diff --git a/src/main/java/fiji/plugin/trackmate/detection/LogDetectorFactory.java b/src/main/java/fiji/plugin/trackmate/detection/LogDetectorFactory.java index cadfd6643..1c0da0bde 100644 --- a/src/main/java/fiji/plugin/trackmate/detection/LogDetectorFactory.java +++ b/src/main/java/fiji/plugin/trackmate/detection/LogDetectorFactory.java @@ -28,13 +28,6 @@ import javax.swing.ImageIcon; -import net.imagej.ImgPlus; -import net.imglib2.Interval; -import net.imglib2.RandomAccessible; -import net.imglib2.type.NativeType; -import net.imglib2.type.numeric.RealType; -import net.imglib2.view.Views; - import org.jdom2.Element; import org.scijava.plugin.Plugin; @@ -43,6 +36,13 @@ import fiji.plugin.trackmate.gui.ConfigurationPanel; import fiji.plugin.trackmate.gui.panels.detector.LogDetectorConfigurationPanel; import fiji.plugin.trackmate.util.TMUtils; +import net.imagej.ImgPlus; +import net.imagej.axis.Axes; +import net.imglib2.Interval; +import net.imglib2.RandomAccessible; +import net.imglib2.type.NativeType; +import net.imglib2.type.numeric.RealType; +import net.imglib2.view.Views; @Plugin( type = SpotDetectorFactory.class ) public class LogDetectorFactory< T extends RealType< T > & NativeType< T >> implements SpotDetectorFactory< T > @@ -89,7 +89,7 @@ protected RandomAccessible< T > prepareFrameImg( final int frame ) { final double[] calibration = TMUtils.getSpatialCalibration( img ); RandomAccessible< T > imFrame; - final int cDim = TMUtils.findCAxisIndex( img ); + final int cDim = img.dimensionIndex( Axes.CHANNEL ); if ( cDim < 0 ) { imFrame = img; @@ -101,13 +101,12 @@ protected RandomAccessible< T > prepareFrameImg( final int frame ) imFrame = Views.hyperSlice( img, cDim, channel ); } - int timeDim = TMUtils.findTAxisIndex( img ); + int timeDim = img.dimensionIndex( Axes.TIME ); if ( timeDim >= 0 ) { if ( cDim >= 0 && timeDim > cDim ) - { timeDim--; - } + imFrame = Views.hyperSlice( imFrame, timeDim, frame ); } diff --git a/src/main/java/fiji/plugin/trackmate/detection/semiauto/SemiAutoTracker.java b/src/main/java/fiji/plugin/trackmate/detection/semiauto/SemiAutoTracker.java index 7f42c759c..543922a7a 100644 --- a/src/main/java/fiji/plugin/trackmate/detection/semiauto/SemiAutoTracker.java +++ b/src/main/java/fiji/plugin/trackmate/detection/semiauto/SemiAutoTracker.java @@ -7,6 +7,7 @@ import fiji.plugin.trackmate.util.TMUtils; import ij.ImagePlus; import net.imagej.ImgPlus; +import net.imagej.axis.Axes; import net.imglib2.FinalInterval; import net.imglib2.RandomAccessible; import net.imglib2.realtransform.AffineTransform3D; @@ -49,8 +50,8 @@ protected SearchRegion< T > getNeighborhood( final Spot spot, final int frame ) * Source, rai and transform */ - final int tindex = TMUtils.findTAxisIndex( img ); - final int cindex = TMUtils.findCAxisIndex( img ); + final int tindex = img.dimensionIndex( Axes.TIME ); + final int cindex = img.dimensionIndex( Axes.CHANNEL ); if ( frame >= img.dimension( tindex ) ) { logger.log( "Spot: " + spot + ": No more time-points.\n" ); @@ -105,7 +106,7 @@ protected SearchRegion< T > getNeighborhood( final Spot spot, final int frame ) long[] min; long[] max; - if ( img.dimension( TMUtils.findZAxisIndex( img ) ) > 1 ) + if ( img.dimension( img.dimensionIndex( Axes.Z ) ) > 1 ) { // 3D min = new long[] { x0, y0, z0 };