Merge pull request #63 from mastodon-sc/rename-lineage-registration

Rename Lineage Registration to Spatial Track Matching

src/main/java/org/mastodon/mamut/tomancak/sort_tree/CellLifetimeOrder.java

@@ -34,7 +34,7 @@
 import org.mastodon.mamut.model.Link;
 import org.mastodon.mamut.model.ModelGraph;
 import org.mastodon.mamut.model.Spot;
-import org.mastodon.mamut.tomancak.lineage_registration.BranchGraphUtils;
+import org.mastodon.mamut.tomancak.trackmatching.BranchGraphUtils;
 
 /**
  * A sorting "order" for sorting the lineage tree in a {@link ModelGraph}.

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/BranchGraphUtils.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/BranchGraphUtils.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import net.imglib2.util.Pair;
 import net.imglib2.util.ValuePair;

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/ClosableLock.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/ClosableLock.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 /**
  * Similar to {@link AutoCloseable}, but without the checked exception.

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/ComboBoxDialog.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/ComboBoxDialog.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import java.awt.Component;
 import java.util.Arrays;

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageTreeUtils.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/LineageTreeUtils.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import java.util.function.Predicate;
 

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LockUtils.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/LockUtils.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import java.util.concurrent.locks.Lock;
 

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/RefCollectionUtils.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/RefCollectionUtils.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import java.util.function.Predicate;
 import java.util.function.UnaryOperator;

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/RefMapUtils.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/RefMapUtils.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import java.util.function.BiConsumer;
 

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/RegisteredGraphs.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/RegisteredGraphs.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import org.mastodon.RefPool;
 import org.mastodon.collection.RefDoubleMap;
@@ -36,15 +36,15 @@
 import org.mastodon.mamut.model.Model;
 import org.mastodon.mamut.model.ModelGraph;
 import org.mastodon.mamut.model.Spot;
-import org.mastodon.mamut.tomancak.lineage_registration.spatial_registration.InverseSpatialRegistration;
-import org.mastodon.mamut.tomancak.lineage_registration.spatial_registration.SpatialRegistration;
+import org.mastodon.mamut.tomancak.trackmatching.spatial_registration.InverseSpatialRegistration;
+import org.mastodon.mamut.tomancak.trackmatching.spatial_registration.SpatialRegistration;
 
 /**
  * <p>
  * This datastructure holds two {@link ModelGraph}s and a mapping between them.
  * </p>
  * <p>
- * This is also the return type of {@link LineageRegistrationAlgorithm#run}.
+ * This is also the return type of {@link SpatialTrackMatchingAlgorithm#run}.
  * </p>
  */
 public class RegisteredGraphs

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/RootsPairing.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/RootsPairing.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import java.util.HashSet;
 import java.util.Objects;

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/SelectedProject.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/SelectedProject.java

@@ -26,14 +26,14 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import org.mastodon.mamut.ProjectModel;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.mamut.model.ModelGraph;
 
 /**
- * Used in {@link LineageRegistrationFrame} and {@link LineageRegistrationControlService}
+ * Used in {@link SpatialTrackMatchingFrame} and {@link SpatialTrackMatchingControlService}
  * to exchange information about the selected projects and related sittings.
  */
 public class SelectedProject

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationAlgorithm.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/SpatialTrackMatchingAlgorithm.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import net.imglib2.realtransform.AffineTransform3D;
 
@@ -37,10 +37,10 @@
 import org.mastodon.mamut.model.Model;
 import org.mastodon.mamut.model.ModelGraph;
 import org.mastodon.mamut.model.Spot;
-import org.mastodon.mamut.tomancak.lineage_registration.spatial_registration.NotEnoughPairedRootsException;
-import org.mastodon.mamut.tomancak.lineage_registration.spatial_registration.SpatialRegistration;
-import org.mastodon.mamut.tomancak.lineage_registration.spatial_registration.SpatialRegistrationFactory;
-import org.mastodon.mamut.tomancak.lineage_registration.spatial_registration.SpatialRegistrationMethod;
+import org.mastodon.mamut.tomancak.trackmatching.spatial_registration.NotEnoughPairedRootsException;
+import org.mastodon.mamut.tomancak.trackmatching.spatial_registration.SpatialRegistration;
+import org.mastodon.mamut.tomancak.trackmatching.spatial_registration.SpatialRegistrationFactory;
+import org.mastodon.mamut.tomancak.trackmatching.spatial_registration.SpatialRegistrationMethod;
 import org.mastodon.mamut.tomancak.sort_tree.SortTreeUtils;
 
 /**
@@ -50,7 +50,7 @@
  *
  * @see SortTreeUtils#directionOfCellDevision(ModelGraph, Spot)
  */
-public class LineageRegistrationAlgorithm
+public class SpatialTrackMatchingAlgorithm
 {
 	private static final int TIME_OFFSET = SortTreeUtils.DIVISION_DIRECTION_TIME_OFFSET;
 
@@ -71,7 +71,7 @@ public class LineageRegistrationAlgorithm
 	private final RefDoubleMap< Spot > angles;
 
 	/**
-	 * Runs the lineage registration algorithm for to given graphs. The spots before
+	 * Runs the spatial track matching for to given graphs. The spots before
 	 * the given timepoints are ignored.
 	 *
 	 * @return a {@link RegisteredGraphs} object that contains the two graphs and the
@@ -117,7 +117,7 @@ private static NotEnoughPairedRootsException newDetailedNotEnoughPairedRootsExce
 	public static RegisteredGraphs run( Model modelA, Model modelB,
 			RefRefMap< Spot, Spot > roots, SpatialRegistration spatialRegistration )
 	{
-		LineageRegistrationAlgorithm algorithm = new LineageRegistrationAlgorithm(
+		SpatialTrackMatchingAlgorithm algorithm = new SpatialTrackMatchingAlgorithm(
 				modelA.getGraph(), modelB.getGraph(),
 				roots, spatialRegistration );
 		return new RegisteredGraphs( modelA, modelB, spatialRegistration, algorithm.getMapping(), algorithm.getAngles() );
@@ -128,7 +128,7 @@ private RefDoubleMap< Spot > getAngles()
 		return angles;
 	}
 
-	private LineageRegistrationAlgorithm( ModelGraph graphA, ModelGraph graphB, RefRefMap< Spot, Spot > roots,
+	private SpatialTrackMatchingAlgorithm( ModelGraph graphA, ModelGraph graphB, RefRefMap< Spot, Spot > roots,
 			SpatialRegistration spatialRegistration )
 	{
 		this.spatialRegistration = spatialRegistration;

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationControlService.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/SpatialTrackMatchingControlService.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -41,27 +41,27 @@
 import org.mastodon.mamut.ProjectModel;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.mamut.model.Spot;
-import org.mastodon.mamut.tomancak.lineage_registration.angle_feature.CellDivisionAngleFeature;
-import org.mastodon.mamut.tomancak.lineage_registration.coupling.ModelCoupling;
+import org.mastodon.mamut.tomancak.trackmatching.angle_feature.CellDivisionAngleFeature;
+import org.mastodon.mamut.tomancak.trackmatching.coupling.ModelCoupling;
 import org.mastodon.model.tag.TagSetStructure;
 import org.scijava.plugin.Plugin;
 import org.scijava.service.AbstractService;
 
 /**
- * This class is the controller for the {@link LineageRegistrationFrame}.
+ * This class is the controller for the {@link SpatialTrackMatchingFrame}.
  * It shows the dialog and performs the actions requested by the user.
  * <p>
  * There should be only one instance of this class in the Fiji application.
  * This is ensured by making it an {@link ImageJService}. Being a service,
- * allows the {@link LineageRegistrationPlugin} to access it, and to call
+ * allows the {@link SpatialTrackMatchingPlugin} to access it, and to call
  * {@link #registerMastodonInstance}.
  *
  * @author Matthias Arzt
  */
 @Plugin( type = ImageJService.class )
-public class LineageRegistrationControlService extends AbstractService implements ImageJService
+public class SpatialTrackMatchingControlService extends AbstractService implements ImageJService
 {
-	private LineageRegistrationFrame dialog = null;
+	private SpatialTrackMatchingFrame dialog = null;
 
 	private final List< ProjectModel > projectModels = new ArrayList<>();
 
@@ -87,7 +87,7 @@ public synchronized void showDialog()
 			return;
 		}
 		if ( dialog == null )
-			dialog = new LineageRegistrationFrame( new Listener() );
+			dialog = new SpatialTrackMatchingFrame( new Listener() );
 		dialog.setMastodonInstances( projectModels );
 		dialog.pack();
 		dialog.setVisible( true );
@@ -108,7 +108,7 @@ private static void executeTask( boolean writeLock, SelectedProject projectA, Se
 		} ).start();
 	}
 
-	private class Listener implements LineageRegistrationFrame.Listener
+	private class Listener implements SpatialTrackMatchingFrame.Listener
 	{
 
 		private ModelCoupling coupling = null;
@@ -132,7 +132,7 @@ private void sortSecondTrackScheme( SelectedProject project1, SelectedProject pr
 				dialog.log( "Sort the order of the child cells in the TrackScheme of project \"%s\".", project1.getName() );
 				dialog.log( "Use project \"%s\" as reference...", project2.getName() );
 				RegisteredGraphs registration = runRegistrationAlgorithm( project1, project2 );
-				LineageRegistrationUtils.sortSecondTrackSchemeToMatch( registration );
+				SpatialTrackMatchingUtils.sortSecondTrackSchemeToMatch( registration );
 				project2.getProjectModel().getBranchGraphSync().sync();
 				project2.getModel().setUndoPoint();
 				dialog.log( "done." );
@@ -148,7 +148,7 @@ public void onColorLineagesClicked()
 				dialog.clearLog();
 				dialog.log( "Create tag set \"lineages\" in project \"%s\"...", projectA.getName() );
 				dialog.log( "Create tag set \"lineages\" in project \"%s\"...", projectB.getName() );
-				LineageColoring.tagLineages(
+				TrackColoring.tagLineages(
 						projectA.getModel(), projectA.getFirstTimepoint(),
 						projectB.getModel(), projectB.getFirstTimepoint() );
 				projectA.getModel().setUndoPoint();
@@ -176,7 +176,7 @@ private void copyLabelsFromTo( SelectedProject fromProject, SelectedProject toPr
 				dialog.log( "Copy labels from project \"%s\" to project \"%s\"...",
 						fromProject.getName(), toProject.getName() );
 				RegisteredGraphs registration = runRegistrationAlgorithm( fromProject, toProject );
-				LineageRegistrationUtils.copySpotLabelsFromAtoB( registration );
+				SpatialTrackMatchingUtils.copySpotLabelsFromAtoB( registration );
 				toProject.getModel().setUndoPoint();
 				dialog.log( "done." );
 			} );
@@ -222,7 +222,7 @@ private void copyTagSetFromTo( SelectedProject fromProject, SelectedProject toPr
 						tagSet.getName(), fromProject.getName(), toProject.getName() );
 				String newTagSetName = tagSet.getName() + " (" + fromProject.getName() + ")";
 				RegisteredGraphs registration = runRegistrationAlgorithm( fromProject, toProject );
-				LineageRegistrationUtils.copyTagSetToSecondModel( registration, tagSet, newTagSetName );
+				SpatialTrackMatchingUtils.copyTagSetToSecondModel( registration, tagSet, newTagSetName );
 				toModel.setUndoPoint();
 				dialog.log( "done." );
 			} );
@@ -253,11 +253,11 @@ private void putTags( boolean modifyA, boolean modifyB )
 			executeTask( false, projectA, projectB, () -> {
 				dialog.clearLog();
 				if ( modifyA )
-					dialog.log( "Create tag set \"lineage registration\" in project \"%s\"...", projectA.getName() );
+					dialog.log( "Create tag set \"spatial track matching\" in project \"%s\"...", projectA.getName() );
 				if ( modifyB )
-					dialog.log( "Create tag set \"lineage registration\" in project \"%s\"...", projectB.getName() );
+					dialog.log( "Create tag set \"spatial track matching\" in project \"%s\"...", projectB.getName() );
 				RegisteredGraphs registration = runRegistrationAlgorithm( projectA, projectB );
-				LineageRegistrationUtils.tagCells( registration, modifyA, modifyB );
+				SpatialTrackMatchingUtils.tagCells( registration, modifyA, modifyB );
 				if ( modifyA )
 					projectA.getModel().setUndoPoint();
 				if ( modifyB )
@@ -299,7 +299,7 @@ public void onPlotAnglesClicked()
 			SelectedProject projectB = dialog.getProjectB();
 			RegisteredGraphs registeredGraphs = runRegistrationAlgorithm( projectA, projectB );
 			RefDoubleMap< Spot > anglesA = registeredGraphs.anglesA;
-			LineageRegistrationUtils.plotAngleAgainstTimepoint( anglesA );
+			SpatialTrackMatchingUtils.plotAngleAgainstTimepoint( anglesA );
 		}
 
 		@Override
@@ -316,7 +316,7 @@ public void onAddAnglesFeatureClicked()
 
 	private RegisteredGraphs runRegistrationAlgorithm( SelectedProject projectA, SelectedProject projectB )
 	{
-		return LineageRegistrationAlgorithm.run(
+		return SpatialTrackMatchingAlgorithm.run(
 				projectA.getModel(), projectA.getFirstTimepoint(),
 				projectB.getModel(), projectB.getFirstTimepoint(),
 				dialog.getSpatialRegistrationMethod() );

src/main/java/org/mastodon/mamut/tomancak/lineage_registration/LineageRegistrationFrame.java → src/main/java/org/mastodon/mamut/tomancak/trackmatching/SpatialTrackMatchingFrame.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.mastodon.mamut.tomancak.lineage_registration;
+package org.mastodon.mamut.tomancak.trackmatching;
 
 import java.text.NumberFormat;
 import java.util.ArrayList;
@@ -52,13 +52,13 @@
 import org.mastodon.app.ui.GroupLocksPanel;
 import org.mastodon.mamut.ProjectModel;
 import org.mastodon.mamut.io.project.MamutProject;
-import org.mastodon.mamut.tomancak.lineage_registration.spatial_registration.SpatialRegistrationMethod;
+import org.mastodon.mamut.tomancak.trackmatching.spatial_registration.SpatialRegistrationMethod;
 
 /**
- * Dialog for the {@link LineageRegistrationPlugin}. It allows to select two
+ * Dialog for the {@link SpatialTrackMatchingPlugin}. It allows to select two
  * {@link MamutProject}s and to perform various actions on them.
  */
-public class LineageRegistrationFrame extends JFrame
+public class SpatialTrackMatchingFrame extends JFrame
 {
 	private static final String FIRST_TIMEPOINT_TOOLTIP = "<html><body>"
 			+ "The first time point of a project to be used for the registration.<br>"
@@ -75,7 +75,7 @@ public class LineageRegistrationFrame extends JFrame
 			+ "</body></html>";
 
 	private static final String TAG_CELLS_TOOLTIP = "<html><body>"
-			+ "<b>Creates a new tag set \"lineage registration\" in the selected project.</b><br>"
+			+ "<b>Creates a new tag set \"spatial track matching\" in the selected project.</b><br>"
 			+ "<br>"
 			+ "The tag set contains two tags:"
 			+ "<ul>"
@@ -148,9 +148,9 @@ public class LineageRegistrationFrame extends JFrame
 
 	private final JTextArea logArea;
 
-	public LineageRegistrationFrame( Listener listener )
+	public SpatialTrackMatchingFrame( Listener listener )
 	{
-		super( "Lineage Registration Across Two Mastodon Projects" );
+		super( "Spatial Track Matching Across Two Mastodon Projects" );
 		this.setDefaultCloseOperation( WindowConstants.DISPOSE_ON_CLOSE );
 		this.setLocationByPlatform( true );
 		this.listener = listener;
@@ -265,7 +265,7 @@ private JButton newOperationButton( String title, String hint, Runnable action )
 	private static JTextPane introductionTextPane()
 	{
 		final String introText = "<html><body>"
-				+ "The \"lineage registration\" plugin allows comparing the lineages of two "
+				+ "The \"spatial track matching\" plugin allows comparing the lineages of two "
 				+ "similarly developing embryos in two Mastodon projects. By analyzing the "
 				+ "spindle directions it finds the corresponding cells in both embryos."
 				+ "<br><br>"
@@ -277,10 +277,10 @@ private static JTextPane introductionTextPane()
 				+ "<li>Both projects should show stereotypically developing embryos.</li>"
 				+ "<li>The first frames should show both the embryos at a similar developmental stage.</li>"
 				+ "<li>Root nodes must be labeled, and the labels should match between the two projects.</li>"
-				+ "<li>There needs to be at least three lineages with cell divisions, "
+				+ "<li>There needs to be at least three tracks with cell divisions, "
 				+ "that can be paired based on their names.</li>"
 				+ "</ul>"
-				+ "(Note: The plugin ignores lineages that have no cell divisions.)<br><br>"
+				+ "(Note: The plugin ignores tracks that have no cell divisions.)<br><br>"
 				+ "</body></html>";
 		JTextPane comp = new JTextPane();
 		comp.setContentType( "text/html" );
@@ -528,7 +528,7 @@ public void onAddAnglesFeatureClicked()
 	public static void main( String... args )
 	{
 		// NOTE: Small demo function that only shows the LineageRegistrationDialog. For easy debugging.
-		LineageRegistrationFrame dialog = new LineageRegistrationFrame( new DummyListener() );
+		SpatialTrackMatchingFrame dialog = new SpatialTrackMatchingFrame( new DummyListener() );
 		dialog.pack();
 		dialog.setVisible( true );
 	}