From efc10f4b02d2b22c71b49bd088111feb1449bb9c Mon Sep 17 00:00:00 2001
From: tpietzsch <tobias.pietzsch@gmail.com>
Date: Fri, 5 Apr 2024 21:45:09 +0200
Subject: [PATCH 1/4] POM: Bump parent to pom-scijava-38.0.1

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 16dfbeb1..c2908c8a 100644
--- 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>
 

From 40c94ff9e921a5d3b6430dbc965b5e15e005e200 Mon Sep 17 00:00:00 2001
From: tpietzsch <tobias.pietzsch@gmail.com>
Date: Wed, 28 Aug 2024 12:30:22 +0200
Subject: [PATCH 2/4] POM: Bump dependency versions

        imglib2 -> 7.1.0
        imglib2-realtransform -> 4.0.3
        imglib2-roi -> 0.15.0
        imglib2-cache -> 1.0.0-beta-18
        imglib2-algorithm -> 0.15.3
        bigdataviewer-core -> 10.6.0
---
 pom.xml | 21 ++++++---------------
 1 file changed, 6 insertions(+), 15 deletions(-)

diff --git a/pom.xml b/pom.xml
index c2908c8a..5f8c1fc5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -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>

From 548ed74b4e0bc1017d82fca8be6806349f972866 Mon Sep 17 00:00:00 2001
From: tpietzsch <tobias.pietzsch@gmail.com>
Date: Fri, 5 Apr 2024 21:46:07 +0200
Subject: [PATCH 3/4] Adapt API changes introduced by imglib/imglib2-roi#71

---
 .../labkit/pixel_classification/classification/Trainer.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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
index fefaaa70..1b5b3f67 100644
--- 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);

From 6c1acf88cf82a35edc2f8bc66a7f74aa5bdedf2d Mon Sep 17 00:00:00 2001
From: tpietzsch <tobias.pietzsch@gmail.com>
Date: Fri, 5 Apr 2024 21:46:30 +0200
Subject: [PATCH 4/4] Add missing getType() implementations

---
 .../neighborhood/NeighborhoodRandomAccessible.java          | 6 ++++++
 .../labkit/pixel_classification/utils/views/SimpleRAI.java  | 6 ++++++
 2 files changed, 12 insertions(+)

diff --git a/src/main/java/preview/net/imglib2/algorithm/neighborhood/NeighborhoodRandomAccessible.java b/src/main/java/preview/net/imglib2/algorithm/neighborhood/NeighborhoodRandomAccessible.java
index 6fcdcea9..f0ca390a 100644
--- 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/utils/views/SimpleRAI.java b/src/main/java/sc/fiji/labkit/pixel_classification/utils/views/SimpleRAI.java
index 5eff77ed..5cc46493 100644
--- 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();
+	}
 }