Merge pull request #289 from tpietzsch/feature-rai-getType

Fix error wrt changed API in imglib
trackmate-sc · Aug 29, 2024 · f6e86e5 · f6e86e5
2 parents a3e9a7b + 514d5db
commit f6e86e5
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Showing 3 changed files with 16 additions and 6 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>org.scijava</groupId>
  <artifactId>pom-scijava</artifactId>
- <version>37.0.0</version>
+ <version>38.0.1</version>
  <relativePath />
  </parent>
 
@@ -147,7 +147,14 @@
 
  <fontchooser.version>2.5.2</fontchooser.version>
  <javaGeom.version>0.11.1</javaGeom.version>
- <imglib2.version>6.1.0</imglib2.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>

diff --git a/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java b/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java
@@ -33,6 +33,7 @@
 import ij.gui.PolygonRoi;
 import ij.measure.Measurements;
 import ij.process.FloatPolygon;
+import net.imglib2.Cursor;
 import net.imglib2.Interval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
@@ -280,7 +281,7 @@ public static < R extends IntegerType< R > > List< Spot > fromLabeling(
  while ( iterator.hasNext() )
  {
  final LabelRegion< Integer > region = iterator.next();
- final LabelRegionCursor cursor = region.localizingCursor();
+ final Cursor< Void > cursor = region.inside().localizingCursor();
  final int[] cursorPos = new int[ labeling.numDimensions() ];
  final long[] sum = new long[ 3 ];
  while ( cursor.hasNext() )
@@ -358,7 +359,7 @@ public static < T extends RealType< T >, R extends RealType< R > > List< Spot >
  while ( iterator.hasNext() )
  {
  final LabelRegion< Integer > region = iterator.next();
- final LabelRegionCursor cursor = region.localizingCursor();
+ final Cursor< Void > cursor = region.inside().localizingCursor();
  final int[] cursorPos = new int[ labeling.numDimensions() ];
  final long[] sum = new long[ 3 ];
  double quality = Double.NEGATIVE_INFINITY;

diff --git a/src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java b/src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java
@@ -28,6 +28,8 @@
 import net.imglib2.Sampler;
 import net.imglib2.neighborsearch.NearestNeighborSearch;
 
+
+// TODO: revise for new KDTree implementation, where KDTreeNode are reusable proxies.
 public class NearestNeighborFlagSearchOnKDTree< T > implements NearestNeighborSearch< FlagNode< T > >
 {
 
@@ -78,8 +80,8 @@ protected void searchNode( final KDTreeNode< FlagNode< T > > current )
  final boolean leftIsNearBranch = axisDiff < 0;
 
  // search the near branch
- final KDTreeNode< FlagNode< T > > nearChild = leftIsNearBranch ? current.left : current.right;
- final KDTreeNode< FlagNode< T > > awayChild = leftIsNearBranch ? current.right : current.left;
+ final KDTreeNode< FlagNode< T > > nearChild = leftIsNearBranch ? current.left() : current.right();
+ final KDTreeNode< FlagNode< T > > awayChild = leftIsNearBranch ? current.right() : current.left();
  if ( nearChild != null )
  searchNode( nearChild );