Check the run is still going when the Stop dialog is answered

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AcquisitionTab.java

@@ -236,11 +236,14 @@ private void createEventHandlers() {
                 // confirm first: one stray click discards a run in progress
                 if (DialogUtils.showYesNoDialog(this, "Stop Acquisition",
                         "Stop the current acquisition?")) {
-                    model_.acquisitions().requestStop();
+                    // the run can end while the dialog is open
+                    if (model_.acquisitions().isRunning()) {
+                        model_.acquisitions().requestStop();
+                    }
                 } else {
                     // the press already flipped the toggle, so put it back or the button
                     // reads "Start Acquisition" while the run is still going
-                    btnRunAcquisition_.setState(true);
+                    btnRunAcquisition_.setState(model_.acquisitions().isRunning());
                 }
             }
         });

src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java

@@ -284,6 +284,18 @@ protected boolean isStopRequested() {
         return stopRequested_;
     }
 
+    /**
+     * Returns true from the moment a run is requested until its cleanup has finished. Unlike
+     * {@link #isAcquisitionRunning()}, this includes setup, the wait between separate time points
+     * and the cleanup. {@link #requestStop()} acts only while this is true. A speed test does not
+     * count.
+     *
+     * @return true while a run is in progress
+     */
+    public boolean isRunning() {
+        return acquisitionRequested_;
+    }
+
     /**
      * Records whether a series is waiting between time points, for the stop and abort log lines.
      *