lots of cleanup and add defaults

src/main/java/org/micromanager/lightsheetmanager/api/data/AcquisitionMode.java

@@ -15,7 +15,9 @@
 // Note: Each text string must be unique to support reliable lookup in fromString().
 
 /**
- * Acquisition modes for all microscope geometry types.
+ * Acquisition modes for all microscope geometries.
+ * <p>
+ * Use the {@code modesByType} method to get valid modes based on {@link GeometryType}.
  */
 public enum AcquisitionMode {
     NO_SCAN("No scan (fixed sheet)"),
@@ -71,7 +73,7 @@ public String toString() {
     }
 
     /**
-     * Returns {@code true} if the {@link AcquisitionMode} is a stage scan mode.
+     * Returns {@code true} if the {@code AcquisitionMode} is a stage scan mode.
      *
      * @return {@code true} if the mode is stage scan mode
      */
@@ -85,13 +87,13 @@ public boolean isStageScanMode() {
      * This list is filtered based on hardware capabilities: if {@code hasStageScanning}
      * is {@code false}, all stage-scan related modes are excluded.
      *
-     * @param geometry the {@link GeometryType} to query; if {@code null}, an empty list is returned
+     * @param geometryType the {@link GeometryType} to query; if {@code null}, an empty list is returned
      * @param hasStageScanning {@code true} if stage scan hardware is available
-     * @return a {@code List} of {@link AcquisitionMode} constants
+     * @return an array of {@code AcquisitionMode} constants
      */
-    public static AcquisitionMode[] getValidModes(final GeometryType geometry, final boolean hasStageScanning) {
-        return Optional.ofNullable(geometry)
-                .map(MODES_BY_GEOMETRY::get) // returns null if geometry is not in map
+    public static AcquisitionMode[] modesByType(final GeometryType geometryType, final boolean hasStageScanning) {
+        return Optional.ofNullable(geometryType)
+                .map(MODES_BY_GEOMETRY::get) // returns null if geometryType is not in map
                 .orElse(Collections.emptyList())
                 .stream()
                 .filter(mode -> hasStageScanning || !mode.isStageScanMode())

src/main/java/org/micromanager/lightsheetmanager/api/data/CameraData.java

@@ -35,4 +35,10 @@ public static boolean isCameraActive(final CameraData[] cameras, final String ca
         }
         return false;
     }
+
+    @Override
+    public String toString() {
+        return String.format("%s[name=%s]", getClass().getSimpleName(), name_);
+    }
+
 }

src/main/java/org/micromanager/lightsheetmanager/api/data/CameraMode.java

@@ -1,7 +1,6 @@
 package org.micromanager.lightsheetmanager.api.data;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Map;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
@@ -10,8 +9,6 @@
 
 /**
  * Camera trigger modes.
- *
- * <p>All modes should use hardware triggering.
  */
 public enum CameraMode {
     INTERNAL("Internal"),
@@ -23,15 +20,15 @@ public enum CameraMode {
 
     private final String text_;
 
-    private static final Map<String, CameraMode> stringToEnum =
+    private static final Map<String, CameraMode> STRING_TO_ENUM =
             Stream.of(values()).collect(Collectors.toUnmodifiableMap(Object::toString, e -> e));
 
     CameraMode(final String text) {
         text_ = text;
     }
 
     public static CameraMode fromString(final String symbol) {
-        return stringToEnum.getOrDefault(symbol, CameraMode.EDGE);
+        return STRING_TO_ENUM.getOrDefault(symbol, CameraMode.EDGE);
     }
 
     /**
@@ -53,11 +50,11 @@ public static boolean hasOverlapTrigger(final CameraLibrary camLib) {
      * @param camLib the camera device adapter
      * @return {@code true} if the camera supports the mode
      */
-    private static boolean hasPseudoOverlapTrigger(CameraLibrary camLib) {
+    private static boolean hasPseudoOverlapTrigger(final CameraLibrary camLib) {
         return camLib == CameraLibrary.PCOCAMERA || camLib == CameraLibrary.PVCAM;
     }
 
-    private static boolean hasLevelTrigger(CameraLibrary camLib) {
+    private static boolean hasLevelTrigger(final CameraLibrary camLib) {
         return camLib == CameraLibrary.HAMAMATSU ||
                 camLib == CameraLibrary.ANDORSDK3 ||
                 camLib == CameraLibrary.PCOCAMERA;
@@ -69,37 +66,35 @@ private static boolean hasLevelTrigger(CameraLibrary camLib) {
      * @param camLib the camera device adapter
      * @return {@code true} if the camera supports the mode
      */
-    private static boolean hasLightSheetTrigger(CameraLibrary camLib) {
+    private static boolean hasLightSheetTrigger(final CameraLibrary camLib) {
         return camLib == CameraLibrary.HAMAMATSU ||
                 camLib == CameraLibrary.ANDORSDK3 ||
                 camLib == CameraLibrary.PVCAM || // not sure about this
                 camLib == CameraLibrary.DEMOCAMERA;  // for testing only
     }
 
-    public static boolean isCameraValid(CameraLibrary camLib) {
+    public static boolean isCameraValid(final CameraLibrary camLib) {
         return camLib != CameraLibrary.UNKNOWN;
     }
 
-    public static CameraMode[] getAvailableModes(CameraLibrary camLib) {
+    public static CameraMode[] modesByDeviceLibrary(final CameraLibrary cameraLibrary) {
         ArrayList<CameraMode> modes = new ArrayList<>();
-        if (isCameraValid(camLib)) {
+        if (isCameraValid(cameraLibrary)) {
             modes.add(CameraMode.EDGE);
-            if (hasLevelTrigger(camLib)) {
+            if (hasLevelTrigger(cameraLibrary)) {
                 modes.add(CameraMode.LEVEL);
             }
-            if (hasOverlapTrigger(camLib)) {
+            if (hasOverlapTrigger(cameraLibrary)) {
                 modes.add(CameraMode.OVERLAP);
             }
-            if (hasPseudoOverlapTrigger(camLib)) {
+            if (hasPseudoOverlapTrigger(cameraLibrary)) {
                 modes.add(CameraMode.PSEUDO_OVERLAP);
             }
-            if (hasLightSheetTrigger(camLib)) {
+            if (hasLightSheetTrigger(cameraLibrary)) {
                 modes.add(CameraMode.VIRTUAL_SLIT);
             }
         }
-        return modes.stream()
-                .map(CameraMode::toString)
-                .toArray(CameraMode[]::new);
+        return modes.toArray(CameraMode[]::new);
     }
 
     @Override

src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultAcquisitionSettings.java

@@ -5,17 +5,15 @@
 import org.micromanager.lightsheetmanager.api.AcquisitionSettings;
 import org.micromanager.lightsheetmanager.model.DataStorage;
 
-// TODO: make public instead of abstract? use this in demo mode?
-
 /**
  * Base acquisition settings for all microscopes.
  */
 public abstract class DefaultAcquisitionSettings implements AcquisitionSettings {
 
     public abstract static class Builder<T extends Builder<T>> implements AcquisitionSettings.Builder<T> {
 
-        private String saveDirectory_ = "";
-        private String saveNamePrefix_ = "";
+        private String saveDirectory_ = System.getProperty("user.home");
+        private String saveNamePrefix_ = "Experiment";
         private boolean saveDuringAcq_ = false;
         private boolean demoMode_ = false;
         private DataStorage.SaveMode saveMode_ = DataStorage.SaveMode.ND_TIFF;

src/main/java/org/micromanager/lightsheetmanager/gui/components/CheckBox.java

@@ -9,6 +9,8 @@ public class CheckBox extends JCheckBox {
     public static final int LEFT = SwingConstants.LEFT;
     public static final int RIGHT = SwingConstants.RIGHT;
 
+    private boolean isLocked_ = false;
+
     public CheckBox(final String text, final boolean defaultState) {
         super(text, defaultState);
         setHorizontalTextPosition(RIGHT);
@@ -28,8 +30,59 @@ public CheckBox(final String text, final int fontSize, final boolean defaultStat
         setFocusPainted(false);
     }
 
+    /**
+     * Set the locked state, in the locked state the {@code CheckBox}
+     * will not respond to button presses or mouse clicks.
+     *
+     * @param locked the locked state
+     */
+    public void setLocked(final boolean locked) {
+        isLocked_ = locked;
+        if (locked) {
+            setFont(getFont().deriveFont(java.awt.Font.BOLD));
+        } else {
+            setFont(getFont().deriveFont(java.awt.Font.PLAIN));
+        }
+    }
+
+    /**
+     * Sets the selected state of the {@code CheckBox}.
+     *
+     * @param state the new selection state
+     * @param shouldFire {@code true} fires events, {@code false} updates silently
+     */
+    public void setSelected(boolean state, boolean shouldFire) {
+        if (shouldFire) {
+            // Standard behavior: updates state and triggers events
+            super.setSelected(state);
+        } else {
+            // "Silent" behavior: updates state via model without firing ActionEvents
+            getModel().setSelected(state);
+        }
+    }
+
     public void registerListener(final Method method) {
-        addItemListener(method::run);
+        addActionListener(method::run);
+    }
+
+    @Override
+    public void setSelected(boolean state) {
+        // default to true, always fires events
+        setSelected(state, true);
+    }
+
+    @Override
+    protected void processMouseEvent(java.awt.event.MouseEvent e) {
+        if (!isLocked_) {
+            super.processMouseEvent(e);
+        }
+    }
+
+    @Override
+    protected void processKeyEvent(java.awt.event.KeyEvent e) {
+        if (!isLocked_) {
+            super.processKeyEvent(e);
+        }
     }
 
 }

src/main/java/org/micromanager/lightsheetmanager/gui/components/RadioButton.java

@@ -79,7 +79,8 @@ public void setSelected(final String text, final boolean state) {
         }
     }
 
-    public String getSelectedButtonText() {
+    // Returns the text of the selected button.
+    public String getSelectedText() {
         for (final JRadioButton button : buttons) {
             if (button.isSelected()) {
                 return button.getText();
@@ -88,6 +89,16 @@ public String getSelectedButtonText() {
         return "";
     }
 
+    // Returns the selected index or -1 if nothing is selected.
+    public int getSelectedIndex() {
+        for (int i = 0; i < buttons.size(); i++) {
+            if (buttons.get(i).isSelected()) {
+                return i;
+            }
+        }
+        return -1;
+    }
+
     public void registerListener(final Method method) {
         for (final JRadioButton button : buttons) {
             button.addActionListener(method::run);

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

@@ -166,7 +166,8 @@ private void createUserInterface() {
         // acquisition mode combo box
         final boolean isUsingScanSettings = model_.devices().isUsingStageScanning();
         final GeometryType geometryType = model_.devices().adapter().geometry();
-        cmbAcquisitionModes_ = new ComboBox<>(AcquisitionMode.getValidModes(geometryType, isUsingScanSettings),
+        cmbAcquisitionModes_ = new ComboBox<>(
+                AcquisitionMode.modesByType(geometryType, isUsingScanSettings),
                 acqSettings.acquisitionMode(),
                 180, 24);
 

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

@@ -33,6 +33,7 @@ public class CameraTab extends Panel implements ListeningPanel {
     private RadioButton radPrimaryCamera_;
     private CheckBox cbxUseSimultaneousCameras_;
     private List<CheckBox> cbxCameras_;
+    private int selectedIndex_;
 
     private final TabPanel tabPanel_;
     private final LightSheetManager model_;
@@ -71,7 +72,7 @@ private void createUserInterface() {
         final CameraBase camera = model_.devices().firstImagingCamera();
         if (camera != null) {
             final CameraLibrary camLib = CameraLibrary.fromString(camera.getDeviceLibrary());
-            modes = CameraMode.getAvailableModes(camLib);
+            modes = CameraMode.modesByDeviceLibrary(camLib);
         }
 
         cmbCameraTriggerMode_ = new ComboBox<>(modes,
@@ -112,6 +113,11 @@ private void createUserInterface() {
             cbxCameras_.add(checkBox);
         }
 
+        // we can only set this after we load the settings
+        selectedIndex_ = radPrimaryCamera_.getSelectedIndex();
+        // must not disable the primary camera
+        cbxCameras_.get(selectedIndex_).setLocked(true);
+
         final Panel pnlCameraSelectionRow = new Panel();
         pnlCameraSelectionRow.add(new JLabel("Select Primary Camera"), "wrap");
         pnlCameraSelectionRow.add(radPrimaryCamera_, "");
@@ -177,31 +183,37 @@ private boolean[] activeCameras() {
         return active;
     }
 
+    // Change the order of the imaging camera array based on user input.
     private void computeCameraOrder() {
-        // change the order of the imaging camera array
-        final String selected = radPrimaryCamera_.getSelectedButtonText();
-        final String[] cameraNames = model_.devices().imagingCameraNames();
-        final ArrayList<CameraData> cameraData = new ArrayList<>(cameraNames.length);
+        // cache the previous index
+        final int lastSelectedIndex = selectedIndex_;
 
-        // check if the selected primary camera is active before changing the array order
-        boolean isSelectedActive = true;
-        final boolean[] active = activeCameras();
-        for (int i = 0; i < cameraNames.length; i++) {
-            if (cameraNames[i].equals(selected)) {
-                isSelectedActive = active[i];
-                break;
-            }
-        }
+        // unlock the checkbox for the old primary camera
+        cbxCameras_.get(lastSelectedIndex).setLocked(false);
+
+        // lock the checkbox for the new primary camera
+        final String selected = radPrimaryCamera_.getSelectedText();
+        selectedIndex_ = radPrimaryCamera_.getSelectedIndex();
+        cbxCameras_.get(selectedIndex_).setSelected(true, false);
+        cbxCameras_.get(selectedIndex_).setLocked(true);
 
         // the first array index is the primary camera
-        cameraData.add(new CameraData(selected, isSelectedActive));
+        final String[] cameraNames = model_.devices().imagingCameraNames();
+        final ArrayList<CameraData> cameraData = new ArrayList<>(cameraNames.length);
+        cameraData.add(new CameraData(selected, true));
+
         // TODO(Brandon): uses simple ordering that works for 2 cameras,
-        //   but needs additional work to support 4. Use a reorderable JTable?
+        //   but needs additional work to support 4.
+
+        // add cameras in a linear order for now
+        final boolean[] active = activeCameras();
         for (int i = 0; i < cameraNames.length; i++) {
             if (!selected.equals(cameraNames[i])) {
                 cameraData.add(new CameraData(cameraNames[i], active[i]));
             }
         }
+
+        // update camera order
         model_.acquisitions().settingsBuilder()
                 .imagingCameraOrder(cameraData.toArray(CameraData[]::new));
     }

src/main/java/org/micromanager/lightsheetmanager/gui/utils/DialogUtils.java

@@ -10,7 +10,12 @@
  * A utility class for making dialog boxes.
  *
  */
-public class DialogUtils {
+public final class DialogUtils {
+
+    /** This class should not be instantiated. */
+    private DialogUtils() {
+        throw new AssertionError("Utility class; do not instantiate.");
+    }
 
     /**Standard error reporting or delegate to JTextArea component. */
     public static boolean SEND_ERROR_TO_COMPONENT = false;

src/main/java/org/micromanager/lightsheetmanager/gui/utils/WindowUtils.java

@@ -7,6 +7,11 @@
 
 public final class WindowUtils {
 
+    /** This class should not be instantiated. */
+    private WindowUtils() {
+        throw new AssertionError("Utility class; do not instantiate.");
+    }
+
     /**
      * Returns true if the window is displayable and not null.
      *

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

@@ -85,15 +85,6 @@ boolean setup() {
 //            return false;
 //        }
 
-        // we must have an active camera if we are using simultaneous cameras
-        if (model_.acquisitions().settings().isUsingSimultaneousCameras()) {
-            final CameraData[] cameras = model_.acquisitions().settings().imagingCameraOrder();
-            if (cameras.length > 0 && !cameras[0].isActive()) {
-                studio_.logs().showError("The primary camera MUST be active in simultaneous cameras mode!");
-                return false;
-            }
-        }
-
         // set the "Core-Camera" property to the first logical camera device
         final String cameraName = model_.devices().firstImagingCamera().getDeviceName();
         try {