use a single array of objects for camera order

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

@@ -12,7 +12,7 @@ public class LightSheetManagerPlugin implements MenuPlugin, SciJavaPlugin {
     public static final String copyright = "Applied Scientific Instrumentation (ASI), 2022-2026";
     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 = "0.5.7";
+    public static final String version = "0.5.8";
 
     private Studio studio_;
     private LightSheetManager model_;

src/main/java/org/micromanager/lightsheetmanager/api/AcquisitionSettingsSCAPE.java

@@ -1,6 +1,7 @@
 package org.micromanager.lightsheetmanager.api;
 
 import org.micromanager.lightsheetmanager.api.data.AcquisitionMode;
+import org.micromanager.lightsheetmanager.api.data.CameraData;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
 import org.micromanager.lightsheetmanager.api.internal.DefaultChannelSettings;
 import org.micromanager.lightsheetmanager.api.internal.DefaultScanSettings;
@@ -37,14 +38,7 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
          *
          * @param cameraOrder the imaging camera order
          */
-        T imagingCameraOrder(final String[] cameraOrder);
-
-        /**
-         * Sets the active imaging cameras.
-         *
-         * @param camerasActive the active imaging cameras
-         */
-        T imagingCamerasActive(final boolean[] camerasActive);
+        T imagingCameraOrder(final CameraData[] cameraOrder);
 
         /**
          * Sets the acquisition to acquire from multiple simultaneous cameras.
@@ -213,14 +207,7 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
      *
      * @return the imaging camera order
      */
-    String[] imagingCameraOrder();
-
-    /**
-     * Returns an array of active imaging cameras.
-     *
-     * @return an array of active imaging cameras
-     */
-    boolean[] imagingCamerasActive();
+    CameraData[] imagingCameraOrder();
 
     /**
      * Returns true if acquiring from both imaging cameras.

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

@@ -0,0 +1,38 @@
+package org.micromanager.lightsheetmanager.api.data;
+
+// Used to track imaging camera order for simultaneous imaging cameras.
+public class CameraData {
+
+    private String name_;
+    private boolean isActive_;
+
+    public CameraData(final String name, final boolean isActive) {
+        name_ = name;
+        isActive_ = isActive;
+    }
+
+    public String name() {
+        return name_;
+    }
+
+    public void name(final String name) {
+        name_ = name;
+    }
+
+    public boolean isActive() {
+        return isActive_;
+    }
+
+    public void isActive(final boolean isActive) {
+        isActive_ = isActive;
+    }
+
+    public static boolean isCameraActive(final CameraData[] cameras, final String cameraName) {
+        for (CameraData camera : cameras) {
+            if (camera.name().equals(cameraName)) {
+                return camera.isActive();
+            }
+        }
+        return false;
+    }
+}

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

@@ -2,6 +2,7 @@
 
 import org.micromanager.lightsheetmanager.api.AcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.api.data.AcquisitionMode;
+import org.micromanager.lightsheetmanager.api.data.CameraData;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
 
 public class DefaultAcquisitionSettingsSCAPE extends DefaultAcquisitionSettings implements AcquisitionSettingsSCAPE {
@@ -19,8 +20,7 @@ public static class Builder extends DefaultAcquisitionSettings.Builder<Builder>
         private AcquisitionMode acquisitionMode_ = AcquisitionMode.NO_SCAN;
 
         private CameraMode cameraMode_ = CameraMode.EDGE;
-        private String[] imagingCameraOrder_ = {};
-        private boolean[] imagingCamerasActive_ = {};
+        private CameraData[] imagingCameraOrder_ = {};
         private boolean useSimultaneousCameras_ = true;
 
         private boolean useChannels_ = false;
@@ -58,7 +58,6 @@ public Builder(final DefaultAcquisitionSettingsSCAPE acqSettings) {
             acquisitionMode_ = acqSettings.acquisitionMode_;
             cameraMode_ = acqSettings.cameraMode_;
             imagingCameraOrder_ = acqSettings.imagingCameraOrder_;
-            imagingCamerasActive_ = acqSettings.imagingCamerasActive_;
             useSimultaneousCameras_ = acqSettings.useSimultaneousCameras_;
             useChannels_ = acqSettings.useChannels_;
             useTimePoints_ = acqSettings.useTimePoints_;
@@ -107,22 +106,11 @@ public Builder cameraMode(final CameraMode cameraMode) {
          * @param cameraOrder the imaging camera order
          */
         @Override
-        public Builder imagingCameraOrder(final String[] cameraOrder) {
+        public Builder imagingCameraOrder(final CameraData[] cameraOrder) {
             imagingCameraOrder_ = cameraOrder;
             return this;
         }
 
-        /**
-         * Sets the active imaging cameras.
-         *
-         * @param camerasActive the active imaging cameras
-         */
-        @Override
-        public Builder imagingCamerasActive(final boolean[] camerasActive) {
-            imagingCamerasActive_ = camerasActive;
-            return this;
-        }
-
         /**
          * Sets the acquisition to acquire from multiple simultaneous cameras.
          *
@@ -322,8 +310,7 @@ public String toString() {
     private final AcquisitionMode acquisitionMode_;
 
     private final CameraMode cameraMode_;
-    private final String[] imagingCameraOrder_;
-    private final boolean[] imagingCamerasActive_;
+    private final CameraData[] imagingCameraOrder_;
     private final boolean useSimultaneousCameras_;
 
     private final boolean useChannels_;
@@ -356,7 +343,6 @@ private DefaultAcquisitionSettingsSCAPE(Builder builder) {
         acquisitionMode_ = builder.acquisitionMode_;
         cameraMode_ = builder.cameraMode_;
         imagingCameraOrder_ = builder.imagingCameraOrder_;
-        imagingCamerasActive_ = builder.imagingCamerasActive_;
         useSimultaneousCameras_ = builder.useSimultaneousCameras_;
         useChannels_ = builder.useChannels_;
         useTimePoints_ = builder.useTimePoints_;
@@ -506,20 +492,10 @@ public CameraMode cameraMode() {
      * @return the imaging camera order
      */
     @Override
-    public String[] imagingCameraOrder() {
+    public CameraData[] imagingCameraOrder() {
         return imagingCameraOrder_;
     }
 
-    /**
-     * Returns an array of active imaging cameras.
-     *
-     * @return an array of active imaging cameras
-     */
-    @Override
-    public boolean[] imagingCamerasActive() {
-        return imagingCamerasActive_;
-    }
-
     /**
      * Returns true if acquiring from all active imaging cameras on a single view.
      *

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

@@ -1,5 +1,6 @@
 package org.micromanager.lightsheetmanager.gui.tabs;
 
+import org.micromanager.lightsheetmanager.api.data.CameraData;
 import org.micromanager.lightsheetmanager.api.data.CameraLibrary;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
 import org.micromanager.lightsheetmanager.gui.components.Button;
@@ -31,7 +32,7 @@ public class CameraTab extends Panel implements ListeningPanel {
     private ComboBox cmbCameraTriggerMode_;
     private RadioButton radPrimaryCamera_;
     private CheckBox cbxUseSimultaneousCameras_;
-    private List<CheckBox> cbxActiveCameras_;
+    private List<CheckBox> cbxCameras_;
 
     private final TabPanel tabPanel_;
     private final LightSheetManager model_;
@@ -63,22 +64,30 @@ private void createUserInterface() {
         btnCustomROI_ = new Button("Custom", 140, 30);
         btnGetCurrentROI_ = new Button("Get Current ROI", 140, 30);
 
+        // TODO: use optional here for camera?
+
         // get the imaging camera library
+        String[] modes = {""};
         final CameraBase camera = model_.devices().firstImagingCamera();
-        final CameraLibrary camLib = CameraLibrary.fromString(camera.getDeviceLibrary());
+        if (camera != null) {
+            final CameraLibrary camLib = CameraLibrary.fromString(camera.getDeviceLibrary());
+            modes = CameraMode.getAvailableModes(camLib);
+        }
 
-        cmbCameraTriggerMode_ = new ComboBox(CameraMode.getAvailableModes(camLib),
+        cmbCameraTriggerMode_ = new ComboBox(modes,
                 model_.acquisitions().settings().cameraMode().toString());
 
         // validate that the logical device name exists
         final String[] cameraNames = model_.devices().imagingCameraNames();
-        cbxActiveCameras_ = new ArrayList<>(cameraNames.length);
+        cbxCameras_ = new ArrayList<>(cameraNames.length);
 
         // the first element of the list is the primary camera
         String primaryCamera = "";
-        final String[] cameraOrder =  model_.acquisitions().settings().imagingCameraOrder();
+        final CameraData[] cameraOrder =  model_.acquisitions().settings().imagingCameraOrder();
         if (cameraOrder.length > 0) {
-            primaryCamera = cameraOrder[0];
+            primaryCamera = cameraOrder[0].name();
+        } else {
+            primaryCamera = cameraNames[0]; // default to first camera name
         }
 
         // simultaneous camera settings
@@ -94,11 +103,12 @@ private void createUserInterface() {
                 "[]6[]"
         );
 
-        final boolean[] activeCameras = model_.acquisitions().settings().imagingCamerasActive();
-        for (int i = 0; i < cameraNames.length; i++) {
-            final CheckBox checkBox = new CheckBox("Active", activeCameras[i]);
+        // we already have the camera order array
+        for (String cameraName : cameraNames) {
+            final boolean isActive = CameraData.isCameraActive(cameraOrder, cameraName);
+            final CheckBox checkBox = new CheckBox("Active", isActive);
             pnlCheckboxes.add(checkBox, "wrap");
-            cbxActiveCameras_.add(checkBox);
+            cbxCameras_.add(checkBox);
         }
 
         final Panel pnlCameraSelectionRow = new Panel();
@@ -142,30 +152,12 @@ private void createEventHandlers() {
             tabPanel_.swapSetupPathPanels(cameraMode);
         });
 
-        // TODO(Brandon): uses simple ordering that works for 2 cameras,
-        //   but needs additional work to support 4. Use a reorderable JTable?
-
         // select primary camera
-        radPrimaryCamera_.registerListener(e -> {
-            final String selected = radPrimaryCamera_.getSelectedButtonText();
-            final String[] cameraNames = model_.devices().imagingCameraNames();
-            final List<String> cameraOrder = new ArrayList<>();
-            // the first array index is the primary camera
-            cameraOrder.add(selected);
-            for (String cameraName : cameraNames) {
-                if (!selected.equals(cameraName)) {
-                    cameraOrder.add(cameraName);
-                }
-            }
-            model_.acquisitions().settingsBuilder()
-                    .imagingCameraOrder(cameraOrder.toArray(String[]::new));
-        });
+        radPrimaryCamera_.registerListener(e -> computeCameraOrder());
 
         // active camera check boxes
-        for (CheckBox cbx : cbxActiveCameras_) {
-            cbx.registerListener(e ->
-                    model_.acquisitions().settingsBuilder()
-                            .imagingCamerasActive(activeCameras()));
+        for (CheckBox cbx : cbxCameras_) {
+            cbx.registerListener(e -> computeCameraOrder());
         }
 
         // use all active cameras
@@ -177,13 +169,43 @@ private void createEventHandlers() {
     }
 
     private boolean[] activeCameras() {
-        boolean[] active = new boolean[cbxActiveCameras_.size()];
-        for (int i = 0; i < cbxActiveCameras_.size(); i++) {
-            active[i] = cbxActiveCameras_.get(i).isSelected();
+        boolean[] active = new boolean[cbxCameras_.size()];
+        for (int i = 0; i < cbxCameras_.size(); i++) {
+            active[i] = cbxCameras_.get(i).isSelected();
         }
         return active;
     }
 
+    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);
+
+        // 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;
+            }
+        }
+
+        // the first array index is the primary camera
+        cameraData.add(new CameraData(selected, isSelectedActive));
+        // TODO(Brandon): uses simple ordering that works for 2 cameras,
+        //   but needs additional work to support 4. Use a reorderable JTable?
+        for (int i = 0; i < cameraNames.length; i++) {
+            if (!selected.equals(cameraNames[i])) {
+                System.out.println("cameraNames[i] " + cameraNames[i] + "active[i] " + active[i]);
+                cameraData.add(new CameraData(cameraNames[i], active[i]));
+            }
+        }
+        model_.acquisitions().settingsBuilder()
+                .imagingCameraOrder(cameraData.toArray(CameraData[]::new));
+    }
+
     @Override
     public void selected() {
 

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

@@ -3,6 +3,7 @@
 import mmcorej.Configuration;
 import mmcorej.StrVector;
 import org.micromanager.lightsheetmanager.LightSheetManager;
+import org.micromanager.lightsheetmanager.api.data.CameraData;
 import org.micromanager.lightsheetmanager.api.data.CameraLibrary;
 import mmcorej.CMMCore;
 import mmcorej.DeviceType;
@@ -297,14 +298,12 @@ public CameraBase firstImagingCamera() {
         return (CameraBase) deviceMap_.get(deviceKey);
     }
 
-    // TODO: active needs to be synchronized with the order, since order changes but active does not
     // For simultaneous cameras
     public String firstActiveCameraName() {
-        final String[] cameras = model_.acquisitions().settings().imagingCameraOrder();
-        final boolean[] active = model_.acquisitions().settings().imagingCamerasActive();
-        for (int i = 0; i < cameras.length; i++) {
-            if (active[i]) {
-                return cameras[i];
+        final CameraData[] cameras = model_.acquisitions().settings().imagingCameraOrder();
+        for (CameraData camera : cameras) {
+            if (camera.isActive()) {
+                return camera.name();
             }
         }
         return "";
@@ -348,11 +347,10 @@ public CameraBase[] imagingCameras() {
         String[] cameraNames;
         if (model_.acquisitions().settings().isUsingSimultaneousCameras()) {
             ArrayList<String> names = new ArrayList<>();
-            final String[] cameras = model_.acquisitions().settings().imagingCameraOrder();
-            final boolean[] active = model_.acquisitions().settings().imagingCamerasActive();
-            for (int i = 0; i < cameras.length; i++) {
-                if (active[i]) {
-                    names.add(cameras[i]);
+            final CameraData[] cameras = model_.acquisitions().settings().imagingCameraOrder();
+            for (CameraData camera : cameras) {
+                if (camera.isActive()) {
+                    names.add(camera.name());
                 }
             }
             cameraNames = names.toArray(String[]::new);

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

@@ -86,14 +86,14 @@ boolean setup() {
 //        }
 
         // we must have an active camera if we are using simultaneous cameras
-        if (model_.acquisitions().settings().isUsingSimultaneousCameras()) {
-            final boolean[] active = model_.acquisitions().settings().imagingCamerasActive();
-            if (IntStream.range(0, active.length).noneMatch(i -> active[i])) {
-                studio_.logs().showError("Using simultaneous cameras and no cameras are active!");
-                return false;
-            }
-            // TODO: primary camera must be active
-        }
+//        if (model_.acquisitions().settings().isUsingSimultaneousCameras()) {
+//            final boolean[] active = model_.acquisitions().settings().imagingCamerasActive();
+//            if (IntStream.range(0, active.length).noneMatch(i -> active[i])) {
+//                studio_.logs().showError("Using simultaneous cameras and no cameras are active!");
+//                return false;
+//            }
+//            // TODO: primary camera must be active
+//        }
 
         // this is needed for LSMAcquisitionEvents to work with multiple positions
         if (core_.getFocusDevice().isEmpty()