channels() should return the used channels

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

@@ -2,6 +2,7 @@
 
 import org.micromanager.lightsheetmanager.api.data.AcquisitionMode;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
+import org.micromanager.lightsheetmanager.api.internal.DefaultChannelSettings;
 import org.micromanager.lightsheetmanager.api.internal.DefaultScanSettings;
 import org.micromanager.lightsheetmanager.api.internal.DefaultSheetCalibration;
 import org.micromanager.lightsheetmanager.api.internal.DefaultSliceCalibration;
@@ -116,6 +117,13 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
      */
     //Builder copyBuilder();
 
+    /**
+     * Returns the immutable DefaultChannelSettings instance.
+     *
+     * @return immutable DefaultChannelSettings instance.
+     */
+    DefaultChannelSettings channelSettings();
+
     /**
      * Returns the immutable DefaultTimingSettings instance.
      *

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

@@ -28,6 +28,6 @@ interface Builder {
 
     ChannelSpec[] channels();
 
-    ChannelSpec[] usedChannels();
+    ChannelSpec[] allChannels();
 
 }

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

@@ -349,19 +349,14 @@ private DefaultAcquisitionSettingsSCAPE(Builder builder) {
 //                timePointInterval_,
 //                postMoveDelay_
 //        );
-//    }
-
-//    @Override
-//    public AcquisitionSettingsDISPIM.Builder copyBuilder() {
-//        return null;
 //    }
 
     /**
      * Returns the immutable DefaultChannelSettings instance.
      *
      * @return immutable DefaultChannelSettings instance.
      */
-    //@Override
+    @Override
     public DefaultChannelSettings channelSettings() {
         return channelSettings_;
     }

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

@@ -117,19 +117,25 @@ public String[] channelGroups() {
     }
 
    /**
-    * Returns the channels for the selected channel group.
+    * Returns the used channels for the selected channel group.
     *
-    * @return the channels for the channel group.
+    * @return the channels for the channel group
     */
     @Override
     public ChannelSpec[] channels() {
-        return groups_.getOrDefault(channelGroup_, EMPTY_CHANNELS);
+        return Arrays.stream(groups_.getOrDefault(channelGroup_, EMPTY_CHANNELS))
+              .filter(ChannelSpec::useChannel)
+              .toArray(ChannelSpec[]::new);
     }
 
+   /**
+    * Returns all channels for the selected channel group.
+    *
+    * @return all channels for the selected channel group
+    */
     @Override
-    public ChannelSpec[] usedChannels() {
-        return Arrays.stream(groups_.get(channelGroup_))
-                .filter(ChannelSpec::isUsed)
-                .toArray(ChannelSpec[]::new);
+    public ChannelSpec[] allChannels() {
+        return groups_.getOrDefault(channelGroup_, EMPTY_CHANNELS);
     }
+
 }

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/channels/ChannelTable.java

@@ -31,6 +31,7 @@ public class ChannelTable extends JScrollPane {
     public ChannelTable(final LightSheetManager model) {
         model_ = Objects.requireNonNull(model);
 
+        // set the channel group first to get the correct channel array
         final String channelGroup = model_.acquisitions().settings().channelSettings().channelGroup();
         final ChannelSpec[] channels = model_.acquisitions().settings().channelSettings().channels();
 

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/channels/ChannelTableModel.java

@@ -79,7 +79,7 @@ public Object getValueAt(int row, int col) {
        final ChannelSpec channelSpec = data_.getChannelByIndex(row);
         switch (col) {
             case COLUMN_USE:
-                return channelSpec.isUsed();
+                return channelSpec.useChannel();
             case COLUMN_PRESET:
                 return channelSpec.getName();
             case COLUMN_OFFSET:

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/channels/ChannelTablePanel.java

@@ -74,9 +74,12 @@ private void createEventHandlers() {
         cmbChannelGroup_.registerListener(e -> {
             final String channelGroup = cmbChannelGroup_.getSelected();
             table_.updatePresetComboBoxes(channelGroup);
+            // set the channel group to use when we get the channels
+            model_.acquisitions().settingsBuilder().channelSettingsBuilder().channelGroup(channelGroup);
+            model_.acquisitions().updateAcquisitionSettings();
+            // update the table data model and refresh ui
             table_.getData().setChannels(channelGroup, model_.acquisitions().settings().channelSettings().channels());
             table_.getData().setChannelGroup(channelGroup);
-            model_.acquisitions().settingsBuilder().channelSettingsBuilder().channelGroup(channelGroup);
             table_.refreshData();
         });
 

src/main/java/org/micromanager/lightsheetmanager/model/channels/ChannelSpec.java

@@ -32,10 +32,10 @@ public ChannelSpec(final boolean useChannel, final String group, final String na
     }
 
     public ChannelSpec(final ChannelSpec channel) {
-        this.useChannel_ = channel.useChannel_;
-        this.group_ = channel.group_;
-        this.name_ = channel.name_;
-        this.offset_ = channel.offset_;
+        useChannel_ = channel.useChannel_;
+        group_ = channel.group_;
+        name_ = channel.name_;
+        offset_ = channel.offset_;
     }
 
     public String getName() {
@@ -54,7 +54,7 @@ public void setOffset(final double offset) {
         offset_ = offset;
     }
 
-    public boolean isUsed() {
+    public boolean useChannel() {
         return useChannel_;
     }
 

src/main/java/org/micromanager/lightsheetmanager/model/channels/ChannelTableData.java

@@ -41,7 +41,7 @@ public ChannelSpec[] getChannels() {
 
     public ChannelSpec[] getUsedChannels() {
         return channels_.stream()
-                        .filter(ChannelSpec::isUsed)
+                        .filter(ChannelSpec::useChannel)
                         .toArray(ChannelSpec[]::new);
     }