Merge pull request #12 from mastodon-sc/fix-fit-ellipsoid-test

Fix fit ellipsoid test

src/main/java/org/mastodon/mamut/fitting/FitEllipsoidPlugin.java

@@ -126,17 +126,22 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 
 	private final AbstractNamedAction fitSelectedVerticesAction;
 
-	private ProjectModel projectModel;
+	private MinimalProjectModel minimalProjectModel;
 
 	public FitEllipsoidPlugin()
 	{
 		fitSelectedVerticesAction = new RunnableAction( FIT_SELECTED_VERTICES, this::fitSelectedVertices );
 	}
 
 	@Override
-	public void setAppPluginModel( final ProjectModel model )
+	public void setAppPluginModel( final ProjectModel projectModel )
 	{
-		this.projectModel = model;
+		this.minimalProjectModel = new MinimalProjectModel( projectModel );
+	}
+
+	void setMinimalProjectModel( final MinimalProjectModel minimalProjectModel )
+	{
+		this.minimalProjectModel = minimalProjectModel;
 	}
 
 	@Override
@@ -164,7 +169,7 @@ void fitSelectedVertices()
 	{
 		// TODO: parameters to select which source to act on
 		final int sourceIndex = 0;
-		final SourceAndConverter< ? > source = projectModel.getSharedBdvData().getSources().get( sourceIndex );
+		final SourceAndConverter< ? > source = minimalProjectModel.getSharedBdvData().getSources().get( sourceIndex );
 		if ( !( source.getSpimSource().getType() instanceof RealType ) )
 			throw new IllegalArgumentException( "Expected RealType image source" );
 		process( Cast.unchecked( source ) );
@@ -179,7 +184,7 @@ void fitSelectedVertices()
 	@SuppressWarnings( "unused" )
 	private < T extends RealType< T > > void process( final SourceAndConverter< T > source )
 	{
-		final RefSet< Spot > vertices = projectModel.getSelectionModel().getSelectedVertices();
+		final RefSet< Spot > vertices = minimalProjectModel.getSelectionModel().getSelectedVertices();
 		if ( vertices.isEmpty() )
 			System.err.println( "no vertex selected" );
 
@@ -193,7 +198,7 @@ private < T extends RealType< T > > void process( final SourceAndConverter< T >
 		final ArrayList< Spot > threadSafeVertices = asArrayList( vertices );
 		// NB: RefSet is not thread-safe for iteration.
 		final int totalTasks = vertices.size();
-		final ReentrantReadWriteLock.WriteLock writeLock = projectModel.getModel().getGraph().getLock().writeLock();
+		final ReentrantReadWriteLock.WriteLock writeLock = minimalProjectModel.getModel().getGraph().getLock().writeLock();
 
 		Parallelization.getTaskExecutor().forEach( threadSafeVertices, spot -> {
 			// loop over vertices in parallel using multiple threads
@@ -253,7 +258,7 @@ private < T extends RealType< T > > void process( final SourceAndConverter< T >
 
 		// set undo point if at least one spot was fitted
 		if ( found.get() > 0 )
-			projectModel.getModel().setUndoPoint();
+			minimalProjectModel.getModel().setUndoPoint();
 	}
 
 	private static ArrayList< Spot > asArrayList( final RefSet< Spot > vertices )
@@ -405,7 +410,7 @@ private void showBdvDebugWindow( final SourceAndConverter< ? > source, final dou
 	{
 		final BdvStackSource< FloatType > inputSource =
 				BdvFunctions.show( input, "FloatType input", Bdv.options().sourceTransform( sourceToGlobal ) );
-		final ConverterSetups setups = projectModel.getSharedBdvData().getConverterSetups();
+		final ConverterSetups setups = minimalProjectModel.getSharedBdvData().getConverterSetups();
 		final ConverterSetup cs = setups.getConverterSetup( source );
 		final Bounds bounds = setups.getBounds().getBounds( cs );
 		inputSource.setDisplayRange( cs.getDisplayRangeMin(), cs.getDisplayRangeMax() );

src/main/java/org/mastodon/mamut/fitting/MinimalProjectModel.java

@@ -0,0 +1,53 @@
+package org.mastodon.mamut.fitting;
+
+import org.mastodon.mamut.ProjectModel;
+import org.mastodon.mamut.model.Link;
+import org.mastodon.mamut.model.Model;
+import org.mastodon.mamut.model.Spot;
+import org.mastodon.model.SelectionModel;
+import org.mastodon.views.bdv.SharedBigDataViewerData;
+
+/**
+ * A minimal interface to the data model of a Mastodon project.<p>
+ * This interface facilities testing of the ellipsoid fitting, since it allows to circumvent the fact that the {@link org.mastodon.mamut.ProjectModel} creates GUI components on instantiation.<p>
+ * It contains accessor methods to parts of the {@link org.mastodon.mamut.ProjectModel} that are safe to be used in a headless way.
+ *
+ * @author Stefan Hahmann
+ */
+public class MinimalProjectModel
+{
+	private final Model model;
+
+	private final SharedBigDataViewerData sharedBdvData;
+
+	private final SelectionModel< Spot, Link > selectionModel;
+
+	MinimalProjectModel(
+			final Model model, final SharedBigDataViewerData sharedBdvData, final SelectionModel< Spot, Link > selectionModel
+	)
+	{
+		this.model = model;
+		this.sharedBdvData = sharedBdvData;
+		this.selectionModel = selectionModel;
+	}
+
+	public MinimalProjectModel( final ProjectModel projectModel )
+	{
+		this( projectModel.getModel(), projectModel.getSharedBdvData(), projectModel.getSelectionModel() );
+	}
+
+	public Model getModel()
+	{
+		return model;
+	}
+
+	public SharedBigDataViewerData getSharedBdvData()
+	{
+		return sharedBdvData;
+	}
+
+	public SelectionModel< Spot, Link > getSelectionModel()
+	{
+		return selectionModel;
+	}
+}

src/test/java/org/mastodon/mamut/fitting/ArtificialData.java

@@ -35,8 +35,11 @@
 import org.mastodon.collection.ref.RefObjectHashMap;
 import org.mastodon.mamut.ProjectModel;
 import org.mastodon.mamut.fitting.ellipsoid.Ellipsoid;
+import org.mastodon.mamut.model.Link;
 import org.mastodon.mamut.model.Model;
 import org.mastodon.mamut.model.Spot;
+import org.mastodon.model.DefaultSelectionModel;
+import org.mastodon.model.SelectionModel;
 import org.mastodon.views.bdv.SharedBigDataViewerData;
 import org.scijava.Context;
 
@@ -56,7 +59,7 @@
 import net.imglib2.view.Views;
 
 /**
- * Renders a grid of ellipsoids in 3D, and wraps the result in a {@link MamutAppModel}.
+ * Renders a grid of ellipsoids in 3D, and wraps the result in a {@link ProjectModel}.
  */
 public class ArtificialData
 {
@@ -69,12 +72,15 @@ public class ArtificialData
 
 	private final int numberOfSpots = columns * columns * columns;
 
-	private final ProjectModel appModel;
+	private final Context context;
+
+	private final MinimalProjectModel minimalProjectModel;
 
 	private final RefObjectMap< Spot, Ellipsoid > ellipsoids;
 
 	public ArtificialData( final Context context )
 	{
+		this.context = context;
 		final Model model = new Model();
 		ellipsoids = new RefObjectHashMap<>( model.getGraph().vertices().getRefPool(), numberOfSpots );
 		final Img< FloatType > image = ArrayImgs.floats( columns * size, columns * size, columns * size );
@@ -91,8 +97,9 @@ public ArtificialData( final Context context )
 					ellipsoids.put( spot, ellipsoid );
 					drawSpot( image, interval, ellipsoid );
 				}
-
-		appModel = wrapAsAppModel( image, model, context );
+		SharedBigDataViewerData sharedBDVData = asSharedBdvDataXyz( image );
+		SelectionModel< Spot, Link > selectionModel = new DefaultSelectionModel<>( model.getGraph(), model.getGraphIdBimap() );
+		minimalProjectModel = new MinimalProjectModel( model, sharedBDVData, selectionModel );
 		selectAllVerticies();
 	}
 
@@ -112,8 +119,8 @@ private static SharedBigDataViewerData asSharedBdvDataXyz( final Img< FloatType
 
 	private void selectAllVerticies()
 	{
-		for ( final Spot vertex : appModel.getModel().getGraph().vertices() )
-			appModel.getSelectionModel().setSelected( vertex, true );
+		for ( final Spot vertex : minimalProjectModel.getModel().getGraph().vertices() )
+			minimalProjectModel.getSelectionModel().setSelected( vertex, true );
 	}
 
 	private Ellipsoid randomizedEllipsoid( final double[] center )
@@ -167,15 +174,14 @@ private static AffineTransform3D transposed( final AffineTransform3D transform )
 		return r;
 	}
 
-	private static ProjectModel wrapAsAppModel( final Img< FloatType > image, final Model model, final Context context )
+	public ProjectModel getAppModel()
 	{
-		final SharedBigDataViewerData sharedBigDataViewerData = asSharedBdvDataXyz( image );
-		return ProjectModel.create( context, model, sharedBigDataViewerData, null );
+		return ProjectModel.create( context, minimalProjectModel.getModel(), minimalProjectModel.getSharedBdvData(), null );
 	}
 
-	public ProjectModel getAppModel()
+	public MinimalProjectModel getMinimalProjectModel()
 	{
-		return appModel;
+		return minimalProjectModel;
 	}
 
 	public RefObjectMap< Spot, Ellipsoid> getExpectedEllipsoids()

src/test/java/org/mastodon/mamut/fitting/FitEllipsoidPluginTest.java

@@ -35,6 +35,7 @@
 import org.junit.Test;
 import org.mastodon.collection.RefObjectMap;
 import org.mastodon.mamut.fitting.ellipsoid.Ellipsoid;
+import org.mastodon.mamut.model.ModelGraph;
 import org.mastodon.mamut.model.Spot;
 import org.scijava.Context;
 
@@ -56,18 +57,20 @@ public void testFitEllipsoidPlugin() {
 		final ArtificialData data = new ArtificialData( new Context() );
 		final StopWatch watch = StopWatch.createAndStart();
 		final FitEllipsoidPlugin plugin = new FitEllipsoidPlugin();
-		plugin.setAppPluginModel( data.getAppModel() );
+		plugin.setMinimalProjectModel( data.getMinimalProjectModel() );
 		plugin.fitSelectedVertices();
 		System.out.println( watch );
 		final int success = countCorrectEllipsoids( data );
-		assertEquals( "Not all ellipsoids were fitted correctly.", data.getAppModel().getModel().getGraph().vertices().size(), success );
+		ModelGraph graph = data.getMinimalProjectModel().getModel().getGraph();
+		assertEquals( "Not all ellipsoids were fitted correctly.", graph.vertices().size(), success );
 	}
 
 	private static int countCorrectEllipsoids( final ArtificialData data )
 	{
 		int success = 0;
 		final RefObjectMap< Spot, Ellipsoid > expectedEllipsoids = data.getExpectedEllipsoids();
-		for( final Spot spot : data.getAppModel().getModel().getGraph().vertices() ) {
+		for ( final Spot spot : data.getMinimalProjectModel().getModel().getGraph().vertices() )
+		{
 			final Ellipsoid actualEllipsoid = asEllipsoid( spot );
 			final Ellipsoid expectedEllipsoid = expectedEllipsoids.get( spot );
 			final boolean equal = isEllipsoidEqual( expectedEllipsoid, actualEllipsoid );