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Fix error wrt changed API in imglib #289

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merged 4 commits into from
Aug 29, 2024
Merged

Fix error wrt changed API in imglib #289

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61f65e8
POM: Bump parent to pom-scijava-38.0.1
tpietzsch Apr 5, 2024
a503933
POM: Bump dependency versions
tpietzsch Aug 28, 2024
5e0af52
Addapt API changes introduced by https://github.com/imglib/imglib2-ro…
tpietzsch Apr 5, 2024
514d5db
Adapt API changes introduced by https://github.com/imglib/imglib2/pul…
tpietzsch Apr 5, 2024
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11 changes: 9 additions & 2 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>

Expand Down Expand Up @@ -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>
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5 changes: 3 additions & 2 deletions src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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() )
Expand Down Expand Up @@ -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;
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6 changes: 4 additions & 2 deletions src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java
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Expand Up @@ -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 > >
{

Expand Down Expand Up @@ -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 );

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