make more settings value objects

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

@@ -7,7 +7,7 @@
  */
 public interface AutofocusManager {
 
-    CalibrationSettings calibrate(AutofocusSettings settings);
+    //CalibrationSettings calibrate(AutofocusSettings settings);
 }
 
 // TODO: moved from AutofocusSettings

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

@@ -8,6 +8,59 @@
  */
 public interface AutofocusSettings {
 
+    /**
+     * Returns a builder initialized with the current settings.
+     *
+     * @return a builder to create a modified copy of these settings
+     */
+    Builder copyBuilder();
+
+    /**
+     * Return true if channels are enabled.
+     *
+     * @return true if channels are enabled
+     */
+    boolean enabled();
+
+    /**
+     * Returns the number of images used in for autofocus routine.
+     *
+     * @return the number of images
+     */
+    int numImages();
+
+    /**
+     * Returns the step size between images in microns.
+     *
+     * @return the step size in microns
+     */
+    double stepSizeUm();
+
+    /**
+     * Returns the autofocus mode being used.
+     *
+     * @return the autofocus mode
+     */
+    AutofocusMode mode();
+
+    /**
+     * Returns the type of scoring algorithm used for autofocus.
+     *
+     * @return the type of scoring algorithm
+     */
+    AutofocusType scoringMethod();
+
+    /**
+     * Returns the channel autofocus is being run on.
+     *
+     * @return the autofocus channel
+     */
+    String channel();
+
+    boolean showGraph();
+
+    boolean showImages();
+
     interface Builder {
 
         /**
@@ -31,13 +84,6 @@ interface Builder {
          */
         Builder stepSizeUm(final double stepSize);
 
-//        /**
-//         * Sets the tolerance in microns for the autofocus algorithm.
-//         *
-//         * @param value the tolerance in microns
-//         */
-//        Builder toleranceUm(final double value);
-
         /**
          * Set to {@code true} to show the images in the live view window.
          *
@@ -73,29 +119,6 @@ interface Builder {
          */
         Builder channel(final String channel);
 
-        // TODO: maybe denote that these are related to acquisitions
-
-//        /**
-//         * Run autofocus every time we move to the next channel during an acquisition.
-//         *
-//         * @param state true to enable autofocus every stage pass
-//         */
-//        Builder useEveryStagePass(final boolean state);
-//
-//        /**
-//         * Run an autofocus routine before starting the acquisition.
-//         *
-//         * @param state true or false
-//         */
-//        Builder useBeforeAcquisition(final boolean state);
-
-
-//        Builder maxOffset(final double maxOffset); // +/- um
-//
-//        Builder autoUpdateOffset(final boolean state);
-//
-//        Builder autoUpdateMaxOffset(final double um);
-
         /**
          * Creates an immutable instance of AutofocusSettings
          *
@@ -104,85 +127,4 @@ interface Builder {
         AutofocusSettings build();
     }
 
-    /**
-     * Returns a builder initialized with the current settings.
-     *
-     * @return a builder to create a modified copy of these settings
-     */
-    Builder copyBuilder();
-
-    /**
-     * Return true if channels are enabled.
-     *
-     * @return true if channels are enabled
-     */
-    boolean enabled();
-
-    /**
-     * Returns the number of images used in for autofocus routine.
-     *
-     * @return the number of images
-     */
-    int numImages();
-
-    /**
-     * Returns the step size between images in microns.
-     *
-     * @return the step size in microns
-     */
-    double stepSizeUm();
-
-//    /**
-//     * Returns the coefficient of determination used in the autofocus routine.
-//     *
-//     * @return the coefficient of determination
-//     */
-//    double toleranceUm();
-
-    /**
-     * Returns the autofocus mode being used.
-     *
-     * @return the autofocus mode
-     */
-    AutofocusMode mode();
-
-    /**
-     * Returns the type of scoring algorithm used for autofocus.
-     *
-     * @return the type of scoring algorithm
-     */
-    AutofocusType scoringMethod();
-
-    /**
-     * Returns the channel autofocus is being run on.
-     *
-     * @return the autofocus channel
-     */
-    String channel();
-
-//    /**
-//     * Returns true if autofocus is run every stage pass.
-//     *
-//     * @return true if autofocus is run every stage pass
-//     */
-//    boolean useEveryStagePass();
-//
-//    /**
-//     * Returns true if we run an autofocus routine before starting an acquisition.
-//     *
-//     * @return true if enabled
-//     */
-//    boolean useBeforeAcquisition();
-
-   /**
-    * What is this?
-    *
-    * @return
-    */
-//    double maxOffset(); // used during acquisitions
-//
-//    boolean autoUpdateOffset();
-//
-//    double autoUpdateMaxOffset();
-
 }

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

@@ -1,12 +1,23 @@
 package org.micromanager.lightsheetmanager.api;
 
-import org.micromanager.lightsheetmanager.api.internal.DefaultSheetCalibration;
-
 /**
  * Light Sheet Synchronization on "Setup Path #" tabs.
  */
 public interface SheetCalibration {
 
+    Builder copyBuilder();
+
+    // normal camera trigger modes
+    double imagingCenter();
+    double sheetWidth();
+    double sheetOffset();
+    boolean autoSheetWidthEnabled();
+    double autoSheetWidthPerPixel();
+
+    // virtual slit camera trigger mode
+    double scanSpeed();
+    double scanOffset();
+
     interface Builder {
 
         Builder imagingCenter(final double center);
@@ -30,7 +41,7 @@ interface Builder {
          *
          * @param state true to automatically set sheet width
          */
-        Builder useAutoSheetWidth(final boolean state);
+        Builder autoSheetWidthEnabled(final boolean state);
 
         /**
          * Sets the width per pixel when isUsingAutoSheetWidth is true.
@@ -62,17 +73,4 @@ interface Builder {
 
     }
 
-    Builder copyBuilder();
-
-    // normal camera trigger modes
-    double imagingCenter();
-    double sheetWidth();
-    double sheetOffset();
-    boolean isUsingAutoSheetWidth();
-    double autoSheetWidthPerPixel();
-
-    // virtual slit camera trigger mode
-    double scanSpeed();
-    double scanOffset();
-
 }

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

@@ -9,11 +9,16 @@
  */
 public interface SliceCalibration {
 
+    Builder copyBuilder();
+
+    double slope();
+    double offset();
+
     interface Builder {
 
-        Builder sliceSlope(final double slope);
+        Builder slope(final double slope);
 
-        Builder sliceOffset(final double offset);
+        Builder offset(final double offset);
 
         /**
          * Creates an immutable instance of DefaultSliceCalibration
@@ -23,10 +28,4 @@ interface Builder {
         DefaultSliceCalibration build();
     }
 
-    Builder copyBuilder();
-
-    double sliceSlope();
-    double sliceOffset();
-
-
 }

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

@@ -2,7 +2,36 @@
 
 public interface SliceSettings {
 
+    /**
+     * Returns a builder initialized with the current settings.
+     *
+     * @return a builder to create a modified copy of these settings
+     */
+    Builder copyBuilder();
+
+    /**
+     * Returns the slice period in milliseconds.
+     *
+     * @return the slice period in milliseconds
+     */
+    double period();
+
+    /**
+     * Returns the sample exposure time in milliseconds.
+     *
+     * @return the exposure time in milliseconds
+     */
+    double sampleExposure();
+
+    /**
+     * Returns true if the slice period is minimized.
+     *
+     * @return true if slice period is minimized
+     */
+    boolean periodMinimized();
+
     interface Builder {
+
         /**
          * Sets the slice period in milliseconds.
          *
@@ -22,41 +51,15 @@ interface Builder {
          *
          * @param state true to minimize the slice period
          */
-        Builder minimizePeriod(final boolean state);
+        Builder periodMinimized(final boolean state);
 
         /**
          * Creates an immutable instance of SliceSettings
          *
          * @return Immutable version of SliceSettings
          */
         SliceSettings build();
-    }
-
-    /**
-     * Returns a builder initialized with the current settings.
-     *
-     * @return a builder to create a modified copy of these settings
-     */
-    Builder copyBuilder();
-
-    /**
-     * Returns the slice period in milliseconds.
-     *
-     * @return the slice period in milliseconds
-     */
-    double period();
 
-    /**
-     * Returns the sample exposure time in milliseconds.
-     *
-     * @return the exposure time in milliseconds
-     */
-    double sampleExposure();
+    }
 
-    /**
-     * Returns true if the slice period is minimized.
-     *
-     * @return true if slice period is minimized
-     */
-    boolean periodMinimized();
 }