Merge pull request #12 update to imglib2 version 7.1

Merge pull request #12 from juglab/feature-rai-getType Addition of getType() API
juglab · Aug 29, 2024 · cf91e26 · cf91e26
2 parents 3301cdb + 6c1acf8
commit cf91e26
Show file tree

Hide file tree

Showing 4 changed files with 20 additions and 17 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>34.1.0</version>
+		<version>38.0.1</version>
 		<relativePath />
 	</parent>
 
@@ -91,16 +91,12 @@
 		<fastRandomForest.version>r49</fastRandomForest.version>
 		<imagescience.version>3.0.0</imagescience.version>
 
-		<bigdataviewer-core.version>10.4.6</bigdataviewer-core.version>
-		<imagej-deprecated.version>0.2.0</imagej-deprecated.version>
-		<imagej-ops.version>2.0.0</imagej-ops.version>
-		<imglib2.version>6.1.0</imglib2.version>
-		<imglib2-algorithm.version>0.13.2</imglib2-algorithm.version>
-		<imglib2-algorithm-gpl.version>0.3.1</imglib2-algorithm-gpl.version>
-		<imglib2-cache.version>1.0.0-beta-17</imglib2-cache.version>
-		<imglib2-realtransform.version>4.0.1</imglib2-realtransform.version>
-		<imglib2-roi.version>0.14.0</imglib2-roi.version>
-		<scifio.version>0.45.0</scifio.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>
+		<bigdataviewer-core.version>10.6.0</bigdataviewer-core.version>
 	</properties>
 
 	<repositories>
@@ -283,11 +279,6 @@
 			<artifactId>imagej</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>sc.fiji</groupId>
-			<artifactId>bigdataviewer-vistools</artifactId>
-			<scope>test</scope>
-		</dependency>
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>

diff --git a/src/main/java/preview/net/imglib2/algorithm/neighborhood/NeighborhoodRandomAccessible.java b/src/main/java/preview/net/imglib2/algorithm/neighborhood/NeighborhoodRandomAccessible.java
@@ -60,4 +60,10 @@ public RandomAccess<Neighborhood<T>> randomAccess() {
 	public RandomAccess<Neighborhood<T>> randomAccess(final Interval interval) {
 		return new NeighborhoodRandomAccess<T>(source, factory, interval);
 	}
+
+	@Override
+	public Neighborhood< T > getType()
+	{
+		return randomAccess().getType();
+	}
 }
diff --git a/src/main/java/sc/fiji/labkit/pixel_classification/classification/Trainer.java b/src/main/java/sc/fiji/labkit/pixel_classification/classification/Trainer.java
@@ -109,7 +109,7 @@ public <L> void trainLabeledFeatures(
 			if (label == null)
 				continue;
 			LabelRegion<L> region = regions.getLabelRegion(label);
-			Cursor<Void> cursor = region.cursor();
+			Cursor<Void> cursor = region.inside().cursor();
 			while (cursor.hasNext()) {
 				cursor.next();
 				ra.setPosition(cursor);

diff --git a/src/main/java/sc/fiji/labkit/pixel_classification/utils/views/SimpleRAI.java b/src/main/java/sc/fiji/labkit/pixel_classification/utils/views/SimpleRAI.java
@@ -67,4 +67,10 @@ public RandomAccess<T> randomAccess(Interval interval) {
 	public int numDimensions() {
 		return blueprint.numDimensions();
 	}
+
+	@Override
+	public T getType()
+	{
+		return blueprint.getType();
+	}
 }