Add t-SNE computation for spot and branch features

mastodon-sc · Nov 14, 2024 · 0375d7c · 0375d7c
1 parent 1b0101a
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diff --git a/...ava/org/mastodon/mamut/feature/branch/dimensionalityreduction/tsne/BranchTSneFeature.java b/...ava/org/mastodon/mamut/feature/branch/dimensionalityreduction/tsne/BranchTSneFeature.java
@@ -0,0 +1,85 @@
+/*-
+ * #%L
+ * mastodon-deep-lineage
+ * %%
+ * Copyright (C) 2022 - 2024 Stefan Hahmann
+ * %%
+ * 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.branch.dimensionalityreduction.tsne;
+
+import java.util.List;
+
+import org.mastodon.feature.Feature;
+import org.mastodon.feature.FeatureProjectionKey;
+import org.mastodon.feature.FeatureProjectionSpec;
+import org.mastodon.feature.FeatureSpec;
+import org.mastodon.feature.Multiplicity;
+import org.mastodon.mamut.feature.dimensionalityreduction.tsne.feature.AbstractTSneFeature;
+import org.mastodon.mamut.model.branch.BranchSpot;
+import org.mastodon.properties.DoublePropertyMap;
+import org.scijava.plugin.Plugin;
+
+/**
+ * Represents a t-SNE feature for BranchSpots in the Mastodon project.
+ * <br>
+ * This feature is used to store the t-SNE outputs for BranchSpots.
+ * <br>
+ * The t-SNE outputs are stored in a list of {@link DoublePropertyMap}s. The size of the list is equal to the number of dimensions of the t-SNE output.
+ */
+public class BranchTSneFeature extends AbstractTSneFeature< BranchSpot >
+{
+	public static final String KEY = "Branch t-SNE outputs";
+
+	private final BranchSpotTSneFeatureSpec adaptedSpec;
+
+	public static final BranchSpotTSneFeatureSpec GENERIC_SPEC = new BranchSpotTSneFeatureSpec();
+
+	public BranchTSneFeature( final List< DoublePropertyMap< BranchSpot > > outputMaps )
+	{
+		super( outputMaps );
+		FeatureProjectionSpec[] projectionSpecs =
+				projectionMap.keySet().stream().map( FeatureProjectionKey::getSpec ).toArray( FeatureProjectionSpec[]::new );
+		this.adaptedSpec = new BranchSpotTSneFeatureSpec( projectionSpecs );
+	}
+
+	@Plugin( type = FeatureSpec.class )
+	public static class BranchSpotTSneFeatureSpec extends FeatureSpec< BranchTSneFeature, BranchSpot >
+	{
+		public BranchSpotTSneFeatureSpec()
+		{
+			super( KEY, HELP_STRING, BranchTSneFeature.class, BranchSpot.class, Multiplicity.SINGLE );
+		}
+
+		public BranchSpotTSneFeatureSpec( final FeatureProjectionSpec... projectionSpecs )
+		{
+			super( KEY, HELP_STRING, BranchTSneFeature.class, BranchSpot.class, Multiplicity.SINGLE, projectionSpecs );
+		}
+	}
+
+	@Override
+	public FeatureSpec< ? extends Feature< BranchSpot >, BranchSpot > getSpec()
+	{
+		return adaptedSpec;
+	}
+}
diff --git a/...mastodon/mamut/feature/branch/dimensionalityreduction/tsne/BranchTSneFeatureComputer.java b/...mastodon/mamut/feature/branch/dimensionalityreduction/tsne/BranchTSneFeatureComputer.java
@@ -0,0 +1,76 @@
+/*-
+ * #%L
+ * mastodon-deep-lineage
+ * %%
+ * Copyright (C) 2022 - 2024 Stefan Hahmann
+ * %%
+ * 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.branch.dimensionalityreduction.tsne;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.concurrent.locks.ReentrantReadWriteLock;
+
+import org.mastodon.RefPool;
+import org.mastodon.mamut.feature.dimensionalityreduction.tsne.feature.AbstractTSneFeature;
+import org.mastodon.mamut.feature.dimensionalityreduction.tsne.feature.AbstractTSneFeatureComputer;
+import org.mastodon.mamut.model.Model;
+import org.mastodon.mamut.model.branch.BranchLink;
+import org.mastodon.mamut.model.branch.BranchSpot;
+import org.mastodon.mamut.model.branch.ModelBranchGraph;
+import org.mastodon.properties.DoublePropertyMap;
+import org.scijava.Context;
+
+public class BranchTSneFeatureComputer extends AbstractTSneFeatureComputer< BranchSpot, BranchLink, ModelBranchGraph >
+{
+
+	public BranchTSneFeatureComputer( final Model model, final Context context )
+	{
+		super( model, context );
+	}
+
+	@Override
+	protected AbstractTSneFeature< BranchSpot > createFeatureInstance( final List< DoublePropertyMap< BranchSpot > > umapOutputMaps )
+	{
+		return new BranchTSneFeature( umapOutputMaps );
+	}
+
+	@Override
+	protected RefPool< BranchSpot > getRefPool()
+	{
+		return model.getBranchGraph().vertices().getRefPool();
+	}
+
+	@Override
+	protected ReentrantReadWriteLock getLock( final ModelBranchGraph branchGraph )
+	{
+		return branchGraph.getLock();
+	}
+
+	@Override
+	protected Collection< BranchSpot > getVertices()
+	{
+		return model.getBranchGraph().vertices();
+	}
+}
diff --git a/...stodon/mamut/feature/branch/dimensionalityreduction/tsne/BranchTSneFeatureSerializer.java b/...stodon/mamut/feature/branch/dimensionalityreduction/tsne/BranchTSneFeatureSerializer.java
@@ -0,0 +1,72 @@
+/*-
+ * #%L
+ * mastodon-deep-lineage
+ * %%
+ * Copyright (C) 2022 - 2024 Stefan Hahmann
+ * %%
+ * 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.branch.dimensionalityreduction.tsne;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+import org.mastodon.feature.FeatureSpec;
+import org.mastodon.feature.io.FeatureSerializer;
+import org.mastodon.io.FileIdToObjectMap;
+import org.mastodon.io.ObjectToFileIdMap;
+import org.mastodon.mamut.feature.branch.BranchFeatureSerializer;
+import org.mastodon.mamut.feature.branch.dimensionalityreduction.BranchOutputSerializerTools;
+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.scijava.plugin.Plugin;
+
+/**
+ * De-/serializes {@link BranchTSneFeature}
+ */
+@Plugin( type = FeatureSerializer.class )
+public class BranchTSneFeatureSerializer implements BranchFeatureSerializer< BranchTSneFeature, BranchSpot, Spot >
+{
+	@Override
+	public FeatureSpec< BranchTSneFeature, BranchSpot > getFeatureSpec()
+	{
+		return BranchTSneFeature.GENERIC_SPEC;
+	}
+
+	@Override
+	public void serialize( final BranchTSneFeature feature, final ObjectToFileIdMap< Spot > idmap, final ObjectOutputStream oos,
+			final ModelBranchGraph branchGraph, final ModelGraph graph ) throws IOException
+	{
+		BranchOutputSerializerTools.serialize( feature, idmap, oos, branchGraph, graph );
+	}
+
+	@Override
+	public BranchTSneFeature deserialize( final FileIdToObjectMap< Spot > idmap, final ObjectInputStream ois,
+			final ModelBranchGraph branchGraph, final ModelGraph graph ) throws ClassNotFoundException, IOException
+	{
+		return BranchOutputSerializerTools.deserialize( idmap, ois, branchGraph, graph, BranchTSneFeature::new );
+	}
+}
diff --git a/...org/mastodon/mamut/feature/dimensionalityreduction/DimensionalityReductionController.java b/...org/mastodon/mamut/feature/dimensionalityreduction/DimensionalityReductionController.java
@@ -37,11 +37,14 @@
 import org.mastodon.graph.Edge;
 import org.mastodon.graph.ReadOnlyGraph;
 import org.mastodon.graph.Vertex;
+import org.mastodon.mamut.feature.branch.dimensionalityreduction.tsne.BranchTSneFeatureComputer;
 import org.mastodon.mamut.feature.branch.dimensionalityreduction.umap.BranchUmapFeatureComputer;
 import org.mastodon.mamut.feature.dimensionalityreduction.tsne.TSneSettings;
+import org.mastodon.mamut.feature.dimensionalityreduction.tsne.feature.AbstractTSneFeatureComputer;
 import org.mastodon.mamut.feature.dimensionalityreduction.umap.UmapSettings;
 import org.mastodon.mamut.feature.dimensionalityreduction.umap.feature.AbstractUmapFeatureComputer;
 import org.mastodon.mamut.feature.dimensionalityreduction.util.InputDimension;
+import org.mastodon.mamut.feature.spot.dimensionalityreduction.tsne.SpotTSneFeatureComputer;
 import org.mastodon.mamut.feature.spot.dimensionalityreduction.umap.SpotUmapFeatureComputer;
 import org.mastodon.mamut.model.Link;
 import org.mastodon.mamut.model.Model;
@@ -177,10 +180,23 @@ public void setAlgorithm( final DimensionalityReductionAlgorithm algorithm )
 			throw new IllegalArgumentException( "Number of output dimensions (" + commonSettings.getNumberOfOutputDimensions()
 					+ ") must be smaller than the number of input features (" + inputDimensions.size() + ")." );
 		G graph = getGraph( isModelGraph );
-		AbstractUmapFeatureComputer< V, E, G > umapFeatureComputer =
-				isModelGraph ? Cast.unchecked( new SpotUmapFeatureComputer( model, context ) )
-						: Cast.unchecked( new BranchUmapFeatureComputer( model, context ) );
-		umapFeatureComputer.computeFeature( commonSettings, umapSettings, inputDimensions, graph );
+		switch ( algorithm )
+		{
+		case UMAP:
+			AbstractUmapFeatureComputer< V, E, G > umapFeatureComputer =
+					isModelGraph ? Cast.unchecked( new SpotUmapFeatureComputer( model, context ) )
+							: Cast.unchecked( new BranchUmapFeatureComputer( model, context ) );
+			umapFeatureComputer.computeFeature( commonSettings, umapSettings, inputDimensions, graph );
+			break;
+		case TSNE:
+			AbstractTSneFeatureComputer< V, E, G > tSneFeatureComputer =
+					isModelGraph ? Cast.unchecked( new SpotTSneFeatureComputer( model, context ) )
+							: Cast.unchecked( new BranchTSneFeatureComputer( model, context ) );
+			tSneFeatureComputer.computeFeature( commonSettings, tSneSettings, inputDimensions, graph );
+			break;
+		default:
+			throw new IllegalArgumentException( "Unknown algorithm: " + algorithm );
+		}
 	}
 
 	private < V extends Vertex< E >, E extends Edge< V >, G extends ReadOnlyGraph< V, ? > > G getGraph( boolean isSpotGraph )

diff --git a/.../org/mastodon/mamut/feature/dimensionalityreduction/tsne/feature/AbstractTSneFeature.java b/.../org/mastodon/mamut/feature/dimensionalityreduction/tsne/feature/AbstractTSneFeature.java
@@ -0,0 +1,59 @@
+/*-
+ * #%L
+ * mastodon-deep-lineage
+ * %%
+ * Copyright (C) 2022 - 2024 Stefan Hahmann
+ * %%
+ * 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.dimensionalityreduction.tsne.feature;
+
+import java.util.List;
+
+import org.mastodon.graph.Vertex;
+import org.mastodon.mamut.feature.dimensionalityreduction.AbstractOutputFeature;
+import org.mastodon.properties.DoublePropertyMap;
+
+/**
+ * This generic feature is used to store the t-SNE outputs.
+ * <br>
+ * The t-SNE outputs are stored in a list of {@link DoublePropertyMap}s. The size of the list is equal to the number of dimensions of the t-SNE output.
+ */
+public abstract class AbstractTSneFeature< V extends Vertex< ? > > extends AbstractOutputFeature< V >
+{
+	private static final String PROJECTION_NAME_TEMPLATE = "tSNE%d";
+
+	protected static final String HELP_STRING =
+			"Computes the t-SNE according to the selected input dimensions, number of target dimensions, the perplexity value and maximum number of iterations.";
+
+	protected AbstractTSneFeature( final List< DoublePropertyMap< V > > umapOutputMaps )
+	{
+		super( umapOutputMaps );
+	}
+
+	@Override
+	protected String getProjectionNameTemplate()
+	{
+		return PROJECTION_NAME_TEMPLATE;
+	}
+}