LineageRegistrationPlugin: add copy spot labels functionality

mastodon-sc · Jun 14, 2024 · 413b471 · 413b471
1 parent 9c03ba2
commit 413b471
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Showing 4 changed files with 97 additions and 0 deletions.
diff --git a/...a/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationControlService.java b/...a/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationControlService.java
@@ -157,6 +157,31 @@ public void onColorLineagesClicked()
 			} );
 		}
 
+		@Override
+		public void onCopyLabelsAtoB()
+		{
+			copyLabelsFromTo( dialog.getProjectA(), dialog.getProjectB() );
+		}
+
+		@Override
+		public void onCopyLabelsBtoA()
+		{
+			copyLabelsFromTo( dialog.getProjectB(), dialog.getProjectA() );
+		}
+
+		private void copyLabelsFromTo( SelectedProject fromProject, SelectedProject toProject )
+		{
+			executeTask( true, fromProject, toProject, () -> {
+				dialog.clearLog();
+				dialog.log( "Copy labels from project \"%s\" to project \"%s\"...",
+						fromProject.getName(), toProject.getName() );
+				RegisteredGraphs registration = runRegistrationAlgorithm( fromProject, toProject );
+				LineageRegistrationUtils.copySpotLabelsFromAtoB( registration );
+				toProject.getModel().setUndoPoint();
+				dialog.log( "done." );
+			} );
+		}
+
 		@Override
 		public void onCopyTagSetAtoB()
 		{

diff --git a/src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationFrame.java b/src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationFrame.java
@@ -85,6 +85,14 @@ public class LineageRegistrationFrame extends JFrame
 			+ "</ul>"
 			+ "</body></html>";
 
+	private static final String COPY_LABELS_TOOLTIP = "<html><body>"
+			+ "Use the found correspondences to copy spot labels from one project to the other.<br>"
+			+ "<br>"
+			+ "The correspondences are on a level of cells / branches.<br>"
+			+ "That is why the all the spots that belong to a cell / branch will get the same label.<br>"
+			+ "Labels on individual spot can not copied."
+			+ "</body></html>";
+
 	private static final String COPY_TAGSET_TOOLTIP = "<html><body>"
 			+ "Use the found correspondences to copy a tag set from one project to the other.<br>"
 			+ "<br>"
@@ -176,6 +184,9 @@ public LineageRegistrationFrame( Listener listener )
 		add( new JLabel( "Sort TrackScheme:" ) );
 		add( newOperationButton( "project A", SORT_TRACKSCHEME_TOOLTIP, listener::onSortTrackSchemeAClicked ), "split 2" );
 		add( newOperationButton( "project B", SORT_TRACKSCHEME_TOOLTIP, listener::onSortTrackSchemeBClicked ), "wrap" );
+		add( new JLabel( "Copy spot labels:" ) );
+		add( newOperationButton( "from A to B ...", COPY_LABELS_TOOLTIP, listener::onCopyLabelsAtoB ), "split 2" );
+		add( newOperationButton( "from B to A ...", COPY_LABELS_TOOLTIP, listener::onCopyLabelsBtoA ), "wrap" );
 		add( new JLabel( "Copy tag set:" ) );
 		add( newOperationButton( "from A to B ...", COPY_TAGSET_TOOLTIP, listener::onCopyTagSetAtoB ), "split 2" );
 		add( newOperationButton( "from B to A ...", COPY_TAGSET_TOOLTIP, listener::onCopyTagSetBtoA ), "wrap" );
@@ -408,6 +419,10 @@ public interface Listener
 
 		void onColorLineagesClicked();
 
+		void onCopyLabelsAtoB();
+
+		void onCopyLabelsBtoA();
+
 		void onCopyTagSetAtoB();
 
 		void onCopyTagSetBtoA();
@@ -446,6 +461,18 @@ public void onColorLineagesClicked()
 
 		}
 
+		@Override
+		public void onCopyLabelsAtoB()
+		{
+
+		}
+
+		@Override
+		public void onCopyLabelsBtoA()
+		{
+
+		}
+
 		@Override
 		public void onCopyTagSetAtoB()
 		{

diff --git a/src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationUtils.java b/src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationUtils.java
@@ -318,4 +318,28 @@ public static void plotAngleAgainstTimepoint( RefDoubleMap< Spot > angles )
 		frame.pack();
 		frame.setVisible( true );
 	}
+
+	public static void copySpotLabelsFromAtoB( final RegisteredGraphs registration )
+	{
+		final ModelGraph graphB = registration.graphB;
+		final Spot refB = graphB.vertexRef();
+		try
+		{
+			for ( final Spot spotA : registration.mapAB.keySet() )
+			{
+				boolean hasLabel = !Integer.toString( spotA.getInternalPoolIndex() ).equals( spotA.getLabel() );
+				if ( hasLabel )
+				{
+					final Spot spotB = registration.mapAB.get( spotA, refB );
+					final RefList< Spot > spotsOfBranchB = BranchGraphUtils.getBranchSpotsAndLinks( graphB, spotB ).getA();
+					for ( final Spot spot : spotsOfBranchB )
+						spot.setLabel( spotA.getLabel() );
+				}
+			}
+		}
+		finally
+		{
+			graphB.releaseRef( refB );
+		}
+	}
 }
diff --git a/...t/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationUtilsTest.java b/...t/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationUtilsTest.java
@@ -116,6 +116,27 @@ public void testCopyTagSet()
 		assertEquals( set( "B~2 -> B2" ), getTaggedEdges( barB ) );
 	}
 
+	@Test
+	public void testCopyLabels()
+	{
+		// setup: labels for embryoA
+		for ( Spot spot : embryoA.graph.vertices() )
+			spot.setLabel( spot.getLabel() + "_test" );
+		// process
+		LineageRegistrationUtils.copySpotLabelsFromAtoB( registration );
+		// test: labels for embryoB
+		assertEquals( "A_test", embryoB.a.getLabel() );
+		assertEquals( "A_test", embryoB.a.outgoingEdges().get( 0 ).getTarget().getLabel() );
+		assertEquals( "A1_test", embryoB.a1.getLabel() );
+		assertEquals( "A2_test", embryoB.a2.getLabel() );
+		assertEquals( "B_test", embryoB.b.getLabel() );
+		assertEquals( "B2_test", embryoB.b1.getLabel() );
+		assertEquals( "B1_test", embryoB.b2.getLabel() );
+		assertEquals( "C_test", embryoB.c.getLabel() );
+		assertEquals( "C1_test", embryoB.c1.getLabel() );
+		assertEquals( "C2_test", embryoB.c2.getLabel() );
+	}
+
 	private static < T > Set< T > set( T... values )
 	{
 		return new HashSet<>( Arrays.asList( values ) );