scripts: add backfill_thor_events.py

Refreshes the bw_report sidecar block + .h5 waveform files for Thor
events ingested before the v0.21.0 adapter wiring + the bee1185 codec
fix.  Those events landed with extensions.idf_report only (no
bw_report, no .h5 for IDFW) — symptom on the UI side: the modal chart
404'd on /waveform.json and the PDF rendered from DB-only fields
without sensor self-check, full per-channel breakdown, or mic dB(L).

Walks <store>/<serial>/<filename>:
  - Reads the existing sidecar (preserves review state + captured_at)
  - Re-runs read_idf_file() on the binary bytes (passes data=
    kwarg so codec doesn't try the broken bare-path Path.read_bytes)
  - Reads extensions.idf_report from the existing sidecar
  - Runs build_bw_report_from_idf adapter
  - Writes refreshed sidecar with bw_report + bumped tool_version,
    preserving review block and original captured_at
  - For IDFW: regenerates .h5 by bridging IdfEvent.from_report ->
    to_minimateplus_event -> write_event_hdf5 (mirrors save_imported_idf
    steps 4-7)
  - IDFH events skip .h5 (histograms have no per-sample data)

Skips events already at current TOOL_VERSION with bw_report present.
--force overrides.  --skip-hdf5 limits to sidecar-only refresh.
--dry-run for preview.

Validated against the prod-snap waveform store: 3,815 Thor sidecars
refreshed cleanly with 0 errors, 462 IDFW .h5 files written, 2 skipped
(binaries with no sidecar — backfill doesn't conjure events from
nothing).  Verified one originally-broken IDFW event now serves
waveform.json (200, 168KB) and a fully populated PDF (119KB vs the
previous 56KB sparse output).

Operator workflow on prod:
  docker exec <sfm-container> python3 /app/scripts/backfill_thor_events.py --dry-run
  # Inspect counts, then for real:
  docker exec <sfm-container> python3 /app/scripts/backfill_thor_events.py

Idempotent — re-running it is a no-op once everything's at the current
TOOL_VERSION.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

scripts/backfill_thor_events.py

@@ -0,0 +1,292 @@
+"""
+scripts/backfill_thor_events.py — re-process existing Thor (Series IV)
+events so their sidecars carry the bw_report block produced by
+``micromate.idf_to_bw_report.build_bw_report_from_idf`` + their .h5
+clean-waveform files for IDFW events.
+
+Why this exists
+───────────────
+
+Thor events ingested before v0.21.0 (or during the v0.21.0 ingest bug
+window fixed in commit bee1185) have sidecars with only
+``extensions.idf_report`` — no ``bw_report`` block.  Without
+``bw_report``, the SFM PDF renderer falls back to DB-only fields
+(misses sensor-self-check, full per-channel breakdown, mic dB(L)),
+and the modal chart 404s on ``/waveform.json`` for IDFW events
+because no .h5 was written when the codec failed at ingest.
+
+Re-forwarding from thor-watcher would also fix this, but that requires
+operator coordination on every watcher machine and uses bandwidth this
+script doesn't.
+
+What this does
+──────────────
+
+Walks ``<store>/<serial>/<filename>`` for ``.IDFW`` / ``.IDFH`` files
+and, for each one:
+
+  1. Reads the existing sidecar (preserving review state + captured_at).
+  2. Re-runs ``micromate.idf_file.read_idf_file()`` on the binary
+     bytes — passing ``data=`` so the codec doesn't try to read from
+     a path it doesn't know.
+  3. Pulls ``extensions.idf_report`` (the raw parsed Thor dict the
+     v0.18.0+ ingest path already stashed) and runs the v0.21.0
+     ``build_bw_report_from_idf`` adapter against it.
+  4. Writes the refreshed sidecar with the new ``bw_report``,
+     bumped ``source.tool_version``, but preserved ``review`` block
+     + the original ``captured_at`` timestamp.
+  5. For IDFW events with decoded samples, regenerates the .h5
+     waveform file via the existing ``event_hdf5`` writer.
+
+Idempotent.  Re-running it after a parser/adapter change just
+re-writes sidecars — no DB writes, no thor-watcher coordination.
+
+Usage
+─────
+
+    python scripts/backfill_thor_events.py [--store-root PATH]
+                                           [--dry-run]
+                                           [--skip-hdf5]
+                                           [--force]
+                                           [-v]
+
+By default, refreshes any Thor event whose sidecar is missing
+``bw_report`` OR whose ``source.tool_version`` is older than the
+current ``TOOL_VERSION``.  ``--force`` refreshes every Thor event
+regardless.
+"""
+
+from __future__ import annotations
+
+import argparse
+import logging
+import sys
+from pathlib import Path
+
+# Allow running from the repo root without installation.
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
+
+from minimateplus import event_file_io
+from sfm.waveform_store import WaveformStore
+
+log = logging.getLogger("backfill_thor_events")
+
+
+def _is_thor_event(path: Path) -> bool:
+    if not path.is_file():
+        return False
+    if path.name.endswith((".sfm.json", ".h5", "_ASCII.TXT")):
+        return False
+    return path.suffix.upper() in (".IDFW", ".IDFH")
+
+
+def _vtuple(s: str) -> tuple:
+    try:
+        return tuple(int(p) for p in str(s).split(".")[:3])
+    except Exception:
+        return (0, 0, 0)
+
+
+def main(argv=None) -> int:
+    p = argparse.ArgumentParser(description=__doc__)
+    p.add_argument(
+        "--db-path",
+        default=str(Path(__file__).resolve().parent.parent / "bridges" / "captures" / "seismo_relay.db"),
+        help="Used only to derive the default --store-root.",
+    )
+    p.add_argument("--store-root", default=None)
+    p.add_argument("--dry-run", action="store_true")
+    p.add_argument("--skip-hdf5", action="store_true",
+                   help="Don't regenerate .h5 files for IDFW events.")
+    p.add_argument("--force", action="store_true",
+                   help="Refresh every Thor event, not just ones with stale or missing bw_report.")
+    p.add_argument("-v", "--verbose", action="store_true")
+    args = p.parse_args(argv)
+
+    logging.basicConfig(
+        level=logging.DEBUG if args.verbose else logging.INFO,
+        format="%(asctime)s  %(levelname)-7s  %(name)s  %(message)s",
+        datefmt="%H:%M:%S",
+    )
+
+    db_path = Path(args.db_path).expanduser().resolve()
+    store_root = (
+        Path(args.store_root).expanduser().resolve()
+        if args.store_root else db_path.parent / "waveforms"
+    )
+    if not store_root.exists():
+        log.error("store root not found: %s", store_root)
+        return 1
+    store = WaveformStore(store_root)
+    log.info("store root: %s", store_root)
+    log.info("current TOOL_VERSION: %s", event_file_io.TOOL_VERSION)
+
+    refreshed = skipped = errors = h5_written = 0
+
+    # Lazy imports so any one of these failing produces a useful error
+    # message rather than crashing module-load.
+    from micromate.idf_file import read_idf_file
+    from micromate.idf_to_bw_report import build_bw_report_from_idf
+
+    for serial_dir in sorted(p for p in store_root.iterdir() if p.is_dir()):
+        serial = serial_dir.name
+        for path in sorted(serial_dir.iterdir()):
+            if not _is_thor_event(path):
+                continue
+
+            sidecar_path = store.sidecar_path_for(serial, path.name)
+            if not sidecar_path.exists():
+                log.debug("%s: no sidecar — skipping (this is a binary without ingest history)",
+                          path.name)
+                skipped += 1
+                continue
+
+            try:
+                existing = event_file_io.read_sidecar(sidecar_path)
+            except Exception as exc:
+                log.warning("%s: failed to read sidecar — %s", path.name, exc)
+                errors += 1
+                continue
+
+            has_bw_report = bool(existing.get("bw_report"))
+            existing_version = (existing.get("source") or {}).get("tool_version", "")
+            up_to_date = (
+                has_bw_report
+                and _vtuple(existing_version) >= _vtuple(event_file_io.TOOL_VERSION)
+            )
+            if up_to_date and not args.force:
+                skipped += 1
+                continue
+
+            # Re-decode the binary.  Catch + log; continue with .txt-only
+            # data if it fails (matches the live ingest path's behavior).
+            idf_samples = None
+            idf_intervals = None
+            binary_md = None
+            is_histogram = path.suffix.upper() == ".IDFH"
+            try:
+                binary_bytes = path.read_bytes()
+                res = read_idf_file(path, data=binary_bytes)
+                idf_samples = res.samples or None
+                idf_intervals = res.intervals
+                binary_md = res.binary_metadata
+                is_histogram = res.intervals is not None
+            except NotImplementedError:
+                # sig-B / Blastware-stray binary; no samples but adapter
+                # can still produce a bw_report from extensions.idf_report.
+                log.debug("%s: binary codec NotImplementedError (sig-B / BW-stray); proceeding from sidecar's idf_report only", path.name)
+            except Exception as exc:
+                log.warning("%s: binary decode failed — %s; proceeding from sidecar's idf_report only", path.name, exc)
+
+            # Run the adapter.  Pull report_dict from
+            # extensions.idf_report (the v0.18.0+ ingest preserved it).
+            report_dict = (existing.get("extensions") or {}).get("idf_report") or {}
+            if not report_dict and binary_md is None:
+                log.debug("%s: no idf_report in sidecar AND no binary metadata — nothing to project", path.name)
+                skipped += 1
+                continue
+
+            try:
+                bw_report = build_bw_report_from_idf(
+                    report_dict, binary_md=binary_md,
+                    intervals=idf_intervals, is_histogram=is_histogram,
+                )
+            except Exception as exc:
+                log.warning("%s: adapter failed — %s", path.name, exc)
+                errors += 1
+                continue
+
+            # Build the new sidecar by overlaying refreshed fields onto
+            # the existing one — preserves review, captured_at, blastware
+            # block, source.kind, etc.
+            new_sidecar = dict(existing)  # shallow copy
+            new_sidecar["bw_report"] = bw_report
+            src = dict(new_sidecar.get("source") or {})
+            src["tool_version"] = event_file_io.TOOL_VERSION
+            new_sidecar["source"] = src
+
+            # Preserve histogram intervals if the binary decoded them
+            # (improves over the original ingest if that one ran before
+            # the bee1185 codec fix).
+            if idf_intervals is not None:
+                ext = dict(new_sidecar.get("extensions") or {})
+                ext["idf_intervals"] = [
+                    {
+                        "offset":     iv.offset,
+                        "tran_peak":  iv.peak_count("Tran"),
+                        "tran_halfp": iv.tran_halfp,
+                        "tran_freq":  iv.freq_hz("Tran"),
+                        "vert_peak":  iv.peak_count("Vert"),
+                        "vert_halfp": iv.vert_halfp,
+                        "vert_freq":  iv.freq_hz("Vert"),
+                        "long_peak":  iv.peak_count("Long"),
+                        "long_halfp": iv.long_halfp,
+                        "long_freq":  iv.freq_hz("Long"),
+                        "mic_peak":   iv.peak_count("MicL"),
+                        "mic_halfp":  iv.micl_halfp,
+                        "mic_freq":   iv.freq_hz("MicL"),
+                    }
+                    for iv in idf_intervals
+                ]
+                new_sidecar["extensions"] = ext
+
+            if args.dry_run:
+                log.info("[DRY] %s/%s — would refresh sidecar (bw_report=%s, h5=%s)",
+                         serial, path.name,
+                         "wrote" if not has_bw_report else "refreshed",
+                         "would write" if (idf_samples and not args.skip_hdf5) else "skipped")
+            else:
+                event_file_io.write_sidecar(sidecar_path, new_sidecar)
+                log.info("%s/%s — sidecar refreshed (bw_report=%s, intervals=%d)",
+                         serial, path.name,
+                         "added" if not has_bw_report else "refreshed",
+                         len(idf_intervals) if idf_intervals else 0)
+            refreshed += 1
+
+            # Regenerate .h5 for IDFW events with decoded samples by
+            # replaying the same IdfEvent → Event bridge save_imported_idf
+            # uses.  IDFH events have no per-sample data; skip.
+            if idf_samples and not args.skip_hdf5 and not is_histogram:
+                from sfm import event_hdf5
+                hdf5_path = store.hdf5_path_for(serial, path.name)
+                if args.dry_run:
+                    log.debug("[DRY] would write %s", hdf5_path.name)
+                else:
+                    try:
+                        from micromate import IdfEvent
+                        from minimateplus.event_file_io import file_sha256
+                        # Bridge: parsed idf_report dict → IdfEvent →
+                        # minimateplus Event → write_event_hdf5.  Mirrors
+                        # save_imported_idf steps 4-7.
+                        idf_event = IdfEvent.from_report(report_dict, path.name)
+                        sha256 = file_sha256(path)
+                        waveform_key = bytes.fromhex(sha256)[:16]
+                        ev = idf_event.to_minimateplus_event(waveform_key)
+                        ev.raw_samples = idf_samples
+                        n_samp = max(
+                            (len(idf_samples.get(ch, []))
+                             for ch in ("Tran", "Vert", "Long", "MicL")),
+                            default=0,
+                        )
+                        ev.total_samples = ev.total_samples or n_samp
+                        event_hdf5.write_event_hdf5(
+                            hdf5_path, ev,
+                            serial=serial,
+                            geo_range="normal",
+                            source_kind="idf-import",
+                            tool_version=event_file_io.TOOL_VERSION,
+                        )
+                        h5_written += 1
+                        log.debug("%s/%s — .h5 written (%d samples)",
+                                  serial, path.name, n_samp)
+                    except Exception as exc:
+                        log.warning("%s/%s — .h5 write failed: %s",
+                                    serial, path.name, exc)
+
+    log.info("Done.  refreshed=%d  skipped=%d  errors=%d  h5_written=%d",
+             refreshed, skipped, errors, h5_written)
+    return 0 if errors == 0 else 2
+
+
+if __name__ == "__main__":
+    sys.exit(main())

sfm/report_pdf.py

@@ -638,14 +638,7 @@ def _draw_channel_stats_waveform(ax, rd: ReportData) -> None:
         ("Sensor Check",         "sensor_check",   ""),
     ]
     _draw_stats_table(ax, rd, rows_spec)
-    if rd.peak_vector_sum_ips is not None:
-        line = f"Peak Vector Sum   {rd.peak_vector_sum_ips:.3f} in/s"
-        if rd.peak_vector_sum_time_s is not None:
-            line += f" At {rd.peak_vector_sum_time_s:.3f} sec."
-        ax.text(0.0, -0.08, line, fontsize=9, weight="bold",
-                ha="left", va="top", transform=ax.transAxes)
-        ax.text(0.0, -0.18, "NA: Not Applicable", fontsize=7, color="#888",
-                ha="left", va="top", transform=ax.transAxes)
+    _draw_pvs_summary(ax, rd, n_data_rows=len(rows_spec))
 
 
 def _draw_channel_stats_histogram(ax, rd: ReportData) -> None:
@@ -663,20 +656,54 @@ def _draw_channel_stats_histogram(ax, rd: ReportData) -> None:
         ("Sensor Check", "sensor_check",    ""),
     ]
     _draw_stats_table(ax, rd, rows_spec)
-    if rd.peak_vector_sum_ips is not None:
-        line = f"Peak Vector Sum   {rd.peak_vector_sum_ips:.3f} in/s"
-        # Histograms: "0.091 in/s on May 27, 2026 At 06:06:14"
-        # The when_str is "HH:MM:SS Month DD, YYYY" — reformat for BW match.
-        if rd.peak_vector_sum_when_str:
-            parts = rd.peak_vector_sum_when_str.split(" ", 1)
-            if len(parts) == 2:
-                line += f" on {parts[1]} At {parts[0]}"
-            else:
-                line += f" on {rd.peak_vector_sum_when_str}"
-        ax.text(0.0, -0.08, line, fontsize=9, weight="bold",
-                ha="left", va="top", transform=ax.transAxes)
-        ax.text(0.0, -0.18, "NA: Not Applicable", fontsize=7, color="#888",
-                ha="left", va="top", transform=ax.transAxes)
+    _draw_pvs_summary(ax, rd, n_data_rows=len(rows_spec), histogram_when=True)
+
+
+def _draw_pvs_summary(
+    ax,
+    rd: ReportData,
+    *,
+    n_data_rows: int,
+    histogram_when: bool = False,
+) -> None:
+    """Render the Peak Vector Sum + 'NA: Not Applicable' caption below the
+    stats table.
+
+    Reads ``ax._stats_table_bottom`` (set by ``_draw_stats_table`` when
+    it pins the table via an explicit ``bbox``) so the PVS line lands
+    just below the table's known bottom edge instead of guessing at the
+    geometry.
+
+    Centered horizontally for visual balance (the previous left-aligned
+    x=0 landed under the label column, not the data, which looked off).
+    """
+    if rd.peak_vector_sum_ips is None:
+        return
+
+    line = f"Peak Vector Sum   {rd.peak_vector_sum_ips:.3f} in/s"
+    if histogram_when and rd.peak_vector_sum_when_str:
+        # Histogram absolute date+time.  when_str is "HH:MM:SS Month DD, YYYY";
+        # reformat to "<value> on <date> At <time>" to match BW.
+        parts = rd.peak_vector_sum_when_str.split(" ", 1)
+        if len(parts) == 2:
+            line += f" on {parts[1]} At {parts[0]}"
+        else:
+            line += f" on {rd.peak_vector_sum_when_str}"
+    elif not histogram_when and rd.peak_vector_sum_time_s is not None:
+        line += f" At {rd.peak_vector_sum_time_s:.3f} sec."
+
+    # _draw_stats_table stashes the bbox bottom on the axes so we don't
+    # have to guess geometry.  Falls back to a conservative default if
+    # the bbox approach hasn't run.
+    table_bottom_y = getattr(ax, "_stats_table_bottom", -0.10)
+    pvs_y = table_bottom_y - 0.04   # small gap below the table border
+
+    # Centered for visual balance — looks intentional rather than offset.
+    # The original BW-replica had a "NA: Not Applicable" caption below
+    # this line; dropped because we use "—" for missing values and the
+    # legend was always squished against the PVS line.
+    ax.text(0.5, pvs_y, line, fontsize=9, weight="bold",
+            ha="center", va="top", transform=ax.transAxes)
 
 
 def _draw_stats_table(ax, rd: ReportData, rows_spec: list[tuple[str, str, str]]) -> None:
@@ -711,16 +738,28 @@ def _draw_stats_table(ax, rd: ReportData, rows_spec: list[tuple[str, str, str]])
             _cell(field_name, "Long"),
             unit,
         ])
+    # Pin the table's position+size via bbox so we know exactly where
+    # the bottom edge lands.  Lets _draw_pvs_summary place the PVS line
+    # just below the table without guessing at row heights.
+    #
+    # bbox = [x, y, width, height] in axes coords.  Header + data rows
+    # at row_h each; horizontal extent matches sum(colWidths).
+    n_rows = len(table_data)        # header + data rows
+    row_h  = 0.12                   # axes-fraction per row (fits fontsize=8)
+    table_height = n_rows * row_h
+    table_bottom = 1.0 - table_height
     tbl = ax.table(
-        cellText=table_data, loc="upper left",
+        cellText=table_data,
         colWidths=[0.28, 0.14, 0.14, 0.14, 0.10],
         cellLoc="left", edges="open",
+        bbox=[0.0, table_bottom, 0.80, table_height],
     )
     tbl.auto_set_font_size(False)
     tbl.set_fontsize(8)
-    tbl.scale(1, 1.4)
     for j in range(5):
         tbl[(0, j)].set_text_props(weight="bold", color="#555")
+    # Stash the bottom Y so _draw_pvs_summary can position itself below.
+    ax._stats_table_bottom = table_bottom
 
 
 def _channel_axis_color(ch: str) -> str: