fix: stop live mode + pump Qt event loop during run_experiment

faro/core/controller.py

@@ -166,6 +166,42 @@ def stimulator_needs_data(self) -> bool:
             return False
         return isinstance(self.pipeline.stimulator, (StimWithImage, StimWithPipeline))
 
+    @staticmethod
+    def _wait_for_frame_pumping_qt(
+        queue_obj, frame_idx: int, timeout: float, poll_s: float = 0.05
+    ):
+        """Wait for a frame on a ``FrameDispenser`` while pumping Qt events.
+
+        ``FrameDispenser.wait_for_frame`` is a plain ``threading.Condition.wait()``
+        with no Qt awareness. Called from the main thread (as
+        ``Controller._build_stim_slm`` does), it freezes the Qt event loop
+        for as long as the pipeline takes to produce the stim mask -- napari
+        freezes during every stim frame even though the actual GPU work is
+        on the pipeline's executor.
+
+        Poll with a short timeout and call ``QCoreApplication.processEvents``
+        between attempts, preserving the caller-supplied total timeout.
+        Falls back to a plain ``wait_for_frame`` if Qt isn't loaded.
+        """
+        try:
+            from qtpy.QtCore import QCoreApplication
+        except Exception:
+            return queue_obj.wait_for_frame(frame_idx, timeout=timeout)
+        app = QCoreApplication.instance()
+        if app is None:
+            return queue_obj.wait_for_frame(frame_idx, timeout=timeout)
+
+        deadline = time.monotonic() + timeout
+        while True:
+            remaining = deadline - time.monotonic()
+            slice_dt = max(0.0, min(poll_s, remaining))
+            try:
+                return queue_obj.wait_for_frame(frame_idx, timeout=slice_dt)
+            except QueueEmpty:
+                if remaining <= 0:
+                    raise
+                app.processEvents()
+
     def get_stim_mask(
         self, fov_index: int, metadata: dict, *, timeout: float | None = None
     ) -> np.ndarray | None:
@@ -185,8 +221,8 @@ def get_stim_mask(
                 timeout = self._stim_mask_timeout
             frame_idx = metadata.get("timestep", 0)
             try:
-                mask = fov_state.stim_mask_queue.wait_for_frame(
-                    frame_idx, timeout=timeout
+                mask = self._wait_for_frame_pumping_qt(
+                    fov_state.stim_mask_queue, frame_idx, timeout
                 )
             except QueueEmpty as e:
                 # _build_stim_slm still log-and-continues with False, but
@@ -577,6 +613,13 @@ def __init__(self, mic, pipeline, *, writer: Writer | None = None):
             pipeline: ImageProcessingPipeline instance.
             writer: Storage backend. If None, Analyzer uses TiffWriter (default).
                 Pass an OmeZarrWriter for OME-Zarr output.
+
+        Note:
+            ``run_experiment`` automatically stops any continuous sequence
+            acquisition (live mode) before starting MDA, and pumps the Qt
+            event loop while waiting on the MDA worker, so napari-mm's own
+            ``preview`` layer keeps updating throughout the run without the
+            window freezing.
         """
         self._mic = mic
         self._pipeline = pipeline
@@ -836,6 +879,16 @@ def _validate_fov_positions(self, events):
 
     def _run_mda_with_events(self, events, *, stim_mode):
         """Run the MDA event loop — shared by run/continue_experiment."""
+        # Live mode (continuous sequence acquisition) and MDA both drive the
+        # camera. If live is still running when the MDA's first snapImage
+        # fires, the snap buffer is consumed by the live-poll listener (in
+        # napari-micromanager: ``_core_link._image_snapped``) before the
+        # engine calls getImage, and the engine raises "Camera image buffer
+        # read failed". Stop it unconditionally before MDA starts.
+        mmc = getattr(self._mic, "mmc", None)
+        if mmc is not None and mmc.isSequenceRunning():
+            mmc.stopSequenceAcquisition()
+
         self._mic.connect_frame(self._on_frame_ready)
 
         # Set up event queue for extend_experiment support.
@@ -867,7 +920,7 @@ def _run_mda_with_events(self, events, *, stim_mode):
                     break
 
                 while self._queue.qsize() >= 3:
-                    time.sleep(0.1)
+                    self._pump_qt_and_sleep(0.05)
                 self._n_channels = len(rtm_event.channels)
 
                 # In "previous" mode at t=0 there is no predecessor
@@ -909,14 +962,55 @@ def _run_mda_with_events(self, events, *, stim_mode):
             self._event_queue = None
             self._queue.put(self.STOP_EVENT)
             if mda_thread is not None:
-                mda_thread.join()
+                self._qt_join(mda_thread)
             self._mic.disconnect_frame(self._on_frame_ready)
 
         if self._fatal_error is not None:
             fatal = self._fatal_error
             self._fatal_error = None
             raise fatal
 
+    # ------------------------------------------------------------------
+    # Qt-event-loop hygiene
+    # ------------------------------------------------------------------
+    #
+    # _run_mda_with_events runs on the main thread — the same thread napari
+    # paints from. Without explicit pumping, time.sleep / thread.join starve
+    # the Qt event loop, so napari freezes for the duration of the run and
+    # any main-thread-queued updates (e.g. napari-micromanager's preview
+    # layer refreshes) stay in the queue until the cell exits. Both helpers
+    # below fall back to plain blocking if Qt isn't loaded at all.
+
+    @staticmethod
+    def _pump_qt_and_sleep(dt: float) -> None:
+        try:
+            from qtpy.QtCore import QCoreApplication
+        except Exception:
+            time.sleep(dt)
+            return
+        app = QCoreApplication.instance()
+        if app is None:
+            time.sleep(dt)
+            return
+        app.processEvents()
+        time.sleep(dt)
+
+    @staticmethod
+    def _qt_join(thread: threading.Thread, poll_s: float = 0.05) -> None:
+        try:
+            from qtpy.QtCore import QCoreApplication
+        except Exception:
+            thread.join()
+            return
+        app = QCoreApplication.instance()
+        if app is None:
+            thread.join()
+            return
+        while thread.is_alive():
+            app.processEvents()
+            thread.join(timeout=poll_s)
+        app.processEvents()
+
     # ------------------------------------------------------------------
     # Frame handling
     # ------------------------------------------------------------------