Draft PR that tracks the work towards TrackMate v8

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>TrackMate</artifactId>
-	<version>7.14.1-SNAPSHOT</version>
+	<version>8.0.0-SNAPSHOT</version>
 
 	<name>TrackMate</name>
 	<description>TrackMate plugin for Fiji.</description>
@@ -147,14 +147,6 @@
 
 		<fontchooser.version>2.5.2</fontchooser.version>
 		<javaGeom.version>0.11.1</javaGeom.version>
-
-		<imglib2.version>7.1.0</imglib2.version>
-		<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
-		<imglib2-roi.version>0.15.0</imglib2-roi.version>
-		<imglib2-cache.version>1.0.0-beta-18</imglib2-cache.version>
-		<imglib2-algorithm.version>0.15.3</imglib2-algorithm.version>
-		<imglib2-ij.version>2.0.2</imglib2-ij.version>
-		<bigdataviewer-core.version>10.6.0</bigdataviewer-core.version>
 	</properties>
 
 	<dependencies>
@@ -163,6 +155,10 @@
 			<groupId>sc.fiji</groupId>
 			<artifactId>fiji-lib</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>labkit-ui</artifactId>
+		</dependency>
 
 		<!-- ImageJ dependencies -->
 		<dependency>
@@ -215,10 +211,10 @@
 			<groupId>com.github.vlsi.mxgraph</groupId>
 			<artifactId>jgraphx</artifactId>
 		</dependency>
-		<dependency>
+		<!--<dependency>
 			<groupId>com.google.code.gson</groupId>
 			<artifactId>gson</artifactId>
-		</dependency>
+		</dependency> -->
 		<dependency>
 			<groupId>com.itextpdf</groupId>
 			<artifactId>itextpdf</artifactId>

src/main/java/fiji/plugin/trackmate/LoadTrackMatePlugIn.java

@@ -24,6 +24,7 @@
 import static fiji.plugin.trackmate.gui.Icons.TRACKMATE_ICON;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.io.File;
 
 import javax.swing.JFrame;
@@ -65,8 +66,6 @@ public class LoadTrackMatePlugIn extends TrackMatePlugIn
 	@Override
 	public void run( final String filePath )
 	{
-//		GuiUtils.setSystemLookAndFeel();
-
 		final Logger logger = Logger.IJ_LOGGER;
 		File file;
 		if ( null == filePath || filePath.length() == 0 )
@@ -215,6 +214,8 @@ public void run( final String filePath )
 		frame.setIconImage( TRACKMATE_ICON.getImage() );
 		GuiUtils.positionWindow( frame, settings.imp.getWindow() );
 		frame.setVisible( true );
+		final Dimension size = frame.getSize();
+		frame.setSize( size.width, size.height + 1 );
 
 		// Text
 		final LogPanelDescriptor2 logDescriptor = ( LogPanelDescriptor2 ) sequence.logDescriptor();
@@ -230,7 +231,7 @@ public void run( final String filePath )
 		final String warning = reader.getErrorMessage();
 		if ( !warning.isEmpty() )
 		{
-			logger2.log( "Warnings occured during reading the file:\n"
+			logger2.log( "Warnings occurred during reading the file:\n"
 					+ "--------------------\n"
 					+ warning
 					+ "--------------------\n",
@@ -292,11 +293,12 @@ protected TmXmlReader createReader( final File lFile )
 
 	public static void main( final String[] args )
 	{
+		GuiUtils.setSystemLookAndFeel();
 		ImageJ.main( args );
 		final LoadTrackMatePlugIn plugIn = new LoadTrackMatePlugIn();
-		plugIn.run( null );
+//		plugIn.run( null );
 //		plugIn.run( "samples/FakeTracks.xml" );
-//		plugIn.run( "samples/MAX_Merged.xml" );
+		plugIn.run( "samples/MAX_Merged.xml" );
 //		plugIn.run( "c:/Users/tinevez/Development/TrackMateWS/TrackMate-Cellpose/samples/R2_multiC.xml" );
 //		plugIn.run( "/Users/tinevez/Desktop/230901_DeltaRcsB-ZipA-mCh_timestep5min_Stage9_reg/230901_DeltaRcsB-ZipA-mCh_timestep5min_Stage9_reg_merge65.xml" );
 	}

src/main/java/fiji/plugin/trackmate/TrackMate.java

@@ -107,6 +107,12 @@ public class TrackMate implements Benchmark, MultiThreaded, Algorithm, Named, Ca
 	public TrackMate( final Settings settings )
 	{
 		this( new Model(), settings );
+		if ( settings.imp != null && settings.imp.getCalibration() != null )
+		{
+			final String spaceUnits = settings.imp.getCalibration().getXUnit();
+			final String timeUnits = settings.imp.getCalibration().getTimeUnit();
+			model.setPhysicalUnits( spaceUnits, timeUnits );
+		}
 	}
 
 	public TrackMate( final Model model, final Settings settings )

src/main/java/fiji/plugin/trackmate/detection/DetectionUtils.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -39,8 +39,8 @@
 import fiji.plugin.trackmate.SpotCollection;
 import fiji.plugin.trackmate.TrackMate;
 import fiji.plugin.trackmate.detection.util.MedianFilter2D;
-import fiji.plugin.trackmate.util.Threads;
 import fiji.plugin.trackmate.util.TMUtils;
+import fiji.plugin.trackmate.util.Threads;
 import ij.ImagePlus;
 import net.imagej.ImgPlus;
 import net.imagej.axis.Axes;
@@ -69,7 +69,6 @@
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.util.Intervals;
-import net.imglib2.util.Util;
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
 
@@ -82,7 +81,7 @@ public class DetectionUtils
 	 * This method returns immediately and execute the detection in a separate
 	 * thread. It executes the detection in one frame only and writes the
 	 * results in the specified model object.
-	 * 
+	 *
 	 * @param model
 	 *            the model to write detection results in.
 	 * @param settings
@@ -167,7 +166,7 @@ public static final void preview(
 	 * Returns <code>true</code> if the specified image is 2D. It can have
 	 * multiple channels and multiple time-points; this method only looks at
 	 * whether several Z-slices can be found.
-	 * 
+	 *
 	 * @param img
 	 *            the image.
 	 * @return <code>true</code> if the image is 2D, regardless of time and
@@ -189,7 +188,7 @@ public static final boolean is2D( final ImagePlus imp )
 	 * radius specified <b>using calibrated units</b>. The specified calibration
 	 * is used to determine the dimensionality of the kernel and to map it on a
 	 * pixel grid.
-	 * 
+	 *
 	 * @param radius
 	 *            the blob radius (in image unit).
 	 * @param nDims
@@ -277,7 +276,7 @@ public static final < T extends RealType< T > > Img< FloatType > copyToFloatImg(
 		final RandomAccess< T > in = Views.zeroMin( Views.interval( img, interval ) ).randomAccess();
 		final Cursor< FloatType > out = output.cursor();
 		final RealFloatConverter< T > c = new RealFloatConverter<>();
-		
+
 		while ( out.hasNext() )
 		{
 			out.fwd();
@@ -344,7 +343,7 @@ public static final < T extends RealType< T > > List< Spot > findLocalMaxima(
 		 * Find maxima.
 		 */
 
-		final T val = Util.getTypeFromInterval( source ).createVariable();
+		final T val = source.getType().createVariable();
 		val.setReal( threshold );
 		final LocalNeighborhoodCheck< Point, T > localNeighborhoodCheck = new LocalExtrema.MaximumCheck<>( val );
 		final IntervalView< T > dogWithBorder = Views.interval( Views.extendMirrorSingle( source ), Intervals.expand( source, 1 ) );
@@ -492,7 +491,7 @@ else if ( source.numDimensions() > 1 )
 	/**
 	 * Return a view of the specified input image, at the specified channel
 	 * (0-based) and the specified frame (0-based too).
-	 * 
+	 *
 	 * @param <T>
 	 *            the type of the input image.
 	 * @param img
@@ -524,7 +523,7 @@ public static final < T extends Type< T > > RandomAccessibleInterval< T > prepar
 
 	/**
 	 * Normalize the pixel value of an image between 0 and 1.
-	 * 
+	 *
 	 * @param <T>
 	 *            the type of pixels in the image. Must extend {@link RealType}.
 	 * @param input

src/main/java/fiji/plugin/trackmate/detection/DogDetector.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -23,7 +23,6 @@
 
 import net.imglib2.Cursor;
 import net.imglib2.Interval;
-import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.algorithm.dog.DifferenceOfGaussian;
@@ -117,10 +116,8 @@ public boolean process()
 			e.printStackTrace();
 		}
 
-		final IterableInterval< FloatType > dogIterable = Views.iterable( dog );
-		final IterableInterval< FloatType > tmpIterable = Views.iterable( dog2 );
-		final Cursor< FloatType > dogCursor = dogIterable.cursor();
-		final Cursor< FloatType > tmpCursor = tmpIterable.cursor();
+		final Cursor< FloatType > dogCursor = dog.cursor();
+		final Cursor< FloatType > tmpCursor = dog2.cursor();
 		while ( dogCursor.hasNext() )
 			dogCursor.next().sub( tmpCursor.next() );
 

src/main/java/fiji/plugin/trackmate/detection/LabelImageDetector.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -101,9 +101,7 @@ public boolean process()
 	{
 		final long start = System.currentTimeMillis();
 		final RandomAccessibleInterval< T > rai = Views.interval( input, interval );
-		final T type = Util.getTypeFromInterval( rai );
-
-		if ( type instanceof IntegerType )
+		if ( rai.getType() instanceof IntegerType )
 		{
 			processIntegerImg( ( RandomAccessibleInterval ) Views.zeroMin( rai ) );
 		}
@@ -126,7 +124,7 @@ private < R extends IntegerType< R > > void processIntegerImg( final RandomAcces
 	{
 		// Get all labels.
 		final AtomicInteger max = new AtomicInteger( 0 );
-		Views.iterable( rai ).forEach( p -> {
+		rai.forEach( p -> {
 			final int val = p.getInteger();
 			if ( val != 0 && val > max.get() )
 				max.set( val );