WIP: Update to ImgLib2 v7

Depends on upgrade of imagej-common. * Add missing getType() implementations * Follow API changes from imglib/imglib2-roi#71 Signed-off-by: Curtis Rueden <[email protected]>
imagej · Jun 11, 2024 · ccb600e · ccb600e
1 parent d9d1528
commit ccb600e
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Showing 4 changed files with 16 additions and 3 deletions.
diff --git a/pom.xml b/pom.xml
@@ -256,6 +256,13 @@
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
+		<imglib2.version>7.0.3</imglib2.version>
+		<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
+		<imglib2-roi.version>0.15.0</imglib2-roi.version>
+		<imglib2-algorithm.version>0.15.3</imglib2-algorithm.version>
+		<imagej-common.version>2.1.1-SNAPSHOT</imagej-common.version>
+		<enforcer.skip>true</enforcer.skip>
+
 		<scijava-common.version>2.98.0</scijava-common.version>
 	</properties>
 

diff --git a/src/main/java/net/imagej/ops/coloc/ShuffledView.java b/src/main/java/net/imagej/ops/coloc/ShuffledView.java
@@ -134,6 +134,12 @@ public RandomAccess<T> randomAccess(final Interval interval) {
 		return randomAccess(); // FIXME
 	}
 
+	@Override
+	public T getType()
+	{
+		return image.getType();
+	}
+
 	private class ShuffledRandomAccess extends Point implements RandomAccess<T> {
 		private final RandomAccess<T> imageRA;
 		private final long[] blockPos;

diff --git a/src/main/java/net/imagej/ops/geom/geom3d/DefaultInertiaTensor3D.java b/src/main/java/net/imagej/ops/geom/geom3d/DefaultInertiaTensor3D.java
@@ -66,7 +66,7 @@ public void initialize() {
 	@Override
 	public RealMatrix calculate(final IterableRegion<B> input) {
 		final BlockRealMatrix output = new BlockRealMatrix(3, 3);
-		Cursor<Void> c = input.localizingCursor();
+		Cursor<Void> c = input.inside().localizingCursor();
 		double[] pos = new double[3];
 		double[] computedCentroid = new double[3];
 		centroid.calculate(input).localize(computedCentroid);
@@ -87,7 +87,7 @@ public RealMatrix calculate(final IterableRegion<B> input) {
 			output.setEntry(2, 1, output.getEntry(1, 2));
 		}
 
-		final double size = input.size();
+		final double size = input.inside().size();
 		output.setEntry(0, 0, output.getEntry(0, 0) / size);
 		output.setEntry(0, 1, output.getEntry(0, 1) / size);
 		output.setEntry(0, 2, output.getEntry(0, 2) / size);

diff --git a/src/main/java/net/imagej/ops/image/watershed/Watershed.java b/src/main/java/net/imagej/ops/image/watershed/Watershed.java
@@ -137,7 +137,7 @@ public void compute(final RandomAccessibleInterval<T> in, final ImgLabeling<Inte
 		final List<Long> imiList = new ArrayList<>();
 
 		if (mask != null) {
-			final Cursor<Void> c = Regions.iterable(mask).localizingCursor();
+			final Cursor<Void> c = Regions.iterable(mask).inside().localizingCursor();
 			while (c.hasNext()) {
 				c.next();
 				imiList.add(IntervalIndexer.positionToIndex(c, in));