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Add new method to tag set utils #302

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May 17, 2024
Merged

Add new method to tag set utils #302

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9e9a66a
Add new method getFirstSpot to TreeUtils
stefanhahmann Mar 28, 2024
bdbb56f
Add 2 new methods to TagSetUtils
stefanhahmann Mar 28, 2024
1364dfa
Add Spot ref as parameter to TagSetUtils.getTagLabel() and TreeUtils.…
stefanhahmann May 17, 2024
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31 changes: 31 additions & 0 deletions src/main/java/org/mastodon/util/TagSetUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,14 +28,17 @@
*/
package org.mastodon.util;

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;

import org.mastodon.mamut.model.Link;
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.model.tag.ObjTagMap;
import org.mastodon.model.tag.TagSetModel;
import org.mastodon.model.tag.TagSetStructure;
Expand Down Expand Up @@ -351,4 +354,32 @@ public static TagSetStructure.Tag findTag( final TagSetStructure.TagSet tagSet,
return tag;
throw new NoSuchElementException( "Did not find a tag with the given label: " + tagLabel );
}

/**
* Returns the names of all tag sets in the model.
* @param model the model to get the tag-set model from.
* @return the names of all tag sets in the model.
*/
public static List< String > getTagSetNames( final Model model )
{
List< String > tagSetNames = new ArrayList<>();
model.getTagSetModel().getTagSetStructure().getTagSets().forEach( tagSet -> tagSetNames.add( tagSet.getName() ) );
return tagSetNames;
}

/**
* Gets the tag label of the first spot in the given branchSpot within the given tagSet.
* @param model the model to which the branch belongs
* @param branchSpot the branch spot
* @param tagSet the tag set
* @return the tag label
*/
public static String getTagLabel( final Model model, final BranchSpot branchSpot, final TagSetStructure.TagSet tagSet, final Spot ref )
{
if ( model == null || branchSpot == null || tagSet == null )
return null;
Spot first = TreeUtils.getFirstSpot( model, branchSpot, ref );
TagSetStructure.Tag tag = TagSetUtils.getBranchTag( model, tagSet, first );
return tag == null ? null : tag.label();
}
}
12 changes: 12 additions & 0 deletions src/main/java/org/mastodon/util/TreeUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@
import org.mastodon.graph.Vertex;
import org.mastodon.mamut.model.Model;
import org.mastodon.mamut.model.Spot;
import org.mastodon.mamut.model.branch.BranchSpot;

public class TreeUtils
{
Expand Down Expand Up @@ -255,4 +256,15 @@ public static int getMaxTimepoint( final Model model )
max = Math.max( max, spot.getTimepoint() );
return max;
}

/**
* Gets the first {@link Spot} within the given {@link BranchSpot}.
* @param model the {@link Model} to which the {@link BranchSpot} belongs
* @param branchSpot the {@link BranchSpot} to query
* @return the first {@link Spot}
*/
public static Spot getFirstSpot( final Model model, final BranchSpot branchSpot, final Spot ref )
{
return model.getBranchGraph().getFirstLinkedVertex( branchSpot, ref );
}
}
38 changes: 38 additions & 0 deletions src/test/java/org/mastodon/util/TagSetUtilsTest.java
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Expand Up @@ -38,9 +38,13 @@

import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.List;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;

public class TagSetUtilsTest
Expand Down Expand Up @@ -110,4 +114,38 @@ public void tagSpotAndOutgoingEdges()
// 3 links are tagged: spot0 -> spot1, spot2 -> spot3, spot2 -> spot11
assertEquals( 3, model.getTagSetModel().getEdgeTags().getTaggedWith( tag0 ).size() );
}

@Test
public void testGetTagSetNames()
{
ExampleGraph1 exampleGraph1 = new ExampleGraph1();
String tagSetName1 = "TagSet1";
String tagSetName2 = "TagSet2";
String tagSetName3 = "TagSet2";
Collection< Pair< String, Integer > > emptyTagsAndColors = Collections.emptyList();
TagSetUtils.addNewTagSetToModel( exampleGraph1.getModel(), tagSetName1, emptyTagsAndColors );
TagSetUtils.addNewTagSetToModel( exampleGraph1.getModel(), tagSetName2, emptyTagsAndColors );
TagSetUtils.addNewTagSetToModel( exampleGraph1.getModel(), tagSetName3, emptyTagsAndColors );
Collection< String > tagSetNames = TagSetUtils.getTagSetNames( exampleGraph1.getModel() );
List< String > expected = Arrays.asList( tagSetName1, tagSetName2, tagSetName3 );
assertEquals( expected, tagSetNames );
}

@Test
public void testGetTagLabel()
{
ExampleGraph2 exampleGraph2 = new ExampleGraph2();
String tagSetName = "TagSet";
Pair< String, Integer > tag0 = Pair.of( "Tag", 0 );
Collection< Pair< String, Integer > > tagAndColor = Collections.singletonList( tag0 );
TagSetStructure.TagSet tagSet = TagSetUtils.addNewTagSetToModel( exampleGraph2.getModel(), tagSetName, tagAndColor );
TagSetStructure.Tag tag = tagSet.getTags().get( 0 );
TagSetUtils.tagBranch( exampleGraph2.getModel(), tagSet, tag, exampleGraph2.spot5 );
Spot ref = exampleGraph2.getModel().getGraph().vertexRef();
assertEquals( tag.label(), TagSetUtils.getTagLabel( exampleGraph2.getModel(), exampleGraph2.branchSpotD, tagSet, ref ) );
assertNull( TagSetUtils.getTagLabel( null, exampleGraph2.branchSpotD, tagSet, ref ) );
assertNull( TagSetUtils.getTagLabel( exampleGraph2.getModel(), null, tagSet, ref ) );
assertNull( TagSetUtils.getTagLabel( exampleGraph2.getModel(), exampleGraph2.branchSpotD, null, ref ) );
exampleGraph2.getModel().getGraph().releaseRef( ref );
}
}
14 changes: 14 additions & 0 deletions src/test/java/org/mastodon/util/TreeUtilsTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -191,4 +191,18 @@ public void testGetMaxTimepoint()
assertEquals( 3, TreeUtils.getMaxTimepoint( new ExampleGraph1().getModel() ) );
assertEquals( 7, TreeUtils.getMaxTimepoint( new ExampleGraph2().getModel() ) );
}

@Test
public void testGetFirstSpot()
{
ExampleGraph1 exampleGraph1 = new ExampleGraph1();
Spot ref = exampleGraph1.getModel().getGraph().vertexRef();
assertEquals( exampleGraph1.spot0, TreeUtils.getFirstSpot( exampleGraph1.getModel(), exampleGraph1.branchSpotA, ref ) );
exampleGraph1.getModel().getGraph().releaseRef( ref );

ExampleGraph2 exampleGraph2 = new ExampleGraph2();
ref = exampleGraph2.getModel().getGraph().vertexRef();
assertEquals( exampleGraph2.spot5, TreeUtils.getFirstSpot( exampleGraph2.getModel(), exampleGraph2.branchSpotD, ref ) );
exampleGraph2.getModel().getGraph().releaseRef( ref );
}
}
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