internal api improvements

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

@@ -65,8 +65,7 @@ public boolean setup() {
         positionUpdater_.setup();
 
         // create different acq engine based on microscope geometry
-        final GeometryType geometryType = deviceManager_
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = deviceManager_.adapter().geometry();
         switch (geometryType) {
             case SCAPE:
                 acqEngine_ = new AcquisitionEngineSCAPE(this);
@@ -85,7 +84,7 @@ public boolean setup() {
 
         // TODO: put this somewhere better, need to put this value into LSMAcquisitionEvents for now
         LSMAcquisitionEvents.isUsingMultipleCameras =
-              deviceManager_.getDeviceAdapter().getNumSimultaneousCameras() > 1;
+              deviceManager_.adapter().numSimultaneousCameras() > 1;
 
         // if we made it here then everything loaded correctly
         return true;

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

@@ -13,7 +13,6 @@
 import org.micromanager.lightsheetmanager.gui.data.Icons;
 import org.micromanager.lightsheetmanager.gui.tabs.TabPanel;
 import org.micromanager.lightsheetmanager.gui.tabs.navigation.NavigationPanel;
-import org.micromanager.lightsheetmanager.gui.tabs.setup.PositionPanel;
 import org.micromanager.lightsheetmanager.gui.utils.WindowUtils;
 import org.micromanager.internal.utils.WindowPositioning;
 
@@ -46,8 +45,7 @@ public LightSheetManagerFrame(final LightSheetManager model, final boolean isLoa
         // create the user interface
         if (isLoaded) {
             initDialogs();
-            final GeometryType geometryType = model_.devices()
-                    .getDeviceAdapter().getMicroscopeGeometry();
+            final GeometryType geometryType = model_.devices().adapter().geometry();
             switch (geometryType) {
                 case DISPIM:
                 case SCAPE:

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

@@ -162,7 +162,7 @@ private void createUserInterface() {
 
         // acquisition mode combo box
         final boolean isUsingScanSettings = model_.devices().isUsingStageScanning();
-        final GeometryType geometryType = model_.devices().getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
         cmbAcquisitionModes_ = new ComboBox(AcquisitionMode.getLabels(geometryType, isUsingScanSettings),
                 acqSettings.acquisitionMode().toString(),
                 180, 24);

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

@@ -55,6 +55,7 @@ private void createUserInterface() {
 
         // get the imaging camera library
         final CameraBase camera = model_.devices().getFirstImagingCamera();
+
         final CameraLibrary camLib = CameraLibrary.fromString(camera.getDeviceLibrary());
 
         cmbCameraTriggerMode_ = new ComboBox(CameraMode.getAvailableModes(camLib),

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

@@ -37,15 +37,15 @@ private void createUserInterface() {
         btnCreateConfigGroup_ = new Button("Create Devices Configuration Group", 220, 30);
 
         final JLabel lblGeometryType = new JLabel("Microscope Geometry: "
-                + devices_.getDeviceAdapter().getMicroscopeGeometry());
+                + devices_.adapter().geometry());
         final JLabel lblLightSheetType = new JLabel("Light Sheet Type: "
-                + devices_.getDeviceAdapter().getLightSheetType());
+                + devices_.adapter().lightSheetType());
         final JLabel lblNumImagingPaths = new JLabel("Imaging Paths: "
-                + devices_.getDeviceAdapter().getNumImagingPaths());
+                + devices_.adapter().numImagingPaths());
         final JLabel lblNumIlluminationPaths = new JLabel("Illumination Paths: "
-                + devices_.getDeviceAdapter().getNumIlluminationPaths());
+                + devices_.adapter().numIlluminationPaths());
         final JLabel lblNumSimultaneousCameras = new JLabel("Simultaneous Cameras: "
-                + devices_.getDeviceAdapter().getNumSimultaneousCameras());
+                + devices_.adapter().numSimultaneousCameras());
 
         btnCreateConfigGroup_.setToolTipText("Creates or updates the \"LightSheetManager::Devices\" " +
                 "configuration group with all editable properties from the Light Sheet Manager device adapter.");

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

@@ -65,7 +65,7 @@ private void createUserInterface() {
         tabbedPane_.addTab(createTabTitle("Navigation"), navigationTab_);
 
         // create a setup path tab for each imaging path
-        final int numImagingPaths = devices_.getDeviceAdapter().getNumImagingPaths();
+        final int numImagingPaths = devices_.adapter().numImagingPaths();
         for (int i = 0; i < numImagingPaths; i++) {
             SetupPathTab setupPathTab = new SetupPathTab(model_, i + 1);
             tabbedPane_.add(createTabTitle("Setup Path " + (i + 1)), setupPathTab);

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

@@ -30,11 +30,9 @@ public VolumeSettingsPanel(final LightSheetManager model) {
     }
 
     private void createUserInterface() {
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
-        final int numImagingPaths = model_.devices()
-                .getDeviceAdapter().getNumImagingPaths();
+        final int numImagingPaths = model_.devices().adapter().numImagingPaths();
 
         final DefaultVolumeSettings volumeSettings = model_.acquisitions()
                 .settings().volumeSettings();

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

@@ -62,11 +62,11 @@ private void createUserInterface() {
         final String imaging = "Imaging";
 
         // use pre-init property settings and Microscope Geometry data from Device Adapter
-        final LightSheetDeviceManager deviceAdapter = devices_.getDeviceAdapter();
-        final int numImagingPaths = deviceAdapter.getNumImagingPaths();
-        final int numIllumPaths = deviceAdapter.getNumIlluminationPaths();
-        final Map<String, String> deviceMap = deviceAdapter.getDeviceMap();
-        final Map<String, DeviceType> deviceTypeMap = deviceAdapter.getDeviceTypeMap();
+        final LightSheetDeviceManager deviceAdapter = devices_.adapter();
+        final int numImagingPaths = deviceAdapter.numImagingPaths();
+        final int numIllumPaths = deviceAdapter.numIlluminationPaths();
+        final Map<String, String> deviceMap = deviceAdapter.deviceMap();
+        final Map<String, DeviceType> deviceTypeMap = deviceAdapter.deviceTypeMap();
 
         // init ControlPanel arrays
         final ArrayList<ControlPanel> stageProperties = new ArrayList<>();
@@ -83,11 +83,7 @@ private void createUserInterface() {
         // create a ControlPanel for each device
         int devicesFound = 0;
         for (String propertyName : deviceMap.keySet()) {
-
             final String deviceName = deviceMap.get(propertyName);
-            if (deviceName.equals("Undefined")) {
-                continue; // skip this property => device not set
-            }
 
             // TODO: only add certain kinds of devices
             //System.out.println(propertyName);

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

@@ -11,7 +11,6 @@
 import org.micromanager.lightsheetmanager.LightSheetManager;
 
 import javax.swing.JLabel;
-import javax.swing.SwingConstants;
 import java.util.Objects;
 
 public class BeamSheetControlPanel extends Panel {
@@ -63,11 +62,9 @@ public BeamSheetControlPanel(final LightSheetManager model, final int pathNum) {
     }
 
     private void createUserInterface() {
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
-        final DefaultAcquisitionSettingsSCAPE acqSettings = model_.acquisitions()
-                .settings();
+        final DefaultAcquisitionSettingsSCAPE acqSettings = model_.acquisitions().settings();
 
         //setMigLayout("", "[]10[]", "");
 

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

@@ -39,8 +39,7 @@ public CameraPanel(final LightSheetManager model) {
     }
 
     private void createUserInterface() {
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
         setMigLayout(
                 "",
@@ -85,8 +84,7 @@ private void createUserInterface() {
     }
 
     private void createEventHandlers() {
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
         switch (geometryType) {
             case DISPIM:

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

@@ -32,8 +32,7 @@ public ExcitationPanel(final LightSheetManager model) {
     }
 
     private void createUserInterface() {
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
         isUsingPLogic_ = model_.devices().isUsingPLogic();
 

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

@@ -47,8 +47,7 @@ public PiezoCalibrationPanel(final LightSheetManager model, final PositionPanel
     }
 
     private void createUserInterface() {
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
         isUsingPLogic_ = model_.devices().isUsingPLogic();
 

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

@@ -53,8 +53,7 @@ public PositionPanel(final LightSheetManager model, final int pathNum) {
     }
 
     private void createUserInterface() {
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
         isUsingPLogic_ = model_.devices().isUsingPLogic();
 
@@ -173,10 +172,10 @@ private void createUserInterface() {
     // TODO: currently set up for SCAPE geometry, compare to original diSPIM plugin
     private void createEventHandlers() {
         // TODO: find a way to refresh these values
-        if (model_.devices().getDeviceAdapter().hasDevice("ImagingFocus")) {
+        if (model_.devices().adapter().hasDevice("ImagingFocus")) {
             model_.positions().register(this, "ImagingFocus");
         }
-        if (model_.devices().getDeviceAdapter().hasDevice("IllumSlice")) {
+        if (model_.devices().adapter().hasDevice("IllumSlice")) {
             model_.positions().register(this, "IllumSlice");
         }
 

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

@@ -57,7 +57,7 @@ public SetupPanel(final LightSheetManager model, final int pathNum) {
         // TODO: add joystick panel back in
         leftPanel_.add(excitationPanel_, "growx, wrap");
         //leftPanel_.add(joystickPanel_, "growx, wrap");
-        if (model_.devices().getDeviceAdapter().getMicroscopeGeometry() == GeometryType.SCAPE) {
+        if (model_.devices().adapter().geometry() == GeometryType.SCAPE) {
             singleAxisPanel_ = new SingleAxisPanel(model_);
             leftPanel_.add(singleAxisPanel_, "growx, wrap");
         }

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

@@ -71,7 +71,6 @@ public void setup() {
 
         // always add an entry for the device adapter
         final LightSheetDeviceManager lsm = new LightSheetDeviceManager(studio_, deviceAdapterName_);
-        lsm.getPreInitProperties();
         deviceMap_.put("LightSheetDeviceManager", lsm);
 
         // keep track of devices we have already added to the map
@@ -241,36 +240,36 @@ public <T extends DeviceBase> T getDevice(final String deviceName) {
     }
 
     public CameraBase getFirstImagingCamera() {
-        final LightSheetDeviceManager adapter = model_.devices().getDeviceAdapter();
-        if (adapter.getNumSimultaneousCameras() > 1 && adapter.getNumImagingPaths() == 1) {
+        final LightSheetDeviceManager adapter = model_.devices().adapter();
+        if (adapter.numSimultaneousCameras() > 1 && adapter.numImagingPaths() == 1) {
            return (CameraBase)deviceMap_.get("ImagingCamera1");
-        } else if (adapter.getNumSimultaneousCameras() > 1) {
+        } else if (adapter.numSimultaneousCameras() > 1) {
            return (CameraBase)deviceMap_.get("Imaging1Camera1");
-        } else if (adapter.getNumImagingPaths() > 1) {
+        } else if (adapter.numImagingPaths() > 1) {
            return (CameraBase)deviceMap_.get("Imaging1Camera");
         } else {
            return (CameraBase)deviceMap_.get("ImagingCamera");
         }
     }
 
     public CameraBase getImagingCamera(final int view, final int num) {
-        final LightSheetDeviceManager adapter = model_.devices().getDeviceAdapter();
+        final LightSheetDeviceManager adapter = model_.devices().adapter();
         String cameraName = "Imaging";
-        if (adapter.getNumImagingPaths() > 1) {
+        if (adapter.numImagingPaths() > 1) {
             cameraName += String.valueOf(view);
         }
         cameraName += "Camera";
-        if (adapter.getNumSimultaneousCameras() > 1) {
+        if (adapter.numSimultaneousCameras() > 1) {
             cameraName += String.valueOf(num);
         }
         return (CameraBase)deviceMap_.get(cameraName);
     }
 
     public CameraBase[] getImagingCameras() {
         ArrayList<CameraBase> cameraNames = new ArrayList<>();
-        final LightSheetDeviceManager adapter = model_.devices().getDeviceAdapter();
-        final int numImagingPaths = adapter.getNumImagingPaths();
-        final int numCameras  = adapter.getNumSimultaneousCameras();
+        final LightSheetDeviceManager adapter = model_.devices().adapter();
+        final int numImagingPaths = adapter.numImagingPaths();
+        final int numCameras  = adapter.numSimultaneousCameras();
         for (int i = 0; i < numImagingPaths; i++) {
             for (int j = 0; j < numCameras; j++) {
                 String cameraName = "Imaging";
@@ -299,7 +298,7 @@ public CameraBase[] getImagingCameras() {
 //        return deviceMap_.get("Imaging" + view + "Camera" + num);
 //    }
 
-    public LightSheetDeviceManager getDeviceAdapter() {
+    public LightSheetDeviceManager adapter() {
         return (LightSheetDeviceManager)deviceMap_.get("LightSheetDeviceManager");
     }
 
@@ -446,8 +445,8 @@ public void createConfigGroup() {
      */
     private ArrayList<String> updateConfig(final String groupName, final String configName) {
         ArrayList<String> newProperties = new ArrayList<>();
-        final String[] props = getDeviceAdapter().getDevicePropertyNames();
-        final String[] properties = getDeviceAdapter().getEditableProperties(props);
+        final String[] props = adapter().getDevicePropertyNames();
+        final String[] properties = adapter().getEditableProperties(props);
 
         Configuration config;
         try {

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

@@ -89,8 +89,7 @@ public PLogicDISPIM(final LightSheetManager model) {
         lastDistanceStr_ = "";
         lastPosStr_ = "";
 
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
         // populate devices
         switch (geometryType) {
@@ -506,7 +505,7 @@ public boolean prepareControllerForAcquisitionSide(
         }
 
         // TODO: make a separate method for scape? two classes instead? no need for switch
-        if (model_.devices().getDeviceAdapter().getMicroscopeGeometry() == GeometryType.SCAPE) {
+        if (model_.devices().adapter().geometry() == GeometryType.SCAPE) {
             scanner = scanner_;
             piezo = piezo_;
         }
@@ -1012,7 +1011,7 @@ public double getSheetWidth(CameraMode cameraMode, int view) {
         double sheetWidth;
         //final String cameraName = devices_.getMMDevice(cameraDevice);
         String deviceName = "ImagingCamera" + view; // diSPIM
-        if (model_.devices().getDeviceAdapter().getMicroscopeGeometry() == GeometryType.SCAPE) {
+        if (model_.devices().adapter().geometry() == GeometryType.SCAPE) {
             deviceName = "ImagingCamera";
         }
         CameraBase camera = devices_.getDevice(deviceName); // TODO: find a way of adapting to different cameras
@@ -1131,7 +1130,7 @@ public void setPathPreset(int side) {
     }
 
     public void stopSPIMStateMachines() {
-        if (model_.devices().getDeviceAdapter().getMicroscopeGeometry() == GeometryType.SCAPE) {
+        if (model_.devices().adapter().geometry() == GeometryType.SCAPE) {
             scanner_.setSPIMState(ASIScanner.SPIMState.IDLE);
         } else {
             scanner1_.setSPIMState(ASIScanner.SPIMState.IDLE);

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

@@ -906,9 +906,9 @@ public double getSheetWidth(CameraMode cameraMode, int view) {
         double sheetWidth;
         //final String cameraName = devices_.getMMDevice(cameraDevice);
         String deviceName = "ImagingCamera" + view; // diSPIM
-        if (model_.devices().getDeviceAdapter().getMicroscopeGeometry() == GeometryType.SCAPE) {
+        if (model_.devices().adapter().geometry() == GeometryType.SCAPE) {
             deviceName = "ImagingCamera";
-            if (model_.devices().getDeviceAdapter().getNumSimultaneousCameras() > 1 ) {
+            if (model_.devices().adapter().numSimultaneousCameras() > 1 ) {
                 deviceName += String.valueOf(view);
             }
         }

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

@@ -73,8 +73,7 @@ public void clear() {
      */
     public void load() {
         // get json from settings based on microscope geometry type
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
 
         final String key = SETTINGS_PREFIX + geometryType.toString().toUpperCase();
         final String json = settings_.getString(key, SETTINGS_NOT_FOUND);
@@ -116,10 +115,8 @@ public void save() {
         model_.acquisitions().updateAcquisitionSettings();
 
         // settings key based on geometry type
-        final GeometryType geometryType = model_.devices()
-                .getDeviceAdapter().getMicroscopeGeometry();
-        final String key = SETTINGS_PREFIX +
-                geometryType.toString().toUpperCase();
+        final GeometryType geometryType = model_.devices().adapter().geometry();
+        final String key = SETTINGS_PREFIX + geometryType.toString().toUpperCase();
 
         // save acquisition settings
         settings_.putString(key, model_.acquisitions().settings().toJson());

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

@@ -679,7 +679,7 @@ public void recalculateSliceTiming() {
         // don't change timing settings if user is using advanced timing
         if (acqSettings_.isUsingAdvancedTiming()) {
             // TODO: find a better place to set the camera trigger mode for SCAPE
-            if (model_.devices().getDeviceAdapter().getMicroscopeGeometry() == GeometryType.SCAPE) {
+            if (model_.devices().adapter().geometry() == GeometryType.SCAPE) {
                 CameraBase camera = model_.devices().getDevice("ImagingCamera");
                 camera.setTriggerMode(acqSettings_.cameraMode());
                 studio_.logs().logDebugMessage(

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

@@ -539,8 +539,8 @@ public void close() {
             }
             cameraNames = cameraDeviceNames.toArray(new String[0]);
         } else {
-            final LightSheetDeviceManager adapter = model_.devices().getDeviceAdapter();
-            if (adapter.getNumSimultaneousCameras() > 1 && adapter.getNumImagingPaths() == 1) {
+            final LightSheetDeviceManager adapter = model_.devices().adapter();
+            if (adapter.numSimultaneousCameras() > 1 && adapter.numImagingPaths() == 1) {
                // multiple simultaneous cameras
                cameraNames = new String[]{
                      model_.devices().getDevice("ImagingCamera1").getDeviceName(),
@@ -825,7 +825,7 @@ private boolean doHardwareCalculations(PLogicSCAPE plc) {
 
         // TODO: make this more robust
         String cameraName;
-        if (model_.devices().getDeviceAdapter().getNumSimultaneousCameras() > 1) {
+        if (model_.devices().adapter().numSimultaneousCameras() > 1) {
            cameraName = "ImagingCamera1";
         } else {
            cameraName = "ImagingCamera";