- * Adapted from Yury Petrov's Ellipsoid
- * Fit MATLAB function and KalebKE ellipsoidfit.
- *
- * @author Jean-Yves Tinevez
- */
-public class EllipsoidFitter
-{
-
- /**
- * The results of fitting an ellpsoid to a mesh or a collection of points.
- */
- public static final class EllipsoidFit
- {
- /** The ellipsoid center. */
- public final RealLocalizable center;
-
- /** The eigenvector of the smallest axis of the ellipsoid. */
- public final RealLocalizable ev1;
-
- /** The eigenvector of the middle axis of the ellipsoid. */
- public final RealLocalizable ev2;
-
- /** The eigenvector of the largest axis of the ellipsoid. */
- public final RealLocalizable ev3;
-
- /** The radius of the smallest axis of the ellipsoid. */
- public final double r1;
-
- /** The radius of the middle axis of the ellipsoid. */
- public final double r2;
-
- /** The radius of the largest axis of the ellipsoid. */
- public final double r3;
-
- private EllipsoidFit( final RealLocalizable center,
- final RealLocalizable ev1,
- final RealLocalizable ev2,
- final RealLocalizable ev3,
- final double r1,
- final double r2,
- final double r3 )
- {
- this.center = center;
- this.ev1 = ev1;
- this.ev2 = ev2;
- this.ev3 = ev3;
- this.r1 = r1;
- this.r2 = r2;
- this.r3 = r3;
- }
-
- @Override
- public String toString()
- {
- final StringBuilder str = new StringBuilder( super.toString() );
- str.append( "\n - center: " + Util.printCoordinates( center ) );
- str.append( String.format( "\n - axis 1: radius = %.2f, vector = %s", r1, ev1 ) );
- str.append( String.format( "\n - axis 2: radius = %.2f, vector = %s", r2, ev2 ) );
- str.append( String.format( "\n - axis 3: radius = %.2f, vector = %s", r3, ev3 ) );
- return str.toString();
- }
- }
-
- private static final DefaultConvexHull3D cHull = new DefaultConvexHull3D();
-
- /**
- * Fit an ellipsoid to the convex-Hull of a 3D mesh.
- *
- * @param mesh
- * the mesh to fit.
- * @return the fit results.
- */
- public static final EllipsoidFit fit( final Mesh mesh )
- {
- final Mesh ch = cHull.calculate( mesh );
- return fitOnConvexHull( ch );
- }
-
- /**
- * Fit an ellipsoid to a 3D mesh, assuming it is the convex-Hull.
- *
- * @param mesh
- * the convex-Hull of the mesh to fit.
- * @return the fit results.
- */
- public static final EllipsoidFit fitOnConvexHull( final Mesh mesh )
- {
- return fit( mesh.vertices(), ( int ) mesh.vertices().size() );
- }
-
- /**
- * Fit an ellipsoid to a collection of 3D points.
- *
- * @param points
- * an iterable over the points to fit.
- * @param nPoints
- * the number of points to include in the fit. The fit will
- * consider at most the first nPoints of the iterable, or all the
- * points in the iterable, whatever comes first.
- * @return the fit results.
- */
- public static EllipsoidFit fit( final Iterable< ? extends RealLocalizable > points, final int nPoints )
- {
- final RealVector V = solve( points, nPoints );
-
- // To algebraix form.
- final RealMatrix A = toAlgebraicForm( V );
-
- // Find the center of the ellipsoid.
- final RealVector C = findCenter( A );
-
- // Translate the algebraic form of the ellipsoid to the center.
- final RealMatrix R = translateToCenter( C, A );
-
- // Ellipsoid eigenvectors and eigenvalues.
- final EllipsoidFit fit = getFit( R, C );
- return fit;
- }
-
- private static EllipsoidFit getFit( final RealMatrix R, final RealVector C )
- {
- final RealMatrix subr = R.getSubMatrix( 0, 2, 0, 2 );
-
- // subr[i][j] = subr[i][j] / -r[3][3]).
- final double divr = -R.getEntry( 3, 3 );
- for ( int i = 0; i < subr.getRowDimension(); i++ )
- for ( int j = 0; j < subr.getRowDimension(); j++ )
- subr.setEntry( i, j, subr.getEntry( i, j ) / divr );
-
- // Get the eigenvalues and eigenvectors.
- final EigenDecomposition ed = new EigenDecomposition( subr );
- final double[] eigenvalues = ed.getRealEigenvalues();
- final RealVector e1 = ed.getEigenvector( 0 );
- final RealVector e2 = ed.getEigenvector( 1 );
- final RealVector e3 = ed.getEigenvector( 2 );
-
- // Semi-axis length (radius).
- final RealVector SAL = new ArrayRealVector( eigenvalues.length );
- for ( int i = 0; i < eigenvalues.length; i++ )
- SAL.setEntry( i, Math.sqrt( 1. / eigenvalues[ i ] ) );
-
- // Put everything in a fit object.
- final RealPoint center = new RealPoint( C.getEntry( 0 ), C.getEntry( 1 ), C.getEntry( 2 ) );
- final RealPoint ev1 = new RealPoint( e1.getEntry( 0 ), e1.getEntry( 1 ), e1.getEntry( 2 ) );
- final RealPoint ev2 = new RealPoint( e2.getEntry( 0 ), e2.getEntry( 1 ), e2.getEntry( 2 ) );
- final RealPoint ev3 = new RealPoint( e3.getEntry( 0 ), e3.getEntry( 1 ), e3.getEntry( 2 ) );
- return new EllipsoidFit( center, ev1, ev2, ev3, SAL.getEntry( 0 ), SAL.getEntry( 1 ), SAL.getEntry( 2 ) );
- }
-
- /**
- * Translate the algebraic form of the ellipsoid to the center.
- *
- * @param C
- * the center of the ellipsoid.
- * @param A
- * the ellipsoid matrix.
- * @return the center translated form of the algebraic ellipsoid.
- */
- private static final RealMatrix translateToCenter( final RealVector C, final RealMatrix A )
- {
- final RealMatrix T = MatrixUtils.createRealIdentityMatrix( 4 );
- final RealMatrix centerMatrix = new Array2DRowRealMatrix( 1, 3 );
- centerMatrix.setRowVector( 0, C );
- T.setSubMatrix( centerMatrix.getData(), 3, 0 );
- final RealMatrix R = T.multiply( A ).multiply( T.transpose() );
- return R;
- }
-
- /**
- * Find the center of the ellipsoid.
- *
- * @param a
- * the algebraic from of the polynomial.
- * @return a vector containing the center of the ellipsoid.
- */
- private static final RealVector findCenter( final RealMatrix A )
- {
- final RealMatrix subA = A.getSubMatrix( 0, 2, 0, 2 );
-
- for ( int q = 0; q < subA.getRowDimension(); q++ )
- for ( int s = 0; s < subA.getColumnDimension(); s++ )
- subA.multiplyEntry( q, s, -1.0 );
-
- final RealVector subV = A.getRowVector( 3 ).getSubVector( 0, 3 );
-
- final DecompositionSolver solver = new SingularValueDecomposition( subA ).getSolver();
- final RealMatrix subAi = solver.getInverse();
- return subAi.operate( subV );
- }
-
- /**
- * Solve for Ax^2 + By^2 + Cz^2 + 2Dxy + 2Exz + 2Fyz + 2Gx + 2Hy +
- * 2Iz = 1.
- *
- * @param points
- * an iterable over 3D points.
- * @param nPoints
- * the number of points in the iterable.
- * @return
- */
- private static final RealVector solve( final Iterable< ? extends RealLocalizable > points, final int nPoints )
- {
- final RealMatrix M0 = new Array2DRowRealMatrix( nPoints, 9 );
- int i = 0;
- for ( final RealLocalizable point : points )
- {
- final double x = point.getDoublePosition( 0 );
- final double y = point.getDoublePosition( 1 );
- final double z = point.getDoublePosition( 2 );
-
- final double xx = x * x;
- final double yy = y * y;
- final double zz = z * z;
-
- final double xy = 2. * x * y;
- final double xz = 2. * x * z;
- final double yz = 2. * y * z;
-
- M0.setEntry( i, 0, xx );
- M0.setEntry( i, 1, yy );
- M0.setEntry( i, 2, zz );
- M0.setEntry( i, 3, xy );
- M0.setEntry( i, 4, xz );
- M0.setEntry( i, 5, yz );
- M0.setEntry( i, 6, 2. * x );
- M0.setEntry( i, 7, 2. * y );
- M0.setEntry( i, 8, 2. * z );
-
- i++;
- if ( i >= nPoints )
- break;
- }
- final RealMatrix M;
- if ( i == nPoints )
- M = M0;
- else
- M = M0.getSubMatrix( 0, i, 0, 9 );
-
- final RealMatrix M2 = M.transpose().multiply( M );
-
- final RealVector O = new ArrayRealVector( nPoints );
- O.mapAddToSelf( 1 );
-
- final RealVector MO = M.transpose().operate( O );
-
- final DecompositionSolver solver = new SingularValueDecomposition( M2 ).getSolver();
- final RealMatrix I = solver.getInverse();
-
- final RealVector V = I.operate( MO );
- return V;
- }
-
- /**
- * Reshape the fit result vector in the shape of an algebraic matrix.
- *
- *
- * A = [ Ax2 2Dxy 2Exz 2Gx ]
- * [ 2Dxy By2 2Fyz 2Hy ]
- * [ 2Exz 2Fyz Cz2 2Iz ]
- * [ 2Gx 2Hy 2Iz -1 ] ]
- *
- *
- * @param V the fit result.
- * @return a new 4x4 real matrix.
- */
- private static final RealMatrix toAlgebraicForm( final RealVector V )
- {
- final RealMatrix A = new Array2DRowRealMatrix( 4, 4 );
-
- A.setEntry( 0, 0, V.getEntry( 0 ) );
- A.setEntry( 0, 1, V.getEntry( 3 ) );
- A.setEntry( 0, 2, V.getEntry( 4 ) );
- A.setEntry( 0, 3, V.getEntry( 6 ) );
- A.setEntry( 1, 0, V.getEntry( 3 ) );
- A.setEntry( 1, 1, V.getEntry( 1 ) );
- A.setEntry( 1, 2, V.getEntry( 5 ) );
- A.setEntry( 1, 3, V.getEntry( 7 ) );
- A.setEntry( 2, 0, V.getEntry( 4 ) );
- A.setEntry( 2, 1, V.getEntry( 5 ) );
- A.setEntry( 2, 2, V.getEntry( 2 ) );
- A.setEntry( 2, 3, V.getEntry( 8 ) );
- A.setEntry( 3, 0, V.getEntry( 6 ) );
- A.setEntry( 3, 1, V.getEntry( 7 ) );
- A.setEntry( 3, 2, V.getEntry( 8 ) );
- A.setEntry( 3, 3, -1 );
- return A;
- }
-}
diff --git a/src/main/java/fiji/plugin/trackmate/util/mesh/SpotMeshCursor.java b/src/main/java/fiji/plugin/trackmate/util/mesh/SpotMeshCursor.java
index 1dd49e9d5..3f384f969 100644
--- a/src/main/java/fiji/plugin/trackmate/util/mesh/SpotMeshCursor.java
+++ b/src/main/java/fiji/plugin/trackmate/util/mesh/SpotMeshCursor.java
@@ -2,10 +2,9 @@
import fiji.plugin.trackmate.SpotMesh;
import gnu.trove.list.array.TDoubleArrayList;
-import net.imagej.mesh.alg.zslicer.Slice;
import net.imglib2.Cursor;
import net.imglib2.RandomAccess;
-import net.imglib2.Sampler;
+import net.imglib2.mesh.alg.zslicer.Slice;
/**
* A {@link Cursor} that iterates over the pixels inside a mesh.
@@ -197,13 +196,13 @@ public long getLongPosition( final int d )
public Cursor< T > copyCursor()
{
return new SpotMeshCursor<>(
- ra.copyRandomAccess(),
+ ra.copy(),
sm.copy(),
cal.clone() );
}
@Override
- public Sampler< T > copy()
+ public Cursor< T > copy()
{
return copyCursor();
}
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/BVVUtils.java b/src/main/java/fiji/plugin/trackmate/visualization/bvv/BVVUtils.java
new file mode 100644
index 000000000..d3ff277bd
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/BVVUtils.java
@@ -0,0 +1,122 @@
+package fiji.plugin.trackmate.visualization.bvv;
+
+import bvv.vistools.Bvv;
+import bvv.vistools.BvvFunctions;
+import bvv.vistools.BvvHandle;
+import bvv.vistools.BvvSource;
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.SpotMesh;
+import fiji.plugin.trackmate.util.TMUtils;
+import ij.CompositeImage;
+import ij.ImagePlus;
+import ij.process.ImageProcessor;
+import ij.process.LUT;
+import net.imagej.ImgPlus;
+import net.imagej.axis.Axes;
+import net.imglib2.img.display.imagej.ImgPlusViews;
+import net.imglib2.mesh.Meshes;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.nio.BufferMesh;
+import net.imglib2.mesh.obj.transform.TranslateMesh;
+import net.imglib2.type.Type;
+import net.imglib2.type.numeric.ARGBType;
+
+public class BVVUtils
+{
+
+ public static final StupidMesh createMesh( final Spot spot )
+ {
+ if ( spot instanceof SpotMesh )
+ {
+ final SpotMesh sm = ( SpotMesh ) spot;
+ final Mesh mesh = TranslateMesh.translate( sm.getMesh(), spot );
+ final BufferMesh bm = new BufferMesh( ( int ) mesh.vertices().size(), ( int ) mesh.triangles().size() );
+ Meshes.copy( mesh, bm );
+ return new StupidMesh( bm );
+ }
+ return new StupidMesh( Icosahedron.sphere( spot ) );
+ }
+
+ public static final < T extends Type< T > > BvvHandle createViewer( final ImagePlus imp )
+ {
+ final double[] cal = TMUtils.getSpatialCalibration( imp );
+
+ // Convert and split by channels.
+ final ImgPlus< T > img = TMUtils.rawWraps( imp );
+ final int cAxis = img.dimensionIndex( Axes.CHANNEL );
+ final BvvHandle bvvHandle;
+ if ( cAxis < 0 )
+ {
+ final BvvSource source = BvvFunctions.show( img, imp.getShortTitle(),
+ Bvv.options()
+ .maxAllowedStepInVoxels( 0 )
+ .renderWidth( 1024 )
+ .renderHeight( 1024 )
+ .preferredSize( 512, 512 )
+ .frameTitle( "3D view " + imp.getShortTitle() )
+ .sourceTransform( cal ) );
+ source.setDisplayRange( imp.getDisplayRangeMin(), imp.getDisplayRangeMax() );
+ if ( imp.getLuts().length > 0 )
+ {
+ final LUT lut = imp.getLuts()[ 0 ];
+ final int rgb = lut.getColorModel().getRGB( ( int ) imp.getDisplayRangeMax() );
+ source.setColor( new ARGBType( rgb ) );
+ }
+ bvvHandle = source.getBvvHandle();
+ }
+ else
+ {
+ BvvHandle h = null;
+ final long nChannels = img.dimension( cAxis );
+ final String st = imp.getShortTitle();
+ for ( int c = 0; c < nChannels; c++ )
+ {
+ final ImgPlus< T > channel = ImgPlusViews.hyperSlice( img, cAxis, c );
+ final BvvSource source;
+ if ( h == null )
+ {
+ source = BvvFunctions.show( channel, st + "_c" + ( c + 1 ),
+ Bvv.options()
+ .maxAllowedStepInVoxels( 0 )
+ .renderWidth( 1024 )
+ .renderHeight( 1024 )
+ .preferredSize( 512, 512 )
+ .frameTitle( "3D view " + imp.getShortTitle() )
+ .sourceTransform( cal ) );
+ h = source.getBvvHandle();
+ }
+ else
+ {
+ source = BvvFunctions.show( channel, st + "_c" + ( c + 1 ),
+ Bvv.options()
+ .maxAllowedStepInVoxels( 0 )
+ .renderWidth( 1024 )
+ .renderHeight( 1024 )
+ .preferredSize( 512, 512 )
+ .sourceTransform( cal )
+ .addTo( h ) );
+
+ }
+ final int i = imp.getStackIndex( c + 1, 1, 1 );
+ if ( imp instanceof CompositeImage )
+ {
+ final CompositeImage cp = ( CompositeImage ) imp;
+ source.setDisplayRange( cp.getChannelLut( c + 1 ).min, cp.getChannelLut( c + 1 ).max );
+ }
+ else
+ {
+ final ImageProcessor ip = imp.getStack().getProcessor( i );
+ source.setDisplayRange( ip.getMin(), ip.getMax() );
+ }
+ if ( imp.getLuts().length > 0 )
+ {
+ final LUT lut = imp.getLuts()[ c ];
+ final int rgb = lut.getColorModel().getRGB( ( int ) imp.getDisplayRangeMax() );
+ source.setColor( new ARGBType( rgb ) );
+ }
+ }
+ bvvHandle = h;
+ }
+ return bvvHandle;
+ }
+}
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/Icosahedron.java b/src/main/java/fiji/plugin/trackmate/visualization/bvv/Icosahedron.java
new file mode 100644
index 000000000..d77d407d1
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/Icosahedron.java
@@ -0,0 +1,154 @@
+package fiji.plugin.trackmate.visualization.bvv;
+
+import fiji.plugin.trackmate.Spot;
+import net.imglib2.RealLocalizable;
+import net.imglib2.mesh.Meshes;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.Triangle;
+import net.imglib2.mesh.obj.naive.NaiveDoubleMesh;
+import net.imglib2.mesh.obj.nio.BufferMesh;
+
+/**
+ * Icosahedron spheres.
+ *
+ * Based on https://github.com/caosdoar/spheres
+ *
+ * @author Jean-Yves Tinevez
+ */
+public class Icosahedron
+{
+
+ public static final Mesh core()
+ {
+ final NaiveDoubleMesh mesh = new NaiveDoubleMesh();
+
+ // Vertices
+ final double t = ( 1. + Math.sqrt( 5. ) ) / 2.;
+ final double[][] vs = new double[][] {
+ { -1.0, t, 0.0 },
+ { 1.0, t, 0.0 },
+ { -1.0, -t, 0.0 },
+ { 1.0, -t, 0.0 },
+ { 0.0, -1.0, t },
+ { 0.0, 1.0, t },
+ { 0.0, -1.0, -t },
+ { 0.0, 1.0, -t },
+ { t, 0.0, -1.0 },
+ { t, 0.0, 1.0 },
+ { -t, 0.0, -1.0 },
+ { -t, 0.0, 1.0 }
+ };
+ final double[] tmp = new double[ 3 ];
+ for ( final double[] v : vs )
+ {
+ normalize( v, tmp );
+ mesh.vertices().add( tmp[ 0 ], tmp[ 1 ], tmp[ 2 ] );
+ }
+
+ // Faces
+ mesh.triangles().add( 0, 11, 5 );
+ mesh.triangles().add( 0, 5, 1 );
+ mesh.triangles().add( 0, 1, 7 );
+ mesh.triangles().add( 0, 7, 10 );
+ mesh.triangles().add( 0, 10, 11 );
+ mesh.triangles().add( 1, 5, 9 );
+ mesh.triangles().add( 5, 11, 4 );
+ mesh.triangles().add( 11, 10, 2 );
+ mesh.triangles().add( 10, 7, 6 );
+ mesh.triangles().add( 7, 1, 8 );
+ mesh.triangles().add( 3, 9, 4 );
+ mesh.triangles().add( 3, 4, 2 );
+ mesh.triangles().add( 3, 2, 6 );
+ mesh.triangles().add( 3, 6, 8 );
+ mesh.triangles().add( 3, 8, 9 );
+ mesh.triangles().add( 4, 9, 5 );
+ mesh.triangles().add( 2, 4, 11 );
+ mesh.triangles().add( 6, 2, 10 );
+ mesh.triangles().add( 8, 6, 7 );
+ mesh.triangles().add( 9, 8, 1 );
+ return mesh;
+ }
+
+ public static final BufferMesh refine( final Mesh core )
+ {
+ final int nVerticesOut = ( int ) ( 6 * core.triangles().size() );
+ final int nTrianglesOut = ( int ) ( 4 * core.triangles().size() );
+ final BufferMesh out = new BufferMesh( nVerticesOut, nTrianglesOut );
+
+ final double[] tmpIn = new double[ 3 ];
+ final double[] tmpOut = new double[ 3 ];
+ for ( final Triangle t : core.triangles() )
+ {
+ final long v0 = out.vertices().add( t.v0x(), t.v0y(), t.v0z() );
+ final long v1 = out.vertices().add( t.v1x(), t.v1y(), t.v1z() );
+ final long v2 = out.vertices().add( t.v2x(), t.v2y(), t.v2z() );
+
+ tmpIn[ 0 ] = 0.5 * ( t.v0xf() + t.v1xf() );
+ tmpIn[ 1 ] = 0.5 * ( t.v0yf() + t.v1yf() );
+ tmpIn[ 2 ] = 0.5 * ( t.v0zf() + t.v1zf() );
+ normalize( tmpIn, tmpOut );
+ final long v3 = out.vertices().add( tmpOut[ 0 ], tmpOut[ 1 ], tmpOut[ 2 ] );
+
+ tmpIn[ 0 ] = 0.5 * ( t.v2xf() + t.v1xf() );
+ tmpIn[ 1 ] = 0.5 * ( t.v2yf() + t.v1yf() );
+ tmpIn[ 2 ] = 0.5 * ( t.v2zf() + t.v1zf() );
+ normalize( tmpIn, tmpOut );
+ final long v4 = out.vertices().add( tmpOut[ 0 ], tmpOut[ 1 ], tmpOut[ 2 ] );
+
+ tmpIn[ 0 ] = 0.5 * ( t.v0xf() + t.v2xf() );
+ tmpIn[ 1 ] = 0.5 * ( t.v0yf() + t.v2yf() );
+ tmpIn[ 2 ] = 0.5 * ( t.v0zf() + t.v2zf() );
+ normalize( tmpIn, tmpOut );
+ final long v5 = out.vertices().add( tmpOut[ 0 ], tmpOut[ 1 ], tmpOut[ 2 ] );
+
+ out.triangles().add( v0, v3, v5 );
+ out.triangles().add( v3, v1, v4 );
+ out.triangles().add( v5, v4, v2 );
+ out.triangles().add( v3, v4, v5 );
+ }
+
+ return out;
+ }
+
+ public static BufferMesh sphere( final Spot spot )
+ {
+ return sphere( spot, spot.getFeature( Spot.RADIUS ) );
+ }
+
+ public static BufferMesh sphere( final RealLocalizable center, final double radius )
+ {
+ return sphere( center, radius, 3 );
+ }
+
+ public static BufferMesh sphere( final RealLocalizable center, final double radius, final int nSubdivisions )
+ {
+ Mesh mesh = core();
+ for ( int i = 0; i < nSubdivisions; i++ )
+ mesh = refine( mesh );
+
+ scale( mesh, center, radius );
+ final BufferMesh out = new BufferMesh( ( int ) mesh.vertices().size(), ( int ) mesh.triangles().size() );
+ Meshes.calculateNormals( mesh, out );
+ return out;
+ }
+
+ private static void scale( final Mesh mesh, final RealLocalizable center, final double radius )
+ {
+ final long nV = mesh.vertices().size();
+ for ( int i = 0; i < nV; i++ )
+ {
+ final double x = mesh.vertices().x( i ) * radius + center.getDoublePosition( 0 );
+ final double y = mesh.vertices().y( i ) * radius + center.getDoublePosition( 1 );
+ final double z = mesh.vertices().z( i ) * radius + center.getDoublePosition( 2 );
+ mesh.vertices().set( i, x, y, z );
+ }
+ }
+
+ private static void normalize( final double[] v, final double[] tmp )
+ {
+ final double l = Math.sqrt( v[ 0 ] * v[ 0 ] + v[ 1 ] * v[ 1 ] + v[ 2 ] * v[ 2 ] );
+ tmp[ 0 ] = v[ 0 ] / l;
+ tmp[ 1 ] = v[ 1 ] / l;
+ tmp[ 2 ] = v[ 2 ] / l;
+ }
+}
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/StupidMesh.java b/src/main/java/fiji/plugin/trackmate/visualization/bvv/StupidMesh.java
new file mode 100644
index 000000000..46da5742e
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/StupidMesh.java
@@ -0,0 +1,155 @@
+/*-
+ * #%L
+ * Volume rendering of bdv datasets
+ * %%
+ * Copyright (C) 2018 - 2021 Tobias Pietzsch
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package fiji.plugin.trackmate.visualization.bvv;
+
+import static com.jogamp.opengl.GL.GL_FLOAT;
+import static com.jogamp.opengl.GL.GL_TRIANGLES;
+import static com.jogamp.opengl.GL.GL_UNSIGNED_INT;
+
+import java.awt.Color;
+import java.nio.FloatBuffer;
+import java.nio.IntBuffer;
+
+import org.joml.Matrix3f;
+import org.joml.Matrix4f;
+import org.joml.Matrix4fc;
+
+import com.jogamp.opengl.GL;
+import com.jogamp.opengl.GL3;
+
+import bvv.core.backend.jogl.JoglGpuContext;
+import bvv.core.shadergen.DefaultShader;
+import bvv.core.shadergen.Shader;
+import bvv.core.shadergen.generate.Segment;
+import bvv.core.shadergen.generate.SegmentTemplate;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
+import net.imglib2.mesh.obj.nio.BufferMesh;
+
+public class StupidMesh
+{
+ private final Shader prog;
+
+ private final BufferMesh mesh;
+
+ private boolean initialized;
+
+ private int vao;
+
+ private final float[] carr = new float[ 4 ];
+
+ private final float[] scarr = new float[ 4 ];
+
+ public StupidMesh( final BufferMesh mesh )
+ {
+ this.mesh = mesh;
+ final Segment meshVp = new SegmentTemplate( StupidMesh.class, "mesh.vp" ).instantiate();
+ final Segment meshFp = new SegmentTemplate( StupidMesh.class, "mesh.fp" ).instantiate();
+ prog = new DefaultShader( meshVp.getCode(), meshFp.getCode() );
+ DisplaySettings.defaultStyle().getSpotUniformColor().getColorComponents( carr );
+ DisplaySettings.defaultStyle().getHighlightColor().getColorComponents( scarr );
+ }
+
+ private void init( final GL3 gl )
+ {
+ initialized = true;
+
+ final int[] tmp = new int[ 3 ];
+ gl.glGenBuffers( 3, tmp, 0 );
+ final int meshPosVbo = tmp[ 0 ];
+ final int meshNormalVbo = tmp[ 1 ];
+ final int meshEbo = tmp[ 2 ];
+
+ final FloatBuffer vertices = mesh.vertices().verts();
+ vertices.rewind();
+ gl.glBindBuffer( GL.GL_ARRAY_BUFFER, meshPosVbo );
+ gl.glBufferData( GL.GL_ARRAY_BUFFER, vertices.limit() * Float.BYTES, vertices, GL.GL_STATIC_DRAW );
+ gl.glBindBuffer( GL.GL_ARRAY_BUFFER, 0 );
+
+ final FloatBuffer normals = mesh.vertices().normals();
+ normals.rewind();
+ gl.glBindBuffer( GL.GL_ARRAY_BUFFER, meshNormalVbo );
+ gl.glBufferData( GL.GL_ARRAY_BUFFER, normals.limit() * Float.BYTES, normals, GL.GL_STATIC_DRAW );
+ gl.glBindBuffer( GL.GL_ARRAY_BUFFER, 0 );
+
+ final IntBuffer indices = mesh.triangles().indices();
+ indices.rewind();
+ gl.glBindBuffer( GL.GL_ELEMENT_ARRAY_BUFFER, meshEbo );
+ gl.glBufferData( GL.GL_ELEMENT_ARRAY_BUFFER, indices.limit() * Integer.BYTES, indices, GL.GL_STATIC_DRAW );
+ gl.glBindBuffer( GL.GL_ELEMENT_ARRAY_BUFFER, 0 );
+
+ gl.glGenVertexArrays( 1, tmp, 0 );
+ vao = tmp[ 0 ];
+ gl.glBindVertexArray( vao );
+ gl.glBindBuffer( GL.GL_ARRAY_BUFFER, meshPosVbo );
+ gl.glVertexAttribPointer( 0, 3, GL_FLOAT, false, 3 * Float.BYTES, 0 );
+ gl.glEnableVertexAttribArray( 0 );
+ gl.glBindBuffer( GL.GL_ARRAY_BUFFER, meshNormalVbo );
+ gl.glVertexAttribPointer( 1, 3, GL_FLOAT, false, 3 * Float.BYTES, 0 );
+ gl.glEnableVertexAttribArray( 1 );
+ gl.glBindBuffer( GL.GL_ELEMENT_ARRAY_BUFFER, meshEbo );
+ gl.glBindVertexArray( 0 );
+ }
+
+ public void setColor( final Color color, final float alpha )
+ {
+ color.getComponents( carr );
+ carr[ 3 ] = alpha;
+ }
+
+ public void setSelectionColor( final Color selectionColor, final float alpha )
+ {
+ selectionColor.getComponents( scarr );
+ scarr[ 3 ] = alpha;
+ }
+
+ public void draw( final GL3 gl, final Matrix4fc pvm, final Matrix4fc vm, final boolean isSelected )
+ {
+ if ( !initialized )
+ init( gl );
+
+ final JoglGpuContext context = JoglGpuContext.get( gl );
+ final Matrix4f itvm = vm.invert( new Matrix4f() ).transpose();
+
+ prog.getUniformMatrix4f( "pvm" ).set( pvm );
+ prog.getUniformMatrix4f( "vm" ).set( vm );
+ prog.getUniformMatrix3f( "itvm" ).set( itvm.get3x3( new Matrix3f() ) );
+ prog.getUniform4f( "ObjectColor" ).set( carr[ 0 ], carr[ 1 ], carr[ 2 ], carr[ 3 ] );
+ prog.getUniform1f( "IsSelected" ).set( isSelected ? 1f : 0f );
+ prog.getUniform4f( "SelectionColor" ).set( scarr[ 0 ], scarr[ 1 ], scarr[ 2 ], scarr[ 3 ] );
+ prog.setUniforms( context );
+ prog.use( context );
+
+ gl.glBindVertexArray( vao );
+ gl.glEnable( GL.GL_CULL_FACE );
+ gl.glCullFace( GL.GL_BACK );
+ gl.glFrontFace( GL.GL_CCW );
+ gl.glDrawElements( GL_TRIANGLES, ( int ) mesh.triangles().size() * 3, GL_UNSIGNED_INT, 0 );
+ gl.glBindVertexArray( 0 );
+ }
+}
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/TrackMateBVV.java b/src/main/java/fiji/plugin/trackmate/visualization/bvv/TrackMateBVV.java
new file mode 100644
index 000000000..a7c024b5b
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/TrackMateBVV.java
@@ -0,0 +1,189 @@
+package fiji.plugin.trackmate.visualization.bvv;
+
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import org.joml.Matrix4f;
+
+import bdv.viewer.animate.TranslationAnimator;
+import bvv.core.VolumeViewerPanel;
+import bvv.core.util.MatrixMath;
+import bvv.vistools.BvvHandle;
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.ModelChangeEvent;
+import fiji.plugin.trackmate.SelectionModel;
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.features.FeatureUtils;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
+import fiji.plugin.trackmate.visualization.AbstractTrackMateModelView;
+import fiji.plugin.trackmate.visualization.FeatureColorGenerator;
+import ij.ImagePlus;
+import net.imglib2.RealLocalizable;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.Type;
+
+public class TrackMateBVV< T extends Type< T > > extends AbstractTrackMateModelView
+{
+
+ private static final String KEY = "BIGVOLUMEVIEWER";
+
+ private final ImagePlus imp;
+
+ private BvvHandle handle;
+
+ private final Map< Spot, StupidMesh > meshMap;
+
+ public TrackMateBVV( final Model model, final SelectionModel selectionModel, final ImagePlus imp, final DisplaySettings displaySettings )
+ {
+ super( model, selectionModel, displaySettings );
+ this.imp = imp;
+ this.meshMap = new HashMap<>();
+ final Iterable< Spot > it = model.getSpots().iterable( true );
+ it.forEach( s -> meshMap.computeIfAbsent( s, BVVUtils::createMesh ) );
+ updateColor();
+ displaySettings.listeners().add( this::updateColor );
+ selectionModel.addSelectionChangeListener( e -> refresh() );
+ }
+
+ /**
+ * Returns the {@link BvvHandle} that contains this view. Returns
+ * null if this view has not been rendered yet.
+ *
+ * @return the BVV handle, or null.
+ */
+ public BvvHandle getBvvHandle()
+ {
+ return handle;
+ }
+
+ @Override
+ public void render()
+ {
+ this.handle = BVVUtils.createViewer( imp );
+ final VolumeViewerPanel viewer = handle.getViewerPanel();
+ viewer.setRenderScene( ( gl, data ) -> {
+ if ( displaySettings.isSpotVisible() )
+ {
+ final Matrix4f pvm = new Matrix4f( data.getPv() );
+ final Matrix4f view = MatrixMath.affine( data.getRenderTransformWorldToScreen(), new Matrix4f() );
+ final Matrix4f vm = MatrixMath.screen( data.getDCam(), data.getScreenWidth(), data.getScreenHeight(), new Matrix4f() ).mul( view );
+
+ final int t = data.getTimepoint();
+ final Iterable< Spot > it = model.getSpots().iterable( t, true );
+ it.forEach( s -> meshMap.computeIfAbsent( s, BVVUtils::createMesh ).draw( gl, pvm, vm, selectionModel.getSpotSelection().contains( s ) ) );
+ }
+ } );
+ }
+
+ @Override
+ public void refresh()
+ {
+ if ( handle != null )
+ handle.getViewerPanel().requestRepaint();
+ }
+
+ @Override
+ public void clear()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void centerViewOn( final Spot spot )
+ {
+ if ( handle == null )
+ return;
+
+ final VolumeViewerPanel panel = handle.getViewerPanel();
+ panel.setTimepoint( spot.getFeature( Spot.FRAME ).intValue() );
+
+ final AffineTransform3D c = panel.state().getViewerTransform();
+ final double[] translation = getTranslation( c, spot, panel.getWidth(), panel.getHeight() );
+ if ( translation != null )
+ {
+ final TranslationAnimator animator = new TranslationAnimator( c, translation, 300 );
+ animator.setTime( System.currentTimeMillis() );
+ panel.setTransformAnimator( animator );
+ }
+ }
+
+ /**
+ * Returns a translation vector that will put the specified position at the
+ * center of the panel when used with a TranslationAnimator.
+ *
+ * @param t
+ * the viewer panel current view transform.
+ * @param target
+ * the position to focus on.
+ * @param width
+ * the width of the panel.
+ * @param height
+ * the height of the panel.
+ * @return a new double[] array with 3 elements containing the
+ * translation to use.
+ */
+ private static final double[] getTranslation( final AffineTransform3D t, final RealLocalizable target, final int width, final int height )
+ {
+ final double[] pos = new double[ 3 ];
+ final double[] vPos = new double[ 3 ];
+ target.localize( pos );
+ t.apply( pos, vPos );
+
+ final double dx = width / 2 - vPos[ 0 ] + t.get( 0, 3 );
+ final double dy = height / 2 - vPos[ 1 ] + t.get( 1, 3 );
+ final double dz = -vPos[ 2 ] + t.get( 2, 3 );
+
+ return new double[] { dx, dy, dz };
+ }
+
+ @Override
+ public String getKey()
+ {
+ return KEY;
+ }
+
+ @Override
+ public void modelChanged( final ModelChangeEvent event )
+ {
+ switch ( event.getEventID() )
+ {
+ case ModelChangeEvent.SPOTS_FILTERED:
+ case ModelChangeEvent.SPOTS_COMPUTED:
+ case ModelChangeEvent.TRACKS_VISIBILITY_CHANGED:
+ case ModelChangeEvent.TRACKS_COMPUTED:
+ refresh();
+ break;
+ case ModelChangeEvent.MODEL_MODIFIED:
+ {
+ for ( final Spot spot : event.getSpots() )
+ {
+ final StupidMesh mesh = BVVUtils.createMesh( spot );
+ meshMap.put( spot, mesh );
+ }
+ updateColor();
+ refresh();
+ break;
+ }
+ }
+ }
+
+ private void updateColor()
+ {
+ final FeatureColorGenerator< Spot > spotColorGenerator = FeatureUtils.createSpotColorGenerator( model, displaySettings );
+ for ( final Entry< Spot, StupidMesh > entry : meshMap.entrySet() )
+ {
+ final StupidMesh sm = entry.getValue();
+ if ( sm == null )
+ continue;
+
+ final Color color = spotColorGenerator.color( entry.getKey() );
+ final float alpha = ( float ) displaySettings.getSpotTransparencyAlpha();
+ sm.setColor( color, alpha );
+ sm.setSelectionColor( displaySettings.getHighlightColor(), alpha );
+ }
+ refresh();
+ }
+}
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/mesh.fp b/src/main/java/fiji/plugin/trackmate/visualization/bvv/mesh.fp
new file mode 100644
index 000000000..fb732ddd4
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/mesh.fp
@@ -0,0 +1,48 @@
+out vec4 fragColor;
+
+in vec3 Normal;
+in vec3 FragPos;
+
+uniform vec4 ObjectColor;
+uniform float IsSelected;
+uniform vec4 SelectionColor;
+
+const vec3 lightColor1 = 0.5 * vec3(0.9, 0.9, 1);
+const vec3 lightDir1 = normalize(vec3(0, -0.2, -1));
+
+const vec3 lightColor2 = 0.5 * vec3(0.1, 0.1, 1);
+const vec3 lightDir2 = normalize(vec3(1, 1, 0.5));
+
+const vec3 ambient = vec3(0.7, 0.7, 0.7);
+
+const float specularStrength = 5;
+
+vec3 phong(vec3 norm, vec3 viewDir, vec3 lightDir, vec3 lightColor, float shininess, float specularStrength)
+{
+ float diff = max(dot(norm, lightDir), 0.0);
+ vec3 diffuse = diff * lightColor;
+
+ vec3 reflectDir = reflect(-lightDir, norm);
+ float spec = pow(max(dot(viewDir, reflectDir), 0.0), shininess);
+ vec3 specular = specularStrength * spec * lightColor;
+
+ return diffuse + specular;
+}
+
+void main()
+{
+// fragColor = vec4(ObjectColor, 1);
+ vec3 norm = normalize(Normal);
+ vec3 viewDir = normalize(-FragPos);
+
+ vec3 l1 = phong( norm, viewDir, lightDir1, lightColor1, 32, 0.1 );
+ vec3 l2 = phong( norm, viewDir, lightDir2, lightColor2, 32, 0.5 );
+
+ if (IsSelected > 0.5) {
+ fragColor = vec4( (ambient + l1 + l2), SelectionColor[3]) * SelectionColor;
+ } else {
+ float it = dot(norm, viewDir);
+ fragColor = vec4( it * (ambient + l1 + l2), 1) * ObjectColor + (1-it) * vec4(1,1,1,ObjectColor[3]);
+ }
+
+}
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/mesh.vp b/src/main/java/fiji/plugin/trackmate/visualization/bvv/mesh.vp
new file mode 100644
index 000000000..e86810409
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/mesh.vp
@@ -0,0 +1,16 @@
+layout (location = 0) in vec3 aPos;
+layout (location = 1) in vec3 aNormal;
+
+out vec3 FragPos;
+out vec3 Normal;
+
+uniform mat4 pvm;
+uniform mat4 vm;
+uniform mat3 itvm;
+
+void main()
+{
+ gl_Position = pvm * vec4( aPos, 1.0 );
+ FragPos = vec3(vm * vec4(aPos, 1.0));
+ Normal = itvm * aNormal;
+}
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/ModelEditActions.java b/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/ModelEditActions.java
index dfc83d4ed..fded6eef5 100644
--- a/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/ModelEditActions.java
+++ b/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/ModelEditActions.java
@@ -17,7 +17,7 @@
import fiji.plugin.trackmate.Model;
import fiji.plugin.trackmate.SelectionModel;
import fiji.plugin.trackmate.Spot;
-import fiji.plugin.trackmate.SpotShape;
+import fiji.plugin.trackmate.SpotBase;
import fiji.plugin.trackmate.detection.semiauto.SemiAutoTracker;
import fiji.plugin.trackmate.util.ModelTools;
import fiji.plugin.trackmate.util.TMUtils;
@@ -76,7 +76,7 @@ private Spot makeSpot( Point mouseLocation )
SwingUtilities.convertPointFromScreen( mouseLocation, canvas );
}
final double[] calibration = TMUtils.getSpatialCalibration( imp );
- return new Spot(
+ return new SpotBase(
( -0.5 + canvas.offScreenXD( mouseLocation.x ) ) * calibration[ 0 ],
( -0.5 + canvas.offScreenYD( mouseLocation.y ) ) * calibration[ 1 ],
( imp.getSlice() - 1 ) * calibration[ 2 ],
@@ -265,24 +265,14 @@ public void changeSpotRadius( final boolean increase, final boolean fast )
? radius + factor * dx * COARSE_STEP
: radius + factor * dx * FINE_STEP;
-
if ( newRadius <= dx )
return;
// Store new value of radius for next spot creation.
previousRadius = newRadius;
- final SpotShape shape = target.getShape();
- if ( null == shape )
- {
- target.putFeature( Spot.RADIUS, newRadius );
- }
- else
- {
- final double alpha = newRadius / radius;
- shape.scale( alpha );
- target.putFeature( Spot.RADIUS, shape.radius() );
- }
+ // Actually scale the spot.
+ target.scale( radius / newRadius );
model.beginUpdate();
try
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/PaintSpotMesh.java b/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/PaintSpotMesh.java
index af1cc0e7d..158260da4 100644
--- a/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/PaintSpotMesh.java
+++ b/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/PaintSpotMesh.java
@@ -11,9 +11,9 @@
import fiji.plugin.trackmate.SpotMesh;
import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
import ij.ImagePlus;
-import net.imagej.mesh.alg.zslicer.Contour;
-import net.imagej.mesh.alg.zslicer.Slice;
import net.imglib2.RealLocalizable;
+import net.imglib2.mesh.alg.zslicer.Contour;
+import net.imglib2.mesh.alg.zslicer.Slice;
/**
* Utility class to paint the {@link SpotMesh} component of spots.
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/SpotEditTool.java b/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/SpotEditTool.java
index 2b92ea64f..baedb0394 100644
--- a/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/SpotEditTool.java
+++ b/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/SpotEditTool.java
@@ -403,7 +403,6 @@ public void keyPressed( final KeyEvent e )
break;
}
}
-
}
@Override
diff --git a/src/main/resources/fiji/plugin/trackmate/gui/images/TrackMateBVV-logo-16x16.png b/src/main/resources/fiji/plugin/trackmate/gui/images/TrackMateBVV-logo-16x16.png
new file mode 100644
index 000000000..2e5b7d5fa
Binary files /dev/null and b/src/main/resources/fiji/plugin/trackmate/gui/images/TrackMateBVV-logo-16x16.png differ
diff --git a/src/test/java/fiji/plugin/trackmate/mesh/DebugZSlicer.java b/src/test/java/fiji/plugin/trackmate/mesh/DebugZSlicer.java
index 94456b577..9d28c8e35 100644
--- a/src/test/java/fiji/plugin/trackmate/mesh/DebugZSlicer.java
+++ b/src/test/java/fiji/plugin/trackmate/mesh/DebugZSlicer.java
@@ -13,9 +13,9 @@
import ij.CompositeImage;
import ij.ImageJ;
import ij.ImagePlus;
-import net.imagej.mesh.alg.zslicer.Contour;
-import net.imagej.mesh.alg.zslicer.Slice;
-import net.imagej.mesh.alg.zslicer.ZSlicer;
+import net.imglib2.mesh.alg.zslicer.Contour;
+import net.imglib2.mesh.alg.zslicer.Slice;
+import net.imglib2.mesh.alg.zslicer.ZSlicer;
public class DebugZSlicer
{
diff --git a/src/test/java/fiji/plugin/trackmate/mesh/DefaultMesh.java b/src/test/java/fiji/plugin/trackmate/mesh/DefaultMesh.java
index 8ce097ad2..37e6f9961 100644
--- a/src/test/java/fiji/plugin/trackmate/mesh/DefaultMesh.java
+++ b/src/test/java/fiji/plugin/trackmate/mesh/DefaultMesh.java
@@ -16,8 +16,8 @@
import ij.measure.Calibration;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
-import net.imagej.mesh.Mesh;
import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.mesh.obj.Mesh;
import net.imglib2.type.logic.BitType;
public class DefaultMesh
diff --git a/src/test/java/fiji/plugin/trackmate/mesh/Demo3DMesh.java b/src/test/java/fiji/plugin/trackmate/mesh/Demo3DMesh.java
index 84b9912f9..766d92e4b 100644
--- a/src/test/java/fiji/plugin/trackmate/mesh/Demo3DMesh.java
+++ b/src/test/java/fiji/plugin/trackmate/mesh/Demo3DMesh.java
@@ -14,21 +14,20 @@
import ij.gui.PolygonRoi;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.Meshes;
-import net.imagej.mesh.Vertices;
-import net.imagej.mesh.alg.zslicer.Contour;
-import net.imagej.mesh.alg.zslicer.Slice;
-import net.imagej.mesh.alg.zslicer.ZSlicer;
-import net.imagej.mesh.io.ply.PLYMeshIO;
-import net.imagej.mesh.io.stl.STLMeshIO;
-import net.imagej.mesh.naive.NaiveDoubleMesh;
-import net.imagej.mesh.naive.NaiveDoubleMesh.Triangles;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.converter.RealTypeConverters;
import net.imglib2.img.ImgView;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.img.display.imagej.ImgPlusViews;
+import net.imglib2.mesh.Meshes;
+import net.imglib2.mesh.alg.zslicer.Contour;
+import net.imglib2.mesh.alg.zslicer.Slice;
+import net.imglib2.mesh.alg.zslicer.ZSlicer;
+import net.imglib2.mesh.io.ply.PLYMeshIO;
+import net.imglib2.mesh.io.stl.STLMeshIO;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.Vertices;
+import net.imglib2.mesh.obj.naive.NaiveDoubleMesh;
import net.imglib2.roi.labeling.ImgLabeling;
import net.imglib2.roi.labeling.LabelRegion;
import net.imglib2.roi.labeling.LabelRegions;
@@ -112,8 +111,8 @@ public static void main( final String[] args )
static Mesh debugMesh( final long[] min, final long[] max )
{
final NaiveDoubleMesh mesh = new NaiveDoubleMesh();
- final net.imagej.mesh.naive.NaiveDoubleMesh.Vertices vertices = mesh.vertices();
- final Triangles triangles = mesh.triangles();
+ final net.imglib2.mesh.obj.naive.NaiveDoubleMesh.Vertices vertices = mesh.vertices();
+ final net.imglib2.mesh.obj.naive.NaiveDoubleMesh.Triangles triangles = mesh.triangles();
// Coords as X Y Z
@@ -198,11 +197,10 @@ private static void testIO( final Mesh mesh, final int j )
// Serialize to disk.
try
{
- new STLMeshIO().save( mesh, String.format( "samples/mesh/io/STL_%02d.stl", j ) );
+ STLMeshIO.save( mesh, String.format( "samples/mesh/io/STL_%02d.stl", j ) );
- final PLYMeshIO plyio = new PLYMeshIO();
- plyio.save( mesh, String.format( "samples/mesh/io/PLY_%02d.ply", j ) );
- final byte[] bs = plyio.writeAscii( mesh );
+ PLYMeshIO.save( mesh, String.format( "samples/mesh/io/PLY_%02d.ply", j ) );
+ final byte[] bs = PLYMeshIO.writeAscii( mesh );
final String str = new String( bs );
try (final FileWriter writer = new FileWriter(
String.format( "samples/mesh/io/PLYTEXT_%02d.txt", j ) ))
diff --git a/src/test/java/fiji/plugin/trackmate/mesh/ExportMeshForDemo.java b/src/test/java/fiji/plugin/trackmate/mesh/ExportMeshForDemo.java
index 44b560382..890b4a553 100644
--- a/src/test/java/fiji/plugin/trackmate/mesh/ExportMeshForDemo.java
+++ b/src/test/java/fiji/plugin/trackmate/mesh/ExportMeshForDemo.java
@@ -12,7 +12,7 @@
import fiji.plugin.trackmate.detection.ThresholdDetectorFactory;
import ij.IJ;
import ij.ImagePlus;
-import net.imagej.mesh.io.stl.STLMeshIO;
+import net.imglib2.mesh.io.stl.STLMeshIO;
public class ExportMeshForDemo
{
@@ -42,7 +42,6 @@ public static void main( final String[] args )
if ( !file.isDirectory() )
file.delete();
- final STLMeshIO io = new STLMeshIO();
for ( final Spot spot : spots.iterable( true ) )
{
final int t = spot.getFeature( Spot.FRAME ).intValue();
@@ -51,7 +50,7 @@ public static void main( final String[] args )
if ( spot instanceof SpotMesh )
{
final SpotMesh mesh = ( SpotMesh ) spot;
- io.save( mesh.getMesh(), savePath );
+ STLMeshIO.save( mesh.getMesh(), savePath );
}
}
System.out.println( "Export done." );
diff --git a/src/test/java/fiji/plugin/trackmate/mesh/MeshPlayground.java b/src/test/java/fiji/plugin/trackmate/mesh/MeshPlayground.java
new file mode 100644
index 000000000..0c2cb85e7
--- /dev/null
+++ b/src/test/java/fiji/plugin/trackmate/mesh/MeshPlayground.java
@@ -0,0 +1,114 @@
+package fiji.plugin.trackmate.mesh;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import org.joml.Matrix4f;
+import org.scijava.ui.behaviour.io.InputTriggerConfig;
+import org.scijava.ui.behaviour.util.Actions;
+
+import bvv.core.VolumeViewerPanel;
+import bvv.core.util.MatrixMath;
+import bvv.vistools.Bvv;
+import bvv.vistools.BvvFunctions;
+import bvv.vistools.BvvSource;
+import fiji.plugin.trackmate.util.TMUtils;
+import fiji.plugin.trackmate.visualization.bvv.StupidMesh;
+import ij.IJ;
+import ij.ImagePlus;
+import net.imagej.ImgPlus;
+import net.imagej.axis.Axes;
+import net.imglib2.img.display.imagej.ImgPlusViews;
+import net.imglib2.mesh.Meshes;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.naive.NaiveDoubleMesh;
+import net.imglib2.mesh.obj.nio.BufferMesh;
+import net.imglib2.type.Type;
+import net.imglib2.type.numeric.ARGBType;
+
+public class MeshPlayground
+{
+ public static < T extends Type< T > > void main( final String[] args )
+ {
+ final String filePath = "samples/mesh/CElegansMask3D.tif";
+ final ImagePlus imp = IJ.openImage( filePath );
+
+ final ImgPlus< T > img = TMUtils.rawWraps( imp );
+ final ImgPlus< T > c1 = ImgPlusViews.hyperSlice( img, img.dimensionIndex( Axes.CHANNEL ), 1 );
+ final ImgPlus< T > t1 = ImgPlusViews.hyperSlice( c1, c1.dimensionIndex( Axes.TIME ), 0 );
+ final double[] cal = TMUtils.getSpatialCalibration( t1 );
+
+ final BvvSource source = BvvFunctions.show( c1, "t1",
+ Bvv.options()
+ .maxAllowedStepInVoxels( 0 )
+ .renderWidth( 1024 )
+ .renderHeight( 1024 )
+ .preferredSize( 512, 512 )
+ .sourceTransform( cal ) );
+
+ source.setDisplayRangeBounds( 0, 1024 );
+ source.setColor( new ARGBType( 0xaaffaa ) );
+
+
+ final List< StupidMesh > meshes = new ArrayList<>();
+ for ( int j = 1; j <= 3; ++j )
+ {
+ final String fn = String.format( "samples/mesh/CElegansMask3D_%02d.stl", j );
+ meshes.add( new StupidMesh( load( fn ) ) );
+ }
+
+ final VolumeViewerPanel viewer = source.getBvvHandle().getViewerPanel();
+
+ final AtomicBoolean showMeshes = new AtomicBoolean( true );
+ viewer.setRenderScene( ( gl, data ) -> {
+ if ( showMeshes.get() )
+ {
+ final Matrix4f pvm = new Matrix4f( data.getPv() );
+ final Matrix4f view = MatrixMath.affine( data.getRenderTransformWorldToScreen(), new Matrix4f() );
+ final Matrix4f vm = MatrixMath.screen( data.getDCam(), data.getScreenWidth(), data.getScreenHeight(), new Matrix4f() ).mul( view );
+ meshes.forEach( mesh -> mesh.draw( gl, pvm, vm, false ) );
+ }
+ } );
+
+ final Actions actions = new Actions( new InputTriggerConfig() );
+ actions.install( source.getBvvHandle().getKeybindings(), "my-new-actions" );
+ actions.runnableAction( () -> {
+ showMeshes.set( !showMeshes.get() );
+ viewer.requestRepaint();
+ }, "toggle meshes", "G" );
+
+ viewer.requestRepaint();
+ }
+
+
+ private static BufferMesh load( final String fn )
+ {
+ BufferMesh mesh = null;
+ try
+ {
+ final NaiveDoubleMesh nmesh = new NaiveDoubleMesh();
+ net.imglib2.mesh.io.stl.STLMeshIO.read( nmesh, new File( fn ) );
+ mesh = calculateNormals(
+ nmesh
+// Meshes.removeDuplicateVertices( nmesh, 5 )
+ );
+ }
+ catch ( final IOException e )
+ {
+ e.printStackTrace();
+ }
+ return mesh;
+ }
+
+ private static BufferMesh calculateNormals( final Mesh mesh )
+ {
+ final int nvertices = ( int ) mesh.vertices().size();
+ final int ntriangles = ( int ) mesh.triangles().size();
+ final BufferMesh bufferMesh = new BufferMesh( nvertices, ntriangles, true );
+ Meshes.calculateNormals( mesh, bufferMesh );
+ return bufferMesh;
+ }
+}
diff --git a/src/test/java/fiji/plugin/trackmate/mesh/TestEllipsoidFit.java b/src/test/java/fiji/plugin/trackmate/mesh/TestEllipsoidFit.java
index c5fabdd62..f5172a51c 100644
--- a/src/test/java/fiji/plugin/trackmate/mesh/TestEllipsoidFit.java
+++ b/src/test/java/fiji/plugin/trackmate/mesh/TestEllipsoidFit.java
@@ -5,10 +5,10 @@
import org.junit.Test;
-import fiji.plugin.trackmate.util.mesh.EllipsoidFitter;
-import fiji.plugin.trackmate.util.mesh.EllipsoidFitter.EllipsoidFit;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.naive.NaiveDoubleMesh;
+import net.imglib2.mesh.alg.EllipsoidFitter;
+import net.imglib2.mesh.alg.EllipsoidFitter.EllipsoidFit;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.naive.NaiveDoubleMesh;
public class TestEllipsoidFit
{