micro-manager · bls337 · Sep 3, 2024 · Sep 3, 2024
diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/frames/XYZGridFrame.java b/src/main/java/org/micromanager/lightsheetmanager/gui/frames/XYZGridFrame.java
@@ -63,6 +63,7 @@ private void createUserInterface() {
                 "[]10[]"
         ));
 
+        Spinner.setDefaultSize(7);
         Button.setDefaultSize(160, 26);
         btnComputeGrid_ = new Button("Compute Grid");
         btnEditPositionList_ = new Button("Edit Position List...");
@@ -80,7 +81,7 @@ private void createUserInterface() {
 
         Panel.setMigLayoutDefault(
                 "insets 10 10 10 10",
-                "[]15[]",
+                "[]10[]",
                 "[]10[]"
         );
         final Panel pnlX = new Panel(cbxUseX_);
@@ -89,29 +90,29 @@ private void createUserInterface() {
         final Panel pnlButtons = new Panel();
 
         // X
-        final JLabel lblXStart = new JLabel("X start [\u00B5m]:");
-        final JLabel lblXStop = new JLabel("X stop [\u00B5m]:");
-        final JLabel lblXDelta = new JLabel("X delta [\u00B5m]:");
+        final JLabel lblXStart = new JLabel("X start [µm]:");
+        final JLabel lblXStop = new JLabel("X stop [µm]:");
+        final JLabel lblXDelta = new JLabel("X delta [µm]:");
         final JLabel lblXCount = new JLabel("Slice count:");
 
         spnXStart_ = Spinner.createDoubleSpinner(0.0, -Double.MAX_VALUE, Double.MAX_VALUE, 100.0);
         spnXStop_ = Spinner.createDoubleSpinner(0.0, -Double.MAX_VALUE, Double.MAX_VALUE, 100.0);
         spnXDelta_ = Spinner.createDoubleSpinner(0.0, -Double.MAX_VALUE, Double.MAX_VALUE, 100.0);
 
         // Y
-        final JLabel lblYStart = new JLabel("Y start [\u00B5m]:");
-        final JLabel lblYStop = new JLabel("Y stop [\u00B5m]:");
-        final JLabel lblYDelta = new JLabel("Y delta [\u00B5m]:");
+        final JLabel lblYStart = new JLabel("Y start [µm]:");
+        final JLabel lblYStop = new JLabel("Y stop [µm]:");
+        final JLabel lblYDelta = new JLabel("Y delta [µm]:");
         final JLabel lblYCount = new JLabel("Y count:");
 
         spnYStart_ = Spinner.createDoubleSpinner(0.0, -Double.MAX_VALUE, Double.MAX_VALUE, 100.0);
         spnYStop_ = Spinner.createDoubleSpinner(0.0, -Double.MAX_VALUE, Double.MAX_VALUE, 100.0);
         spnYDelta_ = Spinner.createDoubleSpinner(0.0, -Double.MAX_VALUE, Double.MAX_VALUE, 100.0);
 
         // Z
-        final JLabel lblZStart = new JLabel("Z start [\u00B5m]:");
-        final JLabel lblZStop = new JLabel("Z stop [\u00B5m]:");
-        final JLabel lblZDelta = new JLabel("Z delta [\u00B5m]:");
+        final JLabel lblZStart = new JLabel("Z start [µm]:");
+        final JLabel lblZStop = new JLabel("Z stop [µm]:");
+        final JLabel lblZDelta = new JLabel("Z delta [µm]:");
         final JLabel lblZCount = new JLabel("Z count:");
 
         spnZStart_ = Spinner.createDoubleSpinner(0.0, -Double.MAX_VALUE, Double.MAX_VALUE, 100.0);
@@ -120,6 +121,7 @@ private void createUserInterface() {
 
         final Panel pnlSettings = new Panel("Grid Settings");
         final JLabel lblOverlap = new JLabel("Overlap (Y and Z) [%]");
+        Spinner.setDefaultSize(4);
         spnOverlapYZ_ = Spinner.createIntegerSpinner(10, 0, 100, 1);
         cbxClearPositions_ = new CheckBox("Clear position list if YZ unused", false);
 
@@ -160,12 +162,13 @@ private void createUserInterface() {
         pnlButtons.add(btnRunOverviewAcq_, "");
 
         add(pnlY, "growx");
-        add(pnlZ, "wrap");
+        add(pnlZ, "growx, wrap");
         add(pnlX, "growx");
         add(pnlSettings, "wrap");
         add(pnlButtons, "");
 
-        pack();
+        pack(); // fit window size to layout
+        setIconImage(Icons.MICROSCOPE.getImage());
     }
 
     private void createEventHandlers() {

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AcquisitionTab.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AcquisitionTab.java
@@ -112,7 +112,7 @@ private void createUserInterface() {
                 "Multiple positions (XY)", acqSettings.isUsingMultiplePositions());
         pnlMultiPositions_ = new MultiPositionPanel(model_, cbxUseMultiplePositions_);
         // disable elements based on acqSettings
-        pnlMultiPositions_.setEnabled(acqSettings.isUsingMultiplePositions());
+        pnlMultiPositions_.setPanelEnabled(acqSettings.isUsingMultiplePositions());
 
         // time points
         cbxUseTimePoints_ = new CheckBox(
@@ -308,6 +308,10 @@ public SliceSettingsPanel getSliceSettingsPanel() {
         return pnlSliceSettings_;
     }
 
+    public MultiPositionPanel getMultiPositionPanel() {
+        return pnlMultiPositions_;
+    }
+
     private void acqFinishedCallback() {
         try {
             SwingUtilities.invokeAndWait(() -> {

diff --git a/...main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/MultiPositionPanel.java b/...main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/MultiPositionPanel.java
@@ -1,6 +1,5 @@
 package org.micromanager.lightsheetmanager.gui.tabs.acquisition;
 
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.components.Button;
 import org.micromanager.lightsheetmanager.gui.components.CheckBox;
 import org.micromanager.lightsheetmanager.gui.components.Label;
@@ -30,17 +29,17 @@ public MultiPositionPanel(final LightSheetManager model, final CheckBox cbxUseMu
     }
 
     private void createUserInterface() {
-        final DefaultAcquisitionSettingsSCAPE acqSettings =
-                model_.acquisitions().settings();
 
-        Spinner.setDefaultSize(7);
+        // post move delay
         lblPostMoveDelay_ = new Label("Post-move delay [ms]:");
+        Spinner.setDefaultSize(8);
         spnPostMoveDelay_ = Spinner.createIntegerSpinner(
-                acqSettings.postMoveDelay(), 0, Integer.MAX_VALUE, 100);
-        btnEditPositionList_ = new Button("Edit Position List", 120, 24);
-        btnOpenXYZGrid_ = new Button("XYZ Grid", 80, 24);
+                model_.acquisitions().settings().postMoveDelay(),
+                0, Integer.MAX_VALUE, 100);
 
-        btnOpenXYZGrid_.setEnabled(false);
+        // XYZ grid
+        btnEditPositionList_ = new Button("Edit Position List...", 130, 24);
+        btnOpenXYZGrid_ = new Button("XYZ Grid...", 90, 24);
 
         add(btnEditPositionList_, "");
         add(btnOpenXYZGrid_, "wrap");
@@ -50,21 +49,32 @@ private void createUserInterface() {
 
     private void createEventHandlers() {
 
-        btnOpenXYZGrid_.registerListener(e -> xyzGridFrame_.setVisible(true));
+        // open XYZ grid
+        btnOpenXYZGrid_.registerListener(e -> {
+            if (model_.devices().hasDevice("SampleXY")
+                    && model_.devices().hasDevice("SampleZ")) {
+                xyzGridFrame_.setVisible(true);
+            } else {
+                model_.studio().logs().showError(
+                        "SampleXY and SampleZ must not be \"Undefined\" to use the XYZ grid.");
+            }
+        });
+
+        // open position list
         btnEditPositionList_.registerListener(e -> model_.studio().app().showPositionList());
 
-        spnPostMoveDelay_.registerListener(e -> {
-            model_.acquisitions().settingsBuilder().postMoveDelay(spnPostMoveDelay_.getInt());
-            //System.out.println("getPostMoveDelay: " + model_.acquisitions().getAcquisitionSettings().getPostMoveDelay());
-        });
+        spnPostMoveDelay_.registerListener(e -> model_.acquisitions()
+                .settingsBuilder().postMoveDelay(spnPostMoveDelay_.getInt()));
 
     }
 
-    @Override
-    public void setEnabled(final boolean state) {
+    public void setPanelEnabled(final boolean state) {
         lblPostMoveDelay_.setEnabled(state);
         spnPostMoveDelay_.setEnabled(state);
         btnEditPositionList_.setEnabled(state);
     }
 
+    public XYZGridFrame getXYZGridFrame() {
+        return xyzGridFrame_;
+    }
 }
diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/TimePointsPanel.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/TimePointsPanel.java
@@ -35,6 +35,7 @@ private void createUserInterface() {
                 "[]5[]"
         );
 
+        Spinner.setDefaultSize(6);
         lblNumTimePoints_ = new Label("Number:");
         lblTimePointInterval_ = new Label("Interval [s]:");
         spnNumTimePoints_ = Spinner.createIntegerSpinner(

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/DeviceManager.java b/src/main/java/org/micromanager/lightsheetmanager/model/DeviceManager.java
@@ -45,7 +45,8 @@ public class DeviceManager {
     private final Studio studio_;
     private final CMMCore core_;
 
-    private Map<String, DeviceBase> deviceMap_;
+    /* Maps the Device Adapter device name to a Device object */
+    private final Map<String, DeviceBase> deviceMap_;
 
     private static String deviceAdapterName_;
 
@@ -463,4 +464,13 @@ public void checkDevices(final JFrame frame) {
         }
     }
 
+    /**
+     * Return true if the device is set to a value other than "Undefined".
+     *
+     * @param deviceName the device adapter name ("SampleXY", "SampleZ", etc.)
+     * @return true if the device is present
+     */
+    public boolean hasDevice(final String deviceName) {
+        return !deviceMap_.get(deviceName).getDeviceName().equals("Undefined");
+    }
 }
diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/XYZGrid.java b/src/main/java/org/micromanager/lightsheetmanager/model/XYZGrid.java
@@ -4,9 +4,8 @@
 import org.micromanager.PositionList;
 import org.micromanager.StagePosition;
 import org.micromanager.lightsheetmanager.LightSheetManager;
-import org.micromanager.lightsheetmanager.api.data.DISPIMDevice;
-import org.micromanager.lightsheetmanager.model.devices.vendor.ASIXYStage;
-import org.micromanager.lightsheetmanager.model.devices.vendor.ASIZStage;
+import org.micromanager.lightsheetmanager.model.devices.Stage;
+import org.micromanager.lightsheetmanager.model.devices.XYStage;
 import org.micromanager.lightsheetmanager.model.utils.GeometryUtils;
 import org.micromanager.lightsheetmanager.model.utils.NumberUtils;
 
@@ -38,7 +37,7 @@ public class XYZGrid {
     private int overlapYZ_;
     private boolean clearYZ_;
 
-    private LightSheetManager model_;
+    private final LightSheetManager model_;
 
     public XYZGrid(final LightSheetManager model) {
         model_ = Objects.requireNonNull(model);
@@ -88,8 +87,8 @@ private int updateGridZCount() {
      */
     public void computeGrid() {
 
-        ASIXYStage xyStage = model_.devices().getDevice(DISPIMDevice.SAMPLE_XY);
-        ASIZStage zStage = model_.devices().getDevice(DISPIMDevice.SAMPLE_Z);
+        XYStage xyStage = model_.devices().getDevice("SampleXY");
+        Stage zStage = model_.devices().getDevice("SampleZ");
 
         final int numX = useX_ ? updateGridXCount() : 1;
         final int numY = useY_ ? updateGridYCount() : 1;

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/devices/Stage.java b/src/main/java/org/micromanager/lightsheetmanager/model/devices/Stage.java
@@ -7,4 +7,22 @@ public class Stage extends DeviceBase {
     public Stage(final Studio studio, final String deviceName) {
         super(studio, deviceName);
     }
+
+    public void setPosition(final double position) {
+        try {
+            core_.setPosition(deviceName_, position);
+        } catch (Exception e) {
+            studio_.logs().showError("could not set position for " + deviceName_);
+        }
+    }
+
+    public double getPosition() {
+        try {
+            return core_.getPosition(deviceName_);
+        } catch (Exception e) {
+            studio_.logs().showError("could not get position for " + deviceName_);
+            return 0.0;
+        }
+    }
+
 }
diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/devices/XYStage.java b/src/main/java/org/micromanager/lightsheetmanager/model/devices/XYStage.java
@@ -24,7 +24,7 @@ public void setRelativeXYPosition(final int x, final int y) {
         }
     }
 
-    public void setXYPosition(final int x, final int y) {
+    public void setXYPosition(final double x, final double y) {
         try {
             core_.setXYPosition(deviceName_, x, y);
         } catch (Exception e) {