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- Number of incoming and outgoing links on a spot. Useful to fish for cells that have a division or a merge, and debug unwanted linking events. - Oriented time-difference for links. Useful to detect buggy links introduced by improper semi-auto tracking. Debugging without this feature is really a pain.
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src/main/java/org/mastodon/mamut/feature/LinkDeltaFrameFeature.java
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| /*- | ||
| * #%L | ||
| * Mastodon | ||
| * %% | ||
| * Copyright (C) 2014 - 2023 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; | ||
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| import static org.mastodon.feature.FeatureProjectionKey.key; | ||
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| import java.util.Collections; | ||
| import java.util.Set; | ||
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| 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.FeatureSpec; | ||
| import org.mastodon.feature.Multiplicity; | ||
| import org.mastodon.mamut.model.Link; | ||
| import org.mastodon.mamut.model.ModelGraph; | ||
| import org.mastodon.mamut.model.Spot; | ||
| import org.scijava.plugin.Plugin; | ||
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| public class LinkDeltaFrameFeature implements Feature< Link > | ||
| { | ||
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| private static final String KEY = "Link delta T"; | ||
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| private static final String HELP_STRING = "The time difference in number of time-points between the target and source of links."; | ||
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| private static final FeatureProjectionSpec PROJECTION_SPEC = new FeatureProjectionSpec( KEY, Dimension.NONE ); | ||
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| public static final Spec SPEC = new Spec(); | ||
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| final ModelGraph graph; | ||
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| @Plugin( type = FeatureSpec.class ) | ||
| public static class Spec extends FeatureSpec< LinkDeltaFrameFeature, Link > | ||
| { | ||
| public Spec() | ||
| { | ||
| super( | ||
| KEY, | ||
| HELP_STRING, | ||
| LinkDeltaFrameFeature.class, | ||
| Link.class, | ||
| Multiplicity.SINGLE, | ||
| PROJECTION_SPEC ); | ||
| } | ||
| } | ||
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| public LinkDeltaFrameFeature( final ModelGraph graph ) | ||
| { | ||
| this.graph = graph; | ||
| } | ||
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| @Override | ||
| public FeatureProjection< Link > project( final FeatureProjectionKey key ) | ||
| { | ||
| return key( PROJECTION_SPEC ).equals( key ) ? new MyProjection( graph ) : null; | ||
| } | ||
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| @Override | ||
| public Set< FeatureProjection< Link > > projections() | ||
| { | ||
| return Collections.singleton( new MyProjection( graph ) ); | ||
| } | ||
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| @Override | ||
| public Spec getSpec() | ||
| { | ||
| return SPEC; | ||
| } | ||
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| @Override | ||
| public void invalidate( final Link link ) | ||
| {} | ||
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| private static final class MyProjection implements FeatureProjection< Link > | ||
| { | ||
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| private final Spot ref1; | ||
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| private final Spot ref2; | ||
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| public MyProjection( final ModelGraph graph ) | ||
| { | ||
| this.ref1 = graph.vertexRef(); | ||
| this.ref2 = graph.vertexRef(); | ||
| } | ||
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| @Override | ||
| public FeatureProjectionKey getKey() | ||
| { | ||
| return key( PROJECTION_SPEC ); | ||
| } | ||
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| @Override | ||
| public boolean isSet( final Link link ) | ||
| { | ||
| return true; | ||
| } | ||
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| @Override | ||
| public synchronized double value( final Link link ) | ||
| { | ||
| final Spot source = link.getSource( ref1 ); | ||
| final Spot target = link.getTarget( ref2 ); | ||
| return target.getTimepoint() - source.getTimepoint(); | ||
| } | ||
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| @Override | ||
| public String units() | ||
| { | ||
| return Dimension.NONE_UNITS; | ||
| } | ||
| } | ||
| } |
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