set cameras to internal on setup tab live buttons; fix No scan (fixed…

… sheet) error
micro-manager · Jul 29, 2024 · 419438c · 419438c
1 parent c54a2c1
commit 419438c
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Showing 15 changed files with 68 additions and 50 deletions.
diff --git a/src/main/java/org/micromanager/lightsheetmanager/LightSheetManagerPlugin.java b/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), 2022-2024";
     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 = "0.4.3";
+    public static final String version = "0.4.4";
 
     private Studio studio_;
     private LightSheetManagerFrame frame_;

diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/data/AcquisitionMode.java b/src/main/java/org/micromanager/lightsheetmanager/api/data/AcquisitionMode.java
@@ -2,6 +2,9 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Map;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 // TODO: account for different naming on each geometry type (SLICE_SCAN_ONLY)
 
@@ -21,6 +24,9 @@ public enum AcquisitionMode {
 
     private final String text_;
 
+    private static final Map<String, AcquisitionMode> stringToEnum =
+            Stream.of(values()).collect(Collectors.toMap(Object::toString, e -> e));
+
     AcquisitionMode(final String text) {
         text_ = text;
     }
@@ -30,8 +36,8 @@ public String toString() {
         return text_;
     }
 
-    public static AcquisitionMode getByIndex(final int index) {
-        return values()[index];
+    public static AcquisitionMode fromString(final String symbol) {
+        return stringToEnum.getOrDefault(symbol, AcquisitionMode.NONE);
     }
 
     public static String[] toArray() {

diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/data/AutofocusFitType.java b/src/main/java/org/micromanager/lightsheetmanager/api/data/AutofocusFitType.java
@@ -18,7 +18,7 @@ public enum AutofocusFitType {
             Stream.of(values()).collect(Collectors.toMap(Object::toString, e -> e));
 
     AutofocusFitType(final String text) {
-        this.text_ = text;
+        text_ = text;
     }
 
     public static String[] toArray() {

diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/data/AutofocusMode.java b/src/main/java/org/micromanager/lightsheetmanager/api/data/AutofocusMode.java
@@ -12,13 +12,13 @@ public enum AutofocusMode {
     FIXED_PIEZO_SWEEP_SLICE("Fixed piezo, sweep slice"),
     FIXED_SLICE_SWEEP_PIEZO("Fixed slice, sweep piezo");
 
-    private final String name;
+    private final String name_;
 
     private static final Map<String, AutofocusMode> stringToEnum =
             Stream.of(values()).collect(Collectors.toMap(Object::toString, e -> e));
 
     AutofocusMode(final String name) {
-        this.name = name;
+        name_ = name;
     }
 
     public static String[] toArray() {
@@ -33,7 +33,7 @@ public static AutofocusMode fromString(final String symbol) {
 
     @Override
     public String toString() {
-        return name;
+        return name_;
     }
 
 }
diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/data/AutofocusType.java b/src/main/java/org/micromanager/lightsheetmanager/api/data/AutofocusType.java
@@ -22,13 +22,13 @@ public enum AutofocusType {
     FFT_BANDPASS("FFTBandpass"),
     TENENGRAD("Tenengrad");
 
-    private final String name;
+    private final String name_;
 
     private static final Map<String, AutofocusType> stringToEnum =
             Stream.of(values()).collect(Collectors.toMap(Object::toString, e -> e));
 
     AutofocusType(final String name) {
-        this.name = name;
+        name_ = name;
     }
 
     public static String[] toArray() {
@@ -43,7 +43,7 @@ public static AutofocusType fromString(final String symbol) {
 
     @Override
     public String toString() {
-        return name;
+        return name_;
     }
 
 }
diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/data/CameraMode.java b/src/main/java/org/micromanager/lightsheetmanager/api/data/CameraMode.java
@@ -21,23 +21,19 @@ public enum CameraMode {
     PSEUDO_OVERLAP("Pseudo Overlap"),
     VIRTUAL_SLIT("Virtual Slit");
 
-    private final String text;
+    private final String text_;
 
     private static final Map<String, CameraMode> stringToEnum =
             Stream.of(values()).collect(Collectors.toMap(Object::toString, e -> e));
 
     CameraMode(final String text) {
-        this.text = text;
+        text_ = text;
     }
 
     public static CameraMode fromString(final String symbol) {
         return stringToEnum.getOrDefault(symbol, CameraMode.EDGE);
     }
 
-    public static CameraMode getByIndex(final int index) {
-        return values()[index];
-    }
-
     /**
      * @return an array of Strings containing all possible camera trigger modes.
      */
@@ -117,7 +113,7 @@ public static String[] getAvailableModes(CameraLibrary camLib) {
 
     @Override
     public String toString() {
-        return text;
+        return text_;
     }
 
 }
diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/data/GeometryType.java b/src/main/java/org/micromanager/lightsheetmanager/api/data/GeometryType.java
@@ -16,15 +16,15 @@ public enum GeometryType {
     private static final Map<String, GeometryType> stringToEnum =
             Stream.of(values()).collect(Collectors.toMap(Object::toString, e -> e));
 
-    private final String label;
+    private final String label_;
 
     GeometryType(final String label) {
-        this.label = label;
+        label_ = label;
     }
 
     @Override
     public String toString() {
-        return label;
+        return label_;
     }
 
     public static GeometryType fromString(final String symbol) {

diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/data/LightSheetType.java b/src/main/java/org/micromanager/lightsheetmanager/api/data/LightSheetType.java
@@ -12,15 +12,15 @@ public enum LightSheetType {
     private static final Map<String, LightSheetType> stringToEnum =
             Stream.of(values()).collect(Collectors.toMap(Object::toString, e -> e));
 
-    private final String label;
+    private final String label_;
 
     LightSheetType(final String label) {
-        this.label = label;
+        label_ = label;
     }
 
     @Override
     public String toString() {
-        return label;
+        return label_;
     }
 
     public static LightSheetType fromString(final String symbol) {

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AcquisitionTab.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AcquisitionTab.java
@@ -264,8 +264,9 @@ private void createEventHandlers() {
 
         // select the acquisition mode
         cmbAcquisitionModes_.registerListener(e -> {
-            final int index = cmbAcquisitionModes_.getSelectedIndex();
-            model_.acquisitions().settingsBuilder().acquisitionMode(AcquisitionMode.getByIndex(index));
+            final String selected = cmbAcquisitionModes_.getSelected();
+            model_.acquisitions().settingsBuilder()
+                    .acquisitionMode(AcquisitionMode.fromString(selected));
         });
 
         // TODO: should timing recalc be part of setting use advanced timing value in model?

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/CameraPanel.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/CameraPanel.java
@@ -1,10 +1,12 @@
 package org.micromanager.lightsheetmanager.gui.tabs.setup;
 
+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.Panel;
 import org.micromanager.lightsheetmanager.gui.data.Icons;
 import org.micromanager.lightsheetmanager.model.LightSheetManagerModel;
+import org.micromanager.lightsheetmanager.model.devices.cameras.CameraBase;
 
 import java.util.Objects;
 
@@ -96,26 +98,37 @@ private void createEventHandlers() {
                 btnInvertedPath_.registerListener(e -> {
                     // TODO: make this work, needs Device Adapter pull request and name for camera...
                     closeLiveModeWindow();
-                    final String cameraName = model_.devices()
-                            .getDevice("PreviewCamera").getDeviceName();
-                    try {
-                        model_.studio().core().setCameraDevice(cameraName);
-                    } catch (Exception ex) {
-                        model_.studio().logs().showError("could not set camera to " + cameraName);
+                    final CameraBase camera = model_.devices().getDevice("PreviewCamera");
+                    if (camera != null) {
+                        try {
+                            model_.studio().core().setCameraDevice(camera.getDeviceName());
+                            camera.setTriggerMode(CameraMode.INTERNAL);
+                        } catch (Exception ex) {
+                            model_.studio().logs().showError("could not set camera to " + camera.getDeviceName());
+                        }
+                        model_.studio().live().setLiveModeOn(true);
+                    } else {
+                        model_.studio().logs().showError(
+                                "No device for \"PreviewCamera\" set in the device adapter.");
                     }
-                    model_.studio().live().setLiveModeOn(true);
                 });
 
+                // live mode
                 btnLiveMode_.registerListener(e -> {
                     closeLiveModeWindow();
-                    final String cameraName = model_.devices()
-                            .getDevice("ImagingCamera").getDeviceName();
-                    try {
-                        model_.studio().core().setCameraDevice(cameraName);
-                    } catch (Exception ex) {
-                        model_.studio().logs().showError("could not set camera to " + cameraName);
+                    final CameraBase camera = model_.devices().getDevice("ImagingCamera");
+                    if (camera != null) {
+                        try {
+                            model_.studio().core().setCameraDevice(camera.getDeviceName());
+                            camera.setTriggerMode(CameraMode.INTERNAL);
+                        } catch (Exception ex) {
+                            model_.studio().logs().showError("could not set camera to " + camera.getDeviceName());
+                        }
+                        model_.studio().live().setLiveModeOn(true);
+                    } else {
+                        model_.studio().logs().showError(
+                                "No device for \"ImagingCamera\" set in the device adapter.");
                     }
-                    model_.studio().live().setLiveModeOn(true);
                 });
                 break;
             default:

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/DeviceManager.java b/src/main/java/org/micromanager/lightsheetmanager/model/DeviceManager.java
@@ -220,21 +220,22 @@ private void createXYStageDevice() {
 //        return deviceMap_.get(deviceName);
 //    }
 
+    // TODO: consider using Optional to improve the API
     /**
-     * Returns the device given by {@code deviceName} as type {@code T}.
+     * Returns the device given by {@code deviceName} as type {@code T},
+     * if the device is not found, {@code null} is returned.
      * The caller is responsible for assigning the returned
      * value to the correct type.
      * <P><P>
      * Typesafe: The client can only cast the return value to a subclass
      * of DeviceBase, avoiding the ClassCastException at compile time.
      *
      * @param deviceName the device name
-     * @return the device as a subclass of DeviceBase
+     * @return the device or null if device not found
      * @param <T> the generic type to cast the result to
      */
     @SuppressWarnings("unchecked")
     public <T extends DeviceBase> T getDevice(final String deviceName) {
-        //System.out.println(deviceName + " " + deviceMap_.get(deviceName).getDeviceName());
         return (T) deviceMap_.get(deviceName);
     }
 

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/LightSheetManagerModel.java b/src/main/java/org/micromanager/lightsheetmanager/model/LightSheetManagerModel.java
@@ -27,9 +27,8 @@ public class LightSheetManagerModel implements LightSheetManager {
     private UserSettings userSettings_;
     private PluginSettings pluginSettings_;
 
-    private DeviceManager deviceManager_;
-
-    private XYZGrid xyzGrid_;
+    private final XYZGrid xyzGrid_;
+    private final DeviceManager deviceManager_;
 
     private AcquisitionEngine acqEngine_;
     private AcquisitionTableData acqTableData_;
@@ -41,9 +40,9 @@ public LightSheetManagerModel(final Studio studio) {
         pluginSettings_ = new PluginSettings();
         userSettings_ = new UserSettings(this);
         xyzGrid_ = new XYZGrid(this);
+        deviceManager_ = new DeviceManager(studio_, this);
 
-        // set during setup if there is an error
-        // displayed in the error ui
+        // set during setup if there is an errordisplayed in the error ui
         errorText_ = "";
     }
 
@@ -54,8 +53,6 @@ public LightSheetManagerModel(final Studio studio) {
      */
     public boolean setup() {
 
-        deviceManager_ = new DeviceManager(studio_, this);
-
         // first we check to see if the device adapter is present
         if (!deviceManager_.hasDeviceAdapter()) {
             return false;

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java b/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java
@@ -126,6 +126,7 @@ public Future<?> requestRun(boolean speedTest) {
                 } else {
                     studio_.logs().logMessage("Preparing Acquisition: plugin version " + LightSheetManagerPlugin.version);
                     // TODO: put this here? generic setup tasks? put in own method?
+                    System.out.println("acqSettings_.acquisitionMode(): " + acqSettings_.acquisitionMode());
                     if (acqSettings_.acquisitionMode() == AcquisitionMode.NONE) {
                         studio_.logs().showError("please select a valid acquisition mode!");
                         return; // early exit

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/devices/cameras/CameraBase.java b/src/main/java/org/micromanager/lightsheetmanager/model/devices/cameras/CameraBase.java
@@ -87,6 +87,7 @@ public int roiReadoutRowsSplitReadout(Rectangle roi, Rectangle sensor) {
 
     @Override
     public void setTriggerMode(CameraMode cameraMode) {
+        System.out.println("this!");
         mode_ = cameraMode;
     }
 

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/devices/cameras/DemoCamera.java b/src/main/java/org/micromanager/lightsheetmanager/model/devices/cameras/DemoCamera.java
@@ -27,7 +27,9 @@ public DemoCamera(Studio studio, String deviceName) {
 
     @Override
     public void setTriggerMode(final CameraMode cameraMode) {
-        // do nothing - no camera trigger modes - always internal
+        // do nothing - no camera trigger modes - always internal - log for debug convenience
+        studio_.logs().logMessage(
+                "setTriggerMode(" + cameraMode + ") called but the DemoCamera is always in internal mode.");
     }
 
     @Override