Refactor UMAP test to use Properties for configuration and update parameter setup

Author: Stefan Hahmann

src/main/java/org/mastodon/mamut/feature/dimensionalityreduction/tsne/feature/AbstractTSneFeatureComputer.java

@@ -30,7 +30,6 @@
 
 import java.lang.invoke.MethodHandles;
 import java.util.List;
-import java.util.Properties;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 
 import org.mastodon.RefPool;

src/test/java/org/mastodon/mamut/feature/dimensionalityreduction/umap/UmapSmileTest.java

@@ -4,22 +4,20 @@
 
 import java.lang.invoke.MethodHandles;
 import java.util.Arrays;
+import java.util.Properties;
 
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.mastodon.mamut.feature.dimensionalityreduction.DimensionalityReductionTestUtils;
 import org.mastodon.mamut.feature.dimensionalityreduction.RandomDataTools;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import smile.manifold.UMAP;
-import smile.math.MathEx;
 
 class UmapSmileTest
 {
 	private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
 
-	/*
 	@Test
 	void test()
 	{
@@ -29,11 +27,24 @@ void test()
 		double[][] sampleData = RandomDataTools.generateSampleData( numCluster1, numCluster2 );
 
 		// Recommendations for UMAP defaults: https://github.com/lmcinnes/umap/blob/a012b9d8751d98b94935ca21f278a54b3c3e1b7f/umap/umap_.py#L1073
-		int iterations = sampleData.length < 10_000 ? 500 : 200;
 		double minDist = 0.1;
 		int nNeighbors = 15;
+		int d = 2;
+		double learningRate = 1.0;
+		double spread = 1.0;
+		int negativeSampleRate = 5;
+		double repulsionStrength = 1.0;
 		long t0 = System.currentTimeMillis();
-		double[][] umapResult = UMAP.of( sampleData, MathEx::distance, nNeighbors, 2, iterations, 1, minDist, 1.0, 5, 1 );
+		Properties props = new Properties();
+		props.setProperty( "smile.umap.k", String.valueOf( nNeighbors ) );
+		props.setProperty( "smile.umap.d", String.valueOf( d ) );
+		props.setProperty( "smile.umap.learning_rate", String.valueOf( learningRate ) );
+		props.setProperty( "smile.umap.min_dist", String.valueOf( minDist ) );
+		props.setProperty( "smile.umap.spread", String.valueOf( spread ) );
+		props.setProperty( "smile.umap.negative_samples", String.valueOf( negativeSampleRate ) );
+		props.setProperty( "smile.umap.repulsion_strength", String.valueOf( repulsionStrength ) );
+
+		double[][] umapResult = UMAP.fit( sampleData, UMAP.Options.of( props ) );
 		logger.info( "UMAP took {} ms", System.currentTimeMillis() - t0 );
 
 		assertEquals( 2, umapResult[ 0 ].length );
@@ -44,6 +55,4 @@ void test()
 
 		DimensionalityReductionTestUtils.testNonOverlappingClusters( umapResult1, umapResult2 ); // should pass
 	}
-	
-	 */
 }