Add scale factor to LineageMotifsUtils

Author: Stefan Hahmann

src/main/java/org/mastodon/mamut/lineagemotifs/ui/FindLineageMotifsCommand.java

@@ -117,8 +117,9 @@ private void findModules( boolean runOnBranchGraph )
 		{
 			BranchSpotTree lineageMotif = LineageMotifsUtils.getSelectedMotif( model, projectModel.getSelectionModel() );
 			String lineageMotifName = lineageMotif.getStartSpotName();
-			List< Pair< BranchSpotTree, Double > > similarModules = LineageMotifsUtils.getMostSimilarMotifs( lineageMotif,
-					numberOfSimilarLineage, SimilarityMeasure.getByName( similarityMeasure ), spotRef, branchSpotRef, !runOnBranchGraph );
+			List< Pair< BranchSpotTree, Double > > similarModules =
+					LineageMotifsUtils.getMostSimilarMotifs( lineageMotif, numberOfSimilarLineage,
+							SimilarityMeasure.getByName( similarityMeasure ), 1d, spotRef, branchSpotRef, !runOnBranchGraph );
 			int numberOfDivisions = lineageMotif.getNumberOfDivisions();
 			String optionalPlural = numberOfDivisions == 1 ? "" : "s";
 			tagSetName = TAG_SET_NAME + lineageMotifName + " (" + numberOfDivisions + " division" + optionalPlural + ")";

src/main/java/org/mastodon/mamut/lineagemotifs/util/LineageMotifsUtils.java

@@ -108,10 +108,11 @@ static int getEndTimepoint( final Spot selectedRoot, final Model model, final Se
 	 * @param lineageMotif the {@link BranchSpotTree} representing the given lineage motif
 	 * @param branchRef a reference to the branch graph
 	 * @param similarityMeasure the {@link SimilarityMeasure} to use for calculating the similarity
+	 * @param scaleFactor a scaling factor (i.e. in time) to apply to the similarity measure
 	 * @return a {@link RefDoubleMap} of {@link Spot}s and their respective similarity to the given lineage motif
 	 */
 	static RefDoubleMap< Spot > getMotifSimilarityBySpotIteration( final BranchSpotTree lineageMotif,
-			final SimilarityMeasure similarityMeasure, final BranchSpot branchRef )
+			final SimilarityMeasure similarityMeasure, final BranchSpot branchRef, final double scaleFactor )
 	{
 		Model model = lineageMotif.getModel();
 		final int motifLength = lineageMotif.getDuration();
@@ -129,7 +130,7 @@ static RefDoubleMap< Spot > getMotifSimilarityBySpotIteration( final BranchSpotT
 					int endTimepoint = startTimepoint + motifLength;
 					BranchSpot branchSpot = model.getBranchGraph().getBranchVertex( spot, branchRef );
 					BranchSpotTree candidateMotif = new BranchSpotTree( branchSpot, startTimepoint, endTimepoint, model );
-					double distance = similarityMeasure.compute( lineageMotif, candidateMotif, 1d );
+					double distance = similarityMeasure.compute( lineageMotif, candidateMotif, scaleFactor );
 					candidates.put( spot, distance );
 				}
 			} );
@@ -143,10 +144,11 @@ static RefDoubleMap< Spot > getMotifSimilarityBySpotIteration( final BranchSpotT
 	 *
 	 * @param lineageMotif the {@link BranchSpotTree} representing the given lineage module
 	 * @param similarityMeasure the {@link SimilarityMeasure} to use for calculating the similarity
+	 * @param scaleFactor a scaling factor (i.e. in time) to apply to the similarity measure
 	 * @return a {@link RefDoubleMap} of {@link Spot}s and their respective similarity to the given lineage module
 	 */
 	static RefDoubleMap< Spot > getMotifSimilarityByBranchSpotIteration( final BranchSpotTree lineageMotif,
-			final SimilarityMeasure similarityMeasure )
+			final SimilarityMeasure similarityMeasure, final double scaleFactor )
 	{
 		final int motifLength = lineageMotif.getDuration();
 		int moduleStartTimepoint = lineageMotif.getStartTimepoint();
@@ -162,7 +164,7 @@ static RefDoubleMap< Spot > getMotifSimilarityByBranchSpotIteration( final Branc
 			{
 				int endTimepoint = startTimepoint + motifLength;
 				BranchSpotTree candidateMotif = new BranchSpotTree( branchSpot, startTimepoint, endTimepoint, model );
-				double distance = similarityMeasure.compute( lineageMotif, candidateMotif, 1d );
+				double distance = similarityMeasure.compute( lineageMotif, candidateMotif, scaleFactor );
 				Iterator< Spot > spotIterator = model.getBranchGraph().vertexBranchIterator( branchSpot );
 				// we need to iterate over the spots in the branch to get the correct spot for the candidate
 				boolean foundMatchingSpot = false;
@@ -193,22 +195,23 @@ static RefDoubleMap< Spot > getMotifSimilarityByBranchSpotIteration( final Branc
 	 * @param lineageMotif    the {@link BranchSpotTree} representing the lineage motif to compare
 	 * @param maxNumberOfMotifs the maximum number of similar motifs to retrieve
 	 * @param similarityMeasure the {@link SimilarityMeasure} used to compute the similarity between motifs
+	 * @param scaleFactor      a scaling factor (i.e. in time) to apply to the similarity measure
 	 * @param spotRef         a reference {@link Spot} used for accessing the graph's objects
 	 * @param branchRef       a reference {@link BranchSpot} associated with the branch graph
 	 * @param isSpotIteration  a boolean indicating whether to use spot iteration or branch spot iteration for similarity calculation.
 	 * Spot iteration may take significantly longer than branch spot iteration, but it is more accurate.
 	 * @return a {@link List} of {@link BranchSpotTree} objects representing the most similar lineage motifs, including their similarity scores.
 	 */
 	public static List< Pair< BranchSpotTree, Double > > getMostSimilarMotifs( final BranchSpotTree lineageMotif,
-			int maxNumberOfMotifs, final SimilarityMeasure similarityMeasure, final Spot spotRef, final BranchSpot branchRef,
-			boolean isSpotIteration )
+			int maxNumberOfMotifs, final SimilarityMeasure similarityMeasure, final double scaleFactor, final Spot spotRef,
+			final BranchSpot branchRef, boolean isSpotIteration )
 	{
 		int motifLength = lineageMotif.getDuration();
 		RefDoubleMap< Spot > candidates;
 		if ( isSpotIteration )
-			candidates = getMotifSimilarityBySpotIteration( lineageMotif, similarityMeasure, branchRef );
+			candidates = getMotifSimilarityBySpotIteration( lineageMotif, similarityMeasure, branchRef, 1d );
 		else
-			candidates = getMotifSimilarityByBranchSpotIteration( lineageMotif, similarityMeasure );
+			candidates = getMotifSimilarityByBranchSpotIteration( lineageMotif, similarityMeasure, 1d );
 
 		Model model = lineageMotif.getModel();
 		RefPool< Spot > refPool = model.getGraph().vertices().getRefPool();

src/test/java/org/mastodon/mamut/lineagemotifs/util/LineageMotifsUtilsTest.java

@@ -321,9 +321,9 @@ void testGetSimilarMotifs() throws IOException, SpimDataException
 				}
 				BranchSpotTree motif = LineageMotifsUtils.getSelectedMotif( model, selectionModel );
 				List< Pair< BranchSpotTree, Double > > similarMotifsSpotIteration = LineageMotifsUtils.getMostSimilarMotifs( motif, 20,
-						SimilarityMeasure.NORMALIZED_ZHANG_DIFFERENCE, spotRef, branchSpotRef, true );
+						SimilarityMeasure.NORMALIZED_ZHANG_DIFFERENCE, 1d, spotRef, branchSpotRef, true );
 				List< Pair< BranchSpotTree, Double > > similarMotifsBranchSpotIteration = LineageMotifsUtils.getMostSimilarMotifs( motif,
-						20, SimilarityMeasure.NORMALIZED_ZHANG_DIFFERENCE, spotRef, branchSpotRef, false );
+						20, SimilarityMeasure.NORMALIZED_ZHANG_DIFFERENCE, 1d, spotRef, branchSpotRef, false );
 				boolean containsZeroValueSpotIteration = similarMotifsSpotIteration.stream().anyMatch( pair -> pair.getValue() == 0.0 );
 				boolean containsBranchSpot220SpotIteration =
 						similarMotifsSpotIteration.stream().anyMatch( pair -> pair.getKey().getBranchSpot().getLabel().equals( "220" ) );