Add Fusion menu with Angle Alignment (rotation+translation registration)

Adds a background worker that aligns every scan angle onto one shared,
zero-padded canvas using a rigid transform only (no scaling): rotation
is taken analytically from the known scan angle, and only the residual
translation is found via FFT phase correlation of each angle's
binarized CH4 dc-mask. An "Aligned View" toggle then redisplays the
currently selected angle/channel resampled onto that shared canvas,
with ROI, CSV export, and waveform-click inspection all kept working.

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

sras_viewer.py

@@ -28,6 +28,7 @@ import struct
 import faulthandler
 import numpy as np
 from pathlib import Path
+from dataclasses import dataclass
 import os
 
 faulthandler.enable()   # print a native stack trace on SIGSEGV/SIGABRT/etc.
@@ -59,6 +60,7 @@ except ImportError:
     pass
 
 import scipy.fft as scipy_fft
+import scipy.ndimage as scipy_ndimage
 
 # Runtime-mutable settings changed via FftOptionsDialog
 _fft_backend = "numpy"   # "numpy" or "pyfftw"
@@ -707,6 +709,274 @@ def compute_rf_image(sras: SrasFile, angle_idx: int,
     return img
 
 
+# ---------------------------------------------------------------------------
+# Angle alignment (Fusion menu)
+#
+# Puts every angle's images onto one shared, zero-padded pixel grid using a
+# rigid transform only (rotation + translation, never scale). Rotation for
+# angle `a` is the *known* scan-angle delta relative to a reference angle —
+# never searched. Only the residual translation is found, via FFT phase
+# correlation of each angle's binarized CH4 ("dc-mask") image.
+#
+# Rotation is done in physical mm space rather than on raw pixel indices:
+# the x-pixel pitch (SrasFile.pixel_x_mm) is file-wide constant but the
+# y-pixel pitch (row spacing) can differ from it, and for v6 files can even
+# vary per angle. Rotating the raw index grid directly would implicitly
+# assume square pixels and shear a non-square-pixel image — an unwanted
+# effective anisotropic scale. Instead each angle gets one affine that maps
+# shared-canvas pixel index -> mm -> undo rotation/shift -> that angle's own
+# local mm -> that angle's own raw pixel index, matching the output->input
+# convention scipy.ndimage.affine_transform expects.
+# ---------------------------------------------------------------------------
+
+@dataclass
+class AngleTransform:
+    rotation_deg: float
+    shift_mm: tuple[float, float]      # (dx_mm, dy_mm) found by phase correlation
+    matrix: np.ndarray                 # (2,2): canvas (row,col) -> this angle's raw (row,col)
+    offset: np.ndarray                 # (2,)
+
+
+@dataclass
+class AlignmentResult:
+    ref_angle_idx: int
+    dc_threshold_mv: float
+    canvas_shape: tuple[int, int]          # (n_rows, n_cols)
+    canvas_dx_mm: float
+    canvas_dy_mm: float
+    canvas_origin_mm: tuple[float, float]  # mm at canvas pixel index (0, 0)
+    per_angle: dict[int, AngleTransform]
+
+
+def _pixel_pitch_mm(sras: SrasFile, angle_idx: int) -> tuple[float, float]:
+    """(dx, dy) mm/pixel for one angle: dx is the file-wide constant
+    pixel_x_mm; dy is this angle's own row spacing (assumed uniform, same
+    assumption _redraw_image already makes when it builds the display
+    extent)."""
+    dx = sras.pixel_x_mm
+    y = sras.y_positions_mm(angle_idx)
+    dy = float(y[1] - y[0]) if len(y) > 1 else 1.0
+    return dx, dy
+
+
+def _bbox_center_mm(sras: SrasFile, angle_idx: int) -> tuple[float, float]:
+    x = sras.x_axis_mm(angle_idx)
+    y = sras.y_positions_mm(angle_idx)
+    return float((x[0] + x[-1]) / 2.0), float((y[0] + y[-1]) / 2.0)
+
+
+def _bbox_corners_mm(sras: SrasFile, angle_idx: int) -> np.ndarray:
+    """4 corners (x, y) of this angle's raw mm bounding box, shape (4, 2)."""
+    x = sras.x_axis_mm(angle_idx)
+    y = sras.y_positions_mm(angle_idx)
+    return np.array([[xx, yy] for xx in (x[0], x[-1]) for yy in (y[0], y[-1])])
+
+
+def _rotation_matrix(theta_deg: float) -> np.ndarray:
+    t = np.radians(theta_deg)
+    c, s = np.cos(t), np.sin(t)
+    return np.array([[c, -s], [s, c]])   # CCW rotation acting on (x, y)
+
+
+def _build_affine_canvas_to_raw(sras: SrasFile, angle_idx: int, ref_idx: int,
+                                shift_mm: tuple[float, float],
+                                canvas_dx: float, canvas_dy: float,
+                                canvas_origin_mm: tuple[float, float]
+                                ) -> tuple[np.ndarray, np.ndarray]:
+    """matrix, offset s.t. raw_index = matrix @ [row_out, col_out] + offset,
+    matching scipy.ndimage.affine_transform's output->input convention.
+
+    Pipeline (all mm unless noted):
+      [X;Y]   = A_out @ [row_out;col_out] + b_out        # canvas idx -> ref-frame mm
+      [lx;ly] = R(theta)^T @ ([X;Y]-c_ref-shift) + c_a    # undo rotation+shift -> angle a's local mm
+      [row;col] = D @ ([lx;ly] - [x_start_a; y0_a])       # local mm -> angle a's raw idx
+
+    where theta = angles_deg[angle_idx] - angles_deg[ref_idx], c_ref/c_a are
+    each angle's own raw-bbox mm centroid (the rotation pivot — this keeps
+    rotated content centered, minimizing required canvas padding), and
+    A_out/D are the index<->mm scaling matrices for the canvas pitch and
+    this angle's own native pitch respectively.
+    """
+    theta = float(sras.angles_deg[angle_idx] - sras.angles_deg[ref_idx])
+    Rinv = _rotation_matrix(theta).T
+    cx_a, cy_a = _bbox_center_mm(sras, angle_idx)
+    cx_ref, cy_ref = _bbox_center_mm(sras, ref_idx)
+    dx_a, dy_a = _pixel_pitch_mm(sras, angle_idx)
+    x0_a = float(sras.x_start_mm[angle_idx])
+    y0_a = float(sras.y_positions_mm(angle_idx)[0])
+
+    A_out = np.array([[0.0, canvas_dx], [canvas_dy, 0.0]])   # [row,col] -> [X,Y]
+    b_out = np.array(canvas_origin_mm, dtype=np.float64)
+    D = np.array([[0.0, 1.0 / dy_a], [1.0 / dx_a, 0.0]])     # [x,y] -> [row,col]
+    shift = np.array(shift_mm, dtype=np.float64)
+    c_ref_v = np.array([cx_ref, cy_ref])
+    c_a_v = np.array([cx_a, cy_a])
+    origin_a = np.array([x0_a, y0_a])
+
+    matrix = D @ Rinv @ A_out
+    offset = D @ Rinv @ (b_out - c_ref_v - shift) + D @ (c_a_v - origin_a)
+    return matrix, offset
+
+
+def apply_alignment(result: AlignmentResult, angle_idx: int, img: np.ndarray,
+                     order: int = 0) -> np.ndarray:
+    """Resample any already-computed 2D image for `angle_idx` (same shape as
+    that angle's raw (n_rows, n_frames) — e.g. compute_dc_image /
+    compute_rf_image output) onto the shared alignment canvas. order=0
+    (nearest) avoids blending real data with zero-padding or with
+    masked-out (0-valued) CH1/velocity pixels at mask edges. Channel-
+    agnostic: the same per-angle transform (found from the CH4 mask) works
+    for any channel's image of that angle."""
+    t = result.per_angle[angle_idx]
+    return scipy_ndimage.affine_transform(
+        img.astype(np.float32, copy=False), t.matrix, offset=t.offset,
+        output_shape=result.canvas_shape, order=order,
+        mode="constant", cval=0.0)
+
+
+def _block_mean_downsample(img: np.ndarray, factor: int) -> np.ndarray:
+    if factor <= 1:
+        return img
+    h, w = img.shape
+    h2, w2 = (h // factor) * factor, (w // factor) * factor
+    trimmed = img[:h2, :w2]
+    return trimmed.reshape(h2 // factor, factor, w2 // factor, factor).mean(axis=(1, 3))
+
+
+def _phase_correlate_shift(ref_img: np.ndarray, mov_img: np.ndarray) -> tuple[int, int]:
+    """FFT normalized cross-power-spectrum phase correlation. Returns the
+    integer (dr, dc) pixel shift of mov_img relative to ref_img; both must
+    be the same shape. Risk: if the true shift is near +/- half the array
+    size, wraparound can bias the peak — mitigated by the generous
+    margin_frac padding in _working_canvas_for_pair, which keeps the true
+    residual shift small relative to the correlation canvas."""
+    F1 = scipy_fft.fft2(ref_img.astype(np.float64))
+    F2 = scipy_fft.fft2(mov_img.astype(np.float64))
+    R = F1 * np.conj(F2)
+    R /= np.maximum(np.abs(R), 1e-12)
+    corr = scipy_fft.ifft2(R).real
+    dr, dc = np.unravel_index(np.argmax(corr), corr.shape)
+    h, w = corr.shape
+    if dr > h // 2:
+        dr -= h
+    if dc > w // 2:
+        dc -= w
+    return int(dr), int(dc)
+
+
+def _working_canvas_for_pair(sras: SrasFile, ref_idx: int, a_idx: int,
+                             dx: float, dy: float, margin_frac: float = 0.3
+                             ) -> tuple[tuple[float, float], tuple[int, int]]:
+    """Union of the reference's own raw bbox and angle a's raw bbox rotated
+    (about its own center) into the ref frame with zero shift, padded by
+    margin_frac on each side — sized generously so the true phase-
+    correlation shift lands well inside the canvas (see
+    _phase_correlate_shift's wraparound note)."""
+    theta = float(sras.angles_deg[a_idx] - sras.angles_deg[ref_idx])
+    R = _rotation_matrix(theta)
+    c_a = np.array(_bbox_center_mm(sras, a_idx))
+    c_ref = np.array(_bbox_center_mm(sras, ref_idx))
+    pts = list(_bbox_corners_mm(sras, ref_idx))
+    for corner in _bbox_corners_mm(sras, a_idx):
+        pts.append(R @ (corner - c_a) + c_ref)
+    pts = np.array(pts)
+    x_min, y_min = pts.min(axis=0)
+    x_max, y_max = pts.max(axis=0)
+    pad_x, pad_y = (x_max - x_min) * margin_frac, (y_max - y_min) * margin_frac
+    x_min, x_max = x_min - pad_x, x_max + pad_x
+    y_min, y_max = y_min - pad_y, y_max + pad_y
+    n_cols = int(np.ceil((x_max - x_min) / dx)) + 1
+    n_rows = int(np.ceil((y_max - y_min) / abs(dy))) + 1
+    origin = (x_min, y_min if dy > 0 else y_max)
+    return origin, (n_rows, n_cols)
+
+
+def _compute_angle_alignment(sras: SrasFile, ref_angle_idx: int,
+                             dc_threshold_mv: float,
+                             progress_cb=None) -> AlignmentResult:
+    """Top-level alignment driver. Runs on a background thread (see
+    AngleAlignmentWorker) — deliberately recomputes CH4 DC images from
+    scratch via compute_dc_image rather than reading the GUI-thread
+    _dc_cache dict, mirroring PreprocessWorker's existing precedent."""
+    n = sras.n_angles   # already the *complete*-angle count for aborted v6 scans
+    dx_ref, dy_ref = _pixel_pitch_mm(sras, ref_angle_idx)
+
+    # ---- Step 1: binarized CH4 mask per angle, native per-angle grid -----
+    masks: dict[int, np.ndarray] = {}
+    for a in range(n):
+        dc4 = adc_to_mv(compute_dc_image(sras, a, CH4_IDX),
+                        sras.ch_ymult_mv[CH4_IDX], sras.ch_yoff_adc[CH4_IDX],
+                        sras.ch_yzero_mv[CH4_IDX])
+        masks[a] = (dc4 >= dc_threshold_mv).astype(np.float32)
+        if progress_cb:
+            progress_cb(int((a + 1) / n * 25))
+
+    # ---- Step 2: coarse correlation stage (downsample first, then rotate)
+    # Downsampling before affine_transform (not after) is what keeps this
+    # tractable for a v6 scan with thousands of rows/frames per angle.
+    max_dim = max(max(m.shape) for m in masks.values())
+    factor = max(1, int(np.ceil(max_dim / 1024)))
+    dx_c, dy_c = dx_ref * factor, dy_ref * factor
+    masks_small = {a: _block_mean_downsample(m, factor) for a, m in masks.items()}
+
+    shifts_mm: dict[int, tuple[float, float]] = {ref_angle_idx: (0.0, 0.0)}
+    for a in range(n):
+        if a == ref_angle_idx:
+            continue
+        work_origin, work_shape = _working_canvas_for_pair(
+            sras, ref_angle_idx, a, dx_c, dy_c, margin_frac=0.3)
+
+        # Coarse canvas->raw affine at native pitch, then rescale by /factor
+        # so it maps coarse-canvas idx -> coarse (downsampled) raw idx —
+        # exact for block-mean downsampling (up to the trimmed remainder).
+        m_a, o_a = _build_affine_canvas_to_raw(
+            sras, a, ref_angle_idx, (0.0, 0.0), dx_c, dy_c, work_origin)
+        m_ref, o_ref = _build_affine_canvas_to_raw(
+            sras, ref_angle_idx, ref_angle_idx, (0.0, 0.0), dx_c, dy_c, work_origin)
+        rotated_a = scipy_ndimage.affine_transform(
+            masks_small[a], m_a / factor, offset=o_a / factor,
+            output_shape=work_shape, order=0, mode="constant", cval=0.0)
+        embedded_ref = scipy_ndimage.affine_transform(
+            masks_small[ref_angle_idx], m_ref / factor, offset=o_ref / factor,
+            output_shape=work_shape, order=0, mode="constant", cval=0.0)
+
+        dr, dc = _phase_correlate_shift(embedded_ref, rotated_a)
+        shifts_mm[a] = (dc * dx_c, dr * dy_c)
+        if progress_cb:
+            progress_cb(25 + int((a + 1) / n * 50))
+
+    # ---- Step 3: union bounding box over all angles (rotation+shift applied)
+    corners_ref_frame = []
+    for a in range(n):
+        theta = float(sras.angles_deg[a] - sras.angles_deg[ref_angle_idx])
+        R = _rotation_matrix(theta)
+        c_a = np.array(_bbox_center_mm(sras, a))
+        c_ref = np.array(_bbox_center_mm(sras, ref_angle_idx))
+        shift = np.array(shifts_mm[a])
+        for corner in _bbox_corners_mm(sras, a):
+            corners_ref_frame.append(R @ (corner - c_a) + c_ref + shift)
+    corners_ref_frame = np.array(corners_ref_frame)
+    x_min, y_min = corners_ref_frame.min(axis=0)
+    x_max, y_max = corners_ref_frame.max(axis=0)
+    n_cols = int(np.ceil((x_max - x_min) / dx_ref)) + 1
+    n_rows = int(np.ceil((y_max - y_min) / abs(dy_ref))) + 1
+    canvas_origin_mm = (float(x_min), float(y_min if dy_ref > 0 else y_max))
+    canvas_shape = (n_rows, n_cols)
+
+    # ---- Step 4: final per-angle full-resolution affine (canvas -> raw idx)
+    per_angle: dict[int, AngleTransform] = {}
+    for a in range(n):
+        matrix, offset = _build_affine_canvas_to_raw(
+            sras, a, ref_angle_idx, shifts_mm[a], dx_ref, dy_ref, canvas_origin_mm)
+        theta = float(sras.angles_deg[a] - sras.angles_deg[ref_angle_idx])
+        per_angle[a] = AngleTransform(theta, shifts_mm[a], matrix, offset)
+        if progress_cb:
+            progress_cb(75 + int((a + 1) / n * 25))
+
+    return AlignmentResult(ref_angle_idx, dc_threshold_mv, canvas_shape,
+                           dx_ref, dy_ref, canvas_origin_mm, per_angle)
+
+
 # ---------------------------------------------------------------------------
 # Background workers
 # ---------------------------------------------------------------------------
@@ -880,6 +1150,31 @@ class PreprocessWorker(QObject):
             self.finished.emit(str(exc))
 
 
+class AngleAlignmentWorker(QObject):
+    """Computes rotation+translation alignment for every angle in *sras*,
+    referenced to *ref_angle_idx*, from each angle's binarized CH4 mask.
+    Rotation is analytic (from sras.angles_deg); only translation is found
+    by phase correlation. Mirrors PreprocessWorker's progress/finished shape.
+    """
+    progress = pyqtSignal(int)             # 0–100
+    finished = pyqtSignal(object, str)     # AlignmentResult|None, error msg ("" = success)
+
+    def __init__(self, sras: SrasFile, ref_angle_idx: int, dc_threshold_mv: float):
+        super().__init__()
+        self._sras      = sras
+        self._ref       = ref_angle_idx
+        self._threshold = dc_threshold_mv
+
+    def run(self):
+        try:
+            result = _compute_angle_alignment(
+                self._sras, self._ref, self._threshold,
+                progress_cb=lambda pct: self.progress.emit(pct))
+            self.finished.emit(result, "")
+        except Exception as exc:
+            self.finished.emit(None, str(exc))
+
+
 # ---------------------------------------------------------------------------
 # ROI (free quadrilateral in data coordinates)
 # ---------------------------------------------------------------------------
@@ -1516,6 +1811,13 @@ class SrasViewerWindow(QMainWindow):
         self._dc_precompute_worker: DcPrecomputeWorker | None = None
         self._dc_generation: int = 0
 
+        # Angle alignment ("Fusion" menu)
+        self._alignment_result: AlignmentResult | None = None
+        self._alignment_thread: QThread | None = None
+        self._alignment_worker: AngleAlignmentWorker | None = None
+        self._alignment_generation: int = 0
+        self._aligned_cache: dict[tuple, np.ndarray] = {}
+
         self._build_ui()
 
         if initial_path:
@@ -1637,6 +1939,18 @@ class SrasViewerWindow(QMainWindow):
         self.chk_bg_sub.toggled.connect(self._on_bg_sub_toggled)
         vl.addWidget(self.chk_bg_sub)
 
+        # Aligned View (Fusion → Angle Alignment result)
+        self.chk_aligned_view = QCheckBox("Aligned View (Fusion)")
+        self.chk_aligned_view.setChecked(False)
+        self.chk_aligned_view.setEnabled(False)
+        self.chk_aligned_view.setToolTip(
+            "Show the current angle/channel resampled onto the shared,\n"
+            "rotation+translation-aligned canvas from Fusion → Angle\n"
+            "Alignment. Uncheck to see the raw per-angle scan grid."
+        )
+        self.chk_aligned_view.toggled.connect(self._on_aligned_view_toggled)
+        vl.addWidget(self.chk_aligned_view)
+
         # Velocity settings (visible only in velocity mode)
         self.grp_velocity = QGroupBox("Velocity Settings  (CH1 only)")
         vel_l = QVBoxLayout(self.grp_velocity)
@@ -1805,6 +2119,15 @@ class SrasViewerWindow(QMainWindow):
         self._preprocess_act.triggered.connect(self._on_preprocess)
         fft_menu.addAction(self._preprocess_act)
 
+        fusion_menu = menubar.addMenu("&Fusion")
+        self._alignment_act = QAction("Angle &Alignment", self)
+        self._alignment_act.setStatusTip(
+            "Compute a rotation+translation alignment across all angles "
+            "(from CH4 masks) and enable Aligned View. Requires >1 angle.")
+        self._alignment_act.setEnabled(False)
+        self._alignment_act.triggered.connect(self._on_angle_alignment)
+        fusion_menu.addAction(self._alignment_act)
+
     # ------------------------------------------------------------------
     # Drag-and-drop
     # ------------------------------------------------------------------
@@ -1872,6 +2195,18 @@ class SrasViewerWindow(QMainWindow):
         self._fft_cache = {}
         self.lbl_dc_precompute.setText("")
 
+        # Same for any alignment result — belongs to the previous file's
+        # geometry. Bump the generation counter so a still-running
+        # alignment worker's result is discarded when it lands (see
+        # _on_alignment_done).
+        self._alignment_result = None
+        self._aligned_cache = {}
+        self._alignment_generation += 1
+        self.chk_aligned_view.blockSignals(True)
+        self.chk_aligned_view.setChecked(False)
+        self.chk_aligned_view.setEnabled(False)
+        self.chk_aligned_view.blockSignals(False)
+
         # A ROI from the previous file no longer matches the new scan's
         # geometry, so discard it on every load.
         self.image_canvas.clear_roi()
@@ -1968,6 +2303,12 @@ class SrasViewerWindow(QMainWindow):
         can_preprocess = (enabled and s is not None and s.version != 6
                           and self._preprocess_thread is None)
         self._preprocess_act.setEnabled(can_preprocess)
+        # Angle alignment: needs >1 angle and no alignment already running
+        can_align = (enabled and s is not None and s.n_angles > 1
+                    and self._alignment_thread is None)
+        self._alignment_act.setEnabled(can_align)
+        self.chk_aligned_view.setEnabled(
+            enabled and self._alignment_result is not None)
         self._update_roi_ui()
 
     def _on_channel_changed(self):
@@ -2056,6 +2397,10 @@ class SrasViewerWindow(QMainWindow):
         npix = 0
         if self._sras is not None:
             try:
+                # Deliberately always the raw per-angle grid, even when
+                # Aligned View is on: _on_export_roi_csv also exports on the
+                # raw grid (never synthetically-resampled pixels), so this
+                # readout must match what Export ROI actually writes.
                 mask = roi.mask_for_grid(self._sras.x_axis_mm(self._current_angle),
                                          self._sras.y_positions_mm(self._current_angle))
                 npix = int(mask.sum())
@@ -2191,6 +2536,35 @@ class SrasViewerWindow(QMainWindow):
             return freq_mhz * self.spin_grating_um.value()
         return freq_mhz
 
+    # ------------------------------------------------------------------
+    # Aligned View (Fusion) display helpers
+    # ------------------------------------------------------------------
+
+    def _aligned_cache_key(self, angle_idx: int, ch_idx: int) -> tuple:
+        """Mirrors _fft_cache's key granularity so a stale aligned image is
+        never shown after bg_sub/threshold/pad/grating changes."""
+        if ch_idx in CH1_DERIVED_MODES:
+            return (angle_idx, ch_idx, self.chk_bg_sub.isChecked(),
+                    self._current_n_fft(), self.spin_threshold_mv.value(),
+                    self.spin_grating_um.value() if ch_idx == VELOCITY_MODE_IDX else None)
+        return (angle_idx, ch_idx)
+
+    def _aligned_canvas_axes(self) -> tuple[np.ndarray, np.ndarray]:
+        r = self._alignment_result
+        n_rows, n_cols = r.canvas_shape
+        x_axis = r.canvas_origin_mm[0] + np.arange(n_cols) * r.canvas_dx_mm
+        y_axis = r.canvas_origin_mm[1] + np.arange(n_rows) * r.canvas_dy_mm
+        return x_axis, y_axis
+
+    def _get_aligned_display_image(self, raw_img: np.ndarray, angle_idx: int,
+                                    ch_idx: int) -> np.ndarray:
+        key = self._aligned_cache_key(angle_idx, ch_idx)
+        cached = self._aligned_cache.get(key)
+        if cached is None:
+            cached = apply_alignment(self._alignment_result, angle_idx, raw_img)
+            self._aligned_cache[key] = cached
+        return cached
+
     def _refresh_display(self):
         """Show the image for the current angle/channel/threshold, using
         cached data whenever possible and only falling back to a
@@ -2398,8 +2772,19 @@ class SrasViewerWindow(QMainWindow):
     def _redraw_image(self, img: np.ndarray):
         s = self._sras
         angle_idx = self._current_angle
-        x_axis = s.x_axis_mm(angle_idx)
+        ch_idx    = self._current_ch
-        y_axis = s.y_positions_mm(angle_idx)
+
+        aligned = (self.chk_aligned_view.isChecked()
+                  and self._alignment_result is not None
+                  and angle_idx in self._alignment_result.per_angle)
+        if aligned:
+            display_img = self._get_aligned_display_image(img, angle_idx, ch_idx)
+            x_axis, y_axis = self._aligned_canvas_axes()
+        else:
+            display_img = img
+            x_axis = s.x_axis_mm(angle_idx)
+            y_axis = s.y_positions_mm(angle_idx)
+
         dx = x_axis[1] - x_axis[0] if len(x_axis) > 1 else s.pixel_x_mm
         dy = float(y_axis[1] - y_axis[0]) if len(y_axis) > 1 else 1.0
 
@@ -2411,7 +2796,7 @@ class SrasViewerWindow(QMainWindow):
         ]
 
         if self.chk_auto.isChecked():
-            vmin, vmax = float(img.min()), float(img.max())
+            vmin, vmax = float(display_img.min()), float(display_img.max())
             for spin, val in ((self.spin_vmin, vmin), (self.spin_vmax, vmax)):
                 spin.blockSignals(True)
                 spin.setValue(val)
@@ -2420,7 +2805,6 @@ class SrasViewerWindow(QMainWindow):
             vmin = self.spin_vmin.value()
             vmax = self.spin_vmax.value()
 
-        ch_idx    = self._current_ch
         angle_deg = s.angles_deg[self._current_angle]
         ch_label  = CH_LABELS[ch_idx]
 
@@ -2440,9 +2824,11 @@ class SrasViewerWindow(QMainWindow):
             colorbar_label = "mV"
 
         title = f"{CH_NAMES[ch_idx]}  |  {mode_str}  |  {angle_deg:.1f}°"
+        if aligned:
+            title += "  [Aligned]"
 
         self.image_canvas.show_image(
-            img, extent,
+            display_img, extent,
             cmap=self.combo_cmap.currentText(),
             vmin=vmin, vmax=vmax,
             xlabel="X (mm)", ylabel="Y (mm)",
@@ -2451,7 +2837,8 @@ class SrasViewerWindow(QMainWindow):
         )
         self.statusBar().showMessage(
             f"{s.path.name}  |  {ch_label}  @  {angle_deg:.1f}°  "
-            f"|  {img.shape[1]} × {img.shape[0]} px  |  {unit}"
+            f"|  {display_img.shape[1]} × {display_img.shape[0]} px  |  {unit}"
+            f"{'  |  Aligned' if aligned else ''}"
         )
 
     # ------------------------------------------------------------------
@@ -2461,16 +2848,31 @@ class SrasViewerWindow(QMainWindow):
     def _on_pixel_clicked(self, row_idx: int, frame_idx: int):
         if self._sras is None or self._current_image is None:
             return
+        angle_idx = self._current_angle
+        if (self.chk_aligned_view.isChecked() and self._alignment_result is not None
+                and angle_idx in self._alignment_result.per_angle):
+            # The click landed on the shared aligned canvas — invert the
+            # same canvas->raw affine used to display it back to a raw
+            # (row, frame) index before looking up the waveform.
+            t = self._alignment_result.per_angle[angle_idx]
+            raw = t.matrix @ np.array([row_idx, frame_idx], dtype=np.float64) + t.offset
+            row_idx, frame_idx = int(round(raw[0])), int(round(raw[1]))
+            n_rows_a   = int(self._sras.n_rows[angle_idx])
+            n_frames_a = int(self._sras.n_frames[angle_idx])
+            if not (0 <= row_idx < n_rows_a and 0 <= frame_idx < n_frames_a):
+                self.statusBar().showMessage(
+                    "No source waveform here (padding region of the aligned canvas).")
+                return
         self.lbl_wave_hint.hide()
         ch_idx = self._current_ch
         if ch_idx in CH1_DERIVED_MODES:
             self.wave_canvas.show_rf_waveform(
-                self._sras, self._current_angle, row_idx, frame_idx,
+                self._sras, angle_idx, row_idx, frame_idx,
                 apply_bg_sub=self.chk_bg_sub.isChecked(),
             )
         else:
             self.wave_canvas.show_dc_waveform(
-                self._sras, self._current_angle, ch_idx, row_idx, frame_idx
+                self._sras, angle_idx, ch_idx, row_idx, frame_idx
             )
 
     # ------------------------------------------------------------------
@@ -2565,6 +2967,74 @@ class SrasViewerWindow(QMainWindow):
         self._preprocess_act.setEnabled(
             self._sras is not None and self._sras.version != 6)
 
+    # ------------------------------------------------------------------
+    # Fusion: angle alignment
+    # ------------------------------------------------------------------
+
+    def _on_angle_alignment(self):
+        if self._sras is None or self._sras.n_angles <= 1:
+            return
+        if self._alignment_thread is not None:
+            return
+        ref_idx      = 0
+        threshold_mv = self.spin_threshold_mv.value()
+        generation   = self._alignment_generation
+
+        # Claim self._alignment_thread before anything below that can pump
+        # the Qt event loop — see the comment in _start_compute for why.
+        self._alignment_worker = AngleAlignmentWorker(self._sras, ref_idx, threshold_mv)
+        self._alignment_thread = QThread()
+        self._alignment_worker.moveToThread(self._alignment_thread)
+        self._alignment_thread.started.connect(self._alignment_worker.run)
+        self._alignment_worker.progress.connect(self._on_alignment_progress)
+        self._alignment_worker.finished.connect(
+            lambda result, err, g=generation: self._on_alignment_done(g, result, err))
+        self._alignment_worker.finished.connect(self._alignment_thread.quit)
+        self._alignment_thread.finished.connect(self._on_alignment_thread_finished)
+
+        self._alignment_act.setEnabled(False)
+        self._show_progress(
+            f"Computing angle alignment ({self._sras.n_angles} angles, "
+            f"ref=angle 0, CH4 mask ≥ {threshold_mv:.3f} mV)…"
+        )
+        self._alignment_thread.start()
+
+    def _on_alignment_progress(self, pct: int):
+        if self._progress_dlg is not None:
+            self._progress_dlg.setValue(pct)
+
+    def _on_alignment_thread_finished(self):
+        # See the comment in _on_compute_thread_finished: wait() before
+        # releasing our reference to avoid destroying a QThread whose OS
+        # thread hasn't fully joined yet.
+        if self._alignment_thread is not None:
+            self._alignment_thread.wait()
+        self._alignment_thread = None
+        self._update_controls_enabled(self._sras is not None)
+
+    def _on_alignment_done(self, generation: int, result, error_msg: str):
+        self._close_progress()
+        if generation != self._alignment_generation:
+            return   # a new file was loaded while this was computing — discard
+        if error_msg:
+            self.statusBar().showMessage(f"Angle alignment failed: {error_msg}")
+            return
+        self._alignment_result = result
+        self._aligned_cache = {}
+        self.chk_aligned_view.setEnabled(True)
+        self.chk_aligned_view.blockSignals(True)
+        self.chk_aligned_view.setChecked(True)
+        self.chk_aligned_view.blockSignals(False)
+        nr, nc = result.canvas_shape
+        self.statusBar().showMessage(
+            f"Angle alignment computed ({self._sras.n_angles} angles, "
+            f"canvas {nc}×{nr} px).")
+        self._refresh_display()
+
+    def _on_aligned_view_toggled(self, checked: bool):
+        if self._current_image is not None:
+            self._redraw_image(self._current_image)
+
     # ------------------------------------------------------------------
     # FFT Options
     # ------------------------------------------------------------------
@@ -2597,7 +3067,7 @@ class SrasViewerWindow(QMainWindow):
         if self._dc_precompute_worker is not None:
             self._dc_precompute_worker.stop()
         for attr in ("_load_thread", "_compute_thread", "_preprocess_thread",
-                     "_dc_precompute_thread"):
+                     "_dc_precompute_thread", "_alignment_thread"):
             t = getattr(self, attr, None)
             if t is not None:
                 t.quit()