Add unit tests

src/test/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsControllerTest.java

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+package org.mastodon.mamut.segment;
+
+import bdv.util.AbstractSource;
+import bdv.util.RandomAccessibleIntervalSource;
+import io.scif.img.ImgOpener;
+import io.scif.img.SCIFIOImgPlus;
+import mpicbg.spim.data.sequence.TimePoint;
+import net.imglib2.img.Img;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.test.RandomImgs;
+import net.imglib2.type.numeric.integer.IntType;
+import net.imglib2.util.Cast;
+import org.junit.Before;
+import org.junit.Test;
+import org.mastodon.mamut.model.Model;
+import org.mastodon.mamut.model.ModelGraph;
+import org.mastodon.mamut.model.Spot;
+import org.mastodon.mamut.model.branch.BranchSpot;
+import org.mastodon.mamut.model.branch.ModelBranchGraph;
+import org.mastodon.mamut.segment.config.LabelOptions;
+import org.scijava.Context;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertThrows;
+
+public class SegmentUsingEllipsoidsControllerTest
+{
+	private Model model;
+
+	private Spot spot;
+
+	private BranchSpot branchSpot;
+
+	private int timepoint;
+
+	private final long[] center = new long[] { 50, 50, 50 };
+
+	@Before
+	public void setUp()
+	{
+		model = new Model();
+		ModelGraph modelGraph = model.getGraph();
+		spot = modelGraph.addVertex();
+		ModelBranchGraph modelBranchGraph = model.getBranchGraph();
+		modelBranchGraph.graphRebuilt();
+		branchSpot = modelBranchGraph.getBranchVertex( spot, modelBranchGraph.vertexRef() );
+		timepoint = 0;
+		spot.init( timepoint, Arrays.stream( center ).asDoubleStream().toArray(), 5d );
+	}
+
+	@Test
+	public void testSaveEllipsoidSegmentationToFile() throws IOException
+	{
+		AbstractSource< IntType > source = createRandomSource();
+		Context context = new Context();
+		TimePoint timePoint = new TimePoint( timepoint );
+		List< TimePoint > timePoints = Collections.singletonList( timePoint );
+		SegmentUsingEllipsoidsController segmentUsingEllipsoidsController =
+				new SegmentUsingEllipsoidsController( model, timePoints, Cast.unchecked( source ), context );
+		File outputSpot = getTempFile( "resultSpot" );
+		File outputBranchSpot = getTempFile( "resultBranchSpot" );
+		segmentUsingEllipsoidsController.saveEllipsoidSegmentationToFile( LabelOptions.SPOT_ID, outputSpot, true, false );
+		segmentUsingEllipsoidsController.saveEllipsoidSegmentationToFile( LabelOptions.BRANCH_SPOT_ID, outputBranchSpot, true, false );
+
+		ImgOpener imgOpener = new ImgOpener( context );
+		SCIFIOImgPlus< IntType > imgSpot = getIntTypeSCIFIOImgPlus( imgOpener, outputSpot );
+		SCIFIOImgPlus< IntType > imgBranchSpot = getIntTypeSCIFIOImgPlus( imgOpener, outputBranchSpot );
+
+		// check that the random content has been replaced by the spot id in the center of the spot
+		assertEquals( spot.getInternalPoolIndex(), imgSpot.getAt( center ).get() );
+		assertEquals( branchSpot.getInternalPoolIndex(), imgBranchSpot.getAt( center ).get() );
+		// check that the random content has NOT been replaced outside the ellipsoid of the spot
+		long[] corner = new long[] { 0, 0, 0 };
+		assertNotEquals( spot.getInternalPoolIndex(), imgSpot.getAt( corner ).get() );
+		assertNotEquals( branchSpot.getInternalPoolIndex(), imgBranchSpot.getAt( corner ).get() );
+	}
+
+	private static SCIFIOImgPlus< IntType > getIntTypeSCIFIOImgPlus( ImgOpener imgOpener, File outputSpot )
+	{
+		List< SCIFIOImgPlus< ? > > imgsSpot = imgOpener.openImgs( outputSpot.getAbsolutePath() );
+		SCIFIOImgPlus< ? > imgSpot = imgsSpot.get( 0 );
+		return Cast.unchecked( imgSpot );
+	}
+
+	private static File getTempFile( final String prefix ) throws IOException
+	{
+		File outputSpot = File.createTempFile( prefix, ".tif" );
+		outputSpot.deleteOnExit();
+		return outputSpot;
+	}
+
+	@Test
+	public void testExceptions() throws IOException
+	{
+		SegmentUsingEllipsoidsController controller =
+				new SegmentUsingEllipsoidsController( model, Collections.emptyList(), null, new Context() );
+		File file = File.createTempFile( "foo", "foo" );
+		file.deleteOnExit();
+		assertThrows(
+				IllegalArgumentException.class,
+				() -> controller.saveEllipsoidSegmentationToFile( LabelOptions.SPOT_ID, null, true, false )
+		);
+		assertThrows( IllegalArgumentException.class, () -> controller.saveEllipsoidSegmentationToFile( null, file, true, false ) );
+		assertThrows( IllegalArgumentException.class, () -> controller.showEllipsoidSegmentationInBDV( null ) );
+	}
+
+	private static AbstractSource< IntType > createRandomSource()
+	{
+		Img< IntType > randomImg = RandomImgs.seed( 0 ).nextImage( new IntType() {}, 100, 100, 100 );
+		return new RandomAccessibleIntervalSource<>( randomImg, new IntType(), new AffineTransform3D(), "Segmentation" );
+	}
+
+	@Test
+	public void testShowEllipsoidSegmentationInBDV()
+	{
+		AbstractSource< IntType > source = createRandomSource();
+		Context context = new Context();
+		TimePoint timePoint = new TimePoint( timepoint );
+		List< TimePoint > timePoints = Collections.singletonList( timePoint );
+		SegmentUsingEllipsoidsController segmentUsingEllipsoidsController =
+				new SegmentUsingEllipsoidsController( model, timePoints, Cast.unchecked( source ), context );
+		segmentUsingEllipsoidsController.showEllipsoidSegmentationInBDV( LabelOptions.SPOT_ID );
+
+		// check that the random content has been replaced by the spot id in the center of the spot
+		assertEquals( spot.getInternalPoolIndex(), source.getSource( timepoint, 0 ).getAt( center ).get() );
+		// check that the random content has NOT been replaced outside the ellipsoid of the spot
+		long[] corner = new long[] { 0, 0, 0 };
+		assertNotEquals( spot.getInternalPoolIndex(), source.getSource( timepoint, 0 ).getAt( corner ).get() );
+	}
+
+}

src/test/java/org/mastodon/mamut/segment/config/LabelOptionsTest.java

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+package org.mastodon.mamut.segment.config;
+
+import org.junit.Test;
+
+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( "BranchSpot Id" ) );
+	}
+
+	@Test
+	public void getName()
+	{
+		assertEquals( "Spot Id", LabelOptions.SPOT_ID.getName() );
+		assertEquals( "BranchSpot Id", LabelOptions.BRANCH_SPOT_ID.getName() );
+	}
+}

src/test/java/org/mastodon/mamut/segment/config/SegmentationTaskTest.java

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+package org.mastodon.mamut.segment.config;
+
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class SegmentationTaskTest
+{
+
+	@Test
+	public void getByName()
+	{
+		assertEquals( SegmentationTask.SEGMENT_ELLIPSOIDS_BDV, SegmentationTask.getByName( "Show segmentation in BigDataViewer" ) );
+	}
+
+	@Test
+	public void getName()
+	{
+		assertEquals( "Show segmentation in BigDataViewer", SegmentationTask.SEGMENT_ELLIPSOIDS_BDV.getName() );
+		assertEquals( "Save segmentation result to file", SegmentationTask.SEGMENT_ELLIPSOIDS_IMAGEJ.getName() );
+	}
+}