#!/usr/bin/env python3 """ SRAS Scan File Viewer PyQt6 application for visualizing channel data from .sras binary scan files. Channel semantics (fixed by sc3_aui_app.py acquisition settings): CH1 — RF Acoustic Packet (AC-coupled, 100 mV/div): FFT → peak frequency CH3 — Bias A (DC-coupled, 50 mV/div): waveform mean CH4 — Bias B (DC-coupled, 50 mV/div): waveform mean RF images are masked: pixels where CH4_dc < dc_threshold show 0. File parsing lives in sras_format, image/alignment math in sras_compute, and background workers in sras_workers — the first two import neither Qt nor matplotlib so multiprocessing children can load them cheaply. """ import faulthandler import sys from pathlib import Path import matplotlib as mpl import numpy as np from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg, NavigationToolbar2QT from matplotlib.figure import Figure from matplotlib.patches import Polygon from matplotlib.path import Path as MplPath from PyQt6.QtCore import QObject, Qt, QThread, pyqtSignal from PyQt6.QtGui import QAction, QKeyEvent from PyQt6.QtWidgets import ( QApplication, QButtonGroup, QCheckBox, QComboBox, QDialog, QDialogButtonBox, QDoubleSpinBox, QFileDialog, QFormLayout, QFrame, QGroupBox, QHBoxLayout, QLabel, QMainWindow, QMessageBox, QProgressDialog, QPushButton, QRadioButton, QScrollArea, QSizePolicy, QSpinBox, QSplitter, QVBoxLayout, QWidget, ) import sras_compute as compute from sras_compute import ( PYFFTW_AVAILABLE, ManualAngleParams, apply_alignment, build_manual_alignment, delete_manual_alignment, load_manual_alignment, save_manual_alignment, sidecar_path, ) from sras_format import ( CH1_IDX, CH3_IDX, CH4_IDX, CH_NAMES, SrasFile, adc_to_mv, mv_to_adc, _FALLBACK_YMULT_MV, _FALLBACK_YOFF_ADC, ) from sras_workers import ( AngleAlignmentWorker, BatchCacheWorker, Ch4MaskWorker, ComputeWorker, DcPrecomputeWorker, LoadWorker, ) faulthandler.enable() # print a native stack trace on SIGSEGV/SIGABRT/etc. # --------------------------------------------------------------------------- # Display constants # --------------------------------------------------------------------------- CH_LABELS = [ "CH1 — RF (FFT peak freq)", "CH3 — Bias A (DC mean)", "CH4 — Bias B (DC mean)", "CH1 — Velocity (SRAS)", ] # Combo index for the derived velocity mode (uses CH1_IDX data) VELOCITY_MODE_IDX = 3 # All modes that operate on CH1 waveforms CH1_DERIVED_MODES = (CH1_IDX, VELOCITY_MODE_IDX) CMAPS = ["gray", "viridis", "plasma", "inferno", "hot", "jet", "RdBu_r", "seismic"] # (mode_str, status-bar unit, colorbar label) per channel index _CHANNEL_DISPLAY = { CH1_IDX: ("RF", "Peak frequency (MHz)", "MHz"), CH3_IDX: ("DC", "DC mean (mV)", "mV"), CH4_IDX: ("DC", "DC mean (mV)", "mV"), VELOCITY_MODE_IDX: ("Velocity", "Velocity (m/s)", "m/s"), } _CSS_HINT = "font-size: 11px; color: #aaa;" _CSS_INFO = "font-size: 11px;" _CSS_MUTED = "color: #888; font-size: 11px;" _CSS_WARN = "color: #e07000; font-size: 11px;" _CSS_BUSY = "color: #4a90d9; font-size: 11px;" # Side-panel column widths (the scroll areas that hold the controls). _LEFT_PANEL_W = 288 _RIGHT_PANEL_W = 272 # Minimum width for a spin box so its value + suffix are never clipped. _SPIN_MIN_W = 96 # --------------------------------------------------------------------------- # Small layout helpers # --------------------------------------------------------------------------- def _wrap_label(text: str = "", css: str | None = None) -> QLabel: """A word-wrapped QLabel that reports its *wrapped* height to the layout. A plain word-wrapped QLabel advertises a single-line minimum height, so in a fixed-width column the layout happily shrinks it and the extra lines get clipped. Enabling height-for-width makes the box layout ask for the real height at the column's width instead. """ lbl = QLabel(text) lbl.setWordWrap(True) sp = lbl.sizePolicy() sp.setVerticalPolicy(QSizePolicy.Policy.Minimum) sp.setHeightForWidth(True) lbl.setSizePolicy(sp) if css: lbl.setStyleSheet(css) return lbl def _group(title: str) -> tuple[QGroupBox, QVBoxLayout]: """A group box with consistent, non-cramped internal margins.""" grp = QGroupBox(title) lay = QVBoxLayout(grp) lay.setContentsMargins(10, 8, 10, 10) lay.setSpacing(6) return grp, lay def _form() -> QFormLayout: """A label/field form layout for a narrow side panel.""" form = QFormLayout() form.setContentsMargins(0, 0, 0, 0) form.setHorizontalSpacing(8) form.setVerticalSpacing(6) form.setLabelAlignment(Qt.AlignmentFlag.AlignRight | Qt.AlignmentFlag.AlignVCenter) form.setFormAlignment(Qt.AlignmentFlag.AlignLeft | Qt.AlignmentFlag.AlignTop) form.setFieldGrowthPolicy( QFormLayout.FieldGrowthPolicy.AllNonFixedFieldsGrow) form.setRowWrapPolicy(QFormLayout.RowWrapPolicy.DontWrapRows) return form def _scroll_panel(inner: QWidget, width: int) -> QScrollArea: """Put a side panel in a fixed-width scroll area. Without this the panels are sized by the window: a short window squeezes the controls past their minimum heights, which is what makes text overlap the widget below it. Scrolling keeps every control at its natural size. """ area = QScrollArea() area.setWidget(inner) area.setWidgetResizable(True) area.setFrameShape(QFrame.Shape.NoFrame) area.setHorizontalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAlwaysOff) area.setVerticalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAsNeeded) area.setFixedWidth(width) area.viewport().setAutoFillBackground(False) inner.setAutoFillBackground(False) return area # --------------------------------------------------------------------------- # ROI (free quadrilateral in data coordinates) # --------------------------------------------------------------------------- class RoiQuad: """Free quadrilateral defined in data coordinates (mm). Stored as 4 corner points (shape (4, 2)) in CCW order: BL, BR, TR, TL. Each corner can be positioned independently, allowing skewed / non-orthogonal regions of interest. Because it lives in scan/data coords it persists unchanged when the displayed channel/mode switches. """ def __init__(self, pts: np.ndarray): """pts : array-like, shape (4, 2).""" self._pts = np.asarray(pts, dtype=np.float64).reshape(4, 2).copy() @classmethod def from_bbox(cls, x0: float, y0: float, x1: float, y1: float) -> "RoiQuad": """Create an axis-aligned rectangle from two opposite corners.""" lx, rx = min(x0, x1), max(x0, x1) by, ty = min(y0, y1), max(y0, y1) return cls(np.array([[lx, by], [rx, by], [rx, ty], [lx, ty]])) def copy(self) -> "RoiQuad": return RoiQuad(self._pts.copy()) def corners(self) -> np.ndarray: """World-coord corners, shape (4, 2), CCW: BL, BR, TR, TL.""" return self._pts.copy() def centroid(self) -> np.ndarray: return self._pts.mean(axis=0) def bbox_size(self) -> np.ndarray: """Width and height of the axis-aligned bounding box, shape (2,).""" return self._pts.max(axis=0) - self._pts.min(axis=0) def contains(self, x: float, y: float) -> bool: return bool(MplPath(self._pts).contains_point((x, y))) def mask_for_grid(self, x_axis: np.ndarray, y_axis: np.ndarray) -> np.ndarray: """Boolean mask (n_rows, n_frames) of pixels whose centres lie inside the quadrilateral. Only the quad's axis-aligned bounding box is tested — meshgrid and contains_points over the *whole* grid would be tens of millions of point-in-polygon tests (and hundreds of MB of float64 temporaries) on a large scan, on every ROI edit. """ x = np.asarray(x_axis, dtype=np.float64) y = np.asarray(y_axis, dtype=np.float64) mask = np.zeros((y.size, x.size), dtype=bool) (x0, y0), (x1, y1) = self._pts.min(axis=0), self._pts.max(axis=0) cols = np.nonzero((x >= x0) & (x <= x1))[0] rows = np.nonzero((y >= y0) & (y <= y1))[0] if cols.size == 0 or rows.size == 0: return mask c0, c1 = int(cols[0]), int(cols[-1]) + 1 r0, r1 = int(rows[0]), int(rows[-1]) + 1 X, Y = np.meshgrid(x[c0:c1], y[r0:r1]) inside = MplPath(self._pts).contains_points( np.column_stack([X.ravel(), Y.ravel()])) mask[r0:r1, c0:c1] = inside.reshape(X.shape) return mask # --------------------------------------------------------------------------- # Matplotlib canvases # --------------------------------------------------------------------------- class ImageCanvas(FigureCanvasQTAgg): pixel_clicked = pyqtSignal(int, int) # row_idx, frame_idx roi_changed = pyqtSignal() # ROI created / edited / cleared draw_mode_changed = pyqtSignal(bool) # "draw new ROI" arm toggled # Interaction state values _IDLE = "idle" _DRAW_NEW = "draw_new" _MOVE = "move" _DRAG_CORNER = "drag_corner" # Hit tolerance (display pixels) for handles. _HANDLE_PX = 12 _CLICK_THRESH_PX = 4 # releases within this of press count as a click def __init__(self, parent=None): fig = Figure(figsize=(7, 5), tight_layout=True) self.ax = fig.add_subplot(111) super().__init__(fig) self.setParent(parent) self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding) self._extent = None self._img_shape = None # ROI state self._roi: RoiQuad | None = None self._roi_artists: list = [] self._state = self._IDLE self._draw_mode = False # Per-interaction snapshots / anchors self._press_xy: tuple[float, float] | None = None self._press_pixel: tuple[float, float] | None = None self._press_button = None self._snapshot: RoiQuad | None = None self._drag_corner_idx: int = -1 self._move_anchor = None # press-point in world coords self._draw_previous: RoiQuad | None = None self.mpl_connect("button_press_event", self._on_press) self.mpl_connect("motion_notify_event", self._on_motion) self.mpl_connect("button_release_event", self._on_release) # ------------------------------------------------------------------ # Public API # ------------------------------------------------------------------ def show_image(self, img: np.ndarray, extent: list[float], cmap: str, vmin: float, vmax: float, xlabel: str, ylabel: str, title: str, colorbar_label: str = ""): self.figure.clf() self.ax = self.figure.add_subplot(111) # Patches and lines are destroyed by figure.clf(); drop stale refs. self._roi_artists = [] self._extent = extent self._img_shape = img.shape im = self.ax.imshow( img, aspect="auto", origin="upper", extent=extent, cmap=cmap, vmin=vmin, vmax=vmax, interpolation="nearest", ) cb = self.figure.colorbar(im, ax=self.ax, fraction=0.046, pad=0.04) if colorbar_label: cb.set_label(colorbar_label) self.ax.set_xlabel(xlabel) self.ax.set_ylabel(ylabel) self.ax.set_title(title) # Re-draw the ROI (if any) on top of the fresh image so it persists # unchanged across mode / angle / channel switches. self._draw_roi() self.draw() def get_roi(self) -> RoiQuad | None: return self._roi def set_roi(self, roi: RoiQuad | None): self._roi = roi.copy() if roi is not None else None self._draw_roi() self.draw_idle() self.roi_changed.emit() def clear_roi(self): self._roi = None self._remove_roi_artists() self.draw_idle() self.roi_changed.emit() def start_drawing(self): """Arm the next click+drag on the image to create a new ROI, replacing any existing one.""" self._draw_mode = True self.setCursor(Qt.CursorShape.CrossCursor) self.draw_mode_changed.emit(True) def cancel_drawing(self): if self._draw_mode: self._draw_mode = False self.setCursor(Qt.CursorShape.ArrowCursor) self.draw_mode_changed.emit(False) # ------------------------------------------------------------------ # Rendering # ------------------------------------------------------------------ def _remove_roi_artists(self): for a in self._roi_artists: try: a.remove() except (ValueError, AttributeError, NotImplementedError): pass self._roi_artists = [] def _draw_roi(self): self._remove_roi_artists() if self._roi is None or self.ax is None: return corners = self._roi.corners() # Filled quad, then a sharp unfilled edge for visibility over bright # images, then draggable corner handles. for kwargs in ( dict(fill=True, facecolor="#ffd93a", edgecolor="#e53935", alpha=0.22, linewidth=2.0, zorder=10), dict(fill=False, edgecolor="#e53935", linewidth=1.8, zorder=11), ): patch = Polygon(corners, closed=True, **kwargs) self.ax.add_patch(patch) self._roi_artists.append(patch) self._roi_artists.append(self.ax.scatter( corners[:, 0], corners[:, 1], s=60, c="white", edgecolors="#e53935", linewidths=1.6, zorder=13)) # ------------------------------------------------------------------ # Hit testing (display pixels for handles, data coords for "inside") # ------------------------------------------------------------------ def _hit_test(self, event) -> tuple[str, int | None] | None: if self._roi is None or self.ax is None: return None if event.x is None or event.y is None: return None corners_disp = self.ax.transData.transform(self._roi.corners()) click = np.array([event.x, event.y]) for i in range(4): if np.hypot(*(corners_disp[i] - click)) <= self._HANDLE_PX: return ("corner", i) if event.xdata is not None and event.ydata is not None: if self._roi.contains(event.xdata, event.ydata): return ("inside", None) return None # ------------------------------------------------------------------ # Mouse event handlers # ------------------------------------------------------------------ def _on_press(self, event): if event.inaxes is not self.ax or self._extent is None: return if event.button != 1: # only left mouse button return # If the matplotlib toolbar is in pan / zoom mode, let it handle # the interaction instead of starting a ROI manipulation. tb = getattr(self, "toolbar", None) if tb is not None and getattr(tb, "mode", ""): return self._press_xy = (event.xdata, event.ydata) self._press_pixel = (event.x, event.y) self._press_button = event.button if self._draw_mode: self._draw_previous = self._roi.copy() if self._roi else None self._roi = RoiQuad.from_bbox(event.xdata, event.ydata, event.xdata, event.ydata) self._state = self._DRAW_NEW self._draw_roi() self.draw_idle() return hit = self._hit_test(event) if hit is None: self._state = self._IDLE return kind, idx = hit self._snapshot = self._roi.copy() if kind == "corner": self._state = self._DRAG_CORNER self._drag_corner_idx = idx else: self._state = self._MOVE self._move_anchor = (event.xdata, event.ydata) def _on_motion(self, event): if self._state == self._IDLE: return if event.xdata is None or event.ydata is None: return if event.inaxes is not self.ax: return if self._state == self._DRAW_NEW: x0, y0 = self._press_xy self._roi = RoiQuad.from_bbox(x0, y0, event.xdata, event.ydata) elif self._state == self._MOVE: delta = np.array([event.xdata - self._move_anchor[0], event.ydata - self._move_anchor[1]]) self._roi._pts = self._snapshot.corners() + delta elif self._state == self._DRAG_CORNER: self._roi._pts[self._drag_corner_idx] = [event.xdata, event.ydata] self._draw_roi() self.draw_idle() def _on_release(self, event): if event.button != 1 and self._press_button != 1: return prev_state = self._state self._state = self._IDLE try: if prev_state == self._DRAW_NEW: self._finish_draw() elif prev_state in (self._MOVE, self._DRAG_CORNER): self._draw_roi() self.draw_idle() self.roi_changed.emit() else: self._maybe_emit_pixel_click(event) finally: self._press_xy = self._press_pixel = None self._press_button = None def _finish_draw(self): """Commit (or reject) a freshly-dragged quad.""" if self._extent is not None: x0, x1, y_bot, y_top = self._extent min_w = abs(x1 - x0) * 0.01 # minimum: 1% of each axis range min_h = abs(y_bot - y_top) * 0.01 else: min_w = min_h = 1e-6 if self._roi is None: too_small = True else: bbox = self._roi.bbox_size() too_small = bbox[0] < min_w or bbox[1] < min_h if too_small: self._roi = self._draw_previous self._draw_previous = None self.cancel_drawing() self._draw_roi() self.draw_idle() self.roi_changed.emit() def _maybe_emit_pixel_click(self, event): """A release close enough to its press counts as a pixel click.""" if (self._press_pixel is None or event.x is None or event.y is None or self._extent is None or event.inaxes is not self.ax or event.xdata is None): return dx_px = event.x - self._press_pixel[0] dy_px = event.y - self._press_pixel[1] if dx_px * dx_px + dy_px * dy_px > self._CLICK_THRESH_PX ** 2: return x0, x1, y_bot, y_top = self._extent n_rows, n_frames = self._img_shape col = int((event.xdata - x0) / (x1 - x0) * n_frames) row = int((event.ydata - y_top) / (y_bot - y_top) * n_rows) self.pixel_clicked.emit(max(0, min(row, n_rows - 1)), max(0, min(col, n_frames - 1))) class WaveformCanvas(FigureCanvasQTAgg): def __init__(self, parent=None): fig = Figure(figsize=(8, 3), tight_layout=True) self.ax_wave = fig.add_subplot(121) self.ax_right = fig.add_subplot(122) super().__init__(fig) self.setParent(parent) self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding) def show_rf_waveform(self, sras: SrasFile, angle_idx: int, row_idx: int, frame_idx: int, apply_bg_sub: bool = True): """CH1 RF: time-domain + FFT spectrum. If apply_bg_sub is True and sras.background is not None, the background waveform is overlaid on the time-domain plot and the FFT is computed on the subtracted signal. The unsubtracted FFT is also shown faintly for comparison. """ data = sras.data[angle_idx] waveform = data[row_idx, CH1_IDX, frame_idx, :].astype(np.float32) t_ns = sras.time_axis_ns() f_mhz = sras.freq_axis_mhz() dc3_val = data[row_idx, CH3_IDX, frame_idx, :].astype(np.float32).mean() dc4_val = data[row_idx, CH4_IDX, frame_idx, :].astype(np.float32).mean() bg = sras.background if (apply_bg_sub and sras.background is not None) else None waveform_plot = waveform - bg if bg is not None else waveform self.ax_wave.cla() self.ax_right.cla() if bg is not None: self.ax_wave.plot(t_ns, waveform, linewidth=0.5, color="#aaaaaa", label="raw", zorder=1) self.ax_wave.plot(t_ns, bg, linewidth=0.5, color="#e07030", linestyle="--", label="background", zorder=2) self.ax_wave.plot(t_ns, waveform_plot, linewidth=0.7, color="#4488cc", label="subtracted", zorder=3) self.ax_wave.legend(fontsize=7, loc="upper right") else: self.ax_wave.plot(t_ns, waveform, linewidth=0.7, color="#4488cc") self.ax_wave.set_xlabel("Time (ns)") self.ax_wave.set_ylabel("ADC counts") bg_tag = " [bg sub]" if bg is not None else "" dc3_mv = adc_to_mv(dc3_val, *sras.cal(CH3_IDX)) dc4_mv = adc_to_mv(dc4_val, *sras.cal(CH4_IDX)) self.ax_wave.set_title( f"CH1 RF row={row_idx} frame={frame_idx}{bg_tag}\n" f"CH3={dc3_val:.1f} CH4={dc4_val:.1f} " f"({dc3_mv:.2f} / {dc4_mv:.2f} mV)", fontsize=8, ) # FFT of the (possibly subtracted) waveform power_sub = np.abs(np.fft.rfft(waveform_plot)) ** 2 power_sub[0] = 0.0 peak_mhz = f_mhz[int(np.argmax(power_sub))] if bg is not None: # Also show the unsubtracted FFT for reference power_raw = np.abs(np.fft.rfft(waveform)) ** 2 power_raw[0] = 0.0 self.ax_right.plot(f_mhz, power_raw, linewidth=0.5, color="#aaaaaa", label="raw FFT", zorder=1) self.ax_right.plot(f_mhz, power_sub, linewidth=0.7, color="#4488cc", label="subtracted FFT" if bg is not None else None, zorder=2) self.ax_right.axvline(peak_mhz, color="tomato", linestyle="--", linewidth=1.2, label=f"peak = {peak_mhz:.1f} MHz") self.ax_right.set_xlabel("Frequency (MHz)") self.ax_right.set_ylabel("Power (arb.)") self.ax_right.set_title("FFT Power Spectrum") self.ax_right.set_xlim(0, 500) self.ax_right.legend(fontsize=8) self.draw() def show_dc_waveform(self, sras: SrasFile, angle_idx: int, ch_idx: int, row_idx: int, frame_idx: int): """CH3 or CH4 DC: time-domain + mean annotation.""" waveform = sras.data[angle_idx][row_idx, ch_idx, frame_idx, :].astype(np.float32) mean_val = float(waveform.mean()) mean_mv = adc_to_mv(mean_val, *sras.cal(ch_idx)) self.ax_wave.cla() self.ax_right.cla() self.ax_wave.plot(sras.time_axis_ns(), waveform, linewidth=0.7, color="#4488cc") self.ax_wave.axhline(mean_val, color="tomato", linestyle="--", linewidth=1.2, label=f"mean = {mean_val:.2f} ADC") self.ax_wave.set_xlabel("Time (ns)") self.ax_wave.set_ylabel("ADC counts") self.ax_wave.set_title( f"{CH_NAMES[ch_idx]} DC row={row_idx} frame={frame_idx}") self.ax_wave.legend(fontsize=8) self.ax_right.text( 0.5, 0.5, f"DC mode\n\nmean = {mean_val:.3f} ADC\n = {mean_mv:.3f} mV", ha="center", va="center", transform=self.ax_right.transAxes, fontsize=11, ) self.ax_right.set_axis_off() self.draw() # --------------------------------------------------------------------------- # FFT Options dialog # --------------------------------------------------------------------------- class FftOptionsDialog(QDialog): """Configure FFT backend and zero-padding. Changes take effect only when the user clicks Apply. Cancel discards all pending edits. The live 'frequency resolution' label updates as the user adjusts the pad factor so they can see the trade-off before committing. """ def __init__(self, parent=None, *, current_backend: str, current_pad_factor: int, samples_per_frame: int | None, sample_rate_hz: float | None, grating_um: float): super().__init__(parent) self.setWindowTitle("FFT Options") self.setModal(True) self.setMinimumWidth(380) self._samples_per_frame = samples_per_frame self._sample_rate_hz = sample_rate_hz self._grating_um = grating_um layout = QVBoxLayout(self) # ---- Backend --------------------------------------------------- grp_backend = QGroupBox("FFT Backend") bl = QVBoxLayout(grp_backend) self._btn_numpy = QRadioButton("NumPy FFT (always available)") self._btn_pyfftw = QRadioButton( "pyFFTW (faster for large arrays)" if PYFFTW_AVAILABLE else "pyFFTW (not installed — run: pip install pyfftw)") self._btn_pyfftw.setEnabled(PYFFTW_AVAILABLE) self._backend_group = QButtonGroup(self) self._backend_group.addButton(self._btn_numpy, id=0) self._backend_group.addButton(self._btn_pyfftw, id=1) if current_backend == "pyfftw" and PYFFTW_AVAILABLE: self._btn_pyfftw.setChecked(True) else: self._btn_numpy.setChecked(True) bl.addWidget(self._btn_numpy) bl.addWidget(self._btn_pyfftw) layout.addWidget(grp_backend) # ---- Zero-padding ---------------------------------------------- grp_zp = QGroupBox("Zero-Padding") zl = QVBoxLayout(grp_zp) pad_row = QHBoxLayout() pad_row.addWidget(QLabel("Pad factor:")) self._spin_pad = QSpinBox() self._spin_pad.setRange(1, 256) self._spin_pad.setValue(max(1, current_pad_factor)) self._spin_pad.setToolTip( "Multiply the waveform length by this factor via zero-padding\n" "before computing the FFT.\n" "1 = no padding (natural length).\n" "Powers of 2 (2, 4, 8 …) give the best performance." ) self._spin_pad.valueChanged.connect(self._update_info) pad_row.addWidget(self._spin_pad) zl.addLayout(pad_row) self._lbl_nfft = QLabel() self._lbl_freq_res = QLabel() self._lbl_vel_res = QLabel() for lbl in (self._lbl_nfft, self._lbl_freq_res, self._lbl_vel_res): lbl.setStyleSheet(_CSS_HINT) zl.addWidget(lbl) layout.addWidget(grp_zp) # ---- Buttons --------------------------------------------------- buttons = QDialogButtonBox() buttons.addButton("Apply", QDialogButtonBox.ButtonRole.AcceptRole ).clicked.connect(self.accept) buttons.addButton("Cancel", QDialogButtonBox.ButtonRole.RejectRole ).clicked.connect(self.reject) layout.addWidget(buttons) self._update_info() def _update_info(self): spf = self._samples_per_frame sr = self._sample_rate_hz pad = self._spin_pad.value() if spf is None or sr is None: self._lbl_nfft.setText("Load a file to preview FFT parameters.") self._lbl_freq_res.setText("") self._lbl_vel_res.setText("") return n_fft = spf * pad freq_res_hz = sr / n_fft freq_res_mhz = freq_res_hz / 1e6 # v (m/s) = freq (MHz) × grating (µm) vel_res_ms = freq_res_mhz * self._grating_um self._lbl_nfft.setText(f"FFT points: {spf} × {pad} = {n_fft:,}") self._lbl_freq_res.setText( f"Frequency bin: {freq_res_mhz:.4f} MHz ({freq_res_hz / 1e3:.2f} kHz)") self._lbl_vel_res.setText( f"Velocity bin: {vel_res_ms:.3f} m/s " f"(at grating = {self._grating_um:.2f} µm)") def get_backend(self) -> str: return "pyfftw" if self._btn_pyfftw.isChecked() and PYFFTW_AVAILABLE else "numpy" def get_pad_factor(self) -> int: return max(1, self._spin_pad.value()) # --------------------------------------------------------------------------- # Manual alignment dialog (Fusion -> Manual Alignment...) # --------------------------------------------------------------------------- class ManualAlignOverlayCanvas(FigureCanvasQTAgg): """Renders ManualAlignmentDialog's multi-angle mask overlay and turns keyboard input into translate/rotate nudge requests for whichever angle the dialog currently has active. A pure input+render widget — it holds no alignment state and never touches SrasFile itself; ManualAlignmentDialog owns all of that and decides, from these signals, whether a cheap single-layer refresh or a full preview-canvas rebuild is needed. FigureCanvasQTAgg is a real QWidget, so keyPressEvent works like on any other widget, but Qt only ever delivers key events to whichever widget currently has focus — StrongFocus, plus grabbing focus on click and once right after the dialog is shown, are both required or arrow keys silently do nothing. Rotate keys are letters (Q/E), not punctuation (comma/period or brackets): Shift+letter still reports the same Qt.Key on every platform, whereas Shift+comma/bracket can report a different virtual key (Key_Less / Key_BraceLeft) depending on platform and keyboard layout — which would silently break the "Shift = coarse step" modifier for rotation specifically. Arrow keys have no such hazard. """ nudge_translate = pyqtSignal(int, int, bool) # dir_x, dir_y in {-1,0,1}; coarse nudge_rotate = pyqtSignal(int, bool) # dir in {-1,1} (CCW/CW); coarse _TRANSLATE_KEYS = { Qt.Key.Key_Left: (-1, 0), Qt.Key.Key_Right: (1, 0), Qt.Key.Key_Up: (0, -1), Qt.Key.Key_Down: (0, 1), } _ROTATE_KEYS = {Qt.Key.Key_Q: 1, Qt.Key.Key_E: -1} # CCW, CW def __init__(self, parent=None): fig = Figure(figsize=(6, 6), tight_layout=True) self.ax = fig.add_subplot(111) super().__init__(fig) self.setParent(parent) self.setFocusPolicy(Qt.FocusPolicy.StrongFocus) self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding) self.mpl_connect("button_press_event", lambda _e: self.setFocus()) def show_overlay(self, rgba: np.ndarray, extent: list[float], title: str): self.figure.clf() self.ax = self.figure.add_subplot(111) self.ax.imshow(rgba, extent=extent, origin="upper", aspect="auto") self.ax.set_xlabel("X (mm)") self.ax.set_ylabel("Y (mm)") self.ax.set_title(title) self.draw_idle() # coalesces rapid redraws — matters for key-repeat. def keyPressEvent(self, event: QKeyEvent): key = event.key() coarse = bool(event.modifiers() & Qt.KeyboardModifier.ShiftModifier) if key in self._TRANSLATE_KEYS: dx, dy = self._TRANSLATE_KEYS[key] self.nudge_translate.emit(dx, dy, coarse) event.accept() elif key in self._ROTATE_KEYS: self.nudge_rotate.emit(self._ROTATE_KEYS[key], coarse) event.accept() else: super().keyPressEvent(event) class ManualAlignmentDialog(QDialog): """Non-modal manual angle-alignment editor (Fusion -> Manual Alignment...). Shows every angle's binarized CH4 (Bias B) mask overlaid in a distinct color at partial opacity on one shared canvas, so translation/rotation misalignment is visible by eye — the thing the automatic phase- correlation step (compute_angle_alignment) sometimes gets wrong. The user picks an "active" angle and nudges its rotation+translation with the keyboard; Auto De-rotate sets every non-reference angle's rotation to the known, analytic scan-angle delta without touching any translation the user has already dialed in. Save writes a JSON sidecar next to the .sras file and hands a freshly-built, full-resolution AlignmentResult back to the main window — the exact same object shape compute_angle_alignment produces, so every existing Aligned-View code path (apply_alignment, _aligned_canvas_axes, the pixel-inspector inverse-transform) works completely unmodified. Non-modal by design (shown via .show(), never .exec() or setModal(True)) so the user can still interact with the main window. Talks back to SrasViewerWindow two ways: it reuses parent._run_worker/_jobs directly for its own (rare) background mask-fetch step, so the main window's existing shutdown/lifecycle plumbing covers it for free, and it emits alignment_saved / alignment_cleared signals for the two moments that should actually mutate the main window's persistent state — everything else (nudging, Auto De-rotate, threshold edits) stays purely local to this dialog until Save. """ alignment_saved = pyqtSignal(object, str) # AlignmentResult, sidecar path (str) alignment_cleared = pyqtSignal() _PREVIEW_MARGIN_FRAC = 0.15 _BASE_ALPHA = 0.42 _ACTIVE_ALPHA = 0.75 _MAX_PREVIEW_DIM = 1024 def __init__(self, parent: "SrasViewerWindow", sras: SrasFile, *, ref_angle_idx: int, dc_threshold_mv: float, seed_per_angle: dict[int, ManualAngleParams] | None, cached_dc4_mv: dict[int, np.ndarray]): super().__init__(parent) self._parent = parent self._sras = sras self._ref_angle_idx = ref_angle_idx self._downsample_factor = 1 self._dc4_mv: dict[int, np.ndarray] = {} self._masks_small: dict[int, np.ndarray] = {} self._preview_layers: dict[int, np.ndarray] = {} self._preview_origin_mm = (0.0, 0.0) self._preview_shape = (1, 1) self._preview_dx_mm = self._preview_dy_mm = 1.0 self._masks_ready = False self.setWindowTitle(f"Manual Alignment — {sras.path.name}") self.resize(1150, 760) self._seed_initial_params(seed_per_angle) n = sras.n_angles cmap = mpl.colormaps["tab10"] if n <= 10 else mpl.colormaps["tab20"] self._angle_colors = {a: cmap(a % cmap.N)[:3] for a in range(n)} self._active_angle = 1 if ref_angle_idx == 0 and n > 1 else 0 self._build_ui(dc_threshold_mv) self._set_controls_enabled(False) # re-enabled once masks are ready self._start_mask_prep(cached_dc4_mv) def showEvent(self, event): super().showEvent(event) self.canvas.setFocus() # ------------------------------------------------------------------ # Construction # ------------------------------------------------------------------ def _seed_initial_params(self, seed_per_angle: dict[int, ManualAngleParams] | None): seed = seed_per_angle or {} self._angle_params: dict[int, ManualAngleParams] = { a: (ManualAngleParams(seed[a].rotation_deg, seed[a].shift_mm) if a in seed else ManualAngleParams()) for a in range(self._sras.n_angles) } self._angle_params[self._ref_angle_idx] = ManualAngleParams() def _build_ui(self, dc_threshold_mv: float): root = QHBoxLayout(self) self.canvas = ManualAlignOverlayCanvas() left = QWidget() left_l = QVBoxLayout(left) left_l.setContentsMargins(0, 0, 0, 0) left_l.setSpacing(4) left_l.addWidget(NavigationToolbar2QT(self.canvas, left)) left_l.addWidget(self.canvas) root.addWidget(left, stretch=1) panel = QWidget() panel_l = QVBoxLayout(panel) panel_l.setContentsMargins(0, 0, 0, 0) panel_l.setSpacing(8) # ---- Active Angle ------------------------------------------------- grp_angle, al = _group("Active Angle") self.combo_active_angle = QComboBox() for a in range(self._sras.n_angles): label = f"Angle {a} ({self._sras.angles_deg[a]:.1f}°)" if a == self._ref_angle_idx: label += " [reference]" self.combo_active_angle.addItem(label) al.addWidget(self.combo_active_angle) self.lbl_active_note = _wrap_label("", _CSS_WARN) al.addWidget(self.lbl_active_note) panel_l.addWidget(grp_angle) # ---- Manual Adjustment --------------------------------------------- self.grp_manual_adjust, mform_box = _group("Manual Adjustment") mform = _form() self.spin_active_rotation_deg = QDoubleSpinBox() self.spin_active_rotation_deg.setRange(-3600.0, 3600.0) self.spin_active_rotation_deg.setDecimals(3) self.spin_active_rotation_deg.setSuffix(" °") self.spin_active_rotation_deg.setMinimumWidth(_SPIN_MIN_W) mform.addRow("Rotation:", self.spin_active_rotation_deg) self.spin_active_shift_x_mm = QDoubleSpinBox() self.spin_active_shift_x_mm.setRange(-1e5, 1e5) self.spin_active_shift_x_mm.setDecimals(4) self.spin_active_shift_x_mm.setSuffix(" mm") self.spin_active_shift_x_mm.setMinimumWidth(_SPIN_MIN_W) mform.addRow("Shift X:", self.spin_active_shift_x_mm) self.spin_active_shift_y_mm = QDoubleSpinBox() self.spin_active_shift_y_mm.setRange(-1e5, 1e5) self.spin_active_shift_y_mm.setDecimals(4) self.spin_active_shift_y_mm.setSuffix(" mm") self.spin_active_shift_y_mm.setMinimumWidth(_SPIN_MIN_W) mform.addRow("Shift Y:", self.spin_active_shift_y_mm) mform_box.addLayout(mform) panel_l.addWidget(self.grp_manual_adjust) # ---- Nudge Step Sizes ------------------------------------------------ self.grp_step_sizes, sl = _group("Nudge Step Sizes") sform = _form() self.spin_step_translate_mm = QDoubleSpinBox() self.spin_step_translate_mm.setRange(0.0001, 1000.0) self.spin_step_translate_mm.setDecimals(4) self.spin_step_translate_mm.setSuffix(" mm") self.spin_step_translate_mm.setValue(0.01) self.spin_step_translate_mm.setMinimumWidth(_SPIN_MIN_W) sform.addRow("Translate step:", self.spin_step_translate_mm) self.spin_step_rotate_deg = QDoubleSpinBox() self.spin_step_rotate_deg.setRange(0.001, 90.0) self.spin_step_rotate_deg.setDecimals(3) self.spin_step_rotate_deg.setSuffix(" °") self.spin_step_rotate_deg.setValue(0.1) self.spin_step_rotate_deg.setMinimumWidth(_SPIN_MIN_W) sform.addRow("Rotate step:", self.spin_step_rotate_deg) self.spin_step_multiplier = QDoubleSpinBox() self.spin_step_multiplier.setRange(1.0, 1000.0) self.spin_step_multiplier.setDecimals(1) self.spin_step_multiplier.setValue(10.0) self.spin_step_multiplier.setMinimumWidth(_SPIN_MIN_W) sform.addRow("Coarse × (Shift):", self.spin_step_multiplier) sl.addLayout(sform) sl.addWidget(_wrap_label( "Arrow keys nudge X/Y translation; Q/E nudge rotation (CCW/CW). " "Hold Shift for the coarse step. Click the image once so it has " "keyboard focus.", _CSS_HINT)) panel_l.addWidget(self.grp_step_sizes) # ---- Mask Threshold --------------------------------------------------- self.grp_mask_threshold, tl = _group("Mask Threshold") tform = _form() self.spin_mask_threshold_mv = QDoubleSpinBox() self.spin_mask_threshold_mv.setRange(-500.0, 500.0) self.spin_mask_threshold_mv.setDecimals(3) self.spin_mask_threshold_mv.setSuffix(" mV") self.spin_mask_threshold_mv.setValue(dc_threshold_mv) self.spin_mask_threshold_mv.setMinimumWidth(_SPIN_MIN_W) tform.addRow("DC threshold:", self.spin_mask_threshold_mv) tl.addLayout(tform) panel_l.addWidget(self.grp_mask_threshold) # ---- Actions ------------------------------------------------------ grp_actions, acl = _group("Actions") self.btn_auto_derotate = QPushButton("Auto De-rotate (use known angles)") self.btn_save = QPushButton("Save Alignment") self.btn_clear = QPushButton("Clear Alignment…") self.btn_close = QPushButton("Close") for btn in (self.btn_auto_derotate, self.btn_save, self.btn_clear, self.btn_close): acl.addWidget(btn) panel_l.addWidget(grp_actions) self.lbl_status = _wrap_label("", _CSS_MUTED) panel_l.addWidget(self.lbl_status) panel_l.addStretch() root.addWidget(_scroll_panel(panel, 300)) self.combo_active_angle.currentIndexChanged.connect(self._on_active_angle_changed) self.spin_active_rotation_deg.editingFinished.connect(self._on_rotation_spin_edited) self.spin_active_shift_x_mm.editingFinished.connect(self._on_shift_spin_edited) self.spin_active_shift_y_mm.editingFinished.connect(self._on_shift_spin_edited) self.spin_mask_threshold_mv.editingFinished.connect(self._on_mask_threshold_edited) self.btn_auto_derotate.clicked.connect(self._on_auto_derotate) self.btn_save.clicked.connect(self._on_save) self.btn_clear.clicked.connect(self._on_clear) self.btn_close.clicked.connect(self.close) self.canvas.nudge_translate.connect(self._on_nudge_translate) self.canvas.nudge_rotate.connect(self._on_nudge_rotate) self.combo_active_angle.blockSignals(True) self.combo_active_angle.setCurrentIndex(self._active_angle) self.combo_active_angle.blockSignals(False) self._on_active_angle_changed(self._active_angle) # ------------------------------------------------------------------ # Mask preparation (initial CH4 fetch + threshold + downsample) # ------------------------------------------------------------------ def _start_mask_prep(self, cached_dc4_mv: dict[int, np.ndarray]): self._dc4_mv = dict(cached_dc4_mv) missing = [a for a in range(self._sras.n_angles) if a not in self._dc4_mv] if not missing: self._finish_mask_prep() return self.lbl_status.setText(f"Preparing masks: 0/{len(missing)} angle(s) needed…") started = self._parent._run_worker( "manual_align_masks", Ch4MaskWorker(self._sras, missing), connect=( ("angle_done", self._on_mask_angle_done), ("error", lambda msg: self.lbl_status.setText(f"Mask prep error: {msg}")), ), on_done=self._finish_mask_prep) if not started: self.lbl_status.setText( "Could not start mask preparation (busy) — close and reopen.") def _on_mask_angle_done(self, angle_idx: int, dc4_mv: np.ndarray): self._dc4_mv[angle_idx] = dc4_mv self.lbl_status.setText( f"Preparing masks: {len(self._dc4_mv)}/{self._sras.n_angles} ready…") def _finish_mask_prep(self): if len(self._dc4_mv) < self._sras.n_angles: return # a mask-worker error left some angles unfetched max_dim = max(max(img.shape) for img in self._dc4_mv.values()) self._downsample_factor = max(1, int(np.ceil(max_dim / self._MAX_PREVIEW_DIM))) self._recompute_masks_small() self._rebuild_preview_canvas() self._set_controls_enabled(True) self.lbl_status.setText("Ready.") def _recompute_masks_small(self): """Threshold + downsample every angle's already-in-memory full-res CH4 mV image. Cheap (a compare + block-mean), so this re-runs in full whenever the mask-threshold spin box changes — no re-fetch.""" threshold = self.spin_mask_threshold_mv.value() factor = self._downsample_factor self._masks_small = { a: compute._block_mean_downsample( (img >= threshold).astype(np.float32), factor) for a, img in self._dc4_mv.items() } # ------------------------------------------------------------------ # Preview canvas: full rebuild vs. incremental single-layer refresh # ------------------------------------------------------------------ def _rebuild_preview_canvas(self): """Full geometry rebuild: recomputes the shared preview canvas's origin/shape (rotation can grow the union bbox — translation alone cannot, per the padding baked in via _PREVIEW_MARGIN_FRAC) and every angle's reprojected mask layer. Triggered by: dialog open, mask-threshold change, Auto De-rotate, a rotation nudge/edit of the active angle. NOT triggered by a translation-only nudge — see _refresh_active_preview_layer.""" dx_ref, dy_ref = compute._pixel_pitch_mm(self._sras, self._ref_angle_idx) factor = self._downsample_factor dx_c, dy_c = dx_ref * factor, dy_ref * factor origin, shape = compute.union_canvas_mm( self._sras, self._ref_angle_idx, dx_c, dy_c, self._angle_params, margin_frac=self._PREVIEW_MARGIN_FRAC) self._preview_origin_mm, self._preview_shape = origin, shape self._preview_dx_mm, self._preview_dy_mm = dx_c, dy_c self._preview_layers = { a: compute.reproject_mask( self._sras, a, self._ref_angle_idx, self._masks_small[a], self._angle_params[a].rotation_deg, self._angle_params[a].shift_mm, dx_c, dy_c, origin, shape) for a in range(self._sras.n_angles) } self._redraw_overlay() def _refresh_active_preview_layer(self): """Cheap path for a translation-only nudge/edit of the active angle: reproject just that one angle's downsampled mask onto the *existing* preview canvas — every other angle's cached layer is untouched.""" a = self._active_angle self._preview_layers[a] = compute.reproject_mask( self._sras, a, self._ref_angle_idx, self._masks_small[a], self._angle_params[a].rotation_deg, self._angle_params[a].shift_mm, self._preview_dx_mm, self._preview_dy_mm, self._preview_origin_mm, self._preview_shape) self._redraw_overlay() def _redraw_overlay(self): """Alpha-composite every angle's colored mask layer into one RGBA image ("all thresholds overlaid with varying opacity"). Each angle keeps a fixed, distinct color regardless of which is active; the active angle is drawn last (on top) at a visibly higher alpha so it's easy to track while nudging.""" if not self._preview_layers: return # mask prep hasn't finished yet — nothing to draw n_rows, n_cols = self._preview_shape rgba = np.zeros((n_rows, n_cols, 4), dtype=np.float32) order = sorted(range(self._sras.n_angles), key=lambda a: a == self._active_angle) for a in order: layer = self._preview_layers.get(a) if layer is None: continue alpha = self._ACTIVE_ALPHA if a == self._active_angle else self._BASE_ALPHA color = self._angle_colors[a] fg_a = layer * alpha for c in range(3): rgba[..., c] = color[c] * fg_a + rgba[..., c] * rgba[..., 3] * (1 - fg_a) rgba[..., 3] = fg_a + rgba[..., 3] * (1 - fg_a) x0, y0 = self._preview_origin_mm dx, dy = self._preview_dx_mm, self._preview_dy_mm x_axis = x0 + np.arange(n_cols) * dx y_axis = y0 + np.arange(n_rows) * dy extent = [x_axis[0] - dx / 2, x_axis[-1] + dx / 2, y_axis[-1] + dy / 2, y_axis[0] - dy / 2] title = (f"Angle {self._active_angle} active " f"({self._sras.angles_deg[self._active_angle]:.1f}°)") self.canvas.show_overlay(rgba, extent, title) # ------------------------------------------------------------------ # Angle selection / nudge / edit handlers # ------------------------------------------------------------------ def _on_active_angle_changed(self, angle_idx: int): self._active_angle = angle_idx is_ref = angle_idx == self._ref_angle_idx self.grp_manual_adjust.setEnabled(self._masks_ready and not is_ref) self.lbl_active_note.setText( "Reference angle — defines the shared origin, not adjustable." if is_ref else "") self._sync_active_spinboxes() self._redraw_overlay() def _sync_active_spinboxes(self): p = self._angle_params[self._active_angle] for spin, val in ((self.spin_active_rotation_deg, p.rotation_deg), (self.spin_active_shift_x_mm, p.shift_mm[0]), (self.spin_active_shift_y_mm, p.shift_mm[1])): spin.blockSignals(True) spin.setValue(val) spin.blockSignals(False) def _on_nudge_translate(self, dir_x: int, dir_y: int, coarse: bool): if not self._masks_ready or self._active_angle == self._ref_angle_idx: return step = self.spin_step_translate_mm.value() if coarse: step *= self.spin_step_multiplier.value() p = self._angle_params[self._active_angle] p.shift_mm = (p.shift_mm[0] + dir_x * step, p.shift_mm[1] + dir_y * step) self._sync_active_spinboxes() self._refresh_active_preview_layer() def _on_nudge_rotate(self, direction: int, coarse: bool): if not self._masks_ready or self._active_angle == self._ref_angle_idx: return step = self.spin_step_rotate_deg.value() if coarse: step *= self.spin_step_multiplier.value() self._angle_params[self._active_angle].rotation_deg += direction * step self._sync_active_spinboxes() self._rebuild_preview_canvas() def _on_rotation_spin_edited(self): if self._active_angle == self._ref_angle_idx: return self._angle_params[self._active_angle].rotation_deg = self.spin_active_rotation_deg.value() self._rebuild_preview_canvas() def _on_shift_spin_edited(self): if self._active_angle == self._ref_angle_idx: return p = self._angle_params[self._active_angle] p.shift_mm = (self.spin_active_shift_x_mm.value(), self.spin_active_shift_y_mm.value()) self._refresh_active_preview_layer() def _on_mask_threshold_edited(self): if not self._masks_ready: return self._recompute_masks_small() self._rebuild_preview_canvas() # ------------------------------------------------------------------ # Actions # ------------------------------------------------------------------ def _on_auto_derotate(self): n_changed = 0 for a in range(self._sras.n_angles): if a == self._ref_angle_idx: continue self._angle_params[a].rotation_deg = compute._theta_deg( self._sras, a, self._ref_angle_idx) n_changed += 1 self._sync_active_spinboxes() self._rebuild_preview_canvas() self.lbl_status.setText( f"Rotation set to the known scan angle for {n_changed} angle(s) " "(translation left untouched).") def _on_save(self): threshold = self.spin_mask_threshold_mv.value() resolved = dict(self._angle_params) # already concrete floats try: path = save_manual_alignment(self._sras, self._ref_angle_idx, threshold, resolved) result = build_manual_alignment(self._sras, self._ref_angle_idx, threshold, resolved) except OSError as exc: QMessageBox.warning(self, "Save Alignment Failed", str(exc)) return self.lbl_status.setText(f"Saved to {path.name}.") self.alignment_saved.emit(result, str(path)) def _on_clear(self): reply = QMessageBox.question( self, "Clear Alignment", "This resets every angle back to raw/unaligned (0° rotation, no " "shift) and deletes the saved alignment file for this scan, if " "any. This cannot be undone. Continue?", QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No, QMessageBox.StandardButton.No) if reply != QMessageBox.StandardButton.Yes: return try: existed = delete_manual_alignment(self._sras) except OSError as exc: QMessageBox.warning(self, "Clear Alignment Failed", f"Could not delete the saved alignment file: {exc}") return self._angle_params = {a: ManualAngleParams() for a in range(self._sras.n_angles)} self._sync_active_spinboxes() self._rebuild_preview_canvas() self.lbl_status.setText( "Alignment cleared; saved file removed." if existed else "Alignment cleared (there was no saved file).") self.alignment_cleared.emit() def _set_controls_enabled(self, enabled: bool): self._masks_ready = enabled self.combo_active_angle.setEnabled(enabled) self.grp_manual_adjust.setEnabled(enabled and self._active_angle != self._ref_angle_idx) self.grp_step_sizes.setEnabled(enabled) self.grp_mask_threshold.setEnabled(enabled) self.btn_auto_derotate.setEnabled(enabled) self.btn_save.setEnabled(enabled) self.btn_clear.setEnabled(enabled) # --------------------------------------------------------------------------- # Main window # --------------------------------------------------------------------------- class SrasViewerWindow(QMainWindow): def __init__(self, initial_path: str | None = None): super().__init__() self.setWindowTitle("SRAS Scan Viewer") self.resize(1560, 840) self.setMinimumSize(960, 560) self.setAcceptDrops(True) self._sras: SrasFile | None = None self._current_image: np.ndarray | None = None self._current_angle: int = 0 self._current_ch: int = 0 self._pending_angle: int = 0 self._pending_ch: int = 0 self._pending_bg_sub: bool = True self._pending_threshold: float = 50.0 # mV self._pending_fft_pad_factor: int = 1 # Live background jobs, keyed by role — see _run_worker. self._jobs: dict[str, tuple] = {} self._progress_dlgs: dict[str, QProgressDialog] = {} # FFT settings (configured via FFT Options dialog) self._fft_pad_factor: int = 1 # 1 = no padding # Convert menu: batch DC/FFT compute-and-store (v6 -> v7) self._batch_errors: list[str] = [] # Display-only settings (colormap, grating) never trigger a # recompute — they're applied to cached data on redraw. DC images # (CH3/CH4) are cheap and precomputed for every angle in the # background right after load. CH1/Velocity FFT images are # computed lazily (with a progress popup) the first time an # angle/threshold combination is viewed — using the cached DC4 # image to skip the FFT entirely for masked-out pixels — and # cached per (angle, bg_sub, n_fft, threshold) so revisiting the # same combination is free. self._dc_cache: dict[tuple[int, int], np.ndarray] = {} self._fft_cache: dict[tuple[int, bool, int | None, float], np.ndarray] = {} self._dc_precompute_worker: DcPrecomputeWorker | None = None self._dc_generation: int = 0 # Angle alignment ("Fusion" menu) self._alignment_result = None self._alignment_generation: int = 0 self._aligned_cache: dict[tuple, np.ndarray] = {} self._manual_align_dialog: ManualAlignmentDialog | None = None self._build_ui() if initial_path: self._load_file(initial_path) # ------------------------------------------------------------------ # Background job plumbing # ------------------------------------------------------------------ def _run_worker(self, key: str, worker: QObject, *, connect: tuple = (), quit_on: tuple = ("finished",), on_done=None) -> bool: """Move *worker* onto its own QThread and start it. Returns False if a job under *key* is already running. Centralises two lifetime hazards that each cost a process abort: 1. The job is claimed in self._jobs *before* start() and before anything below that can pump the Qt event loop (a QProgressDialog.show() does on first display). If it weren't, a re-entrant editingFinished could slip past the busy check, start a second thread, and then have the first call's own assignment clobber — and destroy while still running — that second QThread. 2. thread.finished fires as the thread winds down but does not guarantee the OS thread has joined. Dropping the last reference to a QThread whose thread is still running logs "QThread: Destroyed while thread is still running" and aborts, so wait() first. """ if key in self._jobs: return False thread = QThread() self._jobs[key] = (thread, worker, on_done) # claim before anything pumps worker.moveToThread(thread) thread.started.connect(worker.run) for signal_name, slot in connect: getattr(worker, signal_name).connect(slot) for signal_name in quit_on: getattr(worker, signal_name).connect(thread.quit) thread.finished.connect(lambda k=key: self._on_job_finished(k)) thread.start() return True def _on_job_finished(self, key: str): job = self._jobs.pop(key, None) if job is None: return thread, _worker, on_done = job thread.wait() # join before releasing our last reference if on_done is not None: on_done() def _job_running(self, key: str) -> bool: return key in self._jobs # ------------------------------------------------------------------ # UI construction # ------------------------------------------------------------------ def _build_ui(self): central = QWidget() self.setCentralWidget(central) root = QHBoxLayout(central) root.setContentsMargins(8, 8, 8, 8) root.setSpacing(8) root.addWidget(self._build_left_panel()) root.addWidget(self._build_canvases(), stretch=1) root.addWidget(self._build_right_panel()) self.statusBar().showMessage("Open an .sras file to begin.") self._build_menus() def _build_left_panel(self) -> QWidget: panel = QWidget() panel_layout = QVBoxLayout(panel) panel_layout.setContentsMargins(0, 0, 0, 0) panel_layout.setSpacing(8) # ---- File ------------------------------------------------------- grp_file, fl = _group("File") self.btn_open = QPushButton("Open .sras…") self.btn_open.clicked.connect(self._on_open) self.lbl_filename = _wrap_label("No file loaded", _CSS_MUTED) fl.addWidget(self.btn_open) fl.addWidget(self.lbl_filename) panel_layout.addWidget(grp_file) # ---- Scan info -------------------------------------------------- grp_info, il = _group("Scan Info") il.setSpacing(3) self._info = {} for key in ("Angles", "Rows", "Frames / row", "Samples / frame", "Sample rate", "X start", "Pixel Δx", "Laser freq"): lbl = _wrap_label(f"{key}: —", _CSS_INFO) il.addWidget(lbl) self._info[key] = lbl # frame-count / format notes self.lbl_frame_warn = _wrap_label("", _CSS_WARN) il.addWidget(self.lbl_frame_warn) # background DC-precompute progress self.lbl_dc_precompute = _wrap_label("", _CSS_BUSY) il.addWidget(self.lbl_dc_precompute) panel_layout.addWidget(grp_info) # ---- View settings ---------------------------------------------- grp_view, vl = _group("View Settings") view_form = _form() self.spin_angle = QSpinBox() self.spin_angle.setRange(0, 0) self.spin_angle.setEnabled(False) self.spin_angle.setMinimumWidth(64) self.spin_angle.editingFinished.connect(self._on_view_changed) self.lbl_angle_deg = QLabel("—") angle_field = QWidget() ar = QHBoxLayout(angle_field) ar.setContentsMargins(0, 0, 0, 0) ar.setSpacing(6) ar.addWidget(self.spin_angle) ar.addWidget(self.lbl_angle_deg) ar.addStretch() view_form.addRow("Angle:", angle_field) self.combo_channel = QComboBox() self.combo_channel.addItems(CH_LABELS) self.combo_channel.setEnabled(False) self.combo_channel.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed) self.combo_channel.setSizeAdjustPolicy( QComboBox.SizeAdjustPolicy.AdjustToMinimumContentsLengthWithIcon) self.combo_channel.setMinimumContentsLength(12) self.combo_channel.currentIndexChanged.connect(self._on_channel_changed) view_form.addRow("Channel:", self.combo_channel) vl.addLayout(view_form) sep = QFrame() sep.setFrameShape(QFrame.Shape.HLine) sep.setStyleSheet("color: #555;") vl.addWidget(sep) # DC threshold (for RF / CH1 masking) self.grp_threshold, tl = _group("RF Mask Threshold (CH1 only)") thr_form = _form() self.spin_threshold_mv = QDoubleSpinBox() self.spin_threshold_mv.setRange(-500.0, 500.0) self.spin_threshold_mv.setDecimals(3) self.spin_threshold_mv.setSingleStep(0.025) self.spin_threshold_mv.setSuffix(" mV") self.spin_threshold_mv.setValue(50.0) self.spin_threshold_mv.setEnabled(False) self.spin_threshold_mv.setMinimumWidth(_SPIN_MIN_W) self.spin_threshold_mv.editingFinished.connect(self._on_threshold_changed) thr_form.addRow("DC threshold:", self.spin_threshold_mv) tl.addLayout(thr_form) self.lbl_threshold_adc = _wrap_label( f"≈ {mv_to_adc(50.0):.1f} ADC counts", _CSS_MUTED) tl.addWidget(self.lbl_threshold_adc) vl.addWidget(self.grp_threshold) # Background subtraction (v4+ files only) self.chk_bg_sub = QCheckBox("Background subtraction (CH1 only)") self.chk_bg_sub.setChecked(True) self.chk_bg_sub.setEnabled(False) self.chk_bg_sub.setToolTip( "Subtract the stored background waveform from each CH1 frame\n" "before computing the FFT (v4+ files only)." ) 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) self.btn_export_csv = QPushButton("Export Image as CSV…") self.btn_export_csv.setEnabled(False) self.btn_export_csv.setToolTip( "Save the current CH1 image (one scan row per CSV line).") self.btn_export_csv.clicked.connect(self._on_export_csv) vl.addWidget(self.btn_export_csv) panel_layout.addWidget(grp_view) # ---- ROI --------------------------------------------------------- grp_roi, rl = _group("ROI (Region of Interest)") self.btn_draw_roi = QPushButton("Draw ROI") self.btn_draw_roi.setCheckable(True) self.btn_draw_roi.setEnabled(False) self.btn_draw_roi.setToolTip( "Arm next click+drag on the image to draw a new ROI\n" "(replaces any existing one). Click again to cancel.\n" "After drawing, drag inside to move, or grab corners to reshape.\n" "The ROI is persistent across channels / modes / angles." ) self.btn_draw_roi.toggled.connect(self._on_draw_roi_toggled) rl.addWidget(self.btn_draw_roi) self.btn_clear_roi = QPushButton("Clear ROI") self.btn_clear_roi.setEnabled(False) self.btn_clear_roi.clicked.connect(self._on_clear_roi) rl.addWidget(self.btn_clear_roi) self.btn_export_roi = QPushButton("Export ROI as CSV…") self.btn_export_roi.setEnabled(False) self.btn_export_roi.setToolTip( "Save every pixel whose centre lies inside the ROI as CSV.\n" "Columns: row, frame, x_mm, y_mm, value.\n" "Corner coordinates of the quad are written in the file header." ) self.btn_export_roi.clicked.connect(self._on_export_roi_csv) rl.addWidget(self.btn_export_roi) self.lbl_roi_center = _wrap_label("centroid: —", _CSS_HINT) self.lbl_roi_size = _wrap_label("bbox: —", _CSS_HINT) self.lbl_roi_npix = _wrap_label("pixels inside: —", _CSS_HINT) for lbl in (self.lbl_roi_center, self.lbl_roi_size, self.lbl_roi_npix): rl.addWidget(lbl) panel_layout.addWidget(grp_roi) panel_layout.addStretch() return _scroll_panel(panel, _LEFT_PANEL_W) def _build_canvases(self) -> QWidget: splitter = QSplitter(Qt.Orientation.Vertical) splitter.setChildrenCollapsible(False) img_widget = QWidget() img_vl = QVBoxLayout(img_widget) img_vl.setContentsMargins(0, 0, 0, 0) img_vl.setSpacing(4) self.image_canvas = ImageCanvas() self.image_canvas.setMinimumHeight(220) self.image_canvas.pixel_clicked.connect(self._on_pixel_clicked) self.image_canvas.roi_changed.connect(self._update_roi_ui) self.image_canvas.draw_mode_changed.connect(self._on_draw_mode_changed) img_vl.addWidget(NavigationToolbar2QT(self.image_canvas, img_widget)) img_vl.addWidget(self.image_canvas) splitter.addWidget(img_widget) wave_widget = QWidget() wave_vl = QVBoxLayout(wave_widget) wave_vl.setContentsMargins(0, 0, 0, 0) wave_vl.setSpacing(4) self.lbl_wave_hint = QLabel( "Click a pixel in the image above to inspect its waveform.") self.lbl_wave_hint.setAlignment(Qt.AlignmentFlag.AlignCenter) self.lbl_wave_hint.setStyleSheet(_CSS_MUTED) self.wave_canvas = WaveformCanvas() self.wave_canvas.setMinimumHeight(150) wave_vl.addWidget(self.lbl_wave_hint) wave_vl.addWidget(self.wave_canvas) splitter.addWidget(wave_widget) splitter.setStretchFactor(0, 3) splitter.setStretchFactor(1, 1) splitter.setSizes([580, 250]) return splitter def _build_right_panel(self) -> QWidget: # Velocity settings (visible only in velocity mode) self.grp_velocity, vel_l = _group("Velocity Settings (CH1 only)") vel_form = _form() self.spin_grating_um = QDoubleSpinBox() self.spin_grating_um.setRange(0.1, 1000.0) self.spin_grating_um.setDecimals(2) self.spin_grating_um.setSingleStep(0.5) self.spin_grating_um.setSuffix(" µm") self.spin_grating_um.setValue(25) self.spin_grating_um.setEnabled(False) self.spin_grating_um.setMinimumWidth(_SPIN_MIN_W) self.spin_grating_um.editingFinished.connect(self._on_grating_changed) vel_form.addRow("Grating size:", self.spin_grating_um) vel_l.addLayout(vel_form) vel_l.addWidget(_wrap_label("v (m/s) = freq (MHz) × grating (µm)", "font-size: 10px; color: #888;")) self.grp_velocity.setVisible(False) grp_display, dl = _group("Display Options") cmap_form = _form() self.combo_cmap = QComboBox() self.combo_cmap.addItems(CMAPS) self.combo_cmap.setCurrentText("gray") self.combo_cmap.setEnabled(False) self.combo_cmap.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed) self.combo_cmap.currentIndexChanged.connect(self._on_cmap_changed) cmap_form.addRow("Colormap:", self.combo_cmap) dl.addLayout(cmap_form) self.chk_auto = QCheckBox("Auto-scale colormap") self.chk_auto.setChecked(True) self.chk_auto.toggled.connect(self._on_autoscale_toggled) dl.addWidget(self.chk_auto) range_form = _form() for label, attr in (("min:", "spin_vmin"), ("max:", "spin_vmax")): spin = QDoubleSpinBox() spin.setRange(-1e9, 1e9) spin.setDecimals(4) spin.setEnabled(False) spin.setMinimumWidth(_SPIN_MIN_W) spin.editingFinished.connect(self._on_manual_range_changed) setattr(self, attr, spin) range_form.addRow(label, spin) dl.addLayout(range_form) right_panel = QWidget() layout = QVBoxLayout(right_panel) layout.setContentsMargins(0, 0, 0, 0) layout.setSpacing(8) layout.addWidget(self.grp_velocity) layout.addWidget(grp_display) layout.addStretch() return _scroll_panel(right_panel, _RIGHT_PANEL_W) def _build_menus(self): menubar = self.menuBar() fft_menu = menubar.addMenu("&FFT") fft_act = QAction("FFT &Options…", self) fft_act.setStatusTip("Configure FFT backend and zero-padding") fft_act.triggered.connect(self._on_fft_options) fft_menu.addAction(fft_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) self._manual_align_act = QAction("&Manual Alignment…", self) self._manual_align_act.setStatusTip( "Open an interactive dialog to align angles by eye: overlaid CH4 " "threshold masks, keyboard nudge (translate + rotate), auto " "de-rotate to the known scan angles, and save/clear a persistent " "alignment.") self._manual_align_act.setEnabled(False) self._manual_align_act.triggered.connect(self._on_manual_alignment) fusion_menu.addAction(self._manual_align_act) convert_menu = menubar.addMenu("&Convert") self._batch_dc_act = QAction("Batch Compute DC and &Store…", self) self._batch_dc_act.setStatusTip( "Select .sras files and compute+store DC images (CH3/CH4 mean) " "for every angle, converting v6 files to v7 in place.") self._batch_dc_act.triggered.connect(lambda: self._on_batch_compute("dc")) convert_menu.addAction(self._batch_dc_act) self._batch_fft_act = QAction("Batch Compute FFT and Sto&re…", self) self._batch_fft_act.setStatusTip( "Select .sras files and compute+store FFT peak-frequency images " "for every angle, converting v6 files to v7 in place.") self._batch_fft_act.triggered.connect(lambda: self._on_batch_compute("fft")) convert_menu.addAction(self._batch_fft_act) # ------------------------------------------------------------------ # Drag-and-drop # ------------------------------------------------------------------ def dragEnterEvent(self, event): urls = event.mimeData().urls() if urls and urls[0].toLocalFile().lower().endswith(".sras"): event.acceptProposedAction() def dropEvent(self, event): self._load_file(event.mimeData().urls()[0].toLocalFile()) # ------------------------------------------------------------------ # File loading # ------------------------------------------------------------------ def _on_open(self): path, _ = QFileDialog.getOpenFileName( self, "Open SRAS File", "", "SRAS Files (*.sras);;All Files (*)") if path: self._load_file(path) def _load_file(self, path: str): started = self._run_worker( "load", LoadWorker(path), connect=( ("finished", self._on_load_done), ("error", lambda msg: self.statusBar().showMessage(f"Error: {msg}")), ), ) if not started: return self.btn_open.setEnabled(False) self.statusBar().showMessage(f"Loading {Path(path).name}…") self._show_progress("main", f"Loading {Path(path).name}…") def _on_load_done(self, sras): self._close_progress("main") self.btn_open.setEnabled(True) if sras is None: return self._sras = sras self._current_image = None # A manual-alignment dialog bound to the previous file must not # survive a reload — its per-angle state (and the sras it was # constructed against) no longer matches the new file's geometry. if self._manual_align_dialog is not None: self._manual_align_dialog.close() self._manual_align_dialog = None # Caches (and any in-flight DC precompute) belong to the previous # file's geometry — discard and start fresh. Bumping the generation # counters makes any still-running worker's result get dropped when # it lands. self._dc_cache = {} self._fft_cache = {} self._dc_generation += 1 self.lbl_dc_precompute.setText("") 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) # Silently restore a previously-saved manual alignment, if any, so # the work survives closing and reopening the file. sidecar = load_manual_alignment(sras) if sidecar is not None: try: self._alignment_result = build_manual_alignment( sras, sidecar.ref_angle_idx, sidecar.dc_threshold_mv, sidecar.per_angle) self.chk_aligned_view.blockSignals(True) self.chk_aligned_view.setChecked(True) self.chk_aligned_view.blockSignals(False) self.statusBar().showMessage( f"Restored saved manual alignment from " f"{sidecar_path(sras.path).name}") except Exception as exc: # A corrupt/foreign sidecar or a rescan that shrank n_angles # below ref_angle_idx must not block opening the .sras file. self.statusBar().showMessage( f"Could not restore saved alignment: {exc}") # 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() self.lbl_filename.setText(sras.path.name) self.spin_angle.blockSignals(True) self.spin_angle.setRange(0, max(0, sras.n_angles - 1)) self.spin_angle.setValue(0) self.spin_angle.blockSignals(False) # DC channels are cheap and give an instant, fluid overview of a # scan; CH1/Velocity require an FFT per pixel that can take minutes # on a large scan, so don't default to it. self.combo_channel.blockSignals(True) self.combo_channel.setCurrentIndex(CH4_IDX) self.combo_channel.blockSignals(False) self._update_controls_enabled(True) self._on_threshold_changed() # refresh ADC label with file calibration self._on_view_changed() self._start_dc_precompute() # ------------------------------------------------------------------ # Scan info panel # ------------------------------------------------------------------ def _update_scan_info_labels(self): s = self._sras if s is None: return a = self.spin_angle.value() for key, text in ( ("Angles", f"{s.n_angles}"), ("Rows", f"{s.n_rows[a]}"), ("Frames / row", f"{s.n_frames[a]}"), ("Samples / frame", f"{s.samples_per_frame}"), ("Sample rate", f"{s.sample_rate_hz / 1e9:.4g} GS/s"), ("X start", f"{s.x_start_mm[a]:.4g} mm"), ("Pixel Δx", f"{s.pixel_x_mm * 1e3:.3g} µm"), ("Laser freq", f"{s.laser_freq_hz / 1e3:.4g} kHz"), ): self._info[key].setText(f"{key}: {text}") notes = [] if s.frame_count_mismatch: notes.append(f"! Header n_frames={s.n_frames_header}, " f"actual={s.n_frames[a]} (scanner bug — corrected)") if s.scan_aborted: notes.append(f"! Scan aborted: {s.n_angles}/{s.n_angles_declared} " "angles complete") if s.background is not None: notes.append(f"Background waveform: {len(s.background)} samples") if s.version in (6, 7): notes.append("v6/v7 format: rows / frames / x_start are per-angle") n_dc = sum(1 for x in s.precomputed_dc4_mv if x is not None) n_fft = sum(1 for x in s.precomputed_freq_mhz if x is not None) if n_dc or n_fft: bg_note = " (bg-sub)" if s.precomputed_bg_sub else " (no bg-sub)" notes.append( f"Cached images: DC {n_dc}/{s.n_angles} angles, " f"FFT {n_fft}/{s.n_angles} angles{bg_note if n_fft else ''} " "— display is instant for cached angles") elif s.version == 7: notes.append("v7 format: no cache blocks stored yet") self.lbl_frame_warn.setText("\n".join(notes)) # ------------------------------------------------------------------ # Controls # ------------------------------------------------------------------ def _update_controls_enabled(self, enabled: bool): s = self._sras has_file = enabled and s is not None ch_idx = self.combo_channel.currentIndex() is_ch1 = enabled and ch_idx in CH1_DERIVED_MODES is_vel = enabled and ch_idx == VELOCITY_MODE_IDX self.spin_angle.setEnabled(has_file and s.n_angles > 1) self.combo_channel.setEnabled(enabled) self.combo_cmap.setEnabled(enabled) self.chk_auto.setEnabled(enabled) manual = enabled and not self.chk_auto.isChecked() self.spin_vmin.setEnabled(manual) self.spin_vmax.setEnabled(manual) # Threshold and bg-sub apply to all CH1 modes self.spin_threshold_mv.setEnabled(is_ch1) self.chk_bg_sub.setEnabled(has_file and s.background is not None and is_ch1) self.spin_grating_um.setEnabled(is_vel) self.grp_velocity.setVisible(is_vel) self.btn_export_csv.setEnabled(is_ch1 and self._current_image is not None) # ROI: always usable once a file is loaded (independent of channel) self.btn_draw_roi.setEnabled(has_file) # Batch Convert actions pick their own files, independent of # whatever's currently open — only gated on no batch already running. can_batch = not self._job_running("batch") self._batch_dc_act.setEnabled(can_batch) self._batch_fft_act.setEnabled(can_batch) self._alignment_act.setEnabled( has_file and s.n_angles > 1 and not self._job_running("align")) self._manual_align_act.setEnabled( has_file and s.n_angles > 1 and not self._job_running("align")) self.chk_aligned_view.setEnabled(enabled and self._alignment_result is not None) self._update_roi_ui() def _on_channel_changed(self): self._update_controls_enabled(self._sras is not None) self._on_view_changed() def _on_bg_sub_toggled(self): # Background subtraction changes the FFT input, so it genuinely # invalidates the cached raw FFT (the cache key includes it) — # _refresh_display() recomputes only on a miss for the new state. if self._sras is not None and self.combo_channel.currentIndex() in CH1_DERIVED_MODES: self._refresh_display() def _on_grating_changed(self): # Grating is a pure post-multiply on the cached frequency image — # never needs a recompute. if self._sras is not None and self.combo_channel.currentIndex() == VELOCITY_MODE_IDX: self._refresh_display() def _on_threshold_changed(self): mv = self.spin_threshold_mv.value() cal = (self._sras.cal(CH4_IDX) if self._sras is not None else (_FALLBACK_YMULT_MV, _FALLBACK_YOFF_ADC, 0.0)) self.lbl_threshold_adc.setText(f"≈ {mv_to_adc(mv, *cal):.1f} ADC counts") # Threshold decides which pixels get an FFT at all, so changing it is # a genuine cache-key change — but the recompute reuses the cached DC4 # image to skip masked-out pixels. if self._sras is not None and self.combo_channel.currentIndex() in CH1_DERIVED_MODES: self._refresh_display() def _on_autoscale_toggled(self, checked: bool): manual = not checked self.spin_vmin.setEnabled(manual and self._sras is not None) self.spin_vmax.setEnabled(manual and self._sras is not None) if self._sras is not None and self._current_image is not None: self._redraw_image(self._current_image) def _on_manual_range_changed(self): if not self.chk_auto.isChecked() and self._current_image is not None: self._redraw_image(self._current_image) def _on_cmap_changed(self): # Colormap is purely how the existing image is rendered. if self._current_image is not None: self._redraw_image(self._current_image) def _on_view_changed(self): if self._sras is None: return idx = self.spin_angle.value() self.lbl_angle_deg.setText(f"({self._sras.angles_deg[idx]:.1f}°)") self._update_scan_info_labels() self._refresh_display() def _on_aligned_view_toggled(self, checked: bool): if self._current_image is not None: self._redraw_image(self._current_image) # ------------------------------------------------------------------ # CSV export # ------------------------------------------------------------------ def _on_export_csv(self): if self._current_image is None or self._sras is None: return default_name = (f"{self._sras.path.stem}_angle{self._current_angle}" f"_{CH_NAMES[self._current_ch]}.csv") path, _ = QFileDialog.getSaveFileName( self, "Export Image as CSV", str(self._sras.path.parent / default_name), "CSV files (*.csv);;All files (*)") if not path: return np.savetxt(path, self._current_image, delimiter=",", fmt="%.6g") self.statusBar().showMessage(f"Exported {Path(path).name}") def _on_export_roi_csv(self): if self._current_image is None or self._sras is None: return roi = self.image_canvas.get_roi() if roi is None: self.statusBar().showMessage("No ROI — draw one first") return s = self._sras x_axis = s.x_axis_mm(self._current_angle) y_axis = s.y_positions_mm(self._current_angle) mask = roi.mask_for_grid(x_axis, y_axis) if not mask.any(): self.statusBar().showMessage("ROI does not overlap any pixel") return img = self._current_image if img.shape != mask.shape: self.statusBar().showMessage( f"ROI shape {mask.shape} does not match image {img.shape}") return X, Y = np.meshgrid(np.asarray(x_axis, dtype=np.float64), np.asarray(y_axis, dtype=np.float64)) rows_idx, frames_idx = np.where(mask) n_pix = int(mask.sum()) ch_name = CH_NAMES[self._current_ch] angle = self._current_angle default_name = f"{s.path.stem}_angle{angle}_{ch_name}_ROI.csv" path, _ = QFileDialog.getSaveFileName( self, "Export ROI as CSV", str(s.path.parent / default_name), "CSV files (*.csv);;All files (*)") if not path: return corners_str = " ".join(f"({p[0]:.6g},{p[1]:.6g})" for p in roi.corners()) header = ( f"# ROI quad corners (BL BR TR TL) mm: {corners_str}\n" f"# source: {s.path.name}, channel={ch_name}, " f"angle_idx={angle}, angle_deg={s.angles_deg[angle]:.4g}\n" f"# n_pixels={n_pix}\n" "row,frame,x_mm,y_mm,value" ) data = np.column_stack([ rows_idx.astype(np.int64), frames_idx.astype(np.int64), X[mask], Y[mask], img[mask].astype(np.float64), ]) # integer columns first, floats after — use a per-column format list np.savetxt(path, data, delimiter=",", fmt=["%d", "%d", "%.6g", "%.6g", "%.6g"], header=header, comments="") self.statusBar().showMessage( f"Exported ROI ({n_pix} pixels) to {Path(path).name}") # ------------------------------------------------------------------ # ROI # ------------------------------------------------------------------ def _on_draw_roi_toggled(self, checked: bool): if checked: self.image_canvas.start_drawing() self.statusBar().showMessage( "Click and drag on the image to draw a new rectangle.") else: self.image_canvas.cancel_drawing() def _on_draw_mode_changed(self, active: bool): # Keep the toggle button's visual state in sync with the canvas. self.btn_draw_roi.blockSignals(True) self.btn_draw_roi.setChecked(active) self.btn_draw_roi.blockSignals(False) def _on_clear_roi(self): self.image_canvas.clear_roi() self.statusBar().showMessage("ROI cleared") def _update_roi_ui(self): roi = self.image_canvas.get_roi() if roi is None: self.lbl_roi_center.setText("centroid: —") self.lbl_roi_size.setText("bbox: —") self.lbl_roi_npix.setText("pixels inside: —") self.btn_clear_roi.setEnabled(False) self.btn_export_roi.setEnabled(False) return cen = roi.centroid() bbox = roi.bbox_size() self.lbl_roi_center.setText(f"centroid: ({cen[0]:.3f}, {cen[1]:.3f}) mm") self.lbl_roi_size.setText(f"bbox: {bbox[0]:.3f} × {bbox[1]:.3f} mm") 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()) except Exception: npix = 0 self.lbl_roi_npix.setText(f"pixels inside: {npix}") self.btn_clear_roi.setEnabled(True) self.btn_export_roi.setEnabled(self._current_image is not None and npix > 0) # ------------------------------------------------------------------ # Display # ------------------------------------------------------------------ def _current_n_fft(self) -> int | None: if self._fft_pad_factor <= 1 or self._sras is None: return None return self._sras.samples_per_frame * self._fft_pad_factor def _scale_for_display(self, freq_mhz: np.ndarray, ch_idx: int) -> np.ndarray: """Velocity is a pure post-multiply of the (already DC-masked) cached frequency image — never worth a recompute on its own.""" if ch_idx == VELOCITY_MODE_IDX: return freq_mhz * self.spin_grating_um.value() return freq_mhz def _fft_cache_key(self, angle_idx: int) -> tuple: return (angle_idx, self.chk_bg_sub.isChecked(), self._current_n_fft(), self.spin_threshold_mv.value()) 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 (*self._fft_cache_key(angle_idx), ch_idx, 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 return (r.canvas_origin_mm[0] + np.arange(n_cols) * r.canvas_dx_mm, r.canvas_origin_mm[1] + np.arange(n_rows) * r.canvas_dy_mm) 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 background compute (with progress popup) when genuinely nothing is cached yet.""" if self._sras is None: return angle_idx = self.spin_angle.value() ch_idx = self.combo_channel.currentIndex() if ch_idx in CH1_DERIVED_MODES: raw = self._fft_cache.get(self._fft_cache_key(angle_idx)) if raw is not None: self._show_image_now(self._scale_for_display(raw, ch_idx), angle_idx, ch_idx) return else: cached = self._dc_cache.get((angle_idx, ch_idx)) if cached is not None: self._show_image_now(cached, angle_idx, ch_idx) return # Nothing cached for these settings — need a real compute. Changing # the DC threshold changes *which* pixels get an FFT at all, so it # can't be satisfied from the cache — but with the DC map already # known, the recompute skips the FFT for masked-out pixels. self._start_compute() def _show_image_now(self, img: np.ndarray, angle_idx: int, ch_idx: int): """Display an already-available image with no compute involved.""" self._current_image = img self._current_angle = angle_idx self._current_ch = ch_idx self.btn_export_csv.setEnabled(ch_idx in CH1_DERIVED_MODES) self._redraw_image(img) self._update_roi_ui() def _redraw_image(self, img: np.ndarray): s = self._sras angle_idx = self._current_angle ch_idx = self._current_ch 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 extent = [x_axis[0] - dx / 2, x_axis[-1] + dx / 2, y_axis[-1] + dy / 2, y_axis[0] - dy / 2] if self.chk_auto.isChecked(): 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) spin.blockSignals(False) else: vmin, vmax = self.spin_vmin.value(), self.spin_vmax.value() angle_deg = s.angles_deg[angle_idx] mode_str, unit, colorbar_label = _CHANNEL_DISPLAY[ch_idx] if ch_idx == VELOCITY_MODE_IDX: ch_label = f"Velocity [grating={self.spin_grating_um.value():.2f} µm]" else: ch_label = CH_LABELS[ch_idx] title = f"{CH_NAMES[ch_idx]} | {mode_str} | {angle_deg:.1f}°" if aligned: title += " [Aligned]" self.image_canvas.show_image( display_img, extent, cmap=self.combo_cmap.currentText(), vmin=vmin, vmax=vmax, xlabel="X (mm)", ylabel="Y (mm)", title=title, colorbar_label=colorbar_label, ) self.statusBar().showMessage( f"{s.path.name} | {ch_label} @ {angle_deg:.1f}° " f"| {display_img.shape[1]} × {display_img.shape[0]} px | {unit}" f"{' | Aligned' if aligned else ''}" ) # ------------------------------------------------------------------ # Background compute (only reached on a genuine cache miss) # ------------------------------------------------------------------ def _start_compute(self): if self._sras is None or self._job_running("compute"): return # re-checked when the running compute finishes angle_idx = self.spin_angle.value() ch_idx = self.combo_channel.currentIndex() is_fft = ch_idx in CH1_DERIVED_MODES self._pending_angle = angle_idx self._pending_ch = ch_idx self._pending_bg_sub = self.chk_bg_sub.isChecked() self._pending_threshold = self.spin_threshold_mv.value() self._pending_fft_pad_factor = self._fft_pad_factor worker = ComputeWorker( self._sras, angle_idx, ch_idx, apply_bg_sub=self._pending_bg_sub, n_fft=self._current_n_fft(), dc_threshold_mv=self._pending_threshold, # Reuse the cached DC4 image (if the precompute has reached this # angle) so the FFT skips masked-out pixels entirely and doesn't # need to re-read the CH4 channel from disk. dc4_mv=self._dc_cache.get((angle_idx, CH4_IDX)), is_fft_mode=is_fft, ) if not self._run_worker( "compute", worker, connect=( ("finished", self._on_compute_done), ("error", lambda msg: self.statusBar().showMessage( f"Compute error: {msg}")), ), on_done=self._after_compute): return if is_fft: self.statusBar().showMessage("Computing FFT…") self._show_progress( "main", f"Computing FFT for angle {angle_idx}…\n" "This can take a while on a large scan — result is cached " "so revisiting this angle/mode/threshold will be instant.") else: self.statusBar().showMessage("Computing DC image…") self._show_progress("main", f"Computing DC image for angle {angle_idx}…") def _after_compute(self): """If settings changed while the compute was running, re-dispatch through the cache-aware path — the now-current combination may already be cached.""" if (self.spin_angle.value(), self.combo_channel.currentIndex(), self.chk_bg_sub.isChecked(), self.spin_threshold_mv.value(), self._fft_pad_factor) != ( self._pending_angle, self._pending_ch, self._pending_bg_sub, self._pending_threshold, self._pending_fft_pad_factor): self._refresh_display() def _on_compute_done(self, result): self._close_progress("main") if result is None: return # cancelled mid-compute; the partial image must not cache angle_idx = self._pending_angle ch_idx = self._pending_ch if ch_idx in CH1_DERIVED_MODES: self._fft_cache[(angle_idx, self._pending_bg_sub, self._current_n_fft(), self._pending_threshold)] = result img = self._scale_for_display(result, ch_idx) else: img = result self._dc_cache[(angle_idx, ch_idx)] = img self._show_image_now(img, angle_idx, ch_idx) # ------------------------------------------------------------------ # Background DC precompute (all angles, so switching is fluid) # ------------------------------------------------------------------ def _start_dc_precompute(self): if self._sras is None: return generation = self._dc_generation n_angles = self._sras.n_angles worker = DcPrecomputeWorker(self._sras) self._dc_precompute_worker = worker started = self._run_worker( "dc_precompute", worker, connect=( ("angle_done", lambda a, dc3, dc4, g=generation: self._on_dc_precompute_angle_done(g, a, dc3, dc4, n_angles)), ("error", lambda msg: self.statusBar().showMessage( f"DC precompute error: {msg}", 5000)), ), quit_on=("finished", "error"), on_done=lambda: setattr(self, "_dc_precompute_worker", None), ) if not started: self._dc_precompute_worker = None def _on_dc_precompute_angle_done(self, generation: int, angle_idx: int, dc3_mv: np.ndarray, dc4_mv: np.ndarray, n_angles: int): if generation != self._dc_generation: return # stale result from a previously-loaded file — discard self._dc_cache[(angle_idx, CH3_IDX)] = dc3_mv self._dc_cache[(angle_idx, CH4_IDX)] = dc4_mv done = sum(1 for a in range(n_angles) if (a, CH4_IDX) in self._dc_cache) self.lbl_dc_precompute.setText( f"Precomputing DC images: {done}/{n_angles} angles ready…" if done < n_angles else "DC images ready for all angles.") # If we just finished the angle/channel the user is currently looking # at and it wasn't shown yet (they switched here before the precompute # caught up and are still waiting), show it now. current_ch = self.combo_channel.currentIndex() if (angle_idx == self.spin_angle.value() and not self._job_running("compute") and current_ch in (CH3_IDX, CH4_IDX) and (self._current_angle != angle_idx or self._current_ch != current_ch)): self._refresh_display() # ------------------------------------------------------------------ # Pixel inspector # ------------------------------------------------------------------ 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, n_frames_a = self._sras.image_shape(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() if self._current_ch in CH1_DERIVED_MODES: self.wave_canvas.show_rf_waveform( 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, angle_idx, self._current_ch, row_idx, frame_idx) # ------------------------------------------------------------------ # Progress dialogs # ------------------------------------------------------------------ def _show_progress(self, key: str, message: str, maximum: int = 0): """Show (or relabel) the progress dialog under *key*. maximum=0 gives an indeterminate busy indicator.""" dlg = self._progress_dlgs.get(key) if dlg is not None: dlg.setLabelText(message) return dlg = QProgressDialog(message, "", 0, maximum, self) dlg.setWindowTitle("Please wait…") dlg.setCancelButton(None) dlg.setWindowModality(Qt.WindowModality.WindowModal) dlg.setMinimumDuration(300) # only appears if it takes > 300 ms dlg.show() self._progress_dlgs[key] = dlg def _set_progress(self, key: str, pct: int): dlg = self._progress_dlgs.get(key) if dlg is not None: dlg.setValue(pct) def _close_progress(self, key: str): dlg = self._progress_dlgs.pop(key, None) if dlg is not None: dlg.close() # ------------------------------------------------------------------ # Convert menu: batch DC/FFT compute-and-store (v6 -> v7) # ------------------------------------------------------------------ def _on_batch_compute(self, mode: str): if self._job_running("batch"): return label = "DC" if mode == "dc" else "FFT" paths, _ = QFileDialog.getOpenFileNames( self, f"Select .sras files to batch-compute {label}", "", "SRAS files (*.sras);;All files (*)") if not paths: return self._batch_errors = [] worker = BatchCacheWorker(paths, mode, self.chk_bg_sub.isChecked()) started = self._run_worker( "batch", worker, connect=( ("progress", lambda pct: self._set_progress("batch", pct)), ("file_done", self._on_batch_file_done), ("finished", lambda p=paths: self._on_batch_finished(p)), ), on_done=self._after_batch, ) if not started: return # a second trigger snuck in while the file dialog was open self._batch_dc_act.setEnabled(False) self._batch_fft_act.setEnabled(False) self._show_progress( "batch", f"Batch computing {label} for {len(paths)} file(s)…", maximum=100) def _on_batch_file_done(self, path: str, err: str): if err: self._batch_errors.append(f"{Path(path).name} — {err}") self._show_progress("batch", f"Processed {Path(path).name}…") def _on_batch_finished(self, paths: list[str]): self._close_progress("batch") n_total = len(paths) n_failed = len(self._batch_errors) n_ok = n_total - n_failed if n_failed: summary = (f"Batch store: {n_ok}/{n_total} file(s) updated, " f"{n_failed} failed: {'; '.join(self._batch_errors)}") else: summary = f"Batch store: {n_ok}/{n_total} file(s) updated." self.statusBar().showMessage(summary) self._batch_errors = [] # If the currently-open file was in this batch, reload it so the GUI # picks up the newly-written v7 cache instead of stale state. if self._sras is not None and str(self._sras.path) in paths: self._load_file(str(self._sras.path)) def _after_batch(self): self._batch_dc_act.setEnabled(True) self._batch_fft_act.setEnabled(True) # ------------------------------------------------------------------ # Fusion: angle alignment # ------------------------------------------------------------------ def _on_angle_alignment(self): if self._sras is None or self._sras.n_angles <= 1: return ref_idx = 0 threshold_mv = self.spin_threshold_mv.value() generation = self._alignment_generation started = self._run_worker( "align", AngleAlignmentWorker(self._sras, ref_idx, threshold_mv), connect=( ("progress", lambda pct: self._set_progress("main", pct)), ("finished", lambda result, err, g=generation: self._on_alignment_done(g, result, err)), ), on_done=lambda: self._update_controls_enabled(self._sras is not None), ) if not started: return self._alignment_act.setEnabled(False) self._show_progress( "main", f"Computing angle alignment ({self._sras.n_angles} angles, " f"ref=angle 0, CH4 mask ≥ {threshold_mv:.3f} mV)…", maximum=100) def _on_alignment_done(self, generation: int, result, error_msg: str): self._close_progress("main") 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() # ------------------------------------------------------------------ # Fusion: manual alignment # ------------------------------------------------------------------ def _on_manual_alignment(self): if self._sras is None or self._sras.n_angles <= 1: return if self._manual_align_dialog is not None: self._manual_align_dialog.raise_() self._manual_align_dialog.activateWindow() return ref_idx = 0 threshold_mv = self.spin_threshold_mv.value() seed: dict[int, ManualAngleParams] = {} if (self._alignment_result is not None and self._alignment_result.ref_angle_idx == ref_idx): seed = {a: ManualAngleParams(t.rotation_deg, t.shift_mm) for a, t in self._alignment_result.per_angle.items()} threshold_mv = self._alignment_result.dc_threshold_mv else: sidecar = load_manual_alignment(self._sras) if sidecar is not None and sidecar.ref_angle_idx == ref_idx: seed = dict(sidecar.per_angle) threshold_mv = sidecar.dc_threshold_mv cached_dc4 = {a: img for (a, ch), img in self._dc_cache.items() if ch == CH4_IDX} dlg = ManualAlignmentDialog( self, self._sras, ref_angle_idx=ref_idx, dc_threshold_mv=threshold_mv, seed_per_angle=seed, cached_dc4_mv=cached_dc4) dlg.alignment_saved.connect(self._on_manual_alignment_saved) dlg.alignment_cleared.connect(self._on_manual_alignment_cleared) dlg.finished.connect(self._on_manual_align_dialog_closed) dlg.setAttribute(Qt.WidgetAttribute.WA_DeleteOnClose) self._manual_align_dialog = dlg dlg.show() def _on_manual_align_dialog_closed(self, _result_code: int): self._manual_align_dialog = None def _on_manual_alignment_saved(self, result, sidecar_path_str: str): self._alignment_result = result self._aligned_cache = {} self._alignment_generation += 1 self.chk_aligned_view.setEnabled(True) self.chk_aligned_view.blockSignals(True) self.chk_aligned_view.setChecked(True) self.chk_aligned_view.blockSignals(False) self._update_controls_enabled(self._sras is not None) self.statusBar().showMessage( f"Manual alignment saved to {Path(sidecar_path_str).name}") if self._current_image is not None: self._refresh_display() def _on_manual_alignment_cleared(self): 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) self._update_controls_enabled(self._sras is not None) self.statusBar().showMessage("Manual alignment cleared.") if self._current_image is not None: self._refresh_display() # ------------------------------------------------------------------ # FFT Options # ------------------------------------------------------------------ def _on_fft_options(self): dlg = FftOptionsDialog( self, current_backend=compute.get_fft_backend(), current_pad_factor=self._fft_pad_factor, samples_per_frame=self._sras.samples_per_frame if self._sras else None, sample_rate_hz=self._sras.sample_rate_hz if self._sras else None, grating_um=self.spin_grating_um.value(), ) if dlg.exec() != QDialog.DialogCode.Accepted: return compute.set_fft_backend(dlg.get_backend()) self._fft_pad_factor = dlg.get_pad_factor() # Pad factor changes the FFT bin count, so it genuinely invalidates # the cached raw FFT (part of the cache key) — _refresh_display() # recomputes only on a cache miss. if self._sras is not None and self.combo_channel.currentIndex() in CH1_DERIVED_MODES: self._refresh_display() # ------------------------------------------------------------------ def closeEvent(self, event): if self._manual_align_dialog is not None: self._manual_align_dialog.close() # Signal every cancellable worker first, then wait. Waiting without # signalling means sitting out whatever is in flight — on a large # scan a single angle is ~40 s. jobs = list(self._jobs.values()) for _thread, worker, _on_done in jobs: stop = getattr(worker, "stop", None) if callable(stop): stop() for thread, _worker, _on_done in jobs: thread.quit() thread.wait(5000) super().closeEvent(event) # --------------------------------------------------------------------------- def main(): app = QApplication(sys.argv) window = SrasViewerWindow( initial_path=sys.argv[1] if len(sys.argv) > 1 else None) window.show() sys.exit(app.exec()) if __name__ == "__main__": main()