- * 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 0c88e45ed..3f384f969 100644
--- a/src/main/java/fiji/plugin/trackmate/util/mesh/SpotMeshCursor.java
+++ b/src/main/java/fiji/plugin/trackmate/util/mesh/SpotMeshCursor.java
@@ -2,9 +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.mesh.alg.zslicer.Slice;
/**
* A {@link Cursor} that iterates over the pixels inside a mesh.
@@ -196,7 +196,7 @@ public long getLongPosition( final int d )
public Cursor< T > copyCursor()
{
return new SpotMeshCursor<>(
- ra.copyRandomAccess(),
+ ra.copy(),
sm.copy(),
cal.clone() );
}
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/BVVUtils.java b/src/main/java/fiji/plugin/trackmate/visualization/bvv/BVVUtils.java
index 61d6c848a..d3ff277bd 100644
--- a/src/main/java/fiji/plugin/trackmate/visualization/bvv/BVVUtils.java
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/BVVUtils.java
@@ -13,11 +13,11 @@
import ij.process.LUT;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.Meshes;
-import net.imagej.mesh.nio.BufferMesh;
-import net.imagej.mesh.obj.transform.TranslateMesh;
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;
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/Icosahedron.java b/src/main/java/fiji/plugin/trackmate/visualization/bvv/Icosahedron.java
index a825b3705..d77d407d1 100644
--- a/src/main/java/fiji/plugin/trackmate/visualization/bvv/Icosahedron.java
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/Icosahedron.java
@@ -1,12 +1,12 @@
package fiji.plugin.trackmate.visualization.bvv;
import fiji.plugin.trackmate.Spot;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.Meshes;
-import net.imagej.mesh.Triangle;
-import net.imagej.mesh.naive.NaiveDoubleMesh;
-import net.imagej.mesh.nio.BufferMesh;
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.
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/StupidMesh.java b/src/main/java/fiji/plugin/trackmate/visualization/bvv/StupidMesh.java
index 89a85bd65..46da5742e 100644
--- a/src/main/java/fiji/plugin/trackmate/visualization/bvv/StupidMesh.java
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/StupidMesh.java
@@ -49,7 +49,7 @@
import bvv.core.shadergen.generate.Segment;
import bvv.core.shadergen.generate.SegmentTemplate;
import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
-import net.imagej.mesh.nio.BufferMesh;
+import net.imglib2.mesh.obj.nio.BufferMesh;
public class StupidMesh
{
@@ -116,13 +116,13 @@ private void init( final GL3 gl )
gl.glBindVertexArray( 0 );
}
- public void setColor( final Color color, float alpha )
+ public void setColor( final Color color, final float alpha )
{
color.getComponents( carr );
carr[ 3 ] = alpha;
}
- public void setSelectionColor( final Color selectionColor, float alpha )
+ public void setSelectionColor( final Color selectionColor, final float alpha )
{
selectionColor.getComponents( scarr );
scarr[ 3 ] = alpha;
diff --git a/src/main/java/fiji/plugin/trackmate/visualization/bvv/TrackMateBVV.java b/src/main/java/fiji/plugin/trackmate/visualization/bvv/TrackMateBVV.java
index 82020e27f..a7c024b5b 100644
--- a/src/main/java/fiji/plugin/trackmate/visualization/bvv/TrackMateBVV.java
+++ b/src/main/java/fiji/plugin/trackmate/visualization/bvv/TrackMateBVV.java
@@ -1,15 +1,10 @@
package fiji.plugin.trackmate.visualization.bvv;
-import static fiji.plugin.trackmate.gui.Icons.TRACKMATE_ICON;
-
import java.awt.Color;
-import java.io.File;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
-import javax.swing.JFrame;
-
import org.joml.Matrix4f;
import bdv.viewer.animate.TranslationAnimator;
@@ -19,20 +14,11 @@
import fiji.plugin.trackmate.Model;
import fiji.plugin.trackmate.ModelChangeEvent;
import fiji.plugin.trackmate.SelectionModel;
-import fiji.plugin.trackmate.Settings;
import fiji.plugin.trackmate.Spot;
-import fiji.plugin.trackmate.TrackMate;
import fiji.plugin.trackmate.features.FeatureUtils;
-import fiji.plugin.trackmate.gui.GuiUtils;
import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
-import fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence;
-import fiji.plugin.trackmate.gui.wizard.WizardSequence;
-import fiji.plugin.trackmate.io.TmXmlReader;
import fiji.plugin.trackmate.visualization.AbstractTrackMateModelView;
import fiji.plugin.trackmate.visualization.FeatureColorGenerator;
-import fiji.plugin.trackmate.visualization.TrackMateModelView;
-import fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer;
-import ij.ImageJ;
import ij.ImagePlus;
import net.imglib2.RealLocalizable;
import net.imglib2.realtransform.AffineTransform3D;
@@ -81,8 +67,8 @@ public void render()
if ( displaySettings.isSpotVisible() )
{
final Matrix4f pvm = new Matrix4f( data.getPv() );
- Matrix4f view = MatrixMath.affine( data.getRenderTransformWorldToScreen(), new Matrix4f() );
- Matrix4f vm = MatrixMath.screen( data.getDCam(), data.getScreenWidth(), data.getScreenHeight(), new Matrix4f() ).mul( view );
+ 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 );
@@ -194,55 +180,10 @@ private void updateColor()
continue;
final Color color = spotColorGenerator.color( entry.getKey() );
- float alpha = ( float ) displaySettings.getSpotTransparencyAlpha();
+ final float alpha = ( float ) displaySettings.getSpotTransparencyAlpha();
sm.setColor( color, alpha );
sm.setSelectionColor( displaySettings.getHighlightColor(), alpha );
}
refresh();
}
-
- public static < T extends Type< T > > void main( final String[] args )
- {
- try
- {
-// final String filePath = "samples/mesh/CElegansMask3D.tif";
- final String filePath = "samples/CElegans3D-smoothed-mask-orig.xml";
-// final String filePath = "../TrackMate-StarDist/samples/CTC-Fluo-N3DH-SIM-multiC.xml";
-
- ImageJ.main( args );
- final TmXmlReader reader = new TmXmlReader( new File( filePath ) );
- if ( !reader.isReadingOk() )
- {
- System.err.println( reader.getErrorMessage() );
- return;
- }
- final ImagePlus imp = reader.readImage();
- final Settings settings = reader.readSettings( imp );
- imp.show();
-
- final Model model = reader.getModel();
- final SelectionModel selectionModel = new SelectionModel( model );
- final DisplaySettings ds = reader.getDisplaySettings();
- final TrackMate trackmate = new TrackMate( model, settings );
-
- // Main view
- final TrackMateModelView displayer = new HyperStackDisplayer( model, selectionModel, imp, ds );
- displayer.render();
-
- // Wizard.
- final WizardSequence sequence = new TrackMateWizardSequence( trackmate, selectionModel, ds );
- sequence.setCurrent( "ConfigureViews" );
- final JFrame frame = sequence.run( "TrackMate on " + imp.getShortTitle() );
- frame.setIconImage( TRACKMATE_ICON.getImage() );
- GuiUtils.positionWindow( frame, settings.imp.getWindow() );
- frame.setVisible( true );
-
- final TrackMateBVV< T > tbvv = new TrackMateBVV<>( model, selectionModel, imp, ds );
- tbvv.render();
- }
- catch ( final Exception e )
- {
- e.printStackTrace();
- }
- }
}
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/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/Demo3DMeshTrackMate.java b/src/test/java/fiji/plugin/trackmate/mesh/Demo3DMeshTrackMate.java
index 39e1add05..52a32b51c 100644
--- a/src/test/java/fiji/plugin/trackmate/mesh/Demo3DMeshTrackMate.java
+++ b/src/test/java/fiji/plugin/trackmate/mesh/Demo3DMeshTrackMate.java
@@ -14,8 +14,8 @@ public static void main( final String[] args )
{
ImageJ.main( args );
- final String filePath = "samples/CElegans3D-smoothed-mask-orig.tif";
-// final String filePath = "samples/Celegans-5pc-17timepoints.tif";
+// final String filePath = "samples/CElegans3D-smoothed-mask-orig-t7.tif";
+ final String filePath = "samples/Celegans-5pc-17timepoints.tif";
final ImagePlus imp = IJ.openImage( filePath );
imp.show();
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
index 7e3f4e7dc..0c2cb85e7 100644
--- a/src/test/java/fiji/plugin/trackmate/mesh/MeshPlayground.java
+++ b/src/test/java/fiji/plugin/trackmate/mesh/MeshPlayground.java
@@ -21,12 +21,11 @@
import ij.ImagePlus;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.Meshes;
-import net.imagej.mesh.io.stl.STLMeshIO;
-import net.imagej.mesh.naive.NaiveDoubleMesh;
-import net.imagej.mesh.nio.BufferMesh;
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;
@@ -55,7 +54,7 @@ public static < T extends Type< T > > void main( final String[] args )
final List< StupidMesh > meshes = new ArrayList<>();
- for ( int j = 1; j <= 3; ++j)
+ for ( int j = 1; j <= 3; ++j )
{
final String fn = String.format( "samples/mesh/CElegansMask3D_%02d.stl", j );
meshes.add( new StupidMesh( load( fn ) ) );
@@ -68,8 +67,8 @@ public static < T extends Type< T > > void main( final String[] args )
if ( showMeshes.get() )
{
final Matrix4f pvm = new Matrix4f( data.getPv() );
- Matrix4f view = MatrixMath.affine( data.getRenderTransformWorldToScreen(), new Matrix4f() );
- Matrix4f vm = MatrixMath.screen( data.getDCam(), data.getScreenWidth(), data.getScreenHeight(), new Matrix4f() ).mul( view );
+ 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 ) );
}
} );
@@ -91,8 +90,7 @@ private static BufferMesh load( final String fn )
try
{
final NaiveDoubleMesh nmesh = new NaiveDoubleMesh();
- final STLMeshIO meshIO = new STLMeshIO();
- meshIO.read( nmesh, new File( fn ) );
+ net.imglib2.mesh.io.stl.STLMeshIO.read( nmesh, new File( fn ) );
mesh = calculateNormals(
nmesh
// Meshes.removeDuplicateVertices( nmesh, 5 )
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
{