From 12dcb90d38786f17c72d330003372ab81d1fa8ff Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <jean-yves.tinevez@pasteur.fr>
Date: Tue, 23 Jul 2024 11:41:37 +0200
Subject: [PATCH] Add the smoothing scale param to the 2D labeling methods as
 well.

Not implemented yet, but at least symmetric with the 2D case.
---
 .../plugin/trackmate/detection/SpotRoiUtils.java | 16 ++++++++++++++--
 .../trackmate/gui/editor/LabkitImporter.java     |  1 +
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/main/java/fiji/plugin/trackmate/detection/SpotRoiUtils.java b/src/main/java/fiji/plugin/trackmate/detection/SpotRoiUtils.java
index 0a4ba51f2..5e3078861 100644
--- a/src/main/java/fiji/plugin/trackmate/detection/SpotRoiUtils.java
+++ b/src/main/java/fiji/plugin/trackmate/detection/SpotRoiUtils.java
@@ -121,7 +121,13 @@ public static < R extends IntegerType< R >, S extends RealType< S > > List< Spot
 			final double smoothingScale,
 			final RandomAccessibleInterval< S > qualityImage )
 	{
-		final Map< Integer, List< Spot > > map = from2DLabelingWithROIMap( labeling, origin, calibration, simplify, qualityImage );
+		final Map< Integer, List< Spot > > map = from2DLabelingWithROIMap(
+				labeling,
+				origin,
+				calibration,
+				simplify,
+				smoothingScale,
+				qualityImage );
 		final List< Spot > spots = new ArrayList<>();
 		for ( final List< Spot > s : map.values() )
 			spots.addAll( s );
@@ -144,7 +150,7 @@ public static < R extends IntegerType< R >, S extends RealType< S > > List< Spot
 	 * @param <S>
 	 *            the type of the quality image. Must be real, scalar.
 	 * @param labeling
-	 *            the labeling, must be zero-min and 2D..
+	 *            the labeling, must be zero-min and 2D.
 	 * @param origin
 	 *            the origin (min pos) of the interval the labeling was
 	 *            generated from, used to reposition the spots from the zero-min
@@ -154,6 +160,11 @@ public static < R extends IntegerType< R >, S extends RealType< S > > List< Spot
 	 * @param simplify
 	 *            if <code>true</code> the polygon will be post-processed to be
 	 *            smoother and contain less points.
+	 * @param smoothingScale
+	 *            if strictly larger than 0, the mask will be smoothed before
+	 *            creating the mesh, resulting in smoother meshes. The scale
+	 *            value sets the (Gaussian) filter radius and is specified in
+	 *            physical units. If 0 or lower than 0, no smoothing is applied.
 	 * @param qualityImage
 	 *            the image in which to read the quality value.
 	 * @return a map linking the label integer value to the list of spots, with
@@ -164,6 +175,7 @@ public static < R extends IntegerType< R >, S extends RealType< S > > Map< Integ
 			final double[] origin,
 			final double[] calibration,
 			final boolean simplify,
+			final double smoothingScale,
 			final RandomAccessibleInterval< S > qualityImage )
 	{
 		if ( labeling.numDimensions() != 2 )
diff --git a/src/main/java/fiji/plugin/trackmate/gui/editor/LabkitImporter.java b/src/main/java/fiji/plugin/trackmate/gui/editor/LabkitImporter.java
index 95bb352dd..2cc4b82d2 100644
--- a/src/main/java/fiji/plugin/trackmate/gui/editor/LabkitImporter.java
+++ b/src/main/java/fiji/plugin/trackmate/gui/editor/LabkitImporter.java
@@ -305,6 +305,7 @@ private Map< Integer, List< Spot > > getSpots( final RandomAccessibleInterval< T
 					new double[] { 0., 0. },
 					calibration,
 					simplify,
+					smoothingScale,
 					rai );
 	}