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(); - } - } }