Expose burst acquisition in the app; refresh scan_format acquisition docs

Wires the burst_mode flag through QtScanController to ScanEngine and adds a
checkbox to the scan panel. The setting persists via ScanDefaults like the
other scan fields, defaulting to off — per-row acquisition stays the default
path until burst mode has run on the rig and the gate-off preflight has
settled which TRIGOUT value idles the pin low.

scan_format.md — the acquisition settings table had drifted from the code it
claimed to describe: it attributed the settings to sc3_aui_app.py (they moved
to core/scope_sras.py in the Phase 2 extraction), listed a 1.24 V trigger
level and 0 % offset where the code sets 0.500 V and HORizontal:POSition 30,
and did not mention the logic-AND scan trigger at all. Corrected, pointed at
the module that actually owns them, and noted that none of it affects byte
layout — only where the acoustic packet lands inside a frame.

Added an acquisition-paths section: the two paths write byte-identical files
and the choice is a runtime flag that is not recorded in the file, so a
reader never needs to care which produced it. Documents where row boundaries
come from in a burst and that either path squares rows up to n_frames.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

core/config.py

@@ -23,6 +23,7 @@ class ScanDefaults:
     oscope_ip: str = "192.168.0.1"
     save_dir: str = str(DEFAULTS_PATH.parent / "scans")
     helios_port: str = "/dev/ttyUSB2"
+    burst_mode: bool = False
 
     @classmethod
     def load(cls, path: Path = DEFAULTS_PATH) -> "ScanDefaults":

core/scan_engine.py

@@ -15,7 +15,7 @@ from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Callable
 
-from core import scope_sras
+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, create_scan_file
@@ -95,7 +95,8 @@ class ScanEngine:
     def __init__(self, stage, scope, rotator: RotationAxis | None,
                  plan: ScanPlan, out_path: Path,
                  resume: ResumeState | None = None,
-                 callbacks: ScanCallbacks | None = None):
+                 callbacks: ScanCallbacks | None = None,
+                 burst_mode: bool = False):
         self._stage = stage
         self._scope = scope
         self._rotator = rotator
@@ -103,6 +104,11 @@ class ScanEngine:
         self._out_path = Path(out_path)
         self._resume = resume
         self._cb = callbacks if callbacks is not None else ScanCallbacks()
+        # Burst mode acquires as many whole rows per FastFrame acquisition as
+        # the scope's frame memory holds, instead of one row per acquisition.
+        self._burst_mode = burst_mode
+        self._max_frames = 0
+        self._preflight_done = False
 
         self._abort = threading.Event()
         self._resume_event = threading.Event()
@@ -207,6 +213,14 @@ class ScanEngine:
             self._scan_loop(scan_file, samples_per_frame, result)
         finally:
             scan_file.close()
+            # Leave the X trigger output inactive.  Burst mode toggles it every
+            # row and could exit from either state; the per-row path used to
+            # leave TRIGOUT_MAXV armed for the rest of the session, which keeps
+            # driving the gate line on every later jog.
+            try:
+                self._stage.set_trigger_gate_off(AXIS_X)
+            except Exception:
+                logger.exception("Could not return the X trigger output to idle")
             # Return the GR axis home regardless of abort or error
             if rotator_ready and abs(self._rotator.current_deg) > 0.001:
                 self._cb.on_status("Returning GR to home …")
@@ -242,7 +256,13 @@ class ScanEngine:
                                  acceleration=SCAN_ACCEL_MM_S2)
         ctrl.set_velocity_params(AXIS_Y, max_velocity=SCAN_VELOCITY_MM_S,
                                  acceleration=SCAN_ACCEL_MM_S2)
-        # X trigger: logic-high output while the stage is at maximum velocity
+        # X trigger: logic-high output while the stage is at maximum velocity.
+        # Burst mode arms it per acquiring pass instead — a burst spans several
+        # rows with the scope running throughout, so leaving it armed would let
+        # the flyback trigger frames between rows.
+        if self._burst_mode:
+            ctrl.arm_scan_gate(AXIS_X, False)
+        else:
             ctrl.set_trigger_trigout_maxv(AXIS_X)
 
     def _prepare_scope(self) -> int:
@@ -290,6 +310,16 @@ class ScanEngine:
             )
 
         scope_sras.configure_scan_trigger(self._scope)
+
+        if self._burst_mode:
+            # Horizontal settings are fixed by now, so the capacity is stable
+            # for the whole scan; only rows-per-burst varies (n_frames is
+            # per-angle).
+            self._max_frames = scope_burst.max_frames(self._scope)
+            self._cb.on_status(
+                f"Burst mode: scope holds {self._max_frames} frames "
+                f"({samples_per_frame} samples/frame)"
+            )
         return samples_per_frame
 
     def _open_output(self, samples_per_frame: int, result: ScanResult):
@@ -309,7 +339,6 @@ class ScanEngine:
         plan = self._plan
         n_angles = plan.n_angles
         x_ramp_total = SCAN_RAMP_MM + SCAN_RAMP_BUFFER_MM
-        ctrl = self._stage
         scope = self._scope
 
         targets_by_ai = None
@@ -337,9 +366,28 @@ class ScanEngine:
                         f"Rotating GR to {pa.angle_deg:.1f}° (Δ{delta:+.1f}°) …")
                     self._rotator.rotate_to(pa.angle_deg)
 
-            # Each angle's bounding box gives it its own points/row count, so
-            # the scope's FastFrame count must be re-armed per angle.
+            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
+                # nothing to re-arm per angle here.
+                self._scan_rows_burst(scan_file, pa, ai, n_angles,
+                                      samples_per_frame, result, x_ramp_total)
+            else:
+                # Each angle's bounding box gives it its own points/row count,
+                # so the scope's FastFrame count must be re-armed per angle.
                 scope.set_fastframe_count(pa.n_frames)
+                self._scan_rows_serial(scan_file, pa, ai, n_angles,
+                                       samples_per_frame, result, x_ramp_total)
+
+            result.angles_acquired.append(ai)
+
+    # ── Per-row acquisition (one FastFrame acquisition per row) ───────────────
+
+    def _scan_rows_serial(self, scan_file, pa, ai: int, n_angles: int,
+                          samples_per_frame: int, result: ScanResult,
+                          x_ramp_total: float):
+        ctrl = self._stage
+        scope = self._scope
 
         for ri, y_pos in enumerate(pa.y_positions):
             self._pause_point()
@@ -363,31 +411,208 @@ class ScanEngine:
             ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
 
             scope_sras.finish_row(scope)
-                self._write_row(scan_file, samples_per_frame, ri)
+            self._write_row(scan_file, samples_per_frame, ri, pa.n_frames)
 
             result.rows_written += 1
             self._cb.on_row_done(ri + 1, pa.n_rows, ai + 1, n_angles)
 
-            result.angles_acquired.append(ai)
-
-    def _write_row(self, scan_file, samples_per_frame: int, row_idx: int):
+    def _write_row(self, scan_file, samples_per_frame: int, row_idx: int,
+                   n_frames: int):
         """Stream every channel from the scope into the file.
 
         CH3 is the max-vel gate signal — no useful waveform data — so zeroed
         frames are written to keep the file layout intact.
         """
         scope = self._scope
+        ch_bytes = n_frames * samples_per_frame
         for ch in SCAN_CHANNELS:
             if ch == 3:
                 self._cb.on_status("Writing zeroed CH3 frames …")
-                zero_frame = bytes(samples_per_frame)
-                for _ in range(scope_sras.frames_acquired(scope)):
-                    scan_file.write(zero_frame)
+                scan_file.write(bytes(ch_bytes))
                 continue
 
             self._cb.on_status(f"Fetching CH{ch} data …")
             waveforms = scope_sras.transfer_channel(scope, ch)
-            if ch == 4 and waveforms:
-                self._cb.on_dc_bias(row_idx + 1, scope_sras.frame_means(waveforms))
-            for w in waveforms:
-                scan_file.write(w)
+            if ch == SCAN_CHANNELS[0]:
+                self._warn_frame_delta(row_idx, len(waveforms), n_frames)
+            row = scope_burst.normalize_row(
+                b"".join(waveforms), 0, len(waveforms), n_frames, samples_per_frame)
+            if ch == 4:
+                self._cb.on_dc_bias(row_idx + 1, scope_burst.frame_means_block(
+                    row, 0, n_frames, samples_per_frame))
+            scan_file.write(row)
+
+    # ── Burst acquisition (many whole rows per FastFrame acquisition) ─────────
+
+    def _scan_rows_burst(self, scan_file, pa, ai: int, n_angles: int,
+                         samples_per_frame: int, result: ScanResult,
+                         x_ramp_total: float):
+        """Acquire the angle in bursts of as many whole rows as the scope holds.
+
+        One ACQuire:STATE RUN spans the whole burst, so the gate is armed only
+        for each acquiring pass and dropped for the flyback — otherwise the
+        return move would reach max velocity and inject frames between rows.
+        """
+        scope = self._scope
+        n_frames = pa.n_frames
+        x_lead_in = pa.x_start - x_ramp_total
+        x_end = pa.x_start + pa.x_delta + x_ramp_total
+
+        if not self._preflight_done:
+            # Once per scan: the gate wiring can't change between angles, and
+            # the check costs two row-times.
+            self._gate_off_preflight(x_lead_in, x_end)
+            self._preflight_done = True
+
+        row = 0
+        while row < pa.n_rows:
+            self._pause_point()
+            n_burst = scope_burst.rows_per_burst(
+                self._max_frames, n_frames, samples_per_frame, pa.n_rows - row)
+            self._cb.on_status(
+                f"Angle {ai+1}/{n_angles}  Rows {row+1}-{row+n_burst}/{pa.n_rows} "
+                f"in one acquisition ({n_burst * n_frames} frames) …"
+            )
+
+            burst_start = scan_file.tell()
+            cumulative = []
+            baseline = scope_burst.start_burst(scope, self._max_frames)
+            try:
+                for r in range(n_burst):
+                    self._check_abort()
+                    self._cb.on_row_started(row + r + 1, pa.n_rows,
+                                            ai + 1, n_angles)
+                    self._acquire_gated_row(pa.y_positions[row + r],
+                                            x_lead_in, x_end)
+                    total = scope_burst.frames_acquired(scope)
+                    if total >= self._max_frames:
+                        raise RuntimeError(
+                            f"FastFrame buffer full ({total}/{self._max_frames} "
+                            f"frames) at row {row + r + 1} — later rows in this "
+                            "burst would be misattributed.  Raise "
+                            "scope_burst.BURST_FRAME_HEADROOM and rerun."
+                        )
+                    cumulative.append(total - baseline)
+            finally:
+                scope_burst.stop_burst(scope)
+
+            counts = scope_burst.split_row_counts(cumulative)
+            self._write_burst(scan_file, burst_start, row, counts,
+                              n_frames, samples_per_frame)
+
+            for r in range(n_burst):
+                result.rows_written += 1
+                self._cb.on_row_done(row + r + 1, pa.n_rows, ai + 1, n_angles)
+            row += n_burst
+
+    def _acquire_gated_row(self, y_pos: float, x_lead_in: float, x_end: float):
+        """One row: step Y, fly back gated off, then acquire on the +X pass."""
+        ctrl = self._stage
+        ctrl.move_axis_absolute(AXIS_Y, y_pos, timeout=60.0)
+        ctrl.move_axis_absolute(AXIS_X, x_lead_in, timeout=30.0)
+        ctrl.arm_scan_gate(AXIS_X, True)
+        ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
+        ctrl.arm_scan_gate(AXIS_X, False)
+        time.sleep(scope_burst.BURST_ROW_SETTLE_S)
+
+    def _gate_off_preflight(self, x_lead_in: float, x_end: float):
+        """Prove the gate really gates before trusting a multi-row burst.
+
+        The value that makes the BBD trigger output idle low is not settled by
+        the protocol docs (see apt_constants.TRIGOUT_GATE_OFF), and getting it
+        wrong fills every burst with flyback frames that silently shift the
+        file.  The scope already measures the gate on CH3, so this needs no
+        bench probe: one gated-off flyback must acquire nothing, and one gated
+        pass must acquire something — the second half is what stops a dark
+        laser from making the first half pass vacuously.
+
+        Leaves the stage parked at x_end, where the burst loop expects it.
+        """
+        ctrl, scope = self._stage, self._scope
+        self._cb.on_status("Burst preflight: checking the stage gate …")
+
+        ctrl.arm_scan_gate(AXIS_X, False)
+        ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
+        baseline = scope_burst.start_burst(scope, self._max_frames)
+        ctrl.move_axis_absolute(AXIS_X, x_lead_in, timeout=120.0)
+        scope_burst.stop_burst(scope)
+        leaked = scope_burst.frames_acquired(scope) - baseline
+
+        ctrl.arm_scan_gate(AXIS_X, True)
+        baseline = scope_burst.start_burst(scope, self._max_frames)
+        ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
+        ctrl.arm_scan_gate(AXIS_X, False)
+        scope_burst.stop_burst(scope)
+        gated = scope_burst.frames_acquired(scope) - baseline
+
+        if gated <= 0:
+            raise RuntimeError(
+                "Burst preflight: no frames acquired with the gate armed. "
+                "Check that the Genesis laser is pulsing (CH2) and that the "
+                "BBD X trigger output reaches CH3 before scanning."
+            )
+        if leaked:
+            raise RuntimeError(
+                f"Burst preflight: {leaked} frame(s) acquired during a flyback "
+                "that should have been gated off — the BBD trigger output is "
+                "not idling low.  Set apt_constants.TRIGOUT_GATE_OFF to "
+                "TriggerBitsServo.TRIGOUT_HIGH and retry, or use per-row "
+                "acquisition."
+            )
+        self._cb.on_status(
+            f"Burst preflight OK ({gated} frames gated on, 0 leaked).")
+
+    def _write_burst(self, scan_file, burst_start: int, first_row: int,
+                     counts: list[int], n_frames: int, samples_per_frame: int):
+        """Deinterleave one burst into the file's per-row, per-channel blocks.
+
+        The wire is channel-major (every row of CH1, then every row of CH4);
+        the file is row-major with channels inner.  Writing one channel at a
+        time to strided offsets keeps peak memory at a single channel's burst
+        instead of the whole thing.
+        """
+        scope = self._scope
+        ch_bytes = n_frames * samples_per_frame
+        row_bytes = len(SCAN_CHANNELS) * ch_bytes
+        total_frames = sum(counts)
+
+        for r, count in enumerate(counts):
+            self._warn_frame_delta(first_row + r, count, n_frames)
+
+        for ch_idx, ch in enumerate(SCAN_CHANNELS):
+            if ch == 3:
+                self._cb.on_status("Writing zeroed CH3 frames …")
+                blob = None
+            else:
+                self._cb.on_status(
+                    f"Fetching CH{ch} burst ({total_frames} frames) …")
+                blob = scope_burst.transfer_burst(scope, ch, total_frames,
+                                                  samples_per_frame)
+            src = 0
+            zeros = bytes(ch_bytes) if blob is None else None
+            for r, count in enumerate(counts):
+                scan_file.seek(burst_start + r * row_bytes + ch_idx * ch_bytes)
+                if blob is None:
+                    scan_file.write(zeros)
+                else:
+                    row = scope_burst.normalize_row(
+                        blob, src, count, n_frames, samples_per_frame)
+                    if ch == 4:
+                        self._cb.on_dc_bias(
+                            first_row + r + 1,
+                            scope_burst.frame_means_block(
+                                row, 0, n_frames, samples_per_frame))
+                    scan_file.write(row)
+                src += count * samples_per_frame
+            del blob
+
+        scan_file.seek(burst_start + len(counts) * row_bytes)
+
+    def _warn_frame_delta(self, row_idx: int, count: int, n_frames: int):
+        if count == n_frames:
+            return
+        verb = "zero-padded" if count < n_frames else "truncated"
+        msg = (f"Row {row_idx + 1}: {count} frames acquired, {n_frames} "
+               f"expected — {verb} to keep the file layout intact.")
+        logger.warning(msg)
+        self._cb.on_status(msg)

core/scope_burst.py

@@ -0,0 +1,149 @@
+"""Burst-mode FastFrame acquisition policy.
+
+Per-row acquisition pays a full arm/stop/transfer round trip for every row,
+and the transfer alone is one IEEE-488.2 block read per frame (~16k frames a
+row).  A burst instead runs one FastFrame acquisition across as many complete
+rows as the scope's frame memory holds, then pulls the whole thing in a single
+transaction — amortising the round trip over `rows_per_burst` rows.
+
+The scope reports its capacity with ``HORizontal:FASTframe:MAXFRames?`` once
+the horizontal settings are fixed; ``rows_per_burst`` turns that into a row
+count.  Everything here that computes rather than talks to hardware is a free
+function, so the row-splitting logic is testable without a rig.
+
+The catch is that the burst contains no row markers: the scope hands back one
+flat run of frames.  Boundaries come from polling ``ACQuire:NUMFRAMESACQuired?``
+after each row's acquiring pass, while the stage gate is already low — see
+``split_row_counts``.
+"""
+from __future__ import annotations
+
+import logging
+import time
+
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
+# Peak transfer buffer, per channel.  The writer holds one channel at a time
+# (see ScanEngine._scan_rows_burst), so this is the real high-water mark.
+BURST_MEMORY_BUDGET_BYTES = 512 * 1024 * 1024
+
+# Extra frames budgeted per row on top of n_frames.  0 gives the plain
+# floor(max_frames / n_frames) row count; raise it if the acquiring pass
+# routinely over-triggers (watch the pad/truncate warnings).
+BURST_FRAME_HEADROOM = 0
+
+BURST_ARM_SETTLE_S = 0.05   # after ACQuire:STATE RUN, before the first move
+BURST_ROW_SETTLE_S = 0.05   # after the gate drops, before reading the counter
+
+
+# ── Pure helpers ─────────────────────────────────────────────────────────────
+
+def rows_per_burst(max_frames: int, n_frames: int, samples_per_frame: int,
+                   rows_remaining: int,
+                   memory_budget: int = BURST_MEMORY_BUDGET_BYTES,
+                   headroom: int = BURST_FRAME_HEADROOM) -> int:
+    """How many complete rows fit in one acquisition.
+
+    Rounds down — a partial row is worthless, since a row must be transferred
+    whole to be written.  Clamped by the transfer buffer budget and by the rows
+    actually left in the angle, and never below 1 (a single row always goes,
+    even if it exceeds the budget, so the scan can still make progress).
+    """
+    if n_frames < 1 or samples_per_frame < 1:
+        raise ValueError(f"n_frames={n_frames} samples_per_frame={samples_per_frame}")
+
+    by_scope = max_frames // (n_frames + headroom)
+    by_memory = memory_budget // (n_frames * samples_per_frame)
+    return max(1, min(by_scope, by_memory, rows_remaining))
+
+
+def split_row_counts(cumulative: list[int]) -> list[int]:
+    """Per-row frame counts from the cumulative counter sampled after each row.
+
+    ``cumulative`` is ``ACQuire:NUMFRAMESACQuired?`` read once per row, already
+    rebased on the value at burst start.
+    """
+    counts = []
+    prev = 0
+    for i, c in enumerate(cumulative):
+        if c < prev:
+            raise RuntimeError(
+                f"FastFrame counter went backwards at row {i} ({prev} → {c}) — "
+                "the acquisition was restarted mid-burst"
+            )
+        counts.append(c - prev)
+        prev = c
+    return counts
+
+
+def normalize_row(buf, offset: int, count: int, n_frames: int,
+                  samples_per_frame: int):
+    """Coerce one row's frames to exactly ``n_frames``.
+
+    The v6 format commits to n_frames per row in the header and has no per-row
+    length field, so a row that over- or under-triggers must be squared up or
+    every later row in the file shifts.  Short rows are zero-padded, long rows
+    lose their trailing frames.  Returns something writable directly.
+    """
+    want = n_frames * samples_per_frame
+    end = min(offset + count * samples_per_frame, offset + want, len(buf))
+    chunk = memoryview(buf)[offset:end]
+    if len(chunk) == want:
+        return chunk
+    return bytes(chunk) + bytes(want - len(chunk))
+
+
+def frame_means_block(buf, offset: int, n_frames: int,
+                      samples_per_frame: int) -> list[float]:
+    """Per-frame DC mean over one row's slice of a burst buffer."""
+    n = n_frames * samples_per_frame
+    block = np.frombuffer(buf, dtype=np.int8, count=n, offset=offset)
+    return block.reshape(n_frames, samples_per_frame).mean(
+        axis=1, dtype=np.float32).tolist()
+
+
+# ── Instrument control ───────────────────────────────────────────────────────
+
+def max_frames(scope) -> int:
+    """Frames the scope can hold under the current horizontal settings."""
+    try:
+        m = scope.get_fastframe_max_frames()
+    except Exception as exc:
+        raise RuntimeError(
+            "Scope did not answer HORizontal:FASTframe:MAXFRames? — burst mode "
+            "cannot size a burst without it.  Use per-row acquisition on this "
+            f"firmware. ({exc})"
+        ) from exc
+    if m < 1:
+        raise RuntimeError(f"Scope reports a FastFrame capacity of {m} frames")
+    return m
+
+
+def start_burst(scope, frame_count: int) -> int:
+    """Arm one burst; returns the counter baseline to subtract from later reads.
+
+    Reading the baseline back beats assuming the counter resets to 0 on RUN —
+    any residual is simply subtracted out instead of being misattributed to the
+    first row.
+    """
+    scope.set_fastframe_count(frame_count)
+    scope.write("ACQuire:STATE RUN")
+    time.sleep(BURST_ARM_SETTLE_S)
+    return frames_acquired(scope)
+
+
+def stop_burst(scope) -> None:
+    time.sleep(BURST_ROW_SETTLE_S)
+    scope.write("ACQuire:STATE STOP")
+
+
+def frames_acquired(scope) -> int:
+    return int(scope.query("ACQuire:NUMFRAMESACQuired?"))
+
+
+def transfer_burst(scope, ch: int, frame_count: int, samples_per_frame: int):
+    """Pull a whole burst for one channel in a single CURVe? transaction."""
+    scope.set_data_source(ch)
+    return scope.transfer_fastframe_bulk(frame_count, samples_per_frame)

core/scope_sras.py

@@ -10,8 +10,6 @@ import logging
 import time
 from dataclasses import dataclass
 
-import numpy as np
-
 logger = logging.getLogger(__name__)
 
 SAMPLE_RATE_HZ = 6.25e9    # 6.25 GS/s → 160 ps/sample
@@ -66,6 +64,11 @@ 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)
+    # 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.
+    scope.set_data_encoding("RIBinary")
+    scope.set_data_width(1)
     scope.set_sample_rate(SAMPLE_RATE_HZ)
     scope.write("HORizontal:POSition 30")  # 10 % trigger offset
     time.sleep(0.3)                        # let the timebase settle before reading back
@@ -140,28 +143,7 @@ def finish_row(scope) -> None:
     scope.write("ACQuire:STATE STOP")
 
 
-def frames_acquired(scope) -> int:
-    return int(scope.query("ACQuire:NUMFRAMESACQuired?"))
-
-
 def transfer_channel(scope, ch: int) -> list[bytes]:
     """Fetch one channel's FastFrame block as raw int8 frames."""
     scope.set_data_source(ch)
     return scope.transfer_fastframe(parse=False)
-
-
-def frame_means(waveforms: list[bytes]) -> list[float]:
-    """Per-frame DC mean of a raw int8 FastFrame block.
-
-    numpy over the joined buffer: the per-frame struct.unpack this replaces
-    allocated a tuple of Python ints per frame (~16k frames per row).
-    """
-    if not waveforms:
-        return []
-    n = len(waveforms[0])
-    if n == 0 or any(len(w) != n for w in waveforms):
-        # Ragged block (shouldn't happen) — fall back to per-frame means.
-        return [float(np.frombuffer(w, dtype=np.int8).mean()) if len(w) else 0.0
-                for w in waveforms]
-    block = np.frombuffer(b"".join(waveforms), dtype=np.int8).reshape(len(waveforms), n)
-    return block.mean(axis=1, dtype=np.float32).tolist()

gui/scan_bridge.py

@@ -32,7 +32,7 @@ class QtScanController(QObject):
     paused_changed = pyqtSignal(bool)                 # True while paused at a row boundary
 
     def __init__(self, stage, scope, rotator, plan, out_path,
-                 resume=None, on_scan_active=None):
+                 resume=None, on_scan_active=None, burst_mode=False):
         super().__init__()
         self._prompt_event = threading.Event()
         self._on_scan_active = on_scan_active
@@ -47,7 +47,8 @@ class QtScanController(QObject):
             prompt=self._blocking_prompt,
         )
         self._engine = ScanEngine(stage, scope, rotator, plan, out_path,
-                                  resume=resume, callbacks=callbacks)
+                                  resume=resume, callbacks=callbacks,
+                                  burst_mode=burst_mode)
 
     # ── Engine control (called from the GUI thread) ───────────────────────────
 

hardware/pybbd202/apt_constants.py

@@ -45,5 +45,20 @@ class TriggerBitsServo(IntFlag):
     TRIGOUT_MAXV = TRIGOUT_HIGH | TRIGOUT_MAXVELOCITY
 
 
+# Gate off: no trigger-out function selected, so the pin idles inactive.
+#
+# Treat this as unverified until it has been checked on the rig.  §7.6 of
+# docs/hardware/BBD203_Communications_Protocol.md documents `mode` as an
+# enumeration capping at 0x11, which flatly contradicts the bitmask this
+# driver actually sends (TRIGOUT_MAXV = 0x90, known working), so the doc
+# cannot settle what makes the pin idle low.  Under the bitmask reading 0x00
+# clears everything and the pin sits low.  If instead TRIGOUT_HIGH is an
+# active-high *polarity* bit, clearing it means active-low and the pin idles
+# HIGH — which in burst mode floods the acquisition with flyback frames.
+# ScanEngine's gate-off preflight catches that; if it trips, change this to
+# TriggerBitsServo.TRIGOUT_HIGH.
+TRIGOUT_GATE_OFF = TriggerBitsServo(0)
+
+
 
 

hardware/pybbd202/bbd20x.py

@@ -7,7 +7,7 @@
 import time
 from threading import Thread, Event
 from queue import Queue, Empty
-from .apt_constants import StatusBits, TriggerBitsServo
+from .apt_constants import StatusBits, TriggerBitsServo, TRIGOUT_GATE_OFF
 from .apt_messages import APTProtocol
 from .serial_comms import SerialSnooper
 
@@ -465,3 +465,42 @@ class ThorlabsServoDriver():
     def set_trigger_trigout_maxv(self, axis):
         '''Set trigger output high + pulse at max velocity (TRIGOUT_MAXV).'''
         self.set_trigger(axis, TriggerBitsServo.TRIGOUT_MAXV)
+
+    def set_trigger_gate_off(self, axis):
+        '''Drive the trigger output inactive, so no pulses reach the gate.'''
+        self.set_trigger(axis, TRIGOUT_GATE_OFF)
+
+    def arm_scan_gate(self, axis, armed, verify=True):
+        '''
+            arm_scan_gate(axis, armed): Arms or drops the max-velocity trigger
+            output the oscilloscope AND-gate uses.
+
+            Burst acquisition runs one scope acquisition across many rows, so
+            the gate must be armed only for the acquiring pass and dropped for
+            the flyback — otherwise the return move hits max velocity and
+            injects frames between rows.
+        '''
+        mode = TriggerBitsServo.TRIGOUT_MAXV if armed else TRIGOUT_GATE_OFF
+        if verify:
+            self.set_trigger_verified(axis, mode)
+        else:
+            self.set_trigger(axis, mode)
+
+    def set_trigger_verified(self, axis, mode, timeout=5.0, retries=2):
+        '''
+            set_trigger_verified(axis, mode): Sets the trigger mode and reads
+            it back to confirm it landed.
+
+            set_trigger is fire-and-forget over the shared TX queue.  Burst
+            acquisition toggles the gate between every row, and a dropped
+            change there silently fills the acquisition with flyback frames —
+            so confirm rather than assume.
+        '''
+        for _ in range(retries + 1):
+            self.set_trigger(axis, mode)
+            if int(self.get_trigger(axis, timeout=timeout)) == int(mode):
+                return
+        raise RuntimeError(
+            f"Axis 0x{axis:02X} did not accept trigger mode 0x{int(mode):02X} "
+            f"after {retries + 1} attempts"
+        )

hardware/tektronix_base.py

@@ -183,6 +183,10 @@ class TektronixOscilloscopeBase:
 
         self.write(f"HORizontal:FASTframe:COUNt {count}")
 
+    def get_fastframe_max_frames(self):
+        """Query how many FastFrame frames the current horizontal settings allow."""
+        return int(self.query("HORizontal:FASTframe:MAXFRames?"))
+
     def get_record_length(self):
         """Query the current horizontal record length."""
         response = self.query("HORizontal:MODe:RECOrdlength?")
@@ -361,6 +365,21 @@ class TektronixOscilloscopeBase:
 
         self.write(f"DATa:SOUrce {source}")
 
+    def set_data_encoding(self, encoding):
+        """Set the curve transfer encoding (e.g. RIBinary = signed int, MSB first)."""
+        valid = ('ASCII', 'RIBinary', 'RPBinary', 'FPBinary',
+                 'SRIbinary', 'SRPbinary', 'SFPbinary')
+        if encoding.upper() not in [v.upper() for v in valid]:
+            raise ValueError(f"Invalid data encoding: {encoding}. "
+                             f"Valid options: {', '.join(valid)}")
+        self.write(f"DATa:ENCdg {encoding}")
+
+    def set_data_width(self, width):
+        """Set bytes per sample for curve transfers."""
+        if width not in (1, 2):
+            raise ValueError(f"Invalid data width: {width}. Must be 1 or 2")
+        self.write(f"DATa:WIDth {width}")
+
     def query_wfmoutpre(self):
         """Query all waveform output preamble parameters."""
         return self.query("WFMOutpre?")
@@ -455,6 +474,43 @@ class TektronixOscilloscopeBase:
 
         return waveforms
 
+    def transfer_fastframe_bulk(self, frame_count, samples_per_frame,
+                                bytes_per_sample=1):
+        """Transfer a whole FastFrame burst as one contiguous buffer.
+
+        Unlike transfer_fastframe this does not care how the scope frames the
+        response — it accumulates blocks until it has the expected byte count,
+        so one large IEEE block and one block per frame both work.  Returns a
+        bytearray of frame_count * samples_per_frame * bytes_per_sample bytes.
+        """
+        if not self.get_fastframe_state():
+            raise RuntimeError("FastFrame is not enabled. Enable it with set_fastframe_state(True)")
+
+        expected = frame_count * samples_per_frame * bytes_per_sample
+        if expected <= 0:
+            raise RuntimeError(
+                f"Nothing to transfer: {frame_count} frames × "
+                f"{samples_per_frame} samples × {bytes_per_sample} bytes"
+            )
+
+        self.write("CURVe?")
+
+        buf = bytearray()
+        while len(buf) < expected:
+            block = self.read_raw(expected_bytes=expected - len(buf))
+            if not block:
+                raise RuntimeError(
+                    f"Scope returned an empty block {len(buf)}/{expected} bytes "
+                    "into the burst transfer"
+                )
+            buf += block
+
+        if len(buf) != expected:
+            raise RuntimeError(
+                f"Burst transfer overran: got {len(buf)} bytes, expected {expected}"
+            )
+        return buf
+
     def parse_curve_data(self, curve_bytes, byte_count=1, signed=True, byte_order='MSB'):
         """Parse raw curve data into integer array."""
         if byte_count not in (1, 2):
@@ -526,7 +582,19 @@ class TektronixOscilloscopeBase:
 
         return response.decode('ascii').strip()
 
-    def read_raw(self):
+    def _recv_exact(self, count):
+        """Read exactly `count` bytes; recv() is free to return fewer."""
+        chunks = []
+        remaining = count
+        while remaining > 0:
+            chunk = self.socket.recv(min(remaining, 65536))
+            if not chunk:
+                raise RuntimeError("Connection closed while reading data")
+            chunks.append(chunk)
+            remaining -= len(chunk)
+        return b''.join(chunks)
+
+    def read_raw(self, expected_bytes=None):
         """
         Read raw binary data from the instrument.
 
@@ -535,6 +603,10 @@ class TektronixOscilloscopeBase:
         where N is a digit indicating how many digits follow,
         and those digits specify the length of the data block.
 
+        `#0` announces an indeterminate-length block, normally delimited by EOI
+        — which a raw socket never sees.  Pass expected_bytes to say how many
+        bytes to take in that case.
+
         Returns:
             bytes: Raw binary data (without IEEE 488.2 header)
 
@@ -564,27 +636,24 @@ class TektronixOscilloscopeBase:
 
         num_digits = int(length_of_length)
 
-        # Read the data length
-        length_bytes = self.socket.recv(num_digits)
-        if len(length_bytes) != num_digits:
-            raise RuntimeError("Failed to read data length")
+        if num_digits == 0:
+            # Indeterminate length: no byte count follows, and the EOI that
+            # would delimit it does not exist on a raw socket.
+            if expected_bytes is None:
+                raise RuntimeError(
+                    "Scope returned an indeterminate-length block (#0); "
+                    "read_raw needs expected_bytes to size it over a socket"
+                )
+            data_length = expected_bytes
+        else:
+            data_length = int(self._recv_exact(num_digits))
 
-        data_length = int(length_bytes)
+        data = self._recv_exact(data_length)
 
-        # Read the actual binary data
-        chunks = []
-        remaining = data_length
-        while remaining > 0:
-            chunk = self.socket.recv(min(remaining, 65536))
-            if not chunk:
-                raise RuntimeError("Connection closed while reading data")
-            chunks.append(chunk)
-            remaining -= len(chunk)
+        # Read the trailing newline / block separator
+        self._recv_exact(1)
 
-        # Read the trailing newline
-        self.socket.recv(1)
-
-        return b''.join(chunks)
+        return data
 
     @property
     def is_connected(self):

sc3-aui-main.ui

@@ -997,6 +997,16 @@
         </property>
        </widget>
       </item>
+      <item>
+       <widget class="QCheckBox" name="burst_mode_check">
+        <property name="toolTip">
+         <string>Acquire as many whole rows per FastFrame acquisition as the scope can hold, and transfer each burst in one CURVe? transaction. The stage trigger output is gated off for the flyback between rows.</string>
+        </property>
+        <property name="text">
+         <string>Burst acquisition (multi-row FastFrame)</string>
+        </property>
+       </widget>
+      </item>
       <item>
        <widget class="QPushButton" name="start_scan_btn">
         <property name="text">

sc3_aui_app.py

@@ -917,6 +917,7 @@ class MainWindow(QMainWindow):
         self.row_spacing_edit.setText("0.250")
         self.scan_prefix_edit.setText("scan")
         self.scan_save_dir_edit.setText(DEFAULTS.save_dir)
+        self.burst_mode_check.setChecked(DEFAULTS.burst_mode)
 
         # Hide the old T3R manual controls; the connect toggle becomes the panel button.
         for w in (
@@ -977,6 +978,7 @@ class MainWindow(QMainWindow):
         self.t3r_comport_edit.editingFinished.connect(self._persist_defaults)
         self.bbd202_comport_edit.editingFinished.connect(self._persist_defaults)
         self.oscope_ip_edit.editingFinished.connect(self._persist_defaults)
+        self.burst_mode_check.toggled.connect(self._persist_defaults)
 
         # Camera
         self.show_camera_toggle.toggled.connect(self._on_camera_toggle)
@@ -1134,6 +1136,7 @@ class MainWindow(QMainWindow):
         DEFAULTS.bbd_port = self.bbd202_comport_edit.text().strip()
         DEFAULTS.oscope_ip = self.oscope_ip_edit.text().strip()
         DEFAULTS.save_dir = self.scan_save_dir_edit.text().strip()
+        DEFAULTS.burst_mode = self.burst_mode_check.isChecked()
         DEFAULTS.save()
 
     # ── Camera toggle ─────────────────────────────────────────────────────────
@@ -1257,6 +1260,7 @@ class MainWindow(QMainWindow):
             # a worker concern, not the engine's.
             on_scan_active=lambda active: setattr(
                 self._bbd_worker, "scanning_active", active),
+            burst_mode=self.burst_mode_check.isChecked(),
         )
         self._scan_worker.moveToThread(self._scan_thread)
         self._scan_thread.started.connect(self._scan_worker.run)

scan_format.md

@@ -183,19 +183,49 @@ using that angle's `x_start` from the Per-Angle Geometry Table (not
 
 ---
 
-## Acquisition Settings (fixed by sc3_aui_app.py)
+## Acquisition Settings (fixed by core/scope_sras.py)
 
 | Parameter            | Value                                    |
-|-----------------------|------------------------------|
-| Oscilloscope trigger | CH2, rising edge, 1.24 V     |
-| Trigger offset       | 0 % (trigger at left edge)   |
+|-----------------------|------------------------------------------|
+| Setup trigger        | CH2, rising edge, 0.500 V (`TRIG_LEVEL_V`) |
+| Scan trigger         | Logic AND, CH2 HIGH ∧ CH3 HIGH, 0.500 V  |
+| Horizontal position  | 30 (`HORizontal:POSition`)               |
 | Sample rate          | 6.25 GS/s  (160 ps/sample)               |
+| Transfer format      | `DATa:ENCdg RIBinary`, `DATa:WIDth 1`    |
 | Channels recorded    | CH1, CH3, CH4                            |
 | Stage X velocity     | 100 mm/s                                 |
 | Stage X acceleration | 1500 mm/s²                               |
-| Stage X trigger out  | Logic-high at max velocity   |
+| Stage X trigger out  | Logic-high at max velocity (`TRIGOUT_MAXV`) |
 | Acquisition mode     | FastFrame, Normal trigger                |
 
+None of these are stored in the file, so they do not affect byte layout — but
+they do set where the acoustic packet lands inside each frame.  Read them from
+`core/scope_sras.py`; earlier revisions of this table drifted from the code.
+
+---
+
+## Acquisition Paths
+
+Two acquisition strategies write **byte-identical** files; the choice is a
+runtime flag (`ScanEngine(burst_mode=…)`, exposed as a checkbox in the app) and
+is not recorded in the file.
+
+| | Per-row (default) | Burst |
+|---|---|---|
+| FastFrame acquisitions | one per row | one per `floor(max_frames / n_frames)` rows |
+| 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 |
+
+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
+`ACQuire:NUMFRAMESACQuired?` sampled after each pass — the burst itself carries
+no row markers.  See `core/scope_burst.py`.
+
+Either path squares each row up to the declared `n_frames` (zero-padding a
+short row, dropping the tail of a long one), because the format has no per-row
+length field and a mismatch would shift every later row.
+
 ---
 
 ## Version History

tests/fakes.py

@@ -3,9 +3,24 @@
 Each fake records an ordered call trace, so a test can assert the exact
 command sequence the engine issues — the property that matters when the
 real rig isn't available.
+
+The stage and scope are wired together the way the rig is: an X move at scan
+velocity with the trigger gate armed feeds frames into a running acquisition,
+at the real 20 kHz / 100 mm/s rate.  Per-row and burst acquisition therefore
+get their frame counts from the same model, which is what makes a
+byte-identity comparison between the two paths meaningful — and it means a
+gate the engine forgets to drop shows up as extra frames instead of passing
+silently.
 """
 from __future__ import annotations
 
+from core.scan_engine import (
+    AXIS_X, LASER_FREQ_HZ, SCAN_RAMP_BUFFER_MM, SCAN_RAMP_MM,
+    SCAN_VELOCITY_MM_S,
+)
+
+RAMP_TOTAL_MM = SCAN_RAMP_MM + SCAN_RAMP_BUFFER_MM
+
 
 class Trace:
     """Ordered record of hardware calls, shared by all fakes in one test."""
@@ -29,29 +44,59 @@ class Trace:
 class FakeStage:
     """Stands in for ThorlabsServoDriver."""
 
-    def __init__(self, trace: Trace, homed=(True, True), enabled=(True, True)):
+    def __init__(self, trace: Trace, homed=(True, True), enabled=(True, True),
+                 scope=None):
         self._t = trace
         self.am_homed = list(homed)
         self.am_enabled = list(enabled)
         self.positions = [0.0, 0.0]
+        self._scope = scope
+        self.gate_armed = False
+
+    def attach_scope(self, scope):
+        """Route gated motion into `scope`, as the TRIGOUT pin does on the rig."""
+        self._scope = scope
 
     def enable_axis(self, axis):
         self._t.record("enable_axis", axis)
-        self.am_enabled[0 if axis == 0x21 else 1] = True
+        self.am_enabled[0 if axis == AXIS_X else 1] = True
 
     def home_axis(self, axis, timeout=0.0):
         self._t.record("home_axis", axis)
-        self.am_homed[0 if axis == 0x21 else 1] = True
+        self.am_homed[0 if axis == AXIS_X else 1] = True
 
     def set_velocity_params(self, axis, max_velocity=None, acceleration=None):
         self._t.record("set_velocity_params", axis, max_velocity, acceleration)
 
     def set_trigger_trigout_maxv(self, axis):
         self._t.record("set_trigger_trigout_maxv", axis)
+        if axis == AXIS_X:
+            self.gate_armed = True
+
+    def set_trigger_gate_off(self, axis):
+        self._t.record("set_trigger_gate_off", axis)
+        if axis == AXIS_X:
+            self.gate_armed = False
+
+    def arm_scan_gate(self, axis, armed, verify=True):
+        self._t.record("arm_scan_gate", axis, bool(armed))
+        if axis == AXIS_X:
+            self.gate_armed = bool(armed)
 
     def move_axis_absolute(self, axis, pos, timeout=0.0):
+        idx = 0 if axis == AXIS_X else 1
+        prev = self.positions[idx]
         self._t.record("move_axis_absolute", axis, round(pos, 6))
-        self.positions[0 if axis == 0x21 else 1] = pos
+        self.positions[idx] = pos
+
+        # The gate is high only at max velocity, i.e. over the move minus its
+        # two ramps — direction-agnostic, so a flyback the engine failed to
+        # gate off produces frames instead of quietly producing none.
+        if axis == AXIS_X and self.gate_armed and self._scope is not None:
+            at_speed_mm = abs(pos - prev) - 2 * RAMP_TOTAL_MM
+            if at_speed_mm > 0:
+                self._scope.acquire_frames(
+                    round(at_speed_mm * LASER_FREQ_HZ / SCAN_VELOCITY_MM_S))
 
 
 class FakeScope:
@@ -61,24 +106,42 @@ class FakeScope:
     against an expected byte pattern.
     """
 
-    def __init__(self, trace: Trace, samples_per_frame=8, n_frames=4):
+    def __init__(self, trace: Trace, samples_per_frame=8, max_frames=4096):
         self._t = trace
         self.samples_per_frame = samples_per_frame
-        self._n_frames = n_frames
+        self.max_frames = max_frames
         self._acq_polls = 0
-        self.frame_seq = 0
+        self._running = False
+        self._acquired = 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.
+        self._next_frame: dict[int, int] = {}
+
+    # -- driven by FakeStage ------------------------------------------------
+    def acquire_frames(self, n):
+        if self._running:
+            self._acquired += n
 
     # -- writes / queries ---------------------------------------------------
     def write(self, cmd):
         self._t.record("write", cmd)
+        if cmd == "ACQuire:STATE RUN":
+            self._running = True
+            self._acquired = 0
+        elif cmd == "ACQuire:STATE STOP":
+            self._running = False
 
     def query(self, cmd):
         self._t.record("query", cmd)
         if cmd == "ACQuire:STATE?":
             self._acq_polls += 1
+            # STOPAfter SEQuence self-stops when the sequence completes, so
+            # reporting "stopped" and staying armed would be inconsistent.
+            self._running = False
             return "0"                      # background average finished
         if cmd == "ACQuire:NUMFRAMESACQuired?":
-            return str(self._n_frames)
+            return str(self._acquired)
         return ""
 
     # -- typed setters used by core.scope_sras ------------------------------
@@ -102,7 +165,13 @@ class FakeScope:
 
     def set_fastframe_count(self, n):
         self._t.record("set_fastframe_count", n)
-        self._n_frames = n
+
+    def get_fastframe_state(self):
+        return 1
+
+    def get_fastframe_max_frames(self):
+        self._t.record("get_fastframe_max_frames")
+        return self.max_frames
 
     def set_sample_rate(self, sr):
         self._t.record("set_sample_rate", sr)
@@ -114,6 +183,12 @@ class FakeScope:
         self._t.record("set_data_source", ch)
         self._source = ch
 
+    def set_data_encoding(self, encoding):
+        self._t.record("set_data_encoding", encoding)
+
+    def set_data_width(self, width):
+        self._t.record("set_data_width", width)
+
     def query_wfmoutpre(self):
         return f"WFMOUTPRE:CH{self._source};YMULT 1.5625E-3;YOFF -87.04;YZERO 0.0"
 
@@ -121,14 +196,22 @@ class FakeScope:
         self._t.record("transfer_curve")
         return bytes(range(self.samples_per_frame))
 
-    def transfer_fastframe(self, parse=True):
+    def _frames(self, ch, count):
+        spf = self.samples_per_frame
+        start = self._next_frame.get(ch, 0)
+        self._next_frame[ch] = start + count
+        return [bytes((ch * 31 + g + s) % 256 for s in range(spf))
+                for g in range(start, start + count)]
+
+    def transfer_fastframe(self, parse=True, byte_count=1, signed=True,
+                           byte_order='MSB'):
         self._t.record("transfer_fastframe", self._source)
-        frames = []
-        for i in range(self._n_frames):
-            frames.append(bytes((self.frame_seq + i + s) % 256
-                                for s in range(self.samples_per_frame)))
-        self.frame_seq += 1
-        return frames
+        return self._frames(self._source, self._acquired)
+
+    def transfer_fastframe_bulk(self, frame_count, samples_per_frame,
+                                bytes_per_sample=1):
+        self._t.record("transfer_fastframe_bulk", self._source, frame_count)
+        return bytearray(b"".join(self._frames(self._source, frame_count)))
 
     # channel config (only used by configure_channels)
     def set_channel_label_name(self, ch, name):

tests/test_scan_engine.py

@@ -20,22 +20,24 @@ from fakes import FakeScope, FakeStage, FakeT3R, Trace
 SPF = 8
 
 
-def make_plan(num_angles=1):
-    # Small ROI well inside the stage limits: 1 row, few frames per angle.
-    return build_plan(40.0, 30.0, 0.02, 0.005, num_angles, 0.01,
+def make_plan(num_angles=1, y_delta=0.005):
+    # Small ROI well inside the stage limits: few rows, few frames per angle.
+    return build_plan(40.0, 30.0, 0.02, y_delta, num_angles, 0.01,
                       laser_freq_hz=20000.0, velocity_mm_s=100.0)
 
 
-def build(tmp_path, num_angles=1, callbacks=None, resume=None, **kw):
+def build(tmp_path, num_angles=1, callbacks=None, resume=None, plan=None,
+          burst_mode=False, max_frames=4096, out_name="out.sras", **kw):
     trace = Trace()
-    stage = FakeStage(trace)
-    scope = FakeScope(trace, samples_per_frame=SPF)
+    scope = FakeScope(trace, samples_per_frame=SPF, max_frames=max_frames)
+    stage = FakeStage(trace, scope=scope)
     t3r = FakeT3R(trace, **kw)
     rotator = RotationAxis(t3r, RotationSettings())
-    plan = make_plan(num_angles)
-    engine = ScanEngine(stage, scope, rotator, plan, tmp_path / "out.sras",
+    plan = plan if plan is not None else make_plan(num_angles)
+    engine = ScanEngine(stage, scope, rotator, plan, tmp_path / out_name,
                         resume=resume,
-                        callbacks=callbacks or ScanCallbacks())
+                        callbacks=callbacks or ScanCallbacks(),
+                        burst_mode=burst_mode)
     return engine, trace, plan
 
 
@@ -192,8 +194,8 @@ def test_dc_bias_callback_reports_per_frame_means(tmp_path):
 
 def test_offstage_plan_rejected_before_touching_hardware(tmp_path):
     trace = Trace()
-    stage = FakeStage(trace)
     scope = FakeScope(trace, samples_per_frame=SPF)
+    stage = FakeStage(trace, scope=scope)
     # X range that runs off the 110 mm stage once ramps are added
     plan = build_plan(80.0, 30.0, 40.0, 5.0, 1, 0.25,
                       laser_freq_hz=20000.0, velocity_mm_s=100.0)
@@ -265,6 +267,137 @@ def test_resume_record_length_mismatch_rejected(tmp_path):
         engine2.run()
 
 
+# ── Burst acquisition ────────────────────────────────────────────────────────
+
+# 6 rows × 4 frames/row; max_frames=14 gives 14//4 = 3 rows per burst, so the
+# angle needs two bursts and the second is not a whole burst wide.
+BURST_PLAN = dict(y_delta=0.05)
+BURST_MAX_FRAMES = 14
+
+
+def test_burst_and_serial_produce_identical_files(tmp_path):
+    """The whole point: burst mode must be a pure acquisition optimisation."""
+    plan = make_plan(**BURST_PLAN)
+    assert plan.per_angle[0].n_rows == 6 and plan.per_angle[0].n_frames == 4
+
+    serial, _, _ = build(tmp_path, plan=plan, out_name="serial.sras")
+    serial.run()
+    burst, _, _ = build(tmp_path, plan=plan, out_name="burst.sras",
+                        burst_mode=True, max_frames=BURST_MAX_FRAMES)
+    burst.run()
+
+    assert (tmp_path / "burst.sras").read_bytes() == \
+           (tmp_path / "serial.sras").read_bytes()
+
+
+def test_burst_multi_angle_file_is_complete(tmp_path):
+    plan = make_plan(num_angles=3, **BURST_PLAN)
+    engine, trace, _ = build(tmp_path, plan=plan, burst_mode=True,
+                             max_frames=BURST_MAX_FRAMES)
+    result = engine.run()
+
+    assert result.rows_written == plan.total_rows
+    assert result.angles_acquired == [0, 1, 2]
+    sras = SrasFile(tmp_path / "out.sras")
+    assert [s.status for s in sras.angle_status()] == ["OK"] * 3
+
+
+def test_burst_gates_the_flyback_and_runs_once_per_burst(tmp_path):
+    plan = make_plan(**BURST_PLAN)
+    engine, trace, _ = build(tmp_path, plan=plan, burst_mode=True,
+                             max_frames=BURST_MAX_FRAMES)
+    engine.run()
+
+    # Two bursts (3 + 3 rows), two preflight acquisitions, one background.
+    runs = [c for c in trace.of("write") if c[1] == "ACQuire:STATE RUN"]
+    assert len(runs) == 5
+
+    # Every acquiring pass is bracketed by an arm/disarm, so the gate is low
+    # for each flyback.  6 rows + 1 preflight pass = 7 arms.
+    gate = [c[2] for c in trace.of("arm_scan_gate")]
+    assert gate.count(True) == 7
+    # No two arms without a disarm between them — that is what would let a
+    # flyback into the acquisition.  (A repeated disarm is just defensive.)
+    for a, b in zip(gate, gate[1:], strict=False):
+        assert not (a and b), f"acquiring pass with no disarm before it: {gate}"
+    assert gate[-1] is False, "scan left the gate armed"
+
+    # One bulk transfer per data channel per burst, none per row.
+    assert [(c[1], c[2]) for c in trace.of("transfer_fastframe_bulk")] == [
+        (1, 12), (4, 12), (1, 12), (4, 12)]
+    assert trace.count("transfer_fastframe") == 0
+
+
+def test_burst_preflight_rejects_a_leaky_gate(tmp_path):
+    plan = make_plan(**BURST_PLAN)
+    engine, trace, _ = build(tmp_path, plan=plan, burst_mode=True,
+                             max_frames=BURST_MAX_FRAMES)
+    stage = engine._stage
+
+    # A gate that ignores the disable request — the failure mode the preflight
+    # exists to catch (TRIGOUT_GATE_OFF set to the wrong mode value).
+    def stuck_gate(axis, armed, verify=True):
+        trace.record("arm_scan_gate", axis, bool(armed))
+        stage.gate_armed = True
+    stage.arm_scan_gate = stuck_gate
+
+    with pytest.raises(RuntimeError, match="not idling low"):
+        engine.run()
+
+
+def test_burst_preflight_rejects_a_dark_laser(tmp_path):
+    """A gate that never fires would let a leak check pass vacuously."""
+    plan = make_plan(**BURST_PLAN)
+    engine, trace, _ = build(tmp_path, plan=plan, burst_mode=True,
+                             max_frames=BURST_MAX_FRAMES)
+    engine._stage.attach_scope(None)      # no pulses ever reach the scope
+
+    with pytest.raises(RuntimeError, match="no frames acquired"):
+        engine.run()
+
+
+@pytest.mark.parametrize("burst_mode", [False, True])
+def test_short_row_is_padded_to_declared_frame_count(tmp_path, burst_mode):
+    """A clipped row must not shift every later row in the file.
+
+    v6 declares n_frames per row up front and has no per-row length, so an
+    under-triggered row has to be squared up.  In burst mode this also proves
+    the splitter advances by what actually arrived, not by n_frames.
+    """
+    warnings = []
+    plan = make_plan(**BURST_PLAN)
+    engine, trace, _ = build(
+        tmp_path, plan=plan, burst_mode=burst_mode,
+        max_frames=BURST_MAX_FRAMES,
+        callbacks=ScanCallbacks(on_status=warnings.append))
+    # The preflight is covered by its own tests; skipping it keeps the
+    # acquiring-pass count below identical in both modes.
+    engine._preflight_done = True
+
+    scope = engine._scope
+    real_acquire = scope.acquire_frames
+    passes = {"n": 0}
+
+    def clipped(n):
+        if scope._running:
+            passes["n"] += 1
+            if passes["n"] == 2:        # second data row loses one frame
+                n -= 1
+        real_acquire(n)
+    scope.acquire_frames = clipped
+
+    result = engine.run()
+
+    assert result.rows_written == 6
+    assert any("Row 2: 3 frames acquired, 4 expected" in w for w in warnings)
+    assert any("zero-padded" in w for w in warnings)
+    sras = SrasFile(tmp_path / "out.sras")
+    assert [s.status for s in sras.angle_status()] == ["OK"]
+    # The padding lands at the end of the short row, not in the next one.
+    assert bytes(sras.load_row(0, 1, 0)[-1]) == bytes(SPF)
+    assert bytes(sras.load_row(0, 2, 0)[0]) != bytes(SPF)
+
+
 def test_engine_imports_without_qt():
     """The engine must be usable from a non-Qt front end."""
     import subprocess

tests/test_scope_burst.py

@@ -0,0 +1,103 @@
+"""Burst sizing and row-splitting, exercised without any instrument."""
+import pytest
+
+from core.scope_burst import (
+    frame_means_block, normalize_row, rows_per_burst, split_row_counts,
+)
+
+SPF = 8
+
+
+# ── rows_per_burst ───────────────────────────────────────────────────────────
+
+def test_rows_per_burst_rounds_down():
+    # 9.7 rows' worth of capacity is 9 rows: a partial row is unusable.
+    assert rows_per_burst(97, 10, SPF, rows_remaining=100) == 9
+    assert rows_per_burst(100, 10, SPF, rows_remaining=100) == 10
+
+
+def test_rows_per_burst_clamped_by_rows_remaining():
+    assert rows_per_burst(1000, 10, SPF, rows_remaining=3) == 3
+
+
+def test_rows_per_burst_clamped_by_memory_budget():
+    # Budget holds 4 rows of 10 frames × 8 samples; the scope would hold 100.
+    assert rows_per_burst(1000, 10, SPF, rows_remaining=100,
+                          memory_budget=4 * 10 * SPF) == 4
+
+
+def test_rows_per_burst_headroom_reserves_slack_per_row():
+    assert rows_per_burst(100, 10, SPF, rows_remaining=100, headroom=0) == 10
+    assert rows_per_burst(100, 10, SPF, rows_remaining=100, headroom=2) == 8
+
+
+def test_rows_per_burst_never_returns_zero():
+    """A row too big for any budget still goes, or the scan cannot progress."""
+    assert rows_per_burst(5, 10, SPF, rows_remaining=100) == 1
+    assert rows_per_burst(1000, 10, SPF, rows_remaining=100,
+                          memory_budget=1) == 1
+
+
+def test_rows_per_burst_rejects_degenerate_geometry():
+    with pytest.raises(ValueError):
+        rows_per_burst(100, 0, SPF, rows_remaining=1)
+
+
+# ── split_row_counts ─────────────────────────────────────────────────────────
+
+def test_split_row_counts_differences_the_cumulative_counter():
+    assert split_row_counts([4, 8, 12]) == [4, 4, 4]
+    assert split_row_counts([4, 7, 12]) == [4, 3, 5]
+    assert split_row_counts([]) == []
+
+
+def test_split_row_counts_rejects_a_counter_that_went_backwards():
+    # Only happens if the acquisition restarted mid-burst, which would
+    # misattribute every later row.
+    with pytest.raises(RuntimeError, match="backwards"):
+        split_row_counts([8, 4])
+
+
+# ── normalize_row ────────────────────────────────────────────────────────────
+
+def test_normalize_row_passes_an_exact_row_through():
+    buf = bytes(range(4 * SPF))
+    assert bytes(normalize_row(buf, 0, 4, 4, SPF)) == buf
+
+
+def test_normalize_row_pads_a_short_row():
+    buf = bytes(range(3 * SPF))
+    out = bytes(normalize_row(buf, 0, 3, 4, SPF))
+    assert len(out) == 4 * SPF
+    assert out[:3 * SPF] == buf
+    assert out[3 * SPF:] == bytes(SPF)
+
+
+def test_normalize_row_truncates_a_long_row():
+    buf = bytes(range(6 * SPF))
+    out = bytes(normalize_row(buf, 0, 6, 4, SPF))
+    assert out == buf[:4 * SPF]
+
+
+def test_normalize_row_reads_at_an_offset():
+    buf = bytes(range(8 * SPF))
+    out = bytes(normalize_row(buf, 2 * SPF, 4, 4, SPF))
+    assert out == buf[2 * SPF:6 * SPF]
+
+
+def test_normalize_row_pads_a_buffer_that_ends_early():
+    """Defensive: a truncated transfer must not shorten the row on disk."""
+    out = bytes(normalize_row(bytes(2 * SPF), 0, 4, 4, SPF))
+    assert len(out) == 4 * SPF
+
+
+# ── frame_means_block ────────────────────────────────────────────────────────
+
+def test_frame_means_block_is_per_frame():
+    buf = bytes([1] * SPF + [3] * SPF)
+    assert frame_means_block(buf, 0, 2, SPF) == [1.0, 3.0]
+
+
+def test_frame_means_block_reads_signed_samples_at_an_offset():
+    buf = bytes([0] * SPF) + bytes([0xFF] * SPF)     # 0xFF == -1 as int8
+    assert frame_means_block(buf, SPF, 1, SPF) == [-1.0]