diff --git a/src/main/java/viewer/render/labelling/Demo.java b/src/main/java/viewer/render/labelling/Demo.java
index 1888ca80ffdf170b928abf32611bc0f555191556..94908f2bb4d2cd72567dbe66e4694e464f714d65 100644
--- a/src/main/java/viewer/render/labelling/Demo.java
+++ b/src/main/java/viewer/render/labelling/Demo.java
@@ -43,245 +43,286 @@ import viewer.render.SourceState;
import viewer.render.ViewerState;
import viewer.util.Affine3DHelpers;
-public class Demo {
+public class Demo
+{
+
+ private LabelingSource< ? > overlay;
- private LabelingSource overlay;
private final SpimViewer viewer;
+
private int nTimepoints;
- private List<SourceAndConverter<?>> sources;
+
+ private List< SourceAndConverter< ? >> sources;
+
private SetupAssignments setupAssignments;
+
private final BrightnessDialog brightnessDialog;
+
private boolean editMode = false;
- private TransformEventHandler<AffineTransform3D> transformEventHandler;
- private RegionGrowingAnnotationTool<?> regionGrowingAnnotationTool;
- public Demo(final File file) throws ParserConfigurationException, SAXException, IOException, InstantiationException, IllegalAccessException, ClassNotFoundException, JDOMException {
+ private TransformEventHandler< AffineTransform3D > transformEventHandler;
+
+ private RegionGrowingAnnotationTool< ? > regionGrowingAnnotationTool;
+
+ public Demo( final File file ) throws ParserConfigurationException, SAXException, IOException, InstantiationException, IllegalAccessException, ClassNotFoundException, JDOMException
+ {
/*
* Load image source
*/
- prepareSources(file);
+ prepareSources( file );
viewer = newViewer();
- initTransform(viewer, 800, 600);
- initBrightness(viewer, 0, 1);
+ initTransform( viewer, 800, 600 );
+ initBrightness( viewer, 0, 1 );
/*
* Brightness
*/
- brightnessDialog = new BrightnessDialog(null, setupAssignments);
+ brightnessDialog = new BrightnessDialog( null, setupAssignments );
}
- private void prepareSources(final File dataFile) throws ParserConfigurationException, SAXException, IOException, InstantiationException, IllegalAccessException, ClassNotFoundException, JDOMException {
- final SequenceViewsLoader loader = new SequenceViewsLoader(dataFile.getAbsolutePath());
+ @SuppressWarnings( { "rawtypes", "unchecked" } )
+ private void prepareSources( final File dataFile ) throws ParserConfigurationException, SAXException, IOException, InstantiationException, IllegalAccessException, ClassNotFoundException, JDOMException
+ {
+ final SequenceViewsLoader loader = new SequenceViewsLoader( dataFile.getAbsolutePath() );
final SequenceDescription seq = loader.getSequenceDescription();
nTimepoints = seq.numTimepoints();
- sources = new ArrayList<SourceAndConverter<?>>();
- final ArrayList<ConverterSetup> converterSetups = new ArrayList<ConverterSetup>();
- for (int setup = 0; setup < seq.numViewSetups(); ++setup) {
- final RealARGBColorConverter<UnsignedShortType> converter = new RealARGBColorConverter<UnsignedShortType>(0, 65535);
- converter.setColor(new ARGBType(ARGBType.rgba(255, 255, 255, 255)));
- sources.add(new SourceAndConverter<UnsignedShortType>(new SpimSource(loader, setup, "angle " + seq.setups.get(setup).getAngle()), converter));
+ sources = new ArrayList< SourceAndConverter< ? >>();
+ final ArrayList< ConverterSetup > converterSetups = new ArrayList< ConverterSetup >();
+ for ( int setup = 0; setup < seq.numViewSetups(); ++setup )
+ {
+ final RealARGBColorConverter< UnsignedShortType > converter = new RealARGBColorConverter< UnsignedShortType >( 0, 65535 );
+ converter.setColor( new ARGBType( ARGBType.rgba( 255, 255, 255, 255 ) ) );
+ sources.add( new SourceAndConverter< UnsignedShortType >( new SpimSource( loader, setup, "angle " + seq.setups.get( setup ).getAngle() ), converter ) );
final int id = setup;
- converterSetups.add(new ConverterSetup() {
+ converterSetups.add( new ConverterSetup()
+ {
@Override
- public void setDisplayRange(final int min, final int max) {
- converter.setMin(min);
- converter.setMax(max);
+ public void setDisplayRange( final int min, final int max )
+ {
+ converter.setMin( min );
+ converter.setMax( max );
requestRepaintAllViewers();
}
@Override
- public void setColor(final ARGBType color) {
- converter.setColor(color);
+ public void setColor( final ARGBType color )
+ {
+ converter.setColor( color );
requestRepaintAllViewers();
}
@Override
- public int getSetupId() {
+ public int getSetupId()
+ {
return id;
}
@Override
- public int getDisplayRangeMin() {
- return (int) converter.getMin();
+ public int getDisplayRangeMin()
+ {
+ return ( int ) converter.getMin();
}
@Override
- public int getDisplayRangeMax() {
- return (int) converter.getMax();
+ public int getDisplayRangeMax()
+ {
+ return ( int ) converter.getMax();
}
@Override
- public ARGBType getColor() {
+ public ARGBType getColor()
+ {
return converter.getColor();
}
- });
+ } );
}
/*
* Create setup assignments (for managing brightness and color).
*/
- setupAssignments = new SetupAssignments(converterSetups, 0, 65535);
- final MinMaxGroup group = setupAssignments.getMinMaxGroups().get(0);
- for (final ConverterSetup setup : setupAssignments.getConverterSetups()) {
- setupAssignments.moveSetupToGroup(setup, group);
+ setupAssignments = new SetupAssignments( converterSetups, 0, 65535 );
+ final MinMaxGroup group = setupAssignments.getMinMaxGroups().get( 0 );
+ for ( final ConverterSetup setup : setupAssignments.getConverterSetups() )
+ {
+ setupAssignments.moveSetupToGroup( setup, group );
}
-
- overlay = new LabelingSource(sources.get(0).getSpimSource());
- sources.add(new SourceAndConverter<ARGBType>(overlay, new TypeIdentity<ARGBType>()));
+ // Use 2nd level
+ overlay = new LabelingSource( sources.get( 0 ).getSpimSource(), 2 );
+ sources.add( new SourceAndConverter< ARGBType >( overlay, new TypeIdentity< ARGBType >() ) );
}
- private SpimViewer newViewer() {
- final SpimViewer viewer = new SpimViewer(800, 600, sources, nTimepoints);
+ private SpimViewer newViewer()
+ {
+ final SpimViewer viewer = new SpimViewer( 800, 600, sources, nTimepoints );
- viewer.addKeyAction(KeyStroke.getKeyStroke("ESCAPE"), new AbstractAction("toggle mode") {
+ viewer.addKeyAction( KeyStroke.getKeyStroke( "ESCAPE" ), new AbstractAction( "toggle mode" )
+ {
@Override
- public void actionPerformed(final ActionEvent arg0) {
+ public void actionPerformed( final ActionEvent arg0 )
+ {
toggleMode();
}
private static final long serialVersionUID = 1L;
- });
+ } );
- viewer.addKeyAction(KeyStroke.getKeyStroke("S"), new AbstractAction("brightness settings") {
+ viewer.addKeyAction( KeyStroke.getKeyStroke( "S" ), new AbstractAction( "brightness settings" )
+ {
@Override
- public void actionPerformed(final ActionEvent arg0) {
+ public void actionPerformed( final ActionEvent arg0 )
+ {
toggleBrightnessDialog();
}
private static final long serialVersionUID = 1L;
- });
+ } );
return viewer;
}
- public void toggleBrightnessDialog() {
- brightnessDialog.setVisible(!brightnessDialog.isVisible());
+ public void toggleBrightnessDialog()
+ {
+ brightnessDialog.setVisible( !brightnessDialog.isVisible() );
}
- private void requestRepaintAllViewers() {
- if (null != viewer) {
+ private void requestRepaintAllViewers()
+ {
+ if ( null != viewer )
+ {
viewer.requestRepaint();
}
}
- private void initBrightness(final SpimViewer viewer, final double cumulativeMinCutoff, final double cumulativeMaxCutoff) {
+ private void initBrightness( final SpimViewer viewer, final double cumulativeMinCutoff, final double cumulativeMaxCutoff )
+ {
final ViewerState state = viewer.getState();
- final Source<?> source = state.getSources().get(state.getCurrentSource()).getSpimSource();
- @SuppressWarnings({ "rawtypes", "unchecked" })
- final RandomAccessibleInterval<UnsignedShortType> img = (RandomAccessibleInterval) source.getSource(state.getCurrentTimepoint(), source.getNumMipmapLevels() - 1);
- final long z = (img.min(2) + img.max(2) + 1) / 2;
+ final Source< ? > source = state.getSources().get( state.getCurrentSource() ).getSpimSource();
+ @SuppressWarnings( { "rawtypes", "unchecked" } )
+ final RandomAccessibleInterval< UnsignedShortType > img = ( RandomAccessibleInterval ) source.getSource( state.getCurrentTimepoint(), source.getNumMipmapLevels() - 1 );
+ final long z = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 2;
final int numBins = 6535;
- final Histogram1d<UnsignedShortType> histogram = new Histogram1d<UnsignedShortType>(Views.iterable(Views.hyperSlice(img, 2, z)), new Real1dBinMapper<UnsignedShortType>(0, 65535, numBins, false));
+ final Histogram1d< UnsignedShortType > histogram = new Histogram1d< UnsignedShortType >( Views.iterable( Views.hyperSlice( img, 2, z ) ), new Real1dBinMapper< UnsignedShortType >( 0, 65535, numBins, false ) );
final DiscreteFrequencyDistribution dfd = histogram.dfd();
final long[] bin = new long[] { 0 };
double cumulative = 0;
int i = 0;
- for (; i < numBins && cumulative < cumulativeMinCutoff; ++i) {
- bin[0] = i;
- cumulative += dfd.relativeFrequency(bin);
+ for ( ; i < numBins && cumulative < cumulativeMinCutoff; ++i )
+ {
+ bin[ 0 ] = i;
+ cumulative += dfd.relativeFrequency( bin );
}
final int min = i * 65535 / numBins;
- for (; i < numBins && cumulative < cumulativeMaxCutoff; ++i) {
- bin[0] = i;
- cumulative += dfd.relativeFrequency(bin);
+ for ( ; i < numBins && cumulative < cumulativeMaxCutoff; ++i )
+ {
+ bin[ 0 ] = i;
+ cumulative += dfd.relativeFrequency( bin );
}
final int max = i * 65535 / numBins;
- final MinMaxGroup minmax = setupAssignments.getMinMaxGroups().get(0);
- minmax.getMinBoundedValue().setCurrentValue(min);
- minmax.getMaxBoundedValue().setCurrentValue(max);
+ final MinMaxGroup minmax = setupAssignments.getMinMaxGroups().get( 0 );
+ minmax.getMinBoundedValue().setCurrentValue( min );
+ minmax.getMaxBoundedValue().setCurrentValue( max );
}
- private void initTransform(final SpimViewer viewer, final int viewerWidth, final int viewerHeight) {
+ private void initTransform( final SpimViewer viewer, final int viewerWidth, final int viewerHeight )
+ {
final int cX = viewerWidth / 2;
final int cY = viewerHeight / 2;
final ViewerState state = viewer.getState();
- final SourceState<?> source = state.getSources().get(state.getCurrentSource());
+ final SourceState< ? > source = state.getSources().get( state.getCurrentSource() );
final int timepoint = state.getCurrentTimepoint();
- final AffineTransform3D sourceTransform = source.getSpimSource().getSourceTransform(timepoint, 0);
+ final AffineTransform3D sourceTransform = source.getSpimSource().getSourceTransform( timepoint, 0 );
- final Interval sourceInterval = source.getSpimSource().getSource(timepoint, 0);
- final double sX0 = sourceInterval.min(0);
- final double sX1 = sourceInterval.max(0);
- final double sY0 = sourceInterval.min(1);
- final double sY1 = sourceInterval.max(1);
- final double sZ0 = sourceInterval.min(2);
- final double sZ1 = sourceInterval.max(2);
- final double sX = (sX0 + sX1 + 1) / 2;
- final double sY = (sY0 + sY1 + 1) / 2;
- final double sZ = (sZ0 + sZ1 + 1) / 2;
+ final Interval sourceInterval = source.getSpimSource().getSource( timepoint, 0 );
+ final double sX0 = sourceInterval.min( 0 );
+ final double sX1 = sourceInterval.max( 0 );
+ final double sY0 = sourceInterval.min( 1 );
+ final double sY1 = sourceInterval.max( 1 );
+ final double sZ0 = sourceInterval.min( 2 );
+ final double sZ1 = sourceInterval.max( 2 );
+ final double sX = ( sX0 + sX1 + 1 ) / 2;
+ final double sY = ( sY0 + sY1 + 1 ) / 2;
+ final double sZ = ( sZ0 + sZ1 + 1 ) / 2;
- final double[][] m = new double[3][4];
+ final double[][] m = new double[ 3 ][ 4 ];
// rotation
- final double[] qSource = new double[4];
- final double[] qViewer = new double[4];
- Affine3DHelpers.extractApproximateRotationAffine(sourceTransform, qSource, 2);
- LinAlgHelpers.quaternionInvert(qSource, qViewer);
- LinAlgHelpers.quaternionToR(qViewer, m);
+ final double[] qSource = new double[ 4 ];
+ final double[] qViewer = new double[ 4 ];
+ Affine3DHelpers.extractApproximateRotationAffine( sourceTransform, qSource, 2 );
+ LinAlgHelpers.quaternionInvert( qSource, qViewer );
+ LinAlgHelpers.quaternionToR( qViewer, m );
// translation
final double[] centerSource = new double[] { sX, sY, sZ };
- final double[] centerGlobal = new double[3];
- final double[] translation = new double[3];
- sourceTransform.apply(centerSource, centerGlobal);
- LinAlgHelpers.quaternionApply(qViewer, centerGlobal, translation);
- LinAlgHelpers.scale(translation, -1, translation);
- LinAlgHelpers.setCol(3, translation, m);
+ final double[] centerGlobal = new double[ 3 ];
+ final double[] translation = new double[ 3 ];
+ sourceTransform.apply( centerSource, centerGlobal );
+ LinAlgHelpers.quaternionApply( qViewer, centerGlobal, translation );
+ LinAlgHelpers.scale( translation, -1, translation );
+ LinAlgHelpers.setCol( 3, translation, m );
final AffineTransform3D viewerTransform = new AffineTransform3D();
- viewerTransform.set(m);
+ viewerTransform.set( m );
// scale
final double[] pSource = new double[] { sX1, sY1, sZ };
- final double[] pGlobal = new double[3];
- final double[] pScreen = new double[3];
- sourceTransform.apply(pSource, pGlobal);
- viewerTransform.apply(pGlobal, pScreen);
- final double scaleX = cX / pScreen[0];
- final double scaleY = cY / pScreen[1];
- final double scale = Math.min(scaleX, scaleY);
- viewerTransform.scale(scale);
+ final double[] pGlobal = new double[ 3 ];
+ final double[] pScreen = new double[ 3 ];
+ sourceTransform.apply( pSource, pGlobal );
+ viewerTransform.apply( pGlobal, pScreen );
+ final double scaleX = cX / pScreen[ 0 ];
+ final double scaleY = cY / pScreen[ 1 ];
+ final double scale = Math.min( scaleX, scaleY );
+ viewerTransform.scale( scale );
// window center offset
- viewerTransform.set(viewerTransform.get(0, 3) + cX, 0, 3);
- viewerTransform.set(viewerTransform.get(1, 3) + cY, 1, 3);
+ viewerTransform.set( viewerTransform.get( 0, 3 ) + cX, 0, 3 );
+ viewerTransform.set( viewerTransform.get( 1, 3 ) + cY, 1, 3 );
- viewer.setCurrentViewerTransform(viewerTransform);
+ viewer.setCurrentViewerTransform( viewerTransform );
}
- @SuppressWarnings({ "rawtypes", "unchecked" })
- private void toggleMode() {
+ @SuppressWarnings( { "rawtypes", "unchecked" } )
+ private void toggleMode()
+ {
this.editMode = !editMode;
- System.out.println(editMode);// DEBUG
+ System.out.println( editMode );// DEBUG
- if (editMode) {
+ if ( editMode )
+ {
transformEventHandler = viewer.getDisplay().getTransformEventHandler();
- viewer.getDisplay().removeHandler(transformEventHandler);
+ viewer.getDisplay().removeHandler( transformEventHandler );
- final int currentSource = viewer.getState().getCurrentSource();
final int timePoint = viewer.getState().getCurrentTimepoint();
- regionGrowingAnnotationTool = new RegionGrowingAnnotationTool(viewer, sources.get(currentSource).getSpimSource(), overlay, timePoint);
- viewer.getDisplay().addHandler(regionGrowingAnnotationTool);
- } else {
- viewer.getDisplay().removeHandler(regionGrowingAnnotationTool);
- viewer.getDisplay().addHandler(transformEventHandler);
+ regionGrowingAnnotationTool = new RegionGrowingAnnotationTool( viewer, overlay, timePoint );
+ viewer.getDisplay().addHandler( regionGrowingAnnotationTool );
+ }
+ else
+ {
+ viewer.getDisplay().removeHandler( regionGrowingAnnotationTool );
+ viewer.getDisplay().addHandler( transformEventHandler );
}
}
- public static void main(final String[] args) throws ParserConfigurationException, SAXException, IOException, InstantiationException, IllegalAccessException, ClassNotFoundException, JDOMException {
- ImageJ.main(args);
+ public static void main( final String[] args ) throws ParserConfigurationException, SAXException, IOException, InstantiationException, IllegalAccessException, ClassNotFoundException, JDOMException
+ {
+ ImageJ.main( args );
+
+ // final File file = new File(
+ // "/Users/tinevez/Desktop/Data/Mamut/parhyale-crop/parhyale-crop-2.xml"
+ // );
+ final File file = new File( "E:/Users/JeanYves/Desktop/Data/Celegans.xml" );
- final File file = new File("/Users/tinevez/Desktop/Data/Mamut/parhyale-crop/parhyale-crop-2.xml");
- new Demo(file);
+ new Demo( file );
}
}
diff --git a/src/main/java/viewer/render/labelling/RegionGrowingAnnotationTool.java b/src/main/java/viewer/render/labelling/RegionGrowingAnnotationTool.java
index 456965515a61780fe821b86df36ce3d192e4b470..9a4a160c132acd8f6bae5bd9556e0cc68ad0fd1f 100644
--- a/src/main/java/viewer/render/labelling/RegionGrowingAnnotationTool.java
+++ b/src/main/java/viewer/render/labelling/RegionGrowingAnnotationTool.java
@@ -23,38 +23,49 @@ import net.imglib2.roi.IterableRegionOfInterest;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.IntType;
import viewer.SpimViewer;
-import viewer.render.Source;
-public class RegionGrowingAnnotationTool<T extends RealType<T>> implements MouseListener, MouseMotionListener {
+public class RegionGrowingAnnotationTool< T extends RealType< T >> implements MouseListener, MouseMotionListener
+{
private final SpimViewer viewer;
- private Map<long[], Integer> seed;
- private final LabelingSource labelingSource;
+
+ private Map< long[], Integer > seed;
+
+ private final LabelingSource< T > labelingSource;
+
private int label = 0;
+
private final long[][] structuringElement;
+
private final GrowingMode growingMode;
- private final NativeImgLabeling<Integer, IntType> labeling;
+
+ private final NativeImgLabeling< Integer, IntType > labeling;
+
/**
* A {@link RandomAccess} to the source image.
*/
- private final RandomAccess<T> ra;
+ private final RandomAccess< T > ra;
+
/**
* The transform that maps source coordinates to mouse coordinates.
*/
private final AffineTransform3D sourceToGlobal;
- public RegionGrowingAnnotationTool(final SpimViewer viewer, final Source<T> source, final LabelingSource labellingSource, final int t) {
+ public RegionGrowingAnnotationTool( final SpimViewer viewer, final LabelingSource< T > labelingSource, final int t )
+ {
this.viewer = viewer;
- this.labelingSource = labellingSource;
- this.labeling = labellingSource.getLabeling(t);
- this.ra = source.getSource(t, 0).randomAccess();
- this.sourceToGlobal = source.getSourceTransform(t, 0);
- this.structuringElement = AbstractRegionGrowing.get8ConStructuringElement(3);
+ this.labelingSource = labelingSource;
+ this.labeling = labelingSource.getLabeling( t );
+ this.ra = labelingSource.getImgSource().getSource( t, labelingSource.getLevel() ).randomAccess();
+ this.sourceToGlobal = labelingSource.getImgSource().getSourceTransform( t, labelingSource.getLevel() );
+ this.structuringElement = AbstractRegionGrowing.get8ConStructuringElement( 3 );
this.growingMode = GrowingMode.SEQUENTIAL;
int freeLabel = 0;
- for (final Integer existingLabel : labeling.getLabels()) {
- if (existingLabel.intValue() > freeLabel) {
+ for ( final Integer existingLabel : labeling.getLabels() )
+ {
+ if ( existingLabel.intValue() > freeLabel )
+ {
freeLabel = existingLabel.intValue();
}
}
@@ -62,71 +73,88 @@ public class RegionGrowingAnnotationTool<T extends RealType<T>> implements Mouse
}
@Override
- public void mouseClicked(final MouseEvent e) {}
+ public void mouseClicked( final MouseEvent e )
+ {}
@Override
- public void mouseEntered(final MouseEvent e) {}
+ public void mouseEntered( final MouseEvent e )
+ {}
@Override
- public void mouseExited(final MouseEvent e) {}
+ public void mouseExited( final MouseEvent e )
+ {}
@Override
- public void mousePressed(final MouseEvent e) {
+ public void mousePressed( final MouseEvent e )
+ {
final Point point = getLocationOnCurrentSource();
- final long[] pos = new long[3];
- point.localize(pos);
+ final long[] pos = new long[ 3 ];
+ point.localize( pos );
- if (!labeling.getLabels().isEmpty()) {
+ if ( !labeling.getLabels().isEmpty() )
+ {
- final RandomAccess<LabelingType<Integer>> randomAccess = labeling.randomAccess();
- randomAccess.setPosition(point);
+ final RandomAccess< LabelingType< Integer >> randomAccess = labeling.randomAccess();
+ randomAccess.setPosition( point );
- final List<Integer> existingLabels = randomAccess.get().getLabeling();
- if (!existingLabels.isEmpty()) {
+ final List< Integer > existingLabels = randomAccess.get().getLabeling();
+ if ( !existingLabels.isEmpty() )
+ {
- label = existingLabels.get(0).intValue(); // For future new annotation
+ label = existingLabels.get( 0 ).intValue(); // For future new
+ // annotation
- for (final Integer existingLabel : existingLabels) {
+ for ( final Integer existingLabel : existingLabels )
+ {
- final IterableRegionOfInterest roi = labeling.getIterableRegionOfInterest(existingLabel);
- final IterableInterval<LabelingType<Integer>> overROI = roi.getIterableIntervalOverROI(labeling);
- for (final LabelingType<Integer> labelingType : overROI) {
- final ArrayList<Integer> labels = new ArrayList<Integer>(labelingType.getLabeling());
+ final IterableRegionOfInterest roi = labeling.getIterableRegionOfInterest( existingLabel );
+ final IterableInterval< LabelingType< Integer >> overROI = roi.getIterableIntervalOverROI( labeling );
+ for ( final LabelingType< Integer > labelingType : overROI )
+ {
+ final ArrayList< Integer > labels = new ArrayList< Integer >( labelingType.getLabeling() );
labels.clear();
- labelingType.setLabeling(labels);
+ labelingType.setLabeling( labels );
}
}
- } else {
+ }
+ else
+ {
label++;
}
- } else {
+ }
+ else
+ {
label++;
}
- seed = new HashMap<long[], Integer>(1);
- seed.put(pos, Integer.valueOf(label));
+ seed = new HashMap< long[], Integer >( 1 );
+ seed.put( pos, Integer.valueOf( label ) );
}
@Override
- public void mouseReleased(final MouseEvent e) {}
+ public void mouseReleased( final MouseEvent e )
+ {}
@Override
- public void mouseDragged(final MouseEvent arg0) {
+ public void mouseDragged( final MouseEvent arg0 )
+ {
/*
* Remove old stuff
*/
- if (labeling.getLabels().contains(Integer.valueOf(label))) {
+ if ( labeling.getLabels().contains( Integer.valueOf( label ) ) )
+ {
- final IterableRegionOfInterest iterableRegionOfInterest = labeling.getIterableRegionOfInterest(Integer.valueOf(label));
- for (final LabelingType<Integer> ll : iterableRegionOfInterest.getIterableIntervalOverROI(labeling)) {
- final ArrayList<Integer> labels = new ArrayList<Integer>(ll.getLabeling());
- labels.remove(Integer.valueOf(label));
- ll.setLabeling(labels);
+ final IterableRegionOfInterest iterableRegionOfInterest = labeling.getIterableRegionOfInterest( Integer.valueOf( label ) );
+ for ( final LabelingType< Integer > ll : iterableRegionOfInterest.getIterableIntervalOverROI( labeling ) )
+ {
+ final ArrayList< Integer > labels = new ArrayList< Integer >( ll.getLabeling() );
+ labels.remove( Integer.valueOf( label ) );
+ ll.setLabeling( labels );
}
}
@@ -136,10 +164,10 @@ public class RegionGrowingAnnotationTool<T extends RealType<T>> implements Mouse
*/
final Point current = getLocationOnCurrentSource();
- ra.setPosition(current);
+ ra.setPosition( current );
final T threshold = ra.get().copy();
- final ThresholdRegionGrowing<T, Integer> regionGrowing = new ThresholdRegionGrowing<T, Integer>(ra, threshold, seed, growingMode, structuringElement, labeling);
+ final ThresholdRegionGrowing< T, Integer > regionGrowing = new ThresholdRegionGrowing< T, Integer >( ra, threshold, seed, growingMode, structuringElement, labeling );
regionGrowing.checkInput();
regionGrowing.process();
@@ -149,15 +177,17 @@ public class RegionGrowingAnnotationTool<T extends RealType<T>> implements Mouse
}
@Override
- public void mouseMoved(final MouseEvent arg0) {}
+ public void mouseMoved( final MouseEvent arg0 )
+ {}
- private Point getLocationOnCurrentSource() {
- final double[] coordinates = new double[3];
- final RealPoint click = RealPoint.wrap(coordinates);
- viewer.getGlobalMouseCoordinates(click);
+ private Point getLocationOnCurrentSource()
+ {
+ final double[] coordinates = new double[ 3 ];
+ final RealPoint click = RealPoint.wrap( coordinates );
+ viewer.getGlobalMouseCoordinates( click );
- final Point roundedSourcePos = new Point(3);
- sourceToGlobal.applyInverse(new Round<Point>(roundedSourcePos), click);
+ final Point roundedSourcePos = new Point( 3 );
+ sourceToGlobal.applyInverse( new Round< Point >( roundedSourcePos ), click );
return roundedSourcePos;
}
}