add path select buttons, piezo moves to center, deskew plugin works for galvo scan

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

@@ -14,7 +14,7 @@ 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 = "0.6.5";
+    public static final String version = "0.6.6";
 
     private Studio studio_;
     private LightSheetManager model_;

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

@@ -292,7 +292,7 @@ private void createEventHandlers() {
             if (selected) {
                 pnlAdvancedTiming_.updateSpinners();
             } else {
-                model_.acquisitions().updateAcquisitionSettings();
+                model_.acquisitions().updateSettings();
                 model_.acquisitions().recalculateSliceTiming();
             }
         });

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

@@ -181,7 +181,7 @@ public void createEventHandlers() {
                     }
                 }
                 // update settings and save to file
-                model_.acquisitions().updateAcquisitionSettings();
+                model_.acquisitions().updateSettings();
                 FileUtils.writeStringToFile(file.toString(), model_.acquisitions().settings().toPrettyJson());
                 model_.studio().logs().logMessage("Acquisition settings saved to: " + file);
             }

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

@@ -101,23 +101,23 @@ private void createEventHandlers() {
             model_.acquisitions().settingsBuilder()
                     .sliceBuilder().periodMinimized(selected);
             // update slice timing
-            model_.acquisitions().updateAcquisitionSettings();
+            model_.acquisitions().updateSettings();
             model_.acquisitions().recalculateSliceTiming();
         });
 
         spnSlicePeriod_.registerListener(() -> {
             model_.acquisitions().settingsBuilder()
                     .sliceBuilder().period(spnSlicePeriod_.getDouble());
             // update slice timing
-            model_.acquisitions().updateAcquisitionSettings();
+            model_.acquisitions().updateSettings();
             model_.acquisitions().recalculateSliceTiming();
         });
 
         spnSampleExposure_.registerListener(() -> {
             model_.acquisitions().settingsBuilder()
                     .sliceBuilder().sampleExposure(spnSampleExposure_.getDouble());
             // update slice timing
-            model_.acquisitions().updateAcquisitionSettings();
+            model_.acquisitions().updateSettings();
             model_.acquisitions().recalculateSliceTiming();
         });
 

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

@@ -81,7 +81,7 @@ private void createEventHandlers() {
             table_.updatePresetComboBoxes(channelGroup);
             // set the channel group to use when we get the channels
             model_.acquisitions().settingsBuilder().channelBuilder().group(channelGroup);
-            model_.acquisitions().updateAcquisitionSettings();
+            model_.acquisitions().updateSettings();
             // update the table data model and refresh ui
             table_.getData().setChannels(channelGroup, model_.acquisitions().settings().channels().used());
             table_.getData().setChannelGroup(channelGroup);

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

@@ -1,16 +1,16 @@
 package org.micromanager.lightsheetmanager.gui.tabs.setup;
 
-import com.google.common.eventbus.Subscribe;
-import org.micromanager.events.LiveModeEvent;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
 import org.micromanager.lightsheetmanager.gui.components.Button;
+import org.micromanager.lightsheetmanager.gui.components.ComboBox;
 import org.micromanager.lightsheetmanager.gui.components.Panel;
 import org.micromanager.lightsheetmanager.gui.components.ToggleButton;
 import org.micromanager.lightsheetmanager.gui.data.Icons;
 import org.micromanager.lightsheetmanager.LightSheetManager;
 import org.micromanager.lightsheetmanager.model.devices.cameras.CameraBase;
 
+import javax.swing.JLabel;
 import java.util.Objects;
 
 
@@ -19,6 +19,8 @@
  */
 public class CameraPanel extends Panel {
 
+    public static final String CONFIG_GROUP = "Path Select";
+
     private boolean isPreviewPressed = false;
     private boolean isLivePressed = false;
 
@@ -29,6 +31,9 @@ public class CameraPanel extends Panel {
     private ToggleButton btnInvertedPath_;
     private ToggleButton btnLiveMode_;
 
+    // path selection for SCAPE
+    private ComboBox<String> cmbPreset_;
+
     private final LightSheetManager model_;
 
     public CameraPanel(final LightSheetManager model) {
@@ -62,6 +67,19 @@ private void createUserInterface() {
                 Icons.CAMERA, Icons.CANCEL
         );
 
+        // populate the combo box if the group exists
+        String selected = "";
+        String[] presets = {""};
+        if (model_.core().isGroupDefined(CONFIG_GROUP)) {
+            presets = model_.core().getAvailableConfigs(CONFIG_GROUP).toArray();
+            try {
+                selected = model_.core().getCurrentConfig(CONFIG_GROUP);
+            } catch (Exception e) {
+                // ignore => use default value
+            }
+        }
+        cmbPreset_ = new ComboBox<>(presets, selected, 165, 26);
+
         switch (geometryType) {
             case DISPIM:
                 add(btnImagingPath_, "");
@@ -72,7 +90,9 @@ private void createUserInterface() {
                 break;
             case SCAPE:
                 add(btnInvertedPath_, "wrap");
-                add(btnLiveMode_, "");
+                add(btnLiveMode_, "wrap");
+                add(new JLabel("Path Preset:"), "wrap");
+                add(cmbPreset_, "");
                 break;
             default:
                 break;
@@ -85,23 +105,18 @@ private void createEventHandlers() {
         switch (geometryType) {
             case DISPIM:
                 btnImagingPath_.registerListener(() -> {
-
                 });
 
                 btnMultiPath_.registerListener(() -> {
-
                 });
 
                 btnEpiPath_.registerListener(() -> {
-
                 });
 
                 btnInvertedPath_.registerListener(() -> {
-
                 });
 
                 btnLiveMode_.registerListener(() -> {
-
                 });
                 break;
             case SCAPE:
@@ -157,6 +172,18 @@ private void createEventHandlers() {
             default:
                 break;
         }
+
+        // select path preset
+        cmbPreset_.registerListener(() -> {
+            final String selected = cmbPreset_.getSelected();
+            try {
+                model_.core().setConfig(CONFIG_GROUP, selected);
+                model_.studio().app().refreshGUI();
+            } catch (Exception e) {
+                model_.studio().logs().showError("Failed to set configuration: " + e.getMessage());
+            }
+        });
+
     }
 
     /**

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

@@ -2,6 +2,7 @@
 
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
 import org.micromanager.lightsheetmanager.gui.components.Button;
+import org.micromanager.lightsheetmanager.gui.components.ListeningPanel;
 import org.micromanager.lightsheetmanager.gui.components.Panel;
 import org.micromanager.lightsheetmanager.gui.components.TextField;
 import org.micromanager.lightsheetmanager.LightSheetManager;
@@ -15,7 +16,7 @@
 import java.awt.geom.Point2D;
 import java.util.Objects;
 
-public class PositionPanel extends Panel implements Subscriber {
+public class PositionPanel extends Panel implements Subscriber, ListeningPanel {
 
     private JLabel lblImagingCenterValue_;
 
@@ -58,9 +59,9 @@ private void createUserInterface() {
         isUsingPLogic_ = model_.devices().isUsingPLogic();
 
         final JLabel lblImagingCenter = new JLabel("Imaging Center:");
-        final double imagingCenter = model_.acquisitions().settings()
-                .sheetCalibration().imagingCenter();
-        lblImagingCenterValue_ = new JLabel(imagingCenter + " μm");
+        final String imagingCenter = String.format("%.3f μm",
+                model_.acquisitions().settings().sheetCalibration().imagingCenter());
+        lblImagingCenterValue_ = new JLabel(imagingCenter);
 
         setMigLayout(
                 "",
@@ -116,7 +117,7 @@ private void createUserInterface() {
             lblSlicePositionValue_.setText(scannerPositionStr);
         }
 
-        // test fields
+        // text fields
         txtSlicePosition_.setText("0");
         txtImagingPosition_.setText("0");
         txtIllumPosition_.setText("0");
@@ -193,6 +194,7 @@ private void createEventHandlers() {
 
             btnImagingCenterGo_.registerListener(() -> {
                 // FIXME: make sure this is the same as original plugin, diSPIM also moves Scanner with computeGalvoFromPiezo
+                // TODO: (also check if the move when the tab is selected is correct)
                 final double imagingCenter = model_.acquisitions().settingsBuilder().build()
                         .sheetCalibration().imagingCenter();
                 piezo.setPosition(imagingCenter);
@@ -238,4 +240,20 @@ public void update(String topic, Object value) {
             }
         });
     }
+
+    @Override
+    public void selected() {
+        if (model_.devices().isUsingPLogic()) {
+            // TODO: check the fixme above
+            final double imagingCenter = model_.acquisitions().settingsBuilder().build()
+                    .sheetCalibration().imagingCenter();
+            final ASIPiezo piezo = model_.devices().device("ImagingFocus");
+            piezo.setPosition(imagingCenter);
+        }
+    }
+
+    @Override
+    public void unselected() {
+
+    }
 }

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

@@ -72,10 +72,7 @@ private void createEventHandlers() {
         if (isUsingPLogic_) {
             final ASIScanner scanner = model_.devices().device("IllumSlice");
 
-            cbxBeamExc_.registerListener(() -> {
-                scanner.setBeamOn(cbxBeamExc_.isSelected());
-                //System.out.println("set beam on: " + cbxBeamExc_.isSelected());
-            });
+            cbxBeamExc_.registerListener(() -> scanner.setBeamOn(cbxBeamExc_.isSelected()));
         }
 
         if (model_.devices().adapter().geometry() == GeometryType.DISPIM) {
@@ -90,17 +87,13 @@ private void createEventHandlers() {
         }
     }
 
-    // TODO: only handles SCAPE for now
     @Override
     public void selected() {
-        final boolean isBeamOn = cbxBeamExc_.isSelected();
-
         if (isUsingPLogic_) {
-            final ASIScanner scanner =
-                    model_.devices().device("IllumSlice");
-            if (scanner != null && isBeamOn && !scanner.isBeamOn()) {
-                scanner.setBeamOn(true);
-            }
+//            final ASIScanner scanner = model_.devices().device("IllumSlice");
+//            if (scanner != null && !scanner.isBeamOn()) {
+//                scanner.setBeamOn(true);
+//            }
         }
     }
 

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

@@ -52,7 +52,6 @@ public SetupPanel(final LightSheetManager model, final int pathNum) {
         scannerPanel_ = new ScannerPanel(model_);
         cameraPanel_ = new CameraPanel(model_);
 
-        // TODO: add joystick panel back in
         leftPanel_.add(scannerPanel_, "growx, wrap");
         leftPanel_.add(joystickPanel_, "growx, wrap");
         if (model_.devices().adapter().geometry() == GeometryType.SCAPE) {
@@ -80,6 +79,7 @@ public int getPathNum() {
     @Override
     public void selected() {
         scannerPanel_.selected();
+        positionPanel_.selected();
     }
 
     @Override

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

@@ -404,7 +404,7 @@ public void useDefaultImagingCameraOrder() {
         // update settings with default camera order
         model_.acquisitions().settingsBuilder()
                 .imagingCameraOrder(cameras.toArray(new CameraData[0]));
-        model_.acquisitions().updateAcquisitionSettings();
+        model_.acquisitions().updateSettings();
     }
 
     public DeviceAdapter adapter() {

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

@@ -258,7 +258,7 @@ public void convert(final String json) {
         }
 
         // build the settings from builder and update the ui
-        model_.acquisitions().updateAcquisitionSettings();
+        model_.acquisitions().updateSettings();
         model_.userSettings().notifyListeners(model_.acquisitions().settings());
     }
 

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

@@ -129,7 +129,7 @@ public void loadFromJson(final String json, final boolean notify) {
      */
     public void save() {
         // make settings current before saving
-        model_.acquisitions().updateAcquisitionSettings();
+        model_.acquisitions().updateSettings();
 
         // settings key based on geometry type
         final GeometryType geometryType = model_.devices().adapter().geometry();