Merge pull request #39 from mastodon-sc/branch_spot_id_feature

Add new SpotBranchIdFeature

src/main/java/org/mastodon/mamut/feature/spot/SpotBranchIDFeature.java

@@ -0,0 +1,86 @@
+package org.mastodon.mamut.feature.spot;
+
+import org.mastodon.feature.Dimension;
+import org.mastodon.feature.Feature;
+import org.mastodon.feature.FeatureProjection;
+import org.mastodon.feature.FeatureProjectionKey;
+import org.mastodon.feature.FeatureProjectionSpec;
+import org.mastodon.feature.FeatureProjections;
+import org.mastodon.feature.FeatureSpec;
+import org.mastodon.feature.IntFeatureProjection;
+import org.mastodon.feature.Multiplicity;
+import org.mastodon.mamut.model.Spot;
+import org.mastodon.properties.IntPropertyMap;
+import org.scijava.plugin.Plugin;
+
+import java.util.Collections;
+import java.util.Set;
+
+import static org.mastodon.feature.FeatureProjectionKey.key;
+
+public class SpotBranchIDFeature implements Feature< Spot >
+{
+
+	public static final String KEY = "Branch spot ID";
+
+	private static final String HELP_STRING = "Returns the ID of the branch each spot belongs to.";
+
+	public static final FeatureProjectionSpec PROJECTION_SPEC = new FeatureProjectionSpec( KEY );
+
+	public static final SpotBranchIDFeature.Spec SPEC = new SpotBranchIDFeature.Spec();
+
+	final IntPropertyMap< Spot > map;
+
+	private final IntFeatureProjection< Spot > projection;
+
+	@Plugin(type = FeatureSpec.class)
+	public static class Spec extends FeatureSpec< SpotBranchIDFeature, Spot >
+	{
+		public Spec()
+		{
+			super(
+					KEY,
+					HELP_STRING,
+					SpotBranchIDFeature.class,
+					Spot.class,
+					Multiplicity.SINGLE,
+					PROJECTION_SPEC
+			);
+		}
+	}
+
+	SpotBranchIDFeature( final IntPropertyMap< Spot > map )
+	{
+		this.map = map;
+		this.projection = FeatureProjections.project( key( PROJECTION_SPEC ), map, Dimension.NONE_UNITS );
+	}
+
+	public int get( final Spot spot )
+	{
+		return map.getInt( spot );
+	}
+
+	@Override
+	public FeatureProjection< Spot > project( final FeatureProjectionKey key )
+	{
+		return projection.getKey().equals( key ) ? projection : null;
+	}
+
+	@Override
+	public Set< FeatureProjection< Spot > > projections()
+	{
+		return Collections.singleton( projection );
+	}
+
+	@Override
+	public SpotBranchIDFeature.Spec getSpec()
+	{
+		return SPEC;
+	}
+
+	@Override
+	public void invalidate( final Spot spot )
+	{
+		map.remove( spot );
+	}
+}

src/main/java/org/mastodon/mamut/feature/spot/SpotBranchIDFeatureComputer.java

@@ -0,0 +1,86 @@
+/*-
+ * #%L
+ * Mastodon
+ * %%
+ * Copyright (C) 2014 - 2022 Tobias Pietzsch, Jean-Yves Tinevez
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.mastodon.mamut.feature.spot;
+
+import org.mastodon.mamut.feature.CancelableImpl;
+import org.mastodon.mamut.feature.MamutFeatureComputer;
+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.properties.IntPropertyMap;
+import org.scijava.ItemIO;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+@Plugin(type = MamutFeatureComputer.class)
+@SuppressWarnings({ "UnusedDeclaration" })
+public class SpotBranchIDFeatureComputer extends CancelableImpl implements MamutFeatureComputer
+{
+
+	@Parameter
+	@SuppressWarnings({ "UnusedDeclaration" })
+	private ModelGraph graph;
+
+	@Parameter
+	@SuppressWarnings({ "UnusedDeclaration" })
+	private ModelBranchGraph branchGraph;
+
+	@Parameter(type = ItemIO.OUTPUT)
+	private SpotBranchIDFeature output;
+
+	@Override
+	public void createOutput()
+	{
+		if ( null == output )
+			output = new SpotBranchIDFeature( new IntPropertyMap<>( graph.vertices().getRefPool(), -1 ) );
+	}
+
+	@Override
+	public void run()
+	{
+		output.map.beforeClearPool();
+
+		if ( graph.vertices().isEmpty() )
+			return;
+		if ( branchGraph.vertices().isEmpty() )
+			return;
+
+		BranchSpot ref = branchGraph.vertexRef();
+		for ( Spot spot : graph.vertices() )
+		{
+			if ( isCanceled() )
+				return;
+			final BranchSpot branchSpot = branchGraph.getBranchVertex( spot, ref );
+			if ( branchSpot != null )
+				output.map.set( spot, branchSpot.getInternalPoolIndex() );
+		}
+		branchGraph.releaseRef( ref );
+	}
+}

src/main/java/org/mastodon/mamut/feature/spot/SpotBranchIDFeatureSerializer.java

@@ -0,0 +1,76 @@
+/*-
+ * #%L
+ * Mastodon
+ * %%
+ * Copyright (C) 2014 - 2022 Tobias Pietzsch, Jean-Yves Tinevez
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.mastodon.mamut.feature.spot;
+
+import org.mastodon.collection.RefCollection;
+import org.mastodon.feature.io.FeatureSerializer;
+import org.mastodon.io.FileIdToObjectMap;
+import org.mastodon.io.ObjectToFileIdMap;
+import org.mastodon.io.properties.IntPropertyMapSerializer;
+import org.mastodon.mamut.model.Spot;
+import org.mastodon.properties.IntPropertyMap;
+import org.scijava.plugin.Plugin;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+@Plugin(type = FeatureSerializer.class)
+@SuppressWarnings({ "UnusedDeclaration" })
+public class SpotBranchIDFeatureSerializer implements FeatureSerializer< SpotBranchIDFeature, Spot >
+{
+
+	@Override
+	public SpotBranchIDFeature.Spec getFeatureSpec()
+	{
+		return SpotBranchIDFeature.SPEC;
+	}
+
+	@Override
+	public void serialize(
+			final SpotBranchIDFeature feature, final ObjectToFileIdMap< Spot > idmap,
+			final ObjectOutputStream oos
+	) throws IOException
+	{
+		final IntPropertyMapSerializer< Spot > propertyMapSerializer = new IntPropertyMapSerializer<>( feature.map );
+		propertyMapSerializer.writePropertyMap( idmap, oos );
+	}
+
+	@Override
+	public SpotBranchIDFeature deserialize(
+			final FileIdToObjectMap< Spot > idmap, final RefCollection< Spot > pool,
+			final ObjectInputStream ois
+	) throws IOException, ClassNotFoundException
+	{
+		final IntPropertyMap< Spot > map = new IntPropertyMap<>( pool, -1 );
+		final IntPropertyMapSerializer< Spot > propertyMapSerializer = new IntPropertyMapSerializer<>( map );
+		propertyMapSerializer.readPropertyMap( idmap, ois );
+		return new SpotBranchIDFeature( map );
+	}
+}

src/test/java/org/mastodon/mamut/feature/AbstractFeatureTest.java

@@ -0,0 +1,23 @@
+package org.mastodon.mamut.feature;
+
+import org.mastodon.feature.Feature;
+import org.mastodon.feature.FeatureProjection;
+import org.mastodon.feature.FeatureProjectionKey;
+import org.mastodon.feature.FeatureProjectionSpec;
+
+import java.io.IOException;
+
+public abstract class AbstractFeatureTest< T >
+{
+
+	protected FeatureProjection< T > getProjection( Feature< T > ellipsoidFeature, FeatureProjectionSpec featureProjectionSpec )
+	{
+		return ellipsoidFeature.project( FeatureProjectionKey.key( featureProjectionSpec ) );
+	}
+
+	public abstract void testFeatureComputation();
+
+	public abstract void testFeatureSerialization() throws IOException;
+
+	public abstract void testFeatureInvalidate();
+}

src/test/java/org/mastodon/mamut/feature/spot/SpotBranchIDFeatureTest.java

@@ -0,0 +1,74 @@
+package org.mastodon.mamut.feature.spot;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.mastodon.feature.Feature;
+import org.mastodon.feature.FeatureProjection;
+import org.mastodon.mamut.feature.AbstractFeatureTest;
+import org.mastodon.mamut.feature.FeatureComputerTestUtils;
+import org.mastodon.mamut.feature.FeatureSerializerTestUtils;
+import org.mastodon.mamut.feature.branch.exampleGraph.ExampleGraph2;
+import org.mastodon.mamut.model.Spot;
+import org.scijava.Context;
+
+import java.io.IOException;
+import java.util.Collections;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertTrue;
+
+public class SpotBranchIDFeatureTest extends AbstractFeatureTest< Spot >
+{
+	private Feature< Spot > feature;
+
+	private final ExampleGraph2 graph = new ExampleGraph2();
+
+	@Before
+	public void setUp()
+	{
+		try (Context context = new Context())
+		{
+			feature = FeatureComputerTestUtils.getFeature( context, graph.getModel(), SpotBranchIDFeature.SPEC );
+		}
+	}
+
+	@Override
+	@Test
+	public void testFeatureComputation()
+	{
+		FeatureProjection< Spot > featureProjection = getProjection( feature, SpotBranchIDFeature.PROJECTION_SPEC );
+		assertEquals( graph.branchSpotA.getInternalPoolIndex(), ( int ) featureProjection.value( graph.spot0 ) );
+		assertEquals( graph.branchSpotE.getInternalPoolIndex(), ( int ) featureProjection.value( graph.spot10 ) );
+	}
+
+	@Override
+	@Test
+	public void testFeatureSerialization() throws IOException
+	{
+		SpotBranchIDFeature featureReloaded;
+		try (Context context = new Context())
+		{
+			featureReloaded = ( SpotBranchIDFeature ) FeatureSerializerTestUtils.saveAndReload( context, graph.getModel(), feature );
+		}
+		// check that the feature has correct values after saving and reloading
+		assertTrue( FeatureSerializerTestUtils.checkFeatureProjectionEquality( feature, featureReloaded,
+				Collections.singleton( graph.spot0 )
+		) );
+	}
+
+	@Override
+	@Test
+	public void testFeatureInvalidate()
+	{
+		Spot spot = graph.spot0;
+		// test, if features have a non "-1" value before invalidation
+		assertNotEquals( -1, ( int ) getProjection( feature, SpotBranchIDFeature.PROJECTION_SPEC ).value( spot ) );
+
+		// invalidate feature
+		feature.invalidate( spot );
+
+		// test, if features are "-1" after invalidation
+		assertEquals( -1, ( int ) getProjection( feature, SpotBranchIDFeature.PROJECTION_SPEC ).value( spot ) );
+	}
+}

src/test/java/org/mastodon/mamut/feature/spot/ellipsoid/AbstractEllipsoidFeatureTest.java

@@ -1,16 +1,11 @@
 package org.mastodon.mamut.feature.spot.ellipsoid;
 
-import org.mastodon.feature.Feature;
-import org.mastodon.feature.FeatureProjection;
-import org.mastodon.feature.FeatureProjectionKey;
-import org.mastodon.feature.FeatureProjectionSpec;
+import org.mastodon.mamut.feature.AbstractFeatureTest;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.mamut.model.ModelGraph;
 import org.mastodon.mamut.model.Spot;
 
-import java.io.IOException;
-
-public abstract class AbstractEllipsoidFeatureTest
+public abstract class AbstractEllipsoidFeatureTest extends AbstractFeatureTest< Spot >
 {
 	protected final Model model = new Model();
 
@@ -36,16 +31,4 @@ private static Spot initEllipsoidSpot( ModelGraph graph )
 		spot.setCovariance( new double[][] { { 6, 2, 3 }, { 2, 7, 4 }, { 3, 4, 8 } } );
 		return spot;
 	}
-
-	protected static FeatureProjection< Spot > getProjection( Feature< Spot > ellipsoidFeature,
-			FeatureProjectionSpec featureProjectionSpec )
-	{
-		return ellipsoidFeature.project( FeatureProjectionKey.key( featureProjectionSpec ) );
-	}
-
-	abstract void testFeatureComputation();
-
-	abstract void testFeatureSerialization() throws IOException;
-
-	abstract void testFeatureInvalidate();
 }