Add FFT cross-correlation to Manual Alignment, with tunable options

Manual mode previously offered only Auto De-rotate (rotation from known
scan angles) plus keyboard nudging, so every angle's translation had to
be found entirely by eye — fine for a small correction, unworkable for
the tens-of-mm scatter a real many-angle scan can have between angles
before any translation search runs at all.

Add an "Auto Cross-Correlate (vs Reference)" action that, for every
non-reference angle, sets rotation to the known analytic angle (same as
Auto De-rotate) and translation to the FFT-phase-correlation best fit
against angle #0 (always the reference/ground truth). This is meant to
land every angle's outline roughly stacked on the others so keyboard
nudging only has to make small corrections afterward, per the intended
workflow: cross-correlate first, then nudge.

Exposes two tunable options, since real data may correlate better one
way than the other: "Correlate on" (raw CH4 signal, minus its own
minimum -- the default, robust to a shared threshold not suiting every
angle's real signal level -- or the thresholded binary mask), and
"Search margin" (how far a shift the phase correlation searches before
wraparound bias becomes a risk).

Runs on a background thread (new CrossCorrelateWorker in
sras_workers.py) since correlating many high-resolution angles can take
long enough to visibly freeze the dialog otherwise.

The underlying per-angle correlation math is factored out of
compute_angle_alignment's Step 2 into a new, reusable
correlate_translation_mm, so the existing automatic Fusion -> Angle
Alignment action and the new manual button now share one implementation
instead of two copies of the same phase-correlation logic.

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

tools/test_gui.py

@@ -278,6 +278,16 @@ def main():
                          -(float(s.angles_deg[a]) - float(s.angles_deg[0])))
               for a in range(s.n_angles)))
 
+    # --- FFT phase correlation recovers a known synthetic pixel shift ------
+    rng = np.random.default_rng(0)
+    corr_ref = np.zeros((40, 50), dtype=np.float32)
+    corr_ref[10:25, 15:35] = 1.0
+    corr_ref += 0.05 * rng.standard_normal(corr_ref.shape).astype(np.float32)
+    corr_mov = np.roll(corr_ref, shift=(4, -7), axis=(0, 1))
+    dr, dc = compute._phase_correlate_shift(corr_ref, corr_mov)
+    check("phase correlation recovers the shift that aligns mov onto ref",
+          (dr, dc) == (-4, 7), f"got (dr, dc)={(dr, dc)}")
+
     # --- Open: must NOT seed from the still-live automatic AlignmentResult --
     # The automatic result's translation comes from FFT phase correlation --
     # the very thing manual mode exists to work around -- so manual mode
@@ -344,6 +354,29 @@ def main():
     check("reference angle stays identity after auto de-rotate",
           dlg._angle_params[dlg._ref_angle_idx].rotation_deg == 0.0)
 
+    # --- Auto Cross-Correlate: rotation + FFT-correlated shift, backgrounded -
+    check("cross-correlate action enabled once masks are ready",
+          dlg.btn_auto_correlate.isEnabled())
+    dlg._on_auto_correlate()
+    check("auto cross-correlate completed", wait_until(
+        lambda: not win._job_running("manual_align_correlate"), timeout_ms=30000))
+    check("auto cross-correlate set the known analytic angle for every angle",
+          all(abs(dlg._angle_params[a].rotation_deg
+                  - compute._theta_deg(s, a, dlg._ref_angle_idx)) < 1e-6
+              for a in range(s.n_angles) if a != dlg._ref_angle_idx))
+    check("auto cross-correlate reference angle stays identity",
+          dlg._angle_params[dlg._ref_angle_idx] == compute.ManualAngleParams())
+    check("auto cross-correlate re-enabled controls when done",
+          dlg.grp_correlate.isEnabled() and dlg.btn_save.isEnabled())
+    check("preview canvas rebuilt after cross-correlate",
+          len(dlg._preview_layers) == s.n_angles)
+
+    # The thresholded-mask option should also work end to end.
+    dlg.combo_correlate_source.setCurrentIndex(1)   # thresholded mask
+    dlg._on_auto_correlate()
+    check("auto cross-correlate (thresholded-mask option) completed", wait_until(
+        lambda: not win._job_running("manual_align_correlate"), timeout_ms=30000))
+
     # --- Save -----------------------------------------------------------------
     dlg._on_save()
     sidecar = compute.sidecar_path(s.path)