Don't use methods removed in TMUtils to find an axis.

trackmate-sc · Jan 17, 2021 · a3659d8 · a3659d8
1 parent 95fd4de
commit a3659d8
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Showing 2 changed files with 14 additions and 14 deletions.
diff --git 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
@@ -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 };