Phase 4: extract headless ScanEngine; de-Qt the T3R driver

The headline of the refactor. Scan orchestration no longer lives inside a
QObject that reaches through Qt workers for its hardware handles.

core/scan_engine.py — ScanEngine(stage, scope, rotator, plan, out_path,
resume, callbacks). Takes the concrete drivers, blocks in run(), reports
via plain callables, and prompts through an injected blocking callable.
No Qt import anywhere in the path (test_engine_imports_without_qt proves
it), so a simpler GUI or a CLI can drive the identical acquisition.

Supporting extractions, all Qt-free:
- core/scope_sras.py  — SCPI policy: channel profiles, trigger programming,
  background average, per-row FastFrame transfer
- core/rotation.py    — RotationAxis + RotationSettings (the GR_* constants)
- core/scan_resume.py — frontier contiguity rule + settings compatibility
- gui/scan_bridge.py  — QtScanController, exposing exactly the signal
  surface the old ScanWorker had, so MainWindow's connections are unchanged

hardware/t3r_driver.py is now Qt-free: a plain Signal class, a threading
reader, and a polling thread instead of QObject/QThread/QTimer.
gui/qt_t3r.py re-emits its callbacks as queued Qt signals for the panels.

Fixes carried by the extraction:
- rotation waits on the driver's MOTION_DONE event instead of
  time.sleep(estimate + 0.5)
- abort during an operator prompt now takes effect; the old
  _prompt_event.wait() had no timeout and could not be interrupted
- the poll timer is a thread, so an I/O error tearing down the driver no
  longer calls QTimer.stop() from the wrong thread
- T3RDriver.disconnect() renamed close(); it shadowed QObject.disconnect()
- per-frame DC means use np.frombuffer over the joined block instead of
  struct.unpack per frame (~16k tuple allocations per row)

tests/fakes.py + test_scan_engine.py (14 tests) assert the exact command
sequence, file layout, resume seeking, abort/pause, and geometry
rejection before any hardware call; test_scan_resume.py covers the
frontier rule. 58 passing.

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

core/rotation.py

@@ -0,0 +1,87 @@
+"""GR rotation axis: the T3R configuration and move policy for scanning.
+
+Qt-free façade over hardware.t3r_driver.T3RDriver that owns the drive
+settings the scan depends on, so the engine never re-derives them.
+"""
+from __future__ import annotations
+
+import logging
+from dataclasses import dataclass
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass(frozen=True)
+class RotationSettings:
+    """Drive settings for the GR axis during a scan."""
+    microsteps: int = 8          # microsteps/full-step on the GR axis (ch3)
+    velocity: int = 4000         # steps/s for inter-angle moves
+    accel: int = 2000            # steps/s² for inter-angle moves
+    run_current_ma: int = 1200   # drive current while moving
+    hold_current_ma: int = 400   # standstill current
+    ihold_delay: int = 6         # run→hold current ramp delay (TMC IHOLDDELAY units)
+    # The sample rotates CW instead of CCW to clear wiring and avoid a stall.
+    rotation_sign: int = -1
+
+
+DEFAULT_ROTATION = RotationSettings()
+
+
+class RotationAxis:
+    """Blocking rotation control for the GR axis.
+
+    ``configure()`` must run before any move: ``steps_for_angle()`` assumes
+    the configured microstep setting, so the device has to be told to match
+    rather than trusting whatever the T3R panel or firmware default left it
+    at.
+    """
+
+    def __init__(self, driver, settings: RotationSettings = DEFAULT_ROTATION):
+        self.driver = driver
+        self.settings = settings
+        self._current_deg = 0.0
+
+    @property
+    def is_available(self) -> bool:
+        return self.driver is not None and self.driver.is_open
+
+    @property
+    def current_deg(self) -> float:
+        return self._current_deg
+
+    def configure(self) -> None:
+        s = self.settings
+        ch = self.driver.GR_AXIS_CH
+        self.driver.set_microstep(ch, s.microsteps)
+        self.driver.set_current(ch, s.run_current_ma, s.hold_current_ma, s.ihold_delay)
+        self.driver.enable(ch)
+
+    def estimate_move_secs(self, delta_deg: float) -> float:
+        """Trapezoidal move time: cruise + accel/decel ramps."""
+        s = self.settings
+        steps = abs(self.driver.steps_for_angle(delta_deg, s.microsteps))
+        return steps / s.velocity + s.velocity / s.accel
+
+    def rotate_to(self, angle_deg: float, timeout_margin_s: float = 5.0) -> float:
+        """Rotate to an absolute angle and block until the move completes.
+
+        Returns the estimated move time (for status reporting).  Waits on the
+        driver's MOTION_DONE event rather than sleeping for a guessed
+        duration; falls back to the estimate only if the event never arrives.
+        """
+        delta_deg = angle_deg - self._current_deg
+        if abs(delta_deg) <= 0.001:
+            return 0.0
+        s = self.settings
+        est_secs = self.estimate_move_secs(delta_deg)
+        self.driver.rotate_stage(delta_deg, s.microsteps, s.velocity, s.accel)
+        if not self.driver.wait_motion_done(self.driver.GR_AXIS_CH,
+                                            est_secs + timeout_margin_s):
+            logger.warning(
+                "GR axis did not report MOTION_DONE within %.1f s for a "
+                "%.1f° move; continuing", est_secs + timeout_margin_s, delta_deg)
+        self._current_deg = angle_deg
+        return est_secs
+
+    def return_to_zero(self) -> float:
+        return self.rotate_to(0.0)

core/scan_engine.py

@@ -0,0 +1,393 @@
+"""Headless SRAS scan engine.
+
+Takes plain hardware drivers, a ScanPlan, and callbacks — no Qt, no
+widgets.  ``run()`` blocks, so the caller owns the thread; GUIs wrap this
+with gui.scan_bridge.QtScanController, which adapts the callbacks to Qt
+signals.  A CLI or a simpler GUI can drive the same engine with nothing but
+functions.
+"""
+from __future__ import annotations
+
+import logging
+import threading
+import time
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import Callable
+
+from core import 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
+
+logger = logging.getLogger(__name__)
+
+SCAN_VELOCITY_MM_S = 100.0
+SCAN_ACCEL_MM_S2 = 1500.0
+LASER_FREQ_HZ = 20000.0    # laser pulse frequency during data acquisition
+# Theoretical ramp distance: d = v² / (2a) = 100² / (2×1500) ≈ 3.33 mm
+SCAN_RAMP_MM = SCAN_VELOCITY_MM_S**2 / (2.0 * SCAN_ACCEL_MM_S2)
+# Extra buffer added to both ends of the ramp.  The BBD202 controller begins
+# decelerating slightly before the theoretical point to avoid overshoot,
+# which drops TRIGOUT_MAXV early and clips the last few data points.
+SCAN_RAMP_BUFFER_MM = 1.0
+
+AXIS_X = 0x21
+AXIS_Y = 0x22
+
+
+class ScanAborted(Exception):
+    """Raised inside the engine thread to unwind a scan cleanly."""
+
+
+@dataclass
+class ResumeTarget:
+    """One angle selected for (re)acquisition in an existing file."""
+    angle_idx: int
+    data_offset: int
+    n_rows: int
+    angle_deg: float
+
+
+@dataclass
+class ResumeState:
+    path: Path
+    targets: list[ResumeTarget]
+    samples_per_frame: int
+
+    @property
+    def target_indices(self) -> set[int]:
+        return {t.angle_idx for t in self.targets}
+
+
+@dataclass
+class ScanCallbacks:
+    """Progress reporting hooks.  Every one is optional."""
+    on_status: Callable[[str], None] = lambda msg: None
+    on_started: Callable[[], None] = lambda: None
+    on_row_started: Callable[[int, int, int, int], None] = lambda r, nr, a, na: None
+    on_row_done: Callable[[int, int, int, int], None] = lambda r, nr, a, na: None
+    on_dc_bias: Callable[[int, list], None] = lambda row, means: None
+    on_paused_changed: Callable[[bool], None] = lambda paused: None
+    # Blocking operator prompt: must not return until acknowledged.
+    prompt: Callable[[str, str], None] = lambda title, msg: None
+
+
+@dataclass
+class ScanResult:
+    path: Path
+    rows_written: int = 0
+    aborted: bool = False
+    angles_acquired: list[int] = field(default_factory=list)
+
+
+class ScanEngine:
+    """Runs a full SRAS acquisition: stage, rotation, scope, and file output.
+
+    Constructed with the concrete drivers (not worker/queue wrappers), so
+    any front end can reuse it::
+
+        engine = ScanEngine(stage, scope, rotator, plan, out_path,
+                            callbacks=ScanCallbacks(on_status=print))
+        result = engine.run()          # blocking
+    """
+
+    def __init__(self, stage, scope, rotator: RotationAxis | None,
+                 plan: ScanPlan, out_path: Path,
+                 resume: ResumeState | None = None,
+                 callbacks: ScanCallbacks | None = None):
+        self._stage = stage
+        self._scope = scope
+        self._rotator = rotator
+        self._plan = plan
+        self._out_path = Path(out_path)
+        self._resume = resume
+        self._cb = callbacks if callbacks is not None else ScanCallbacks()
+
+        self._abort = threading.Event()
+        self._resume_event = threading.Event()
+        self._resume_event.set()   # set = running, cleared = pause requested
+
+    # ── External control (thread-safe) ────────────────────────────────────────
+
+    def abort(self):
+        self._abort.set()
+        self._resume_event.set()   # unblock a paused scan so it can exit
+
+    def pause(self):
+        """Request a pause; takes effect at the next row boundary."""
+        self._resume_event.clear()
+
+    def resume(self):
+        self._resume_event.set()
+
+    @property
+    def aborted(self) -> bool:
+        return self._abort.is_set()
+
+    # ── Internals ─────────────────────────────────────────────────────────────
+
+    def _check_abort(self):
+        if self._abort.is_set():
+            raise ScanAborted("Scan aborted by user.")
+
+    def _pause_point(self):
+        """Block here (between rows, hardware idle) while a pause is requested."""
+        if self._resume_event.is_set():
+            self._check_abort()
+            return
+        self._cb.on_status(
+            "Scan paused — lasers may be switched off. "
+            "Turn lasers back on before resuming."
+        )
+        self._cb.on_paused_changed(True)
+        while not self._resume_event.wait(0.2):
+            if self._abort.is_set():
+                break
+        self._cb.on_paused_changed(False)
+        self._check_abort()
+        self._cb.on_status("Scan resumed.")
+
+    def _prompt(self, title: str, message: str):
+        self._cb.prompt(title, message)
+        self._check_abort()
+
+    # ── Main sequence ─────────────────────────────────────────────────────────
+
+    def run(self) -> ScanResult:
+        """Execute the scan.  Blocking; returns a ScanResult.
+
+        Raises ScanGeometryError for an unrunnable plan, RuntimeError for
+        missing/mismatched hardware, or ScanAborted if the operator aborts.
+        """
+        plan = self._plan
+        per_angle = plan.per_angle
+        n_angles = plan.n_angles
+        result = ScanResult(path=self._out_path)
+
+        validate_plan(plan, SCAN_RAMP_MM, SCAN_RAMP_BUFFER_MM)
+
+        geometry_summary = ", ".join(
+            f"{pa.angle_deg:.1f}°: {pa.n_rows} row(s) × {pa.n_frames} pts/row"
+            for pa in per_angle
+        )
+        self._cb.on_status(
+            f"Scan geometry: {n_angles} angle(s), {plan.total_rows} row(s) total "
+            f"(per-angle bounding box)  |  save → {self._out_path.parent}\n"
+            f"{geometry_summary}"
+        )
+        self._cb.on_started()
+
+        if self._stage is None:
+            raise RuntimeError("BBD202 not connected")
+        if self._scope is None:
+            raise RuntimeError("Oscilloscope not connected")
+        rotator_ready = self._rotator is not None and self._rotator.is_available
+        if n_angles > 1 and not rotator_ready:
+            raise RuntimeError(
+                f"NumAngles={n_angles} requires the T3R rotation stage (GR-axis), "
+                "but it is not connected. Connect T3R from the T3R panel before "
+                "starting a multi-angle scan, or set NumAngles to 1."
+            )
+
+        if rotator_ready:
+            s = self._rotator.settings
+            self._cb.on_status(
+                f"Configuring GR axis: {s.microsteps} µsteps, "
+                f"{s.run_current_ma}/{s.hold_current_ma} mA run/hold …"
+            )
+            self._rotator.configure()
+            time.sleep(0.2)
+
+        self._prepare_stage()
+        samples_per_frame = self._prepare_scope()
+        scan_file = self._open_output(samples_per_frame, result)
+
+        try:
+            self._scan_loop(scan_file, samples_per_frame, result)
+        finally:
+            scan_file.close()
+            # 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 …")
+                try:
+                    self._rotator.return_to_zero()
+                except Exception:
+                    logger.exception("GR return-to-home failed")
+
+        if self._abort.is_set():
+            result.aborted = True
+            raise ScanAborted("Scan aborted by user.")
+        self._cb.on_status("Scan complete.")
+        return result
+
+    def _prepare_stage(self):
+        ctrl = self._stage
+        self._cb.on_status("Enabling stage axes …")
+        if not ctrl.am_enabled[0]:
+            ctrl.enable_axis(AXIS_X)
+        if not ctrl.am_enabled[1]:
+            ctrl.enable_axis(AXIS_Y)
+        time.sleep(0.2)
+
+        if not ctrl.am_homed[0] or not ctrl.am_homed[1]:
+            self._cb.on_status("Homing stage (may take up to 2 min) …")
+            if not ctrl.am_homed[0]:
+                ctrl.home_axis(AXIS_X, timeout=120.0)
+            if not ctrl.am_homed[1]:
+                ctrl.home_axis(AXIS_Y, timeout=120.0)
+
+        self._cb.on_status("Setting scan velocity …")
+        ctrl.set_velocity_params(AXIS_X, max_velocity=SCAN_VELOCITY_MM_S,
+                                 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
+        ctrl.set_trigger_trigout_maxv(AXIS_X)
+
+    def _prepare_scope(self) -> int:
+        self._cb.on_status("Configuring oscilloscope …")
+        samples_per_frame = scope_sras.configure_acquisition(self._scope)
+
+        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
+            # preambles are reused as-is (the format has no way to replace
+            # them without rewriting the whole file), so background capture is
+            # skipped.  Sanity-check that this scope still produces the same
+            # record 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) "
+                    f"does not match the {self._resume.samples_per_frame} samples/frame "
+                    f"this scan file was started with — cannot safely resume."
+                )
+            targets = ", ".join(str(t.angle_idx + 1) for t in self._resume.targets)
+            self._prompt(
+                "Resume Scan",
+                f"Resuming {self._resume.path.name} — will (re)acquire "
+                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"
+                "then click OK to continue scanning."
+            )
+
+        scope_sras.configure_scan_trigger(self._scope)
+        return samples_per_frame
+
+    def _open_output(self, samples_per_frame: int, result: ScanResult):
+        if self._resume is not None:
+            result.path = self._resume.path
+            self._cb.on_status(
+                f"Resuming {self._resume.path.name} — "
+                f"{len(self._resume.targets)} angle(s) to (re)acquire …"
+            )
+            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,
+        )
+
+    def _scan_loop(self, scan_file, samples_per_frame: int, result: ScanResult):
+        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
+        if self._resume is not None:
+            targets_by_ai = {t.angle_idx: t for t in self._resume.targets}
+
+        # Both fresh and resumed scans assume the GR axis starts at home (0°)
+        # — the resume prompt instructs the operator to re-home it — so the
+        # first move always rotates directly from 0° to the starting angle.
+        for ai, pa in enumerate(plan.per_angle):
+            if targets_by_ai is not None and ai not in targets_by_ai:
+                continue    # not selected for (re)acquisition
+            self._pause_point()
+
+            if targets_by_ai 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)
+
+            if self._rotator is not None and self._rotator.is_available:
+                delta = pa.angle_deg - self._rotator.current_deg
+                if abs(delta) > 0.001:
+                    self._cb.on_status(
+                        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.
+            scope.set_fastframe_count(pa.n_frames)
+
+            for ri, y_pos in enumerate(pa.y_positions):
+                self._pause_point()
+
+                self._cb.on_row_started(ri + 1, pa.n_rows, ai + 1, n_angles)
+                self._cb.on_status(
+                    f"Angle {ai+1}/{n_angles}  Row {ri+1}/{pa.n_rows}  "
+                    f"(Y={y_pos:.3f} mm)"
+                )
+
+                # Position the stage one ramp-length + buffer before the data
+                # window so it is at full velocity before x_start.
+                ctrl.move_axis_absolute(AXIS_Y, y_pos, timeout=60.0)
+                ctrl.move_axis_absolute(AXIS_X, pa.x_start - x_ramp_total, timeout=30.0)
+
+                scope_sras.arm_row(scope)
+
+                # Data window + ramp + buffer run-off, so the stage does not
+                # begin decelerating before the last point.
+                x_end = pa.x_start + pa.x_delta + x_ramp_total
+                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)
+
+                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):
+        """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
+        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)
+                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)

core/scan_resume.py

@@ -0,0 +1,64 @@
+"""Resume planning: turn a file's frontier into a set of angles to re-acquire.
+
+Pure logic, no Qt and no file I/O beyond what SrasFile already parsed, so
+the non-obvious contiguity rule is testable on its own.
+"""
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+
+from core.scan_engine import ResumeState, ResumeTarget
+from core.sras_format import SrasFile
+
+
+@dataclass
+class ResumePlan:
+    targets: list[ResumeTarget]
+    auto_added: list[int] = field(default_factory=list)   # indices forced in
+    frontier_idx: int = 0
+
+    @property
+    def total_rows(self) -> int:
+        return sum(t.n_rows for t in self.targets)
+
+    def to_state(self, sras: SrasFile) -> ResumeState:
+        return ResumeState(path=sras.path, targets=self.targets,
+                           samples_per_frame=sras.header.samples_per_frame)
+
+
+def plan_resume(statuses, selected: set[int]) -> ResumePlan:
+    """Expand an operator's angle selection into a runnable resume plan.
+
+    Waveform data is one contiguous append-only stream, so nothing can be
+    written past a gap: if the operator picks an angle at or beyond the
+    frontier (the first incomplete angle), every angle from the frontier up
+    to it must be re-acquired too.  Those extras are reported in
+    ``auto_added`` so the UI can say so.
+    """
+    frontier_idx = next((s.index for s in statuses if not s.complete), len(statuses))
+
+    at_or_past = {i for i in selected if i >= frontier_idx}
+    if at_or_past:
+        final = selected | set(range(frontier_idx, max(at_or_past) + 1))
+    else:
+        final = set(selected)
+
+    targets = [
+        ResumeTarget(angle_idx=s.index, 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,
+                      auto_added=sorted(final - set(selected)),
+                      frontier_idx=frontier_idx)
+
+
+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."""
+    h = sras.header
+    return (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
+            and abs(h.sample_rate - sample_rate) <= 1.0)

core/scope_sras.py

@@ -0,0 +1,167 @@
+"""Oscilloscope SCPI policy for SRAS acquisition.
+
+All the Tektronix-specific instrument setup the scan depends on, in one
+Qt-free place: per-channel display/coupling config, trigger programming,
+the background average, and per-row FastFrame transfer.
+"""
+from __future__ import annotations
+
+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
+TRIG_LEVEL_V = 0.500
+BACKGROUND_AVERAGES = 1024
+BACKGROUND_TIMEOUT_S = 60.0
+
+
+@dataclass(frozen=True)
+class ChannelProfile:
+    """Display/input configuration for one scope channel."""
+    label: str
+    scale_v_div: float
+    position_div: float
+    termination_ohm: int
+    coupling: str
+    bandwidth_hz: float
+
+
+# Standard SRAS front-end configuration.
+SRAS_CHANNELS = {
+    1: ChannelProfile("RF Acoustic Packet", 0.07, 0.0, 50, "DC", 250e6),
+    2: ChannelProfile("Trigger Signal", 0.5, -2.72, 1_000_000, "DC", 20e6),
+    3: ChannelProfile("Max Vel Gate", 1.0, -2.72, 1_000_000, "DC", 20e6),
+    4: ChannelProfile("Bias - B", 0.1, -2.72, 1_000_000, "DC", 20e6),
+}
+
+
+def configure_channels(scope, profiles=None) -> None:
+    """Apply the standard SRAS channel configuration."""
+    profiles = profiles if profiles is not None else SRAS_CHANNELS
+    for ch, p in profiles.items():
+        scope.write(f"SELect:CH{ch} ON")
+        scope.set_channel_label_name(ch, p.label)
+        scope.set_channel_scale(ch, p.scale_v_div)
+        scope.set_channel_position(ch, p.position_div)
+        scope.set_channel_termination(ch, p.termination_ohm)
+        scope.set_channel_coupling(ch, p.coupling)
+        scope.set_channel_bandwidth(ch, p.bandwidth_hz)
+
+
+def configure_acquisition(scope) -> int:
+    """Program the edge trigger and timebase; returns samples per frame.
+
+    Edge trigger on the rising edge of CH2 (laser pulse).  FastFrame stays
+    off here so the background capture runs as a single record.
+    """
+    scope.write("TRIGger:A:TYPe EDGE")
+    scope.set_trigger_source(2)
+    scope.set_trigger_slope("RISE")
+    scope.set_trigger_level(2, TRIG_LEVEL_V)
+    scope.set_trigger_mode("NORMAL")       # wait for trigger (don't auto-sweep)
+    scope.set_acquire_mode("SAMPLE")
+    scope.set_fastframe_state(False)
+    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
+    return scope.get_record_length()
+
+
+def read_preambles(scope, channels) -> list[str]:
+    """Snapshot WFMOutpre per channel (captures YMULT/YOFF/YZERO)."""
+    preambles = []
+    for ch in channels:
+        scope.set_data_source(ch)
+        preambles.append(scope.query_wfmoutpre())
+    return preambles
+
+
+def capture_background(scope, should_abort=lambda: False,
+                       on_status=lambda msg: None) -> bytes:
+    """Capture one CH1 waveform averaged over BACKGROUND_AVERAGES shots.
+
+    The scope auto-stops after the sequence; poll ACQuire:STATE until it
+    does rather than assuming a duration.
+    """
+    on_status(f"Capturing background waveform ({BACKGROUND_AVERAGES}-average) …")
+    scope.set_acquire_mode("AVERAGE")
+    scope.write(f"ACQuire:NUMAVg {BACKGROUND_AVERAGES}")
+    scope.write("ACQuire:STOPAfter SEQuence")
+    scope.set_data_source(1)
+    scope.write("ACQuire:STATE RUN")
+
+    deadline = time.time() + BACKGROUND_TIMEOUT_S
+    while time.time() < deadline:
+        if should_abort():
+            break
+        if scope.query("ACQuire:STATE?").strip() == "0":
+            break
+        time.sleep(0.25)
+    else:
+        scope.write("ACQuire:STATE STOP")
+        on_status("Warning: background average timed out; stopping early.")
+    time.sleep(0.1)
+    return scope.transfer_curve()
+
+
+def configure_scan_trigger(scope) -> None:
+    """Switch to the scan-time logic-AND trigger (CH2 HIGH AND CH3 HIGH).
+
+    CH3 is the BBD202 TRIGOUT_MAXV gate, so frames only accumulate while the
+    stage is at full scan velocity.
+    """
+    scope.write("ACQuire:STOPAfter RUNSTop")
+    scope.set_acquire_mode("SAMPLE")
+    scope.set_fastframe_state(True)
+
+    scope.write("TRIGger:A:TYPe LOGIc")
+    scope.write("TRIGger:A:LOGIc:FUNCtion AND")
+    scope.set_trigger_level(2, TRIG_LEVEL_V)
+    scope.set_trigger_level(3, TRIG_LEVEL_V)
+    scope.write("TRIGger:A:LOGICPattern:CH2 HIGH")
+    scope.write("TRIGger:A:LOGICPattern:CH3 HIGH")
+    time.sleep(0.2)
+
+
+def arm_row(scope) -> None:
+    """Start acquisition for one scan row."""
+    scope.write("ACQuire:STATE RUN")
+    time.sleep(0.05)
+
+
+def finish_row(scope) -> None:
+    """Wait for trailing frames, then stop acquisition."""
+    time.sleep(0.2)
+    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/__init__.py

@@ -0,0 +1 @@
+"""Shared PyQt6 layer: adapters and widgets used by more than one app."""

gui/qt_t3r.py

@@ -0,0 +1,55 @@
+"""Qt adapter over the (Qt-free) T3RDriver.
+
+The driver fires its callbacks on the reader thread.  This adapter turns
+each one into a Qt signal emitted from that thread; because the adapter
+lives on the GUI thread, Qt queues the delivery and slots run on the GUI
+thread — which is what widget code requires.
+
+Command methods are forwarded to the driver, so panels can hold the adapter
+alone and use it exactly like the old QObject driver.
+"""
+
+from __future__ import annotations
+
+from PyQt6.QtCore import QObject, pyqtSignal
+
+from hardware.t3r_driver import T3RDriver
+
+
+class QtT3RAdapter(QObject):
+    port_opened = pyqtSignal()
+    handshake_ok = pyqtSignal(int, int, int)   # proto_ver, fw_ver, num_channels
+    disconnected = pyqtSignal(str)             # reason ("" = user-initiated)
+    info_updated = pyqtSignal(int, object)     # ch, proto.Info
+    drv_status_updated = pyqtSignal(int, object)
+    position_updated = pyqtSignal(int, int)
+    motion_done = pyqtSignal(int, int)
+    stopped = pyqtSignal(int, int)
+    fault_occurred = pyqtSignal(int, int)
+    ack_received = pyqtSignal(int, int)
+    frame_received = pyqtSignal(int, bytes)
+
+    _EVENTS = ("port_opened", "handshake_ok", "disconnected", "info_updated",
+               "drv_status_updated", "position_updated", "motion_done",
+               "stopped", "fault_occurred", "ack_received", "frame_received")
+
+    def __init__(self, driver: T3RDriver | None = None, parent=None):
+        super().__init__(parent)
+        self.driver = driver if driver is not None else T3RDriver()
+        for name in self._EVENTS:
+            getattr(self.driver, name).connect(getattr(self, name).emit)
+
+    # Class attributes (constants) the panels read off the driver
+    CHANNEL_NAMES = T3RDriver.CHANNEL_NAMES
+    GR_AXIS_CH = T3RDriver.GR_AXIS_CH
+
+    @property
+    def is_open(self) -> bool:
+        return self.driver.is_open
+
+    def __getattr__(self, name):
+        # Only reached for attributes this QObject doesn't define, i.e. the
+        # driver's command API (open/close/move/jog/enable/...).
+        if name.startswith("_"):
+            raise AttributeError(name)
+        return getattr(object.__getattribute__(self, "driver"), name)

gui/scan_bridge.py

@@ -0,0 +1,96 @@
+"""Qt bridge over the headless ScanEngine.
+
+Exposes exactly the signal surface the old in-GUI ScanWorker had, so window
+code connects to it unchanged, and adapts prompts/progress to Qt.  The
+engine itself stays Qt-free and reusable by any other front end.
+"""
+from __future__ import annotations
+
+import threading
+import traceback
+
+from PyQt6.QtCore import QObject, pyqtSignal, pyqtSlot
+
+from core.scan_engine import ScanAborted, ScanCallbacks, ScanEngine
+
+
+class QtScanController(QObject):
+    """Runs a ScanEngine on the caller's QThread and republishes its events.
+
+    Move this to a QThread and connect `started` → `run`, exactly like the
+    previous ScanWorker.
+    """
+
+    started = pyqtSignal()
+    completed = pyqtSignal()
+    dc_bias_updated = pyqtSignal(int, object)         # row index, per-frame DC means
+    failed = pyqtSignal(str)
+    row_started = pyqtSignal(int, int, int, int)      # row, n_rows, angle_idx, n_angles
+    row_done = pyqtSignal(int, int, int, int)
+    status_msg = pyqtSignal(str)
+    user_prompt = pyqtSignal(str, str)                # title, message
+    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):
+        super().__init__()
+        self._prompt_event = threading.Event()
+        self._on_scan_active = on_scan_active
+
+        callbacks = ScanCallbacks(
+            on_status=self.status_msg.emit,
+            on_started=self.started.emit,
+            on_row_started=self.row_started.emit,
+            on_row_done=self.row_done.emit,
+            on_dc_bias=self.dc_bias_updated.emit,
+            on_paused_changed=self.paused_changed.emit,
+            prompt=self._blocking_prompt,
+        )
+        self._engine = ScanEngine(stage, scope, rotator, plan, out_path,
+                                  resume=resume, callbacks=callbacks)
+
+    # ── Engine control (called from the GUI thread) ───────────────────────────
+
+    def abort(self):
+        self._engine.abort()
+        self._prompt_event.set()   # release a scan parked on a prompt
+
+    def pause(self):
+        self._engine.pause()
+
+    def resume(self):
+        self._engine.resume()
+
+    def acknowledge_prompt(self):
+        """Called from the GUI thread when the operator dismisses a prompt."""
+        self._prompt_event.set()
+
+    # ── Callback plumbing ─────────────────────────────────────────────────────
+
+    def _blocking_prompt(self, title: str, message: str):
+        """Ask the GUI thread, then block the scan thread until answered.
+
+        Polls rather than waiting forever so an abort during a prompt takes
+        effect immediately instead of deadlocking the scan thread.
+        """
+        self._prompt_event.clear()
+        self.user_prompt.emit(title, message)
+        while not self._prompt_event.wait(0.2):
+            if self._engine.aborted:
+                return
+
+    @pyqtSlot()
+    def run(self):
+        if self._on_scan_active is not None:
+            self._on_scan_active(True)
+        try:
+            self._engine.run()
+            self.completed.emit()
+        except ScanAborted as exc:
+            self.failed.emit(str(exc))
+        except Exception as exc:
+            traceback.print_exc()
+            self.failed.emit(str(exc))
+        finally:
+            if self._on_scan_active is not None:
+                self._on_scan_active(False)

hardware/t3r_driver.py

@@ -1,8 +1,12 @@
 """T3R Stepper Controller driver for ScanEngine-3.
 
-Qt-based driver that owns the serial connection and an internal reader QThread.
+Owns the serial connection and an internal reader thread.  Events are
-All events arrive as Qt signals; all commands are fire-and-forget writes.
+delivered as plain-Python callbacks (see ``Signal``); commands are
-Create in the main (GUI) thread; no additional thread management required.
+fire-and-forget writes.  No Qt — GUIs wrap this with gui.qt_t3r.QtT3RAdapter,
+which re-emits every event as a queued Qt signal on the GUI thread.
+
+Callbacks run on the reader thread.  Keep them short, and never touch Qt
+widgets from one directly.
 
 Gear train (stage rotation via GR-axis, ch3):
     Motor  →  10T pinion  →  30T idler  →  125T index gear (stage)
@@ -11,23 +15,53 @@ Gear train (stage rotation via GR-axis, ch3):
 
 from __future__ import annotations
 
+import logging
 import threading
 
-import serial
-from PyQt6.QtCore import QObject, QThread, QTimer, pyqtSignal
-
 from . import t3r_protocol as proto
+from .serial_util import open_8n1
+
+logger = logging.getLogger(__name__)
 
 
-class _T3RReader(QThread):
+class Signal:
-    """Blocking read loop — runs on its own QThread."""
+    """Minimal observer slot: ``connect(fn)`` then ``emit(*args)``.
 
-    frame = pyqtSignal(int, bytes)         # (cmd, payload) for each valid frame
+    Mirrors the pyqtSignal API used by the existing panels so the same call
-    finished_reason = pyqtSignal(str)      # "" = clean stop, else I/O error string
+    sites work against either this driver or a Qt adapter over it.  A raising
+    subscriber is logged and skipped so one bad listener cannot kill the
+    reader thread.
+    """
 
-    def __init__(self, ser: serial.Serial):
+    __slots__ = ("_subs", "_name")
-        super().__init__()
+
+    def __init__(self, name: str = ""):
+        self._subs: list = []
+        self._name = name
+
+    def connect(self, fn) -> None:
+        self._subs.append(fn)
+
+    def disconnect(self, fn) -> None:
+        if fn in self._subs:
+            self._subs.remove(fn)
+
+    def emit(self, *args) -> None:
+        for fn in list(self._subs):
+            try:
+                fn(*args)
+            except Exception:
+                logger.exception("T3R %s subscriber failed", self._name)
+
+
+class _Reader(threading.Thread):
+    """Blocking read loop — decodes frames and hands them to `on_frame`."""
+
+    def __init__(self, ser, on_frame, on_finished):
+        super().__init__(daemon=True, name="T3RReader")
         self._ser = ser
+        self._on_frame = on_frame
+        self._on_finished = on_finished
         self._running = True
         self._parser = proto.FrameParser()
 
@@ -44,20 +78,20 @@ class _T3RReader(QThread):
                 break
             if data:
                 for cmd, payload in self._parser.feed(data):
-                    self.frame.emit(cmd, payload)
+                    self._on_frame(cmd, payload)
-        self.finished_reason.emit(reason)
+        self._on_finished(reason)
 
 
-class T3RDriver(QObject):
+class T3RDriver:
-    """Qt-based driver for the T3R four-channel stepper controller.
+    """Driver for the T3R four-channel stepper controller.
 
     Usage::
 
         driver = T3RDriver()
-        driver.handshake_ok.connect(lambda pv, fw, nc: print("connected"))
+        driver.handshake_ok.connect(lambda pv, fw, nc: ...)
-        driver.info_updated.connect(on_info)
+        driver.open("/dev/ttyUSB0")
-        driver.connect("/dev/ttyUSB0")
         driver.move(0, steps=3200, velocity=8000, accel=4000)
+        driver.wait_motion_done(0, timeout=30.0)
     """
 
     CHANNEL_NAMES = ["T-axis (focus)", "Axis 1", "Axis 2", "GR-axis"]
@@ -68,32 +102,33 @@ class T3RDriver(QObject):
     GEAR_TEETH_MOTOR = 10
     GEAR_TEETH_STAGE = 125  # idler is 30T but does not change ratio
 
-    # ── Signals ───────────────────────────────────────────────────────────────
+    POLL_INTERVAL_S = 0.25
 
-    port_opened = pyqtSignal()              # serial port open; PING sent
+    def __init__(self):
-    handshake_ok = pyqtSignal(int, int, int)  # proto_ver, fw_ver, num_channels
+        self._ser = None
-    disconnected = pyqtSignal(str)          # reason ("" = user-initiated)
+        self._reader: _Reader | None = None
-
-    info_updated = pyqtSignal(int, object)        # ch, proto.Info
-    drv_status_updated = pyqtSignal(int, object)  # ch, proto.DrvStatus
-    position_updated = pyqtSignal(int, int)       # ch, position (microsteps)
-    motion_done = pyqtSignal(int, int)            # ch, final_position
-    stopped = pyqtSignal(int, int)                # ch, final_position
-    fault_occurred = pyqtSignal(int, int)         # ch, fault_mask
-    ack_received = pyqtSignal(int, int)           # req_cmd, status (0=OK)
-    frame_received = pyqtSignal(int, bytes)       # raw (cmd, payload) for log
-
-    def __init__(self, parent=None):
-        super().__init__(parent)
-        self._ser: serial.Serial | None = None
-        self._reader: _T3RReader | None = None
         self._write_lock = threading.Lock()
         self._tearing_down = False
         self._is_open = False
 
-        self._poll_timer = QTimer(self)
+        self._poll_stop = threading.Event()
-        self._poll_timer.setInterval(250)
+        self._poll_thread: threading.Thread | None = None
-        self._poll_timer.timeout.connect(self._poll)
+
+        # Per-channel motion-completion events, so a caller can block on a
+        # move finishing instead of guessing its duration.
+        self._motion_events = [threading.Event() for _ in range(proto.NUM_CHANNELS)]
+
+        self.port_opened = Signal("port_opened")              # ()
+        self.handshake_ok = Signal("handshake_ok")            # proto_ver, fw_ver, n_ch
+        self.disconnected = Signal("disconnected")            # reason ("" = user)
+        self.info_updated = Signal("info_updated")            # ch, proto.Info
+        self.drv_status_updated = Signal("drv_status_updated")  # ch, proto.DrvStatus
+        self.position_updated = Signal("position_updated")    # ch, position
+        self.motion_done = Signal("motion_done")              # ch, final_position
+        self.stopped = Signal("stopped")                      # ch, final_position
+        self.fault_occurred = Signal("fault_occurred")        # ch, fault_mask
+        self.ack_received = Signal("ack_received")            # req_cmd, status
+        self.frame_received = Signal("frame_received")        # raw cmd, payload
 
     # ── Connection ────────────────────────────────────────────────────────────
 
@@ -101,26 +136,24 @@ class T3RDriver(QObject):
     def is_open(self) -> bool:
         return self._is_open
 
-    def connect(self, port: str, baud: int = 115200) -> None:
+    def open(self, port: str, baud: int = 115200) -> None:
-        """Open the serial port and start the reader. Emits port_opened on success."""
+        """Open the serial port and start the reader; emits port_opened."""
         if self._is_open:
-            self.disconnect()
+            self.close()
         try:
-            self._ser = serial.Serial(port, baudrate=baud, timeout=0.05)
+            self._ser = open_8n1(port, baudrate=baud, timeout=0.05)
         except Exception as exc:
             raise RuntimeError(f"Cannot open {port}: {exc}") from exc
 
         self._tearing_down = False
         self._is_open = True
-        self._reader = _T3RReader(self._ser)
+        self._reader = _Reader(self._ser, self._on_frame, self._on_reader_finished)
-        self._reader.frame.connect(self._on_frame)
-        self._reader.finished_reason.connect(self._on_reader_finished)
         self._reader.start()
         self.port_opened.emit()
         self.send_frame(proto.ping())   # handshake; polling starts on PONG
 
-    def disconnect(self) -> None:
+    def close(self) -> None:
-        """Close port and stop polling."""
+        """Close the port and stop polling."""
         self._teardown("")
 
     def _on_reader_finished(self, reason: str):
@@ -131,16 +164,21 @@ class T3RDriver(QObject):
         if self._tearing_down or not self._is_open:
             return
         self._tearing_down = True
-        self._poll_timer.stop()
+        self.stop_polling()
         self._is_open = False
 
+        # Release anyone blocked in wait_motion_done so a disconnect during a
+        # move raises there instead of hanging until the timeout.
+        for ev in self._motion_events:
+            ev.set()
+
         reader, self._reader = self._reader, None
         ser, self._ser = self._ser, None
 
         if reader is not None:
             reader.stop()
-            if QThread.currentThread() is not reader:
+            if threading.current_thread() is not reader:
-                reader.wait(1000)
+                reader.join(1.0)
         if ser is not None:
             try:
                 ser.close()
@@ -186,6 +224,7 @@ class T3RDriver(QObject):
         self.send_frame(proto.set_current(ch, run_ma, hold_ma, ihold_delay))
 
     def move(self, ch: int, steps: int, velocity: int, accel: int):
+        self._motion_events[ch].clear()
         self.send_frame(proto.move(ch, steps, velocity, accel))
 
     def jog(self, ch: int, velocity: int, accel: int):
@@ -215,30 +254,44 @@ class T3RDriver(QObject):
     # ── Rotation helpers ──────────────────────────────────────────────────────
 
     def steps_for_angle(self, angle_deg: float, microsteps: int) -> int:
-        """Compute GR-axis microsteps needed to rotate the stage by angle_deg."""
+        """GR-axis microsteps needed to rotate the stage by angle_deg."""
         gear_ratio = self.GEAR_TEETH_STAGE / self.GEAR_TEETH_MOTOR
         steps_per_stage_rev = self.MOTOR_FULL_STEPS_PER_REV * microsteps * gear_ratio
         return round(steps_per_stage_rev * angle_deg / 360.0)
 
     def rotate_stage(self, angle_deg: float, microsteps: int,
                      velocity: int = 8000, accel: int = 4000):
-        """Move GR-axis by the number of steps that rotate the stage by angle_deg."""
+        """Move GR-axis by the steps that rotate the stage by angle_deg."""
-        steps = self.steps_for_angle(angle_deg, microsteps)
+        self.move(self.GR_AXIS_CH, self.steps_for_angle(angle_deg, microsteps),
-        self.move(self.GR_AXIS_CH, steps, velocity, accel)
+                  velocity, accel)
+
+    def wait_motion_done(self, ch: int, timeout: float) -> bool:
+        """Block until the channel reports MOTION_DONE.  False on timeout.
+
+        Cleared by ``move()``, set by the MOTION_DONE event and by teardown,
+        so a disconnect mid-move unblocks immediately.
+        """
+        return self._motion_events[ch].wait(timeout)
 
     # ── Polling ───────────────────────────────────────────────────────────────
 
     def start_polling(self):
-        self._poll_timer.start()
+        if self._poll_thread is not None and self._poll_thread.is_alive():
+            return
+        self._poll_stop.clear()
+        self._poll_thread = threading.Thread(target=self._poll_loop, daemon=True,
+                                             name="T3RPoll")
+        self._poll_thread.start()
 
     def stop_polling(self):
-        self._poll_timer.stop()
+        self._poll_stop.set()
 
-    def _poll(self):
+    def _poll_loop(self):
-        if not self._is_open:
+        while not self._poll_stop.wait(self.POLL_INTERVAL_S):
-            return
+            if not self._is_open:
-        for ch in range(proto.NUM_CHANNELS):
+                break
-            self.send_frame(proto.get_info(ch))
+            for ch in range(proto.NUM_CHANNELS):
+                self.send_frame(proto.get_info(ch))
 
     # ── Frame dispatcher ──────────────────────────────────────────────────────
 
@@ -274,14 +327,17 @@ class T3RDriver(QObject):
         elif cmd == proto.EVT_MOTION_DONE:
             ev = proto.decode_event_position(payload)
             if ev and 0 <= ev.ch < proto.NUM_CHANNELS:
+                self._motion_events[ev.ch].set()
                 self.motion_done.emit(ev.ch, ev.position)
 
         elif cmd == proto.EVT_STOPPED:
             ev = proto.decode_event_position(payload)
             if ev and 0 <= ev.ch < proto.NUM_CHANNELS:
+                self._motion_events[ev.ch].set()
                 self.stopped.emit(ev.ch, ev.position)
 
         elif cmd == proto.EVT_FAULT:
             ev = proto.decode_fault(payload)
             if ev and 0 <= ev.ch < proto.NUM_CHANNELS:
+                self._motion_events[ev.ch].set()
                 self.fault_occurred.emit(ev.ch, ev.position)

sc3_aui_app.py

@@ -10,7 +10,6 @@ import struct
 import sys
 import time
 from pathlib import Path
-import threading
 from threading import Thread
 
 import numpy as np
@@ -29,13 +28,19 @@ ROOT = Path(__file__).parent
 sys.path.insert(0, str(ROOT))
 
 from core.config import ScanDefaults
-from core.scan_geometry import ScanPlan, EtaEstimator, build_plan, format_eta, validate_plan
+from core.rotation import DEFAULT_ROTATION, RotationAxis
-from core.sras_format import (
+from core.scan_engine import (
-    SCAN_CHANNELS, SrasFile, create_scan_file, plan_from_header,
+    ResumeState,
+    LASER_FREQ_HZ, SCAN_VELOCITY_MM_S,
 )
+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, SrasFile, plan_from_header
+from gui.qt_t3r import QtT3RAdapter
+from gui.scan_bridge import QtScanController
 from hardware.helios_laser import HeliosLaser
 from hardware.pybbd202 import AXIS_X, AXIS_Y, ThorlabsServoDriver
-from hardware.t3r_driver import T3RDriver
 from hardware.tektronix_base import TektronixOscilloscopeBase
 from hardware.uc480_camera import (
     CameraStreamThread, UC480Camera, find_camera_bus_conflicts,
@@ -44,31 +49,6 @@ from t3r_control_panel import T3RControlPanel
 
 DEFAULTS = ScanDefaults.load()
 
-# ── Scan constants ───────────────────────────────────────────────────────────
-
-SCAN_VELOCITY_MM_S  = 100.0
-SCAN_ACCEL_MM_S2    = 1500.0
-LASER_FREQ_HZ       = 20000.0    # laser pulse frequency during data acquisition
-# Theoretical ramp distance: d = v² / (2a) = 100² / (2×1500) ≈ 3.33 mm
-SCAN_RAMP_MM        = SCAN_VELOCITY_MM_S**2 / (2.0 * SCAN_ACCEL_MM_S2)
-# Extra buffer added to both ends of the ramp.  The BBD202 controller begins
-# decelerating slightly before the theoretical point to avoid overshoot, which
-# causes TRIGOUT_MAXV to drop early and clip the last few data points.
-# 1 mm at 100 mm/s and 2000 Hz corresponds to 20 extra trigger windows.
-SCAN_RAMP_BUFFER_MM = 1.0
-SCOPE_SAMPLE_RATE   = 6.25e9    # 6.25 GS/s → 160 ps/sample
-SCOPE_TRIG_LEVEL_V  = 0.500
-
-# GR-axis rotation defaults (used by ScanWorker between angles)
-GR_MICROSTEPS       = 8         # microsteps/full-step on GR axis (ch3)
-GR_MOVE_VELOCITY    = 4000      # steps/s for inter-angle moves
-GR_MOVE_ACCEL       = 2000      # steps/s² for inter-angle moves
-GR_RUN_CURRENT_MA   = 1200      # drive current while moving
-GR_HOLD_CURRENT_MA  = 400       # standstill current
-GR_IHOLD_DELAY      = 6         # run→hold current ramp delay (TMC IHOLDDELAY units)
-# Sample rotates CW instead of CCW to clear wiring and avoid a stall condition.
-GR_ROTATION_SIGN    = -1
-
 BBD_DEFAULT_JOG_MM  = 0.5       # default jog step for BBD202
 
 
@@ -317,52 +297,12 @@ class OscopeWorker(QObject):
         try:
             self.scope = TektronixOscilloscopeBase(resource_name=ip, port=4000, timeout=10.0)
             self.scope.connect()
-            self._configure_channels()
+            configure_channels(self.scope)
             self.is_connected = True
             self.connected.emit()
         except Exception as e:
             self.connection_failed.emit(str(e))
 
-    def _configure_channels(self):
-        """Apply standard SRAS channel configuration after connecting."""
-        s = self.scope
-
-        # Turn on all four channels
-        for ch in (1, 2, 3, 4):
-            s.write(f"SELect:CH{ch} ON")
-
-        # ── CH1 — RF Acoustic Packet ──────────────────────────────────────────
-        s.set_channel_label_name(1, "RF Acoustic Packet")
-        s.set_channel_scale(1, 0.07)            # 70 mV/div
-        s.set_channel_position(1, 0.0)         # 0 divs
-        s.set_channel_termination(1, 50)       # 50 Ohm
-        s.set_channel_coupling(1, "DC")
-        s.set_channel_bandwidth(1, 250E6)      # 250Mhz Low-Pass
-
-        # ── CH2 — Trigger Signal ──────────────────────────────────────────────
-        s.set_channel_label_name(2, "Trigger Signal")
-        s.set_channel_scale(2, 0.5)            # 500 mV/div
-        s.set_channel_position(2, -2.72)       # -2.72 divs
-        s.set_channel_termination(2, 1000000)       # 50 Ohm
-        s.set_channel_coupling(2, "DC")
-        s.set_channel_bandwidth(2, 20E6)       # 20 MHz
-
-        # ── CH3 — Max Velocity Gate ───────────────────────────────────────────
-        s.set_channel_label_name(3, "Max Vel Gate")
-        s.set_channel_scale(3, 1.0)            # 1 V/div
-        s.set_channel_position(3, -2.72)       # -2.72 divs
-        s.set_channel_termination(3, 1000000)  # 1 MOhm
-        s.set_channel_coupling(3, "DC")
-        s.set_channel_bandwidth(3, 20E6)       # 20 MHz
-
-        # ── CH4 — Bias B ──────────────────────────────────────────────────────
-        s.set_channel_label_name(4, "Bias - B")
-        s.set_channel_scale(4, 0.1)            # 100 mV/div
-        s.set_channel_position(4, -2.72)       # -2.72 divs
-        s.set_channel_termination(4, 1000000)       # 1 Mohm
-        s.set_channel_coupling(4, "DC")
-        s.set_channel_bandwidth(4, 20E6)       # 20 MHz
-
     def _do_disconnect(self):
         if self.scope:
             try:
@@ -968,424 +908,6 @@ class ScanProgressWindow(QWidget):
 
 # ── Scan worker ───────────────────────────────────────────────────────────────
 
-class ScanWorker(QObject):
-    """Runs the full SRAS scan sequence in a background thread.
-
-    Accesses hardware drivers directly (not through worker queues) so it can
-    make blocking calls.  BBD202Worker.scanning_active is set to True for the
-    duration to suppress position polling in the BBD worker thread.
-    """
-    started         = pyqtSignal()
-    completed       = pyqtSignal()
-    dc_bias_updated = pyqtSignal(int, object)        # row index, list[float] per-frame DC means
-    failed          = pyqtSignal(str)
-    row_started     = pyqtSignal(int, int, int, int)  # row, n_rows, angle_idx, n_angles
-    row_done        = pyqtSignal(int, int, int, int)  # row, n_rows, angle_idx, n_angles
-    status_msg      = pyqtSignal(str)
-    user_prompt     = pyqtSignal(str, str)            # title, message
-    paused_changed  = pyqtSignal(bool)                # True while paused at a row boundary
-
-    def __init__(self, bbd: BBD202Worker, t3r: T3RDriver | None,
-                 oscope: OscopeWorker, plan: ScanPlan, prefix: str,
-                 save_dir: str, resume_info: dict | None = None):
-        super().__init__()
-        self._bbd    = bbd
-        self._t3r    = t3r
-        self._oscope = oscope
-        self._plan   = plan
-        self._prefix = prefix
-        self._save_dir = save_dir
-        self._resume_info = resume_info
-        self._abort  = False
-        self._prompt_event = threading.Event()
-        self._resume_event = threading.Event()
-        self._resume_event.set()   # set = running, cleared = pause requested
-
-    def abort(self):
-        self._abort = True
-        self._resume_event.set()   # unblock a paused scan so it can exit
-
-    def pause(self):
-        """Request a pause; takes effect at the next row boundary."""
-        self._resume_event.clear()
-
-    def resume(self):
-        self._resume_event.set()
-
-    def _pause_point(self):
-        """Block here (between rows, hardware idle) while a pause is requested."""
-        if self._resume_event.is_set() or self._abort:
-            return
-        self.status_msg.emit(
-            "Scan paused — lasers may be switched off. "
-            "Turn lasers back on before resuming."
-        )
-        self.paused_changed.emit(True)
-        while not self._resume_event.wait(0.2):
-            if self._abort:
-                break
-        self.paused_changed.emit(False)
-        if not self._abort:
-            self.status_msg.emit("Scan resumed.")
-
-    def acknowledge_prompt(self):
-        """Called from UI thread when user clicks OK on a prompt dialog."""
-        self._prompt_event.set()
-
-    def _request_user_prompt(self, title: str, message: str):
-        """Emit a prompt signal and block until the UI thread acknowledges it."""
-        self._prompt_event.clear()
-        self.user_prompt.emit(title, message)
-        self._prompt_event.wait()
-
-    @pyqtSlot()
-    def run(self):
-        try:
-            self._run_scan()
-        except Exception as e:
-            import traceback
-            traceback.print_exc()
-            self.failed.emit(str(e))
-
-    def _run_scan(self):
-        plan      = self._plan
-        per_angle = plan.per_angle
-        n_angles  = plan.n_angles
-        save_dir  = Path(self._save_dir)
-
-        # The actual X move starts one ramp-length + buffer before x_start and
-        # ends one ramp-length + buffer after x_start + x_delta, so the stage
-        # is at full velocity across the whole data window.
-        _x_ramp_total = SCAN_RAMP_MM + SCAN_RAMP_BUFFER_MM
-        validate_plan(plan, SCAN_RAMP_MM, SCAN_RAMP_BUFFER_MM)
-
-        geometry_summary = ", ".join(
-            f"{pa.angle_deg:.1f}°: {pa.n_rows} row(s) × {pa.n_frames} pts/row"
-            for pa in per_angle
-        )
-        self.status_msg.emit(
-            f"Scan geometry: {n_angles} angle(s), {plan.total_rows} row(s) total "
-            f"(per-angle bounding box)  |  save → {save_dir}\n{geometry_summary}"
-        )
-        self.started.emit()
-
-        # ── Validate hardware ─────────────────────────────────────────────────
-        ctrl  = self._bbd.controller
-        scope = self._oscope.scope
-        if ctrl is None:
-            raise RuntimeError("BBD202 not connected")
-        if scope is None:
-            raise RuntimeError("Oscilloscope not connected")
-        if n_angles > 1 and (self._t3r is None or not self._t3r.is_open):
-            raise RuntimeError(
-                f"NumAngles={n_angles} requires the T3R rotation stage (GR-axis), "
-                "but it is not connected. Connect T3R from the T3R panel before "
-                "starting a multi-angle scan, or set NumAngles to 1."
-            )
-
-        # ── Configure GR rotation axis ────────────────────────────────────────
-        # steps_for_angle() assumes GR_MICROSTEPS, so the device must be set to
-        # match — never rely on whatever the T3R panel (or firmware default)
-        # last left it at.  Also set drive current and energise the channel.
-        if self._t3r is not None and self._t3r.is_open:
-            self.status_msg.emit(
-                f"Configuring GR axis: {GR_MICROSTEPS} µsteps, "
-                f"{GR_RUN_CURRENT_MA}/{GR_HOLD_CURRENT_MA} mA run/hold …"
-            )
-            gr_ch = self._t3r.GR_AXIS_CH
-            self._t3r.set_microstep(gr_ch, GR_MICROSTEPS)
-            self._t3r.set_current(gr_ch, GR_RUN_CURRENT_MA,
-                                  GR_HOLD_CURRENT_MA, GR_IHOLD_DELAY)
-            self._t3r.enable(gr_ch)
-            time.sleep(0.2)
-
-        # ── Prepare stage ─────────────────────────────────────────────────────
-        self.status_msg.emit("Enabling stage axes …")
-        if not ctrl.am_enabled[0]:
-            ctrl.enable_axis(AXIS_X)
-        if not ctrl.am_enabled[1]:
-            ctrl.enable_axis(AXIS_Y)
-        time.sleep(0.2)
-
-        if not ctrl.am_homed[0] or not ctrl.am_homed[1]:
-            self.status_msg.emit("Homing stage (may take up to 2 min) …")
-            if not ctrl.am_homed[0]:
-                ctrl.home_axis(AXIS_X, timeout=120.0)
-            if not ctrl.am_homed[1]:
-                ctrl.home_axis(AXIS_Y, timeout=120.0)
-
-        self.status_msg.emit("Setting scan velocity …")
-        ctrl.set_velocity_params(AXIS_X, max_velocity=SCAN_VELOCITY_MM_S,
-                                 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 when stage is at maximum velocity
-        ctrl.set_trigger_trigout_maxv(AXIS_X)
-
-        # ── Configure oscilloscope ────────────────────────────────────────────
-        self.status_msg.emit("Configuring oscilloscope …")
-        # Edge trigger: rising edge of CH2 (laser pulse) at 1.0 V.
-        scope.write("TRIGger:A:TYPe EDGE")
-        scope.set_trigger_source(2)
-        scope.set_trigger_slope("RISE")
-        scope.set_trigger_level(2, SCOPE_TRIG_LEVEL_V)
-        scope.set_trigger_mode("NORMAL")       # wait for trigger (don't auto-sweep)
-        scope.set_acquire_mode("SAMPLE")
-        scope.set_fastframe_state(False)       # start non-FF for background capture
-        scope.set_sample_rate(SCOPE_SAMPLE_RATE)
-        scope.write("HORizontal:POSition 30")  # 10 % trigger offset
-        time.sleep(0.3)
-        samples_per_frame = scope.get_record_length()
-
-        resume_info = self._resume_info
-        if resume_info is None:
-            # ── Snapshot WFMOutpre for each channel (captures YMULT/YOFF/YZERO) ──
-            preambles = []
-            for ch in SCAN_CHANNELS:
-                scope.set_data_source(ch)
-                preambles.append(scope.query_wfmoutpre())
-
-            # ── Background subtraction capture ──────────────────────────────────
-            # Prompt user to ensure Helios is ON and Genesis is OFF.
-            self._request_user_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."
-            )
-            if self._abort:
-                self.failed.emit("Scan aborted by user.")
-                return
-
-            # Capture a single averaged CH1 frame (1024 waveforms averaged).
-            self.status_msg.emit("Capturing background waveform (1024-average) …")
-            scope.set_acquire_mode("AVERAGE")
-            scope.write("ACQuire:NUMAVg 1024")
-            scope.write("ACQuire:STOPAfter SEQuence")  # auto-stop after all 1024 averages
-            scope.set_data_source(1)
-            scope.write("ACQuire:STATE RUN")
-            # Poll until the scope finishes all 1024 averages and auto-stops.
-            # Timeout: 1024 averages at 2 kHz (worst case) = ~0.5 s; allow 60 s.
-            _bg_deadline = time.time() + 60.0
-            while time.time() < _bg_deadline:
-                if self._abort:
-                    break
-                if scope.query("ACQuire:STATE?").strip() == "0":
-                    break
-                time.sleep(0.25)
-            else:
-                scope.write("ACQuire:STATE STOP")
-                self.status_msg.emit("Warning: background average timed out; stopping early.")
-            time.sleep(0.1)
-            background_waveform = scope.transfer_curve()
-
-            # Prompt user to turn Genesis back on before the actual scan.
-            self._request_user_prompt(
-                "Begin Scanning",
-                "Background captured successfully.\n\n"
-                "Please ensure the Genesis laser is back ON,\n"
-                "then click OK to begin scanning."
-            )
-            if self._abort:
-                self.failed.emit("Scan aborted by user.")
-                return
-        else:
-            # Resuming an existing file: the background waveform and channel
-            # preambles it already contains are reused as-is (the format has
-            # no way to replace them without rewriting the whole file), so
-            # background capture is skipped entirely.  Sanity-check that this
-            # scope is still producing the same record length the file was
-            # started with — a mismatch would silently corrupt the ragged
-            # per-row byte layout on append.
-            if samples_per_frame != resume_info["samples_per_frame"]:
-                raise RuntimeError(
-                    f"Oscilloscope record length ({samples_per_frame} samples/frame) "
-                    f"does not match the {resume_info['samples_per_frame']} samples/frame "
-                    f"this scan file was started with — cannot safely resume."
-                )
-            target_angles = ", ".join(str(t["ai"] + 1) for t in resume_info["targets"])
-            self._request_user_prompt(
-                "Resume Scan",
-                f"Resuming {resume_info['path'].name} — will (re)acquire "
-                f"angle(s) {target_angles} of {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"
-                "then click OK to continue scanning."
-            )
-            if self._abort:
-                self.failed.emit("Scan aborted by user.")
-                return
-
-        # Restore SAMPLE mode and FastFrame for the actual scan.  FastFrame
-        # count (points/row) is set per-angle in the scan loop below, since
-        # it depends on that angle's bounding-box X extent.
-        scope.write("ACQuire:STOPAfter RUNSTop")
-        scope.set_acquire_mode("SAMPLE")
-        scope.set_fastframe_state(True)
-
-        # Restore logic-AND trigger (CH2 HIGH AND CH3 HIGH) for the scan loop:
-        # CH3 is the BBD202 TRIGOUT_MAXV gate, so frames only accumulate while
-        # the stage is at full scan velocity.
-        scope.write("TRIGger:A:TYPe LOGIc")
-        scope.write("TRIGger:A:LOGIc:FUNCtion AND")
-        scope.set_trigger_level(2, SCOPE_TRIG_LEVEL_V)
-        scope.set_trigger_level(3, SCOPE_TRIG_LEVEL_V)
-        scope.write("TRIGger:A:LOGICPattern:CH2 HIGH")
-        scope.write("TRIGger:A:LOGICPattern:CH3 HIGH")
-        time.sleep(0.2)
-
-        # ── Open output file (entire scan in one .sras) ─────────────────────────
-        if resume_info is not None:
-            targets_by_ai = {t["ai"]: t for t in resume_info["targets"]}
-            scan_file = open(resume_info["path"], "r+b")
-            self.status_msg.emit(
-                f"Resuming {resume_info['path'].name} — "
-                f"{len(targets_by_ai)} angle(s) to (re)acquire …"
-            )
-        else:
-            targets_by_ai = None
-            fname = save_dir / f"{self._prefix}.sras"
-            scan_file = create_scan_file(
-                fname, plan, samples_per_frame, SCOPE_SAMPLE_RATE,
-                preambles, background_waveform,
-            )
-
-        # ── Scan loop ─────────────────────────────────────────────────────────
-        self._bbd.scanning_active = True
-        # Both fresh and resumed scans assume the GR axis starts at home (0°)
-        # — the resume prompt instructs the operator to re-home it before
-        # continuing — so the first move always rotates directly from 0°
-        # to the starting angle.
-        prev_gr_deg = 0.0
-        try:
-            for ai, pa in enumerate(per_angle):
-                if targets_by_ai is not None and ai not in targets_by_ai:
-                    continue    # not selected for (re)acquisition
-                self._pause_point()
-                if self._abort:
-                    break
-
-                angle       = pa.angle_deg
-                a_x_start   = pa.x_start
-                a_x_delta   = pa.x_delta
-                a_n_rows    = pa.n_rows
-                a_n_frames  = pa.n_frames
-                y_positions = pa.y_positions
-
-                if targets_by_ai is not None:
-                    # Interior angles may already have valid data on either
-                    # side of them, 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"])
-
-                # ── Rotate GR ─────────────────────────────────────────────────
-                if self._t3r is not None and self._t3r.is_open:
-                    delta_deg = angle - prev_gr_deg
-                    if abs(delta_deg) > 0.001:
-                        steps = self._t3r.steps_for_angle(delta_deg, GR_MICROSTEPS)
-                        # Trapezoidal move time: cruise + accel/decel ramps
-                        est_secs = (abs(steps) / GR_MOVE_VELOCITY
-                                    + GR_MOVE_VELOCITY / GR_MOVE_ACCEL)
-                        self.status_msg.emit(
-                            f"Rotating GR to {angle:.1f}° (Δ{delta_deg:+.1f}°, "
-                            f"≈{est_secs:.1f} s) …"
-                        )
-                        self._t3r.rotate_stage(delta_deg, GR_MICROSTEPS,
-                                               GR_MOVE_VELOCITY, GR_MOVE_ACCEL)
-                        time.sleep(est_secs + 0.5)
-                prev_gr_deg = angle
-
-                # This 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(a_n_frames)
-
-                # ── Row loop ──────────────────────────────────────────────────
-                for ri, y_pos in enumerate(y_positions):
-                    self._pause_point()
-                    if self._abort:
-                        break
-
-                    self.row_started.emit(ri + 1, a_n_rows, ai + 1, n_angles)
-                    self.status_msg.emit(
-                        f"Angle {ai+1}/{n_angles}  Row {ri+1}/{a_n_rows}  "
-                        f"(Y={y_pos:.3f} mm)"
-                    )
-
-                    # Position stage one ramp-length + buffer before the data
-                    # window so the stage is at full velocity before x_start.
-                    ctrl.move_axis_absolute(AXIS_Y, y_pos,                          timeout=60.0)
-                    ctrl.move_axis_absolute(AXIS_X, a_x_start - _x_ramp_total,      timeout=30.0)
-
-                    # Arm oscilloscope — trigger is gated with TRIGOUT_MAXV so
-                    # frames only accumulate once the stage reaches full velocity
-                    scope.write("ACQuire:STATE RUN")
-                    time.sleep(0.05)
-
-                    # Execute scan move: data window + ramp + buffer run-off so
-                    # the stage does not begin decelerating before the last point.
-                    x_end = a_x_start + a_x_delta + _x_ramp_total
-                    ctrl.move_axis_absolute(AXIS_X, x_end, timeout=120.0)
-
-                    # Brief settle: wait for trailing frames then stop acquisition
-                    time.sleep(0.2)
-                    scope.write("ACQuire:STATE STOP")
-
-                    # Stream all channels from oscilloscope and append to file.
-                    # CH3 is the max-vel gate signal — no useful waveform data,
-                    # so write zeroed frames to keep the file format intact.
-                    for ch in SCAN_CHANNELS:
-                        if ch == 3:
-                            self.status_msg.emit("Writing zeroed CH3 frames …")
-                            zero_frame = bytes(samples_per_frame)
-                            n_frames_acquired = int(scope.query("ACQuire:NUMFRAMESACQuired?"))
-                            for _ in range(n_frames_acquired):
-                                scan_file.write(zero_frame)
-                        elif ch == 4:
-                            self.status_msg.emit(f"Fetching CH{ch} data …")
-                            scope.set_data_source(ch)
-                            waveforms: list[bytes] = scope.transfer_fastframe(parse=False)
-                            if waveforms:
-                                frame_avgs = []
-                                for w in waveforms:
-                                    n = len(w)
-                                    frame_avgs.append(
-                                        sum(struct.unpack(f"{n}b", w)) / n if n > 0 else 0.0
-                                    )
-                                self.dc_bias_updated.emit(ri + 1, frame_avgs)
-                            for w in waveforms:
-                                scan_file.write(w)
-                        else:
-                            self.status_msg.emit(f"Fetching CH{ch} data …")
-                            scope.set_data_source(ch)
-                            waveforms: list[bytes] = scope.transfer_fastframe(parse=False)
-                            for w in waveforms:
-                                scan_file.write(w)
-
-                    self.row_done.emit(ri + 1, a_n_rows, ai + 1, n_angles)
-
-        finally:
-            scan_file.close()
-            self._bbd.scanning_active = False
-            # Return GR axis to home (0°) regardless of abort or error
-            if self._t3r is not None and self._t3r.is_open and abs(prev_gr_deg) > 0.001:
-                return_deg = -prev_gr_deg
-                est_secs = (abs(self._t3r.steps_for_angle(return_deg, GR_MICROSTEPS))
-                            / GR_MOVE_VELOCITY + GR_MOVE_VELOCITY / GR_MOVE_ACCEL)
-                self.status_msg.emit(
-                    f"Returning GR to home ({return_deg:+.1f}°, ≈{est_secs:.1f} s) …"
-                )
-                self._t3r.rotate_stage(return_deg, GR_MICROSTEPS,
-                                       GR_MOVE_VELOCITY, GR_MOVE_ACCEL)
-                time.sleep(est_secs + 0.5)
-
-        if self._abort:
-            self.failed.emit("Scan aborted by user.")
-        else:
-            self.status_msg.emit("Scan complete.")
-            self.completed.emit()
-
-
 # ── Main window ───────────────────────────────────────────────────────────────
 
 class MainWindow(QMainWindow):
@@ -1394,8 +916,10 @@ class MainWindow(QMainWindow):
         uic.loadUi(ROOT / "sc3-aui-main.ui", self)
         self.setWindowTitle("Scanengine-3 AUI")
 
-        # ── T3R driver (owns serial + reader QThread internally) ─────────────
+        # ── T3R driver (owns serial + reader thread internally) ──────────────
-        self._t3r_driver  = T3RDriver(self)
+        # QtT3RAdapter re-emits the driver's thread-side callbacks as queued
+        # Qt signals so widget slots run on the GUI thread.
+        self._t3r_driver  = QtT3RAdapter(parent=self)
         self._t3r_panel: T3RControlPanel | None = None
 
         # ── Worker threads ────────────────────────────────────────────────────
@@ -1419,8 +943,8 @@ class MainWindow(QMainWindow):
         self._helios_win    = HeliosWindow(self._helios_worker)
         self._scan_progress = ScanProgressWindow()
 
-        self._scan_worker: ScanWorker | None = None
+        self._scan_worker: QtScanController | None = None
-        self._scan_thread:  QThread   | None = None
+        self._scan_thread:  QThread | None = None
 
         self._bbd_active_jog: tuple[str, int] | None = None   # (axis, direction)
         self._bbd_jog_timer = QTimer(self)
@@ -1739,11 +1263,9 @@ class MainWindow(QMainWindow):
             QMessageBox.warning(self, "Cannot Resume Scan", f"Could not read scan file:\n\n{e}")
             return
 
-        hdr = sras.header
+        if not is_compatible(sras, velocity=SCAN_VELOCITY_MM_S,
-        if (hdr.bytes_per_sample != 1 or hdr.n_channels != len(SCAN_CHANNELS)
+                             laser_freq=LASER_FREQ_HZ, sample_rate=SAMPLE_RATE_HZ,
-                or abs(hdr.velocity - SCAN_VELOCITY_MM_S) > 1e-3
+                             n_channels=len(SCAN_CHANNELS)):
-                or abs(hdr.laser_freq - LASER_FREQ_HZ) > 1e-3
-                or abs(hdr.sample_rate - SCOPE_SAMPLE_RATE) > 1.0):
             QMessageBox.warning(
                 self, "Cannot Resume Scan",
                 f"{path.name} was recorded with acquisition settings that don't "
@@ -1760,59 +1282,47 @@ class MainWindow(QMainWindow):
         if not selected:
             return
 
-        # Data is one contiguous stream, so angles past the frontier (the
+        resume_plan = plan_resume(statuses, selected)
-        # first incomplete one) can't be skipped over — back-fill the range.
+        if resume_plan.auto_added:
-        frontier_idx = next((s.index for s in statuses if not s.complete), len(statuses))
-        at_or_past_frontier = {i for i in selected if i >= frontier_idx}
-        if at_or_past_frontier:
-            final = selected | set(range(frontier_idx, max(at_or_past_frontier) + 1))
-        else:
-            final = selected
-
-        auto_added = sorted(final - selected)
-        if auto_added:
             QMessageBox.information(
                 self, "Additional Angles Required",
                 "The scan file has no data yet past angle "
-                f"{frontier_idx + 1}, so angle(s) can't be skipped over. "
+                f"{resume_plan.frontier_idx + 1}, so angle(s) can't be skipped over. "
                 "The following angle(s) will also be (re)acquired so there's "
-                f"no gap: {[i + 1 for i in auto_added]}"
+                f"no gap: {[i + 1 for i in resume_plan.auto_added]}"
             )
 
-        targets = [
+        angle_list = ", ".join(str(t.angle_idx + 1) for t in resume_plan.targets)
-            {
-                "ai": s.index, "data_offset": s.data_offset,
-                "n_rows": s.n_rows, "angle_deg": s.angle_deg,
-            }
-            for s in statuses if s.index in final
-        ]
-        total_rows = sum(t["n_rows"] for t in targets)
-        angle_list = ", ".join(f"{t['ai'] + 1}" for t in targets)
         reply = QMessageBox.question(
             self, "Resume Scan",
             f"Resume {path.name}?\n\n"
             f"Angle(s) to (re)acquire: {angle_list}\n"
-            f"Total rows to acquire: {total_rows}\n\n"
+            f"Total rows to acquire: {resume_plan.total_rows}\n\n"
             "Existing data for these angle(s) (if any) will be overwritten.",
             QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
         )
         if reply != QMessageBox.StandardButton.Yes:
             return
 
-        plan = plan_from_header(sras)
+        self._launch_scan_worker(plan_from_header(sras), path.stem,
-        resume_info = {
+                                 str(path.parent), resume_plan.to_state(sras))
-            "path": path,
-            "targets": targets,
-            "samples_per_frame": hdr.samples_per_frame,
-        }
-        self._launch_scan_worker(plan, path.stem, str(path.parent), resume_info)
 
     def _launch_scan_worker(self, plan: ScanPlan, prefix: str, save_dir: str,
-                            resume_info: dict | None = None):
+                            resume: ResumeState | None = None):
+        rotator = RotationAxis(self._t3r_driver.driver, DEFAULT_ROTATION)
+
         self._scan_thread = QThread(self)
-        self._scan_worker = ScanWorker(
+        self._scan_worker = QtScanController(
-            self._bbd_worker, self._t3r_driver, self._oscope_worker,
+            stage=self._bbd_worker.controller,
-            plan, prefix, save_dir, resume_info
+            scope=self._oscope_worker.scope,
+            rotator=rotator,
+            plan=plan,
+            out_path=Path(save_dir) / f"{prefix}.sras",
+            resume=resume,
+            # Suppress BBD position polling for the duration of the scan —
+            # a worker concern, not the engine's.
+            on_scan_active=lambda active: setattr(
+                self._bbd_worker, "scanning_active", active),
         )
         self._scan_worker.moveToThread(self._scan_thread)
         self._scan_thread.started.connect(self._scan_worker.run)
@@ -1827,13 +1337,11 @@ class MainWindow(QMainWindow):
 
         self.start_scan_btn.setEnabled(False)
         self._scan_progress.reset_pause_btn()
-        if resume_info is None:
+        ai0 = 0 if resume is None else resume.targets[0].angle_idx
-            self._scan_progress.update_progress(0, plan.per_angle[0].n_rows, 0, plan.n_angles)
+        self._scan_progress.update_progress(
-        else:
+            0, plan.per_angle[ai0].n_rows,
-            ai0 = resume_info["targets"][0]["ai"]
+            0 if resume is None else ai0 + 1, plan.n_angles
-            self._scan_progress.update_progress(
+        )
-                0, plan.per_angle[ai0].n_rows, ai0 + 1, plan.n_angles
-            )
         self._scan_progress.show()
         self._scan_thread.start()
 
@@ -1855,7 +1363,7 @@ class MainWindow(QMainWindow):
             _i(self.num_angles_edit, "NumAngles"),
             _f(self.row_spacing_edit, "RowSpacing"),
             laser_freq_hz=LASER_FREQ_HZ, velocity_mm_s=SCAN_VELOCITY_MM_S,
-            rotation_sign=GR_ROTATION_SIGN,
+            rotation_sign=DEFAULT_ROTATION.rotation_sign,
         )
         prefix = self.scan_prefix_edit.text().strip() or "scan"
         save_dir = self.scan_save_dir_edit.text().strip() or DEFAULTS.save_dir
@@ -1901,7 +1409,7 @@ class MainWindow(QMainWindow):
     def _disconnect_all_and_close(self):
         """Cleanly disconnect all hardware then quit."""
         if self._t3r_driver.is_open:
-            self._t3r_driver.disconnect()
+            self._t3r_driver.close()
         if self._bbd_worker.is_connected:
             self._bbd_worker.queue_disconnect()
         if self._oscope_worker.is_connected:
@@ -1930,7 +1438,7 @@ class MainWindow(QMainWindow):
         self._scan_progress.close()
         self._helios_win.close()
         if self._t3r_driver.is_open:
-            self._t3r_driver.disconnect()
+            self._t3r_driver.close()
         for w in (self._bbd_worker, self._oscope_worker, self._helios_worker):
             w.stop_worker()
         for t in (self._bbd_thread, self._oscope_thread, self._helios_thread):

t3r_control_panel.py

@@ -27,8 +27,9 @@ from PyQt6.QtWidgets import (
     QSpinBox, QSplitter, QVBoxLayout, QWidget,
 )
 
-from hardware.t3r_driver import T3RDriver
+from gui.qt_t3r import QtT3RAdapter
 from hardware.serial_util import scored_ports
+from hardware.t3r_driver import T3RDriver   # class constants (gear train, channel names)
 import hardware.t3r_protocol as proto
 
 
@@ -62,7 +63,7 @@ def _spin(lo: int, hi: int, val: int) -> QSpinBox:
 class ChannelPanel(QGroupBox):
     """Controls and live readouts for one T3R axis."""
 
-    def __init__(self, ch: int, driver: T3RDriver):
+    def __init__(self, ch: int, driver: QtT3RAdapter):
         label = f"Axis {ch} — {T3RDriver.CHANNEL_NAMES[ch]}"
         super().__init__(label)
         self.ch = ch
@@ -278,7 +279,7 @@ class ChannelPanel(QGroupBox):
 class GroupPanel(QGroupBox):
     """Ganged motion — selected axes step in lockstep."""
 
-    def __init__(self, driver: T3RDriver, log_fn):
+    def __init__(self, driver: QtT3RAdapter, log_fn):
         super().__init__("Ganged / synchronised motion — selected axes move in lockstep")
         self._driver = driver
         self._log = log_fn
@@ -389,7 +390,7 @@ class RotationPanel(QGroupBox):
         Ratio = 125/10 = 12.5
     """
 
-    def __init__(self, driver: T3RDriver):
+    def __init__(self, driver: QtT3RAdapter):
         super().__init__(
             f"Stage Rotation  (GR-axis ch{T3RDriver.GR_AXIS_CH}) — "
             f"gear: {T3RDriver.GEAR_TEETH_MOTOR}T motor → 30T idler → "
@@ -481,12 +482,12 @@ class RotationPanel(QGroupBox):
 class T3RControlPanel(QDialog):
     """User-hidable T3R control window.
 
-    Pass a T3RDriver instance. The panel connects to its signals and forwards
+    Pass a QtT3RAdapter instance. The panel connects to its signals and forwards
     commands via its API. Connection management (port open/close) is handled
     inside the panel itself.
     """
 
-    def __init__(self, driver: T3RDriver, parent=None):
+    def __init__(self, driver: QtT3RAdapter, parent=None):
         super().__init__(parent)
         self.setWindowTitle("T3R Stepper Controller")
         self.setWindowFlags(
@@ -624,14 +625,14 @@ class T3RControlPanel(QDialog):
 
     def _toggle_connect(self):
         if self._driver.is_open:
-            self._driver.disconnect()
+            self._driver.close()
             return
         port = self.port_combo.currentData()
         if not port:
             self._log("No serial port selected", "err")
             return
         try:
-            self._driver.connect(port)
+            self._driver.open(port)
         except Exception as exc:
             self._log(f"Connect failed: {exc}", "err")
             self.conn_lbl.setText("connect failed")

tests/fakes.py

@@ -0,0 +1,185 @@
+"""Recording fake hardware for headless ScanEngine tests.
+
+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.
+"""
+from __future__ import annotations
+
+
+class Trace:
+    """Ordered record of hardware calls, shared by all fakes in one test."""
+
+    def __init__(self):
+        self.calls: list[tuple] = []
+
+    def record(self, *entry):
+        self.calls.append(entry)
+
+    def names(self) -> list[str]:
+        return [c[0] for c in self.calls]
+
+    def of(self, name: str) -> list[tuple]:
+        return [c for c in self.calls if c[0] == name]
+
+    def count(self, name: str) -> int:
+        return len(self.of(name))
+
+
+class FakeStage:
+    """Stands in for ThorlabsServoDriver."""
+
+    def __init__(self, trace: Trace, homed=(True, True), enabled=(True, True)):
+        self._t = trace
+        self.am_homed = list(homed)
+        self.am_enabled = list(enabled)
+        self.positions = [0.0, 0.0]
+
+    def enable_axis(self, axis):
+        self._t.record("enable_axis", axis)
+        self.am_enabled[0 if axis == 0x21 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
+
+    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)
+
+    def move_axis_absolute(self, axis, pos, timeout=0.0):
+        self._t.record("move_axis_absolute", axis, round(pos, 6))
+        self.positions[0 if axis == 0x21 else 1] = pos
+
+
+class FakeScope:
+    """Stands in for TektronixOscilloscopeBase.
+
+    Returns deterministic frame bytes so the written file can be compared
+    against an expected byte pattern.
+    """
+
+    def __init__(self, trace: Trace, samples_per_frame=8, n_frames=4):
+        self._t = trace
+        self.samples_per_frame = samples_per_frame
+        self._n_frames = n_frames
+        self._acq_polls = 0
+        self.frame_seq = 0
+
+    # -- writes / queries ---------------------------------------------------
+    def write(self, cmd):
+        self._t.record("write", cmd)
+
+    def query(self, cmd):
+        self._t.record("query", cmd)
+        if cmd == "ACQuire:STATE?":
+            self._acq_polls += 1
+            return "0"                      # background average finished
+        if cmd == "ACQuire:NUMFRAMESACQuired?":
+            return str(self._n_frames)
+        return ""
+
+    # -- typed setters used by core.scope_sras ------------------------------
+    def set_trigger_source(self, ch):
+        self._t.record("set_trigger_source", ch)
+
+    def set_trigger_slope(self, slope):
+        self._t.record("set_trigger_slope", slope)
+
+    def set_trigger_level(self, ch, level):
+        self._t.record("set_trigger_level", ch, level)
+
+    def set_trigger_mode(self, mode):
+        self._t.record("set_trigger_mode", mode)
+
+    def set_acquire_mode(self, mode):
+        self._t.record("set_acquire_mode", mode)
+
+    def set_fastframe_state(self, on):
+        self._t.record("set_fastframe_state", on)
+
+    def set_fastframe_count(self, n):
+        self._t.record("set_fastframe_count", n)
+        self._n_frames = n
+
+    def set_sample_rate(self, sr):
+        self._t.record("set_sample_rate", sr)
+
+    def get_record_length(self):
+        return self.samples_per_frame
+
+    def set_data_source(self, ch):
+        self._t.record("set_data_source", ch)
+        self._source = ch
+
+    def query_wfmoutpre(self):
+        return f"WFMOUTPRE:CH{self._source};YMULT 1.5625E-3;YOFF -87.04;YZERO 0.0"
+
+    def transfer_curve(self):
+        self._t.record("transfer_curve")
+        return bytes(range(self.samples_per_frame))
+
+    def transfer_fastframe(self, parse=True):
+        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
+
+    # channel config (only used by configure_channels)
+    def set_channel_label_name(self, ch, name):
+        self._t.record("set_channel_label_name", ch, name)
+
+    def set_channel_scale(self, ch, v):
+        self._t.record("set_channel_scale", ch, v)
+
+    def set_channel_position(self, ch, v):
+        self._t.record("set_channel_position", ch, v)
+
+    def set_channel_termination(self, ch, v):
+        self._t.record("set_channel_termination", ch, v)
+
+    def set_channel_coupling(self, ch, v):
+        self._t.record("set_channel_coupling", ch, v)
+
+    def set_channel_bandwidth(self, ch, v):
+        self._t.record("set_channel_bandwidth", ch, v)
+
+
+class FakeT3R:
+    """Stands in for the (Qt-free) T3RDriver, for RotationAxis."""
+
+    GR_AXIS_CH = 3
+    MOTOR_FULL_STEPS_PER_REV = 200
+    GEAR_TEETH_MOTOR = 10
+    GEAR_TEETH_STAGE = 125
+
+    def __init__(self, trace: Trace, is_open=True, motion_completes=True):
+        self._t = trace
+        self.is_open = is_open
+        self._motion_completes = motion_completes
+
+    def set_microstep(self, ch, micro):
+        self._t.record("t3r_set_microstep", ch, micro)
+
+    def set_current(self, ch, run_ma, hold_ma, ihold):
+        self._t.record("t3r_set_current", ch, run_ma, hold_ma, ihold)
+
+    def enable(self, ch):
+        self._t.record("t3r_enable", ch)
+
+    def steps_for_angle(self, angle_deg, microsteps):
+        ratio = self.GEAR_TEETH_STAGE / self.GEAR_TEETH_MOTOR
+        return round(self.MOTOR_FULL_STEPS_PER_REV * microsteps * ratio
+                     * angle_deg / 360.0)
+
+    def rotate_stage(self, angle_deg, microsteps, velocity, accel):
+        self._t.record("t3r_rotate", round(angle_deg, 6))
+
+    def wait_motion_done(self, ch, timeout):
+        self._t.record("t3r_wait_motion_done", ch)
+        return self._motion_completes

tests/test_scan_engine.py

@@ -0,0 +1,282 @@
+"""Headless ScanEngine tests driven entirely by fake hardware.
+
+These cover what can't be checked without the rig: the command sequence,
+the written file layout, and abort/pause behaviour.
+"""
+import threading
+import time
+
+import pytest
+
+from core.rotation import RotationAxis, RotationSettings
+from core.scan_engine import (
+    AXIS_X, AXIS_Y, ScanAborted, ScanCallbacks, ScanEngine, ResumeState,
+    ResumeTarget,
+)
+from core.scan_geometry import ScanGeometryError, build_plan
+from core.sras_format import SCAN_CHANNELS, SrasFile
+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,
+                      laser_freq_hz=20000.0, velocity_mm_s=100.0)
+
+
+def build(tmp_path, num_angles=1, callbacks=None, resume=None, **kw):
+    trace = Trace()
+    stage = FakeStage(trace)
+    scope = FakeScope(trace, samples_per_frame=SPF)
+    t3r = FakeT3R(trace, **kw)
+    rotator = RotationAxis(t3r, RotationSettings())
+    plan = make_plan(num_angles)
+    engine = ScanEngine(stage, scope, rotator, plan, tmp_path / "out.sras",
+                        resume=resume,
+                        callbacks=callbacks or ScanCallbacks())
+    return engine, trace, plan
+
+
+def test_single_angle_scan_writes_readable_file(tmp_path):
+    engine, trace, plan = build(tmp_path)
+    result = engine.run()
+
+    assert not result.aborted
+    assert result.rows_written == plan.per_angle[0].n_rows
+    assert result.angles_acquired == [0]
+
+    sras = SrasFile(result.path)
+    assert sras.header.n_angles == 1
+    assert sras.header.samples_per_frame == SPF
+    assert sras.header.n_channels == len(SCAN_CHANNELS)
+    # 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))
+
+
+def test_command_sequence_order(tmp_path):
+    engine, trace, plan = build(tmp_path)
+    engine.run()
+    names = trace.names()
+
+    def first(name):
+        return names.index(name)
+
+    # Stage prepared, then scope configured, then rows executed
+    assert first("set_trigger_trigout_maxv") < first("set_sample_rate")
+    assert first("set_sample_rate") < first("transfer_fastframe")
+    # Velocity set for both axes before any scan move
+    assert trace.count("set_velocity_params") == 2
+    # Per row: Y positioned, then X pre-ramp, then X run
+    moves = trace.of("move_axis_absolute")
+    assert moves[0][1] == AXIS_Y
+    assert moves[1][1] == AXIS_X and moves[2][1] == AXIS_X
+    assert moves[1][2] < moves[2][2]          # pre-ramp start < run-off end
+    # Data channels transferred (CH3 is synthesized, not read)
+    assert [c[1] for c in trace.of("transfer_fastframe")] == [1, 4]
+
+
+def test_multi_angle_rotates_and_returns_home(tmp_path):
+    engine, trace, plan = build(tmp_path, num_angles=3)
+    engine.run()
+
+    rotations = [c[1] for c in trace.of("t3r_rotate")]
+    # Three angles at 0/-90/-180 → two moves out, then one back to 0
+    assert rotations == [-90.0, -90.0, 180.0]
+    # Every move waits for completion instead of sleeping a guess
+    assert trace.count("t3r_wait_motion_done") == len(rotations)
+    # GR configured once, before any rotation
+    assert trace.names().index("t3r_set_microstep") < trace.names().index("t3r_rotate")
+
+    sras = SrasFile(tmp_path / "out.sras")
+    assert [s.status for s in sras.angle_status()] == ["OK"] * 3
+
+
+def test_fastframe_count_rearmed_per_angle(tmp_path):
+    engine, trace, plan = build(tmp_path, num_angles=3)
+    engine.run()
+    counts = [c[1] for c in trace.of("set_fastframe_count")]
+    assert counts == [pa.n_frames for pa in plan.per_angle]
+
+
+def test_abort_before_start_raises_and_stops_early(tmp_path):
+    engine, trace, _ = build(tmp_path)
+    engine.abort()
+    with pytest.raises(ScanAborted):
+        engine.run()
+    assert trace.count("transfer_fastframe") == 0
+
+
+def test_abort_during_prompt_unblocks(tmp_path):
+    """A prompt that never returns must not deadlock an aborting scan."""
+    released = threading.Event()
+
+    def prompt(title, msg):
+        # Simulates the GUI bridge: waits until abort flips the flag.
+        while not engine.aborted:
+            if released.wait(0.01):
+                return
+
+    engine, trace, _ = build(tmp_path, callbacks=ScanCallbacks(prompt=prompt))
+
+    errors = []
+
+    def run():
+        try:
+            engine.run()
+        except ScanAborted:
+            errors.append("aborted")
+
+    t = threading.Thread(target=run, daemon=True)
+    t.start()
+    time.sleep(0.2)   # let it reach the first prompt
+    engine.abort()
+    t.join(timeout=5)
+    assert not t.is_alive(), "engine deadlocked on a prompt during abort"
+    assert errors == ["aborted"]
+
+
+def test_pause_and_resume_at_row_boundary(tmp_path):
+    states = []
+    engine, trace, plan = build(
+        tmp_path, num_angles=1,
+        callbacks=ScanCallbacks(on_paused_changed=states.append))
+    engine.pause()
+
+    done = threading.Event()
+
+    def run():
+        try:
+            engine.run()
+        except ScanAborted:
+            pass          # only reachable via the failure escape hatch below
+        finally:
+            done.set()
+
+    t = threading.Thread(target=run, daemon=True)
+    t.start()
+    try:
+        # The engine's instrument-settling sleeps run before the first row,
+        # so poll for the pause rather than assuming a fixed delay.
+        deadline = time.monotonic() + 10.0
+        while not states and time.monotonic() < deadline:
+            time.sleep(0.05)
+        paused = bool(states)
+        assert paused and states[0] is True, "engine did not report the pause"
+    finally:
+        # Always release the scan thread; if the pause never arrived, abort
+        # too, so a failed assertion can't leave it parked forever.
+        if not states:
+            engine.abort()
+        engine.resume()
+    t.join(timeout=10)
+    assert done.is_set()
+    assert states[-1] is False
+
+
+def test_dc_bias_callback_reports_per_frame_means(tmp_path):
+    rows = []
+    engine, trace, plan = build(
+        tmp_path, callbacks=ScanCallbacks(on_dc_bias=lambda r, m: rows.append((r, m))))
+    engine.run()
+
+    assert len(rows) == plan.per_angle[0].n_rows
+    row_idx, means = rows[0]
+    assert row_idx == 1
+    assert len(means) == plan.per_angle[0].n_frames
+    assert all(isinstance(v, float) for v in means)
+
+
+def test_offstage_plan_rejected_before_touching_hardware(tmp_path):
+    trace = Trace()
+    stage = FakeStage(trace)
+    scope = FakeScope(trace, samples_per_frame=SPF)
+    # 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)
+    engine = ScanEngine(stage, scope, None, plan, tmp_path / "bad.sras")
+    with pytest.raises(ScanGeometryError):
+        engine.run()
+    assert trace.calls == [], "hardware touched despite invalid geometry"
+
+
+def test_multi_angle_without_rotator_raises(tmp_path):
+    trace = Trace()
+    engine = ScanEngine(FakeStage(trace), FakeScope(trace, samples_per_frame=SPF),
+                        None, make_plan(3), tmp_path / "x.sras")
+    with pytest.raises(RuntimeError, match="T3R rotation stage"):
+        engine.run()
+
+
+def test_missing_hardware_raises(tmp_path):
+    trace = Trace()
+    with pytest.raises(RuntimeError, match="BBD202"):
+        ScanEngine(None, FakeScope(trace), None, make_plan(),
+                   tmp_path / "x.sras").run()
+    with pytest.raises(RuntimeError, match="Oscilloscope"):
+        ScanEngine(FakeStage(trace), None, None, make_plan(),
+                   tmp_path / "x.sras").run()
+
+
+def test_resume_seeks_to_angle_offset_and_skips_others(tmp_path):
+    # First produce a complete 3-angle file
+    engine, trace, plan = build(tmp_path, num_angles=3)
+    engine.run()
+    path = tmp_path / "out.sras"
+    original = path.read_bytes()
+
+    sras = SrasFile(path)
+    statuses = sras.angle_status()
+    target = statuses[1]
+    resume = ResumeState(
+        path=path,
+        targets=[ResumeTarget(target.index, target.data_offset,
+                              target.n_rows, target.angle_deg)],
+        samples_per_frame=SPF,
+    )
+
+    engine2, trace2, _ = build(tmp_path, num_angles=3, resume=resume)
+    result = engine2.run()
+
+    assert result.angles_acquired == [1]
+    # Only the middle angle's rows were re-acquired
+    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)
+    a1_start, a1_end = target.data_offset, 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:]
+
+
+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)],
+                         samples_per_frame=SPF + 1)   # scope changed
+    engine2, _, _ = build(tmp_path, resume=resume)
+    with pytest.raises(RuntimeError, match="record length"):
+        engine2.run()
+
+
+def test_engine_imports_without_qt():
+    """The engine must be usable from a non-Qt front end."""
+    import subprocess
+    import sys
+    code = (
+        "import sys;"
+        "sys.modules['PyQt6'] = None;"
+        "import core.scan_engine, core.rotation, core.scope_sras,"
+        " core.scan_resume, core.sras_format, core.scan_geometry;"
+        "print('ok')"
+    )
+    out = subprocess.run([sys.executable, "-c", code], capture_output=True,
+                         text=True, cwd=str(__import__('pathlib').Path(__file__).parent.parent))
+    assert out.returncode == 0, out.stderr
+    assert "ok" in out.stdout

tests/test_scan_resume.py

@@ -0,0 +1,77 @@
+"""core.scan_resume: the frontier contiguity rule, over real fixture files."""
+from pathlib import Path
+
+from core.scan_resume import is_compatible, plan_resume
+from core.sras_format import SrasFile
+
+GOLDEN = Path(__file__).parent / "golden"
+
+
+def _statuses(name):
+    return SrasFile(GOLDEN / name).angle_status()
+
+
+def test_complete_file_frontier_is_past_the_end():
+    st = _statuses("complete.sras")
+    plan = plan_resume(st, selected={0})
+    assert plan.frontier_idx == len(st)
+    assert [t.angle_idx for t in plan.targets] == [0]
+    assert plan.auto_added == []
+
+
+def test_selecting_past_frontier_backfills_the_gap():
+    # angle 0 complete, angle 1 truncated → frontier = 1
+    st = _statuses("trunc_rowboundary_a1.sras")
+    assert st[0].complete and not st[1].complete
+
+    plan = plan_resume(st, selected={1})
+    assert plan.frontier_idx == 1
+    assert [t.angle_idx for t in plan.targets] == [1]
+    assert plan.auto_added == []
+
+
+def test_selection_before_frontier_is_untouched():
+    st = _statuses("trunc_rowboundary_a1.sras")
+    plan = plan_resume(st, selected={0})
+    assert [t.angle_idx for t in plan.targets] == [0]
+    assert plan.auto_added == []
+
+
+def test_selecting_only_a_later_angle_pulls_in_the_frontier():
+    """Data is one contiguous stream, so angle 1 can't be skipped to reach 2."""
+    st = _statuses("header_only.sras")   # nothing written: frontier = 0
+    assert plan_resume(st, selected={0}).frontier_idx == 0
+
+    plan = plan_resume(st, selected={1})
+    assert [t.angle_idx for t in plan.targets] == [0, 1]
+    assert plan.auto_added == [0]
+
+
+def test_targets_carry_offsets_and_rows():
+    st = _statuses("complete.sras")
+    plan = plan_resume(st, selected={0, 1})
+    for target, status in zip(plan.targets, st, strict=True):
+        assert target.data_offset == status.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)
+
+
+def test_to_state_carries_samples_per_frame():
+    sras = SrasFile(GOLDEN / "complete.sras")
+    state = plan_resume(sras.angle_status(), selected={0}).to_state(sras)
+    assert state.path == sras.path
+    assert state.samples_per_frame == sras.header.samples_per_frame
+    assert state.target_indices == {0}
+
+
+def test_is_compatible_checks_acquisition_settings():
+    sras = SrasFile(GOLDEN / "complete.sras")
+    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)
+    assert not is_compatible(sras, **{**ok, "velocity": h.velocity + 1})
+    assert not is_compatible(sras, **{**ok, "laser_freq": h.laser_freq * 2})
+    assert not is_compatible(sras, **{**ok, "sample_rate": h.sample_rate * 2})
+    assert not is_compatible(sras, **{**ok, "n_channels": h.n_channels + 1})