improve settings

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

@@ -1,13 +1,7 @@
 package org.micromanager.lightsheetmanager.api;
 
+import org.micromanager.lightsheetmanager.api.data.CameraData;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
-import org.micromanager.lightsheetmanager.api.internal.DefaultChannelSettings;
-import org.micromanager.lightsheetmanager.api.internal.DefaultSheetCalibration;
-import org.micromanager.lightsheetmanager.api.internal.DefaultSliceCalibration;
-import org.micromanager.lightsheetmanager.api.internal.DefaultSliceSettings;
-import org.micromanager.lightsheetmanager.api.internal.DefaultSliceSettingsLS;
-import org.micromanager.lightsheetmanager.api.internal.DefaultTimingSettings;
-import org.micromanager.lightsheetmanager.api.internal.DefaultVolumeSettings;
 import org.micromanager.lightsheetmanager.api.data.AcquisitionMode;
 
 /**
@@ -20,7 +14,7 @@ public interface AcquisitionSettingsDispim extends AcquisitionSettings {
      *
      * @return a builder to create a modified copy of these settings
      */
-    //Builder copyBuilder();
+    Builder copyBuilder();
 
     /**
      * Returns the immutable DefaultChannelSettings instance.
@@ -34,28 +28,28 @@ public interface AcquisitionSettingsDispim extends AcquisitionSettings {
      *
      * @return immutable DefaultTimingSettings instance.
      */
-    DefaultTimingSettings timing();
+    TimingSettings timing();
 
     /**
      * Returns the immutable DefaultVolumeSettings instance.
      *
      * @return immutable DefaultVolumeSettings instance.
      */
-    DefaultVolumeSettings volume();
+    VolumeSettings volume();
 
     /**
      * Returns the immutable DefaultSliceSettings instance.
      *
      * @return immutable DefaultSliceSettings instance.
      */
-    DefaultSliceSettings slice();
+    SliceSettings slice();
 
     /**
      * Returns the immutable DefaultSliceSettingsLS instance.
      *
      * @return immutable DefaultSliceSettingsLS instance.
      */
-    DefaultSliceSettingsLS sliceLS();
+    SliceSettingsLightSheet sliceLS();
 
     /**
      * Returns the immutable DefaultScanSettings instance.
@@ -69,15 +63,14 @@ public interface AcquisitionSettingsDispim extends AcquisitionSettings {
      *
      * @return immutable DefaultSheetCalibration instance.
      */
-    DefaultSheetCalibration sheetCalibration(final int view);
+    SheetCalibration sheetCalibration(final int view);
 
     /**
      * Returns the immutable DefaultSliceCalibration instance.
      *
      * @return immutable DefaultSliceCalibration instance.
      */
-    DefaultSliceCalibration sliceCalibration(final int view);
-    //DefaultSliceCalibration sliceCalibration();
+    SliceCalibration sliceCalibration(final int view);
 
     /**
      * Returns the acquisition mode.
@@ -93,6 +86,13 @@ public interface AcquisitionSettingsDispim extends AcquisitionSettings {
      */
     CameraMode cameraMode();
 
+    /**
+     * Returns the imaging camera order.
+     *
+     * @return the imaging camera order
+     */
+    CameraData[] imagingCameraOrder();
+
     /**
      * Returns true if using time points.
      *
@@ -162,6 +162,14 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
          */
         T cameraMode(final CameraMode cameraMode);
 
+        /**
+         * Sets the imaging camera order.
+         *
+         * @param order the imaging camera order
+         * @return {@code this} builder
+         */
+        T imagingCameraOrder(final CameraData[] order);
+
         /**
          * Sets the acquisition to use time points.
          *

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

@@ -3,11 +3,6 @@
 import org.micromanager.lightsheetmanager.api.data.AcquisitionMode;
 import org.micromanager.lightsheetmanager.api.data.CameraData;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
-import org.micromanager.lightsheetmanager.api.internal.DefaultSheetCalibration;
-import org.micromanager.lightsheetmanager.api.internal.DefaultSliceCalibration;
-import org.micromanager.lightsheetmanager.api.internal.DefaultSliceSettings;
-import org.micromanager.lightsheetmanager.api.internal.DefaultTimingSettings;
-import org.micromanager.lightsheetmanager.api.internal.DefaultVolumeSettings;
 
 /**
  * Acquisition settings for SCAPE microscopes.
@@ -19,12 +14,12 @@ public interface AcquisitionSettingsScape extends AcquisitionSettings {
      *
      * @return a builder to create a modified copy of these settings
      */
-    //Builder copyBuilder();
+    Builder copyBuilder();
 
     /**
-     * Returns the immutable DefaultChannelSettings instance.
+     * Returns the immutable ChannelSettings instance.
      *
-     * @return immutable DefaultChannelSettings instance.
+     * @return immutable ChannelSettings instance.
      */
     ChannelSettings channels();
 
@@ -33,19 +28,19 @@ public interface AcquisitionSettingsScape extends AcquisitionSettings {
      *
      * @return immutable DefaultTimingSettings instance.
      */
-    DefaultTimingSettings timing();
+    TimingSettings timing();
 
     /**
      * Returns the immutable DefaultVolumeSettings instance.
      *
      * @return immutable DefaultVolumeSettings instance.
      */
-    DefaultVolumeSettings volume();
+    VolumeSettings volume();
 
     /**
-     * Returns the immutable DefaultSliceSettings instance.
+     * Returns the immutable SliceSettings instance.
      *
-     * @return immutable DefaultSliceSettings instance.
+     * @return immutable SliceSettings instance.
      */
     SliceSettings slice();
 
@@ -61,14 +56,14 @@ public interface AcquisitionSettingsScape extends AcquisitionSettings {
      *
      * @return immutable DefaultSheetCalibration instance.
      */
-    DefaultSheetCalibration sheetCalibration();
+    SheetCalibration sheetCalibration();
 
     /**
      * Returns the immutable DefaultSliceCalibration instance.
      *
      * @return immutable DefaultSliceCalibration instance.
      */
-    DefaultSliceCalibration sliceCalibration();
+    SliceCalibration sliceCalibration();
 
     /**
      * Returns the acquisition mode.
@@ -144,6 +139,9 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
 
         /**
          * Sets the acquisition mode.
+         * <p>
+         * If the mode is a stage scanning mode,
+         * set the stage scanning flag to true.
          *
          * @param mode the acquisition mode
          * @return {@code this} builder

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

@@ -92,9 +92,9 @@ interface Builder {
          */
         Builder delayBeforeView(final double viewDelayMs);
 
-        Builder slicesPerView(final int n);
+        Builder slicesPerView(final int numSlices);
 
-        Builder sliceStepSize(final double um);
+        Builder sliceStepSize(final double stepSizeUm);
 
         /**
          * Sets the volume bounds, automatically computing numSlices and centerPosition.

src/main/java/org/micromanager/lightsheetmanager/api/internal/BaseAcquisitionSettings.java

@@ -5,8 +5,12 @@
 import com.google.gson.JsonDeserializer;
 import org.micromanager.lightsheetmanager.api.AcquisitionSettings;
 import org.micromanager.lightsheetmanager.api.ChannelSettings;
+import org.micromanager.lightsheetmanager.api.SheetCalibration;
+import org.micromanager.lightsheetmanager.api.SliceCalibration;
 import org.micromanager.lightsheetmanager.api.SliceSettings;
 import org.micromanager.lightsheetmanager.api.StageScanSettings;
+import org.micromanager.lightsheetmanager.api.TimingSettings;
+import org.micromanager.lightsheetmanager.api.VolumeSettings;
 import org.micromanager.lightsheetmanager.model.DataStorage;
 
 /**
@@ -221,21 +225,41 @@ public String toPrettyJson() {
 
     public static <T extends AcquisitionSettings> T fromJson(final String json, final Class<T> cls) {
         Gson gson = new GsonBuilder()
-                .registerTypeAdapter(StageScanSettings.class, (JsonDeserializer<StageScanSettings>)
+                .registerTypeAdapter(ChannelSettings.class, (JsonDeserializer<ChannelSettings>)
                         (jsonElement, typeOfT, context) -> {
                             // This forces Gson to use the concrete implementation class
-                            return context.deserialize(jsonElement, DefaultStageScanSettings.class);
+                            return context.deserialize(jsonElement, DefaultChannelSettings.class);
                         })
-                .registerTypeAdapter(ChannelSettings.class, (JsonDeserializer<ChannelSettings>)
+                .registerTypeAdapter(TimingSettings.class, (JsonDeserializer<TimingSettings>)
                         (jsonElement, typeOfT, context) -> {
                             // This forces Gson to use the concrete implementation class
-                            return context.deserialize(jsonElement, DefaultChannelSettings.class);
+                            return context.deserialize(jsonElement, DefaultTimingSettings.class);
+                        })
+                .registerTypeAdapter(VolumeSettings.class, (JsonDeserializer<VolumeSettings>)
+                        (jsonElement, typeOfT, context) -> {
+                            // This forces Gson to use the concrete implementation class
+                            return context.deserialize(jsonElement, DefaultVolumeSettings.class);
+                        })
+                .registerTypeAdapter(StageScanSettings.class, (JsonDeserializer<StageScanSettings>)
+                        (jsonElement, typeOfT, context) -> {
+                            // This forces Gson to use the concrete implementation class
+                            return context.deserialize(jsonElement, DefaultStageScanSettings.class);
                         })
                 .registerTypeAdapter(SliceSettings.class, (JsonDeserializer<SliceSettings>)
                         (jsonElement, typeOfT, context) -> {
                             // This forces Gson to use the concrete implementation class
                             return context.deserialize(jsonElement, DefaultSliceSettings.class);
                         })
+                .registerTypeAdapter(SheetCalibration.class, (JsonDeserializer<SheetCalibration>)
+                        (jsonElement, typeOfT, context) -> {
+                            // This forces Gson to use the concrete implementation class
+                            return context.deserialize(jsonElement, DefaultSheetCalibration.class);
+                        })
+                .registerTypeAdapter(SliceCalibration.class, (JsonDeserializer<SliceCalibration>)
+                        (jsonElement, typeOfT, context) -> {
+                            // This forces Gson to use the concrete implementation class
+                            return context.deserialize(jsonElement, DefaultSliceCalibration.class);
+                        })
                 .create();
         return gson.fromJson(json, cls);
     }

src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSheetCalibration.java

@@ -24,6 +24,11 @@ private DefaultSheetCalibration(Builder builder) {
         scanOffset_ = builder.scanOffset_;
     }
 
+    // Note: used by GSON library for deserialization
+    private DefaultSheetCalibration() {
+        this(new Builder());
+    }
+
     public static Builder builder() {
         return new Builder();
     }

src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultSliceCalibration.java

@@ -14,6 +14,11 @@ private DefaultSliceCalibration(Builder builder) {
         offset_ = builder.offset_;
     }
 
+    // Note: used by GSON library for deserialization
+    private DefaultSliceCalibration() {
+        this(new Builder());
+    }
+
     public static Builder builder() {
         return new Builder();
     }

src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultTimingSettings.java

@@ -30,6 +30,11 @@ private DefaultTimingSettings(Builder builder) {
         alternateScanDirection_ = builder.alternateScanDirection_;
     }
 
+    // Note: used by GSON library for deserialization
+    private DefaultTimingSettings() {
+        this(new Builder());
+    }
+
     public static Builder builder() {
         return new Builder();
     }