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Stefan Hahmann
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Add PCA Feature, Computer and Serializer classes
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‎src/main/java/org/mastodon/mamut/feature/branch/dimensionalityreduction/pca/BranchPcaFeature.java‎

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/*-
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* #%L
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* mastodon-deep-lineage
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* %%
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* Copyright (C) 2022 - 2024 Stefan Hahmann
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.feature.branch.dimensionalityreduction.pca;
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import java.util.List;
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import org.mastodon.feature.Feature;
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import org.mastodon.feature.FeatureProjectionKey;
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import org.mastodon.feature.FeatureProjectionSpec;
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import org.mastodon.feature.FeatureSpec;
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import org.mastodon.feature.Multiplicity;
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import org.mastodon.mamut.feature.dimensionalityreduction.pca.AbstractPcaFeature;
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import org.mastodon.mamut.model.branch.BranchSpot;
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import org.mastodon.properties.DoublePropertyMap;
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import org.scijava.plugin.Plugin;
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/**
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* Represents a PCA feature for BranchSpots in the Mastodon project.
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* <br>
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* This feature is used to store the PCA outputs for BranchSpots.
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* <br>
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* The PCA outputs are stored in a list of {@link DoublePropertyMap}s. The size of the list is equal to the number of dimensions of the PCA output.
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*/
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public class BranchPcaFeature extends AbstractPcaFeature< BranchSpot >
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{
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public static final String KEY = "Branch PCA outputs";
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private final BranchSpotPcaFeatureSpec adaptedSpec;
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public static final BranchSpotPcaFeatureSpec GENERIC_SPEC = new BranchSpotPcaFeatureSpec();
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public BranchPcaFeature( final List< DoublePropertyMap< BranchSpot > > outputMaps )
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{
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super( outputMaps );
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FeatureProjectionSpec[] projectionSpecs =
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projectionMap.keySet().stream().map( FeatureProjectionKey::getSpec ).toArray( FeatureProjectionSpec[]::new );
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this.adaptedSpec = new BranchSpotPcaFeatureSpec( projectionSpecs );
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}
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@Plugin( type = FeatureSpec.class )
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public static class BranchSpotPcaFeatureSpec extends FeatureSpec< BranchPcaFeature, BranchSpot >
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{
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public BranchSpotPcaFeatureSpec()
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{
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super( KEY, HELP_STRING, BranchPcaFeature.class, BranchSpot.class, Multiplicity.SINGLE );
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}
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public BranchSpotPcaFeatureSpec( final FeatureProjectionSpec... projectionSpecs )
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{
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super( KEY, HELP_STRING, BranchPcaFeature.class, BranchSpot.class, Multiplicity.SINGLE, projectionSpecs );
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}
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}
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@Override
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public FeatureSpec< ? extends Feature< BranchSpot >, BranchSpot > getSpec()
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{
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return adaptedSpec;
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}
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}

‎src/main/java/org/mastodon/mamut/feature/branch/dimensionalityreduction/pca/BranchPcaFeatureComputer.java‎

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/*-
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* #%L
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* mastodon-deep-lineage
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* %%
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* Copyright (C) 2022 - 2024 Stefan Hahmann
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.feature.branch.dimensionalityreduction.pca;
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import java.util.Collection;
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import java.util.List;
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import java.util.concurrent.locks.ReentrantReadWriteLock;
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import org.mastodon.RefPool;
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import org.mastodon.mamut.feature.dimensionalityreduction.pca.AbstractPcaFeature;
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import org.mastodon.mamut.feature.dimensionalityreduction.pca.AbstractPcaFeatureComputer;
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import org.mastodon.mamut.model.Model;
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import org.mastodon.mamut.model.branch.BranchLink;
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import org.mastodon.mamut.model.branch.BranchSpot;
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import org.mastodon.mamut.model.branch.ModelBranchGraph;
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import org.mastodon.properties.DoublePropertyMap;
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import org.scijava.Context;
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public class BranchPcaFeatureComputer extends AbstractPcaFeatureComputer< BranchSpot, BranchLink, ModelBranchGraph >
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{
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public BranchPcaFeatureComputer( final Model model, final Context context )
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{
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super( model, context );
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}
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@Override
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protected AbstractPcaFeature< BranchSpot > createFeatureInstance( final List< DoublePropertyMap< BranchSpot > > umapOutputMaps )
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{
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return new BranchPcaFeature( umapOutputMaps );
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}
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@Override
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protected RefPool< BranchSpot > getRefPool()
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{
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return model.getBranchGraph().vertices().getRefPool();
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}
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@Override
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protected ReentrantReadWriteLock getLock( final ModelBranchGraph branchGraph )
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{
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return branchGraph.getLock();
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}
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@Override
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protected Collection< BranchSpot > getVertices()
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{
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return model.getBranchGraph().vertices();
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}
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}

‎src/main/java/org/mastodon/mamut/feature/branch/dimensionalityreduction/pca/BranchPcaFeatureSerializer.java‎

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/*-
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* #%L
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* mastodon-deep-lineage
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* %%
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* Copyright (C) 2022 - 2024 Stefan Hahmann
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.mastodon.mamut.feature.branch.dimensionalityreduction.pca;
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import java.io.IOException;
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import java.io.ObjectInputStream;
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import java.io.ObjectOutputStream;
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import org.mastodon.feature.FeatureSpec;
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import org.mastodon.feature.io.FeatureSerializer;
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import org.mastodon.io.FileIdToObjectMap;
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import org.mastodon.io.ObjectToFileIdMap;
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import org.mastodon.mamut.feature.branch.BranchFeatureSerializer;
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import org.mastodon.mamut.feature.branch.dimensionalityreduction.BranchOutputSerializerTools;
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import org.mastodon.mamut.model.ModelGraph;
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import org.mastodon.mamut.model.Spot;
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import org.mastodon.mamut.model.branch.BranchSpot;
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import org.mastodon.mamut.model.branch.ModelBranchGraph;
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import org.scijava.plugin.Plugin;
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/**
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* De-/serializes {@link BranchPcaFeature}
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*/
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@Plugin( type = FeatureSerializer.class )
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public class BranchPcaFeatureSerializer implements BranchFeatureSerializer< BranchPcaFeature, BranchSpot, Spot >
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{
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@Override
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public FeatureSpec< BranchPcaFeature, BranchSpot > getFeatureSpec()
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{
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return BranchPcaFeature.GENERIC_SPEC;
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}
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@Override
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public void serialize( final BranchPcaFeature feature, final ObjectToFileIdMap< Spot > idmap, final ObjectOutputStream oos,
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final ModelBranchGraph branchGraph, final ModelGraph graph ) throws IOException
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{
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BranchOutputSerializerTools.serialize( feature, idmap, oos, branchGraph, graph );
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}
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@Override
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public BranchPcaFeature deserialize( final FileIdToObjectMap< Spot > idmap, final ObjectInputStream ois,
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final ModelBranchGraph branchGraph, final ModelGraph graph ) throws ClassNotFoundException, IOException
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{
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return BranchOutputSerializerTools.deserialize( idmap, ois, branchGraph, graph, BranchPcaFeature::new );
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}
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}

‎src/main/java/org/mastodon/mamut/feature/dimensionalityreduction/pca/AbstractPcaFeature.java‎

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/*-
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* #%L
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* mastodon-deep-lineage
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* %%
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* Copyright (C) 2022 - 2024 Stefan Hahmann
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* %%
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* Redistribution and use in source and binary forms, with or without
8+
* modification, are permitted provided that the following conditions are met:
9+
*
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* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
12+
* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
14+
* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
18+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
22+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
23+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
24+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
25+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
27+
* #L%
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*/
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package org.mastodon.mamut.feature.dimensionalityreduction.pca;
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import java.util.List;
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import org.mastodon.graph.Vertex;
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import org.mastodon.mamut.feature.dimensionalityreduction.AbstractOutputFeature;
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import org.mastodon.properties.DoublePropertyMap;
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/**
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* This generic feature is used to store the PCA outputs.
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* <br>
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* The PCA outputs are stored in a list of {@link DoublePropertyMap}s. The size of the list is equal to the number of dimensions of the PCA output.
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*/
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public abstract class AbstractPcaFeature< V extends Vertex< ? > > extends AbstractOutputFeature< V >
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{
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private static final String PROJECTION_NAME_TEMPLATE = "PCA%d";
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protected static final String HELP_STRING =
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"Computes the PCA according to the selected input dimensions and the number of target dimensions.";
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protected AbstractPcaFeature( final List< DoublePropertyMap< V > > outputMaps )
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{
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super( outputMaps );
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}
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@Override
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protected String getProjectionNameTemplate()
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{
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return PROJECTION_NAME_TEMPLATE;
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}
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}

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