Auto-align: level the sample on the DC bias levels from the camera window

The operator frames a good spot, confirms the two DC levels the detector
reads there, and the rig then measures its own tilt: step 1.5 mm either side
on X and then on Y, and tilt the platform until those levels come back.  The
correction that fixes an offset point is the correction that levels the whole
travel — height error and tilt effect are both proportional to the offset —
so the procedure ends by applying it and leaving it applied.

Both directions are measured from the same starting tilt and averaged, which
makes their disagreement a flatness read-out rather than something averaged
away silently.

core/auto_align.py holds the geometry and the search, Qt-free.  The three
T-axes' azimuths are the whole geometry: T1 lies along +X so it alone tilts
along X, and T0/T2 move as an equal-and-opposite pair to tilt along Y without
touching X (tilt_response derives that, and the tests pin it — an axis map
that drifts would still converge, on the wrong axis).  The search is a secant
null on the split-detector difference: probe once to learn what a microstep
is worth, sign included, then step at the null.  It refuses to servo on a
scope that has not re-triggered, escalates a probe that reads as no response
before calling an axis dead, and stops at a per-axis travel limit.

gui/align_bridge.py runs it on a worker thread; stopping is a threading.Event
rather than a queued command, because the worker is inside a long handler for
the whole run.  The camera window carries the button and the progress window,
and locks the scan panel and the jog pads while a run owns the stage.

Adds immediate MEAN measurements and an acquisition count to the scope
driver, and read_bias_mv to core/scope_inspect — the one scalar the
inspection state was missing.

KNOWN_ISSUES.md records what only the rig can settle: the probe step, the
travel limit, the hold current, and whether the piston the X phase applies
alongside its tilt matters.

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

tests/fakes.py

@@ -258,6 +258,9 @@ class FakeT3R:
         self._t = trace
         self.is_open = is_open
         self._motion_completes = motion_completes
+        # Microsteps commanded per channel, so a test can read the tilt the
+        # platform ended up at rather than replaying the move trace.
+        self.positions = {ch: 0 for ch in range(4)}
 
     def set_microstep(self, ch, micro):
         self._t.record("t3r_set_microstep", ch, micro)
@@ -273,9 +276,113 @@ class FakeT3R:
         return round(self.MOTOR_FULL_STEPS_PER_REV * microsteps * ratio
                      * angle_deg / 360.0)
 
+    def move(self, ch, steps, velocity, accel):
+        self._t.record("t3r_move", ch, steps)
+        self.positions[ch] += steps
+
     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
+
+
+class FakeAlignRig:
+    """A tilted sample on the tilt platform, as the DC levels would read it.
+
+    The detection beam is fixed and the stage carries the sample under it, so
+    the height error under the beam is the sample's slope times how far the
+    stage has moved off the reference point.  The T-axes tilt the sample the
+    other way: their three heights define a plane, and its slope adds to the
+    sample's.  Nulling the split-detector difference therefore means cancelling
+    the sample slope — which is exactly what an aligner has to work out.
+
+    The plane is fitted by least squares here, rather than reusing
+    core.auto_align's closed form, so the two are independent statements of
+    the same geometry.
+
+    ``curvature_mv_per_mm2`` bends the surface: a curved sample needs opposite
+    corrections at +1.5 mm and -1.5 mm, which is the disagreement the
+    procedure is supposed to report instead of averaging away.
+    """
+
+    # Actuator azimuths on the platform, in degrees from stage +X.
+    AZIMUTH_DEG = {0: 120.0, 1: 0.0, 2: 240.0}
+
+    def __init__(self, stage, t3r, ref_mm=(50.0, 40.0),
+                 x_slope_mv_per_mm=40.0, y_slope_mv_per_mm=-25.0,
+                 tilt_gain_mv_per_mm=0.2, base_mv=400.0,
+                 curvature_mv_per_mm2=0.0, jitter_mv=0.0):
+        self._stage = stage
+        self._t3r = t3r
+        self.ref_mm = ref_mm
+        self.x_slope_mv_per_mm = x_slope_mv_per_mm
+        self.y_slope_mv_per_mm = y_slope_mv_per_mm
+        self.tilt_gain_mv_per_mm = tilt_gain_mv_per_mm
+        self.base_mv = base_mv
+        self.curvature_mv_per_mm2 = curvature_mv_per_mm2
+        self.jitter_mv = jitter_mv
+        self._reads = 0
+
+    # -- geometry -----------------------------------------------------------
+    def platform_tilt(self):
+        """(x_tilt, y_tilt) of the plane through the three actuator heights."""
+        import numpy as np
+        rows, heights = [], []
+        for ch, azimuth in self.AZIMUTH_DEG.items():
+            theta = np.radians(azimuth)
+            rows.append([1.0, np.cos(theta), np.sin(theta)])
+            heights.append(float(self._t3r.positions[ch]))
+        _, x_tilt, y_tilt = np.linalg.lstsq(np.array(rows), np.array(heights),
+                                            rcond=None)[0]
+        return float(x_tilt), float(y_tilt)
+
+    def slopes_mv_per_mm(self):
+        """The residual sample slope the beam sees, after the platform tilt."""
+        x_tilt, y_tilt = self.platform_tilt()
+        return (self.x_slope_mv_per_mm + self.tilt_gain_mv_per_mm * x_tilt,
+                self.y_slope_mv_per_mm + self.tilt_gain_mv_per_mm * y_tilt)
+
+    def difference_mv(self):
+        x_off = self._stage.positions[0] - self.ref_mm[0]
+        y_off = self._stage.positions[1] - self.ref_mm[1]
+        slope_x, slope_y = self.slopes_mv_per_mm()
+        return (slope_x * x_off + slope_y * y_off
+                + self.curvature_mv_per_mm2 * (x_off ** 2 + y_off ** 2))
+
+    # -- what the scope reports ---------------------------------------------
+    def level_v(self, channel):
+        """CH3 and CH4 as volts: the difference straddling a constant sum.
+
+        The sum is fixed because tilt steers the beam across the detector
+        rather than changing how much light comes back — so a nulled
+        difference does put both levels back where they were.
+        """
+        self._reads += 1
+        # A deterministic alternating wobble, so a test can check the median
+        # of several reads is what keeps the loop stable.
+        jitter = self.jitter_mv * (1 if self._reads % 2 else -1)
+        half = 0.5 * self.difference_mv()
+        mv = self.base_mv + (half if channel == 3 else -half) + jitter
+        return mv / 1000.0
+
+
+class FakeAlignScope(FakeScope):
+    """FakeScope that also answers the DC measurements auto-align reads."""
+
+    def __init__(self, trace: Trace, rig: FakeAlignRig, samples_per_frame=8,
+                 acquisitions_advance=True):
+        super().__init__(trace, samples_per_frame=samples_per_frame)
+        self._rig = rig
+        self._acq = 0
+        self._advance = acquisitions_advance
+
+    def measure_immediate(self, channel, measurement_type="MEAN"):
+        self._t.record("measure_immediate", channel, measurement_type)
+        return self._rig.level_v(channel)
+
+    def get_acquisition_count(self):
+        if self._advance:
+            self._acq += 1
+        return self._acq