Merge dev-per-angle-background: one background per angle in the data block

KNOWN_ISSUES.md

@@ -48,3 +48,19 @@ rig, check whether the camera apps run without the shim; if they do, delete
 `lib/ueye_loader.{c,so}`. Either way, record in SETUP.md where
 `libueye_api64.so.3.82` came from (IDS SDK version) and how the loader is
 meant to be used.
+
+## Per-angle background: trigger round trip mid-scan
+
+Every angle now captures its own background, so the scope switches from the
+scan-time logic-AND trigger back to the single-record edge trigger and
+returns to it once per angle (`core/scope_sras.py`:
+`configure_background_trigger` → `capture_background` →
+`configure_scan_trigger`). Before this, that transition happened once per
+scan, with the stage idle and nothing depending on how long it took.
+
+**Bench check:** run a multi-angle scan and watch the first row after each
+background. If frames go missing at the start of an angle, the 0.2 s settle
+in `configure_scan_trigger` is not enough for FastFrame to re-arm after an
+AVERAGE-mode sequence, and the row-packing warning ("N frames acquired, M
+expected") will say so in the log. Raise the settle rather than the ramp
+buffer — the stage geometry is not what changed.

README.md

@@ -12,10 +12,12 @@ scanengine-3 is a unified platform for scanning acoustic microscopy and precisio
 - **Laser Systems**: Helios pulsed laser and Genesis CW laser control
 - **Data Acquisition**: Tektronix oscilloscope integration with fast-frame support
 - **Scan Planning**: Automated raster scan generation and execution
+- **Per-Angle Background**: every angle opens with its own background
+  capture (Genesis off, Helios on), stored ahead of that angle's data
 - **Angle Inspection**: Park the rig at random points across a plan's angles
   to check the SAW response on the scope before committing to a long scan
 - **SAW Quality Check**: Acquire one row per angle — the row-wise middle of
-  the ROI — as a v10 `.sras`, then compare every angle's SAW frequency on one
+  the ROI — as a v11 `.sras`, then compare every angle's SAW frequency on one
   graph to judge the alignment before a full run
 - **Real-time Monitoring**: Live status updates and progress tracking
 
@@ -65,7 +67,7 @@ scanengine-3/
 │   ├── angle_inspect.py           # AngleInspector — park on a point per angle
 │   ├── saw_check.py               # Middle-row SAW check: plan + alignment read-out
 │   ├── rotation.py                # GR rotation axis settings + moves
-│   ├── sras_format.py             # v6/v10 .sras writer/reader (memory-mapped)
+│   ├── sras_format.py             # v7/v11 .sras writer, v6/v10 reader (mmap)
 │   ├── sras_analysis.py           # Image reducers + SAW matched filter
 │   └── config.py                  # ScanDefaults ⇄ aui_defaults.json
 │
@@ -98,7 +100,7 @@ scanengine-3/
 ├── sc3-aui-*.ui                   # Qt Designer files loaded at runtime
 │
 ├── tests/                         # pytest suite
-│   ├── golden/                    # v6 .sras + geometry fixtures
+│   ├── golden/                    # legacy v6 .sras + geometry fixtures
 │   ├── fakes.py                   # Recording fake stage/scope/rotator
 │   └── test_*.py
 │
@@ -220,7 +222,7 @@ print(f"wrote {result.rows_written} rows to {result.path}")
 ### Running a SAW quality check
 
 Same engine, same hardware sequence — the plan is reduced to one row per
-angle and the result is tagged v10 so the viewer knows it is a check rather
+angle and the result is tagged v11 so the viewer knows it is a check rather
 than a scan cut short:
 
 ```python

core/saw_check.py

@@ -6,7 +6,7 @@ without the other:
 
 *Acquisition* — ``middle_row_plan`` reduces a full ScanPlan to a single row
 per angle, the row-wise middle of the ROI.  ScanEngine runs the result
-exactly like any other scan and writes it as a v10 .sras file
+exactly like any other scan and writes it as a v11 .sras file
 (``sras_format.VERSION_SAW_CHECK``), so a check costs one row-time per angle
 instead of the hours a full multi-angle scan takes.
 
@@ -55,7 +55,7 @@ def middle_row_plan(plan: ScanPlan) -> ScanPlan:
 
     An even row count has no exact middle; the upper of the two central rows
     is taken (``n_rows // 2``), which is also the row the viewer picks when it
-    reads the middle row out of a full v6 scan.
+    reads the middle row out of a full scan.
     """
     if plan.n_angles == 0:
         raise ScanGeometryError("Cannot build a SAW check from a plan with no angles")
@@ -181,18 +181,24 @@ class AlignmentSummary:
 
 
 def frequency_traces(sras: SrasFile, *, dc_threshold_mv: float = 0.0,
-                     background: np.ndarray | None = None,
+                     subtract_background: bool = False,
                      gate_start_ns: float | None = None,
                      gate_end_ns: float | None = None,
                      calib: ChannelCalibration | None = None,
                      on_progress=lambda done, total: None) -> list[AngleTrace]:
     """Peak SAW frequency along the middle row of every angle in ``sras``.
 
-    Works on a v10 check (one row per angle, so the middle row is the only
+    Works on a v11 check (one row per angle, so the middle row is the only
-    row) and on a full v6 scan alike — the same middle row the check would
+    row) and on a full scan alike — the same middle row the check would
     have acquired is pulled out of the scan, which is what lets a finished
     scan be re-examined with the check's own read-out.
 
+    ``subtract_background`` takes each angle's own background out of its
+    frames (v6/v10 files have only the one, which every angle then shares).
+    Doing it per angle is the point of the per-angle capture: comparing
+    angles is exactly what this read-out is for, so they must not be
+    referenced against one background taken at whichever angle came first.
+
     Angles with nothing on disk (an aborted file) are skipped rather than
     reported as flat zero.
     """
@@ -210,6 +216,7 @@ def frequency_traces(sras: SrasFile, *, dc_threshold_mv: float = 0.0,
         row = middle_row_index(st.n_rows_available)
         view = sras.load_angle(st.index, n_rows=st.n_rows_available)[row:row + 1]
 
+        background = sras.background_array(st.index) if subtract_background else None
         img = compute_rf_image(view, calib, freq_axis, dc_threshold_mv,
                                background=background,
                                gate_start_ns=gate_start_ns, gate_end_ns=gate_end_ns,

core/scan_engine.py

@@ -18,7 +18,10 @@ from typing import Callable
 from core import scope_burst, scope_sras
 from core.rotation import RotationAxis
 from core.scan_geometry import ScanPlan, validate_plan
-from core.sras_format import SCAN_CHANNELS, VERSION, create_scan_file
+from core.sras_format import (
+    BG_LEN_SIZE, SCAN_CHANNELS, VERSION, create_scan_file,
+    write_background_block,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -42,8 +45,15 @@ class ScanAborted(Exception):
 
 @dataclass
 class ResumeTarget:
-    """One angle selected for (re)acquisition in an existing file."""
+    """One angle selected for (re)acquisition in an existing file.
+
+    ``bg_offset`` is where the angle's background block starts and
+    ``data_offset`` where its rows do; the gap between them is the room the
+    file already has for a background, which a re-acquired angle must fill
+    exactly or every row behind it would shift.
+    """
     angle_idx: int
+    bg_offset: int
     data_offset: int
     n_rows: int
     angle_deg: float
@@ -280,27 +290,14 @@ class ScanEngine:
 
         if self._resume is None:
             self._preambles = scope_sras.read_preambles(self._scope, SCAN_CHANNELS)
-            self._prompt(
-                "Background Capture",
-                "Please ensure the Helios laser is ON and the Genesis laser is OFF,\n"
-                "then click OK to capture the background waveform."
-            )
-            self._background = scope_sras.capture_background(
-                self._scope, should_abort=self._abort.is_set,
-                on_status=self._cb.on_status)
-            self._prompt(
-                "Begin Scanning",
-                "Background captured successfully.\n\n"
-                "Please ensure the Genesis laser is back ON,\n"
-                "then click OK to begin scanning."
-            )
         else:
-            # Resuming: the file's existing background waveform and channel
+            # Resuming: the file's channel preambles are reused as-is (the
-            # preambles are reused as-is (the format has no way to replace
+            # format has no way to replace them without rewriting the whole
-            # them without rewriting the whole file), so background capture is
+            # file).  Each re-acquired angle still captures its own fresh
-            # skipped.  Sanity-check that this scope still produces the same
+            # background, which is rewritten in place over the old one.
-            # record length the file was started with — a mismatch would
+            # Sanity-check that this scope still produces the same record
-            # silently corrupt the ragged per-row byte layout on append.
+            # length the file was started with — a mismatch would silently
+            # corrupt the ragged per-row byte layout on append.
             if samples_per_frame != self._resume.samples_per_frame:
                 raise RuntimeError(
                     f"Oscilloscope record length ({samples_per_frame} samples/frame) "
@@ -314,8 +311,8 @@ class ScanEngine:
                 f"angle(s) {targets} of {self._plan.n_angles}.\n\n"
                 "Please re-home the GR axis to 0° before continuing — the scan "
                 "will rotate it directly from angle to angle before scanning resumes.\n\n"
-                "Please ensure the Genesis laser is ON,\n"
+                "Each angle begins with its own background capture, so you will "
-                "then click OK to continue scanning."
+                "be asked to switch the Genesis laser off and on again per angle."
             )
 
         scope_sras.configure_scan_trigger(self._scope)
@@ -341,7 +338,7 @@ class ScanEngine:
             return open(self._resume.path, "r+b")
         return create_scan_file(
             self._out_path, self._plan, samples_per_frame,
-            scope_sras.SAMPLE_RATE_HZ, self._preambles, self._background,
+            scope_sras.SAMPLE_RATE_HZ, self._preambles,
             version=self._file_version,
         )
 
@@ -363,11 +360,12 @@ class ScanEngine:
                 continue    # not selected for (re)acquisition
             self._pause_point()
 
-            if targets_by_ai is not None:
+            target = None if targets_by_ai is None else targets_by_ai[ai]
+            if target is not None:
                 # Interior angles may already have valid data on either side,
                 # so seek to this angle's fixed offset rather than relying on
                 # the file's current position.
-                scan_file.seek(targets_by_ai[ai].data_offset)
+                scan_file.seek(target.bg_offset)
 
             if self._rotator is not None and self._rotator.is_available:
                 delta = pa.angle_deg - self._rotator.current_deg
@@ -376,6 +374,9 @@ class ScanEngine:
                         f"Rotating GR to {pa.angle_deg:.1f}° (Δ{delta:+.1f}°) …")
                     self._rotator.rotate_to(pa.angle_deg)
 
+            self._write_angle_background(scan_file, ai, n_angles,
+                                         pa.angle_deg, target)
+
             if self._burst_mode:
                 # Burst mode sizes the FastFrame count from the scope's whole
                 # capacity instead (see scope_burst.start_burst), so there is
@@ -391,6 +392,49 @@ class ScanEngine:
 
             result.angles_acquired.append(ai)
 
+    def _write_angle_background(self, scan_file, ai: int, n_angles: int,
+                                angle_deg: float, target: ResumeTarget | None):
+        """Capture this angle's background and write it ahead of its rows.
+
+        The Genesis laser has to be off for the capture and back on for the
+        scan, so every angle costs two operator prompts and one averaged
+        record.  That buys a background taken minutes from the data it will
+        be subtracted from, instead of one taken hours earlier at angle 1.
+
+        On resume the block is overwritten in place, so it has to be exactly
+        as long as the one already there — anything else would shift every
+        row behind it.  Checked before the write, not after.
+        """
+        scope = self._scope
+        scope_sras.configure_background_trigger(scope)
+        self._prompt(
+            f"Background Capture — Angle {ai + 1}/{n_angles}",
+            f"Angle {ai + 1} of {n_angles} ({angle_deg:.1f}°) starts with its "
+            "own background capture.\n\n"
+            "Please switch the Genesis laser OFF — leave the Helios laser ON —\n"
+            "then click OK to capture the background waveform."
+        )
+        background = scope_sras.capture_background(
+            scope, should_abort=self._abort.is_set, on_status=self._cb.on_status)
+        self._prompt(
+            f"Begin Angle {ai + 1}/{n_angles}",
+            "Background captured successfully.\n\n"
+            "Please switch the Genesis laser back ON,\n"
+            f"then click OK to scan angle {ai + 1} of {n_angles}."
+        )
+        scope_sras.configure_scan_trigger(scope)
+
+        if target is not None:
+            room = target.data_offset - target.bg_offset
+            if BG_LEN_SIZE + len(background) != room:
+                raise RuntimeError(
+                    f"Angle {ai + 1}: the new background block is "
+                    f"{BG_LEN_SIZE + len(background)} bytes but the file has room "
+                    f"for {room} — writing it would shift every row behind it, "
+                    "so the scan stops here."
+                )
+        write_background_block(scan_file, background)
+
     # ── Per-row acquisition (one FastFrame acquisition per row) ───────────────
 
     def _scan_rows_serial(self, scan_file, pa, ai: int, n_angles: int,

core/scan_resume.py

@@ -8,7 +8,7 @@ from __future__ import annotations
 from dataclasses import dataclass, field
 
 from core.scan_engine import ResumeState, ResumeTarget
-from core.sras_format import SrasFile
+from core.sras_format import WRITABLE_VERSIONS, SrasFile
 
 
 @dataclass
@@ -44,8 +44,9 @@ def plan_resume(statuses, selected: set[int]) -> ResumePlan:
         final = set(selected)
 
     targets = [
-        ResumeTarget(angle_idx=s.index, data_offset=s.data_offset,
+        ResumeTarget(angle_idx=s.index, bg_offset=s.bg_offset,
-                     n_rows=s.n_rows, angle_deg=s.angle_deg)
+                     data_offset=s.data_offset, n_rows=s.n_rows,
+                     angle_deg=s.angle_deg)
         for s in statuses if s.index in final
     ]
     return ResumePlan(targets=targets,
@@ -55,9 +56,15 @@ def plan_resume(statuses, selected: set[int]) -> ResumePlan:
 
 def is_compatible(sras: SrasFile, *, velocity: float, laser_freq: float,
                   sample_rate: float, n_channels: int) -> bool:
-    """Whether appending to this file with the current settings is safe."""
+    """Whether appending to this file with the current settings is safe.
+
+    A legacy v6/v10 file is not: it has one background for the whole scan,
+    and every angle this engine acquires writes a background block of its
+    own, which the older layout has no room for.
+    """
     h = sras.header
-    return (h.bytes_per_sample == 1
+    return (sras.version in WRITABLE_VERSIONS
+            and h.bytes_per_sample == 1
             and h.n_channels == n_channels
             and abs(h.velocity - velocity) <= 1e-3
             and abs(h.laser_freq - laser_freq) <= 1e-3

core/scope_sras.py

@@ -51,11 +51,13 @@ def configure_channels(scope, profiles=None) -> None:
         scope.set_channel_bandwidth(ch, p.bandwidth_hz)
 
 
-def configure_acquisition(scope) -> int:
+def configure_background_trigger(scope) -> None:
-    """Program the edge trigger and timebase; returns samples per frame.
+    """Program the edge trigger used for a background capture.
 
-    Edge trigger on the rising edge of CH2 (laser pulse).  FastFrame stays
+    Edge trigger on the rising edge of CH2 (laser pulse), FastFrame off so
-    off here so the background capture runs as a single record.
+    the capture runs as a single record.  Every angle starts with a fresh
+    background, so the scan comes back here between angles from the
+    logic-AND trigger configure_scan_trigger leaves behind.
     """
     scope.write("TRIGger:A:TYPe EDGE")
     scope.set_trigger_source(2)
@@ -64,6 +66,11 @@ def configure_acquisition(scope) -> int:
     scope.set_trigger_mode("NORMAL")       # wait for trigger (don't auto-sweep)
     scope.set_acquire_mode("SAMPLE")
     scope.set_fastframe_state(False)
+
+
+def configure_acquisition(scope) -> int:
+    """Program the edge trigger and timebase; returns samples per frame."""
+    configure_background_trigger(scope)
     # Pin the transfer format instead of inheriting front-panel state — the
     # file header hardcodes bytes_per_sample=1, and a scope left on 2 bytes
     # would corrupt every frame written.

core/sras_format.py

@@ -1,4 +1,5 @@
-"""SRAS binary scan-file format (v6 and v10) — the single implementation.
+"""SRAS binary scan-file format (v7/v11, reading v6/v10 too) — the single
+implementation.
 
 Full byte-level spec: scan_format.md.  Summary:
 
@@ -9,20 +10,33 @@ Full byte-level spec: scan_format.md.  Summary:
     geometry table             n_angles × >ffIH  (x_start x_delta n_frames n_rows)
     row tables (ragged)        per angle: n_rows × >f  (y positions)
     preambles                  n_channels × (>H length + utf-8 WFMOutpre string)
-    background block           >I length + raw int8 CH1 average
+    data block                 per angle: [background][rows]
-    waveform data              angle-major, row-minor, channel-inner:
+                               background = >I length + raw int8 CH1 average
-                               for each angle, for each row, for each channel,
+                               rows       = for each row, for each channel,
                                n_frames × samples_per_frame × bytes_per_sample
 
+Every angle carries its own background: the operator switches the Genesis
+laser off before each angle and the engine averages a fresh CH1 record, so
+the reference a reader subtracts was taken minutes — not hours — from the
+data it is subtracted from.  That is the whole difference between v7 and v6,
+which held a single background for the entire file, ahead of the data block.
+
 Incomplete files are valid: the data block is one contiguous append-only
 stream, so the readable prefix defines a single frontier past which nothing
-has been written yet (see ``SrasFile.angle_status``).
+has been written yet (see ``SrasFile.angle_status``).  Because the background
+blocks are length-prefixed, the per-angle offsets come from a walk of that
+stream at parse time rather than from arithmetic on the geometry table.
 
-Version 10 is the SAW quality check (core.saw_check): byte layout identical
+Version 11 is the SAW quality check (core.saw_check): byte layout identical
-to v6, but every angle declares exactly one row — the row-wise middle of the
+to v7, but every angle declares exactly one row — the row-wise middle of the
 ROI.  The version byte is the whole difference, and it exists so a reader can
 tell a one-row-per-angle check from a full scan that was aborted after its
 first row.  ``create_scan_file`` enforces the one-row rule at write time.
+
+v6 and v10 are the pre-per-angle-background versions of the same two files.
+They are still read (every scan taken before this change is one); nothing
+writes them any more, and a v6 file cannot be resumed into, since appending
+v7 blocks to it would shift its data.
 """
 from __future__ import annotations
 
@@ -37,14 +51,21 @@ import numpy as np
 from core.scan_geometry import AngleGeometry, ScanPlan
 
 MAGIC = b"SRAS"
-VERSION = 6
+VERSION = 7
 # One row per angle, taken from the middle of the ROI — see core.saw_check.
-VERSION_SAW_CHECK = 10
+VERSION_SAW_CHECK = 11
-SUPPORTED_VERSIONS = (VERSION, VERSION_SAW_CHECK)
+# v6/v10: the same two files with one background for the whole scan, written
+# ahead of the data block instead of once per angle.  Read-only.
+LEGACY_VERSIONS = (6, 10)
+WRITABLE_VERSIONS = (VERSION, VERSION_SAW_CHECK)
+SUPPORTED_VERSIONS = tuple(sorted(WRITABLE_VERSIONS + LEGACY_VERSIONS))
+SAW_CHECK_VERSIONS = (10, VERSION_SAW_CHECK)
 HDR_FMT = ">4sBHfffffffIdBB"
 HDR_SIZE = struct.calcsize(HDR_FMT)   # 49 bytes
 GEOM_FMT = ">ffIH"
 GEOM_SIZE = struct.calcsize(GEOM_FMT)  # 14 bytes
+BG_LEN_FMT = ">I"
+BG_LEN_SIZE = struct.calcsize(BG_LEN_FMT)   # 4 bytes
 
 # Oscilloscope channels recorded, in on-disk order.
 SCAN_CHANNELS = [1, 3, 4]
@@ -78,7 +99,8 @@ class AngleStatus:
     angle_deg: float
     n_rows: int              # declared
     row_bytes: int
-    data_offset: int
+    bg_offset: int           # start of this angle's background block
+    data_offset: int         # start of its rows, i.e. just past that block
     n_rows_available: int
     status: str              # STATUS_OK / STATUS_TRUNCATED / STATUS_MISSING
 
@@ -86,33 +108,38 @@ class AngleStatus:
     def complete(self) -> bool:
         return self.status == STATUS_OK
 
+    @property
+    def bg_bytes(self) -> int:
+        """Size of the background block ahead of the rows (0 on v6/v10)."""
+        return self.data_offset - self.bg_offset
+
 
 def create_scan_file(path: Path, plan: ScanPlan, samples_per_frame: int,
                      sample_rate: float, preambles: list[str],
-                     background_waveform: bytes,
                      version: int = VERSION) -> BinaryIO:
     """Create a new .sras file and write the header + tables.
 
     ``version`` selects which kind of file this is — VERSION for a full scan,
     VERSION_SAW_CHECK for a middle-row quality check.  The layout is the same
-    either way; the one-row-per-angle rule that gives v10 its meaning is
+    either way; the one-row-per-angle rule that gives v11 its meaning is
-    checked here, since nothing downstream can recover from a v10 file that
+    checked here, since nothing downstream can recover from a v11 file that
     breaks it.
 
-    Returns an open binary file positioned at the start of the data block;
+    Returns an open binary file positioned at the start of the data block.
-    the caller appends waveform rows and must close it (try/finally).
+    The caller writes each angle as ``write_background_block()`` followed by
+    that angle's rows, and must close the file (try/finally).
     """
-    if version not in SUPPORTED_VERSIONS:
+    if version not in WRITABLE_VERSIONS:
         raise ValueError(
             f"Cannot write SRAS format version {version} "
-            f"(supported: {', '.join(str(v) for v in SUPPORTED_VERSIONS)})"
+            f"(writable: {', '.join(str(v) for v in WRITABLE_VERSIONS)})"
         )
     if version == VERSION_SAW_CHECK:
         bad = [f"{pa.angle_deg:.1f}° has {pa.n_rows}"
                for pa in plan.per_angle if pa.n_rows != 1]
         if bad:
             raise ValueError(
-                "A v10 SAW-check file holds exactly one row per angle, but "
+                "A v11 SAW-check file holds exactly one row per angle, but "
                 + ", ".join(bad) + " — build the plan with "
                 "core.saw_check.middle_row_plan()."
             )
@@ -140,19 +167,33 @@ def create_scan_file(path: Path, plan: ScanPlan, samples_per_frame: int,
         enc = p.encode("utf-8")
         f.write(struct.pack(">H", len(enc)))
         f.write(enc)
-    f.write(struct.pack(">I", len(background_waveform)))
-    f.write(background_waveform)
     return f
 
 
+def write_background_block(f: BinaryIO, waveform: bytes) -> int:
+    """Write one angle's background block; returns the bytes written.
+
+    Every angle's rows are preceded by one of these, so a reader walking the
+    data block knows where that angle's frames start.
+    """
+    f.write(struct.pack(BG_LEN_FMT, len(waveform)))
+    f.write(waveform)
+    return BG_LEN_SIZE + len(waveform)
+
+
 @dataclass
 class SrasFile:
-    """Parsed .sras file (v6 or v10): header, tables, and lazy (memmap) access.
+    """Parsed .sras file (v7/v11, or legacy v6/v10): header, tables, and lazy
+    (memmap) access.
 
-    Parsing reads only the header/tables — never the waveform block — so
+    Parsing reads only the header/tables and the per-angle background blocks
-    opening a multi-GB file is cheap.  ``load_angle``/``load_row`` return
+    — never the waveform block — so opening a multi-GB file is cheap.
-    read-only numpy views backed by a shared mmap; no data is copied until
+    ``load_angle``/``load_row`` return read-only numpy views backed by a
-    the caller computes on it.
+    shared mmap; no data is copied until the caller computes on it.
+
+    ``backgrounds[i]`` is angle *i*'s own background (v7/v11) or the file's
+    single background repeated for every angle (v6/v10), so a reader never
+    has to branch on the version to subtract the right one.
     """
     path: Path
     version: int = field(init=False)
@@ -160,7 +201,7 @@ class SrasFile:
     per_angle: list[AngleGeometry] = field(init=False)
     preambles: list[str] = field(init=False)
     preambles_raw: list[bytes] = field(init=False)
-    background: bytes = field(init=False)
+    backgrounds: list[bytes] = field(init=False)
     data_start_offset: int = field(init=False)
     file_size: int = field(init=False)
 
@@ -215,15 +256,65 @@ class SrasFile:
                 self.preambles_raw.append(f.read(plen))
             self.preambles = [p.decode("utf-8", errors="replace") for p in self.preambles_raw]
 
-            (n_bg,) = struct.unpack(">I", f.read(4))
+            shared_bg = None
-            self.background = f.read(n_bg)
+            if self.is_legacy_layout:
+                # v6/v10: one background for the whole file, ahead of the data.
+                (n_bg,) = struct.unpack(BG_LEN_FMT, f.read(BG_LEN_SIZE))
+                shared_bg = f.read(n_bg)
 
             self.data_start_offset = f.tell()
+            self._walk_data_block(f, shared_bg)
+
+    def _walk_data_block(self, f, shared_bg: bytes | None):
+        """Locate every angle's background block and the rows behind it.
+
+        v7 interleaves a length-prefixed background ahead of each angle's
+        rows, so the offsets are no longer pure arithmetic over the geometry
+        table — the walk reads each prefix as it goes.  Past the frontier of
+        a partial file there is nothing to read, so the remaining offsets are
+        predicted from the block a writer would have produced (a full record),
+        which is exactly where a resumed scan writes.
+        """
+        expected_bg = BG_LEN_SIZE + self.header.samples_per_frame
+        self.backgrounds, self._bg_present = [], []
+        self._bg_offsets, self._data_offsets = [], []
+        cursor = self.data_start_offset
+        for ai, pa in enumerate(self.per_angle):
+            if shared_bg is not None:
+                bg, bg_bytes, present = shared_bg, 0, True
+            else:
+                bg, bg_bytes, present = self._read_background(f, cursor, expected_bg)
+            self.backgrounds.append(bg)
+            self._bg_present.append(present)
+            self._bg_offsets.append(cursor)
+            cursor += bg_bytes
+            self._data_offsets.append(cursor)
+            cursor += self.row_bytes(ai) * pa.n_rows
+
+    def _read_background(self, f, offset: int, expected_bytes: int):
+        """One angle's background block as (waveform, block_bytes, present).
+
+        A block that runs past the end of the file was never written: the
+        walk keeps going with the size a writer would have used, and the
+        angle is reported MISSING.
+        """
+        if offset + BG_LEN_SIZE > self.file_size:
+            return b"", expected_bytes, False
+        f.seek(offset)
+        (n_bg,) = struct.unpack(BG_LEN_FMT, f.read(BG_LEN_SIZE))
+        if offset + BG_LEN_SIZE + n_bg > self.file_size:
+            return b"", expected_bytes, False
+        return f.read(n_bg), BG_LEN_SIZE + n_bg, True
 
     @property
     def is_saw_check(self) -> bool:
-        """True for a v10 middle-row SAW quality check rather than a scan."""
+        """True for a middle-row SAW quality check rather than a scan."""
-        return self.version == VERSION_SAW_CHECK
+        return self.version in SAW_CHECK_VERSIONS
+
+    @property
+    def is_legacy_layout(self) -> bool:
+        """True for v6/v10: one background for the file, not one per angle."""
+        return self.version in LEGACY_VERSIONS
 
     # ── Frontier / truncation analysis ───────────────────────────────────────
 
@@ -237,40 +328,48 @@ class SrasFile:
 
         Because the data is one contiguous append-only stream, once an angle
         is found short every later angle is necessarily absent too — there is
-        a single frontier past which nothing has been written yet.
+        a single frontier past which nothing has been written yet.  An angle
+        whose background block never made it to disk is short by definition,
+        even though no row of it was due yet.
         """
         statuses = []
-        cursor = self.data_start_offset
         frontier_seen = False
         for ai, pa in enumerate(self.per_angle):
             row_bytes = self.row_bytes(ai)
-            data_offset = cursor
+            data_offset = self._data_offsets[ai]
-            if frontier_seen:
+            if frontier_seen or not self._bg_present[ai]:
                 n_rows_available = 0
                 status = STATUS_MISSING
+                frontier_seen = True
             else:
                 declared_bytes = row_bytes * pa.n_rows
-                if row_bytes > 0 and cursor + declared_bytes <= self.file_size:
+                if row_bytes > 0 and data_offset + declared_bytes <= self.file_size:
                     n_rows_available = pa.n_rows
                     status = STATUS_OK
-                    cursor += declared_bytes
                 else:
-                    remaining = max(0, self.file_size - cursor)
+                    remaining = max(0, self.file_size - data_offset)
                     n_rows_available = remaining // row_bytes if row_bytes > 0 else 0
                     status = STATUS_MISSING if n_rows_available == 0 else STATUS_TRUNCATED
                     frontier_seen = True
             statuses.append(AngleStatus(
                 index=ai, angle_deg=pa.angle_deg, n_rows=pa.n_rows,
-                row_bytes=row_bytes, data_offset=data_offset,
+                row_bytes=row_bytes, bg_offset=self._bg_offsets[ai],
+                data_offset=data_offset,
                 n_rows_available=n_rows_available, status=status,
             ))
         return statuses
 
     def angle_data_offset(self, angle_idx: int) -> int:
-        offset = self.data_start_offset
+        """Where angle ``angle_idx``'s rows start (past its background)."""
-        for ai in range(angle_idx):
+        return self._data_offsets[angle_idx]
-            offset += self.row_bytes(ai) * self.per_angle[ai].n_rows
+
-        return offset
+    def angle_block_offset(self, angle_idx: int) -> int:
+        """Where angle ``angle_idx``'s block starts, background included.
+
+        Equal to ``angle_data_offset`` on v6/v10, which have no per-angle
+        background block.
+        """
+        return self._bg_offsets[angle_idx]
 
     # ── Lazy data access ─────────────────────────────────────────────────────
 
@@ -286,6 +385,11 @@ class SrasFile:
     def _dtype(self) -> np.dtype:
         return np.dtype(np.int16 if self.header.bytes_per_sample == 2 else np.int8)
 
+    def background_array(self, angle_idx: int) -> np.ndarray | None:
+        """One angle's background as float32 ADC counts, or None if absent."""
+        bg = np.frombuffer(self.backgrounds[angle_idx], dtype=self._dtype())
+        return bg.astype(np.float32) if bg.size else None
+
     def load_angle(self, angle_idx: int, n_rows: int | None = None) -> np.ndarray:
         """Read-only view of one angle's data block, shape
         (n_rows, n_channels, n_frames, samples_per_frame).

gui/scan_bridge.py

@@ -12,6 +12,7 @@ import traceback
 from PyQt6.QtCore import QObject, pyqtSignal, pyqtSlot
 
 from core.scan_engine import ScanAborted, ScanCallbacks, ScanEngine
+from core.sras_format import VERSION
 
 
 class QtScanController(QObject):
@@ -33,7 +34,7 @@ class QtScanController(QObject):
 
     def __init__(self, stage, scope, rotator, plan, out_path,
                  resume=None, on_scan_active=None, burst_mode=False,
-                 strict_rows=False):
+                 strict_rows=False, file_version=VERSION):
         super().__init__()
         self._prompt_event = threading.Event()
         self._on_scan_active = on_scan_active
@@ -50,7 +51,8 @@ class QtScanController(QObject):
         self._engine = ScanEngine(stage, scope, rotator, plan, out_path,
                                   resume=resume, callbacks=callbacks,
                                   burst_mode=burst_mode,
-                                  strict_rows=strict_rows)
+                                  strict_rows=strict_rows,
+                                  file_version=file_version)
 
     # ── Engine control (called from the GUI thread) ───────────────────────────
 

saw_check_viewer.py

@@ -2,7 +2,7 @@
 """
 SAW Check Viewer — every angle's frequency on one graph.
 
-Opens a v10 middle-row SAW check (written by the main app's "SAW Quality
+Opens a middle-row SAW check (written by the main app's "SAW Quality
 Check") and plots the peak SAW frequency along each angle's row, all angles
 on the same axes.  ``core.saw_check`` explains why that answers an alignment
 question: every angle's middle row crosses the same ROI centre, so the angles
@@ -17,7 +17,7 @@ Two readings share the window:
   * the summary — each angle's median with ±1σ, plotted against angle, plus
     the same numbers per angle in a table.
 
-A full v6 scan opens too: the same middle row is pulled out of it, so a scan
+A full scan opens too: the same middle row is pulled out of it, so a scan
 can be re-examined with the check's own read-out after the fact.
 """
 
@@ -91,14 +91,17 @@ class LoadedCheck:
     def __init__(self, path: Path):
         self.sras = SrasFile(path)
         self.calib = ChannelCalibration.from_preambles(self.sras.preambles)
-        bg = np.frombuffer(self.sras.background, dtype=np.int8)
+        # Each angle carries its own background (v7/v11); the read-out pulls
-        self.background = bg.astype(np.float32) if len(bg) else None
+        # the right one per angle, so the viewer only needs to know whether
+        # there is anything to subtract at all.
+        self.has_background = any(self.sras.background_array(ai) is not None
+                                  for ai in range(self.sras.header.n_angles))
         self.traces = []
         self.summary = None
 
     def describe(self) -> str:
         h = self.sras.header
-        kind = ("v10 SAW check" if self.sras.is_saw_check
+        kind = (f"v{self.sras.version} SAW check" if self.sras.is_saw_check
                 else f"v{self.sras.version} scan — middle row of each angle")
         return (f"{self.sras.path.name}\n{kind}\n"
                 f"{h.n_angles} angle(s) · {h.samples_per_frame} samples/frame · "
@@ -468,10 +471,11 @@ class SawCheckWindow(QMainWindow):
         self._check = check
         self.setWindowTitle(f"SAW Check Viewer — {path.name}")
         self.lbl_file.setText(check.describe())
+        self.chk_bg_sub.setEnabled(check.has_background)
 
         if not check.sras.is_saw_check:
             self.lbl_status.setText(
-                "Not a v10 check — reading the middle row of each angle "
+                "Not a SAW check file — reading the middle row of each angle "
                 "out of this scan instead.")
         else:
             self.lbl_status.setText("")
@@ -504,7 +508,7 @@ class SawCheckWindow(QMainWindow):
         gated = self.chk_gate.isChecked()
         kwargs = dict(
             dc_threshold_mv=self.spin_threshold_mv.value(),
-            background=check.background if self.chk_bg_sub.isChecked() else None,
+            subtract_background=self.chk_bg_sub.isChecked(),
             gate_start_ns=self.spin_gate_start.value() if gated else None,
             gate_end_ns=self.spin_gate_end.value() if gated else None,
             calib=check.calib,

sc3_aui_app.py

@@ -38,7 +38,8 @@ from core.scan_geometry import ScanPlan, EtaEstimator, build_plan, format_eta
 from core.scan_resume import is_compatible, plan_resume
 from core.scope_sras import SAMPLE_RATE_HZ, configure_channels
 from core.sras_format import (
-    SCAN_CHANNELS, VERSION, VERSION_SAW_CHECK, SrasFile, plan_from_header,
+    SCAN_CHANNELS, VERSION, VERSION_SAW_CHECK, WRITABLE_VERSIONS, SrasFile,
+    plan_from_header,
 )
 from gui.jog_panel import (
     BBD_JOG_ACCEL_MM_S2, BBD_JOG_SPEED_MM_S, BBD_JOG_STEP_MM,
@@ -1369,7 +1370,9 @@ class MainWindow(QMainWindow):
             self, "SAW Quality Check",
             f"Acquire the middle row of the ROI at {check_plan.n_angles} angle(s)?\n\n"
             f"{rows}\n\n"
-            f"Save → {out_path.name}{overwrite}",
+            "Each angle starts with its own background capture, so you will be "
+            "asked to switch the Genesis laser off and back on at every angle."
+            f"\n\nSave → {out_path.name}{overwrite}",
             QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
         )
         if reply != QMessageBox.StandardButton.Yes:
@@ -1519,6 +1522,18 @@ class MainWindow(QMainWindow):
             QMessageBox.warning(self, "Cannot Resume Scan", f"Could not read scan file:\n\n{e}")
             return
 
+        if sras.version not in WRITABLE_VERSIONS:
+            QMessageBox.warning(
+                self, "Cannot Resume Scan",
+                f"{path.name} is a v{sras.version} file, written before each "
+                "angle carried its own background waveform. Every angle this "
+                "app acquires now writes a background block that the older "
+                "layout has no room for, so resuming would shift the file's "
+                "data. Start a new scan instead — the old file still opens in "
+                "the viewer."
+            )
+            return
+
         if not is_compatible(sras, velocity=SCAN_VELOCITY_MM_S,
                              laser_freq=LASER_FREQ_HZ, sample_rate=SAMPLE_RATE_HZ,
                              n_channels=len(SCAN_CHANNELS)):

scan_format.md

@@ -1,17 +1,24 @@
-# SRAS Scan Binary Format — Versions 6 and 10
+# SRAS Scan Binary Format — Versions 7 and 11 (reading 6 and 10)
 
 Each `.sras` file contains **one complete scan**: all GR rotation angles and all
 Y rows.  Files are named `{prefix}.sras`.
 
-Two versions share this layout byte for byte — only the version field differs,
+Two versions are written, sharing this layout byte for byte — only the version
-and with it what the file means:
+field differs, and with it what the file means:
 
 | Version | Meaning | Rows per angle |
 |---------|---------|----------------|
-| 6  | A full scan. | Whatever the ROI needs. |
+| 7  | A full scan. | Whatever the ROI needs. |
-| 10 | A middle-row SAW quality check (`{prefix}-sawcheck.sras`). | Exactly 1. |
+| 11 | A middle-row SAW quality check (`{prefix}-sawcheck.sras`). | Exactly 1. |
 
-See [SAW Quality Check (v10)](#saw-quality-check-v10) below.
+See [SAW Quality Check (v11)](#saw-quality-check-v11) below.
+
+**Versions 6 and 10** are the same two files as they were written before each
+angle carried its own background: a single background block sat between the
+preambles and the data block, and the data block held nothing but rows.  They
+are still read — see [Legacy layout (v6/v10)](#legacy-layout-v6v10) — but
+nothing writes them any more, and a v6 file cannot be resumed into, since the
+background block a resumed angle writes has no room in it.
 
 Starting in v6, each angle only scans the **bounding box of the nominal ROI
 rotated by that specific angle** — not the worst case across all angles — so
@@ -30,10 +37,14 @@ instead of forcing every angle to the largest bounding box.
 [Per-Angle Geometry Table— n_angles × 14 bytes (x_start f32, x_delta f32, n_frames u32, n_rows u16)]
 [Row Table (ragged)      — sum(n_rows) × 4 bytes (float32 per row, angle-major)]
 [Preamble Blocks         — n_channels × (uint16 length + UTF-8 WFMOutpre string)]
-[Background Block        — uint32 n_bg_samples + n_bg_samples × int8 bytes]
+[Data Block (ragged)     — per angle: [Background Block][Waveform Data]]
-[Waveform Data (ragged)  — per angle: n_rows[a] × n_channels × n_frames[a] × samples_per_frame × bps bytes]
+    [Background Block    — uint32 n_bg_samples + n_bg_samples × int8 bytes]
+    [Waveform Data       — n_rows[a] × n_channels × n_frames[a] × samples_per_frame × bps bytes]
 ```
 
+So the data block reads `[background][scan][background][scan] …`, one pair per
+angle, in angle-table order.
+
 All multi-byte integers and floats use **big-endian** byte order
 (`>` in Python's `struct` module).
 
@@ -44,7 +55,7 @@ All multi-byte integers and floats use **big-endian** byte order
 | Offset | Size | Type      | Field              | Description                                      |
 |--------|------|-----------|--------------------|--------------------------------------------------|
 |  0     |  4   | `4s`      | `magic`            | Always `SRAS` (0x53 0x52 0x41 0x53)              |
-|  4     |  1   | `uint8`   | `version`          | Format version — `6` (scan) or `10` (SAW check)  |
+|  4     |  1   | `uint8`   | `version`          | Format version — `7` (scan) or `11` (SAW check)  |
 |  5     |  2   | `uint16`  | `n_angles`         | Number of GR rotation angles                     |
 |  7     |  4   | `float32` | `x_start_nominal`  | Nominal (pre-rotation) X scan start, mm          |
 | 11     |  4   | `float32` | `y_start_nominal`  | Nominal (pre-rotation) Y scan start, mm          |
@@ -127,54 +138,77 @@ to convert raw ADC values to volts.
 
 ---
 
-## Background Block
+## Data Block (ragged)
 
-Immediately after the preamble blocks: a single CH1 waveform captured with the
+Immediately after the preamble blocks, and running to the end of the file:
-**Helios (generation) laser enabled** and the **Genesis (detection) laser
+for each angle in angle-table order, that angle's **background block**
-disabled**.  This provides a noise/background reference for subtraction during
+followed by that angle's **waveform data**.
-post-processing.
+
+```
+for angle a in 0 … n_angles-1:
+  uint32  n_bg_samples                       # background block
+  int8[]  bg_data
+  for row in 0 … n_rows[a]-1:                # waveform data
+    for channel in [CH1, CH3, CH4]:          # 3 channels, fixed order
+      for frame in 0 … n_frames[a]-1:
+        samples[0 … samples_per_frame-1]     # bps bytes each
+```
+
+### Background block
+
+One CH1 waveform captured with the **Helios (generation) laser enabled** and
+the **Genesis (detection) laser disabled**, averaged over 1024 shots
+(`core/scope_sras.py`, `BACKGROUND_AVERAGES`).  It is a noise/background
+reference for subtraction during post-processing.
 
 ```
 uint32  n_bg_samples   — number of samples in the background waveform
 int8[]  bg_data        — raw ADC samples (same encoding as waveform data)
 ```
 
-`n_bg_samples` equals `samples_per_frame` under normal acquisition settings.
+`n_bg_samples` equals `samples_per_frame` under normal acquisition settings,
+but is **not** assumed to: readers take the per-angle offsets from a walk of
+the data block, reading each length prefix as they go, rather than from
+arithmetic over the geometry table alone.
 
----
+Every angle carries its own.  The operator is prompted to switch the Genesis
+laser off before each angle and back on after the capture, so the reference is
+taken minutes from the data it will be subtracted from — a multi-angle scan
+runs for hours, and one background captured at the first angle has drifted by
+the last.  It also makes the angles comparable, which is the entire point of a
+multi-angle scan: each is referenced against its own noise floor rather than
+against whichever angle happened to be scanned first.
 
-## Waveform Data (ragged)
+### Waveform data
 
-Immediately after the background block.  Data is stored in **angle-major,
+Stored in **angle-major, row-minor** order, and each angle contributes a
-row-minor** order, but unlike earlier versions each angle contributes a
 different number of rows (`n_rows[a]`) and a different number of frames per
 row (`n_frames[a]`), both taken from that angle's Per-Angle Geometry Table
 entry.  Within each row, channels are interleaved in ascending channel-index
 order, with each channel's FastFrame data written in frame order.
 
-```
-for angle a in 0 … n_angles-1:
-  for row in 0 … n_rows[a]-1:
-    for channel in [CH1, CH3, CH4]:          # 3 channels, fixed order
-      for frame in 0 … n_frames[a]-1:
-        samples[0 … samples_per_frame-1]     # bps bytes each
-```
-
 Each sample is a raw signed ADC value.  With `bytes_per_sample = 1` this is
 **int8** (−128 … +127).  With `bytes_per_sample = 2` this is **big-endian
 int16**.
 
-Total data size:
+Total data-block size:
 ```
-sum over angles a of: n_rows[a] × 3 × n_frames[a] × samples_per_frame × bytes_per_sample
+sum over angles a of: 4 + n_bg_samples[a]
+                    + n_rows[a] × 3 × n_frames[a] × samples_per_frame × bytes_per_sample
 ```
 
 > **Incomplete files:** If a scan is aborted the file is closed immediately and
-> the data block will be shorter than the expected size. Readers should
+> the data block will be shorter than the expected size. Readers should walk
-> reconstruct the expected per-angle byte offsets from the Per-Angle Geometry
+> the data block from its start — background length prefix, then that angle's
-> Table and check `file_size` against the running total before reshaping —
+> declared row bytes from the Per-Angle Geometry Table — checking `file_size`
-> a fixed `(n_angles, n_rows, ...)` reshape (as in pre-v6 readers) will not
+> against the running total before reshaping.  A fixed
-> work since row/frame counts are no longer uniform across angles.
+> `(n_angles, n_rows, ...)` reshape (as in pre-v6 readers) will not work since
+> row/frame counts are no longer uniform across angles.
+>
+> An angle whose background block is not fully on disk has nothing of itself
+> written yet: it is *missing*, not truncated, and the walk continues past it
+> assuming the block a writer would have produced
+> (`4 + samples_per_frame` bytes), which is where a resumed scan writes.
 
 ---
 
@@ -197,8 +231,9 @@ using that angle's `x_start` from the Per-Angle Geometry Table (not
 
 | Parameter            | Value                                    |
 |-----------------------|------------------------------------------|
-| Setup trigger        | CH2, rising edge, 0.500 V (`TRIG_LEVEL_V`) |
+| Background trigger   | CH2, rising edge, 0.500 V (`TRIG_LEVEL_V`), FastFrame off |
 | Scan trigger         | Logic AND, CH2 HIGH ∧ CH3 HIGH, 0.500 V  |
+| Background average   | 1024 shots (`BACKGROUND_AVERAGES`), once per angle |
 | Horizontal position  | 30 (`HORizontal:POSition`)               |
 | Sample rate          | 6.25 GS/s  (160 ps/sample)               |
 | Transfer format      | `DATa:ENCdg RIBinary`, `DATa:WIDth 1`    |
@@ -226,6 +261,10 @@ is not recorded in the file.
 | Curve transfers | one per channel per row | one per channel per burst |
 | Stage X trigger out | armed for the whole scan | armed per acquiring pass, dropped for the flyback |
 
+Both paths take the same per-angle background: the scope returns to the
+single-record edge trigger for the capture and back to the logic-AND trigger
+before the angle's rows, so the two paths still produce byte-identical files.
+
 Burst mode runs a single acquisition across several rows, so the return move
 must not trigger: the trigger output is dropped before each flyback and
 re-armed for each acquiring pass.  Row boundaries inside the burst come from
@@ -252,21 +291,22 @@ the file always ends on a whole-row boundary.
 
 ---
 
-## SAW Quality Check (v10)
+## SAW Quality Check (v11)
 
 A full multi-angle scan takes hours, and a rig whose angles disagree produces
 all of them before anyone finds out.  The SAW quality check acquires **one row
-per angle — the row-wise middle of the ROI** — and writes it as a v10 file.
+per angle — the row-wise middle of the ROI** — and writes it as a v11 file.
 The cost is one row-time per angle instead of `n_rows` of them.
 
-Nothing about the byte layout changes.  A v10 file is a v6 file in which every
+Nothing about the byte layout changes.  A v11 file is a v7 file in which every
 angle's Per-Angle Geometry Table entry declares `n_rows = 1`, and its Row Table
-holds that angle's single middle Y position.  Every v6 reader that works from
+holds that angle's single middle Y position.  Every v7 reader that works from
-the geometry table (rather than assuming a uniform shape) reads a v10 file
+the geometry table (rather than assuming a uniform shape) reads a v11 file
-unchanged.
+unchanged.  Each angle still carries its own background, so a check costs the
+same two operator prompts per angle a scan does.
 
 The version byte earns its keep because the two are otherwise
-indistinguishable: **a v6 scan aborted after its first row is not a check**,
+indistinguishable: **a v7 scan aborted after its first row is not a check**,
 even though both hold one row per angle.  A reader that guessed from the row
 count would treat a failed scan as a deliberate measurement.
 
@@ -278,12 +318,33 @@ of the rig — which is what makes it an alignment check.  `saw_check_viewer.py`
 plots every angle's frequency on one graph for exactly that comparison.
 
 Writers must honour the one-row rule; `core.sras_format.create_scan_file`
-refuses a v10 write for any plan that breaks it.  Producing the plan is
+refuses a v11 write for any plan that breaks it.  Producing the plan is
 `core.saw_check.middle_row_plan(plan)`, and `n_rows // 2` is the middle-row
 rule (the upper of the two central rows when the count is even).
 
 ---
 
+## Legacy layout (v6/v10)
+
+A v6 or v10 file differs in one place: the background block sits **once**,
+between the preamble blocks and the data block, and the data block is
+waveform data alone.
+
+```
+[Preamble Blocks]
+[Background Block        — uint32 n_bg_samples + n_bg_samples × int8 bytes]
+[Waveform Data (ragged)  — per angle: rows, as above, with no background between]
+```
+
+Everything else — header, tables, row order, spatial mapping — is identical,
+which is why `core.sras_format.SrasFile` reads both: it hands the one legacy
+background to every angle, so a reader that asks for angle *a*'s background
+never has to know which layout it is looking at.  Nothing writes v6/v10 any
+more, and a resume refuses them, because a re-acquired angle writes a
+background block the layout has no room for.
+
+---
+
 ## Version History
 
 | Version | Change |
@@ -294,5 +355,7 @@ rule (the upper of the two central rows when the count is even).
 | 4       | Added background waveform block (CH1, Helios ON / Genesis OFF) after the preamble blocks; stored as `uint32` sample count followed by raw `int8` ADC bytes. |
 | 5       | (skipped) |
 | 6       | Each angle now scans only the bounding box of the nominal ROI rotated by that angle instead of the AABB-expanded worst case across all angles. Header no longer carries a single global `x_start`/`x_delta`/`n_rows` — replaced with `*_nominal` reference fields plus a new Per-Angle Geometry Table (`x_start`, `x_delta`, `n_frames`, `n_rows` per angle) and a ragged Row Table / Waveform Data block sized per angle. **Not compatible with v4 readers** (e.g. `sras_viewer.py`, which has not yet been updated for v6). |
-| 7–9     | (skipped) |
+| 7       | Background moved into the data block, one per angle: the block now reads `[background][scan][background][scan] …`. Each angle is preceded by its own `uint32` + `int8[]` background, captured (Genesis off, Helios on) just before that angle is scanned, so the reference is contemporary with the data and the angles are comparable to each other. Per-angle offsets therefore come from a walk of the data block rather than arithmetic over the geometry table. **v6 files still read; v6 files cannot be resumed into.** |
-| 10      | Middle-row SAW quality check. Byte layout identical to v6, with every angle declaring exactly one row — the row-wise middle of the ROI. A v6 reader that derives its shape from the Per-Angle Geometry Table reads these unchanged; the version byte exists so a check is not confused with a scan aborted after its first row. Written by the main app's *SAW Quality Check*, read by `saw_check_viewer.py`. |
+| 8–9     | (skipped) |
+| 10      | Middle-row SAW quality check on the v6 layout. Byte layout identical to v6, with every angle declaring exactly one row — the row-wise middle of the ROI. Superseded by v11; still read. |
+| 11      | Middle-row SAW quality check on the v7 layout: identical to v7 with every angle declaring exactly one row, per-angle backgrounds included. The version byte exists so a check is not confused with a scan aborted after its first row. Written by the main app's *SAW Quality Check*, read by `saw_check_viewer.py`. |

sras_scan_manager.py

@@ -1,20 +1,22 @@
 #!/opt/srasenv/bin/python3
 """
 SRAS Scan Manager
-Command-line / interactive TUI for inspecting v6 .sras files.
+Command-line / interactive TUI for inspecting .sras files.
 
 A .sras file (see scan_format.md) holds one acquisition run across several
 GR rotation angles, each with its own geometry (x_start, x_delta, n_frames,
-n_rows) and waveform data block. This tool lists those per-angle sub-scans
+n_rows), background waveform, and waveform data block. This tool lists those
-and lets you export a subset to a new .sras file, or delete a subset from
+per-angle sub-scans and lets you export a subset to a new .sras file, or
-the file in place — both operations rewrite the angle/geometry/row tables
+delete a subset from the file in place — both operations rewrite the
-and stream-copy only the selected angles' waveform data, producing a file
+angle/geometry/row tables, carry each kept angle's background across, and
-that is itself a valid .sras readable by sras_viewer.py-style tools
+stream-copy only the selected angles' waveform data, producing a file that is
-(once updated for v6) or sc3_aui_app.py.
+itself a valid .sras readable by sras_viewer.py or sc3_aui_app.py.
 
-Format versions 6 (full scan) and 10 (middle-row SAW check) are supported.
+Format versions 7 (full scan) and 11 (middle-row SAW check) are supported,
-A subset keeps the version of the file it came from — a v10 check exports as
+as are their pre-per-angle-background predecessors 6 and 10. A subset keeps
-a v10 check, since dropping angles from one leaves it one row per angle.
+the version — and therefore the background layout — of the file it came
+from: a v11 check exports as a v11 check, since dropping angles from one
+leaves it one row per angle.
 """
 
 import argparse
@@ -26,7 +28,9 @@ from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).resolve().parent))
 
-from core.sras_format import GEOM_FMT, HDR_FMT, MAGIC, VERSION_SAW_CHECK, SrasFile
+from core.sras_format import (
+    BG_LEN_FMT, GEOM_FMT, HDR_FMT, MAGIC, SrasFile,
+)
 
 
 @dataclass
@@ -39,7 +43,8 @@ class AngleEntry:
     n_rows_declared: int
     y_positions: list  # declared length; may exceed what's actually on disk
     row_bytes: int
-    data_offset: int             # byte offset into the file where this angle's data starts
+    background: bytes            # this angle's own background (v7/v11)
+    data_offset: int             # byte offset into the file where this angle's rows start
     n_rows_available: int = 0
     data_size_available: int = 0
     complete: bool = True
@@ -60,6 +65,7 @@ class SrasScanFile:
         sras = SrasFile(self.path)
         h = sras.header
         self.version = sras.version
+        self.is_saw_check = sras.is_saw_check
         self.x_start_nominal = h.x_start_nominal
         self.y_start_nominal = h.y_start_nominal
         self.x_delta_nominal = h.x_delta_nominal
@@ -72,7 +78,10 @@ class SrasScanFile:
         self.bytes_per_sample = h.bytes_per_sample
         self.n_channels       = h.n_channels
         self.preambles_raw   = sras.preambles_raw
-        self.background_raw  = sras.background
+        self.legacy_layout   = sras.is_legacy_layout
+        # v6/v10 keep one background ahead of the data block; v7/v11 keep one
+        # per angle inside it.  Either way sras.backgrounds is per angle.
+        self.shared_background = sras.backgrounds[0] if sras.is_legacy_layout else b""
         self.data_start_offset = sras.data_start_offset
         self.file_size       = sras.file_size
 
@@ -82,12 +91,13 @@ class SrasScanFile:
                 x_start=pa.x_start, x_delta=pa.x_delta,
                 n_frames=pa.n_frames, n_rows_declared=pa.n_rows,
                 y_positions=pa.y_positions, row_bytes=st.row_bytes,
-                data_offset=st.data_offset,
+                background=bg, data_offset=st.data_offset,
                 n_rows_available=st.n_rows_available,
                 data_size_available=st.n_rows_available * st.row_bytes,
                 complete=st.complete,
             )
-            for pa, st in zip(sras.per_angle, sras.angle_status(), strict=True)
+            for pa, st, bg in zip(sras.per_angle, sras.angle_status(),
+                                  sras.backgrounds, strict=True)
         ]
 
     def get(self, index: int) -> AngleEntry:
@@ -137,10 +147,18 @@ def _write_subset(sf: SrasScanFile, indices: list, dst_path: Path) -> list:
             dst.write(struct.pack(">H", len(praw)))
             dst.write(praw)
 
-        dst.write(struct.pack(">I", len(sf.background_raw)))
+        if sf.legacy_layout:
-        dst.write(sf.background_raw)
+            dst.write(struct.pack(BG_LEN_FMT, len(sf.shared_background)))
+            dst.write(sf.shared_background)
 
         for e in selected:
+            if not sf.legacy_layout:
+                if not e.background:
+                    warnings.append(
+                        f"angle[{e.index}] ({e.angle_deg:.2f} deg): no background "
+                        "on disk — exported with an empty background block")
+                dst.write(struct.pack(BG_LEN_FMT, len(e.background)))
+                dst.write(e.background)
             src.seek(e.data_offset)
             remaining = e.data_size_available
             chunk_size = 1 << 20
@@ -224,7 +242,7 @@ def parse_index_spec(spec: str, max_index: int) -> list:
 
 def print_summary(sf: SrasScanFile, selected: set):
     print()
-    kind = " SAW check" if sf.version == VERSION_SAW_CHECK else ""
+    kind = " SAW check" if sf.is_saw_check else ""
     print(f"File: {sf.path}  (v{sf.version}{kind}, {_human_size(sf.file_size)})")
     print(f"Nominal ROI: x_start={sf.x_start_nominal:.4f} x_delta={sf.x_delta_nominal:.4f} "
           f"y_start={sf.y_start_nominal:.4f} y_delta={sf.y_delta_nominal:.4f} mm  "
@@ -346,7 +364,7 @@ def interactive_loop(path: Path):
 
 def main():
     ap = argparse.ArgumentParser(
-        description="Inspect, export, or delete per-angle sub-scans in a v6 .sras file.")
+        description="Inspect, export, or delete per-angle sub-scans in a .sras file.")
     ap.add_argument("file", type=Path, help="path to a .sras file")
     ap.add_argument("--list", action="store_true", help="print the angle table and exit")
     ap.add_argument("--export", metavar="SPEC", help="angle index spec to export, e.g. '0,2,4-6' or 'all'")

sras_viewer.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 """
 SRAS Scan File Viewer
-PyQt6 application for visualizing channel data from v6 .sras scan files.
+PyQt6 application for visualizing channel data from .sras scan files.
 
 Channel semantics (fixed by sc3_aui_app.py acquisition settings):
   CH1 — RF Acoustic Packet: FFT → peak frequency
@@ -76,11 +76,18 @@ class LoadedScan:
     def __init__(self, path: str):
         self.sras = SrasFile(Path(path))
         self.calib = ChannelCalibration.from_preambles(self.sras.preambles)
-        bg = np.frombuffer(self.sras.background, dtype=np.int8)
+        # One background per angle (v7/v11), captured just before that angle
-        self.background = bg.astype(np.float32) if len(bg) else None
+        # was scanned.  A legacy v6/v10 file has a single one, which SrasFile
+        # repeats for every angle, so nothing here branches on the version.
+        self.backgrounds = [self.sras.background_array(ai)
+                            for ai in range(self.sras.header.n_angles)]
         # Rows actually on disk per angle (aborted/resumed scans)
         self.rows_available = [s.n_rows_available for s in self.sras.angle_status()]
 
+    def background(self, angle_idx: int) -> np.ndarray | None:
+        """That angle's background waveform, or None if it has none."""
+        return self.backgrounds[angle_idx]
+
     def angle_view(self, angle_idx: int) -> np.ndarray:
         """Available rows of one angle: (rows, n_ch, n_frames, spf) int8 view."""
         return self.sras.load_angle(angle_idx, n_rows=self.rows_available[angle_idx])
@@ -123,7 +130,7 @@ def compute_image(scan: LoadedScan, angle_idx: int, ch_idx: int,
     if view.shape[0] == 0:
         return np.zeros((0, 0), dtype=np.float32)
     sras = scan.sras
-    bg = scan.background if apply_bg_sub else None
+    bg = scan.background(angle_idx) if apply_bg_sub else None
 
     if ch_idx in (CH1_IDX, VELOCITY_MODE_IDX):
         return compute_rf_image(
@@ -232,7 +239,7 @@ class WaveformCanvas(FigureCanvasQTAgg):
         dc4_val = float(sras.load_row(angle_idx, row_idx, CH4_IDX)[frame_idx]
                         .mean(dtype=np.float32))
 
-        bg = scan.background if apply_bg_sub else None
+        bg = scan.background(angle_idx) if apply_bg_sub else None
         waveform_plot = waveform - bg if bg is not None else waveform
 
         self.ax_wave.cla()
@@ -696,7 +703,7 @@ class SrasViewerWindow(QMainWindow):
         self.chk_bg_sub.setChecked(True)
         self.chk_bg_sub.setEnabled(False)
         self.chk_bg_sub.setToolTip(
-            "Subtract the stored background waveform from each CH1 frame\n"
+            "Subtract this angle's stored background waveform from each CH1 frame\n"
             "before computing the FFT."
         )
         self.chk_bg_sub.toggled.connect(self._on_bg_sub_toggled)
@@ -1043,7 +1050,7 @@ class SrasViewerWindow(QMainWindow):
         self._on_view_changed()
 
     def _update_angle_info(self):
-        """Per-angle info fields (v6 geometry is ragged across angles)."""
+        """Per-angle info fields (geometry is ragged across angles)."""
         scan = self._scan
         if scan is None:
             return
@@ -1060,8 +1067,9 @@ class SrasViewerWindow(QMainWindow):
         if avail < pa.n_rows:
             notes.append(f"! Angle {ai}: only {avail}/{pa.n_rows} rows on disk "
                          "(scan was aborted or is still running)")
-        if scan.background is not None:
+        bg = scan.background(ai)
-            notes.append(f"Background waveform: {len(scan.background)} samples")
+        if bg is not None:
+            notes.append(f"Background waveform (angle {ai}): {len(bg)} samples")
         self.lbl_frame_warn.setText("\n".join(notes))
 
     # ------------------------------------------------------------------
@@ -1083,7 +1091,7 @@ class SrasViewerWindow(QMainWindow):
         is_ch1 = enabled and ch_idx in CH1_DERIVED_MODES
         is_fft = enabled and ch_idx in (CH1_IDX, VELOCITY_MODE_IDX)
         self.spin_threshold_mv.setEnabled(is_ch1)
-        has_bg = has_file and scan.background is not None
+        has_bg = has_file and scan.background(self.spin_angle.value()) is not None
         self.chk_bg_sub.setEnabled(has_bg and is_ch1)
         # Time gate only for FFT modes (the SAW pipeline has its own gating)
         self.chk_gate.setEnabled(is_fft)
@@ -1197,6 +1205,9 @@ class SrasViewerWindow(QMainWindow):
         idx = self.spin_angle.value()
         self.lbl_angle_deg.setText(f"({self._scan.sras.per_angle[idx].angle_deg:.1f}°)")
         self._update_angle_info()
+        # Backgrounds are per angle, so whether there is one to subtract can
+        # change with the angle (a truncated file may be missing later ones).
+        self._update_controls_enabled(True)
         self._request_compute()
 
     # ------------------------------------------------------------------
@@ -1382,7 +1393,8 @@ class SrasViewerWindow(QMainWindow):
         angle_idx = self.spin_angle.value()
         n_shots_req = self.spin_saw_n_shots.value()
         row_sel, frame_sel = self._last_row, self._last_frame
-        apply_bg = scan.background is not None and self.chk_bg_sub.isChecked()
+        background = scan.background(angle_idx)
+        apply_bg = background is not None and self.chk_bg_sub.isChecked()
 
         if row_sel is not None and frame_sel is not None:
             src_desc = f"selected pixel (row={row_sel}, frame={frame_sel})"
@@ -1405,7 +1417,7 @@ class SrasViewerWindow(QMainWindow):
                 rows, frames = np.divmod(flat, n_frames)
                 shots = view[rows, CH1_IDX, frames].astype(np.float32)
             if apply_bg:
-                shots -= scan.background
+                shots -= background
             pipeline.build_template(shots)
             return None
 

tests/fakes.py

@@ -99,6 +99,16 @@ class FakeStage:
                     round(at_speed_mm * LASER_FREQ_HZ / SCAN_VELOCITY_MM_S))
 
 
+def background_record(n: int, samples_per_frame: int) -> bytes:
+    """The waveform FakeScope returns from its n-th background capture.
+
+    Every angle captures its own, so the tests need to tell one from the
+    next: a background that landed under the wrong angle would otherwise
+    look exactly like the right one.
+    """
+    return bytes((n * 17 + s) % 256 for s in range(samples_per_frame))
+
+
 class FakeScope:
     """Stands in for TektronixOscilloscopeBase.
 
@@ -113,6 +123,7 @@ class FakeScope:
         self._acq_polls = 0
         self._running = False
         self._acquired = 0
+        self._backgrounds_taken = 0
         # Per-channel running frame index.  Frame content is a function of
         # (channel, index) alone, so the same total frame sequence yields the
         # same bytes however it is chopped into transfers.
@@ -194,7 +205,9 @@ class FakeScope:
 
     def transfer_curve(self):
         self._t.record("transfer_curve")
-        return bytes(range(self.samples_per_frame))
+        n = self._backgrounds_taken
+        self._backgrounds_taken += 1
+        return background_record(n, self.samples_per_frame)
 
     def _frames(self, ch, count):
         spf = self.samples_per_frame

tests/golden/sras_expected.json

@@ -141,7 +141,7 @@
         "angle_deg": -180.0,
         "n_rows": 3,
         "row_bytes": 96,
-        "data_offset": 265,
+        "data_offset": 553,
         "n_rows_available": 0,
         "status": "MISSING"
       }
@@ -161,7 +161,7 @@
         "angle_deg": -180.0,
         "n_rows": 3,
         "row_bytes": 96,
-        "data_offset": 265,
+        "data_offset": 553,
         "n_rows_available": 0,
         "status": "MISSING"
       }

tests/golden_util.py

@@ -1,9 +1,18 @@
-"""Shared constants for the golden .sras fixtures.
+"""Shared constants and writers for the .sras test fixtures.
 
-These mirror the values tests/gen_goldens.py used when the fixtures were
+The constants mirror the values tests/gen_goldens.py used when the committed
-generated against the pre-refactor code (commit d185676); they must never
+golden files were generated against the pre-refactor code (commit d185676);
-change, or the byte-identical comparisons stop meaning anything.
+they must never change, or the comparisons against those files stop meaning
+anything.  Those goldens are legacy v6 files — the one background per file
+layout — and are now read-only fixtures for the parser.
+
+``write_v7`` builds the current layout (one background per angle, inside the
+data block) over the same geometry, for the tests that need a file this
+version of the app could actually have written.
 """
+from core.scan_geometry import build_plan
+from core.sras_format import VERSION, create_scan_file, write_background_block
+
 SPF = 8
 SAMPLE_RATE = 6.25e9
 CHANNELS = [1, 3, 4]
@@ -19,3 +28,31 @@ VELOCITY_MM_S = 100.0
 
 def synthetic_frame(ai, ri, ci, fi):
     return bytes((ai * 7 + ri * 5 + ci * 3 + fi + s) % 256 for s in range(SPF))
+
+
+def tiny_plan():
+    """The fixture geometry: 2 angles × 3 rows × 4 frames."""
+    return build_plan(**TINY_PLAN_ARGS, laser_freq_hz=LASER_FREQ_HZ,
+                      velocity_mm_s=VELOCITY_MM_S)
+
+
+def angle_background(ai):
+    """A background that differs per angle, so tests can tell them apart."""
+    return bytes((ai * 11 + s) % 256 for s in range(SPF))
+
+
+def write_v7(path, plan=None, version=None):
+    """Write a complete current-format file: [background][rows] per angle."""
+    plan = plan if plan is not None else tiny_plan()
+    f = create_scan_file(path, plan, SPF, SAMPLE_RATE, PREAMBLES,
+                         version=VERSION if version is None else version)
+    try:
+        for ai, pa in enumerate(plan.per_angle):
+            write_background_block(f, angle_background(ai))
+            for ri in range(pa.n_rows):
+                for ci in range(len(CHANNELS)):
+                    for fi in range(pa.n_frames):
+                        f.write(synthetic_frame(ai, ri, ci, fi))
+    finally:
+        f.close()
+    return plan

tests/test_saw_check.py

@@ -1,7 +1,7 @@
-"""Middle-row SAW quality check: plan reduction, the v10 file, and the read-out.
+"""Middle-row SAW quality check: plan reduction, the v11 file, and the read-out.
 
 The acquisition half runs on the same fake rig as the scan tests; the
-analysis half runs on a synthetic v10 file whose CH1 is a pure sine at a
+analysis half runs on a synthetic v11 file whose CH1 is a pure sine at a
 known FFT bin, so the frequency a trace reports is a number the test knows
 in advance rather than one it copies from the implementation.
 """
@@ -19,6 +19,7 @@ from core.scan_engine import ScanCallbacks, ScanEngine
 from core.scan_geometry import ScanGeometryError, build_plan
 from core.sras_format import (
     SCAN_CHANNELS, VERSION, VERSION_SAW_CHECK, SrasFile, create_scan_file,
+    write_background_block,
 )
 from fakes import FakeScope, FakeStage, FakeT3R, Trace
 
@@ -51,13 +52,19 @@ def sine_frame(k: int) -> bytes:
     return np.round(100 * np.sin(2 * math.pi * k * n / SPF)).astype(np.int8).tobytes()
 
 
-def write_check(path, bins, n_masked_frames=0, plan=None):
+def write_check(path, bins, n_masked_frames=0, plan=None, backgrounds=None):
-    """A synthetic v10 file: angle `i`'s CH1 is a sine at FFT bin `bins[i]`."""
+    """A synthetic v11 file: angle `i`'s CH1 is a sine at FFT bin `bins[i]`.
+
+    ``backgrounds`` supplies each angle's own background block; the default
+    is a flat zero one per angle, which subtracts to nothing.
+    """
     plan = plan if plan is not None else middle_row_plan(full_plan(len(bins)))
-    f = create_scan_file(path, plan, SPF, SAMPLE_RATE, PREAMBLES, bytes(SPF),
+    f = create_scan_file(path, plan, SPF, SAMPLE_RATE, PREAMBLES,
                          version=VERSION_SAW_CHECK)
     try:
         for ai, pa in enumerate(plan.per_angle):
+            write_background_block(
+                f, bytes(SPF) if backgrounds is None else backgrounds[ai])
             wave = sine_frame(bins[ai])
             for ch in SCAN_CHANNELS:
                 for fi in range(pa.n_frames):
@@ -127,9 +134,9 @@ def test_middle_row_plan_rejects_an_angle_with_no_rows():
         middle_row_plan(plan)
 
 
-# ── The v10 file ─────────────────────────────────────────────────────────────
+# ── The v11 file ─────────────────────────────────────────────────────────────
 
-def test_v10_write_read_roundtrip(tmp_path):
+def test_saw_check_write_read_roundtrip(tmp_path):
     out = tmp_path / "check.sras"
     plan = write_check(out, bins=(8, 8, 8))
 
@@ -141,24 +148,25 @@ def test_v10_write_read_roundtrip(tmp_path):
     sras.close()
 
 
-def test_v10_rejects_a_multi_row_plan(tmp_path):
+def test_saw_check_rejects_a_multi_row_plan(tmp_path):
     plan = full_plan(num_angles=2)
     assert any(pa.n_rows > 1 for pa in plan.per_angle)
     with pytest.raises(ValueError, match="exactly one row per angle"):
         create_scan_file(tmp_path / "bad.sras", plan, SPF, SAMPLE_RATE,
-                         PREAMBLES, bytes(SPF), version=VERSION_SAW_CHECK)
+                         PREAMBLES, version=VERSION_SAW_CHECK)
     assert not (tmp_path / "bad.sras").exists()
 
 
 def test_unknown_version_rejected_at_write(tmp_path):
-    with pytest.raises(ValueError, match="version 7"):
+    with pytest.raises(ValueError, match="version 99"):
         create_scan_file(tmp_path / "bad.sras", middle_row_plan(full_plan(1)),
-                         SPF, SAMPLE_RATE, PREAMBLES, bytes(SPF), version=7)
+                         SPF, SAMPLE_RATE, PREAMBLES, version=99)
 
 
-def test_v6_file_is_not_a_saw_check():
+def test_a_scan_is_not_a_saw_check():
-    sras = SrasFile("tests/golden/complete.sras")
+    """Legacy and current scans alike: only the check versions say check."""
-    assert sras.version == VERSION and not sras.is_saw_check
+    assert not SrasFile("tests/golden/complete.sras").is_saw_check
+    assert VERSION not in (10, VERSION_SAW_CHECK)
 
 
 # ── Acquisition through the engine ───────────────────────────────────────────
@@ -176,7 +184,7 @@ def run_engine(tmp_path, num_angles=3):
     return engine.run(), plan, check, trace
 
 
-def test_engine_writes_a_complete_v10_check(tmp_path):
+def test_engine_writes_a_complete_saw_check(tmp_path):
     result, plan, check, _ = run_engine(tmp_path)
 
     assert not result.aborted
@@ -200,7 +208,7 @@ def test_engine_visits_each_middle_row_once(tmp_path):
     assert y_moves == [round(pa.y_positions[0], 4) for pa in check.per_angle]
 
 
-def test_engine_still_writes_v6_by_default(tmp_path):
+def test_engine_still_writes_a_full_scan_by_default(tmp_path):
     trace = Trace()
     scope = FakeScope(trace, samples_per_frame=SPF)
     stage = FakeStage(trace, scope=scope)
@@ -229,6 +237,30 @@ def test_traces_report_the_injected_frequency(tmp_path):
         assert trace.drift_mhz_per_mm == pytest.approx(0.0, abs=1e-6)
 
 
+def test_background_subtraction_uses_each_angles_own(tmp_path):
+    """Every angle is referenced against its own background, not angle 1's.
+
+    Each angle's background here is a copy of that angle's own CH1 wave, so
+    subtracting the right one leaves nothing to read at any angle — where
+    reusing angle 1's everywhere would leave angles 2 and 3 reporting their
+    sine unchanged.
+    """
+    out = tmp_path / "check.sras"
+    bins = (8, 9, 10)
+    backgrounds = [sine_frame(k) for k in bins]
+    write_check(out, bins=bins, backgrounds=backgrounds)
+
+    with SrasFile(out) as sras:
+        assert sras.backgrounds == backgrounds
+        plain = frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV)
+        subtracted = frequency_traces(sras, dc_threshold_mv=DC_THRESHOLD_MV,
+                                      subtract_background=True)
+
+    assert [t.median_mhz for t in plain] == [pytest.approx(bin_mhz(k)) for k in bins]
+    for trace in subtracted:
+        assert np.isnan(trace.freq_mhz).all()
+
+
 def test_masked_pixels_become_nan_not_zero(tmp_path):
     out = tmp_path / "check.sras"
     write_check(out, bins=(8, 8, 8), n_masked_frames=2)

tests/test_scan_engine.py

@@ -14,8 +14,8 @@ from core.scan_engine import (
     ResumeTarget,
 )
 from core.scan_geometry import ScanGeometryError, build_plan
-from core.sras_format import SCAN_CHANNELS, SrasFile
+from core.sras_format import BG_LEN_SIZE, SCAN_CHANNELS, SrasFile
-from fakes import FakeScope, FakeStage, FakeT3R, Trace
+from fakes import FakeScope, FakeStage, FakeT3R, Trace, background_record
 
 SPF = 8
 
@@ -57,7 +57,41 @@ def test_single_angle_scan_writes_readable_file(tmp_path):
     # File is complete: every declared row present on disk
     assert [s.status for s in sras.angle_status()] == ["OK"]
     assert len(sras.preambles) == 3
-    assert sras.background == bytes(range(SPF))
+    assert sras.backgrounds == [background_record(0, SPF)]
+
+
+def test_each_angle_captures_and_stores_its_own_background(tmp_path):
+    """One background per angle, taken after the rotation, kept ahead of it."""
+    prompts = []
+    engine, trace, plan = build(
+        tmp_path, num_angles=3,
+        callbacks=ScanCallbacks(prompt=lambda title, msg: prompts.append(title)))
+    engine.run()
+
+    sras = SrasFile(tmp_path / "out.sras")
+    assert trace.count("transfer_curve") == 3
+    assert sras.backgrounds == [background_record(i, SPF) for i in range(3)]
+    for st in sras.angle_status():
+        assert st.bg_bytes == BG_LEN_SIZE + SPF
+        assert st.status == "OK"
+
+    # Each capture follows the rotation to the angle it belongs to (the last
+    # rotation is the return to home after the final angle).
+    assert [c[0] for c in trace.calls
+            if c[0] in ("t3r_rotate", "transfer_curve")] == [
+        "transfer_curve", "t3r_rotate", "transfer_curve",
+        "t3r_rotate", "transfer_curve", "t3r_rotate"]
+
+    # Two prompts per angle: Genesis off for the capture, back on to scan.
+    assert prompts == [title for i in range(3) for title in
+                       (f"Background Capture — Angle {i + 1}/3",
+                        f"Begin Angle {i + 1}/3")]
+
+    # The scope goes back to the scan trigger after every capture, not just
+    # once at the start — the capture needs the single-record edge trigger.
+    cmds = [c[1] for c in trace.of("write")]
+    assert cmds.count("TRIGger:A:TYPe EDGE") == 4      # prepare + one per angle
+    assert cmds.count("TRIGger:A:TYPe LOGIc") == 4
 
 
 def test_command_sequence_order(tmp_path):
@@ -236,8 +270,9 @@ def test_resume_seeks_to_angle_offset_and_skips_others(tmp_path):
     target = statuses[1]
     resume = ResumeState(
         path=path,
-        targets=[ResumeTarget(target.index, target.data_offset,
+        targets=[ResumeTarget(target.index, target.bg_offset,
-                              target.n_rows, target.angle_deg)],
+                              target.data_offset, target.n_rows,
+                              target.angle_deg)],
         samples_per_frame=SPF,
     )
 
@@ -249,19 +284,51 @@ def test_resume_seeks_to_angle_offset_and_skips_others(tmp_path):
     assert result.rows_written == plan.per_angle[1].n_rows
     rewritten = path.read_bytes()
     assert len(rewritten) == len(original)
-    # Angle 0's block is untouched; angle 1's changed (fresh frame data)
+    # Angle 0's block is untouched; angle 1's changed — background included,
-    a1_start, a1_end = target.data_offset, target.data_offset + target.row_bytes * target.n_rows
+    # since a re-acquired angle captures a fresh one over the old.
+    a1_start = target.bg_offset
+    a1_end = target.data_offset + target.row_bytes * target.n_rows
     assert rewritten[:a1_start] == original[:a1_start]
     assert rewritten[a1_start:a1_end] != original[a1_start:a1_end]
     assert rewritten[a1_end:] == original[a1_end:]
 
+    # The new background is angle 1's own, written in place of its old one.
+    reread = SrasFile(path)
+    assert reread.backgrounds[1] == background_record(0, SPF)
+    assert reread.backgrounds[0] == SrasFile(path).backgrounds[0]
+    assert [s.status for s in reread.angle_status()] == ["OK"] * 3
+
+
+def test_resume_rejects_a_background_that_would_shift_the_file(tmp_path):
+    """A re-acquired angle's background must fit the room the file has.
+
+    Nothing else in the file records where an angle's rows begin, so a longer
+    or shorter background would push every row behind it out of position.
+    """
+    engine, _, _ = build(tmp_path, num_angles=2)
+    engine.run()
+    path = tmp_path / "out.sras"
+    target = SrasFile(path).angle_status()[0]
+    resume = ResumeState(
+        path=path,
+        targets=[ResumeTarget(0, target.bg_offset, target.data_offset,
+                              target.n_rows, target.angle_deg)],
+        samples_per_frame=SPF,
+    )
+    engine2, _, _ = build(tmp_path, num_angles=2, resume=resume)
+    # A scope that hands back a longer record than the file was written with
+    engine2._scope.transfer_curve = lambda: bytes(SPF + 4)
+
+    with pytest.raises(RuntimeError, match="shift every row"):
+        engine2.run()
+
 
 def test_resume_record_length_mismatch_rejected(tmp_path):
     engine, trace, plan = build(tmp_path)
     engine.run()
     path = tmp_path / "out.sras"
     resume = ResumeState(path=path,
-                         targets=[ResumeTarget(0, 0, 1, 0.0)],
+                         targets=[ResumeTarget(0, 0, 0, 1, 0.0)],
                          samples_per_frame=SPF + 1)   # scope changed
     engine2, _, _ = build(tmp_path, resume=resume)
     with pytest.raises(RuntimeError, match="record length"):
@@ -461,7 +528,7 @@ def test_strict_row_packing_writes_nothing_for_the_failed_row(tmp_path):
     # Row 1 was written in full; row 2 aborted before writing anything, so
     # the file ends exactly on a row boundary.
     sras = SrasFile(tmp_path / "out.sras")
-    written = (tmp_path / "out.sras").stat().st_size - sras.data_start_offset
+    written = (tmp_path / "out.sras").stat().st_size - sras.angle_data_offset(0)
     assert written == sras.row_bytes(0)
 
 

tests/test_scan_resume.py

@@ -3,6 +3,7 @@ from pathlib import Path
 
 from core.scan_resume import is_compatible, plan_resume
 from core.sras_format import SrasFile
+from golden_util import write_v7
 
 GOLDEN = Path(__file__).parent / "golden"
 
@@ -47,11 +48,17 @@ def test_selecting_only_a_later_angle_pulls_in_the_frontier():
     assert plan.auto_added == [0]
 
 
-def test_targets_carry_offsets_and_rows():
+def test_targets_carry_offsets_and_rows(tmp_path):
-    st = _statuses("complete.sras")
+    out = tmp_path / "v7.sras"
+    write_v7(out)
+    st = SrasFile(out).angle_status()
     plan = plan_resume(st, selected={0, 1})
     for target, status in zip(plan.targets, st, strict=True):
+        # A re-acquired angle rewrites its background too, so a target has to
+        # know where the block starts as well as where the rows do.
+        assert target.bg_offset == status.bg_offset
         assert target.data_offset == status.data_offset
+        assert target.bg_offset < target.data_offset
         assert target.n_rows == status.n_rows
         assert target.angle_deg == status.angle_deg
     assert plan.total_rows == sum(s.n_rows for s in st)
@@ -65,9 +72,19 @@ def test_to_state_carries_samples_per_frame():
     assert state.target_indices == {0}
 
 
-def test_is_compatible_checks_acquisition_settings():
+def test_is_compatible_rejects_a_legacy_file():
+    """A v6 file has no room for the background block each angle now writes."""
     sras = SrasFile(GOLDEN / "complete.sras")
     h = sras.header
+    assert not is_compatible(sras, velocity=h.velocity, laser_freq=h.laser_freq,
+                             sample_rate=h.sample_rate, n_channels=h.n_channels)
+
+
+def test_is_compatible_checks_acquisition_settings(tmp_path):
+    out = tmp_path / "v7.sras"
+    write_v7(out)
+    sras = SrasFile(out)
+    h = sras.header
     ok = dict(velocity=h.velocity, laser_freq=h.laser_freq,
               sample_rate=h.sample_rate, n_channels=h.n_channels)
     assert is_compatible(sras, **ok)

tests/test_sras_analysis.py

@@ -22,7 +22,9 @@ def _loaded_scan(name="complete.sras"):
 def test_loaded_scan_basics():
     scan = _loaded_scan()
     assert scan.rows_available == [3, 3]
-    assert scan.background is not None and len(scan.background) == 8
+    # A legacy v6 fixture: its one background stands in for every angle.
+    assert all(scan.background(ai) is not None and len(scan.background(ai)) == 8
+               for ai in (0, 1))
     assert len(scan.calib.ymult_mv) == 3
     view = scan.angle_view(0)
     assert view.shape == (3, 3, 4, 8)

tests/test_sras_format.py

@@ -1,21 +1,27 @@
-"""core.sras_format vs the pre-refactor golden fixtures.
+"""core.sras_format: the current writer against the spec, and the parser
+against the pre-refactor golden fixtures.
 
-The goldens were produced by the original sc3_aui_app implementation; the
+The goldens are legacy v6 files produced by the original sc3_aui_app
-extracted module must reproduce them byte-for-byte (writer) and
+implementation — one background for the whole file.  Nothing writes that
-field-for-field (parser + frontier walk).
+layout any more, so they lock the parser (field-for-field, including the
+frontier walk) rather than the writer.  The writer is locked instead against
+bytes this test lays out from scan_format.md itself.
 """
 import json
+import struct
 from dataclasses import asdict
 from pathlib import Path
 
 import numpy as np
 import pytest
 
-from core.scan_geometry import build_plan
+from core.sras_format import (
-from core.sras_format import SrasFile, create_scan_file
+    BG_LEN_FMT, GEOM_FMT, HDR_FMT, MAGIC, VERSION, VERSION_SAW_CHECK,
+    SrasFile, create_scan_file,
+)
 from golden_util import (
-    BACKGROUND, CHANNELS, LASER_FREQ_HZ, PREAMBLES, SAMPLE_RATE, SPF,
+    BACKGROUND, CHANNELS, PREAMBLES, SAMPLE_RATE, SPF, angle_background,
-    TINY_PLAN_ARGS, VELOCITY_MM_S, synthetic_frame,
+    synthetic_frame, tiny_plan, write_v7,
 )
 
 GOLDEN = Path(__file__).parent / "golden"
@@ -27,28 +33,43 @@ def expected():
         return json.load(f)
 
 
-def _tiny_plan():
+def spec_bytes(plan):
-    return build_plan(**TINY_PLAN_ARGS, laser_freq_hz=LASER_FREQ_HZ,
+    """The v7 layout spelled out from scan_format.md, writer not involved."""
-                      velocity_mm_s=VELOCITY_MM_S)
+    buf = bytearray()
+    buf += struct.pack(HDR_FMT, MAGIC, VERSION, plan.n_angles,
+                       plan.x_start_nominal, plan.y_start_nominal,
+                       plan.x_delta_nominal, plan.y_delta_nominal,
+                       plan.row_spacing, plan.velocity_mm_s, plan.laser_freq_hz,
+                       SPF, SAMPLE_RATE, 1, len(CHANNELS))
+    buf += struct.pack(f">{plan.n_angles}f", *plan.angles)
+    for pa in plan.per_angle:
+        buf += struct.pack(GEOM_FMT, pa.x_start, pa.x_delta, pa.n_frames, pa.n_rows)
+    for pa in plan.per_angle:
+        buf += struct.pack(f">{pa.n_rows}f", *pa.y_positions)
+    for pre in PREAMBLES:
+        buf += struct.pack(">H", len(pre)) + pre.encode("utf-8")
+    for ai, pa in enumerate(plan.per_angle):
+        bg = angle_background(ai)
+        buf += struct.pack(BG_LEN_FMT, len(bg)) + bg
+        for ri in range(pa.n_rows):
+            for ci in range(len(CHANNELS)):
+                for fi in range(pa.n_frames):
+                    buf += synthetic_frame(ai, ri, ci, fi)
+    return bytes(buf)
 
 
-def _write_complete(path):
+def test_writer_matches_the_spec_byte_for_byte(tmp_path):
-    plan = _tiny_plan()
+    out = tmp_path / "v7.sras"
-    f = create_scan_file(path, plan, SPF, SAMPLE_RATE, PREAMBLES, BACKGROUND)
+    plan = write_v7(out)
-    try:
+    assert out.read_bytes() == spec_bytes(plan)
-        for ai, pa in enumerate(plan.per_angle):
-            for ri in range(pa.n_rows):
-                for ci in range(len(CHANNELS)):
-                    for fi in range(pa.n_frames):
-                        f.write(synthetic_frame(ai, ri, ci, fi))
-    finally:
-        f.close()
 
 
-def test_writer_byte_identical_to_golden(tmp_path):
+def test_writer_refuses_the_legacy_versions(tmp_path):
-    out = tmp_path / "rewrite.sras"
+    for version in (6, 10):
-    _write_complete(out)
+        with pytest.raises(ValueError, match=f"version {version}"):
-    assert out.read_bytes() == (GOLDEN / "complete.sras").read_bytes()
+            create_scan_file(tmp_path / "bad.sras", tiny_plan(), SPF,
+                             SAMPLE_RATE, PREAMBLES, version=version)
+        assert not (tmp_path / "bad.sras").exists()
 
 
 def test_header_matches_golden(expected):
@@ -75,15 +96,107 @@ def test_header_matches_golden(expected):
 
 
 def test_frontier_all_truncation_variants(expected):
+    """Every field the goldens recorded, plus the one added since.
+
+    The expectations predate AngleStatus.bg_offset, so they are compared key
+    by key; a v6 angle has no background block of its own, which is exactly
+    what bg_offset == data_offset says.
+
+    Two of the recorded data_offsets were corrected when the walk moved into
+    the parser: an angle past the frontier used to report the frontier's own
+    offset, because the old walk stopped advancing its cursor there, which
+    handed a resumed scan the same write position for every missing angle.
+    They are now the declared position each angle will be written at.
+    """
     for name, exp_statuses in expected["statuses"].items():
         statuses = SrasFile(GOLDEN / name).angle_status()
-        assert [asdict(s) for s in statuses] == exp_statuses, f"mismatch for {name}"
+        assert len(statuses) == len(exp_statuses), f"mismatch for {name}"
+        for status, exp in zip(statuses, exp_statuses, strict=True):
+            got = asdict(status)
+            assert {k: got[k] for k in exp} == exp, f"mismatch for {name}"
+            assert status.bg_offset == status.data_offset
+            assert status.bg_bytes == 0
 
 
-def test_preambles_and_background_roundtrip():
+def test_legacy_preambles_and_shared_background():
+    """A v6 file's one background stands in for every angle's."""
     sras = SrasFile(GOLDEN / "complete.sras")
     assert sras.preambles == PREAMBLES
-    assert sras.background == BACKGROUND
+    assert sras.is_legacy_layout
+    assert sras.backgrounds == [BACKGROUND] * sras.header.n_angles
+    assert np.array_equal(sras.background_array(1),
+                          np.frombuffer(BACKGROUND, dtype=np.int8))
+
+
+# ── Per-angle backgrounds (v7/v11) ───────────────────────────────────────────
+
+def test_each_angle_keeps_its_own_background(tmp_path):
+    out = tmp_path / "v7.sras"
+    plan = write_v7(out)
+
+    sras = SrasFile(out)
+    assert not sras.is_legacy_layout
+    assert sras.backgrounds == [angle_background(ai)
+                                for ai in range(plan.n_angles)]
+    assert [s.status for s in sras.angle_status()] == ["OK"] * plan.n_angles
+    # Every angle's rows start just past its own background block …
+    for st in sras.angle_status():
+        assert st.bg_bytes == 4 + SPF
+        assert st.data_offset == st.bg_offset + st.bg_bytes
+    # … and the data itself still reads back frame for frame.
+    assert sras.load_row(1, 2, 0).tobytes() == b"".join(
+        synthetic_frame(1, 2, 0, fi) for fi in range(plan.per_angle[1].n_frames))
+    sras.close()
+
+
+def test_saw_check_version_also_carries_per_angle_backgrounds(tmp_path):
+    from core.saw_check import middle_row_plan
+    out = tmp_path / "check.sras"
+    plan = write_v7(out, plan=middle_row_plan(tiny_plan()),
+                    version=VERSION_SAW_CHECK)
+
+    sras = SrasFile(out)
+    assert sras.is_saw_check and not sras.is_legacy_layout
+    assert sras.backgrounds == [angle_background(ai)
+                                for ai in range(plan.n_angles)]
+    sras.close()
+
+
+def test_angle_missing_its_background_is_the_frontier(tmp_path):
+    """A file cut inside a background block stops at that angle.
+
+    Nothing of that angle is on disk yet — not even the reference its rows
+    would be read against — so it is MISSING rather than TRUNCATED, and its
+    predicted offsets are where a resumed scan would write.
+    """
+    out = tmp_path / "v7.sras"
+    write_v7(out)
+    whole = out.read_bytes()
+    bg1 = SrasFile(out).angle_status()[1].bg_offset
+
+    for cut, expected_status in ((bg1, "MISSING"), (bg1 + 4 + SPF // 2, "MISSING")):
+        out.write_bytes(whole[:cut])
+        statuses = SrasFile(out).angle_status()
+        assert [s.status for s in statuses] == ["OK", expected_status]
+        assert statuses[1].n_rows_available == 0
+        assert statuses[1].bg_offset == bg1
+        # The absent block is predicted at a full record's worth of bytes,
+        # which is what the writer will produce when the scan resumes.
+        assert statuses[1].data_offset == bg1 + 4 + SPF
+
+
+def test_rows_after_a_background_still_truncate_by_row(tmp_path):
+    out = tmp_path / "v7.sras"
+    plan = write_v7(out)
+    whole = out.read_bytes()
+    st1 = SrasFile(out).angle_status()[1]
+
+    out.write_bytes(whole[:st1.data_offset + 2 * st1.row_bytes])
+    statuses = SrasFile(out).angle_status()
+    assert [s.status for s in statuses] == ["OK", "TRUNCATED"]
+    assert statuses[1].n_rows_available == 2
+    assert SrasFile(out).load_angle(1, n_rows=2).shape[0] == 2
+    assert plan.per_angle[1].n_rows == 3
 
 
 def test_load_angle_memmap_equals_eager():