Fix typos and stale comments, and remove unused code

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

@@ -147,9 +147,9 @@ interface Builder<T extends Builder<T>>  {
         T self();
 
         /**
-         * Creates an immutable instance of DefaultAcquisitionSettings
+         * Creates an immutable instance of AcquisitionSettings
          *
-         * @return Immutable version of DefaultAcquisitionSettings
+         * @return Immutable version of AcquisitionSettings
          */
         AcquisitionSettings build();
     }

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

@@ -201,7 +201,6 @@ private void createUserInterface() {
         add(pnlButtons, "");
 
         pack(); // fit window size to layout
-        setIconImage(Icons.MICROSCOPE.getImage());
     }
 
     private void createEventHandlers() {

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

@@ -30,7 +30,7 @@ public class AutofocusTab extends Panel implements ListeningPanel {
     private ComboBox<AutofocusType> cmbScoringMethod_;
     private Button btnRunAutofocus_;
 
-    // autofocus options during setup
+    // autofocus options during acquisition
     private CheckBox cbxAutofocusEveryPass_;
     private CheckBox cbxAutofocusBeforeAcq_;
     private ComboBox<String> cmbAutofocusChannel_; // TODO: impl

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

@@ -372,7 +372,7 @@ private Rectangle customROI() {
     // Computes the ROI based on a scaling factor.
     private Rectangle computeCenterRectangle(final Rectangle rect, final int scale) {
         if (scale < 1) {
-            model_.studio().logs().showError("scale must be > 1; could not compute ROI!");
+            model_.studio().logs().showError("scale must be >= 1; could not compute ROI!");
             return rect;
         }
         if (rect.x != 0 || rect.y != 0) {

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/CameraPanel.java

@@ -56,7 +56,6 @@ private void createUserInterface() {
         cmbCameraMode_ = new ComboBox<>(modes,
                 model_.acquisitions().settings().cameraMode(), 140, 20);
 
-        // validate that the logical device name exists
         final String[] cameraNames = model_.devices().imagingCameraNames();
         cbxCameras_ = new ArrayList<>(cameraNames.length);
 

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

@@ -132,9 +132,6 @@ public String[] getChannelGroups() {
             if (model_.studio().core().getAvailableConfigs(group).size() > 1) {
                 groups.add(group);
             }
-//            StrVector st = model_.studio().core().getAvailableConfigGroups();
-//            for (String s : st)
-//                System.out.println(s);
         }
         return groups.toArray(String[]::new);
     }

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

@@ -68,7 +68,7 @@ private void createUserInterface() {
 
         btnAddChannel_.setToolTipText("Add a new channel to the table.");
         btnRemoveChannel_.setToolTipText("Remove the currently selected channel from the table.");
-        btnRefresh_.setToolTipText("Refresh the channel panel with the latest configuration groups settings.");
+        btnRefresh_.setToolTipText("Refresh the channel panel with the latest configuration group settings.");
 
         final String[] groupLabels = table_.getChannelGroups();
         cmbChannelGroup_ = new ComboBox<>(groupLabels,
@@ -115,8 +115,6 @@ private void createEventHandlers() {
             final ChannelSpec[] channels = table_.getData().getChannels();
             model_.acquisitions().settingsBuilder().channelBuilder().data(channels);
             model_.acquisitions().updateDurationLabels();
-            //System.out.println("add channel");
-            //table_.getData().printChannelData();
         });
 
         // remove channel
@@ -127,7 +125,6 @@ private void createEventHandlers() {
                 final ChannelSpec[] channels = table_.getData().getChannels();
                 model_.acquisitions().settingsBuilder().channelBuilder().data(channels);
                 model_.acquisitions().updateDurationLabels();
-                //System.out.println("remove row index: " + row);
             }
         });
 

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

@@ -15,8 +15,6 @@
 import java.awt.geom.Point2D;
 import java.util.Objects;
 
-// TODO: add tooltips for the buttons!
-
 public class ControlPanel extends Panel implements Subscriber {
 
     public enum Axis {

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/PositionPanel.java

@@ -106,7 +106,7 @@ private void createUserInterface() {
         txtImagingPosition_.setToolTipText(
                 "Type an imaging piezo position in μm and press Enter to move there.");
         //btnImagingCenterSet_.setToolTipText("Set \"Imaging Center\" value to \"Imaging Piezo\" position. ");
-        btnSliceZero_.setToolTipText("Move \"Slice Position\" position to 0 degrees.");
+        btnSliceZero_.setToolTipText("Move \"Slice Position\" to 0 degrees.");
         btnImagingZero_.setToolTipText("Move \"Imaging Piezo\" position to 0 μm.");
         //btnTestAcq_.setToolTipText("Run a test acquisition.");
 

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/SingleAxisPanel.java

@@ -13,7 +13,7 @@
 
 /**
  * A SCAPE panel
- * This is only ever build in SCAPE mode...
+ * This is only ever built in SCAPE mode...
  */
 public class SingleAxisPanel extends Panel {
 

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

@@ -8,7 +8,7 @@
 import javax.swing.JFrame;
 
 /**
- * Utilities for
+ * Utilities for checking, closing and listening to {@link JFrame} windows.
  */
 public final class WindowUtils {
 

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

@@ -195,12 +195,7 @@ public void setup() {
                 createCameraDevice(propertyName, deviceName,
                         CameraLibrary.fromString(deviceLibrary));
             }
-            //deviceMap_.put(propertyName, "");
         }
-        //System.out.println("----------------");
-
-        // we don't need this array anymore
-        //devicesAdded_.clear();
 
         studio_.logs().logMessage("DeviceManager: [End Setup]");
     }
@@ -242,19 +237,6 @@ private void createCameraDevice(final String propertyName, final String deviceNa
         }
     }
 
-    private void createShutterDevice() {
-
-    }
-
-    private void createXYStageDevice() {
-
-    }
-
-    // Note: clients should use var when we support Java 11
-//    public DeviceBase getDevice(final String deviceName) {
-//        return deviceMap_.get(deviceName);
-//    }
-
     // TODO: consider using Optional to improve the API
     /**
      * Returns the device given by {@code deviceName} as type {@code T},
@@ -457,7 +439,7 @@ public String[] getLoadedDevices() {
     /**
      * Returns true if the hardware configuration has the LightSheetManager device adapter. The user can
      * change the device name of the adapter, but not the device library so that's what we detect. Also,
-     * the name of the device adapter is cached for later usage. This also set the error text on the model
+     * the name of the device adapter is cached for later usage. This also sets the error text on the model
      * when an error is encountered, this is used in the error user interface.
      *
      * @return true if the hardware configuration has the device adapter
@@ -474,7 +456,7 @@ public boolean hasDeviceAdapter() {
                     if (count > 1) {
                         model_.setupErrorMessage("You have multiple instances of the LightSheetManager " +
                                 "device adapter in your hardware configuration.");
-                        break; // exit loop because this a failure condition
+                        break; // exit loop because this is a failure condition
                     }
                 }
             } catch (Exception e) {
@@ -537,7 +519,7 @@ public boolean hasStageScanning() {
 
     /**
      * Creates a configuration group named "System" that includes all device properties
-     * the Light Sheet Manager device adapter.
+     * of the Light Sheet Manager device adapter.
      */
     public void createConfigGroup() {
         final String groupName = "System";
@@ -583,7 +565,7 @@ public void createConfigGroup() {
      * Returns a list of new properties added to the configuration group.
      *
      * @param groupName the group name to check
-     * @param configName the configuration group to check
+     * @param configName the configuration preset to check
      * @return an ArrayList of new properties
      */
     private ArrayList<String> updateConfig(final String groupName, final String configName) {

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

@@ -306,36 +306,6 @@ boolean run() {
             }
         }
 
-
-            // --- testing code below ---
-//            StrVector deviceNames = core_.getLoadedDevices();
-//            for (String deviceName : deviceNames) {
-//                System.out.println("deviceName: " + deviceName);
-//                StrVector propertyNames;
-//                try {
-//                    propertyNames = core_.getDevicePropertyNames(deviceName);
-//                } catch (Exception e) {
-//                    propertyNames = null;
-//                }
-//
-//                Gson gsonObj = new Gson();
-//                HashMap<String, String> deviceProps = new HashMap<>();
-//                for (String propName : propertyNames) {
-//                    String propValue;
-//                    try {
-//                        propValue = core_.getProperty(deviceName, propName);
-//                    } catch (Exception e) {
-//                        propValue = "";
-//                        System.out.println("failed!");
-//                    }
-//                    deviceProps.put(propName, propValue);
-//                    //System.out.println(propName);
-//                }
-//
-//                String jsonStr = gsonObj.toJson(deviceProps);
-//                System.out.println(jsonStr);
-//            }
-
         updateSettings();
 
         // The run snapshot: everything below reads this, never acqSettings_, so an edit made while

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

@@ -484,7 +484,7 @@ public AcquisitionEvent next() {
      * describes, against the core's current XY and focus devices.
      *
      * @param positionList the list of positions to iterate over
-     * @return
+     * @return a function that makes one event per position from the event it is given
      */
     public static Function<AcquisitionEvent, Iterator<AcquisitionEvent>> positions(
             PositionList positionList) {

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

@@ -83,11 +83,4 @@ public double getChannelOffset(final String channelName) {
         }
         return 0.0;
     }
-
-    public void printChannelData() {
-        System.out.println("[ChannelTableData]");
-        for (ChannelSpec channel : channels_) {
-            System.out.println(channel);
-        }
-    }
 }

src/main/java/org/micromanager/lightsheetmanager/model/devices/DeviceAdapter.java

@@ -88,7 +88,7 @@ private int parsePropertyInt(final String propertyName, final int defaultValue)
             return Integer.parseInt(getProperty(propertyName));
         } catch (NumberFormatException e) {
             studio_.logs().logError("Error parsing " + propertyName
-                    + " from the device adapter, use default value " + defaultValue);
+                    + " from the device adapter, using default value " + defaultValue);
             return defaultValue;
         }
     }
@@ -161,7 +161,7 @@ public Map<String, DeviceType> deviceTypeMap() {
      * <p>
      * A "Position Device" is a StageDevice, XYStageDevice, or GalvoDevice.
      *
-     * @return an array of internal devices names for all position devices
+     * @return an array of internal device names for all position devices
      */
     public String[] positionDevices() {
         return deviceMap().entrySet().stream()

src/main/java/org/micromanager/lightsheetmanager/model/devices/cameras/AndorCamera.java

@@ -63,7 +63,7 @@ protected void applyTriggerMode(CameraMode cameraMode) {
                 setProperty(Properties.OVERLAP, Values.OFF);
 
                 // Note: the following applies to single view mode, the issue is not present in dual view mode:
-                // only shutter speeds < 4 work with the 200 Mhz slow scan mode, shutter speeds >= 5 will miss 1 image
+                // only shutter speeds < 4 work with the 200 MHz slow scan mode, shutter speeds >= 5 will miss 1 image
 
                 double maxLineScanSpeed = 104166.6667;
                 if (isSlowReadout()) {
@@ -192,7 +192,7 @@ public double getResetTime(CameraMode cameraMode) {
         return cameraReadoutTime + (numRowsOverhead * rowReadoutTime);
     }
 
-    // Note: at some point the Andor Zyla 4.2 camera changed it's PixelReadoutRate property value
+    // Note: at some point the Andor Zyla 4.2 camera changed its PixelReadoutRate property value
     // for the slow scan speed to start with "200 MHz" instead of "216 MHz".
     private boolean isSlowReadout() {
         if (isZyla55()) {

src/main/java/org/micromanager/lightsheetmanager/model/devices/cameras/DemoCamera.java

@@ -6,10 +6,10 @@
 import java.awt.Rectangle;
 
 /**
- * Support for the DemoCamera in DHub.
+ * Support for the DemoCamera device adapter.
  * <p>Note: this is for demo configurations.
- * <p>Device Adapter: DHub
- * <p>Camera Support: DemoCamera
+ * <p>Device Adapter: DemoCamera
+ * <p>Camera Support: DCam
  */
 public class DemoCamera extends CameraBase {
 

src/main/java/org/micromanager/lightsheetmanager/model/devices/cameras/HamamatsuCamera.java

@@ -68,11 +68,10 @@ protected void applyTriggerMode(final CameraMode cameraMode) {
                 try {
                     lowerLimit = core_.getPropertyLowerLimit(deviceName_, Properties.INTERNAL_LINE_INTERVAL);
                 } catch (Exception ignore) {
-                    // ignore => will set the HAMAMATSU_LINE_INTERVAL property
+                    // ignore => will set the INTERNAL_LINE_INTERVAL property
                     // to the rowTime without considering the lower limit
                 }
                 setProperty(Properties.INTERNAL_LINE_INTERVAL, String.valueOf((Math.max(rowTime, lowerLimit))));
-                //props_.setPropValue(devKey, Properties.Keys.HAMAMATSU_LINE_INTERVAL, Math.max(rowTime, lowerLimit));
                 break;
             case EDGE:
                 setProperty(Properties.TRIGGER_ACTIVE, Values.EDGE);
@@ -193,7 +192,7 @@ public double getResetTime(final CameraMode cameraMode) {
             final double resetTimeMs = camReadoutTime + (numRowsOverhead * rowReadoutTime);
             studio_.logs().logDebugMessage("camera reset time computed as "
                     + resetTimeMs + " for camera " + deviceName_);
-            return resetTimeMs; // assume 10ms readout if not otherwise possible to calculate
+            return resetTimeMs;
         }
     }