"""The SrasViewerWindow main window and application entry point.""" import sys from pathlib import Path import numpy as np from matplotlib.backends.backend_qtagg import NavigationToolbar2QT from PyQt6.QtCore import QObject, QSettings, QSignalBlocker, Qt, QThread from PyQt6.QtGui import QAction from PyQt6.QtWidgets import ( QApplication, QCheckBox, QComboBox, QDialog, QFileDialog, QFrame, QHBoxLayout, QLabel, QMainWindow, QProgressDialog, QPushButton, QSizePolicy, QSpinBox, QSplitter, QVBoxLayout, QWidget, ) import sras_compute as compute from sras_compute import ( ManualAngleParams, apply_alignment, build_manual_alignment, load_manual_alignment, sidecar_path, ) from sras_format import ( CH3_IDX, CH4_IDX, CH_NAMES, SrasFile, mv_to_adc, _FALLBACK_YMULT_MV, _FALLBACK_YOFF_ADC, ) from sras_workers import ( AngleAlignmentWorker, BatchCacheWorker, ComputeWorker, DcPrecomputeWorker, LoadWorker, ) from .canvases import ImageCanvas, WaveformCanvas from .common import ( CH1_DERIVED_MODES, CH_LABELS, CMAPS, VELOCITY_MODE_IDX, _CHANNEL_DISPLAY, _CSS_BUSY, _axes_extent, _CSS_HINT, _CSS_INFO, _CSS_MUTED, _CSS_WARN, _LEFT_PANEL_W, _RIGHT_PANEL_W, Jobs, _form, _group, _make_dspin, _scroll_panel, _wrap_label, ) from .dialogs import FftOptionsDialog, ManualAlignmentDialog # --------------------------------------------------------------------------- # 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, persisted across # sessions). IniFormat: predictable cross-platform and redirectable # in tests. self._settings = QSettings(QSettings.Format.IniFormat, QSettings.Scope.UserScope, "sras-viewer", "sras-viewer") compute.set_fft_backend(str(self._settings.value("fft/backend", "scipy"))) try: pad = int(self._settings.value("fft/pad_factor", 1)) except (TypeError, ValueError): pad = 1 self._fft_pad_factor: int = max(1, min(256, pad)) # 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: they come straight from the file's stored # cache when Batch Compute DC has been run for it (see # _stored_dc_image), and are otherwise precomputed for every angle # in the background right after load. CH1/Velocity FFT images come # from the file's own stored cache when Batch Compute FFT has been # run for it (see _stored_fft_image), and are otherwise 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. Either way the result is # 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_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) panel_layout.addWidget(self._build_file_group()) panel_layout.addWidget(self._build_info_group()) panel_layout.addWidget(self._build_view_group()) panel_layout.addWidget(self._build_roi_group()) panel_layout.addStretch() return _scroll_panel(panel, _LEFT_PANEL_W) def _build_file_group(self) -> QWidget: 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) return grp_file def _build_info_group(self) -> QWidget: 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) return grp_info def _build_view_group(self) -> QWidget: 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) # Keyboard tracking off is what makes valueChanged safe to act on: it # stops the signal firing per keystroke, so typing "12" is one change # to angle 12 (on Return or focus-out) rather than a trip to angle 1 # first. Arrow clicks and the wheel still emit immediately, which # editingFinished alone did not — that is why stepping the angle used # to leave the plot on the previous one until the box lost focus. self.spin_angle.setKeyboardTracking(False) self.spin_angle.valueChanged.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 = _make_dspin(-500.0, 500.0, 3, suffix=" mV", value=50.0, step=0.025) self.spin_threshold_mv.setEnabled(False) 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) return grp_view def _build_roi_group(self) -> QWidget: 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) return grp_roi 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 = _make_dspin(0.1, 1000.0, 2, suffix=" µm", value=25, step=0.5) self.spin_grating_um.setEnabled(False) 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 = _make_dspin(-1e9, 1e9, 4) spin.setEnabled(False) 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. Stored " "images are natural-resolution (pad 1); padded views compute live.") 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( Jobs.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._apply_alignment_result(None, view_checked=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._apply_alignment_result( build_manual_alignment( sras, sidecar.ref_angle_idx, sidecar.dc_threshold_mv, sidecar.per_angle), view_checked=True) 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) with QSignalBlocker(self.spin_angle): self.spin_angle.setRange(0, max(0, sras.n_angles - 1)) self.spin_angle.setValue(0) # 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. with QSignalBlocker(self.combo_channel): self.combo_channel.setCurrentIndex(CH4_IDX) 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)" pad_note = (f", pad {s.precomputed_pad_factor}x" if n_fft and s.precomputed_pad_factor > 1 else "") notes.append( f"Cached images: DC {n_dc}/{s.n_angles} angles, " f"FFT {n_fft}/{s.n_angles} angles" f"{bg_note + pad_note if n_fft else ''} " "— display is instant for cached angles") elif s.version == 7: notes.append("v7 format: no cache blocks stored yet") # A stored FFT cache the current settings can't read back is the one # failure here with no other symptom: the images are right there in # the file and every angle still recomputes. Say why. if n_fft: reasons = [] if s.precomputed_pad_factor != self._fft_pad_factor: reasons.append(f"stored at pad {s.precomputed_pad_factor}x, " f"FFT Options is set to {self._fft_pad_factor}x") if s.precomputed_bg_sub != (self.chk_bg_sub.isChecked() and s.background is not None): reasons.append("stored with bg-sub " f"{'on' if s.precomputed_bg_sub else 'off'}") if reasons: notes.append(f"! Cached FFT unusable as configured ({'; '.join(reasons)})" " — CH1/Velocity will recompute. Re-run Convert -> " "Batch Compute FFT to cache at the current settings.") 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(Jobs.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(Jobs.ALIGN)) self._manual_align_act.setEnabled( has_file and s.n_angles > 1 and not self._job_running(Jobs.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. # It can also decide whether the file's stored cache is readable, so # the info panel's verdict on that has to be redrawn with it. self._update_scan_info_labels() if self._is_fft_mode(): 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._is_fft_mode(): 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. with QSignalBlocker(self.btn_draw_roi): self.btn_draw_roi.setChecked(active) 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 _cached_fft_pad_factor(self) -> int | None: """The pad factor the open file's stored FFT images were computed at, or None if it has none stored.""" if self._sras is None or not any(x is not None for x in self._sras.precomputed_freq_mhz): return None return self._sras.precomputed_pad_factor def _is_fft_mode(self) -> bool: """Is the selected channel an FFT-derived (CH1/Velocity) mode?""" return (self._sras is not None and self.combo_channel.currentIndex() in CH1_DERIVED_MODES) 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 _stored_fft_image(self, angle_idx: int) -> np.ndarray | None: """The file's own batch-computed FFT image for this angle, masked for the current threshold — or None if it can't serve the current settings. Batch Compute FFT stores a peak-frequency image per angle in the file itself, and the whole point of paying for that once is that display is then instant. Without this check the viewer only ever found the stored image deep inside ComputeWorker, so every angle change after a batch still dispatched a background job behind a "Computing FFT…" popup for an image that was already sitting on disk. """ img = compute.cached_rf_image( self._sras, angle_idx, dc_threshold_mv=self.spin_threshold_mv.value(), apply_bg_sub=self.chk_bg_sub.isChecked(), n_fft=self._current_n_fft(), dc4_mv=self._dc_cache.get((angle_idx, CH4_IDX)), # Masking is a copy plus a comparison, but *reading* CH4 to build # the mask is a whole-channel read — that case belongs on a worker, # so it returns None here and falls through to _start_compute. allow_dc_recompute=False) if img is not None: self._fft_cache[self._fft_cache_key(angle_idx)] = img return img def _stored_dc_image(self, angle_idx: int, ch_idx: int) -> np.ndarray | None: """The file's own batch-computed DC image for (angle, channel), if it has one — the CH3/CH4 half of _stored_fft_image. The worker this saves would have handed back the very same stored array (dc_image_mv prefers it over recomputing), so all it ever cost was a thread and a progress popup — but that is exactly what made "Batch Compute DC and Store" look like it had done nothing. """ img = self._sras.cached_dc_mv(angle_idx, ch_idx) if img is not None: self._dc_cache[(angle_idx, ch_idx)] = img return img 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 None: raw = self._stored_fft_image(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 None: cached = self._stored_dc_image(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 = _axes_extent(x_axis, y_axis, dx, dy) 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)): with QSignalBlocker(spin): spin.setValue(val) 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(Jobs.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( Jobs.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._run_worker( Jobs.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"), ) 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(Jobs.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(Jobs.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 = [] # Cache at the pad factor currently configured, not a fixed pad 1 — # a cache stored at any other padding is one this viewer can never # read back (see _stored_fft_image). worker = BatchCacheWorker(paths, mode, self.chk_bg_sub.isChecked(), self._fft_pad_factor) started = self._run_worker( Jobs.BATCH, worker, connect=( ("progress", lambda pct: self._set_progress(Jobs.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( Jobs.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(Jobs.BATCH, f"Processed {Path(path).name}…") def _on_batch_finished(self, paths: list[str]): self._close_progress(Jobs.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( Jobs.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 # No generation bump: this result *is* the current generation's. self._apply_alignment_result(result, view_checked=True, bump_generation=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] = {} # Seed only from a previously *saved manual* alignment (this dialog's # own Save also writes this sidecar) -- never from self._alignment_result # when it holds the automatic Fusion -> Angle Alignment's output. That # path's translation comes from FFT phase correlation, which is the # very thing manual mode exists to work around; inheriting it here # would silently reintroduce the same bad translations under a # "manual" label, on top of the (correct) analytic rotation, which is # exactly what makes manual mode look like it "still does the same # thing" the automatic one does. 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 _apply_alignment_result(self, result, *, view_checked: bool, bump_generation: bool = True): """Install (or clear, with result=None) the active alignment: reset the aligned-image cache and set the Aligned View checkbox without firing its change signal.""" self._alignment_result = result self._aligned_cache = {} if bump_generation: self._alignment_generation += 1 with QSignalBlocker(self.chk_aligned_view): self.chk_aligned_view.setChecked(view_checked) self.chk_aligned_view.setEnabled(result is not None) def _manual_alignment_changed(self, result, message: str): self._apply_alignment_result(result, view_checked=result is not None) self._update_controls_enabled(self._sras is not None) self.statusBar().showMessage(message) if self._current_image is not None: self._refresh_display() def _on_manual_alignment_saved(self, result, sidecar_path_str: str): self._manual_alignment_changed( result, f"Manual alignment saved to {Path(sidecar_path_str).name}") def _on_manual_alignment_cleared(self): self._manual_alignment_changed(None, "Manual alignment cleared.") # ------------------------------------------------------------------ # 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(), cached_pad_factor=self._cached_fft_pad_factor(), ) if dlg.exec() != QDialog.DialogCode.Accepted: return compute.set_fft_backend(dlg.get_backend()) self._fft_pad_factor = dlg.get_pad_factor() self._settings.setValue("fft/backend", compute.get_fft_backend()) self._settings.setValue("fft/pad_factor", self._fft_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. It also decides whether the file's # stored cache can be read back at all, which the info panel reports. self._update_scan_info_labels() if self._is_fft_mode(): 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())