Use scijavas new custom labels feature for the config enums

src/main/java/org/mastodon/mamut/clustering/ClusterRootNodesController.java

@@ -128,13 +128,13 @@ private void runClassification()
 	String getParameters()
 	{
 		StringJoiner joiner = new StringJoiner( ", " );
-		joiner.add( "Crop criterion: " + cropCriterion.getName() );
+		joiner.add( "Crop criterion: " + cropCriterion );
 		joiner.add( "Crop start: " + cropStart );
 		joiner.add( "Crop end: " + cropEnd );
 		joiner.add( "Number of classes: " + numberOfClasses );
 		joiner.add( "Minimum cell divisions: " + minCellDivisions );
-		joiner.add( "Similarity measure: " + similarityMeasure.getName() );
-		joiner.add( "Clustering method: " + clusteringMethod.getName() );
+		joiner.add( "Similarity measure: " + similarityMeasure );
+		joiner.add( "Clustering method: " + clusteringMethod );
 		joiner.add( "Resulting lineage trees: " + getRoots().size() );
 		return joiner.toString();
 	}
@@ -244,7 +244,7 @@ public void setInputParams( final CropCriteria cropCriterion, final int cropStar
 		this.cropStart = cropStart;
 		this.cropEnd = cropEnd;
 		this.minCellDivisions = minCellDivisions;
-		logger.debug( "Crop criterion {}, start: {}, end: {}", cropCriterion.getName(), this.cropStart, this.cropEnd );
+		logger.debug( "Crop criterion {}, start: {}, end: {}", cropCriterion, this.cropStart, this.cropEnd );
 	}
 
 	public void setComputeParams( SimilarityMeasure similarityMeasure, ClusteringMethod clusteringMethod, int numberOfClasses )

src/main/java/org/mastodon/mamut/clustering/config/ClusteringMethod.java

@@ -33,8 +33,6 @@
 import com.apporiented.algorithm.clustering.SingleLinkageStrategy;
 import org.mastodon.mamut.clustering.util.AverageLinkageUPGMAStrategy;
 
-import java.util.NoSuchElementException;
-
 public enum ClusteringMethod
 {
 	AVERAGE_LINKAGE( "Average linkage", new AverageLinkageUPGMAStrategy() ),
@@ -51,19 +49,12 @@ public enum ClusteringMethod
 		this.linkageStrategy = linkageStrategy;
 	}
 
-	public String getName()
+	@Override
+	public String toString()
 	{
 		return name;
 	}
 
-	public static ClusteringMethod getByName(final String name) {
-		for (final ClusteringMethod method : values())
-			if (method.getName().equals(name))
-				return method;
-
-		throw new NoSuchElementException();
-	}
-
 	public LinkageStrategy getLinkageStrategy()
 	{
 		return linkageStrategy;

src/main/java/org/mastodon/mamut/clustering/config/CropCriteria.java

@@ -28,8 +28,6 @@
  */
 package org.mastodon.mamut.clustering.config;
 
-import java.util.NoSuchElementException;
-
 public enum CropCriteria
 {
 	TIMEPOINT( "Timepoint", "time" ),
@@ -45,22 +43,14 @@ public enum CropCriteria
 		this.nameShort = nameShort;
 	}
 
-	public static CropCriteria getByName( final String name )
+	public String getNameShort()
 	{
-		for ( final CropCriteria criteria : values() )
-			if ( criteria.getName().equals( name ) )
-				return criteria;
-
-		throw new NoSuchElementException();
+		return nameShort;
 	}
 
-	public String getName()
+	@Override
+	public String toString()
 	{
 		return name;
 	}
-
-	public String getNameShort()
-	{
-		return nameShort;
-	}
 }

src/main/java/org/mastodon/mamut/clustering/config/SimilarityMeasure.java

@@ -32,7 +32,6 @@
 import org.mastodon.mamut.treesimilarity.ZhangUnorderedTreeEditDistance;
 import org.mastodon.mamut.treesimilarity.tree.Tree;
 
-import java.util.NoSuchElementException;
 import java.util.function.BiFunction;
 import java.util.function.BinaryOperator;
 
@@ -53,21 +52,13 @@ public enum SimilarityMeasure
 		this.distanceFunction = distanceFunction;
 	}
 
-	public static SimilarityMeasure getByName(final String name)
-	{
-		for (final SimilarityMeasure measure : values())
-			if (measure.getName().equals(name))
-				return measure;
-
-		throw new NoSuchElementException();
-	}
-
 	public double compute( Tree< Double > tree1, Tree< Double > tree2, BinaryOperator< Double > costFunction )
 	{
 		return distanceFunction.apply( tree1, tree2, costFunction );
 	}
 
-	public String getName()
+	@Override
+	public String toString()
 	{
 		return name;
 	}

src/main/java/org/mastodon/mamut/clustering/ui/ClusterRootNodesView.java

@@ -63,8 +63,8 @@ public class ClusterRootNodesView extends InteractiveCommand
 			+ "</html>\n";
 
 	@SuppressWarnings("all")
-	@Parameter(label = "Crop criterion", choices = { "Timepoint", "Number of cells" }, callback = "update")
-	private String cropCriterion = CropCriteria.TIMEPOINT.getName();
+	@Parameter(label = "Crop criterion", callback = "update")
+	private CropCriteria cropCriterion = CropCriteria.TIMEPOINT;
 
 	@SuppressWarnings("unused")
 	@Parameter(label = "Crop start", min = "0", callback = "update")
@@ -83,18 +83,12 @@ public class ClusterRootNodesView extends InteractiveCommand
 	private int numberOfCellDivisions;
 
 	@SuppressWarnings("all")
-	@Parameter(
-			label = "Similarity measure", choices = { "Normalized Zhang Tree Distance", "Per Branch Spot Zhang Tree Distance",
-			"Zhang Tree Distance" }, callback = "update"
-	)
-	private String similarityMeasure = SimilarityMeasure.NORMALIZED_DIFFERENCE.getName();
+	@Parameter(label = "Similarity measure", callback = "update")
+	private SimilarityMeasure similarityMeasure = SimilarityMeasure.NORMALIZED_DIFFERENCE;
 
 	@SuppressWarnings("all")
-	@Parameter(
-			label = "Linkage strategy for hierarchical clustering", choices = { "Average linkage", "Single Linkage",
-			"Complete Linkage" }, callback = "update"
-	)
-	private String clusteringMethod = ClusteringMethod.AVERAGE_LINKAGE.getName();
+	@Parameter(label = "Linkage strategy for hierarchical clustering", callback = "update")
+	private ClusteringMethod clusteringMethod = ClusteringMethod.AVERAGE_LINKAGE;
 
 	@SuppressWarnings("unused")
 	@Parameter(label = "Feature", choices = "Branch duration", callback = "update")
@@ -129,9 +123,8 @@ public void run()
 	@SuppressWarnings("unused")
 	private void update()
 	{
-		controller.setInputParams( CropCriteria.getByName( cropCriterion ), start, end, numberOfCellDivisions );
-		controller.setComputeParams(
-				SimilarityMeasure.getByName( similarityMeasure ), ClusteringMethod.getByName( clusteringMethod ), numberOfClasses );
+		controller.setInputParams( cropCriterion, start, end, numberOfCellDivisions );
+		controller.setComputeParams( similarityMeasure, clusteringMethod, numberOfClasses );
 		controller.setShowDendrogram( showDendrogram );
 
 		paramFeedback = "<html><body width=" + WIDTH_INPUT + "cm>";

src/main/java/org/mastodon/mamut/io/exporter/labelimage/config/LabelOptions.java

@@ -28,8 +28,6 @@
  */
 package org.mastodon.mamut.io.exporter.labelimage.config;
 
-import java.util.NoSuchElementException;
-
 
 public enum LabelOptions
 {
@@ -46,15 +44,8 @@ public enum LabelOptions
 		this.name = name;
 	}
 
-	public static LabelOptions getByName( final String name )
-	{
-		for ( final LabelOptions options : values() )
-			if ( options.getName().equals( name ) )
-				return options;
-		throw new NoSuchElementException();
-	}
-
-	public String getName()
+	@Override
+	public String toString()
 	{
 		return name;
 	}

src/main/java/org/mastodon/mamut/io/exporter/labelimage/ui/ExportLabelImageView.java

@@ -56,8 +56,8 @@ public class ExportLabelImageView implements Command
 			+ "</html>\n";
 
 	@SuppressWarnings("all")
-	@Parameter(label = "Label Id", choices = { "Spot track Id", "Branch spot ID", "Spot ID" })
-	private String option = LabelOptions.BRANCH_SPOT_ID.getName();
+	@Parameter(label = "Label Id")
+	private LabelOptions option = LabelOptions.BRANCH_SPOT_ID;
 
 	@SuppressWarnings("all")
 	@Parameter(label = "Frame rate reduction", description = "Only export every n-th. 1 means no reduction. Value must be >= 1.", min = "1")
@@ -83,7 +83,6 @@ public class ExportLabelImageView implements Command
 	public void run()
 	{
 		ExportLabelImageController controller = new ExportLabelImageController( projectModel, context );
-		LabelOptions selectedOption = LabelOptions.getByName( option );
-		controller.saveLabelImageToFile( selectedOption, saveTo, showResult, frameRateReduction );
+		controller.saveLabelImageToFile( option, saveTo, showResult, frameRateReduction );
 	}
 }

src/test/java/org/mastodon/mamut/clustering/config/ClusteringMethodTest.java

@@ -38,15 +38,9 @@ public class ClusteringMethodTest
 {
 
 	@Test
-	public void testGetName()
+	public void testToString()
 	{
-		assertEquals( "Average linkage", ClusteringMethod.AVERAGE_LINKAGE.getName() );
+		assertEquals( "Average linkage", ClusteringMethod.AVERAGE_LINKAGE.toString() );
 	}
 
-	@Test
-	public void testGetByName()
-	{
-		assertEquals( ClusteringMethod.AVERAGE_LINKAGE, ClusteringMethod.getByName( "Average linkage" ) );
-		assertThrows( NoSuchElementException.class, () -> ClusteringMethod.getByName( "foo" ) );
-	}
 }

src/test/java/org/mastodon/mamut/clustering/config/CropCriteriaTest.java

@@ -38,15 +38,8 @@ public class CropCriteriaTest
 {
 
 	@Test
-	public void testGetName()
+	public void testToString()
 	{
-		assertEquals( "Timepoint", CropCriteria.TIMEPOINT.getName() );
-	}
-
-	@Test
-	public void testGetByName()
-	{
-		assertEquals( CropCriteria.TIMEPOINT, CropCriteria.getByName( "Timepoint" ) );
-		assertThrows( NoSuchElementException.class, () -> CropCriteria.getByName( "foo" ) );
+		assertEquals( "Timepoint", CropCriteria.TIMEPOINT.toString() );
 	}
 }

src/test/java/org/mastodon/mamut/clustering/config/SimilarityMeasureTest.java

@@ -30,24 +30,14 @@
 
 import org.junit.Test;
 
-import java.util.NoSuchElementException;
-
 import static org.junit.Assert.*;
 
 public class SimilarityMeasureTest
 {
 
 	@Test
-	public void testGetName()
-	{
-		assertEquals( "Normalized Zhang Tree Distance", SimilarityMeasure.NORMALIZED_DIFFERENCE.getName() );
-	}
-
-	@Test
-	public void testGetByName()
+	public void testToString()
 	{
-		assertEquals( SimilarityMeasure.NORMALIZED_DIFFERENCE, SimilarityMeasure.getByName( "Normalized Zhang Tree Distance" ) );
-		assertThrows( NoSuchElementException.class, () -> SimilarityMeasure.getByName( "foo" ) );
+		assertEquals( "Normalized Zhang Tree Distance", SimilarityMeasure.NORMALIZED_DIFFERENCE.toString() );
 	}
-
 }

src/test/java/org/mastodon/mamut/io/exporter/labelimage/config/LabelOptionsTest.java

@@ -29,29 +29,14 @@
 package org.mastodon.mamut.io.exporter.labelimage.config;
 
 import org.junit.Test;
-import org.mastodon.mamut.io.exporter.labelimage.config.LabelOptions;
-
-import java.util.NoSuchElementException;
 
 import static org.junit.Assert.*;
 
 public class LabelOptionsTest
 {
-
-	@Test
-	public void getByName()
-	{
-		assertEquals( LabelOptions.SPOT_ID, LabelOptions.getByName( "Spot ID" ) );
-		assertEquals( LabelOptions.BRANCH_SPOT_ID, LabelOptions.getByName( "Branch spot ID" ) );
-		assertEquals( LabelOptions.TRACK_ID, LabelOptions.getByName( "Spot track Id" ) );
-		assertThrows( NoSuchElementException.class, () -> LabelOptions.getByName( "Foo" ) );
-	}
-
 	@Test
-	public void getName()
+	public void testToString()
 	{
-		assertEquals( "Spot ID", LabelOptions.SPOT_ID.getName() );
-		assertEquals( "Branch spot ID", LabelOptions.BRANCH_SPOT_ID.getName() );
-		assertEquals( "Spot track Id", LabelOptions.TRACK_ID.getName() );
+		assertEquals( "Spot ID", LabelOptions.SPOT_ID.toString() );
 	}
 }