fix slice timing staleness and refuse to arm on unusable timing

src/main/java/org/micromanager/lightsheetmanager/LightSheetManager.java

@@ -3,6 +3,7 @@
 import mmcorej.CMMCore;
 import org.micromanager.Studio;
 import org.micromanager.lightsheetmanager.api.LightSheetManagerApi;
+import org.micromanager.lightsheetmanager.model.Logging;
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
 import org.micromanager.lightsheetmanager.model.DeviceManager;
 import org.micromanager.lightsheetmanager.model.PluginSettings;
@@ -27,6 +28,7 @@ public class LightSheetManager implements LightSheetManagerApi, AutoCloseable {
 
     private PluginSettings pluginSettings_;
 
+    private final Logging logging_;
     private final UserSettings userSettings_;
     private final DeviceManager deviceManager_;
     private final PositionUpdater positionUpdater_;
@@ -40,6 +42,7 @@ public LightSheetManager(final Studio studio) {
         core_ = studio_.core();
 
         pluginSettings_ = new PluginSettings();
+        logging_ = new Logging(this);
         userSettings_ = new UserSettings(this);
 
         deviceManager_ = new DeviceManager(studio_, this);
@@ -164,6 +167,18 @@ public String setupErrorMessage() {
         return errorText_;
     }
 
+    /**
+     * The plugin's logging and error-reporting service.
+     *
+     * <p>This lives on the model rather than the acquisition engine because callers like
+     * {@code DeviceManager} report errors during {@code setup()}, before the engine exists.
+     *
+     * @return the logging service
+     */
+    public Logging logging() {
+        return logging_;
+    }
+
     public UserSettings userSettings() {
         return userSettings_;
     }

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

@@ -31,6 +31,8 @@ public class SettingsTab extends Panel implements ListeningPanel {
 
     private Button btnCreateConfigGroup_;
 
+    private CheckBox cbxAcquireFailQuietly_;
+
     // changes the ui setup
     private boolean isUsingPLogic_;
     private boolean isUsingScanSettings_;
@@ -154,11 +156,17 @@ private void createUserInterface() {
             pnlLightSheet.add(spnLiveScanPeriod_, "");
         }
 
+        cbxAcquireFailQuietly_ = new CheckBox("Acquisition failures are quiet",
+                model_.pluginSettings().isAcquireFailQuietly());
+        cbxAcquireFailQuietly_.setToolTipText("Log acquisition errors instead of showing dialog " +
+                "boxes, so unattended runs (playlist or scripting) can never hang on an error dialog.");
+
         add(pnlScanSettings, "wrap");
         if (isUsingPLogic_) {
             add(pnlLightSheet, "growx, wrap");
         }
 
+        add(cbxAcquireFailQuietly_, "wrap");
         add(btnCreateConfigGroup_, "");
     }
 
@@ -201,6 +209,9 @@ private void createEventHandlers() {
                     () -> scanner.setFilterFreqY(spnSliceAxisFilterFreq_.getDouble()));
         }
 
+        cbxAcquireFailQuietly_.registerListener(() -> model_.pluginSettings()
+                .setAcquireFailQuietly(cbxAcquireFailQuietly_.isSelected()));
+
         btnCreateConfigGroup_.registerListener(() -> model_.devices().createConfigGroup());
 
         // TODO: make this work with diSPIM settings

src/main/java/org/micromanager/lightsheetmanager/model/Logging.java

@@ -0,0 +1,156 @@
+package org.micromanager.lightsheetmanager.model;
+
+import org.micromanager.lightsheetmanager.LightSheetManager;
+import org.micromanager.lightsheetmanager.gui.utils.DialogUtils;
+
+import java.util.Objects;
+
+/**
+ * The plugin's logging and error-reporting service.
+ *
+ * <p>Two method families with different contracts:
+ * <ul>
+ *   <li>{@code logMessage}/{@code logDebugMessage}/{@code logError} write to the CoreLog and
+ *       never show UI, so they are safe from any thread in any mode.</li>
+ *   <li>{@code reportError}/{@code confirmOrDefault} are user-facing and honor the
+ *       "Acquisition failures are quiet" setting: quiet only logs, otherwise the standard
+ *       dialogs are also shown.</li>
+ * </ul>
+ *
+ * <p>Dialogs shown from the acquisition thread block it until someone clicks OK, so an
+ * unattended run (Playlist, scripting) can hang indefinitely on an error. The 1.4 plugin
+ * solved this with {@code MyDialogUtils.showError(..., hideErrors)} and threaded the flag
+ * through the call chain; reading the setting at the report site instead also covers
+ * stop/pause requests arriving outside a run.
+ *
+ * <p>This is deliberately an instance class, not static utilities: the backend it writes
+ * through must be swappable per model instance for headless operation.
+ */
+public final class Logging {
+
+    private final LightSheetManager model_;
+
+    public Logging(final LightSheetManager model) {
+        model_ = Objects.requireNonNull(model);
+    }
+
+    // The setting is read through the model on every call because loading user settings
+    // replaces the PluginSettings object; a reference captured here would go stale.
+    private boolean isQuiet() {
+        return model_.pluginSettings().isAcquireFailQuietly();
+    }
+
+    // --- pure logging - never shows UI ---
+
+    /**
+     * Logs a message.
+     *
+     * @param message the message to log
+     */
+    public void logMessage(final String message) {
+        model_.studio().logs().logMessage(message);
+    }
+
+    /**
+     * Logs a debug message.
+     *
+     * @param message the message to log
+     */
+    public void logDebugMessage(final String message) {
+        model_.studio().logs().logDebugMessage(message);
+    }
+
+    /**
+     * Logs an error message.
+     *
+     * @param message the error message
+     */
+    public void logError(final String message) {
+        model_.studio().logs().logError(message);
+    }
+
+    /**
+     * Logs an exception.
+     *
+     * @param e the exception to log
+     */
+    public void logError(final Exception e) {
+        model_.studio().logs().logError(e);
+    }
+
+    /**
+     * Logs an exception with a message.
+     *
+     * @param e the exception to log
+     * @param message the error message
+     */
+    public void logError(final Exception e, final String message) {
+        model_.studio().logs().logError(e, message);
+    }
+
+    // --- user-facing - honors "Acquisition failures are quiet" ---
+
+    /**
+     * Reports an error message.
+     *
+     * @param message the error message
+     */
+    public void reportError(final String message) {
+        if (isQuiet()) {
+            logError(message);
+        } else {
+            model_.studio().logs().showError(message);
+        }
+    }
+
+    /**
+     * Reports an exception.
+     *
+     * @param e the exception to report
+     */
+    public void reportError(final Exception e) {
+        if (isQuiet()) {
+            logError(e);
+        } else {
+            model_.studio().logs().showError(e);
+        }
+    }
+
+    /**
+     * Reports an exception with a message.
+     *
+     * @param e the exception to report
+     * @param message the error message
+     */
+    public void reportError(final Exception e, final String message) {
+        if (isQuiet()) {
+            logError(e, message);
+        } else {
+            model_.studio().logs().showError(e, message);
+        }
+    }
+
+    /**
+     * Asks the user a yes/no question, unless acquisition failures are quiet, in which case
+     * {@code quietAnswer} is returned without showing a dialog and the choice is logged.
+     *
+     * <p>{@code quietAnswer} should be the answer an attended user is expected to give, so quiet
+     * runs follow the recommended path rather than silently declining it. 1.4 had no quiet
+     * variant of {@code getConfirmDialogResult} at all, so its confirm dialogs could still hang
+     * an unattended acquisition.
+     *
+     * @param title the dialog title
+     * @param message the yes/no question
+     * @param quietAnswer the answer to use without asking when failures are quiet
+     * @return the user's answer, or {@code quietAnswer} when failures are quiet
+     */
+    public boolean confirmOrDefault(final String title, final String message, final boolean quietAnswer) {
+        if (isQuiet()) {
+            logMessage("Quiet acquisition: answered \"" + (quietAnswer ? "Yes" : "No")
+                    + "\" without showing the dialog [" + title + "]: " + message);
+            return quietAnswer;
+        }
+        return DialogUtils.showYesNoDialog(null, title, message);
+    }
+
+}

src/main/java/org/micromanager/lightsheetmanager/model/PLogicDispim.java

@@ -1033,7 +1033,8 @@ public double getSheetWidth(CameraMode cameraMode, int view) {
         } else {
             final boolean autoSheet = model_.acquisitions().settings().sheetCalibration().autoSheetWidthEnabled();
             if (autoSheet) {
-                Rectangle roi = camera.getROI();
+                // unbinned, so the sheet width stays the same regardless of binning
+                Rectangle roi = camera.getUnbinnedROI();
                 if (roi == null || roi.height == 0) {
                     studio_.logs().logDebugMessage("Could not get camera ROI for auto sheet mode");
                 }

src/main/java/org/micromanager/lightsheetmanager/model/PLogicScape.java

@@ -941,7 +941,8 @@ public double getSheetWidth(CameraMode cameraMode, int view) {
         } else {
             final boolean autoSheet = model_.acquisitions().settings().sheetCalibration().autoSheetWidthEnabled();
             if (autoSheet) {
-                Rectangle roi = camera.getROI();
+                // unbinned, so the sheet width stays the same regardless of binning
+                Rectangle roi = camera.getUnbinnedROI();
                 if (roi == null || roi.height == 0) {
                     studio_.logs().logDebugMessage("Could not get camera ROI for auto sheet mode");
                 }

src/main/java/org/micromanager/lightsheetmanager/model/PluginSettings.java

@@ -10,6 +10,9 @@ public class PluginSettings {
 
     private boolean isPollingPositions_ = true;
 
+    // volatile: written from the EDT (Settings tab) and read from the acquisition thread
+    private volatile boolean acquireFailQuietly_ = false;
+
     private final JoystickData joystick_ = new JoystickData();
 
     private final XYZGrid xyzGrid_ = new XYZGrid();
@@ -30,6 +33,14 @@ public boolean isPollingPositions() {
         return isPollingPositions_;
     }
 
+    public void setAcquireFailQuietly(final boolean state) {
+        acquireFailQuietly_ = state;
+    }
+
+    public boolean isAcquireFailQuietly() {
+        return acquireFailQuietly_;
+    }
+
     public String toJson() {
         return new Gson().toJson(this);
     }

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

@@ -81,35 +81,35 @@ protected boolean validateSaveLocation() {
 
         final String saveNamePrefix = acqSettings_.saveNamePrefix();
         if (saveNamePrefix == null || saveNamePrefix.trim().isEmpty()) {
-            studio_.logs().showError("The save name prefix is empty.\n\n"
+            model_.logging().reportError("The save name prefix is empty.\n\n"
                     + "Set a name on the Datastore panel, or uncheck \"Save images during acquisition\".");
             return false;
         }
 
         final String saveDirectory = acqSettings_.saveDirectory();
         if (saveDirectory == null || saveDirectory.trim().isEmpty()) {
-            studio_.logs().showError("The save directory is not set.\n\n"
+            model_.logging().reportError("The save directory is not set.\n\n"
                     + "Set a directory on the Datastore panel, or uncheck "
                     + "\"Save images during acquisition\".");
             return false;
         }
 
         final File directory = new File(saveDirectory);
         if (!directory.exists()) {
-            studio_.logs().showError("The save directory does not exist:\n\n" + saveDirectory
+            model_.logging().reportError("The save directory does not exist:\n\n" + saveDirectory
                     + "\n\nCreate it, or choose another directory on the Datastore panel.");
             return false;
         }
         if (!directory.isDirectory()) {
-            studio_.logs().showError("The save directory is a file, not a directory:\n\n"
+            model_.logging().reportError("The save directory is a file, not a directory:\n\n"
                     + saveDirectory);
             return false;
         }
         // canWrite() is advisory on Windows (it reports the read-only attribute, not the ACL), so it
         // catches the common cases without being authoritative; a real write failure still surfaces
         // at finish(). Cheap enough to be worth keeping.
         if (!directory.canWrite()) {
-            studio_.logs().showError("The save directory is not writable:\n\n" + saveDirectory);
+            model_.logging().reportError("The save directory is not writable:\n\n" + saveDirectory);
             return false;
         }
 
@@ -138,7 +138,7 @@ protected boolean validateCameraFrameSizes() {
         if (mismatch == null) {
             return true;
         }
-        studio_.logs().showError("The imaging cameras have different frame sizes: " + mismatch
+        model_.logging().reportError("The imaging cameras have different frame sizes: " + mismatch
                 + ".\n\nAcquiring with mismatched frame sizes crashes Micro-Manager outright, so this "
                 + "acquisition was not started.\n\nSet the same ROI and binning on every imaging "
                 + "camera from the Camera tab, then try again.");
@@ -157,6 +157,7 @@ public AcquisitionEngine(final LightSheetManager model) {
         acqSettings_ = asb_.build();
     }
 
+
     //public abstract DefaultAcquisitionSettingsDISPIM settings();
 
     //public abstract <T extends DefaultAcquisitionSettings.Builder<Builder>> T settingsBuilder();
@@ -203,7 +204,7 @@ public Future<?> requestRun(boolean speedTest) {
         // Run on a new thread, so it doesn't block the EDT
         Future<?> acqFinished = acquisitionExecutor_.submit(() -> {
             if (currentAcquisition_ != null) {
-                studio_.logs().showError("Acquisition is already running.");
+                model_.logging().reportError("Acquisition is already running.");
                 return;
             }
 
@@ -220,7 +221,7 @@ public Future<?> requestRun(boolean speedTest) {
                               acqSettings_.saveNamePrefix(),
                               core_, acqSettings_.numTimePoints(), true);
                     } catch (Exception e) {
-                        studio_.logs().showError(e);
+                        model_.logging().reportError(e);
                     }
                     return; // early exit => do speed test
                 }
@@ -241,17 +242,17 @@ public Future<?> requestRun(boolean speedTest) {
                         return; // early exit => stop acquisition
                     }
                 } catch (Exception e) {
-                    studio_.logs().showError(e, "Error during acquisition setup");
+                    model_.logging().reportError(e, "Error during acquisition setup");
                     return; // early exit => stop acquisition
                 }
                 run(); // run the acquisition and block until complete
             } catch (Exception e) {
-                studio_.logs().showError(e);
+                model_.logging().reportError(e);
             } finally {
                 try {
                     finish(); // cleanup any resources
                 } catch (Exception e) {
-                    studio_.logs().showError(e, "Error during acquisition cleanup");
+                    model_.logging().reportError(e, "Error during acquisition cleanup");
                 } finally {
                     // must ALWAYS run: if currentAcquisition_ is left set, every future
                     // acquisition is rejected until the plugin restarts
@@ -273,7 +274,7 @@ public Future<?> requestRun(boolean speedTest) {
     @Override
     public void requestStop() {
         if (currentAcquisition_ == null || currentAcquisition_.getDataSink().isFinished()) {
-            studio_.logs().showError("Acquisition is not running.");
+            model_.logging().reportError("Acquisition is not running.");
             return;
         }
         currentAcquisition_.abort();
@@ -282,7 +283,7 @@ public void requestStop() {
     @Override
     public void requestPause() {
         if (currentAcquisition_ == null) {
-            studio_.logs().showError("Acquisition is not running.");
+            model_.logging().reportError("Acquisition is not running.");
         } else {
             currentAcquisition_.setPaused(true);
         }