Merge branch 'feature/batch-export-images' into main

Adds Export -> Batch Export Images... (see 6976cbf for details), plus
the small correctness fixes bundled in that commit.

sras_average.py

@@ -54,8 +54,13 @@ def average_rows(block: np.ndarray, n: int, discard_remainder: bool) -> np.ndarr
     """Average every N frames of one angle's (n_rows, n_ch, n_frames, spf)
     block. Returns int16 of shape (n_rows, n_ch, n_out, spf).
 
-    Averaging is done in float32 and rounded on cast, matching numpy's mean
+    Cast to native int16 (not float32) before calling .mean(): numpy's mean()
-    followed by an int16 cast in the original implementation.
+    uses a float64 accumulator by default for integer input, matching the
+    original implementation exactly (which kept the whole file as int16 and
+    called .mean() directly). A float32 cast here would use a float32
+    accumulator instead — for large group sizes that can round the sum
+    differently than float64 and, after the int16 cast below, occasionally
+    land on a value 1 ADC count away from the original tool's output.
     """
     n_frames = block.shape[2]
     n_full = n_frames // n
@@ -63,11 +68,11 @@ def average_rows(block: np.ndarray, n: int, discard_remainder: bool) -> np.ndarr
 
     parts = []
     if n_full:
-        full = block[:, :, :n_full * n, :].astype(np.float32)
+        full = block[:, :, :n_full * n, :].astype(np.int16)
         full = full.reshape(block.shape[0], block.shape[1], n_full, n, block.shape[3])
         parts.append(full.mean(axis=3).astype(np.int16))
     if remainder and not discard_remainder:
-        tail = block[:, :, n_full * n:, :].astype(np.float32)
+        tail = block[:, :, n_full * n:, :].astype(np.int16)
         parts.append(tail.mean(axis=2, keepdims=True).astype(np.int16))
 
     if not parts:

sras_compute.py

@@ -266,13 +266,19 @@ def compute_rf_image(sras: SrasFile, angle_idx: int,
         budget=budget)
     background = sras.background if (apply_bg_sub and sras.background is not None) else None
     cal4 = sras.cal(CH4_IDX)
+    # DC4 mask source, in the same priority order as the fast path above:
+    # already-cached DC block (skips reading CH4 raw waveforms entirely),
+    # then the caller-supplied image, else recompute per chunk below.
+    dc4_full = sras.cached_dc_mv(angle_idx, CH4_IDX) if dc_threshold_mv is not None else None
+    if dc4_full is None:
+        dc4_full = dc4_mv
 
     def chunk(r0: int, r1: int):
         if dc_threshold_mv is None:
             valid = None
         else:
-            if dc4_mv is not None:
+            if dc4_full is not None:
-                dc4_chunk = dc4_mv[r0:r1]
+                dc4_chunk = dc4_full[r0:r1]
             else:
                 dc4_chunk = adc_to_mv(
                     data[r0:r1, CH4_IDX, :, :].astype(np.float32).mean(axis=-1), *cal4)
@@ -1007,7 +1013,13 @@ def save_manual_alignment(sras: SrasFile, ref_angle_idx: int,
             for a, p in per_angle.items()
         },
     }
-    path.write_text(json.dumps(payload, indent=2))
+    # Write to a temp file in the same directory then rename over the target
+    # — os.replace() is atomic on both POSIX and Windows, so a crash mid-write
+    # leaves either the old sidecar or the new one, never a truncated/corrupt
+    # file that load_manual_alignment would silently treat as "no alignment".
+    tmp_path = path.with_name(path.name + f".tmp{os.getpid()}")
+    tmp_path.write_text(json.dumps(payload, indent=2))
+    os.replace(tmp_path, path)
     return path
 
 

sras_format.py

@@ -523,7 +523,13 @@ class SrasFile:
         final_freq = new_freq_mhz if new_freq_mhz is not None else self.precomputed_freq_mhz
         final_bg_sub = new_bg_sub if new_bg_sub is not None else self.precomputed_bg_sub
 
-        dc_entries = [a for a in range(self.n_angles) if final_dc3[a] is not None]
+        # dc3/dc4 are always populated together by every current caller, but
+        # guard the per-angle pairing explicitly rather than assume it: an
+        # angle present in only one of the two arrays would otherwise crash
+        # below on final_dc4[a].astype(...) (or silently store the wrong
+        # dc3/dc4 pairing for that angle).
+        dc_entries = [a for a in range(self.n_angles)
+                     if final_dc3[a] is not None and final_dc4[a] is not None]
         fft_entries = [a for a in range(self.n_angles) if final_freq[a] is not None]
 
         block_flags = ((CACH_FLAG_DC if dc_entries else 0)
@@ -552,13 +558,23 @@ class SrasFile:
             f.truncate()
             f.flush()
             os.fsync(f.fileno())
-            # Version-byte flip last: if the process dies before this point,
+            # Version-byte flip last: when converting a v6 source (self.version
-            # the file is still readable as plain v6 (v6 parsing only
+            # was 6 on entry), if the process dies before this point the file
-            # bounds-checks per-angle offset+nbytes <= file_size, it never
+            # is still readable as plain v6 (v6 parsing only bounds-checks
-            # asserts exactly how many bytes follow the last angle) — so an
+            # per-angle offset+nbytes <= file_size, it never asserts exactly
-            # interrupted write can never corrupt the file, only leave
+            # how many bytes follow the last angle) — so an interrupted write
-            # harmless trailing bytes that the next successful write
+            # can never corrupt the file, only leave harmless trailing bytes
-            # overwrites via this same deterministic cache offset.
+            # that the next successful write overwrites via this same
+            # deterministic cache offset.
+            #
+            # That guarantee does NOT extend to updating an already-v7 file:
+            # the version byte here is already 7 before this call, so a crash
+            # during the payload write above (before flush/fsync/truncate)
+            # can leave a cache tail that mixes a prefix of the new payload
+            # with a stale suffix of the old one, and this method has no
+            # protection against that case (no atomic rename — the tail is
+            # rewritten in place to avoid copying the, potentially huge,
+            # waveform data that precedes it).
             f.seek(4)
             f.write(struct.pack("B", 7))
             f.flush()

sras_viewer.py

@@ -29,9 +29,10 @@ 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,
+    QDoubleSpinBox, QFileDialog, QFormLayout, QFrame, QGridLayout, QGroupBox,
-    QLabel, QMainWindow, QMessageBox, QProgressDialog, QPushButton, QRadioButton,
+    QHBoxLayout, QLabel, QLineEdit, QMainWindow, QMessageBox, QProgressDialog,
-    QScrollArea, QSizePolicy, QSpinBox, QSplitter, QVBoxLayout, QWidget,
+    QPushButton, QRadioButton, QScrollArea, QSizePolicy, QSpinBox, QSplitter,
+    QVBoxLayout, QWidget,
 )
 
 import sras_compute as compute
@@ -45,8 +46,9 @@ from sras_format import (
     _FALLBACK_YMULT_MV, _FALLBACK_YOFF_ADC,
 )
 from sras_workers import (
-    AngleAlignmentWorker, BatchCacheWorker, Ch4MaskWorker, ComputeWorker,
+    AngleAlignmentWorker, BatchCacheWorker, BatchExportWorker, Ch4MaskWorker,
-    CrossCorrelateWorker, DcPrecomputeWorker, LoadWorker,
+    ComputeWorker, CrossCorrelateWorker, DcPrecomputeWorker, ExportChannel,
+    LoadWorker,
 )
 
 faulthandler.enable()   # print a native stack trace on SIGSEGV/SIGABRT/etc.
@@ -743,6 +745,137 @@ class FftOptionsDialog(QDialog):
         return max(1, self._spin_pad.value())
 
 
+# ---------------------------------------------------------------------------
+# Batch export dialog (Export -> Batch Export Images...)
+# ---------------------------------------------------------------------------
+
+class BatchExportDialog(QDialog):
+    """Configure a batch PNG export of DC/RF/Velocity maps across every angle
+    of the currently open file.
+
+    Each channel's colorbar range is entered here and held fixed for every
+    exported angle (rather than auto-scaled per image, today's live-view
+    default) so the exported images are directly comparable to each other.
+    """
+
+    # (ch_idx, is_velocity, label, colorbar unit, filename tag)
+    _ROWS = [
+        (CH1_IDX, False, CH_LABELS[CH1_IDX], _CHANNEL_DISPLAY[CH1_IDX][2],
+         CH_NAMES[CH1_IDX]),
+        (CH3_IDX, False, CH_LABELS[CH3_IDX], _CHANNEL_DISPLAY[CH3_IDX][2],
+         CH_NAMES[CH3_IDX]),
+        (CH4_IDX, False, CH_LABELS[CH4_IDX], _CHANNEL_DISPLAY[CH4_IDX][2],
+         CH_NAMES[CH4_IDX]),
+        (CH1_IDX, True, CH_LABELS[VELOCITY_MODE_IDX],
+         _CHANNEL_DISPLAY[VELOCITY_MODE_IDX][2], CH_NAMES[VELOCITY_MODE_IDX]),
+    ]
+    # DC is cheap and precomputed on load; CH1/Velocity need a per-pixel FFT
+    # that can take minutes, so don't default to exporting them (same
+    # rationale as SrasViewerWindow._on_load_done's channel default).
+    _DEFAULT_CHECKED = {CH3_IDX, CH4_IDX}
+
+    def __init__(self, parent, *, default_dir: str, default_prefix: str,
+                 default_ranges: dict[tuple[int, bool], tuple[float, float]]):
+        super().__init__(parent)
+        self.setWindowTitle("Batch Export Images")
+        self.setModal(True)
+        self.setMinimumWidth(460)
+
+        layout = QVBoxLayout(self)
+
+        # ---- Output ------------------------------------------------------
+        grp_out, ol = _group("Output")
+        dir_row = QHBoxLayout()
+        self._edit_dir = QLineEdit(default_dir)
+        btn_browse = QPushButton("Browse…")
+        btn_browse.clicked.connect(self._on_browse)
+        dir_row.addWidget(self._edit_dir)
+        dir_row.addWidget(btn_browse)
+        out_form = _form()
+        out_form.addRow("Folder:", dir_row)
+        self._edit_prefix = QLineEdit(default_prefix)
+        out_form.addRow("File prefix:", self._edit_prefix)
+        ol.addLayout(out_form)
+        layout.addWidget(grp_out)
+
+        # ---- Channels ------------------------------------------------------
+        grp_ch, cl = _group("Channels  (fixed range, applied to every angle)")
+        grid = QGridLayout()
+        grid.setHorizontalSpacing(8)
+        grid.setVerticalSpacing(6)
+        grid.addWidget(_wrap_label("min:", _CSS_HINT), 0, 1)
+        grid.addWidget(_wrap_label("max:", _CSS_HINT), 0, 2)
+
+        self._rows: list[tuple[QCheckBox, QDoubleSpinBox, QDoubleSpinBox]] = []
+        for i, (ch_idx, is_velocity, label, unit, _tag) in enumerate(self._ROWS, 1):
+            chk = QCheckBox(label + (f"  [{unit}]" if unit else ""))
+            chk.setChecked(not is_velocity and ch_idx in self._DEFAULT_CHECKED)
+            vmin, vmax = default_ranges.get((ch_idx, is_velocity), (0.0, 1.0))
+            spin_min, spin_max = QDoubleSpinBox(), QDoubleSpinBox()
+            for spin, val in ((spin_min, vmin), (spin_max, vmax)):
+                spin.setRange(-1e9, 1e9)
+                spin.setDecimals(4)
+                spin.setMinimumWidth(_SPIN_MIN_W)
+                spin.setValue(val)
+            grid.addWidget(chk, i, 0)
+            grid.addWidget(spin_min, i, 1)
+            grid.addWidget(spin_max, i, 2)
+            self._rows.append((chk, spin_min, spin_max))
+        cl.addLayout(grid)
+        layout.addWidget(grp_ch)
+
+        # ---- Buttons --------------------------------------------------
+        buttons = QDialogButtonBox()
+        buttons.addButton("Export", QDialogButtonBox.ButtonRole.AcceptRole
+                          ).clicked.connect(self.accept)
+        buttons.addButton("Cancel", QDialogButtonBox.ButtonRole.RejectRole
+                          ).clicked.connect(self.reject)
+        layout.addWidget(buttons)
+
+    def _on_browse(self):
+        d = QFileDialog.getExistingDirectory(
+            self, "Select Output Folder", self._edit_dir.text())
+        if d:
+            self._edit_dir.setText(d)
+
+    def accept(self):
+        """Validate before closing — Cancel bypasses this entirely."""
+        if not self.get_prefix():
+            QMessageBox.warning(self, "Batch Export", "Enter a file prefix.")
+            return
+        if not self.get_output_dir():
+            QMessageBox.warning(self, "Batch Export", "Choose an output folder.")
+            return
+        selected = self.get_selected_channels()
+        if not selected:
+            QMessageBox.warning(
+                self, "Batch Export", "Select at least one channel to export.")
+            return
+        for ch in selected:
+            if not ch.vmin < ch.vmax:
+                QMessageBox.warning(
+                    self, "Batch Export", f"{ch.label}: min must be less than max.")
+                return
+        super().accept()
+
+    def get_output_dir(self) -> str:
+        return self._edit_dir.text().strip()
+
+    def get_prefix(self) -> str:
+        return self._edit_prefix.text().strip()
+
+    def get_selected_channels(self) -> list[ExportChannel]:
+        result = []
+        for (chk, spin_min, spin_max), (ch_idx, is_velocity, label, unit, tag) in zip(
+                self._rows, self._ROWS):
+            if chk.isChecked():
+                result.append(ExportChannel(
+                    ch_idx=ch_idx, is_velocity=is_velocity,
+                    vmin=spin_min.value(), vmax=spin_max.value(),
+                    label=label, unit=unit, tag=tag))
+        return result
+
+
 # ---------------------------------------------------------------------------
 # Manual alignment dialog (Fusion -> Manual Alignment...)
 # ---------------------------------------------------------------------------
@@ -1399,6 +1532,10 @@ class SrasViewerWindow(QMainWindow):
         # Convert menu: batch DC/FFT compute-and-store (v6 -> v7)
         self._batch_errors: list[str] = []
 
+        # Export menu: batch image export
+        self._export_errors: list[str] = []
+        self._export_ok_count: int = 0
+
         # 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
@@ -1412,6 +1549,8 @@ class SrasViewerWindow(QMainWindow):
         self._fft_cache: dict[tuple[int, bool, int | None, float], np.ndarray] = {}
         self._dc_precompute_worker: DcPrecomputeWorker | None = None
         self._dc_generation: int = 0
+        self._compute_generation: int = 0
+        self._pending_compute_generation: int | None = None
 
         # Angle alignment ("Fusion" menu)
         self._alignment_result = None
@@ -1447,6 +1586,19 @@ class SrasViewerWindow(QMainWindow):
            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.
+
+        3. The thread must quit once worker.run() returns, regardless of
+           which signal (if any) run() emitted on its way out. quit_on exists
+           so a worker whose real completion is signalled asynchronously
+           from *within* run() (e.g. angle_done fired from pool threads
+           before run() itself returns) can still opt into quitting earlier,
+           but relying on quit_on alone is fragile: a worker whose run()
+           emits `error` instead of `finished` on an exception path, at a
+           call site that forgot to add "error" to quit_on, would otherwise
+           never quit — silently wedging that job in self._jobs forever.
+           Quitting unconditionally after run() returns closes that gap for
+           every worker, present and future, without requiring every call
+           site to enumerate every signal run() might emit.
         """
         if key in self._jobs:
             return False
@@ -1454,7 +1606,11 @@ class SrasViewerWindow(QMainWindow):
         thread = QThread()
         self._jobs[key] = (thread, worker, on_done)   # claim before anything pumps
         worker.moveToThread(thread)
-        thread.started.connect(worker.run)
+
+        def _run_then_quit():
+            worker.run()
+            thread.quit()
+        thread.started.connect(_run_then_quit)
         for signal_name, slot in connect:
             getattr(worker, signal_name).connect(slot)
         for signal_name in quit_on:
@@ -1792,6 +1948,15 @@ class SrasViewerWindow(QMainWindow):
         self._batch_fft_act.triggered.connect(lambda: self._on_batch_compute("fft"))
         convert_menu.addAction(self._batch_fft_act)
 
+        export_menu = menubar.addMenu("&Export")
+        self._batch_export_act = QAction("&Batch Export Images…", self)
+        self._batch_export_act.setStatusTip(
+            "Export DC/RF/Velocity map PNGs for every angle of the open "
+            "file, with a fixed colorbar range per channel.")
+        self._batch_export_act.setEnabled(False)
+        self._batch_export_act.triggered.connect(self._on_batch_export)
+        export_menu.addAction(self._batch_export_act)
+
     # ------------------------------------------------------------------
     # Drag-and-drop
     # ------------------------------------------------------------------
@@ -1826,10 +1991,10 @@ class SrasViewerWindow(QMainWindow):
             return
         self.btn_open.setEnabled(False)
         self.statusBar().showMessage(f"Loading {Path(path).name}…")
-        self._show_progress("main", f"Loading {Path(path).name}…")
+        self._show_progress("load", f"Loading {Path(path).name}…")
 
     def _on_load_done(self, sras):
-        self._close_progress("main")
+        self._close_progress("load")
         self.btn_open.setEnabled(True)
         if sras is None:
             return
@@ -1850,6 +2015,7 @@ class SrasViewerWindow(QMainWindow):
         self._dc_cache = {}
         self._fft_cache = {}
         self._dc_generation += 1
+        self._compute_generation += 1
         self.lbl_dc_precompute.setText("")
 
         self._alignment_result = None
@@ -1988,6 +2154,8 @@ class SrasViewerWindow(QMainWindow):
         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._batch_export_act.setEnabled(has_file and not self._job_running("export"))
         self._update_roi_ui()
 
     def _on_channel_changed(self):
@@ -2322,6 +2490,11 @@ class SrasViewerWindow(QMainWindow):
         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
+        # Snapshot which file this compute belongs to, so a result that lands
+        # after a *different* file has since been loaded (nothing blocks
+        # opening a new file while a compute is in flight) gets discarded
+        # instead of being cached/displayed against the wrong SrasFile.
+        self._pending_compute_generation = self._compute_generation
 
         worker = ComputeWorker(
             self._sras, angle_idx, ch_idx,
@@ -2347,13 +2520,13 @@ class SrasViewerWindow(QMainWindow):
         if is_fft:
             self.statusBar().showMessage("Computing FFT…")
             self._show_progress(
-                "main",
+                "compute",
                 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}…")
+            self._show_progress("compute", f"Computing DC image for angle {angle_idx}…")
 
     def _after_compute(self):
         """If settings changed while the compute was running, re-dispatch
@@ -2367,7 +2540,10 @@ class SrasViewerWindow(QMainWindow):
             self._refresh_display()
 
     def _on_compute_done(self, result):
-        self._close_progress("main")
+        self._close_progress("compute")
+        generation, self._pending_compute_generation = self._pending_compute_generation, None
+        if generation != self._compute_generation:
+            return   # a different file was loaded while this was computing — discard
         if result is None:
             return   # cancelled mid-compute; the partial image must not cache
         angle_idx = self._pending_angle
@@ -2554,6 +2730,106 @@ class SrasViewerWindow(QMainWindow):
         self._batch_dc_act.setEnabled(True)
         self._batch_fft_act.setEnabled(True)
 
+    # ------------------------------------------------------------------
+    # Export menu: batch image export
+    # ------------------------------------------------------------------
+
+    def _export_default_ranges(self) -> dict[tuple[int, bool], tuple[float, float]]:
+        """Best-effort default min/max per exportable channel, from whatever
+        is already cached — this must never trigger a fresh compute just to
+        seed the dialog (CH1/Velocity in particular can be expensive)."""
+        s = self._sras
+        ranges: dict[tuple[int, bool], tuple[float, float]] = {}
+
+        for ch_idx, precomputed in ((CH3_IDX, s.precomputed_dc3_mv),
+                                    (CH4_IDX, s.precomputed_dc4_mv)):
+            arrays = [self._dc_cache.get((a, ch_idx)) for a in range(s.n_angles)]
+            arrays = [a for a in arrays if a is not None]
+            if not arrays:
+                arrays = [a for a in precomputed if a is not None]
+            if arrays:
+                ranges[(ch_idx, False)] = (
+                    float(min(a.min() for a in arrays)),
+                    float(max(a.max() for a in arrays)))
+
+        freq_arrays = list(self._fft_cache.values())
+        if not freq_arrays:
+            freq_arrays = [a for a in s.precomputed_freq_mhz if a is not None]
+        if freq_arrays:
+            fmin = float(min(a.min() for a in freq_arrays))
+            fmax = float(max(a.max() for a in freq_arrays))
+            ranges[(CH1_IDX, False)] = (fmin, fmax)
+            grating = self.spin_grating_um.value()
+            ranges[(CH1_IDX, True)] = (fmin * grating, fmax * grating)
+
+        return ranges
+
+    def _on_batch_export(self):
+        if self._sras is None or self._job_running("export"):
+            return
+        s = self._sras
+
+        dlg = BatchExportDialog(
+            self, default_dir=str(s.path.parent), default_prefix=s.path.stem,
+            default_ranges=self._export_default_ranges())
+        if dlg.exec() != QDialog.DialogCode.Accepted:
+            return
+
+        output_dir = dlg.get_output_dir()
+        try:
+            Path(output_dir).mkdir(parents=True, exist_ok=True)
+        except OSError as exc:
+            QMessageBox.warning(
+                self, "Batch Export", f"Could not create output folder:\n{exc}")
+            return
+
+        channels = dlg.get_selected_channels()
+        self._export_errors = []
+        self._export_ok_count = 0
+        worker = BatchExportWorker(
+            s, channels, output_dir, dlg.get_prefix(),
+            cmap=self.combo_cmap.currentText(),
+            apply_bg_sub=self.chk_bg_sub.isChecked(),
+            dc_threshold_mv=self.spin_threshold_mv.value(),
+            n_fft=self._current_n_fft(), grating_um=self.spin_grating_um.value())
+        started = self._run_worker(
+            "export", worker,
+            connect=(
+                ("progress", lambda pct: self._set_progress("export", pct)),
+                ("file_done", self._on_export_file_done),
+                ("finished", self._on_export_finished),
+            ),
+            on_done=self._after_export,
+        )
+        if not started:
+            return   # a second trigger snuck in while the dialog was open
+
+        self._batch_export_act.setEnabled(False)
+        self._show_progress(
+            "export", f"Exporting images to {output_dir}…", maximum=100)
+
+    def _on_export_file_done(self, path: str, err: str):
+        if err:
+            self._export_errors.append(f"{Path(path).name if path else '?'} — {err}")
+        else:
+            self._export_ok_count += 1
+            self._show_progress("export", f"Wrote {Path(path).name}…")
+
+    def _on_export_finished(self):
+        self._close_progress("export")
+        n_ok = self._export_ok_count
+        n_failed = len(self._export_errors)
+        if n_failed:
+            summary = (f"Batch export: {n_ok} image(s) written, {n_failed} "
+                       f"failed: {'; '.join(self._export_errors)}")
+        else:
+            summary = f"Batch export: {n_ok} image(s) written."
+        self.statusBar().showMessage(summary)
+        self._export_errors = []
+
+    def _after_export(self):
+        self._update_controls_enabled(self._sras is not None)
+
     # ------------------------------------------------------------------
     # Fusion: angle alignment
     # ------------------------------------------------------------------
@@ -2568,7 +2844,7 @@ class SrasViewerWindow(QMainWindow):
         started = self._run_worker(
             "align", AngleAlignmentWorker(self._sras, ref_idx, threshold_mv),
             connect=(
-                ("progress", lambda pct: self._set_progress("main", pct)),
+                ("progress", lambda pct: self._set_progress("align", pct)),
                 ("finished", lambda result, err, g=generation:
                     self._on_alignment_done(g, result, err)),
             ),
@@ -2579,13 +2855,13 @@ class SrasViewerWindow(QMainWindow):
 
         self._alignment_act.setEnabled(False)
         self._show_progress(
-            "main",
+            "align",
             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")
+        self._close_progress("align")
         if generation != self._alignment_generation:
             return   # a new file was loaded while this was computing — discard
         if error_msg:
@@ -2639,7 +2915,16 @@ class SrasViewerWindow(QMainWindow):
         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)
+        # Deliberately NOT WA_DeleteOnClose: Ch4MaskWorker/CrossCorrelateWorker
+        # have no stop() and are owned by this window's _jobs (not the
+        # dialog), so a background mask-fetch/cross-correlate job can still be
+        # running after the dialog closes. Its signals stay connected to this
+        # dialog's own bound methods (_on_mask_angle_done, _finish_mask_prep,
+        # etc.) until it finishes — if Qt had already destroyed the dialog's
+        # C++ object, those late callbacks would raise "wrapped C/C++ object
+        # ... has been deleted". Leaving the object merely hidden (not
+        # destroyed) lets them land harmlessly; it is garbage-collected once
+        # the job's own references to it are released.
         self._manual_align_dialog = dlg
         dlg.show()
 

sras_workers.py

@@ -10,15 +10,19 @@ everything they need through their constructor and hand results back by signal.
 import os
 from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed
 from concurrent.futures.process import BrokenProcessPool
+from dataclasses import dataclass
+from pathlib import Path
 
 import numpy as np
+from matplotlib.backends.backend_agg import FigureCanvasAgg
+from matplotlib.figure import Figure
 from PyQt6.QtCore import QObject, pyqtSignal
 
 import sras_compute as compute
 from sras_compute import (
     cache_file, compute_angle_alignment, compute_rf_image, dc_image_mv,
 )
-from sras_format import CH3_IDX, CH4_IDX, SrasFile
+from sras_format import CH1_IDX, CH3_IDX, CH4_IDX, SrasFile
 
 # Concurrency caps. Batch conversion runs one process per file, and each of
 # those processes threads internally, so the two must be divided rather than
@@ -281,6 +285,140 @@ class BatchCacheWorker(QObject):
         self.finished.emit()
 
 
+@dataclass
+class ExportChannel:
+    """One row of a batch image export: which raw channel to read, whether
+    to apply the Velocity post-multiply, and the fixed display range/labels
+    to render it with.
+
+    Kept free of sras_viewer's display constants (CH_LABELS, VELOCITY_MODE_IDX,
+    etc.) so BatchExportWorker has no dependency on the GUI module — the
+    caller resolves labels/units/filename tags once, up front.
+    """
+    ch_idx: int        # CH1_IDX, CH3_IDX, or CH4_IDX -- which raw data to read
+    is_velocity: bool  # True only for the derived Velocity map (post-multiply of CH1 freq)
+    vmin: float
+    vmax: float
+    label: str          # e.g. "CH3 -- Bias A (DC mean)"
+    unit: str           # colorbar units, e.g. "mV"
+    tag: str            # filename tag: "CH1", "CH3", "CH4", "VEL"
+
+
+def _render_map_png(img: np.ndarray, extent: list[float], *, cmap: str,
+                    vmin: float, vmax: float, title: str, colorbar_label: str,
+                    out_path: str):
+    """Render one map image to *out_path* with a fixed vmin/vmax, using a
+    headless Agg canvas so this never touches the GUI thread's interactive
+    matplotlib backend. Layout mirrors ImageCanvas.show_image."""
+    fig = Figure(figsize=(7, 5), tight_layout=True)
+    FigureCanvasAgg(fig)
+    ax = fig.add_subplot(111)
+    im = ax.imshow(img, aspect="auto", origin="upper", extent=extent,
+                   cmap=cmap, vmin=vmin, vmax=vmax, interpolation="nearest")
+    cb = fig.colorbar(im, ax=ax, fraction=0.046, pad=0.04)
+    if colorbar_label:
+        cb.set_label(colorbar_label)
+    ax.set_xlabel("X (mm)")
+    ax.set_ylabel("Y (mm)")
+    ax.set_title(title)
+    fig.savefig(out_path, dpi=150)
+
+
+class BatchExportWorker(CancellableWorker):
+    """Renders and saves one PNG per (angle, selected channel) for an
+    already-open SrasFile, with each channel's vmin/vmax held fixed across
+    every angle so the colorbar is directly comparable image to image.
+
+    Takes the SrasFile object directly (like ComputeWorker/DcPrecomputeWorker)
+    rather than a path -- this runs against the file already open in the GUI,
+    not an arbitrary batch of files, so there is no need to reopen it in a
+    subprocess the way BatchCacheWorker does.
+
+    Emits progress(int) (0-100 over all angle x channel pairs), file_done(str,
+    str) (output path, error message or ""), and finished() -- same shape as
+    BatchCacheWorker.
+    """
+    progress = pyqtSignal(int)
+    file_done = pyqtSignal(str, str)
+    finished = pyqtSignal()
+
+    def __init__(self, sras: SrasFile, channels: list[ExportChannel],
+                 output_dir: str, prefix: str, *, cmap: str,
+                 apply_bg_sub: bool, dc_threshold_mv: float,
+                 n_fft: int | None, grating_um: float):
+        super().__init__()
+        self._sras = sras
+        self._channels = channels
+        self._output_dir = Path(output_dir)
+        self._prefix = prefix
+        self._cmap = cmap
+        self._apply_bg_sub = apply_bg_sub
+        self._dc_threshold_mv = dc_threshold_mv
+        self._n_fft = n_fft
+        self._grating_um = grating_um
+
+    def _angle_extent(self, angle_idx: int) -> list[float]:
+        s = self._sras
+        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
+        return [x_axis[0] - dx / 2, x_axis[-1] + dx / 2,
+                y_axis[-1] + dy / 2, y_axis[0] - dy / 2]
+
+    def run(self):
+        try:
+            s = self._sras
+            n_angles = s.n_angles
+            total = n_angles * len(self._channels)
+            done = 0
+            needs_freq = any(c.ch_idx == CH1_IDX for c in self._channels)
+
+            for angle_idx in range(n_angles):
+                if self._stop:
+                    break
+                extent = self._angle_extent(angle_idx)
+                angle_deg = s.angles_deg[angle_idx]
+
+                freq_mhz = None
+                if needs_freq:
+                    freq_mhz = compute_rf_image(
+                        s, angle_idx, dc_threshold_mv=self._dc_threshold_mv,
+                        apply_bg_sub=self._apply_bg_sub, n_fft=self._n_fft,
+                        should_stop=self._stopped)
+
+                for channel in self._channels:
+                    if self._stop:
+                        break
+                    out_path = (self._output_dir
+                               / f"{self._prefix}_angle{angle_idx:02d}_{channel.tag}.png")
+                    try:
+                        if channel.ch_idx == CH1_IDX:
+                            img = (freq_mhz * self._grating_um if channel.is_velocity
+                                  else freq_mhz)
+                        else:
+                            img = dc_image_mv(s, angle_idx, channel.ch_idx,
+                                              should_stop=self._stopped)
+                        title = f"{channel.tag}  |  {angle_deg:.1f}°"
+                        colorbar_label = (f"{channel.label} ({channel.unit})"
+                                         if channel.unit else channel.label)
+                        _render_map_png(
+                            img, extent, cmap=self._cmap,
+                            vmin=channel.vmin, vmax=channel.vmax,
+                            title=title, colorbar_label=colorbar_label,
+                            out_path=str(out_path))
+                        self.file_done.emit(str(out_path), "")
+                    except Exception as exc:
+                        self.file_done.emit(str(out_path), str(exc))
+                    done += 1
+                    self.progress.emit(int(done / max(1, total) * 100))
+
+            self.finished.emit()
+        except Exception as exc:
+            self.file_done.emit("", str(exc))
+            self.finished.emit()
+
+
 class AngleAlignmentWorker(QObject):
     """Computes rotation+translation alignment for every angle in *sras*,
     referenced to *ref_angle_idx*, from each angle's binarized CH4 mask.

tools/make_test_sras.py

@@ -11,12 +11,16 @@ Usage:
 
 import argparse
 import struct
+import sys
 from pathlib import Path
 
 import numpy as np
 
-HDR_FMT_V6 = ">4sBHfffffffIdBB"
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
-GEO_FMT_V6 = ">ffIH"
+
+# Packed straight from sras_format.py's own constants (not a hand-copy) so
+# this generator can never silently drift from what the real parser expects.
+from sras_format import GEO_FMT_V6, HDR_FMT as HDR_FMT_LEGACY, HDR_FMT_V6  # noqa: E402
 
 # Per-angle (n_rows, n_frames) — deliberately different per angle so ragged
 # geometry handling is actually exercised.
@@ -125,9 +129,6 @@ def write(path: Path, n_angles: int = 3, seed: int = 0,
     return meta
 
 
-HDR_FMT_LEGACY = ">4sBHHffffIIdBB"
-
-
 def write_legacy(path: Path, version: int = 4, n_angles: int = 2,
                  n_rows: int = 4, n_frames: int = 10,
                  samples_per_frame: int = 32, seed: int = 0) -> dict:

tools/test_refactor.py

@@ -288,23 +288,30 @@ def test_legacy_parse_and_average(scratch: Path):
         check("background preserved",
               np.array_equal(avg.background, SrasFile(str(src)).background))
         src_data = meta["data"]
-        expect0 = src_data[0][:, :, 0:4, :].astype(np.float32).mean(axis=2).astype(np.int16)
+        # int16 (not float32) before .mean(): matches average_rows' own
+        # float64-accumulator behavior for integer input, so this doesn't
+        # drift from what average_rows actually guarantees.
+        expect0 = src_data[0][:, :, 0:4, :].astype(np.int16).mean(axis=2).astype(np.int16)
         check("first averaged group equals the mean of its 4 source frames",
               np.array_equal(np.asarray(avg.data[0])[:, :, 0, :], expect0))
 
     # Remainder handling: 12 frames / 5 -> 2 full groups + 1 partial.
     dst2 = scratch / "legacy_v4_avg5.sras"
-    subprocess.run([sys.executable, str(repo / "sras_average.py"),
+    proc2 = subprocess.run([sys.executable, str(repo / "sras_average.py"),
                            str(src), str(dst2), "--n", "5"],
                           capture_output=True, text=True, cwd=repo)
+    check("sras_average ran (--n 5)", proc2.returncode == 0,
+          (proc2.stderr or proc2.stdout).strip()[-200:])
     if dst2.exists():
         check("partial trailing group kept by default",
               list(SrasFile(str(dst2)).n_frames) == [3, 3],
               f"{list(SrasFile(str(dst2)).n_frames)}")
     dst3 = scratch / "legacy_v4_avg5d.sras"
-    subprocess.run([sys.executable, str(repo / "sras_average.py"),
+    proc3 = subprocess.run([sys.executable, str(repo / "sras_average.py"),
                            str(src), str(dst3), "--n", "5", "--discard-remainder"],
                           capture_output=True, text=True, cwd=repo)
+    check("sras_average ran (--n 5 --discard-remainder)", proc3.returncode == 0,
+          (proc3.stderr or proc3.stdout).strip()[-200:])
     if dst3.exists():
         check("--discard-remainder drops the partial group",
               list(SrasFile(str(dst3)).n_frames) == [2, 2],