fix(acquisition abort): Aborting acquisitions midway left the ui in a…

…n invalid state (#76)

`34713ec14805b441a1cee7dbeb2c13c337035d31` added the
`self.is_current_acquisition_widget` concept on our acquisition widgets.
This was set to `= False` in two places for each - one in the
`toggle_acquisition` and another in `acquisition_finished`. The
`toggle_acquisition` always ran first (it sent the signal that
eventually resulted in `acquisition_finished` getting called), which
means that the code in `acquisition_finished` was always skipped via the
`if` guard checking for `is_current_acquisition_widget`.

It's not clear if we need `is_current_acquisition_widget` since it's
new-ish, but for now leave it and just make it so `acquisition_finished`
is the only `= False` setter of that flag.

Tested by: running local acquisitions. Before this, the stage control +
acquisition widgets would get wedged in disabled state if you aborted an
acquisition midway. Now, they don't and you can continue using the UI.

software/control/core/core.py

@@ -4,6 +4,7 @@
 
 from control.microcontroller import Microcontroller
 from squid.abc import AbstractStage
+import squid.logging
 
 # qt libraries
 os.environ["QT_API"] = "pyqt5"
@@ -1468,6 +1469,7 @@ def run(self):
         while self.time_point < self.Nt:
             # check if abort acquisition has been requested
             if self.multiPointController.abort_acqusition_requested:
+                self._log.debug("In run, abort_acquisition_requested=True")
                 break
 
             self.run_single_time_point()
@@ -1489,6 +1491,7 @@ def run(self):
                 # wait until it's time to do the next acquisition
                 while time.time() < self.timestamp_acquisition_started + self.time_point * self.dt:
                     if self.multiPointController.abort_acqusition_requested:
+                        self._log.debug("In run wait loop, abort_acquisition_requested=True")
                         break
                     time.sleep(0.05)
 
@@ -2179,7 +2182,7 @@ def __init__(
         parent=None,
     ):
         QObject.__init__(self)
-
+        self._log = squid.logging.get_logger(self.__class__.__name__)
         self.camera = camera
         if DO_FLUORESCENCE_RTP:
             self.processingHandler = ProcessingHandler()
@@ -2533,6 +2536,7 @@ def run_acquisition(self):
         self.thread.start()
 
     def _on_acquisition_completed(self):
+        self._log.debug("MultiPointController._on_acquisition_completed called")
         # restore the previous selected mode
         if self.gen_focus_map:
             self.autofocusController.clear_focus_map()
@@ -3218,6 +3222,7 @@ class NavigationViewer(QFrame):
 
     def __init__(self, objectivestore, sample="glass slide", invertX=False, *args, **kwargs):
         super().__init__(*args, **kwargs)
+        self._log = squid.logging.get_logger(self.__class__.__name__)
         self.setFrameStyle(QFrame.Panel | QFrame.Raised)
         self.sample = sample
         self.objectiveStore = objectivestore
@@ -3493,6 +3498,7 @@ def handle_mouse_click(self, evt):
             x_mm = (mouse_point.x() - self.origin_x_pixel) * self.mm_per_pixel
             y_mm = (mouse_point.y() - self.origin_y_pixel) * self.mm_per_pixel
 
+            self._log.debug(f"Got double click at (x_mm, y_mm) = {x_mm, y_mm}")
             self.signal_coordinates_clicked.emit(x_mm, y_mm)
 
         except Exception as e:

software/control/gui_hcs.py

@@ -1251,6 +1251,7 @@ def toggleWellSelector(self, show):
         self.wellSelectionWidget.setVisible(show)
 
     def toggleAcquisitionStart(self, acquisition_started):
+        self.log.debug(f"toggleAcquisitionStarted({acquisition_started=})")
         if acquisition_started:
             self.log.info("STARTING ACQUISITION")
             if self.is_live_scan_grid_on:  # disconnect live scan grid during acquisition

software/control/widgets.py

@@ -1875,6 +1875,7 @@ def __init__(
     ):
         super().__init__(*args, **kwargs)
         self._log = squid.logging.get_logger(self.__class__.__name__)
+        self.acquisition_start_time = None
         self.last_used_locations = None
         self.last_used_location_ids = None
         self.stage = stage
@@ -2397,6 +2398,7 @@ def update_Nz(self):
         self.entry_NZ.setValue(nz)
 
     def update_region_progress(self, current_fov, num_fovs):
+        self._log.debug(f"Updating region progress for {current_fov=}, {num_fovs=}")
         self.progress_bar.setMaximum(num_fovs)
         self.progress_bar.setValue(current_fov)
 
@@ -2425,6 +2427,9 @@ def update_region_progress(self, current_fov, num_fovs):
             self.eta_timer.start(1000)  # Update every 1000 ms (1 second)
 
     def update_acquisition_progress(self, current_region, num_regions, current_time_point):
+        self._log.debug(
+            f"updating acquisition progress for {current_region=}, {num_regions=}, {current_time_point=}..."
+        )
         self.current_region = current_region
         self.current_time_point = current_time_point
 
@@ -2524,6 +2529,7 @@ def display_stitcher_widget(self, checked):
         self.signal_stitcher_widget.emit(checked)
 
     def toggle_acquisition(self, pressed):
+        self._log.debug(f"FlexibleMultiPointWidget.toggle_acquisition, {pressed=}")
         if self.base_path_is_set == False:
             self.btn_startAcquisition.setChecked(False)
             msg = QMessageBox()
@@ -2585,9 +2591,8 @@ def toggle_acquisition(self, pressed):
             # Start coordinate-based acquisition
             self.multipointController.run_acquisition()
         else:
+            # This must eventually propagate through and call out acquisition_finished.
             self.multipointController.request_abort_aquisition()
-            self.is_current_acquisition_widget = False
-            self.setEnabled_all(True)
 
     def load_last_used_locations(self):
         if self.last_used_locations is None or len(self.last_used_locations) == 0:
@@ -2984,6 +2989,10 @@ def import_location_list(self):
             self._log.debug(self.location_list)
 
     def acquisition_is_finished(self):
+        self._log.debug(
+            f"In FlexibleMultiPointWidget, got acquisition_is_finished with {self.is_current_acquisition_widget=}"
+        )
+
         if not self.is_current_acquisition_widget:
             return  # Skip if this wasn't the widget that started acquisition
 
@@ -3055,6 +3064,7 @@ def __init__(
         **kwargs,
     ):
         super().__init__(*args, **kwargs)
+        self._log = squid.logging.get_logger(self.__class__.__name__)
         self.stage = stage
         self.navigationViewer = navigationViewer
         self.multipointController = multipointController
@@ -3665,6 +3675,7 @@ def update_live_coordinates(self, pos: squid.abc.Pos):
         self._last_y_mm = y_mm
 
     def toggle_acquisition(self, pressed):
+        self._log.debug(f"WellplateMultiPointWidget.toggle_acquisition, {pressed=}")
         if not self.base_path_is_set:
             self.btn_startAcquisition.setChecked(False)
             QMessageBox.warning(self, "Warning", "Please choose base saving directory first")
@@ -3744,11 +3755,14 @@ def toggle_acquisition(self, pressed):
             self.multipointController.run_acquisition()
 
         else:
+            # This must eventually propagate through and call our aquisition_is_finished, or else we'll be left
+            # in an odd state.
             self.multipointController.request_abort_aquisition()
-            self.is_current_acquisition_widget = False
-            self.setEnabled_all(True)
 
     def acquisition_is_finished(self):
+        self._log.debug(
+            f"In WellMultiPointWidget, got acquisition_is_finished with {self.is_current_acquisition_widget=}"
+        )
         if not self.is_current_acquisition_widget:
             return  # Skip if this wasn't the widget that started acquisition