" - + "A new 16-bit image is generated, of same dimension and size that " - + "of the input image. The label image has one channel, with black baground (0 value) " + + "A new 32-bit image is generated, of same dimension and size that " + + "of the input image. The label image has one channel, with black background (0 value) " + "everywhere, except where there are spots. Each spot is painted with " - + "a uniform integer value equal to the trackID it belongs to. " - + "Spots that do not belong to tracks are painted with a unique integer " - + "larger than the last trackID in the dataset. " + + "a uniform integer value, configurable to be the spot ID, the ID of the " + + "track it belongs to, or a simple index, unique to the frame or to the movie. " + "
"
+ "Only visible spots are painted. "
+ "";
@@ -85,7 +86,7 @@ public void execute( final TrackMate trackmate, final SelectionModel selectionMo
final boolean exportSpotsAsDots;
final boolean exportTracksOnly;
- final boolean useSpotIDsAsLabels;
+ final LabelIdPainting labelIdPainting;
if ( gui != null )
{
final LabelImgExporterPanel panel = new LabelImgExporterPanel();
@@ -102,20 +103,20 @@ public void execute( final TrackMate trackmate, final SelectionModel selectionMo
exportSpotsAsDots = panel.isExportSpotsAsDots();
exportTracksOnly = panel.isExportTracksOnly();
- useSpotIDsAsLabels = panel.isUseSpotIDsAsLabels();;
+ labelIdPainting = panel.labelIdPainting();
}
else
{
exportSpotsAsDots = false;
exportTracksOnly = false;
- useSpotIDsAsLabels = false;
+ labelIdPainting = LabelIdPainting.LABEL_IS_INDEX_MOVIE_UNIQUE;
}
/*
* Generate label image.
*/
- createLabelImagePlus( trackmate, exportSpotsAsDots, exportTracksOnly, useSpotIDsAsLabels ,logger ).show();
+ createLabelImagePlus( trackmate, exportSpotsAsDots, exportTracksOnly, labelIdPainting, logger ).show();
}
/**
@@ -131,17 +132,15 @@ public void execute( final TrackMate trackmate, final SelectionModel selectionMo
* of this input image, except for the number of channels, which
* will be 1.
* @param exportSpotsAsDots
- * if true, spots will be painted as single dots
- * instead of ellipsoids.
+ * if true, spots will be painted as single dots. If
+ * false they will be painted with their shape.
* @param exportTracksOnly
* if true, only the spots belonging to visible
* tracks will be painted. If false, spots not
* belonging to a track will be painted with a unique ID,
* different from the track IDs and different for each spot.
- * @param useSpotIDsAsLabels
- * if true, the label mask images will contain
- * the spot ID. If false, the label mask images
- * will contain the track ID.
+ * @param labeIdPainting
+ * specifies how to paint the label ID of spots.
*
* @return a new {@link ImagePlus}.
*/
@@ -149,10 +148,10 @@ public static final ImagePlus createLabelImagePlus(
final TrackMate trackmate,
final boolean exportSpotsAsDots,
final boolean exportTracksOnly,
- final boolean useSpotIDsAsLabels
+ final LabelIdPainting labeIdPainting
)
{
- return createLabelImagePlus( trackmate, exportSpotsAsDots, exportTracksOnly, useSpotIDsAsLabels, Logger.VOID_LOGGER );
+ return createLabelImagePlus( trackmate, exportSpotsAsDots, exportTracksOnly, labeIdPainting, Logger.VOID_LOGGER );
}
/**
@@ -175,10 +174,8 @@ public static final ImagePlus createLabelImagePlus(
* tracks will be painted. If false, spots not
* belonging to a track will be painted with a unique ID,
* different from the track IDs and different for each spot.
- * @param useSpotIDsAsLabels
- * if true, the label mask images will contain
- * the spot ID. If false, the label mask images
- * will contain the track ID.
+ * @param labelIdPainting
+ * specifies how to paint the label ID of spots.
* @param logger
* a {@link Logger} instance, to report progress of the export
* process.
@@ -189,10 +186,10 @@ public static final ImagePlus createLabelImagePlus(
final TrackMate trackmate,
final boolean exportSpotsAsDots,
final boolean exportTracksOnly,
- final boolean useSpotIDsAsLabels,
+ final LabelIdPainting labelIdPainting,
final Logger logger )
{
- return createLabelImagePlus( trackmate.getModel(), trackmate.getSettings().imp, exportSpotsAsDots, exportTracksOnly, useSpotIDsAsLabels, logger );
+ return createLabelImagePlus( trackmate.getModel(), trackmate.getSettings().imp, exportSpotsAsDots, exportTracksOnly, labelIdPainting, logger );
}
/**
@@ -215,10 +212,8 @@ public static final ImagePlus createLabelImagePlus(
* tracks will be painted. If false, spots not
* belonging to a track will be painted with a unique ID,
* different from the track IDs and different for each spot.
- * @param useSpotIDsAsLabels
- * if true, the label mask images will contain
- * the spot ID. If false, the label mask images
- * will contain the track ID.
+ * @param labelIdPainting
+ * specifies how to paint the label ID of spots.
*
* @return a new {@link ImagePlus}.
*/
@@ -227,9 +222,9 @@ public static final ImagePlus createLabelImagePlus(
final ImagePlus imp,
final boolean exportSpotsAsDots,
final boolean exportTracksOnly,
- final boolean useSpotIDsAsLabels )
+ final LabelIdPainting labelIdPainting )
{
- return createLabelImagePlus( model, imp, exportSpotsAsDots, exportTracksOnly, useSpotIDsAsLabels, Logger.VOID_LOGGER );
+ return createLabelImagePlus( model, imp, exportSpotsAsDots, exportTracksOnly, labelIdPainting, Logger.VOID_LOGGER );
}
/**
@@ -252,10 +247,8 @@ public static final ImagePlus createLabelImagePlus(
* tracks will be painted. If false, spots not
* belonging to a track will be painted with a unique ID,
* different from the track IDs and different for each spot.
- * @param useSpotIDsAsLabels
- * if true, the label mask images will contain
- * the spot ID. If false, the label mask images
- * will contain the track ID.
+ * @param labelIdPainting
+ * specifies how to paint the label ID of spots.
* @param logger
* a {@link Logger} instance, to report progress of the export
* process.
@@ -267,7 +260,7 @@ public static final ImagePlus createLabelImagePlus(
final ImagePlus imp,
final boolean exportSpotsAsDots,
final boolean exportTracksOnly,
- boolean useSpotIDsAsLabels,
+ final LabelIdPainting labelIdPainting,
final Logger logger )
{
final int[] dimensions = imp.getDimensions();
@@ -278,7 +271,7 @@ public static final ImagePlus createLabelImagePlus(
imp.getCalibration().pixelDepth,
imp.getCalibration().frameInterval
};
- final ImagePlus lblImp = createLabelImagePlus( model, dims, calibration, exportSpotsAsDots, exportTracksOnly, useSpotIDsAsLabels, logger );
+ final ImagePlus lblImp = createLabelImagePlus( model, dims, calibration, exportSpotsAsDots, exportTracksOnly, labelIdPainting, logger );
lblImp.setCalibration( imp.getCalibration().copy() );
lblImp.setTitle( "LblImg_" + imp.getTitle() );
return lblImp;
@@ -304,11 +297,9 @@ public static final ImagePlus createLabelImagePlus(
* tracks will be painted. If false, spots not
* belonging to a track will be painted with a unique ID,
* different from the track IDs and different for each spot.
- * @param useSpotIDsAsLabels
- * if true, the label mask images will contain
- * the spot ID. If false, the label mask images
- * will contain the track ID.
- *
+ * @param labelIdPainting
+ * specifies how to paint the label ID of spots.
+ *
* @return a new {@link ImagePlus}.
*/
public static final ImagePlus createLabelImagePlus(
@@ -317,9 +308,9 @@ public static final ImagePlus createLabelImagePlus(
final double[] calibration,
final boolean exportSpotsAsDots,
final boolean exportTracksOnly,
- final boolean useSpotIDsAsLabels)
+ final LabelIdPainting labelIdPainting )
{
- return createLabelImagePlus( model, dimensions, calibration, exportSpotsAsDots, exportTracksOnly, useSpotIDsAsLabels, Logger.VOID_LOGGER );
+ return createLabelImagePlus( model, dimensions, calibration, exportSpotsAsDots, exportTracksOnly, labelIdPainting, Logger.VOID_LOGGER );
}
/**
@@ -341,10 +332,8 @@ public static final ImagePlus createLabelImagePlus(
* tracks will be painted. If false, spots not
* belonging to a track will be painted with a unique ID,
* different from the track IDs and different for each spot.
- * @param useSpotIDsAsLabels
- * if true, the label mask images will contain
- * the spot ID. If false, the label mask images
- * will contain the track ID.
+ * @param labelIdPainting
+ * specifies how to paint the label ID of spots.
* @param logger
* a {@link Logger} instance, to report progress of the export
* process.
@@ -357,17 +346,18 @@ public static final ImagePlus createLabelImagePlus(
final double[] calibration,
final boolean exportSpotsAsDots,
final boolean exportTracksOnly,
- final boolean useSpotIDsAsLabels,
+ final LabelIdPainting labelIdPainting,
final Logger logger )
{
final long[] dims = new long[ 4 ];
for ( int d = 0; d < dims.length; d++ )
dims[ d ] = dimensions[ d ];
- final ImagePlus lblImp = ImageJFunctions.wrap( createLabelImg( model, dims, calibration, exportSpotsAsDots, exportTracksOnly, useSpotIDsAsLabels, logger ), "LblImage" );
+ final ImagePlus lblImp = ImageJFunctions.wrap( createLabelImg( model, dims, calibration, exportSpotsAsDots, exportTracksOnly, labelIdPainting, logger ), "LblImage" );
lblImp.setDimensions( 1, dimensions[ 2 ], dimensions[ 3 ] );
+ lblImp.setLut( GlasbeyLut.toLUT() );
+ lblImp.setDisplayRange( 0, 255 );
lblImp.setOpenAsHyperStack( true );
- lblImp.resetDisplayRange();
return lblImp;
}
@@ -390,11 +380,9 @@ public static final ImagePlus createLabelImagePlus(
* tracks will be painted. If false, spots not
* belonging to a track will be painted with a unique ID,
* different from the track IDs and different for each spot.
- * @param useSpotIDsAsLabels
- * if true, the label mask images will contain
- * the spot ID. If false, the label mask images
- * will contain the track ID.
- *
+ * @param labelIdPainting
+ * specifies how to paint the label ID of spots.
+ *
* @return a new {@link Img}.
*/
public static final Img< FloatType > createLabelImg(
@@ -403,9 +391,9 @@ public static final Img< FloatType > createLabelImg(
final double[] calibration,
final boolean exportSpotsAsDots,
final boolean exportTracksOnly,
- final boolean useSpotIDsAsLabels)
+ final LabelIdPainting labelIdPainting )
{
- return createLabelImg( model, dimensions, calibration, exportSpotsAsDots, exportTracksOnly, useSpotIDsAsLabels, Logger.VOID_LOGGER );
+ return createLabelImg( model, dimensions, calibration, exportSpotsAsDots, exportTracksOnly, labelIdPainting, Logger.VOID_LOGGER );
}
/**
@@ -427,10 +415,8 @@ public static final Img< FloatType > createLabelImg(
* tracks will be painted. If false, spots not
* belonging to a track will be painted with a unique ID,
* different from the track IDs and different for each spot.
- * @param useSpotIDsAsLabels
- * if true, the label mask images will contain
- * the spot ID. If false, the label mask images
- * will contain the track ID.
+ * @param labelIdPainting
+ * specifies how to paint the label ID of spots.
* @param logger
* a {@link Logger} instance, to report progress of the export
* process.
@@ -443,7 +429,7 @@ public static final Img< FloatType > createLabelImg(
final double[] calibration,
final boolean exportSpotsAsDots,
final boolean exportTracksOnly,
- final boolean useSpotIDsAsLabels,
+ final LabelIdPainting labelIdPainting,
final Logger logger )
{
/*
@@ -459,16 +445,10 @@ public static final Img< FloatType > createLabelImg(
final ImgPlus< FloatType > imgPlus = new ImgPlus<>( lblImg, "LblImg", axes, calibration );
/*
- * Determine the starting id for spots not in tracks.
+ * How to assign an ID to spots.
*/
- int maxTrackID = -1;
- final Set< Integer > trackIDs = model.getTrackModel().trackIDs( false );
- if ( null != trackIDs )
- for ( final Integer trackID : trackIDs )
- if ( trackID > maxTrackID )
- maxTrackID = trackID.intValue();
- final AtomicInteger lonelySpotID = new AtomicInteger( maxTrackID + 2 );
+ final IdGenerator idGenerator = labelIdPainting.idGenerator( model.getTrackModel(), exportTracksOnly );
/*
* Frame by frame iteration.
@@ -481,29 +461,11 @@ public static final Img< FloatType > createLabelImg(
final SpotWriter spotWriter = exportSpotsAsDots
? new SpotAsDotWriter<>( imgCT )
: new SpotRoiWriter<>( imgCT );
+ idGenerator.nextFrame();
for ( final Spot spot : model.getSpots().iterable( frame, true ) )
{
- final int id;
- final Integer trackID = model.getTrackModel().trackIDOf( spot );
- if ( null == trackID || !model.getTrackModel().isVisible( trackID ) )
- {
- if ( exportTracksOnly )
- continue;
-
- if ( useSpotIDsAsLabels )
- id = spot.ID() + 1;
- else
- id = lonelySpotID.getAndIncrement();
- }
- else
- {
- if ( useSpotIDsAsLabels )
- id = spot.ID() + 1;
- else
- id = 1 + trackID.intValue();
- }
-
+ final int id = idGenerator.id( spot );
spotWriter.write( spot, id );
}
logger.setProgress( ( double ) ( 1 + frame ) / dimensions[ 3 ] );
@@ -600,4 +562,176 @@ public void write( final Spot spot, final int id )
ra.get().setReal( id );
}
}
+
+ /**
+ * Specifies how spots will be labeled in the exported label image.
+ */
+ public static enum LabelIdPainting
+ {
+
+ LABEL_IS_TRACK_ID( "Track ID",
+ "The spot label is the ID of the track it belongs to, plus one (+1). "
+ + "Spots that do not belong to tracks are painted with a unique integer "
+ + "larger than the last trackID in the dataset." ),
+ LABEL_IS_SPOT_ID( "Spot ID",
+ "The spot label is the spot ID, plus one (+1)." ),
+ LABEL_IS_INDEX( "Index unique in frame",
+ "The spot label is an index starting from 1. "
+ + "It is unique within a frame, "
+ + "but can be repeated across frames." ),
+ LABEL_IS_INDEX_MOVIE_UNIQUE( "Unique index",
+ "The spot label is an index starting from 1. "
+ + "It is unique within the whole movie." );
+
+ private final String info;
+
+ private final String methodName;
+
+ private LabelIdPainting( final String methodName, final String info )
+ {
+ this.methodName = methodName;
+ this.info = info;
+ }
+
+ @Override
+ public String toString()
+ {
+ return methodName;
+ }
+
+ public String getInfo()
+ {
+ return info;
+ }
+
+ public IdGenerator idGenerator( final TrackModel tm, final boolean visibleTracksOnly)
+ {
+ switch ( this )
+ {
+ case LABEL_IS_INDEX:
+ return new SpotIndexGeneratorUniqueInFrame( tm, visibleTracksOnly );
+ case LABEL_IS_INDEX_MOVIE_UNIQUE:
+ return new SpotIndexGeneratorUniqueInMovie( tm, visibleTracksOnly );
+ case LABEL_IS_SPOT_ID:
+ return new SpotIdGenerator( tm, visibleTracksOnly );
+ case LABEL_IS_TRACK_ID:
+ return new TrackIdGenerator( tm, visibleTracksOnly );
+ default:
+ throw new IllegalArgumentException( "Unknown painting id mode: " + this );
+ }
+ }
+ }
+
+ private static interface IdGenerator
+ {
+ public int id( Spot spot );
+
+ public default void nextFrame()
+ {};
+ }
+
+ private static abstract class AbstractIdGenerator implements IdGenerator
+ {
+ protected final TrackModel tm;
+
+ protected final boolean visibleTracksOnly;
+
+ public AbstractIdGenerator( final TrackModel tm, final boolean visibleTracksOnly )
+ {
+ this.tm = tm;
+ this.visibleTracksOnly = visibleTracksOnly;
+ }
+ }
+
+ private static class TrackIdGenerator extends AbstractIdGenerator
+ {
+
+ private final AtomicInteger lonelySpotID;
+
+ public TrackIdGenerator( final TrackModel tm, final boolean visibleTracksOnly )
+ {
+ super( tm, visibleTracksOnly );
+ int maxTrackID = -1;
+ final Set< Integer > trackIDs = tm.trackIDs( false );
+ if ( null != trackIDs )
+ for ( final Integer trackID : trackIDs )
+ if ( trackID > maxTrackID )
+ maxTrackID = trackID.intValue();
+ this.lonelySpotID = new AtomicInteger( maxTrackID + 2 );
+ }
+
+ @Override
+ public int id( final Spot spot )
+ {
+ final Integer trackID = tm.trackIDOf( spot );
+ if ( null == trackID || !tm.isVisible( trackID ) )
+ {
+ if ( visibleTracksOnly )
+ return -1;
+ return lonelySpotID.getAndIncrement();
+ }
+ return trackID + 1;
+ }
+ }
+
+ private static class SpotIdGenerator extends AbstractIdGenerator
+ {
+
+ public SpotIdGenerator( final TrackModel tm, final boolean visibleTracksOnly )
+ {
+ super( tm, visibleTracksOnly );
+ }
+
+ @Override
+ public int id( final Spot spot )
+ {
+ final Integer trackID = tm.trackIDOf( spot );
+ if ( null == trackID || !tm.isVisible( trackID ) )
+ {
+ if ( visibleTracksOnly )
+ return -1;
+ }
+ return spot.ID() + 1;
+ }
+ }
+
+ private static class SpotIndexGeneratorUniqueInMovie extends AbstractIdGenerator
+ {
+
+ protected final AtomicInteger index;
+
+ public SpotIndexGeneratorUniqueInMovie( final TrackModel tm, final boolean visibleTracksOnly )
+ {
+ super( tm, visibleTracksOnly );
+ this.index = new AtomicInteger( 0 );
+ }
+
+ @Override
+ public int id( final Spot spot )
+ {
+ final Integer trackID = tm.trackIDOf( spot );
+ if ( null == trackID || !tm.isVisible( trackID ) )
+ {
+ if ( visibleTracksOnly )
+ return -1;
+ }
+ return index.incrementAndGet();
+ }
+ }
+
+
+ private static class SpotIndexGeneratorUniqueInFrame extends SpotIndexGeneratorUniqueInMovie
+ {
+
+ public SpotIndexGeneratorUniqueInFrame( final TrackModel tm, final boolean visibleTracksOnly )
+ {
+ super( tm, visibleTracksOnly );
+ }
+
+ @Override
+ public void nextFrame()
+ {
+ index.set( 0 );
+ }
+ }
}
diff --git a/src/main/java/fiji/plugin/trackmate/action/LabelImgExporterPanel.java b/src/main/java/fiji/plugin/trackmate/action/LabelImgExporterPanel.java
index 9aebd3688..31366fd60 100644
--- a/src/main/java/fiji/plugin/trackmate/action/LabelImgExporterPanel.java
+++ b/src/main/java/fiji/plugin/trackmate/action/LabelImgExporterPanel.java
@@ -21,13 +21,19 @@
*/
package fiji.plugin.trackmate.action;
+import java.awt.Dimension;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
import javax.swing.JPanel;
+import fiji.plugin.trackmate.action.LabelImgExporter.LabelIdPainting;
+import fiji.plugin.trackmate.gui.Fonts;
+
public class LabelImgExporterPanel extends JPanel
{
@@ -37,15 +43,17 @@ public class LabelImgExporterPanel extends JPanel
private final JCheckBox exportTracksOnly;
- private final JCheckBox useSpotIdsAsLabels;
+ private final JComboBox< LabelIdPainting > labelIdPainting;
public LabelImgExporterPanel()
{
+ setPreferredSize( new Dimension( 250, 200 ) );
final GridBagLayout gridBagLayout = new GridBagLayout();
+ gridBagLayout.rowWeights = new double[] { 0., 0., 0., 1. };
setLayout( gridBagLayout );
final GridBagConstraints gbc = new GridBagConstraints();
- gbc.anchor = GridBagConstraints.WEST;
+ gbc.anchor = GridBagConstraints.NORTHWEST;
gbc.insets = new Insets( 5, 5, 5, 5 );
gbc.gridx = 0;
gbc.gridy = 0;
@@ -57,9 +65,24 @@ public LabelImgExporterPanel()
gbc.gridy++;
add( exportTracksOnly, gbc );
- useSpotIdsAsLabels = new JCheckBox( "Use spots IDs as labels", false );
gbc.gridy++;
- add( useSpotIdsAsLabels, gbc );
+ add( new JLabel( "Label ID is:" ), gbc );
+
+ labelIdPainting = new JComboBox<>( LabelIdPainting.values() );
+ gbc.gridy++;
+ add( labelIdPainting, gbc );
+
+ final JLabel info = new JLabel();
+ info.setFont( Fonts.SMALL_FONT );
+ gbc.gridy++;
+ gbc.fill = GridBagConstraints.BOTH;
+ add( info, gbc );
+
+ labelIdPainting.addItemListener( e -> info.setText( ""
+ + ( ( LabelIdPainting ) labelIdPainting.getSelectedItem() ).getInfo()
+ + "" ) );
+ labelIdPainting.setSelectedIndex( 1 );
+ labelIdPainting.setSelectedIndex( 0 );
}
public boolean isExportSpotsAsDots()
@@ -72,8 +95,8 @@ public boolean isExportTracksOnly()
return exportTracksOnly.isSelected();
}
- public boolean isUseSpotIDsAsLabels()
+ public LabelIdPainting labelIdPainting()
{
- return useSpotIdsAsLabels.isSelected();
+ return ( LabelIdPainting ) labelIdPainting.getSelectedItem();
}
}
diff --git a/src/main/java/fiji/plugin/trackmate/tracking/overlap/OverlapTrackerFactory.java b/src/main/java/fiji/plugin/trackmate/tracking/overlap/OverlapTrackerFactory.java
index a1420fa27..5bc05f791 100644
--- a/src/main/java/fiji/plugin/trackmate/tracking/overlap/OverlapTrackerFactory.java
+++ b/src/main/java/fiji/plugin/trackmate/tracking/overlap/OverlapTrackerFactory.java
@@ -106,8 +106,9 @@ public class OverlapTrackerFactory implements SpotTrackerFactory
+ "spot polygon. "
+ "
" + "
"
- + "Careful: this tracker is only suited to 2D images. It treats all the spots "
- + "as 2D objects. The Z dimension is ignored. "
+ + "This tracker works in 2D and 3D. However in 3D, the IoU is computed from the "
+ + "bounding-boxes regardless of the choice of the IoU computation method. "
+ + "The