getAvailableModes should not map to String, make utils final/prevent …

…instantiation

src/main/java/org/micromanager/lightsheetmanager/api/data/AcquisitionMode.java

@@ -15,7 +15,9 @@
 // Note: Each text string must be unique to support reliable lookup in fromString().
 
 /**
- * Acquisition modes for all microscope geometry types.
+ * Acquisition modes for all microscope geometries.
+ * <p>
+ * Use the {@code modesByType} method to get valid modes based on {@link GeometryType}.
  */
 public enum AcquisitionMode {
     NO_SCAN("No scan (fixed sheet)"),
@@ -85,13 +87,13 @@ public boolean isStageScanMode() {
      * This list is filtered based on hardware capabilities: if {@code hasStageScanning}
      * is {@code false}, all stage-scan related modes are excluded.
      *
-     * @param geometry the {@link GeometryType} to query; if {@code null}, an empty list is returned
+     * @param geometryType the {@link GeometryType} to query; if {@code null}, an empty list is returned
      * @param hasStageScanning {@code true} if stage scan hardware is available
-     * @return a {@code List} of {@link AcquisitionMode} constants
+     * @return an array of {@link AcquisitionMode} constants
      */
-    public static AcquisitionMode[] getValidModes(final GeometryType geometry, final boolean hasStageScanning) {
-        return Optional.ofNullable(geometry)
-                .map(MODES_BY_GEOMETRY::get) // returns null if geometry is not in map
+    public static AcquisitionMode[] modesByType(final GeometryType geometryType, final boolean hasStageScanning) {
+        return Optional.ofNullable(geometryType)
+                .map(MODES_BY_GEOMETRY::get) // returns null if geometryType is not in map
                 .orElse(Collections.emptyList())
                 .stream()
                 .filter(mode -> hasStageScanning || !mode.isStageScanMode())

src/main/java/org/micromanager/lightsheetmanager/api/data/CameraMode.java

@@ -97,9 +97,7 @@ public static CameraMode[] getAvailableModes(CameraLibrary camLib) {
                 modes.add(CameraMode.VIRTUAL_SLIT);
             }
         }
-        return modes.stream()
-                .map(CameraMode::toString)
-                .toArray(CameraMode[]::new);
+        return modes.toArray(CameraMode[]::new);
     }
 
     @Override

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

@@ -166,7 +166,8 @@ private void createUserInterface() {
         // acquisition mode combo box
         final boolean isUsingScanSettings = model_.devices().isUsingStageScanning();
         final GeometryType geometryType = model_.devices().adapter().geometry();
-        cmbAcquisitionModes_ = new ComboBox<>(AcquisitionMode.getValidModes(geometryType, isUsingScanSettings),
+        cmbAcquisitionModes_ = new ComboBox<>(
+                AcquisitionMode.modesByType(geometryType, isUsingScanSettings),
                 acqSettings.acquisitionMode(),
                 180, 24);
 

src/main/java/org/micromanager/lightsheetmanager/gui/utils/DialogUtils.java

@@ -10,7 +10,12 @@
  * A utility class for making dialog boxes.
  *
  */
-public class DialogUtils {
+public final class DialogUtils {
+
+    /** This class should not be instantiated. */
+    private DialogUtils() {
+        throw new AssertionError("Utility class; do not instantiate.");
+    }
 
     /**Standard error reporting or delegate to JTextArea component. */
     public static boolean SEND_ERROR_TO_COMPONENT = false;

src/main/java/org/micromanager/lightsheetmanager/gui/utils/WindowUtils.java

@@ -7,6 +7,11 @@
 
 public final class WindowUtils {
 
+    /** This class should not be instantiated. */
+    private WindowUtils() {
+        throw new AssertionError("Utility class; do not instantiate.");
+    }
+
     /**
      * Returns true if the window is displayable and not null.
      *

src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java

@@ -865,6 +865,8 @@ private boolean doHardwareCalculations(PLogicSCAPE plc) {
 
         // TODO: maybe wrap this up into a method for clarity
         double cameraReadoutTime;
+        //final CameraBase camera = model_.devices().device(cameraName);
+        //final double cameraReadoutTime = camera.getReadoutTime(acqSettings_.cameraMode());
         final CameraLibrary cameraLibrary = CameraLibrary.fromString(
                 model_.devices().device(cameraName).getDeviceLibrary());
         switch (cameraLibrary) {

src/main/java/org/micromanager/lightsheetmanager/model/utils/FileUtils.java

@@ -1,16 +1,19 @@
 package org.micromanager.lightsheetmanager.model.utils;
 
+import org.micromanager.internal.MMStudio;
+
 import java.io.File;
 import java.io.IOException;
 
-// TODO: show errors!
-// TODO: better name
-
-
 /**
- * Read and write to text files using Apache Commons.
+ * Utilities to read and write to files.
  */
-public class FileUtils {
+public final class FileUtils {
+
+    /** This class should not be instantiated. */
+    private FileUtils() {
+        throw new AssertionError("Utility class; do not instantiate.");
+    }
 
     /**
      * Reads a text file with UTF-8 encoding into a String.
@@ -23,7 +26,7 @@ public static String readFileToString(final String filePath) {
         try {
             result = org.apache.commons.io.FileUtils.readFileToString(new File(filePath), "UTF-8");
         } catch (IOException e) {
-            //ReportingUtils.showError("IOException: " + e.getMessage());
+            MMStudio.getInstance().logs().logError("FileUtils: readFileToString error");
         }
         return result;
     }
@@ -38,7 +41,7 @@ public static void writeStringToFile(final String filePath, final String content
         try {
             org.apache.commons.io.FileUtils.writeStringToFile(new File(filePath), contents, "UTF-8");
         } catch (IOException e) {
-            //ReportingUtils.showError("IOException: " + e.getMessage());
+            MMStudio.getInstance().logs().logError("FileUtils: writeStringToFile error");
         }
     }
 

src/main/java/org/micromanager/lightsheetmanager/model/utils/GeometryUtils.java

@@ -1,7 +1,12 @@
 package org.micromanager.lightsheetmanager.model.utils;
 
 // TODO: make this generic for diSPIM/SCOPE or have separate static classes
-public class GeometryUtils {
+public final class GeometryUtils {
+
+    /** This class should not be instantiated. */
+    private GeometryUtils() {
+        throw new AssertionError("Utility class; do not instantiate.");
+    }
 
     /***
      * Compute how far we need to shift each image for deskew relative to Z-step size (orthogonal to image) based on user-specified angle

src/main/java/org/micromanager/lightsheetmanager/model/utils/JsonUtils.java

@@ -5,7 +5,12 @@
 
 import java.util.Objects;
 
-public class JsonUtils {
+public final class JsonUtils {
+
+    /** This class should not be instantiated. */
+    private JsonUtils() {
+        throw new AssertionError("Utility class; do not instantiate.");
+    }
 
     public static void putJson(JSONObject json, final String property, final Object value) {
         Objects.requireNonNull(json);

src/main/java/org/micromanager/lightsheetmanager/model/utils/MathUtils.java

@@ -3,10 +3,11 @@
 /**
  * Math utilities.
  */
-public class MathUtils {
+public final class MathUtils {
 
+    /** This class should not be instantiated. */
     private MathUtils() {
-        // prevent instantiation
+        throw new AssertionError("Utility class; do not instantiate.");
     }
 
     /**

src/main/java/org/micromanager/lightsheetmanager/model/utils/NumberUtils.java

@@ -7,7 +7,12 @@
 /**
  * Utilities for dealing with double precision floating point numbers.
  */
-public class NumberUtils {
+public final class NumberUtils {
+
+    /** This class should not be instantiated. */
+    private NumberUtils() {
+        throw new AssertionError("Utility class; do not instantiate.");
+    }
 
     /**
      * Return true if the two doubles are equal according to Apache commons-math3 library.