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Use single mesh for rendering neurons.
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@hanslovsky
hanslovsky committed Nov 4, 2017
1 parent e61bbc1 commit 195dfbd
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Showing 2 changed files with 82 additions and 65 deletions.
133 changes: 70 additions & 63 deletions src/main/java/bdv/bigcat/viewer/viewer3d/NeuronFX.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@
import bdv.bigcat.viewer.viewer3d.marchingCubes.MarchingCubes;
import bdv.bigcat.viewer.viewer3d.util.HashWrapper;
import bdv.util.InvokeOnJavaFXApplicationThread;
import javafx.collections.ObservableFloatArray;
import javafx.scene.Group;
import javafx.scene.paint.Color;
import javafx.scene.paint.PhongMaterial;
import javafx.scene.shape.Box;
import javafx.scene.shape.CullFace;
import javafx.scene.shape.MeshView;
import javafx.scene.shape.ObservableFaceArray;
import javafx.scene.shape.TriangleMesh;
import javafx.scene.shape.VertexFormat;
import net.imglib2.FinalInterval;
Expand All @@ -32,32 +32,34 @@

public class NeuronFX< T >
{
private static float ONE_OVER_255 = 1.0f / 255.0f;

private final NeuronRendererFX< T, ? > generator;

private final Interval interval;

private final Group root;

public NeuronFX( final NeuronRendererFX< T, ? > generator, final Interval interval, final Group root )
{
super();
this.generator = generator;
this.interval = interval;
this.root = root;
}

private final List< MeshView > nodes = new ArrayList<>();

private final List< Future< ? > > futures = new ArrayList<>();

private final List< Box > chunks = new ArrayList<>();

private final Set< HashWrapper< long[] > > offsets = new HashSet<>();

private boolean isCanceled = false;

private final MeshView node;

private final PhongMaterial material;

private final Object meshModificationLock = new Object();

public NeuronFX( final Interval interval, final Group root )
{
super();
this.interval = interval;
this.root = root;
this.node = new MeshView();
this.material = new PhongMaterial();
this.node.setOpacity( 1.0 );
this.node.setCullFace( CullFace.FRONT );
this.node.setMaterial( material );
}

public void render(
final Localizable initialLocationInImageCoordinates,
final RandomAccessible< T > data,
Expand All @@ -68,11 +70,21 @@ public void render(
final int color,
final ExecutorService es )
{
cancel();
this.isCanceled = false;
final long[] gridCoordinates = new long[ initialLocationInImageCoordinates.numDimensions() ];
initialLocationInImageCoordinates.localize( gridCoordinates );
for ( int i = 0; i < gridCoordinates.length; ++i )
gridCoordinates[ i ] /= blockSize[ i ];
submitForOffset( gridCoordinates, data, foregroundCheck, toWorldCoordinates, blockSize, cubeSize, color, es );
try
{
initializeMeshView( color );
submitForOffset( gridCoordinates, data, foregroundCheck, toWorldCoordinates, blockSize, cubeSize, color, es );
}
catch ( final Exception e )
{
e.printStackTrace();
}
}

public void cancel()
Expand All @@ -81,16 +93,14 @@ public void cancel()
{
this.isCanceled = true;
this.futures.forEach( future -> future.cancel( true ) );
InvokeOnJavaFXApplicationThread.invoke( () -> root.getChildren().removeAll( this.chunks ) );
}
}

public void removeSelf()
public void removeSelf() throws InterruptedException
{
cancel();
InvokeOnJavaFXApplicationThread.invoke( () -> {
root.getChildren().removeAll( this.nodes );
root.getChildren().removeAll( this.chunks );
InvokeOnJavaFXApplicationThread.invokeAndWait( () -> {
root.getChildren().remove( node );
} );
}

Expand All @@ -106,6 +116,7 @@ private void submitForOffset(
{
final HashWrapper< long[] > offset = HashWrapper.longArray( gridCoordinates );
final long[] coordinates = IntStream.range( 0, gridCoordinates.length ).mapToLong( d -> gridCoordinates[ d ] * blockSize[ d ] ).toArray();
final TriangleMesh mesh = ( TriangleMesh ) this.node.getMesh();

synchronized ( futures )
{
Expand Down Expand Up @@ -151,50 +162,46 @@ private void submitForOffset(
chunk.setOpacity( 0.3 );
//
InvokeOnJavaFXApplicationThread.invoke( () -> root.getChildren().add( chunk ) );
this.chunks.add( chunk );

final MarchingCubes< T > mc = new MarchingCubes<>( data, interval, toWorldCoordinates, cubeSize );
final float[] vertices = mc.generateMesh( foregroundCheck );

InvokeOnJavaFXApplicationThread.invoke( () -> root.getChildren().remove( chunk ) );

if ( vertices.length > 0 )
{
final float[] normals = new float[ vertices.length ];
// MarchingCubes.surfaceNormals( vertices, normals );
MarchingCubes.averagedSurfaceNormals( vertices, normals );
for ( int i = 0; i < normals.length; ++i )
normals[ i ] *= -1;
final TriangleMesh mesh = new TriangleMesh();
final PhongMaterial material = new PhongMaterial();
material.setDiffuseColor( surfaceColor );
// material.setSpecularColor( Color.WHITE );

final MeshView mv = new MeshView( mesh );
mv.setOpacity( 1.0 );
mv.setCullFace( CullFace.FRONT );
mv.setMaterial( material );
mesh.getPoints().addAll( vertices );
mesh.getNormals().addAll( normals );
mesh.getTexCoords().addAll( 0, 0 );
mesh.setVertexFormat( VertexFormat.POINT_NORMAL_TEXCOORD );
final ObservableFaceArray faces = mesh.getFaces();
final int[] arr = new int[ 3 ];
for ( int i = 0, k = 0; i < vertices.length; i += 3, ++k )
{
arr[ 0 ] = k;
arr[ 1 ] = k;
arr[ 2 ] = 0;
faces.addAll( arr );
}

synchronized ( futures )
synchronized ( meshModificationLock )
{
if ( !isCanceled )
final ObservableFloatArray meshVertices = mesh.getPoints();
final ObservableFloatArray meshNormals = mesh.getNormals();
final int numVerticesInMesh = meshVertices.size() / 3;
final int[] faceIndices = new int[ vertices.length ];
for ( int i = 0, k = numVerticesInMesh; i < vertices.length; i += 3, ++k )
{
this.chunks.remove( chunk );
InvokeOnJavaFXApplicationThread.invoke( () -> root.getChildren().remove( chunk ) );
addNode( mv );
// generator.updateCompleteBoundingBox( mesh.generateBoundingBox() );
faceIndices[ i + 0 ] = k;
faceIndices[ i + 1 ] = k;
faceIndices[ i + 2 ] = 0;
}

try
{
InvokeOnJavaFXApplicationThread.invokeAndWait( () -> {
meshVertices.addAll( vertices );
meshNormals.addAll( normals );
mesh.getFaces().addAll( faceIndices );
} );
}
catch ( final InterruptedException e )
{
e.printStackTrace();
}

}

for ( int d = 0; d < gridCoordinates.length; ++d )
Expand All @@ -207,21 +214,21 @@ private void submitForOffset(
submitForOffset( otherGridCoordinates.clone(), data, foregroundCheck, toWorldCoordinates, blockSize, cubeSize, color, es );
}
}
else
{
this.chunks.remove( chunk );
InvokeOnJavaFXApplicationThread.invoke( () -> root.getChildren().remove( chunk ) );
}
} ) );
}
}

private void addNode( final MeshView node )
private void initializeMeshView( final int color ) throws InterruptedException
{
synchronized ( this.nodes )
{
this.nodes.add( node );
}
InvokeOnJavaFXApplicationThread.invoke( () -> this.root.getChildren().add( node ) );
final TriangleMesh mesh = new TriangleMesh();
mesh.getTexCoords().addAll( 0, 0 );
mesh.setVertexFormat( VertexFormat.POINT_NORMAL_TEXCOORD );
final Color surfaceColor = Color.rgb( color >>> 16 & 0xff, color >>> 8 & 0xff, color >>> 0 & 0xff, 1.0 );
this.node.setMesh( mesh );
this.material.setDiffuseColor( surfaceColor );
this.node.setMaterial( this.material );
InvokeOnJavaFXApplicationThread.invokeAndWait( () -> {
this.root.getChildren().add( this.node );
} );
}
}
14 changes: 12 additions & 2 deletions src/main/java/bdv/bigcat/viewer/viewer3d/NeuronRendererFX.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,17 @@ public synchronized void cancelRendering()
public synchronized void removeSelfFromScene()
{
cancelRendering();
neurons.forEach( NeuronFX::removeSelf );
neurons.forEach( t -> {
try
{
t.removeSelf();
}
catch ( final InterruptedException e )
{
// TODO Auto-generated catch block
e.printStackTrace();
}
} );
}

public synchronized void updateOnStateChange( final boolean updateOnStateChange )
Expand Down Expand Up @@ -144,7 +154,7 @@ public synchronized void render()
{
removeSelfFromScene();
this.neurons.clear();
final NeuronFX< T > neuron = new NeuronFX<>( this, interval, root );
final NeuronFX< T > neuron = new NeuronFX<>( interval, root );
this.neurons.add( neuron );
final float[] blub = new float[ 3 ];
final int color = stream.argb( selectedFragmentId );
Expand Down

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