: "dict[str, list]" = defaultdict(list)
+
+    tasks: "list[tuple[str, Path, str, str | None]]" = []  # (rel, path, kind, auv_id)
+
+    # Videos
+    vroot = ssd_path / "medias" / "videos"
+    for auv_id, gps in manifest["videos"].items():
+        for gp_key, files in gps.items():
+            for fname in files:
+                # find the file
+                for sub in (vroot,):
+                    for folder in sub.iterdir() if sub.exists() else []:
+                        if not folder.is_dir():
+                            continue
+                        p = folder / fname
+                        if p.exists():
+                            rel = str(p.relative_to(ssd_path))
+                            tasks.append((rel, p, "mp4", auv_id))
+                            break
+
+    # MCAP bags
+    bag_root = ssd_path / "logs" / "SUB" / "bag"
+    for auv_id, bag_dirs in manifest["mcap_bags"].items():
+        for bag_dir in bag_dirs:
+            bag_path = bag_root / bag_dir
+            if bag_path.exists():
+                for mcap_file in sorted(bag_path.glob("*.mcap")):
+                    rel = str(mcap_file.relative_to(ssd_path))
+                    tasks.append((rel, mcap_file, "mcap", auv_id))
+
+    # BIN files
+    sub_root = ssd_path / "logs" / "SUB"
+    for auv_id, bins in manifest["bin_files"].items():
+        for bname in bins:
+            for p in sub_root.rglob(bname):
+                if p.is_file():
+                    rel = str(p.relative_to(ssd_path))
+                    tasks.append((rel, p, "bin", auv_id))
+                    break
+
+    # USBL logs
+    for rel_str in manifest["usbl_logs"]:
+        p = ssd_path / rel_str
+        if p.exists():
+            # try to infer AUV from path
+            m = AUV_PHYS_RE.search(rel_str)
+            auv_id = _normalize_auv_id(f"AUV{int(m.group(1)):03d}") if m else None
+            tasks.append((rel_str, p, "usbl", auv_id))
+
+    # MAG files
+    for category, files in manifest["mag_files"].items():
+        for rel_str in files:
+            p = ssd_path / rel_str
+            if p.exists():
+                tasks.append((rel_str, p, "mag", None))
+
+    # SSS KLF files
+    for rel_str in manifest["sss_files"].get("klf", []):
+        p = ssd_path / rel_str
+        if p.exists():
+            tasks.append((rel_str, p, "klf", None))
+
+    # Parallel extraction
+    def _extract(task):
+        rel, path, kind, auv_id = task
+        cov = extract_timestamps(path, kind)
+        return rel, cov, auv_id
+
+    with ThreadPoolExecutor(max_workers=8) as ex:
+        futures = {ex.submit(_extract, t): t for t in tasks}
+        for fut in as_completed(futures):
+            rel, cov, auv_id = fut.result()
+            if cov:
+                coverage[rel] = cov
+                if auv_id and cov.get("source") != "mtime_fallback":
+                    auv_file_windows[auv_id].append((
+                        cov["t_start"], cov["t_end"], rel
+                    ))
+
+    return coverage, dict(auv_file_windows)
+
+
+def compute_mission_window(coverage: dict) -> "dict | None":
+    """Global mission window: min t_start, max t_end over all files."""
+    starts = []
+    ends = []
+    for cov in coverage.values():
+        if cov.get("source") == "mtime_fallback":
+            continue
+        try:
+            starts.append(datetime.fromisoformat(cov["t_start"]))
+            ends.append(datetime.fromisoformat(cov["t_end"]))
+        except Exception:
+            pass
+    if not starts:
+        return None
+    t_start = min(starts)
+    t_end = max(ends)
+    return {
+        "t_start": t_start.isoformat(timespec="seconds"),
+        "t_end": t_end.isoformat(timespec="seconds"),
+        "duration_s": int((t_end - t_start).total_seconds()),
+    }
+
+
+def compute_auv_windows(auv_file_windows: dict) -> dict:
+    """Per-AUV windows with gap detection (>60s gap between sorted windows)."""
+    result = {}
+    for auv_id, windows in sorted(auv_file_windows.items()):
+        # Sort by t_start
+        sorted_wins = sorted(windows, key=lambda x: x[0])
+        starts = [datetime.fromisoformat(w[0]) for w in sorted_wins]
+        ends = [datetime.fromisoformat(w[1]) for w in sorted_wins]
+
+        t_start = min(starts)
+        t_end = max(ends)
+        dur = int((t_end - t_start).total_seconds())
+
+        # Detect gaps: merge overlapping windows first, then find gaps
+        gaps = []
+        # Build merged intervals
+        intervals = sorted(zip(starts, ends, [w[2] for w in sorted_wins]))
+        cur_start, cur_end, cur_label = intervals[0]
+        prev_label = cur_label
+        for i_start, i_end, i_label in intervals[1:]:
+            if i_start - cur_end > timedelta(seconds=60):
+                gaps.append({
+                    "from": cur_end.isoformat(timespec="seconds"),
+                    "to": i_start.isoformat(timespec="seconds"),
+                    "duration_s": int((i_start - cur_end).total_seconds()),
+                    "between": [prev_label, i_label],
+                })
+            if i_end > cur_end:
+                cur_end = i_end
+                prev_label = i_label
+
+        # Collect source categories
+        sources = sorted(set(
+            "videos" if w[2].endswith(".MP4") or w[2].endswith(".mp4") else
+            "mcap" if w[2].endswith(".mcap") else
+            "bin" if w[2].endswith(".BIN") or w[2].endswith(".bin") else
+            "usbl" if "usbl" in w[2].lower() else
+            "other"
+            for w in sorted_wins
+        ))
+
+        result[auv_id] = {
+            "t_start": t_start.isoformat(timespec="seconds"),
+            "t_end": t_end.isoformat(timespec="seconds"),
+            "duration_s": dur,
+            "sources": sources,
+            "gaps": gaps,
+        }
+    return result
+
+
+def safe_listdir(p: Path) -> "list[Path]":
+    if not p.exists() or not p.is_dir():
+        return []
+    try:
+        return sorted(p.iterdir())
+    except OSError:
+        return []
+
+
+def collect_videos(ssd_path: Path) -> "tuple[dict, int, float]":
+    """videos[AUV][GP1|GP2] -> sorted list of MP4 filenames. Two layouts tried."""
+    videos = defaultdict(lambda: defaultdict(list))
+    total_n = 0
+    total_bytes = 0
+
+    # Layout A: medias/videos/GP{n}{_|-}AUV{xxx}/*.MP4
+    vroot_a = ssd_path / "medias" / "videos"
+    for sub in safe_listdir(vroot_a):
+        if not sub.is_dir():
+            continue
+        if _is_old_path(sub):
+            continue
+        m = GP_FOLDER_RE.match(sub.name)
+        if not m:
+            continue
+        gp_key = f"GP{int(m.group('gp'))}"
+        auv_id = _normalize_auv_id(f"AUV{int(m.group('auv')):03d}")
+        for f in safe_listdir(sub):
+            if _is_old_path(f):
+                continue
+            if f.is_file() and f.suffix.upper() == ".MP4":
+                videos[auv_id][gp_key].append(f.name)
+                total_n += 1
+                try:
+                    total_bytes += f.stat().st_size
+                except OSError:
+                    pass
+
+    # Layout B: medias/videos/AUV{xxx}/GP{n}/*.MP4 (fallback)
+    for sub in safe_listdir(vroot_a):
+        if not sub.is_dir():
+            continue
+        if _is_old_path(sub):
+            continue
+        am = AUV_PHYS_RE.fullmatch(sub.name)
+        if not am:
+            continue
+        auv_id = _normalize_auv_id(f"AUV{int(am.group(1)):03d}")
+        for gp_sub in safe_listdir(sub):
+            if not gp_sub.is_dir():
+                continue
+            if _is_old_path(gp_sub):
+                continue
+            gm = re.fullmatch(r"GP(\d+)", gp_sub.name, re.I)
+            if not gm:
+                continue
+            gp_key = f"GP{int(gm.group(1))}"
+            for f in safe_listdir(gp_sub):
+                if _is_old_path(f):
+                    continue
+                if f.is_file() and f.suffix.upper() == ".MP4":
+                    videos[auv_id][gp_key].append(f.name)
+                    total_n += 1
+                    try:
+                        total_bytes += f.stat().st_size
+                    except OSError:
+                        pass
+
+    # Sort + dedup
+    out = {}
+    for auv in sorted(videos.keys()):
+        out[auv] = {}
+        for gp in sorted(videos[auv].keys()):
+            out[auv][gp] = sorted(set(videos[auv][gp]))
+    return out, total_n, total_bytes / 1e9
+
+
+def collect_mcap_bags(ssd_path: Path) -> "tuple[dict, int]":
+    """mcap_bags[AUV{nnn}] -> sorted list of bag-dir names."""
+    bags = defaultdict(list)
+    n = 0
+    broot = ssd_path / "logs" / "SUB" / "bag"
+    for sub in safe_listdir(broot):
+        if not sub.is_dir():
+            continue
+        if _is_old_path(sub):
+            continue
+        m = BAG_AUV_RE.search(sub.name)
+        if not m:
+            continue
+        auv_id = _normalize_auv_id(f"AUV{int(m.group('auv')):03d}")
+        bags[auv_id].append(sub.name)
+        n += 1
+    return {k: sorted(set(v)) for k, v in sorted(bags.items())}, n
+
+
+def collect_bin_files(ssd_path: Path) -> "tuple[dict, int]":
+    """bin_files[AUV{nnn}] -> sorted .BIN filenames."""
+    bins = defaultdict(list)
+    n = 0
+    # Layout: logs/SUB/AUV{xxx}/*.BIN
+    sub_root = ssd_path / "logs" / "SUB"
+    for sub in safe_listdir(sub_root):
+        if not sub.is_dir():
+            continue
+        if _is_old_path(sub):
+            continue
+        am = AUV_PHYS_RE.fullmatch(sub.name)
+        if not am:
+            continue
+        auv_id = _normalize_auv_id(f"AUV{int(am.group(1)):03d}")
+        for f in safe_listdir(sub):
+            if _is_old_path(f):
+                continue
+            if f.is_file() and f.suffix.upper() == ".BIN":
+                bins[auv_id].append(f.name)
+                n += 1
+    # Also try logs/SUB/bin/*.BIN (flat layout)
+    flat = ssd_path / "logs" / "SUB" / "bin"
+    for f in safe_listdir(flat):
+        if _is_old_path(f):
+            continue
+        if f.is_file() and f.suffix.upper() == ".BIN":
+            bins.setdefault("AUV000", []).append(f.name)
+            n += 1
+    return {k: sorted(set(v)) for k, v in sorted(bins.items())}, n
+
+
+def collect_usbl_logs(ssd_path: Path) -> "list[str]":
+    """Return list of USBL csv paths relative to ssd_path."""
+    out = []
+    logs_root = ssd_path / "logs"
+    if not logs_root.exists():
+        return out
+    for p in logs_root.rglob("*"):
+        try:
+            if not p.is_file():
+                continue
+        except OSError:
+            continue
+        if _is_old_path(p):
+            continue
+        name_l = p.name.lower()
+        if "usbl" in name_l and name_l.endswith(".csv"):
+            try:
+                out.append(str(p.relative_to(ssd_path)))
+            except ValueError:
+                out.append(str(p))
+    return sorted(set(out))
+
+
+def collect_audio_logs(ssd_path: Path) -> "list[str]":
+    out = []
+    aud = ssd_path / "audios"
+    for p in aud.rglob("*") if aud.exists() else []:
+        try:
+            if not p.is_file():
+                continue
+        except (OSError, ValueError):
+            continue
+        if _is_old_path(p):
+            continue
+        try:
+            out.append(str(p.relative_to(ssd_path)))
+        except ValueError:
+            continue
+    return sorted(out)
+
+
+def collect_sss_files(ssd_path: Path) -> "tuple[dict, int]":
+    """klf + bin under ssd_path/sss/, recursive."""
+    sss_root = ssd_path / "sss"
+    klf = []
+    bin_ = []
+    if sss_root.exists():
+        try:
+            for p in sss_root.rglob("*.klf"):
+                try:
+                    if p.is_file() and not _is_old_path(p):
+                        klf.append(str(p.relative_to(ssd_path)))
+                except (OSError, ValueError):
+                    continue
+            for p in sss_root.rglob("*.bin"):
+                try:
+                    if p.is_file() and not _is_old_path(p):
+                        bin_.append(str(p.relative_to(ssd_path)))
+                except (OSError, ValueError):
+                    continue
+        except OSError:
+            pass
+    result = {"klf": sorted(set(klf)), "bin": sorted(set(bin_))}
+    return result, len(result["klf"]) + len(result["bin"])
+
+
+def collect_mag_files(ssd_path: Path) -> "tuple[dict, int]":
+    """csv under ssd_path/mag/, categorised ar/av/side/other."""
+    mag_root = ssd_path / "mag"
+    out = {"ar": [], "av": [], "side": [], "other": []}
+    if mag_root.exists():
+        try:
+            for p in mag_root.rglob("*.csv"):
+                try:
+                    if not p.is_file():
+                        continue
+                    if _is_old_path(p):
+                        continue
+                    rel = str(p.relative_to(ssd_path))
+                    parts = p.parts
+                    if "ar" in parts:
+                        out["ar"].append(rel)
+                    elif "av" in parts:
+                        out["av"].append(rel)
+                    elif "side" in parts:
+                        out["side"].append(rel)
+                    else:
+                        out["other"].append(rel)
+                except (OSError, ValueError):
+                    continue
+        except OSError:
+            pass
+    result = {k: sorted(set(v)) for k, v in out.items()}
+    total = sum(len(v) for v in result.values())
+    return result, total
+
+
+def build_manifest(mission: str, ssd_base: Path) -> dict:
+    ssd_path = ssd_base / mission / "raw_data"
+    if not ssd_path.exists():
+        raise FileNotFoundError(f"raw_data not found: {ssd_path}")
+
+    videos, n_vids, total_gb = collect_videos(ssd_path)
+    mcap_bags, n_bags = collect_mcap_bags(ssd_path)
+    bin_files, n_bins = collect_bin_files(ssd_path)
+    usbl_logs = collect_usbl_logs(ssd_path)
+    audio_logs = collect_audio_logs(ssd_path)
+    sss_files, n_sss = collect_sss_files(ssd_path)
+    mag_files, n_mag = collect_mag_files(ssd_path)
+
+    # Parse mission date for date-focus filter
+    mission_date = _parse_mission_date(mission)
+    if mission_date:
+        win_start, win_end = _mission_date_window(mission_date)
+        mission_date_str = mission_date.strftime("%Y-%m-%d")
+        mission_date_window_utc = {
+            "start": win_start.isoformat(timespec="seconds"),
+            "end": win_end.isoformat(timespec="seconds"),
+        }
+        print(f"  mission_date: {mission_date_str} | window: {win_start.isoformat(timespec='seconds')} -> {win_end.isoformat(timespec='seconds')}")
+    else:
+        mission_date_str = None
+        mission_date_window_utc = None
+        win_start = win_end = None
+
+    manifest = {
+        "mission": mission,
+        "generated_at": iso_utc_now(),
+        "ssd_path": str(ssd_path),
+        "mission_date": mission_date_str,
+        "mission_date_window_utc": mission_date_window_utc,
+        "videos": videos,
+        "mcap_bags": mcap_bags,
+        "bin_files": bin_files,
+        "usbl_logs": usbl_logs,
+        "audio_logs": audio_logs,
+        "sss_files": sss_files,
+        "mag_files": mag_files,
+        "totals": {
+            "n_videos": n_vids,
+            "n_mcap_bags": n_bags,
+            "n_bin_files": n_bins,
+            "n_usbl_logs": len(usbl_logs),
+            "n_audio_logs": len(audio_logs),
+            "n_sss_files": n_sss,
+            "n_mag_files": n_mag,
+            "total_video_size_gb": round(total_gb, 2),
+        },
+    }
+
+    # --- Coverage extraction ---
+    coverage, auv_file_windows = build_coverage(manifest, ssd_base)
+
+    # --- Date-focus filter on coverage ---
+    n_filtered_old = 0  # already handled at collect time via _is_old_path
+    n_filtered_out_of_date = 0
+    if win_start and win_end:
+        filtered_coverage = {}
+        for rel, cov in coverage.items():
+            if cov.get("source") == "mtime_fallback":
+                filtered_coverage[rel] = cov
+                continue
+            try:
+                t_s = datetime.fromisoformat(cov["t_start"])
+                # Ensure tz-aware
+                if t_s.tzinfo is None:
+                    t_s = t_s.replace(tzinfo=timezone.utc)
+                if win_start <= t_s <= win_end:
+                    filtered_coverage[rel] = cov
+                else:
+                    n_filtered_out_of_date += 1
+            except Exception:
+                filtered_coverage[rel] = cov
+        if n_filtered_out_of_date:
+            print(f"  date_filter: removed {n_filtered_out_of_date} entries outside mission date window")
+        coverage = filtered_coverage
+
+        # Rebuild auv_file_windows from filtered coverage
+        kept_rels = set(coverage.keys())
+        auv_file_windows_filtered = defaultdict(list)
+        for auv_id, wins in auv_file_windows.items():
+            for w in wins:
+                if w[2] in kept_rels:
+                    auv_file_windows_filtered[auv_id].append(w)
+        auv_file_windows = dict(auv_file_windows_filtered)
+
+    mission_window = compute_mission_window(coverage)
+    auv_windows = compute_auv_windows(auv_file_windows)
+
+    # Coverage stats
+    import collections
+    source_counts = collections.Counter(v["source"] for v in coverage.values())
+    n_fallback = source_counts.get("mtime_fallback", 0)
+    n_total_cov = len(coverage)
+    if n_total_cov:
+        print(f"  coverage: {n_total_cov} files | fallback={n_fallback} "
+              f"({100*n_fallback//n_total_cov}%) | sources={dict(source_counts)}")
+
+    manifest["coverage"] = coverage
+    manifest["mission_window"] = mission_window
+    manifest["auv_windows"] = auv_windows
+    manifest["totals"]["n_filtered_old"] = n_filtered_old
+    manifest["totals"]["n_filtered_out_of_date"] = n_filtered_out_of_date
+
+    return manifest
+
+
+def main(argv=None):
+    ap = argparse.ArgumentParser(description="Stage 01 -- select mission, produce raw manifest.")
+    ap.add_argument("--mission", required=True, help="Mission folder name (e.g. 20260505-Lepradet)")
+    ap.add_argument("--ssd-base", default="/mnt/ssd", help="SSD base path (default /mnt/ssd)")
+    ap.add_argument("--out", default="/home/cosma/cosma-qc/data",
+                    help="Output base dir (manifest written to <out>/<mission>/01_manifest.json)")
+    args = ap.parse_args(argv)
+
+    ssd_base = Path(args.ssd_base)
+    out_base = Path(args.out)
+    out_dir = out_base / args.mission
+    out_dir.mkdir(parents=True, exist_ok=True)
+    out_path = out_dir / "01_manifest.json"
+
+    with track_stage("01_select_mission", args.mission, out_dir,
+                     output_files=[out_path]):
+        manifest = build_manifest(args.mission, ssd_base)
+        tmp = out_path.with_suffix(".json.tmp")
+        tmp.write_text(json.dumps(manifest, indent=2, ensure_ascii=False))
+        tmp.replace(out_path)
+
+        t = manifest["totals"]
+        print(f"[ok] {out_path}")
+        print(f"  videos={t['n_videos']} ({t['total_video_size_gb']} GB) "
+              f"bags={t['n_mcap_bags']} bins={t['n_bin_files']} "
+              f"usbl={t['n_usbl_logs']} audio={t['n_audio_logs']} "
+              f"sss={t['n_sss_files']} mag={t['n_mag_files']}")
+        print(f"  filtered: old={t.get('n_filtered_old', 0)} out_of_date={t.get('n_filtered_out_of_date', 0)}")
+        if manifest.get("mission_window"):
+            mw = manifest["mission_window"]
+            print(f"  mission_window: {mw['t_start']} -> {mw['t_end']} ({mw['duration_s']}s)")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

pipeline/stages/02_mission_run_detect.py

@@ -0,0 +1,835 @@
+#!/usr/bin/env python3
+"""Stage 02 — Mission run detection (v4 state-based).
+
+Détecte runs via transitions /mavros/state (armed + mode) + validation rel_alt.
+Fallback depth-only si topic state absent.
+
+Usage:
+    python3 02_mission_run_detect.py --mission 20260508-sttropez [--ssd-base /mnt/ssd] [--out data/] [--dry-run]
+    python3 02_mission_run_detect.py --mission 20260505-Lepradet --out data/ \
+        --state-modes ALT_HOLD --require-armed --require-descent \
+        --min-mission-depth -2.0 --min-sustained-duration 30 --min-near-bottom-pct 50 --force
+"""
+
+import argparse
+import glob
+import json
+import re
+import statistics
+import sys
+from datetime import datetime, timezone
+from pathlib import Path
+
+from mcap.reader import make_reader
+from mcap_ros2.decoder import DecoderFactory
+
+# Local helper for stage time/memory tracking
+sys.path.insert(0, str(Path(__file__).parent))
+from _meta import track_stage  # noqa: E402
+
+# Mapping ID physique → ID logistique
+AUV_PHYSICAL_MAP = {
+    "AUV010": "AUV210",
+    "AUV012": "AUV212",
+    "AUV013": "AUV213",
+}
+
+TOPIC_REL_ALT = "/mavros/global_position/rel_alt"
+TOPIC_STATE = "/mavros/state"
+THRESHOLD = -0.3        # rel_alt < THRESHOLD → immersé
+NEED_STREAK = 30        # secondes consécutives pour confirmer début/fin
+MIN_DURATION = 60       # secondes minimum par run
+SMOOTH_WINDOW_S = 3     # fenêtre lissage médian (secondes à 1Hz = samples)
+
+# Default modes considérés comme "mission active"
+DEFAULT_STATE_MODES = {"AUTO", "GUIDED"}
+# Modes qui TERMINENT un run (si require-armed=False)
+STATE_STOP_MODES = {"SURFACE", "MANUAL"}
+
+# Filtrage "vraie mission" (modifiables via argparse)
+DEFAULT_MIN_MISSION_DEPTH = -3.0   # rel_alt doit atteindre ce seuil (m) — strict v5 2026-05-14
+DEFAULT_MIN_SUSTAINED_DURATION = 60.0  # pendant au moins N secondes consécutives — strict v5
+DEFAULT_MIN_NEAR_BOTTOM_PCT = 80.0  # % min du run où rel_alt < min_mission_depth — strict v5
+DEFAULT_MIN_DISPLACEMENT_M = 5.0   # futur stage06+: déplacement min USBL — documenté seulement v5
+
+# Filtrage "avant première plongée"
+DEFAULT_FIRST_SUBMERSION_DEPTH = -2.0   # seuil rel_alt pour considérer submergé
+DEFAULT_FIRST_SUBMERSION_DURATION = 5.0  # durée min continue (s) pour confirmer submersion
+
+
+# ---------------------------------------------------------------------------
+# Lecture MCAP rel_alt
+# ---------------------------------------------------------------------------
+
+def parse_mcap_relalt(mcap_path: Path):
+    """Lit rel_alt depuis un fichier mcap. Retourne liste de (epoch_s, rel_alt_m)."""
+    data = []
+    try:
+        with open(mcap_path, "rb") as fp:
+            reader = make_reader(fp, decoder_factories=[DecoderFactory()])
+            for _schema, _channel, message, ros_msg in reader.iter_decoded_messages(topics=[TOPIC_REL_ALT]):
+                ts = message.log_time / 1e9
+                data.append((ts, float(ros_msg.data)))
+    except Exception as exc:
+        print(f"  [WARN] skip {mcap_path.name}: {exc}", file=sys.stderr)
+    return data
+
+
+# ---------------------------------------------------------------------------
+# Lecture MCAP /mavros/state
+# ---------------------------------------------------------------------------
+
+def read_mavros_state(mcap_path: Path, t_start: float = None, t_end: float = None):
+    """
+    Lit /mavros/state depuis un fichier mcap.
+    Retourne liste de (epoch_s, armed:bool, mode:str).
+    Filtrage optionnel sur [t_start, t_end].
+    """
+    data = []
+    try:
+        with open(mcap_path, "rb") as fp:
+            reader = make_reader(fp, decoder_factories=[DecoderFactory()])
+            for _schema, _channel, message, ros_msg in reader.iter_decoded_messages(topics=[TOPIC_STATE]):
+                ts = message.log_time / 1e9
+                if t_start is not None and ts < t_start:
+                    continue
+                if t_end is not None and ts > t_end:
+                    continue
+                data.append((ts, bool(ros_msg.armed), str(ros_msg.mode)))
+    except Exception as exc:
+        # Silent — bag could be corrupt
+        pass
+    return data
+
+
+def parse_mcap_both(mcap_path: Path):
+    """Lit rel_alt ET state depuis un seul fichier mcap en un seul pass."""
+    alt_data = []
+    state_data = []
+    try:
+        with open(mcap_path, "rb") as fp:
+            reader = make_reader(fp, decoder_factories=[DecoderFactory()])
+            for _schema, _channel, message, ros_msg in reader.iter_decoded_messages(
+                    topics=[TOPIC_REL_ALT, TOPIC_STATE]):
+                ts = message.log_time / 1e9
+                if _channel.topic == TOPIC_REL_ALT:
+                    alt_data.append((ts, float(ros_msg.data)))
+                elif _channel.topic == TOPIC_STATE:
+                    state_data.append((ts, bool(ros_msg.armed), str(ros_msg.mode)))
+    except Exception as exc:
+        print(f"  [WARN] skip {mcap_path.name}: {exc}", file=sys.stderr)
+    return alt_data, state_data
+
+
+def extract_auv_id(folder_name: str):
+    """'20260508_054551_AUV010' → 'AUV010'."""
+    m = re.search(r"(AUV\d+)$", folder_name)
+    return m.group(1) if m else None
+
+
+# ---------------------------------------------------------------------------
+# Signal processing
+# ---------------------------------------------------------------------------
+
+def resample_1hz(data):
+    """Resample (epoch, val) → 1Hz par interpolation linéaire. Retourne (times[], vals[])."""
+    if not data:
+        return [], []
+    data = sorted(data)
+    t0 = int(data[0][0])
+    t1 = int(data[-1][0])
+    times = list(range(t0, t1 + 1))
+    vals = []
+    idx = 0
+    for t in times:
+        while idx < len(data) - 1 and data[idx + 1][0] < t:
+            idx += 1
+        if t <= data[0][0]:
+            v = data[0][1]
+        elif t >= data[-1][0]:
+            v = data[-1][1]
+        else:
+            t0_, v0 = data[idx]
+            t1_, v1 = data[idx + 1]
+            dt = t1_ - t0_
+            v = v0 + ((t - t0_) / dt) * (v1 - v0) if dt > 0 else v0
+        vals.append(v)
+    return times, vals
+
+
+def median_filter(vals, window=3):
+    half = window // 2
+    out = []
+    n = len(vals)
+    for i in range(n):
+        lo = max(0, i - half)
+        hi = min(n, i + half + 1)
+        w = sorted(vals[lo:hi])
+        out.append(w[len(w) // 2])
+    return out
+
+
+def find_first_submersion_epoch(rel_alt_times, rel_alt_vals, threshold=-2.0, min_duration=5.0):
+    """
+    Trouve la PREMIÈRE fois où rel_alt < threshold pendant >= min_duration secondes en continu.
+    Retourne epoch du début de cette submersion, ou None si jamais submergé.
+
+    Travaille sur données 1Hz lissées (times/vals déjà resampleés).
+    """
+    n = len(rel_alt_times)
+    if n == 0:
+        return None
+
+    streak_start = None
+    streak_count = 0
+
+    for i in range(n):
+        if rel_alt_vals[i] < threshold:
+            if streak_count == 0:
+                streak_start = rel_alt_times[i]
+            streak_count += 1
+            if streak_count >= min_duration:
+                return float(streak_start)
+        else:
+            streak_count = 0
+            streak_start = None
+
+    return None
+
+
+def detect_runs_depth_only(times, vals, threshold=THRESHOLD, need_streak=NEED_STREAK, min_duration=MIN_DURATION):
+    """
+    Détecte les runs d'immersion via rel_alt seul (fallback).
+
+    Algorithme:
+    - need_streak samples consécutifs < threshold pour confirmer entrée/sortie
+    - min_duration secondes minimum par run
+    Returns liste de (start_epoch, end_epoch).
+    """
+    n = len(times)
+    if n == 0:
+        return []
+
+    under = [v < threshold for v in vals]
+
+    runs = []
+    in_run = False
+    run_start = None
+    streak_under = 0
+    streak_surface = 0
+
+    i = 0
+    while i < n:
+        if not in_run:
+            if under[i]:
+                streak_under += 1
+                if streak_under >= need_streak:
+                    run_start = times[i - need_streak + 1]
+                    in_run = True
+                    streak_surface = 0
+            else:
+                streak_under = 0
+        else:
+            if under[i]:
+                streak_surface = 0
+            else:
+                streak_surface += 1
+                if streak_surface >= need_streak:
+                    run_end = times[i - need_streak + 1]
+                    dur = run_end - run_start
+                    if dur >= min_duration:
+                        runs.append((run_start, run_end))
+                    in_run = False
+                    run_start = None
+                    streak_under = 0
+                    streak_surface = 0
+        i += 1
+
+    if in_run and run_start is not None:
+        run_end = times[-1]
+        dur = run_end - run_start
+        if dur >= min_duration:
+            runs.append((run_start, run_end))
+
+    return runs
+
+
+# ---------------------------------------------------------------------------
+# State-based run detection
+# ---------------------------------------------------------------------------
+
+def detect_runs_state_based(state_data, times_alt, vals_smooth, mission_modes, require_armed,
+                             require_descent, min_duration, min_depth_m=-0.3):
+    """
+    Détecte runs via /mavros/state:
+    - Intervalles continus armed=True (si require_armed) AND mode in mission_modes
+    - Valide via transition rel_alt surface → fond (si require_descent)
+    - min_duration filtre courtes fenêtres
+
+    Returns:
+        list of (start_epoch, end_epoch, dominant_mode)
+    """
+    if not state_data:
+        return []
+
+    state_data_sorted = sorted(state_data)
+
+    # Construire séquence d'états
+    # Identifier intervalles "mission active"
+    intervals = []
+    cur_start = None
+    cur_mode_counts = {}
+
+    for ts, armed, mode in state_data_sorted:
+        active = (not require_armed or armed) and (mode in mission_modes)
+
+        if active and cur_start is None:
+            cur_start = ts
+            cur_mode_counts = {mode: 1}
+        elif active and cur_start is not None:
+            cur_mode_counts[mode] = cur_mode_counts.get(mode, 0) + 1
+        elif not active and cur_start is not None:
+            # Fin de l'intervalle
+            intervals.append((cur_start, ts, cur_mode_counts))
+            cur_start = None
+            cur_mode_counts = {}
+
+    # Flush dernier intervalle
+    if cur_start is not None:
+        intervals.append((cur_start, state_data_sorted[-1][0], cur_mode_counts))
+
+    # Filtrer par durée min
+    runs = []
+    for start_t, end_t, mode_counts in intervals:
+        dur = end_t - start_t
+        if dur < min_duration:
+            continue
+
+        dominant_mode = max(mode_counts, key=mode_counts.get) if mode_counts else "UNKNOWN"
+
+        if require_descent:
+            # Vérifier transition surface → fond dans la fenêtre
+            window_alts = [(t, v) for t, v in zip(times_alt, vals_smooth)
+                           if start_t <= t <= end_t]
+            if not window_alts:
+                # Pas de données alt dans cette fenêtre — skip
+                continue
+            alt_vals = [v for _, v in window_alts]
+            # Début = surface (rel_alt > -1m dans les 60 premiers samples)
+            first_segment = alt_vals[:60]
+            last_segment = alt_vals[-60:]
+            starts_near_surface = any(v > -1.0 for v in first_segment)
+            reaches_depth = any(v <= min_depth_m for v in alt_vals)
+            if not (starts_near_surface and reaches_depth):
+                continue
+
+        runs.append((start_t, end_t, dominant_mode))
+
+    return runs
+
+
+# ---------------------------------------------------------------------------
+# Validation "vraie mission" — filtre oscillations surface
+# ---------------------------------------------------------------------------
+
+def compute_sustained_depth(times, vals_smooth, start_e, end_e, min_depth_m):
+    """
+    Pour un run [start_e, end_e], calcule le plus long segment continu
+    où rel_alt <= min_depth_m (ex: -2.0m).
+    """
+    run_pairs = [(t, v) for t, v in zip(times, vals_smooth) if start_e <= t <= end_e]
+    if not run_pairs:
+        return 0.0, 0.0
+
+    best_dur = 0
+    best_min = 0.0
+    cur_dur = 0
+    cur_min = 0.0
+
+    for _t, v in run_pairs:
+        if v <= min_depth_m:
+            cur_dur += 1
+            cur_min = min(cur_min, v) if cur_dur > 1 else v
+        else:
+            if cur_dur > best_dur:
+                best_dur = cur_dur
+                best_min = cur_min
+            cur_dur = 0
+            cur_min = 0.0
+
+    if cur_dur > best_dur:
+        best_dur = cur_dur
+        best_min = cur_min
+
+    return round(best_min, 2), float(best_dur)
+
+
+def compute_near_bottom_pct(times, vals_smooth, start_e, end_e, min_depth_m):
+    """Calcule le % de samples dans [start_e, end_e] où rel_alt < min_depth_m."""
+    run_vals = [v for t, v in zip(times, vals_smooth) if start_e <= t <= end_e]
+    if not run_vals:
+        return 0.0
+    n_below = sum(1 for v in run_vals if v < min_depth_m)
+    return round(100.0 * n_below / len(run_vals), 1)
+
+
+# ---------------------------------------------------------------------------
+# Processing AUV
+# ---------------------------------------------------------------------------
+
+def process_auv(auv_mcap_id: str, bag_dirs: list, ssd_base: Path,
+                min_mission_depth: float, min_sustained_duration: float,
+                min_near_bottom_pct: float = 0.0,
+                state_modes: set = None, require_armed: bool = True,
+                require_descent: bool = True,
+                first_submersion_depth: float = DEFAULT_FIRST_SUBMERSION_DEPTH,
+                first_submersion_duration: float = DEFAULT_FIRST_SUBMERSION_DURATION):
+    """
+    Agréger tous les bags d'un AUV, détecter runs via state (avec fallback depth-only).
+    Filtre les runs entiers avant la première vraie submersion.
+    """
+    physical_id = AUV_PHYSICAL_MAP.get(auv_mcap_id, auv_mcap_id)
+    if state_modes is None:
+        state_modes = DEFAULT_STATE_MODES
+
+    all_alt_data = []
+    all_state_data = []
+    bags_list = []
+    n_parsed = 0
+    n_skipped = 0
+
+    # Parcourir bags dans l'ordre chronologique
+    for bag_dir in sorted(bag_dirs):
+        bags_list.append(str(bag_dir.name))
+        mcap_files = sorted(bag_dir.glob("*.mcap"))
+        for mcap_path in mcap_files:
+            alt_pts, state_pts = parse_mcap_both(mcap_path)
+            if alt_pts or state_pts:
+                all_alt_data.extend(alt_pts)
+                all_state_data.extend(state_pts)
+                n_parsed += 1
+            else:
+                n_skipped += 1
+            if (n_parsed + n_skipped) % 50 == 0:
+                print(f"  [{auv_mcap_id}] ... {n_parsed + n_skipped} bags processed", file=sys.stderr)
+
+    has_state = len(all_state_data) > 0
+    print(f"  [{auv_mcap_id}] {n_parsed} mcap OK, {n_skipped} skip, "
+          f"{len(all_alt_data)} rel_alt pts, {len(all_state_data)} state pts", file=sys.stderr)
+
+    if not all_alt_data:
+        print(f"  [{auv_mcap_id}] [WARN] aucune donnée rel_alt", file=sys.stderr)
+        return {
+            "mcap_id": auv_mcap_id,
+            "physical_id": physical_id,
+            "bags": bags_list,
+            "total_immersion_s": 0,
+            "runs": [],
+            "runs_rejected": [],
+            "detection_method": "no_data",
+            "first_submersion_epoch": None,
+            "pre_water_rejected_count": 0,
+        }
+
+    # Dédup + tri rel_alt
+    seen = set()
+    deduped_alt = []
+    for t, v in sorted(all_alt_data):
+        key = round(t, 3)
+        if key not in seen:
+            seen.add(key)
+            deduped_alt.append((t, v))
+
+    # Resample 1Hz
+    times, vals = resample_1hz(deduped_alt)
+    print(f"  [{auv_mcap_id}] {len(times)} samples 1Hz [{times[0]:.0f}..{times[-1]:.0f}]", file=sys.stderr)
+
+    # Lissage médian 3s
+    vals_smooth = median_filter(vals, window=SMOOTH_WINDOW_S)
+
+    # Trouver première submersion réelle
+    first_sub_epoch = find_first_submersion_epoch(
+        times, vals_smooth,
+        threshold=first_submersion_depth,
+        min_duration=first_submersion_duration,
+    )
+    if first_sub_epoch is not None:
+        print(f"  [{auv_mcap_id}] Première submersion réelle: {first_sub_epoch:.0f} "
+              f"({datetime.fromtimestamp(first_sub_epoch, tz=timezone.utc).isoformat()})",
+              file=sys.stderr)
+    else:
+        print(f"  [{auv_mcap_id}] [WARN] Aucune submersion réelle détectée "
+              f"(threshold={first_submersion_depth}m, min_dur={first_submersion_duration}s)",
+              file=sys.stderr)
+
+    # Détection runs
+    detection_method = "depth_only"
+    if has_state:
+        # Trier state data
+        all_state_data.sort(key=lambda x: x[0])
+
+        # Extraire modes présents
+        modes_in_data = set(m for _, _, m in all_state_data)
+        modes_active = modes_in_data & state_modes
+        print(f"  [{auv_mcap_id}] state modes found: {modes_in_data}", file=sys.stderr)
+        print(f"  [{auv_mcap_id}] state modes matching --state-modes: {modes_active}", file=sys.stderr)
+
+        if modes_active:
+            raw_runs_with_mode = detect_runs_state_based(
+                all_state_data, times, vals_smooth,
+                mission_modes=state_modes,
+                require_armed=require_armed,
+                require_descent=require_descent,
+                min_duration=MIN_DURATION,
+                min_depth_m=min_mission_depth,
+            )
+            raw_runs = [(s, e) for s, e, _m in raw_runs_with_mode]
+            run_modes = {(s, e): m for s, e, m in raw_runs_with_mode}
+            detection_method = "state_based"
+            print(f"  [{auv_mcap_id}] {len(raw_runs)} candidats state-based", file=sys.stderr)
+        else:
+            print(f"  [{auv_mcap_id}] [WARN] aucun mode {state_modes} dans state data "
+                  f"→ fallback depth-only", file=sys.stderr)
+            raw_runs = detect_runs_depth_only(times, vals_smooth)
+            run_modes = {}
+            detection_method = "depth_only_fallback_no_modes"
+    else:
+        print(f"  [{auv_mcap_id}] [WARN] topic /mavros/state vide → fallback depth-only", file=sys.stderr)
+        raw_runs = detect_runs_depth_only(times, vals_smooth)
+        run_modes = {}
+
+    print(f"  [{auv_mcap_id}] {len(raw_runs)} runs candidats ({detection_method})", file=sys.stderr)
+
+    # Filtrage pre-water: exclure/tronquer runs avant première submersion
+    pre_water_rejected_count = 0
+    if first_sub_epoch is not None:
+        filtered_runs = []
+        for start_e, end_e in raw_runs:
+            if end_e <= first_sub_epoch:
+                # Run entier avant première plongée → rejeter
+                pre_water_rejected_count += 1
+                phys_id_log = AUV_PHYSICAL_MAP.get(auv_mcap_id, auv_mcap_id)
+                print(f"  [{auv_mcap_id}] PRE-WATER REJECT run [{start_e:.0f}..{end_e:.0f}] "
+                      f"(end before first_sub={first_sub_epoch:.0f})", file=sys.stderr)
+            elif start_e < first_sub_epoch < end_e:
+                # Run chevauche → tronquer start
+                new_start = first_sub_epoch
+                print(f"  [{auv_mcap_id}] PRE-WATER TRUNCATE run [{start_e:.0f}..{end_e:.0f}] "
+                      f"→ [{new_start:.0f}..{end_e:.0f}]", file=sys.stderr)
+                # Mettre à jour run_modes si besoin
+                if (start_e, end_e) in run_modes:
+                    run_modes[(new_start, end_e)] = run_modes.pop((start_e, end_e))
+                filtered_runs.append((new_start, end_e))
+            else:
+                filtered_runs.append((start_e, end_e))
+        raw_runs = filtered_runs
+        print(f"  [{auv_mcap_id}] {pre_water_rejected_count} runs rejetés pre-water, "
+              f"{len(raw_runs)} restants", file=sys.stderr)
+
+    # Construire runs enrichis + filtre "vraie mission"
+    runs_out = []
+    runs_rejected = []
+    for idx, (start_e, end_e) in enumerate(raw_runs):
+        dur = end_e - start_e
+        run_id = f"{physical_id}_run_{idx:02d}"
+        dominant_mode = run_modes.get((start_e, end_e), "UNKNOWN")
+
+        run_vals = [v for t, v in zip(times, vals_smooth) if start_e <= t <= end_e]
+        max_depth = round(min(run_vals), 2) if run_vals else 0.0
+        mean_depth = round(statistics.mean(run_vals), 2) if run_vals else 0.0
+
+        sustained_below_m, sustained_duration_s = compute_sustained_depth(
+            times, vals_smooth, start_e, end_e, min_mission_depth
+        )
+        pct_near_bottom = compute_near_bottom_pct(
+            times, vals_smooth, start_e, end_e, min_mission_depth
+        )
+
+        run_entry = {
+            "run_id": run_id,
+            "start_epoch": float(start_e),
+            "end_epoch": float(end_e),
+            "duration_s": round(dur, 1),
+            "max_depth_m": max_depth,
+            "mean_depth_m": mean_depth,
+            "sustained_below_m": sustained_below_m,
+            "sustained_duration_s": sustained_duration_s,
+            "pct_near_bottom": pct_near_bottom,
+            "dominant_mode": dominant_mode,
+            "detection_method": detection_method,
+        }
+
+        reject_reason = None
+        if sustained_duration_s < min_sustained_duration:
+            reject_reason = (
+                f"sustained_depth only {sustained_duration_s:.0f}s "
+                f"(need {min_sustained_duration:.0f}s below {min_mission_depth}m)"
+            )
+        elif min_near_bottom_pct > 0.0 and pct_near_bottom < min_near_bottom_pct:
+            reject_reason = (
+                f"not_enough_immersion: only {pct_near_bottom:.1f}% "
+                f"time below {min_mission_depth}m (need {min_near_bottom_pct:.1f}%)"
+            )
+
+        if reject_reason is None:
+            runs_out.append(run_entry)
+        else:
+            run_entry["rejected_reason"] = reject_reason
+            runs_rejected.append(run_entry)
+            print(
+                f"  [{auv_mcap_id}] REJECT {run_id}: max_depth={max_depth}m "
+                f"sustained={sustained_duration_s:.0f}s pct={pct_near_bottom:.1f}% "
+                f"reason={reject_reason[:60]}",
+                file=sys.stderr,
+            )
+
+    print(
+        f"  [{auv_mcap_id}] {len(runs_out)} runs OK, {len(runs_rejected)} rejetés ({detection_method})",
+        file=sys.stderr,
+    )
+
+    total_immersion_s = round(sum(r["duration_s"] for r in runs_out), 1)
+
+    return {
+        "mcap_id": auv_mcap_id,
+        "physical_id": physical_id,
+        "bags": bags_list,
+        "total_immersion_s": total_immersion_s,
+        "runs": runs_out,
+        "runs_rejected": runs_rejected,
+        "detection_method": detection_method,
+        "first_submersion_epoch": first_sub_epoch,
+        "pre_water_rejected_count": pre_water_rejected_count,
+    }
+
+
+# ---------------------------------------------------------------------------
+# Main
+# ---------------------------------------------------------------------------
+
+def _run(args):
+    bags_root = Path(args.ssd_base) / args.mission / "raw_data" / "logs" / "SUB" / "bag"
+    if not bags_root.exists():
+        print(f"[ERROR] bags dir not found: {bags_root}", file=sys.stderr)
+        sys.exit(1)
+
+    state_modes = set(m.strip() for m in args.state_modes.split(",") if m.strip())
+
+    print(f"[stage02] Mission: {args.mission}")
+    print(f"[stage02] Bags root: {bags_root}", file=sys.stderr)
+    print(f"[stage02] State modes: {state_modes}, require_armed={args.require_armed}, "
+          f"require_descent={args.require_descent}", file=sys.stderr)
+    near_bottom_str = (f" + near_bottom >= {args.min_near_bottom_pct:.0f}%"
+                       if args.min_near_bottom_pct > 0 else "")
+    print(
+        f"[stage02] Filtre mission: sustained >= {args.min_sustained_duration}s "
+        f"below {args.min_mission_depth}m{near_bottom_str}",
+        file=sys.stderr,
+    )
+    print(
+        f"[stage02] Filtre pre-water: first_submersion threshold={args.first_submersion_depth}m "
+        f"min_duration={args.first_submersion_duration}s",
+        file=sys.stderr,
+    )
+
+    # Grouper dossiers bag par AUV ID
+    auv_dirs = {}
+    for d in sorted(bags_root.iterdir()):
+        if not d.is_dir():
+            continue
+        auv_id = extract_auv_id(d.name)
+        if auv_id:
+            auv_dirs.setdefault(auv_id, []).append(d)
+
+    print(f"[stage02] AUVs: {sorted(auv_dirs.keys())}")
+
+    # Traiter chaque AUV
+    auvs_out = {}
+    all_runs_flat = []
+    all_rejected_flat = []
+
+    for auv_mcap_id in sorted(auv_dirs.keys()):
+        physical_id = AUV_PHYSICAL_MAP.get(auv_mcap_id, auv_mcap_id)
+        print(f"\n[stage02] Processing {auv_mcap_id} -> {physical_id} ({len(auv_dirs[auv_mcap_id])} bag dirs)...")
+        result = process_auv(
+            auv_mcap_id,
+            auv_dirs[auv_mcap_id],
+            Path(args.ssd_base),
+            min_mission_depth=args.min_mission_depth,
+            min_sustained_duration=args.min_sustained_duration,
+            min_near_bottom_pct=args.min_near_bottom_pct,
+            state_modes=state_modes,
+            require_armed=args.require_armed,
+            require_descent=args.require_descent,
+            first_submersion_depth=args.first_submersion_depth,
+            first_submersion_duration=args.first_submersion_duration,
+        )
+        auvs_out[physical_id] = result
+        all_runs_flat.extend(result["runs"])
+        all_rejected_flat.extend(result.get("runs_rejected", []))
+
+    # Trier tous les runs par start_epoch
+    all_runs_sorted = sorted(all_runs_flat, key=lambda r: r["start_epoch"])
+    all_rejected_sorted = sorted(all_rejected_flat, key=lambda r: r["start_epoch"])
+
+    # Construire output JSON
+    output = {
+        "mission": args.mission,
+        "generated_at": datetime.now(timezone.utc).isoformat(),
+        "filter_params": {
+            "min_mission_depth_m": args.min_mission_depth,
+            "min_sustained_duration_s": args.min_sustained_duration,
+            "min_near_bottom_pct": args.min_near_bottom_pct,
+            "state_modes": sorted(state_modes),
+            "require_armed": args.require_armed,
+            "require_descent": args.require_descent,
+            "first_submersion_depth_m": args.first_submersion_depth,
+            "first_submersion_duration_s": args.first_submersion_duration,
+        },
+        "auvs": auvs_out,
+        "all_runs_sorted": all_runs_sorted,
+        "all_runs_rejected": all_rejected_sorted,
+    }
+
+    # Summary
+    total_runs = len(all_runs_sorted)
+    total_rejected = len(all_rejected_sorted)
+    all_depths = [r["max_depth_m"] for r in all_runs_sorted]
+    global_max_depth = min(all_depths) if all_depths else 0.0
+    total_immersion = sum(r["duration_s"] for r in all_runs_sorted)
+    total_pre_water = sum(v.get("pre_water_rejected_count", 0) for v in auvs_out.values())
+
+    print(f"\n{'='*60}")
+    print(f"[stage02] SUMMARY — {args.mission}")
+    print(f"{'='*60}")
+    for phys_id, auv in auvs_out.items():
+        deep = [r for r in auv["runs"] if r["max_depth_m"] < -10.0]
+        rej = len(auv.get("runs_rejected", []))
+        method = auv.get("detection_method", "?")
+        fsub = auv.get("first_submersion_epoch")
+        fsub_str = (datetime.fromtimestamp(fsub, tz=timezone.utc).isoformat()
+                    if fsub else "None")
+        pre_w = auv.get("pre_water_rejected_count", 0)
+        print(f"  {phys_id}: {auv['total_immersion_s']}s immersion, "
+              f"{len(auv['runs'])} runs OK, {rej} rejetés, runs>10m: {len(deep)} [{method}]")
+        print(f"    first_submersion: {fsub_str} | pre_water_rejected: {pre_w}")
+    print(f"  Total runs OK: {total_runs}")
+    print(f"  Total runs rejetés: {total_rejected}")
+    print(f"  Total pre-water rejetés: {total_pre_water}")
+    print(f"  Global max depth: {global_max_depth:.1f}m")
+    print(f"  Total immersion: {total_immersion:.0f}s")
+
+    if total_runs == 0:
+        print("[WARN] Aucun run validé!")
+    else:
+        print(f"[QC OK] {total_runs} runs validés")
+        for r in all_runs_sorted:
+            print(f"  {r['run_id']}: {r['duration_s']:.0f}s depth={r['max_depth_m']}m "
+                  f"pct={r['pct_near_bottom']:.1f}% mode={r.get('dominant_mode','?')} "
+                  f"method={r.get('detection_method','?')}")
+
+    if args.dry_run:
+        print(f"\n[dry-run] JSON non écrit.")
+        return
+
+    # Écrire JSON
+    out_dir = Path(args.out) / args.mission
+    out_dir.mkdir(parents=True, exist_ok=True)
+    out_path = out_dir / "02_runs.json"
+
+    with open(out_path, "w") as f:
+        json.dump(output, f, indent=2)
+
+    print(f"[stage02] Written: {out_path}")
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Stage 02 — Detect mission underwater runs (v4 state-based)")
+    parser.add_argument("--mission", required=True, help="Mission folder, e.g. 20260508-sttropez")
+    parser.add_argument("--ssd-base", default="/mnt/ssd", help="SSD root path (READ-ONLY)")
+    parser.add_argument("--out", default="data/", help="Output base dir")
+    parser.add_argument("--dry-run", action="store_true", help="Print stats sans écrire fichier")
+    parser.add_argument(
+        "--min-mission-depth",
+        type=float,
+        default=DEFAULT_MIN_MISSION_DEPTH,
+        help=f"Profondeur seuil (m, négatif) pour valider un run (default: {DEFAULT_MIN_MISSION_DEPTH})",
+    )
+    parser.add_argument(
+        "--min-sustained-duration",
+        type=float,
+        default=DEFAULT_MIN_SUSTAINED_DURATION,
+        help=f"Durée min (s) consécutive sous min-mission-depth (default: {DEFAULT_MIN_SUSTAINED_DURATION})",
+    )
+    parser.add_argument(
+        "--min-near-bottom-pct",
+        type=float,
+        default=DEFAULT_MIN_NEAR_BOTTOM_PCT,
+        help=f"% min du run où rel_alt < min-mission-depth (0=désactivé, default: {DEFAULT_MIN_NEAR_BOTTOM_PCT})",
+    )
+    parser.add_argument(
+        "--state-modes",
+        type=str,
+        default=",".join(sorted(DEFAULT_STATE_MODES)),
+        help="CSV modes ArduSub considérés mission (ex: AUTO,GUIDED ou ALT_HOLD). "
+             f"Default: {','.join(sorted(DEFAULT_STATE_MODES))}",
+    )
+    parser.add_argument(
+        "--require-armed",
+        action="store_true",
+        default=True,
+        help="Exiger armed=True (défaut: True)",
+    )
+    parser.add_argument(
+        "--no-require-armed",
+        action="store_false",
+        dest="require_armed",
+        help="Ne pas exiger armed=True",
+    )
+    parser.add_argument(
+        "--require-descent",
+        action="store_true",
+        default=True,
+        help="Exiger transition surface→fond dans fenêtre (défaut: True)",
+    )
+    parser.add_argument(
+        "--no-require-descent",
+        action="store_false",
+        dest="require_descent",
+        help="Ne pas exiger transition surface→fond",
+    )
+    parser.add_argument(
+        "--first-submersion-depth",
+        type=float,
+        default=DEFAULT_FIRST_SUBMERSION_DEPTH,
+        help=f"Seuil rel_alt (m) pour détecter première submersion réelle "
+             f"(default: {DEFAULT_FIRST_SUBMERSION_DEPTH})",
+    )
+    parser.add_argument(
+        "--first-submersion-duration",
+        type=float,
+        default=DEFAULT_FIRST_SUBMERSION_DURATION,
+        help=f"Durée min continue (s) sous first-submersion-depth pour confirmer mise à l'eau "
+             f"(default: {DEFAULT_FIRST_SUBMERSION_DURATION})",
+    )
+    parser.add_argument(
+        "--force",
+        action="store_true",
+        help="Forcer recalcul même si fichier existe",
+    )
+    args = parser.parse_args()
+
+    if args.dry_run:
+        _run(args)
+        return
+
+    out_dir = Path(args.out) / args.mission
+    out_dir.mkdir(parents=True, exist_ok=True)
+    out_path = out_dir / "02_runs.json"
+    with track_stage("02_mission_run_detect", args.mission, out_dir,
+                     output_files=[out_path]):
+        _run(args)
+
+
+if __name__ == "__main__":
+    main()

pipeline/stages/02b_runs_diag.py

@@ -0,0 +1,352 @@
+#!/usr/bin/env python3
+"""Stage 02b — Diagnostic plots per run candidate.
+
+Reads 02_runs.json + replays MCAP rel_alt + /mavros/state to produce
+4-panel PNG per run (validated + rejected).
+
+Output:
+    data/<MISSION>/02_runs_diag/<RUN_ID>.png
+    data/<MISSION>/02_runs_diag/index.json
+    data/<MISSION>/02_runs_diag/index.html
+
+Usage:
+    python3 02b_runs_diag.py --mission 20260505-Lepradet \
+        [--ssd-base /mnt/ssd] [--out data/] [--padding-s 120]
+"""
+
+import argparse
+import json
+import re
+import sys
+from datetime import datetime, timezone
+from pathlib import Path
+
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from matplotlib.patches import Rectangle
+
+from mcap.reader import make_reader
+from mcap_ros2.decoder import DecoderFactory
+
+TOPIC_REL_ALT = "/mavros/global_position/rel_alt"
+TOPIC_STATE = "/mavros/state"
+TOPIC_HEADING = "/mavros/global_position/compass_hdg"
+
+AUV_PHYSICAL_MAP = {"AUV010": "AUV210", "AUV012": "AUV212", "AUV013": "AUV213"}
+PHYS_TO_MCAP = {v: k for k, v in AUV_PHYSICAL_MAP.items()}
+
+
+def extract_auv_id(folder_name):
+    m = re.search(r"(AUV\d+)$", folder_name)
+    return m.group(1) if m else None
+
+
+def gather_signals_for_auv(bags_root, auv_mcap_id, t_start, t_end):
+    """Read rel_alt + state + heading from all bags for this AUV in [t_start,t_end]."""
+    alt = []  # (t, v)
+    state = []  # (t, armed, mode)
+    hdg = []  # (t, v_deg)
+    for d in sorted(bags_root.iterdir()):
+        if not d.is_dir():
+            continue
+        if extract_auv_id(d.name) != auv_mcap_id:
+            continue
+        for mcap_path in sorted(d.glob("*.mcap")):
+            try:
+                with open(mcap_path, "rb") as fp:
+                    reader = make_reader(fp, decoder_factories=[DecoderFactory()])
+                    for _schema, channel, message, ros_msg in reader.iter_decoded_messages(
+                            topics=[TOPIC_REL_ALT, TOPIC_STATE, TOPIC_HEADING]):
+                        ts = message.log_time / 1e9
+                        if ts < t_start or ts > t_end:
+                            continue
+                        if channel.topic == TOPIC_REL_ALT:
+                            alt.append((ts, float(ros_msg.data)))
+                        elif channel.topic == TOPIC_STATE:
+                            state.append((ts, bool(ros_msg.armed), str(ros_msg.mode)))
+                        elif channel.topic == TOPIC_HEADING:
+                            hdg.append((ts, float(ros_msg.data)))
+            except Exception as exc:
+                print(f"  [WARN] skip {mcap_path.name}: {exc}", file=sys.stderr)
+    alt.sort()
+    state.sort()
+    hdg.sort()
+    return alt, state, hdg
+
+
+def plot_run_diag(run, alt, state, hdg, filter_params, status, reject_reason, out_path):
+    """4-panel diagnostic plot."""
+    start_e = run["start_epoch"]
+    end_e = run["end_epoch"]
+    dur = end_e - start_e
+    run_id = run["run_id"]
+
+    # Convert epoch → relative seconds from start_e for x-axis readability
+    def to_rel(t):
+        return t - start_e
+
+    fig, axes = plt.subplots(4, 1, figsize=(12, 11), gridspec_kw={"height_ratios": [3, 1, 2, 2]})
+    fig.suptitle(
+        f"{run_id} — {status}  |  start={datetime.fromtimestamp(start_e, tz=timezone.utc).strftime('%H:%M:%S UTC')}  duration={dur:.0f}s",
+        fontsize=12, fontweight="bold",
+        color=("#16a34a" if status == "OK" else "#dc2626"),
+    )
+
+    # === Panel A: rel_alt time series ===
+    ax = axes[0]
+    if alt:
+        t_a = [to_rel(t) for t, _ in alt]
+        v_a = [v for _, v in alt]
+        ax.plot(t_a, v_a, color="#1e40af", lw=1.0, label="rel_alt")
+    threshold = filter_params["min_mission_depth_m"]
+    ax.axhline(threshold, color="#dc2626", ls="--", lw=1.0,
+               label=f"threshold {threshold}m")
+    ax.axhline(0, color="#94a3b8", ls=":", lw=0.8, label="surface")
+    # Mark run window
+    ax.axvspan(0, dur, alpha=0.10, color="#16a34a" if status == "OK" else "#dc2626")
+    ax.set_ylabel("rel_alt (m)")
+    ax.set_title(
+        f"(a) Depth — max={run['max_depth_m']}m  mean={run['mean_depth_m']}m  "
+        f"sustained={run['sustained_duration_s']:.0f}s below {threshold}m  "
+        f"pct_near_bottom={run['pct_near_bottom']:.1f}%"
+    )
+    ax.legend(loc="lower right", fontsize=8)
+    ax.grid(True, alpha=0.3)
+    ax.set_xlim(-30, dur + 30)
+
+    # === Panel B: state armed + mode ===
+    ax = axes[1]
+    if state:
+        t_s = [to_rel(t) for t, _, _ in state]
+        armed_y = [1 if a else 0 for _, a, _ in state]
+        ax.step(t_s, armed_y, where="post", color="#16a34a", lw=1.2, label="armed")
+        # Annotate dominant mode + mode transitions
+        prev_mode = None
+        for t, _, m in state:
+            if m != prev_mode:
+                ax.axvline(to_rel(t), color="#7c3aed", lw=0.5, alpha=0.4)
+                ax.text(to_rel(t), 0.5, m, rotation=90, fontsize=7,
+                        color="#7c3aed", va="center", alpha=0.7)
+                prev_mode = m
+    ax.set_ylim(-0.2, 1.3)
+    ax.set_yticks([0, 1])
+    ax.set_yticklabels(["disarmed", "armed"])
+    ax.set_title(f"(b) MAVROS state — dominant mode: {run.get('dominant_mode','?')}")
+    ax.grid(True, alpha=0.3)
+    ax.set_xlim(-30, dur + 30)
+
+    # === Panel C: depth distribution + cumulative time below threshold ===
+    ax = axes[2]
+    # filter alt to run window
+    run_vals = [v for t, v in alt if start_e <= t <= end_e]
+    if run_vals:
+        ax.hist(run_vals, bins=40, color="#3b82f6", alpha=0.7, edgecolor="white")
+        ax.axvline(threshold, color="#dc2626", ls="--", lw=1.0,
+                   label=f"threshold {threshold}m")
+        n_total = len(run_vals)
+        n_below = sum(1 for v in run_vals if v < threshold)
+        ax.set_title(
+            f"(c) Depth distribution within run  |  {n_below}/{n_total} samples below threshold "
+            f"= {100*n_below/n_total:.1f}%"
+        )
+        ax.legend(loc="upper right", fontsize=8)
+    ax.set_xlabel("rel_alt (m)")
+    ax.set_ylabel("samples")
+    ax.grid(True, alpha=0.3)
+
+    # === Panel D: verdict box ===
+    ax = axes[3]
+    ax.axis("off")
+    color = "#16a34a" if status == "OK" else "#dc2626"
+    verdict_text = f"VERDICT: {status}"
+    ax.text(0.02, 0.85, verdict_text, fontsize=18, fontweight="bold",
+            color=color, transform=ax.transAxes)
+
+    # Build criteria summary
+    crit_lines = []
+    min_dur = filter_params["min_sustained_duration_s"]
+    min_pct = filter_params["min_near_bottom_pct"]
+    min_depth = filter_params["min_mission_depth_m"]
+
+    pass_dur = run["sustained_duration_s"] >= min_dur
+    pass_pct = run["pct_near_bottom"] >= min_pct
+    pass_depth = run["max_depth_m"] < min_depth
+
+    crit_lines.append(
+        f"{'OK' if pass_depth else 'KO':3s}  max_depth {run['max_depth_m']}m < {min_depth}m"
+    )
+    crit_lines.append(
+        f"{'OK' if pass_dur else 'KO':3s}  sustained_duration {run['sustained_duration_s']:.0f}s >= {min_dur:.0f}s"
+    )
+    crit_lines.append(
+        f"{'OK' if pass_pct else 'KO':3s}  pct_near_bottom {run['pct_near_bottom']:.1f}% >= {min_pct:.0f}%"
+    )
+    crit_lines.append(
+        f"     duration {run['duration_s']:.0f}s | mode {run.get('dominant_mode','?')} | method {run.get('detection_method','?')}"
+    )
+
+    for i, line in enumerate(crit_lines):
+        ax.text(0.02, 0.65 - i * 0.13, line, fontsize=10, family="monospace",
+                transform=ax.transAxes)
+
+    if reject_reason:
+        ax.text(0.02, 0.05, f"REASON: {reject_reason}", fontsize=9,
+                color="#dc2626", transform=ax.transAxes, family="monospace")
+
+    axes[-2].set_xlabel("time since run start (s)")
+    plt.tight_layout()
+    plt.savefig(out_path, dpi=90, bbox_inches="tight")
+    plt.close(fig)
+
+
+HTML_TEMPLATE = """<!doctype html>
+<html lang="fr">
+<head>
+<meta charset="utf-8">
+<title>02 Runs Diagnostic — {mission}</title>
+<style>
+body {{ font-family: -apple-system, system-ui, sans-serif; background: #0f172a; color: #e2e8f0; margin: 0; padding: 20px; }}
+h1 {{ color: #38bdf8; margin: 0 0 4px 0; }}
+.subtitle {{ color: #94a3b8; margin-bottom: 20px; font-size: 14px; }}
+.params {{ background: #1e293b; padding: 10px 14px; border-radius: 6px; margin-bottom: 24px; font-family: monospace; font-size: 12px; color: #cbd5e1; }}
+.grid {{ display: grid; grid-template-columns: repeat(auto-fit, minmax(560px, 1fr)); gap: 20px; }}
+.card {{ background: #1e293b; border-radius: 8px; padding: 12px; border-left: 6px solid #475569; }}
+.card.ok {{ border-left-color: #16a34a; }}
+.card.ko {{ border-left-color: #dc2626; }}
+.card h3 {{ margin: 0 0 6px 0; font-size: 16px; }}
+.card h3.ok {{ color: #4ade80; }}
+.card h3.ko {{ color: #f87171; }}
+.card img {{ width: 100%; height: auto; border-radius: 4px; }}
+.meta {{ color: #94a3b8; font-size: 12px; margin: 4px 0 8px 0; font-family: monospace; }}
+.reason {{ color: #fca5a5; font-size: 12px; margin-top: 6px; font-family: monospace; }}
+.summary {{ display: flex; gap: 16px; margin-bottom: 20px; }}
+.pill {{ background: #1e293b; padding: 8px 14px; border-radius: 999px; font-size: 13px; }}
+.pill.ok {{ color: #4ade80; }}
+.pill.ko {{ color: #f87171; }}
+</style>
+</head>
+<body>
+<h1>02 Runs Diagnostic — {mission}</h1>
+<div class="subtitle">Generated {generated_at} · filter v5 strict</div>
+<div class="summary">
+  <div class="pill ok">OK: {n_ok}</div>
+  <div class="pill ko">Rejected: {n_ko}</div>
+  <div class="pill">Total candidates: {n_total}</div>
+</div>
+<div class="params">{params}</div>
+<div class="grid">
+{cards}
+</div>
+</body>
+</html>
+"""
+
+CARD_TEMPLATE = """<div class="card {cls}">
+  <h3 class="{cls}">{run_id} — {status}</h3>
+  <div class="meta">duration={duration}s | max_depth={max_depth}m | sustained={sustained}s | pct_near={pct}% | mode={mode}</div>
+  <img src="{png}" alt="{run_id}">
+  {reason_block}
+</div>"""
+
+
+def build_html(mission, filter_params, generated_at, ok_runs, ko_runs, out_dir):
+    cards = []
+    for run, status, reason in [(r, "OK", None) for r in ok_runs] + [(r, "REJECTED", r.get("rejected_reason")) for r in ko_runs]:
+        cls = "ok" if status == "OK" else "ko"
+        reason_block = f'<div class="reason">REASON: {reason}</div>' if reason else ""
+        cards.append(CARD_TEMPLATE.format(
+            cls=cls, run_id=run["run_id"], status=status,
+            duration=f"{run['duration_s']:.0f}",
+            max_depth=run["max_depth_m"],
+            sustained=f"{run['sustained_duration_s']:.0f}",
+            pct=f"{run['pct_near_bottom']:.1f}",
+            mode=run.get("dominant_mode", "?"),
+            png=f"{run['run_id']}.png",
+            reason_block=reason_block,
+        ))
+    html = HTML_TEMPLATE.format(
+        mission=mission,
+        generated_at=generated_at,
+        params=json.dumps(filter_params, indent=2),
+        n_ok=len(ok_runs),
+        n_ko=len(ko_runs),
+        n_total=len(ok_runs) + len(ko_runs),
+        cards="\n".join(cards),
+    )
+    (out_dir / "index.html").write_text(html, encoding="utf-8")
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Stage 02b — runs diagnostic plots")
+    parser.add_argument("--mission", required=True)
+    parser.add_argument("--ssd-base", default="/mnt/ssd")
+    parser.add_argument("--out", default="data/")
+    parser.add_argument("--padding-s", type=float, default=120.0,
+                        help="padding (s) avant/après run pour contexte")
+    args = parser.parse_args()
+
+    mission_dir = Path(args.out) / args.mission
+    runs_json = mission_dir / "02_runs.json"
+    if not runs_json.exists():
+        print(f"[ERROR] {runs_json} missing — run 02_mission_run_detect first", file=sys.stderr)
+        sys.exit(1)
+
+    bags_root = Path(args.ssd_base) / args.mission / "raw_data" / "logs" / "SUB" / "bag"
+    if not bags_root.exists():
+        print(f"[ERROR] bags dir not found: {bags_root}", file=sys.stderr)
+        sys.exit(1)
+
+    data = json.loads(runs_json.read_text())
+    filter_params = data["filter_params"]
+    out_dir = mission_dir / "02_runs_diag"
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    ok_runs = data["all_runs_sorted"]
+    ko_runs = data["all_runs_rejected"]
+    print(f"[stage02b] {len(ok_runs)} OK + {len(ko_runs)} rejected = {len(ok_runs)+len(ko_runs)} runs to plot")
+
+    # Group by AUV → 1 read per AUV bag set covering all runs
+    runs_by_auv = {}
+    for run in ok_runs + ko_runs:
+        # run_id "AUV210_run_00" → AUV210
+        phys = run["run_id"].split("_")[0]
+        runs_by_auv.setdefault(phys, []).append(run)
+
+    pad = args.padding_s
+    for phys_id, runs in runs_by_auv.items():
+        mcap_id = PHYS_TO_MCAP.get(phys_id, phys_id)
+        t_start = min(r["start_epoch"] for r in runs) - pad
+        t_end = max(r["end_epoch"] for r in runs) + pad
+        print(f"  [{phys_id}] reading {mcap_id} bags [{t_start:.0f}..{t_end:.0f}] for {len(runs)} runs")
+        alt, state, hdg = gather_signals_for_auv(bags_root, mcap_id, t_start, t_end)
+        print(f"    {len(alt)} alt pts, {len(state)} state pts, {len(hdg)} hdg pts")
+
+        for run in runs:
+            r_start = run["start_epoch"] - pad
+            r_end = run["end_epoch"] + pad
+            alt_r = [(t, v) for t, v in alt if r_start <= t <= r_end]
+            state_r = [(t, a, m) for t, a, m in state if r_start <= t <= r_end]
+            hdg_r = [(t, v) for t, v in hdg if r_start <= t <= r_end]
+            status = "REJECTED" if run in ko_runs else "OK"
+            reason = run.get("rejected_reason") if status == "REJECTED" else None
+            out_png = out_dir / f"{run['run_id']}.png"
+            plot_run_diag(run, alt_r, state_r, hdg_r, filter_params, status, reason, out_png)
+            print(f"    [{status}] {run['run_id']}.png written")
+
+    # Build index.html + index.json
+    generated_at = datetime.now(timezone.utc).isoformat()
+    index = {
+        "mission": args.mission,
+        "generated_at": generated_at,
+        "filter_params": filter_params,
+        "ok_runs": [r["run_id"] for r in ok_runs],
+        "rejected_runs": [r["run_id"] for r in ko_runs],
+    }
+    (out_dir / "index.json").write_text(json.dumps(index, indent=2))
+    build_html(args.mission, filter_params, generated_at, ok_runs, ko_runs, out_dir)
+    print(f"[stage02b] Done: {out_dir}/index.html")
+
+
+if __name__ == "__main__":
+    main()

pipeline/stages/03b_trim_runs.py

@@ -0,0 +1,228 @@
+#!/usr/bin/env python3
+"""Stage 03b - Trim videos per run (LRV proxies + -c copy, fast).
+
+Inputs:
+  data/<MISSION>/02_runs.json
+  data/<MISSION>/03_video_index.json
+
+Strategy:
+  - Use GoPro LRV proxy files (768x432 H.264 ~720 kbps) instead of 4K HEVC originals.
+  - ffmpeg -c copy per chapter (keyframe-aligned cut) + concat demuxer.
+  - Output: per-run .mp4 + ours_<gp>.mp4 (concat of per-run).
+
+Falls back to MP4 source if matching LRV is missing.
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+from collections import defaultdict
+from datetime import datetime, timezone
+from pathlib import Path
+
+OUT_ROOT = Path("/mnt/ssd/cosma-qc-out/03b_trim_runs")
+
+
+def run_ff(cmd: list[str]) -> None:
+    r = subprocess.run(cmd, capture_output=True, text=True)
+    if r.returncode != 0:
+        sys.stderr.write(" ".join(cmd) + "\n")
+        sys.stderr.write(r.stderr[-3000:] + "\n")
+        raise RuntimeError(f"ffmpeg failed rc={r.returncode}")
+
+
+def lrv_for_chapter(mp4_path: Path) -> Path | None:
+    """Return matching .LRV path if it exists (GoPro low-res proxy)."""
+    name = mp4_path.name
+    if not name.startswith("GX") or not name.upper().endswith(".MP4"):
+        return None
+    lrv_name = "GL" + name[2:-4] + ".LRV"
+    p = mp4_path.parent / lrv_name
+    return p if p.exists() else None
+
+
+def overlap_clips(run_start: float, run_end: float, chapters: list[dict]) -> list[tuple[dict, float, float]]:
+    """Return [(chapter, start_off_s, duration_s)] for chapters overlapping the run."""
+    out = []
+    for ch in sorted(chapters, key=lambda c: c["start_epoch"]):
+        a = max(run_start, ch["start_epoch"])
+        b = min(run_end, ch["end_epoch"])
+        if b - a <= 1.0:
+            continue
+        start_off = max(0.0, run_start - ch["start_epoch"])
+        dur = b - a
+        out.append((ch, start_off, dur))
+    return out
+
+
+def cut_clip(src: Path, start_off: float, duration: float, dst: Path) -> None:
+    """Cut [start_off, start_off+duration] from src using -c copy (keyframe-aligned)."""
+    cmd = [
+        "ffmpeg", "-y", "-loglevel", "error",
+        "-ss", f"{start_off:.3f}",
+        "-i", str(src),
+        "-t", f"{duration:.3f}",
+        "-c", "copy",
+        "-avoid_negative_ts", "make_zero",
+        "-an",
+        str(dst),
+    ]
+    run_ff(cmd)
+
+
+def concat_demux(parts: list[Path], dst: Path) -> None:
+    """Concat parts with ffmpeg concat demuxer (-c copy)."""
+    if not parts:
+        return
+    if len(parts) == 1:
+        shutil.copy2(parts[0], dst)
+        return
+    with tempfile.NamedTemporaryFile("w", suffix=".txt", delete=False) as f:
+        for p in parts:
+            f.write(f"file '{p.resolve()}'\n")
+        listfile = f.name
+    try:
+        cmd = [
+            "ffmpeg", "-y", "-loglevel", "error",
+            "-f", "concat", "-safe", "0",
+            "-i", listfile,
+            "-c", "copy",
+            "-movflags", "+faststart",
+            "-an",
+            str(dst),
+        ]
+        run_ff(cmd)
+    finally:
+        os.unlink(listfile)
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument("--mission", required=True)
+    ap.add_argument("--data-root", default="/home/cosma/cosma-qc/data")
+    ap.add_argument("--skip-existing", action="store_true")
+    ap.add_argument("--prefer-source", choices=["lrv", "mp4"], default="lrv",
+                    help="lrv = use .LRV proxy (default, fast); mp4 = use 4K originals")
+    args = ap.parse_args()
+
+    mission = args.mission
+    data_dir = Path(args.data_root) / mission
+
+    runs = json.loads((data_dir / "02_runs.json").read_text())["runs"]
+    vidx = json.loads((data_dir / "03_video_index.json").read_text())
+    videos = vidx["videos"]
+
+    by_auv_gp: dict[tuple[str, str], list[dict]] = defaultdict(list)
+    for v in videos:
+        by_auv_gp[(v["auv"], v["gp"])].append(v)
+    all_gps = sorted({v["gp"] for v in videos})
+
+    out_dir = OUT_ROOT / mission
+    out_dir.mkdir(parents=True, exist_ok=True)
+    tmp_dir = out_dir / "_tmp"
+    tmp_dir.mkdir(exist_ok=True)
+
+    link = data_dir / "03b_trim_runs"
+    if link.is_symlink():
+        link.unlink()
+    elif link.exists():
+        shutil.rmtree(link)
+    link.symlink_to(out_dir)
+
+    manifest = {
+        "mission": mission,
+        "generated_at": datetime.now(timezone.utc).isoformat(),
+        "output_root": str(out_dir),
+        "source": args.prefer_source,
+        "runs": [],
+        "ours": {},
+    }
+
+    runs_by_chrono = sorted(runs, key=lambda r: r["start_epoch"])
+    ours_parts: dict[str, list[tuple[float, Path, str]]] = defaultdict(list)
+
+    for run in runs_by_chrono:
+        run_id = run["run_id"]
+        auv = run["auv"]
+        r_start = run["start_epoch"]
+        r_end = run["end_epoch"]
+        run_entry = {"run_id": run_id, "auv": auv, "duration_s": run["duration_s"], "outputs": []}
+
+        for gp in all_gps:
+            chapters = by_auv_gp.get((auv, gp), [])
+            if not chapters:
+                continue
+            clips = overlap_clips(r_start, r_end, chapters)
+            if not clips:
+                continue
+
+            out_name = f"{run_id}_{auv}_{gp}.mp4"
+            out_path = out_dir / out_name
+            if args.skip_existing and out_path.exists() and out_path.stat().st_size > 0:
+                print(f"[skip] {out_name}", flush=True)
+            else:
+                # Pick source per chapter
+                resolved: list[tuple[Path, float, float, str]] = []
+                src_tags: list[str] = []
+                for ch, soff, dur in clips:
+                    mp4 = Path(ch["filepath"])
+                    src = mp4
+                    tag = "mp4"
+                    if args.prefer_source == "lrv":
+                        lrv = lrv_for_chapter(mp4)
+                        if lrv:
+                            src = lrv
+                            tag = "lrv"
+                    resolved.append((src, soff, dur, tag))
+                    src_tags.append(tag)
+
+                print(
+                    f"[cut ] {out_name}  chapters={len(resolved)}  src={','.join(src_tags)}",
+                    flush=True,
+                )
+                tmp_parts: list[Path] = []
+                for i, (src, soff, dur, _) in enumerate(resolved):
+                    tp = tmp_dir / f"{run_id}_{auv}_{gp}_p{i:02d}.mp4"
+                    cut_clip(src, soff, dur, tp)
+                    tmp_parts.append(tp)
+                concat_demux(tmp_parts, out_path)
+                for p in tmp_parts:
+                    p.unlink(missing_ok=True)
+
+            sz_mb = round(out_path.stat().st_size / 1024 / 1024, 1)
+            run_entry["outputs"].append({"gp": gp, "file": out_name, "size_mb": sz_mb})
+            ours_parts[gp].append((r_start, out_path, f"{run_id} {auv}"))
+
+        manifest["runs"].append(run_entry)
+
+    for gp, parts in ours_parts.items():
+        parts.sort()
+        ordered_paths = [p for _, p, _ in parts]
+        ours_path = out_dir / f"ours_{gp}.mp4"
+        print(f"[ours] {ours_path.name} <- {len(ordered_paths)} clip(s)", flush=True)
+        concat_demux(ordered_paths, ours_path)
+        sz_mb = round(ours_path.stat().st_size / 1024 / 1024, 1)
+        manifest["ours"][gp] = {
+            "file": ours_path.name,
+            "size_mb": sz_mb,
+            "segments": [lbl for _, _, lbl in parts],
+        }
+
+    (data_dir / "03b_trim_runs.json").write_text(json.dumps(manifest, indent=2))
+    print(f"\n[done] manifest: {data_dir / '03b_trim_runs.json'}", flush=True)
+    print(f"[done] outputs:  {out_dir}", flush=True)
+
+    try:
+        tmp_dir.rmdir()
+    except OSError:
+        pass
+
+
+if __name__ == "__main__":
+    main()