A utility that returns an iterable over a spot in an ImgPlus.

Takes into account whether the spot has a ROI or not, and
borderline cases.

src/main/java/fiji/plugin/trackmate/util/SpotUtil.java

@@ -0,0 +1,53 @@
+package fiji.plugin.trackmate.util;
+
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.SpotRoi;
+import fiji.plugin.trackmate.detection.DetectionUtils;
+import net.imagej.ImgPlus;
+import net.imglib2.FinalInterval;
+import net.imglib2.Interval;
+import net.imglib2.IterableInterval;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.view.Views;
+
+public class SpotUtil
+{
+
+	public static final < T extends RealType< T > > IterableInterval< T > iterable( final Spot spot, final ImgPlus< T > img )
+	{
+		// Prepare neighborhood
+		final IterableInterval< T > neighborhood;
+		final SpotRoi roi = spot.getRoi();
+		if ( null != roi && DetectionUtils.is2D( img ) )
+		{
+			// Operate on ROI only if we have one and the image is 2D.
+			neighborhood = roi.sample( spot, img );
+		}
+		else
+		{
+			// Otherwise default to circle / sphere.
+			neighborhood = new SpotNeighborhood<>( spot, img );
+		}
+
+		final int npixels = ( int ) neighborhood.size();
+		if ( npixels <= 1 )
+		{
+			final double[] calibration = TMUtils.getSpatialCalibration( img );
+			final long[] min = new long[ img.numDimensions() ];
+			final long[] max = new long[ img.numDimensions() ];
+			for ( int d = 0; d < min.length; d++ )
+			{
+				final long center = Math.round( spot.getFeature( Spot.POSITION_FEATURES[ d ] ).doubleValue() / calibration[ d ] );
+				min[ d ] = center;
+				max[ d ] = center + 1;
+			}
+
+			final Interval interval = new FinalInterval( min, max );
+			return Views.interval( img, interval );
+		}
+		else
+		{
+			return neighborhood;
+		}
+	}
+}