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>
This commit is contained in:
Thomas Ales
+97
-19
@@ -46,7 +46,7 @@ from sras_format import (
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)
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from sras_workers import (
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AngleAlignmentWorker, BatchCacheWorker, Ch4MaskWorker, ComputeWorker,
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DcPrecomputeWorker, LoadWorker,
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CrossCorrelateWorker, DcPrecomputeWorker, LoadWorker,
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)
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faulthandler.enable() # print a native stack trace on SIGSEGV/SIGABRT/etc.
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@@ -818,27 +818,31 @@ class ManualAlignmentDialog(QDialog):
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Shows every angle's binarized CH4 (Bias B) mask overlaid in a distinct
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color at partial opacity on one shared canvas, so translation/rotation
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misalignment is visible by eye — the thing the automatic phase-
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correlation step (compute_angle_alignment) sometimes gets wrong. The user
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picks an "active" angle and nudges its rotation+translation with the
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keyboard; Auto De-rotate sets every non-reference angle's rotation to the
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known, analytic scan-angle delta without touching any translation the
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user has already dialed in. Save writes a JSON sidecar next to the .sras
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file and hands a freshly-built, full-resolution AlignmentResult back to
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the main window — the exact same object shape compute_angle_alignment
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produces, so every existing Aligned-View code path (apply_alignment,
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_aligned_canvas_axes, the pixel-inspector inverse-transform) works
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completely unmodified.
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misalignment is visible by eye. Reference angle (always index 0) is
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ground truth and never moves; every other angle is aligned to it. The
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user picks an "active" angle and nudges its rotation+translation with
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the keyboard; Auto De-rotate sets every non-reference angle's rotation to
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the known, analytic scan-angle delta without touching any translation;
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Auto Cross-Correlate does the same rotation and additionally sets
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translation to the FFT-phase-correlation best fit against the reference
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(see compute.correlate_translation_mm) — meant to get every angle roughly
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stacked on top of each other so keyboard nudging only has to make small
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corrections, not find a coarse alignment from scratch. Save writes a
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JSON sidecar next to the .sras file and hands a freshly-built, full-
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resolution AlignmentResult back to the main window — the exact same
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object shape compute_angle_alignment produces, so every existing
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Aligned-View code path (apply_alignment, _aligned_canvas_axes, the
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pixel-inspector inverse-transform) works completely unmodified.
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Non-modal by design (shown via .show(), never .exec() or setModal(True))
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so the user can still interact with the main window. Talks back to
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SrasViewerWindow two ways: it reuses parent._run_worker/_jobs directly
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for its own (rare) background mask-fetch step, so the main window's
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existing shutdown/lifecycle plumbing covers it for free, and it emits
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alignment_saved / alignment_cleared signals for the two moments that
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should actually mutate the main window's persistent state — everything
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else (nudging, Auto De-rotate, threshold edits) stays purely local to
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this dialog until Save.
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for its background mask-fetch and cross-correlate steps, so the main
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window's existing shutdown/lifecycle plumbing covers both for free, and
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it emits alignment_saved / alignment_cleared signals for the two moments
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that should actually mutate the main window's persistent state —
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everything else (nudging, Auto De-rotate, Auto Cross-Correlate, threshold
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edits) stays purely local to this dialog until Save.
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"""
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alignment_saved = pyqtSignal(object, str) # AlignmentResult, sidecar path (str)
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@@ -998,6 +1002,31 @@ class ManualAlignmentDialog(QDialog):
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tl.addLayout(tform)
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panel_l.addWidget(self.grp_mask_threshold)
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# ---- Cross-Correlate (FFT) -----------------------------------------
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self.grp_correlate, cl = _group("Cross-Correlate (FFT)")
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cform = _form()
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self.combo_correlate_source = QComboBox()
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self.combo_correlate_source.addItems(
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["Raw signal (recommended)", "Thresholded mask"])
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cform.addRow("Correlate on:", self.combo_correlate_source)
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self.spin_correlate_margin = QDoubleSpinBox()
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self.spin_correlate_margin.setRange(0.05, 2.0)
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self.spin_correlate_margin.setSingleStep(0.05)
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self.spin_correlate_margin.setDecimals(2)
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self.spin_correlate_margin.setValue(0.30)
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self.spin_correlate_margin.setMinimumWidth(_SPIN_MIN_W)
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cform.addRow("Search margin (× extent):", self.spin_correlate_margin)
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cl.addLayout(cform)
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self.btn_auto_correlate = QPushButton("Auto Cross-Correlate (vs Reference)")
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cl.addWidget(self.btn_auto_correlate)
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cl.addWidget(_wrap_label(
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"Sets rotation to the known scan angle and translation to the "
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"FFT-correlated best fit for every non-reference angle. Run this "
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"first, then use manual nudging only for small corrections.",
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_CSS_HINT))
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panel_l.addWidget(self.grp_correlate)
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# ---- Actions ------------------------------------------------------
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grp_actions, acl = _group("Actions")
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self.btn_auto_derotate = QPushButton("Auto De-rotate (use known angles)")
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@@ -1012,7 +1041,7 @@ class ManualAlignmentDialog(QDialog):
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panel_l.addWidget(self.lbl_status)
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panel_l.addStretch()
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root.addWidget(_scroll_panel(panel, 300))
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root.addWidget(_scroll_panel(panel, 320))
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self.combo_active_angle.currentIndexChanged.connect(self._on_active_angle_changed)
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self.spin_active_rotation_deg.editingFinished.connect(self._on_rotation_spin_edited)
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@@ -1020,6 +1049,7 @@ class ManualAlignmentDialog(QDialog):
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self.spin_active_shift_y_mm.editingFinished.connect(self._on_shift_spin_edited)
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self.spin_mask_threshold_mv.editingFinished.connect(self._on_mask_threshold_edited)
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self.btn_auto_derotate.clicked.connect(self._on_auto_derotate)
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self.btn_auto_correlate.clicked.connect(self._on_auto_correlate)
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self.btn_save.clicked.connect(self._on_save)
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self.btn_clear.clicked.connect(self._on_clear)
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self.btn_close.clicked.connect(self.close)
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@@ -1241,6 +1271,53 @@ class ManualAlignmentDialog(QDialog):
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f"Rotation set to the known scan angle for {n_changed} angle(s) "
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"(translation left untouched).")
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def _on_auto_correlate(self):
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if not self._masks_ready:
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return
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angles = [a for a in range(self._sras.n_angles) if a != self._ref_angle_idx]
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if not angles:
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return
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use_mask = self.combo_correlate_source.currentIndex() == 1
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worker = CrossCorrelateWorker(
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self._sras, self._ref_angle_idx, angles, self._dc4_mv, self._pivot_mm,
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use_mask=use_mask, dc_threshold_mv=self.spin_mask_threshold_mv.value(),
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margin_frac=self.spin_correlate_margin.value())
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self._correlate_done_count = 0
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self._correlate_total = len(angles)
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self._set_controls_enabled(False)
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self.lbl_status.setText(f"Cross-correlating: 0/{self._correlate_total} angle(s)…")
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started = self._parent._run_worker(
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"manual_align_correlate", worker,
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connect=(
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("angle_done", self._on_correlate_angle_done),
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("error", self._on_correlate_error),
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),
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on_done=self._finish_auto_correlate)
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if not started:
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self._set_controls_enabled(True)
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self.lbl_status.setText("Could not start cross-correlation (busy) — try again.")
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def _on_correlate_angle_done(self, angle_idx: int, rotation_deg: float,
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shift_x_mm: float, shift_y_mm: float):
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self._angle_params[angle_idx] = ManualAngleParams(rotation_deg, (shift_x_mm, shift_y_mm))
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self._correlate_done_count += 1
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self.lbl_status.setText(
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f"Cross-correlating: {self._correlate_done_count}/{self._correlate_total} angle(s)…")
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def _on_correlate_error(self, msg: str):
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self.lbl_status.setText(f"Cross-correlation error: {msg}")
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def _finish_auto_correlate(self):
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self._sync_active_spinboxes()
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self._rebuild_preview_canvas()
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self._set_controls_enabled(True)
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source = "thresholded mask" if self.combo_correlate_source.currentIndex() == 1 \
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else "raw signal"
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self.lbl_status.setText(
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f"Cross-correlated {self._correlate_done_count} angle(s) against "
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f"Angle {self._ref_angle_idx} using the {source}. Nudge from here "
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"for any remaining fine correction.")
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def _on_save(self):
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threshold = self.spin_mask_threshold_mv.value()
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resolved = dict(self._angle_params) # already concrete floats
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@@ -1284,6 +1361,7 @@ class ManualAlignmentDialog(QDialog):
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self.grp_manual_adjust.setEnabled(enabled and self._active_angle != self._ref_angle_idx)
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self.grp_step_sizes.setEnabled(enabled)
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self.grp_mask_threshold.setEnabled(enabled)
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self.grp_correlate.setEnabled(enabled)
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self.btn_auto_derotate.setEnabled(enabled)
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self.btn_save.setEnabled(enabled)
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self.btn_clear.setEnabled(enabled)
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