add PluginSettings to store additional settings

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

@@ -14,7 +14,7 @@ public class LightSheetManagerPlugin implements MenuPlugin, SciJavaPlugin {
     public static final String copyright = "Applied Scientific Instrumentation (ASI), 2022-2024";
     public static final String description = "A plugin to control various types of light sheet microscopes.";
     public static final String menuName = "Light Sheet Manager";
-    public static final String version = "0.4.2";
+    public static final String version = "0.4.3";
 
     private Studio studio_;
     private LightSheetManagerFrame frame_;

src/main/java/org/micromanager/lightsheetmanager/gui/LightSheetManagerFrame.java

@@ -135,11 +135,13 @@ private void createUserInterface() {
         tabPanel_.getNavigationTab().getNavigationPanel()
                 .getPositionUpdater().setPositionPanel(positionPanel);
 
-        tabPanel_.getNavigationTab().getNavigationPanel().startPolling();
+        if (model_.pluginSettings().isPollingPositions()) {
+            tabPanel_.getNavigationTab().getNavigationPanel().startPolling();
+        }
 
         WindowUtils.registerWindowClosingEvent(this, event -> {
             tabPanel_.getNavigationTab().getNavigationPanel().stopPolling();
-            model_.getUserSettings().save();
+            model_.userSettings().save();
             studio_.logs().logMessage("user settings saved");
         });
 

src/main/java/org/micromanager/lightsheetmanager/gui/frames/NavigationFrame.java

@@ -18,11 +18,9 @@ public NavigationFrame(final LightSheetManagerModel model) {
         add(navigationPanel_, "");
     }
 
+    // TODO: this would need ui and events
     public void init() {
-        navigationPanel_.createUserInterface();
+        //navigationPanel_.createUserInterface();
     }
 
-    public void stopTimer() {
-        navigationPanel_.stopPolling();
-    }
 }

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/navigation/NavigationPanel.java

@@ -41,13 +41,16 @@ public NavigationPanel(final LightSheetManagerModel model) {
         devices_ = model_.devices();
 
         controlPanels_ = new ArrayList<>();
+        positionUpdater_ = new PositionUpdater(this);
 
         createUserInterface();
         createEventHandlers();
-        positionUpdater_ = new PositionUpdater(this);
     }
 
-    public void createUserInterface() {
+    /**
+     * Create the control panels for each device.
+     */
+    private void createUserInterface() {
 
         Panel.setMigLayoutDefault(
                 "", //""debug 1000",
@@ -57,7 +60,9 @@ public void createUserInterface() {
 
         btnHaltDevices_ = new Button("HALT", 120, 30);
         btnRefreshPanel_ = new Button("Refresh", 120, 30);
-        cbxPollPositions_ = new CheckBox("Poll Positions", true);
+
+        cbxPollPositions_ = new CheckBox("Poll Positions",
+                model_.pluginSettings().isPollingPositions());
 
         final int numImagingPaths = devices_.getDeviceAdapter().getNumImagingPaths();
         final int numIlluminationPaths = devices_.getDeviceAdapter().getNumIlluminationPaths();
@@ -228,22 +233,27 @@ public void createUserInterface() {
 
     private void createEventHandlers() {
 
+        // refresh devices and ui
         btnRefreshPanel_.registerListener(e -> {
             //System.out.println("refresh pressed");
             removeAll();
             createUserInterface();
             createEventHandlers();
+            revalidate();
+            repaint();
             if (cbxPollPositions_.isSelected()) {
                 positionUpdater_.startPolling();
             }
-            revalidate();
-            repaint();
         });
 
+        // halt stage devices
         btnHaltDevices_.registerListener(e -> haltAllDevices());
 
+        // position polling
         cbxPollPositions_.registerListener(e -> {
-            if (cbxPollPositions_.isSelected()) {
+            final boolean isSelected = cbxPollPositions_.isSelected();
+            model_.pluginSettings().setPollingPositions(isSelected);
+            if (isSelected) {
                 positionUpdater_.startPolling();
             } else {
                 positionUpdater_.stopPolling();
@@ -306,4 +316,5 @@ private void haltAllDevices() {
             }
         }
     }
+
 }

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/navigation/PositionUpdater.java

@@ -17,20 +17,22 @@ public class PositionUpdater {
 
     private SwingWorker<Void, Void> worker_;
 
-    private PositionPanel positionPanel_; // TODO: update multiple setup panels
+    private PositionPanel positionPanel_; // TODO: update multiple setup panels for diSPIM
 
     private final NavigationPanel navPanel_;
 
     private final AtomicBoolean isPolling_;
 
     public PositionUpdater(final NavigationPanel navPanel) {
         navPanel_ = Objects.requireNonNull(navPanel);
-        isPolling_ = new AtomicBoolean(true);
+        isPolling_ = new AtomicBoolean(false);
         pollingDelayMs_ = 500;
     }
 
+    /**
+     * Create the polling thread without starting it.
+     */
     private void createPollingTask() {
-        isPolling_.set(true);
         worker_ = new SwingWorker<Void, Void>() {
             @Override
             protected Void doInBackground() {
@@ -40,44 +42,69 @@ protected Void doInBackground() {
                         navPanel_.updatePositions();
                         positionPanel_.updatePositions();
                     } catch (Exception e) {
-                        e.printStackTrace();
-                    }
-                    if (!isPolling_.get()) {
-                        //System.out.println("break!");
-                        break;
+                        //e.printStackTrace();
                     }
                     try {
                         Thread.sleep(pollingDelayMs_);
                     } catch (InterruptedException e) {
                         throw new RuntimeException(e);
                     }
                 }
+                //System.out.println("done!");
                 return null;
             }
         };
     }
 
+    /**
+     * Create the polling task and start the thread.
+     */
     public void startPolling() {
+        isPolling_.set(true);
         createPollingTask();
         worker_.execute();
     }
 
+    /**
+     * Stops the position polling thread.
+     */
     public void stopPolling() {
         isPolling_.set(false);
     }
 
+    /**
+     * Return true if polling positions.
+     *
+     * @return true if polling positions
+     */
     public boolean isPolling() {
         return isPolling_.get();
     }
 
+    /**
+     * Set the polling delay in milliseconds.
+     *
+     * @param delayMs delay in milliseconds
+     */
     public void setPollingDelayMs(final int delayMs) {
         pollingDelayMs_ = delayMs;
     }
 
+    /**
+     * Return the polling delay in milliseconds.
+     *
+     * @return the polling delay in milliseconds
+     */
     public int getPollingDelayMs() {
         return pollingDelayMs_;
     }
 
+    // TODO: better way to connect this?
+    /**
+     * Set the position panel to update in addition to the {@code NavigationPanel}.
+     *
+     * @param panel the reference to the panel
+     */
     public void setPositionPanel(final PositionPanel panel) {
         positionPanel_ = panel;
     }

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

@@ -24,7 +24,8 @@ public class LightSheetManagerModel implements LightSheetManager {
 
     private String errorText_;
 
-    private UserSettings settings_;
+    private UserSettings userSettings_;
+    private PluginSettings pluginSettings_;
 
     private DeviceManager deviceManager_;
 
@@ -37,7 +38,8 @@ public LightSheetManagerModel(final Studio studio) {
         studio_ = Objects.requireNonNull(studio);
         core_ = studio_.core();
 
-        settings_ = new UserSettings(this);
+        pluginSettings_ = new PluginSettings();
+        userSettings_ = new UserSettings(this);
         xyzGrid_ = new XYZGrid(this);
 
         // set during setup if there is an error
@@ -79,7 +81,7 @@ public boolean setup() {
         }
 
         // load settings
-        settings_.load();
+        userSettings_.load();
 
         // if we made it here then everything loaded correctly
         return true;
@@ -114,8 +116,16 @@ public DeviceManager devices() {
         return deviceManager_;
     }
 
-    public UserSettings getUserSettings() {
-        return settings_;
+    public UserSettings userSettings() {
+        return userSettings_;
+    }
+
+    public PluginSettings pluginSettings() {
+        return pluginSettings_;
+    }
+
+    public void pluginSettings(final PluginSettings pluginSettings) {
+        pluginSettings_ = Objects.requireNonNull(pluginSettings);
     }
 
     public CMMCore getCore() {

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

@@ -12,7 +12,9 @@
 import java.util.Optional;
 
 /**
- * This wraps Micro-Manager's settings profiles to store the plugin settings.
+ * Micro-Manager user settings for the current user.
+ * <p>
+ * This class is used to save and load settings using JSON strings.
  */
 public class UserSettings {
 
@@ -34,9 +36,9 @@ public class UserSettings {
     public UserSettings(final LightSheetManagerModel model) {
         model_ = Objects.requireNonNull(model);
         // setup user profile
-        UserProfile profile = model_.getStudio().getUserProfile();
-        userName_ = profile.getProfileName();
+        final UserProfile profile = model_.getStudio().getUserProfile();
         settings_ = profile.getSettings(UserSettings.class);
+        userName_ = profile.getProfileName();
     }
 
     /**
@@ -51,14 +53,14 @@ public MutablePropertyMapView get() {
     /**
      * Returns the name of the user profile.
      *
-     * @return a String containing the name
+     * @return a {@code String} containing the name
      */
     public String getUserName() {
         return userName_;
     }
 
     /**
-     * Clears all user settings associated with this class name.
+     * Clears all user settings associated with this profile name.
      */
     public void clear() {
         settings_.clear();
@@ -92,6 +94,16 @@ public void load() {
                         + model_.acquisitions().settings().toPrettyJson());
             }
         }
+
+        // load plugin settings or default plugin settings
+        final String jsonStr = settings_.getString(SETTINGS_KEY, SETTINGS_NOT_FOUND);
+        if (jsonStr.equals(SETTINGS_NOT_FOUND)) {
+            model_.studio().logs().logDebugMessage("settings not found, using default plugin settings.");
+        } else {
+            model_.pluginSettings(PluginSettings.fromJson(jsonStr));
+            model_.studio().logs().logDebugMessage("loaded PluginSettings from " + SETTINGS_KEY + ": "
+                    + model_.pluginSettings().toPrettyJson());
+        }
     }
 
     /**
@@ -100,17 +112,25 @@ public void load() {
     public void save() {
         // make settings current before saving
         model_.acquisitions().updateAcquisitionSettings();
-        // settings key
+
+        // settings key based on geometry type
         final GeometryType geometryType = model_.devices()
                 .getDeviceAdapter().getMicroscopeGeometry();
         final String key = SETTINGS_PREFIX_KEY +
                 geometryType.toString().toUpperCase();
-        // save in user settings
+
+        // save acquisition settings
         settings_.putString(key, model_.acquisitions().settings().toJson());
         model_.studio().logs().logDebugMessage("saved JSON to " + key + ": "
                 + model_.acquisitions().settings().toPrettyJson());
+
+        // save plugin settings
+        settings_.putString(SETTINGS_KEY, model_.pluginSettings().toJson());
+        model_.studio().logs().logDebugMessage("saved PluginSettings to " + SETTINGS_KEY + ": "
+                + model_.pluginSettings().toPrettyJson());
     }
 
+    // TODO: this can add new keys but doesn't delete renamed keys
     /**
      * Returns the {@code JSONObject} after checking if it matches the schema of the
      * default acquisition settings object. If it does not, then any new settings