Add functionality for the coloring of lineages

Author: maarzt

…mancak/lineage_registration/Glasbey.java …mancak/lineage_registration/Glasbey.javasrc/test/java/org/mastodon/mamut/tomancak/lineage_registration/Glasbey.java renamed to src/main/java/org/mastodon/mamut/tomancak/lineage_registration/Glasbey.java src/test/java/org/mastodon/mamut/tomancak/lineage_registration/Glasbey.java renamed to src/main/java/org/mastodon/mamut/tomancak/lineage_registration/Glasbey.java

@@ -1,11 +1,13 @@
 package org.mastodon.mamut.tomancak.lineage_registration;
 
+import java.util.Collection;
+import java.util.Collections;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import org.jetbrains.annotations.NotNull;
 import org.mastodon.collection.RefCollection;
 import org.mastodon.collection.RefRefMap;
 import org.mastodon.graph.algorithm.traversal.DepthFirstSearch;
@@ -26,26 +28,24 @@ public class LineageColoring
 	 * Creates a new tag set "lineages" in both models.
 	 * A tag is added for all the root nodes that where successfully matched using {@link RootsPairing#pairDividingRoots}.
 	 * The tags of matching roots node gets the same colors assigned.
-	 * Finally the tag is applied to all the descendants of a root node.
+	 * Finally, the tag is applied to all the descendants of a root node.
 	 */
 	public static void tagLineages( Model embryoA, Model embryoB )
 	{
 		RefRefMap< Spot, Spot > roots = RootsPairing.pairDividingRoots( embryoA.getGraph(), embryoB.getGraph() );
-		Set< String > labels = roots.keySet().stream().map( Spot::getLabel ).collect( Collectors.toSet() );
+		List< String > labels = roots.keySet().stream().map( Spot::getLabel ).sorted().collect( Collectors.toList() );
 		Map< String, Integer > colorMap = createColorMap( labels );
 		tagLineages( colorMap, roots.keySet(), embryoA );
 		tagLineages( colorMap, roots.values(), embryoB );
 	}
 
 	private static void tagLineages( Map< String, Integer > colorMap, RefCollection< Spot > roots, Model model )
 	{
-		TagSetStructure.TagSet tagSet = createTagSet( model, colorMap );
+		TagSetStructure.TagSet tagSet = addTagSetToModel( model, colorMap );
 		Map< String, TagSetStructure.Tag > tags = tagSet.getTags().stream()
 				.collect( Collectors.toMap( TagSetStructure.Tag::label, tag -> tag ) );
 		for ( Spot root : roots )
-		{
 			tagLineage( model, root, tagSet, tags.get( root.getLabel() ) );
-		}
 	}
 
 	private static void tagLineage( Model model, Spot root, TagSetStructure.TagSet tagSet, TagSetStructure.Tag tag )
@@ -86,7 +86,7 @@ public void crossComponent( Spot spot, Spot v1, DepthFirstSearch< Spot, Link > s
 		search.start( root );
 	}
 
-	private static TagSetStructure.TagSet createTagSet( Model model, Map< String, Integer > tagsAndColors )
+	private static TagSetStructure.TagSet addTagSetToModel( Model model, Map< String, Integer > tagsAndColors )
 	{
 		TagSetModel< Spot, Link > tagSetModel = model.getTagSetModel();
 		TagSetStructure tss = copy( tagSetModel.getTagSetStructure() );
@@ -103,8 +103,11 @@ private static TagSetStructure copy( TagSetStructure original )
 		return copy;
 	}
 
-	@NotNull
-	private static Map< String, Integer > createColorMap( Set< String > labels )
+	/**
+	 * For a given set of labels, create a map from label to color.
+	 * Colors are taken from the Glasbey lookup table.
+	 */
+	private static Map< String, Integer > createColorMap( Collection< String > labels )
 	{
 		Map< String, Integer > colors = new HashMap<>();
 		int count = 4;

…ineage_registration/LineageColoring.java …ineage_registration/LineageColoring.javasrc/test/java/org/mastodon/mamut/tomancak/lineage_registration/LineageColoring.java renamed to src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageColoring.java src/test/java/org/mastodon/mamut/tomancak/lineage_registration/LineageColoring.java renamed to src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageColoring.java

@@ -83,7 +83,9 @@ public void onSortTrackSchemeBClicked()
 		@Override
 		public void onColorLineagesClicked()
 		{
-			// TODO
+			Model modelA = dialog.getProjectA().getAppModel().getModel();
+			Model modelB = dialog.getProjectB().getAppModel().getModel();
+			LineageColoring.tagLineages( modelA, modelB );
 		}
 
 		@Override