Update code to ImgLib2 7.x

ctrueden · gselzer · commit 5f588b3b0ff5 · 2025-01-15T15:39:05.000-06:00
And fix backwards incompatibilities due to the new getType() method.
diff --git a/scijava-ops-image/pom.xml b/scijava-ops-image/pom.xml
@@ -266,6 +266,11 @@
 		<scijava-maven-plugin.version>3.0.0</scijava-maven-plugin.version>
 		<imglib2-mesh.version>1.0.0</imglib2-mesh.version>
 		<net.imglib2.imglib2-mesh.version>${imglib2-mesh.version}</net.imglib2.imglib2-mesh.version>
+
+		<imglib2.version>7.0.1</imglib2.version>
+		<imglib2-roi.version>0.15.0</imglib2-roi.version>
+		<imglib2-algorithm.version>0.15.1</imglib2-algorithm.version>
+		<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
 	</properties>
 
 	<dependencies>
diff --git a/scijava-ops-image/src/main/java/org/scijava/ops/image/coloc/ShuffledView.java b/scijava-ops-image/src/main/java/org/scijava/ops/image/coloc/ShuffledView.java
@@ -125,6 +125,11 @@ public void shuffleBlocks(long seed) {
 		shuffleBlocks();
 	}
 
+	@Override
+	public T getType() {
+		return image.getType();
+	}
+
 	@Override
 	public RandomAccess<T> randomAccess() {
 		return new ShuffledRandomAccess();
diff --git a/scijava-ops-image/src/main/java/org/scijava/ops/image/geom/geom3d/DefaultInertiaTensor3D.java b/scijava-ops-image/src/main/java/org/scijava/ops/image/geom/geom3d/DefaultInertiaTensor3D.java
@@ -68,7 +68,7 @@ public RealMatrix apply(final IterableRegion<B> input) {
 			"Only three-dimensional inputs allowed!");
 
 		final var output = new BlockRealMatrix(3, 3);
-        var c = input.localizingCursor();
+        var c = input.inside().localizingCursor();
         var pos = new double[3];
         var computedCentroid = new double[3];
 		centroid.apply(input).localize(computedCentroid);
@@ -95,7 +95,7 @@ public RealMatrix apply(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/scijava-ops-image/src/main/java/org/scijava/ops/image/image/watershed/Watershed.java b/scijava-ops-image/src/main/java/org/scijava/ops/image/image/watershed/Watershed.java
@@ -138,7 +138,7 @@ public void compute(final RandomAccessibleInterval<T> in, //
 		final List<Long> imiList = new ArrayList<>();
 
 		if (mask != null) {
-			final var c = Regions.iterable(mask).localizingCursor();
+			final var c = Regions.iterable(mask).inside().localizingCursor();
 			while (c.hasNext()) {
 				c.next();
 				imiList.add(IntervalIndexer.positionToIndex(c, in));
diff --git a/scijava-ops-image/src/main/java/org/scijava/ops/image/image/watershed/WatershedSeeded.java b/scijava-ops-image/src/main/java/org/scijava/ops/image/image/watershed/WatershedSeeded.java
@@ -206,8 +206,7 @@ public void compute( //
 
 		// Only iterate seeds that are not excluded by the mask
 		final var maskRegions = Regions.iterable(mask);
-		final var seedsMasked = Regions.sample(
-			(IterableInterval<Void>) maskRegions, seeds);
+		final var seedsMasked = Regions.sample(maskRegions.inside(), seeds);
 		final var cursorSeeds = seedsMasked
 			.localizingCursor();
 
diff --git a/scijava-ops-image/src/main/java/org/scijava/ops/image/imagemoments/AbstractImageMomentOp.java b/scijava-ops-image/src/main/java/org/scijava/ops/image/imagemoments/AbstractImageMomentOp.java
@@ -46,7 +46,7 @@ public interface AbstractImageMomentOp<I extends RealType<I>, O extends RealType
 	extends Computers.Arity1<RandomAccessibleInterval<I>, O>
 {
 
-	public void computeMoment(RandomAccessibleInterval<I> input, O output);
+	void computeMoment(RandomAccessibleInterval<I> input, O output);
 
 	/**
 	 * TODO
diff --git a/scijava-ops-image/src/main/java/org/scijava/ops/image/labeling/MergeLabeling.java b/scijava-ops-image/src/main/java/org/scijava/ops/image/labeling/MergeLabeling.java
@@ -32,18 +32,14 @@
 import java.util.function.BiFunction;
 import java.util.function.Function;
 
-import net.imglib2.Cursor;
 import net.imglib2.Dimensions;
-import net.imglib2.IterableInterval;
-import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.roi.IterableRegion;
 import net.imglib2.roi.Regions;
 import net.imglib2.roi.labeling.ImgLabeling;
 import net.imglib2.roi.labeling.LabelingType;
 import net.imglib2.type.BooleanType;
 import net.imglib2.type.numeric.IntegerType;
-import net.imglib2.view.Views;
 
 import org.scijava.function.Computers;
 import org.scijava.function.Functions;
@@ -72,24 +68,21 @@ public class MergeLabeling<L, I extends IntegerType<I>, B extends BooleanType<B>
 	 * TODO
 	 *
 	 * @param input1
-	 * @param input1
+	 * @param input2
 	 * @param mask
 	 * @return an {@link ImgLabeling} that combines the labels of {@code input1}
 	 *         and {@code input2}
 	 */
 	@Override
-	@SuppressWarnings({ "unchecked", "rawtypes", "hiding" })
 	public ImgLabeling<L, I> apply( //
 		final ImgLabeling<L, I> input1, //
 		final ImgLabeling<L, I> input2, //
 		@Nullable final RandomAccessibleInterval<B> mask //
 	) {
-		final var output = imgLabelingCreator.apply(input1, Views
-			.iterable(input1.getSource()).firstElement());
+		final var output = imgLabelingCreator.apply(input1, input1.getSource().firstElement());
 		if (mask != null) {
-			final IterableRegion iterable = Regions.iterable(mask);
-			final var sample = Regions.sample(
-				(IterableInterval<Void>) iterable, output);
+			final IterableRegion<B> iterable = Regions.iterable(mask);
+			final var sample = Regions.sample(iterable.inside(), output);
 			final var randomAccess = input1.randomAccess();
 			final var randomAccess2 = input2.randomAccess();
 			final var cursor = sample.cursor();
diff --git a/scijava-ops-image/src/test/java/org/scijava/ops/image/image/watershed/WatershedSeededTest.java b/scijava-ops-image/src/test/java/org/scijava/ops/image/image/watershed/WatershedSeededTest.java
@@ -219,7 +219,7 @@ private void assertResults(final RandomAccessibleInterval<FloatType> in,
 		// count labels
 		Set<Integer> labelSet = new HashSet<>();
 		for (LabelingType<Integer> pixel : Regions.sample(
-			(IterableInterval<Void>) regions, out))
+			regions.inside(), out))
 		{
 			labelSet.addAll(pixel);
 		}
diff --git a/scijava-ops-image/src/test/java/org/scijava/ops/image/image/watershed/WatershedTest.java b/scijava-ops-image/src/test/java/org/scijava/ops/image/image/watershed/WatershedTest.java
@@ -220,7 +220,7 @@ private void assertResults(final RandomAccessibleInterval<FloatType> in,
 		// count labels
 		Set<Integer> labelSet = new HashSet<>();
 		for (LabelingType<Integer> pixel : Regions.sample(
-			(IterableInterval<Void>) regions, out))
+			regions.inside(), out))
 		{
 			labelSet.addAll(pixel);
 		}

Original file line number	Diff line number	Diff line change
`@@ -46,7 +46,7 @@ public interface AbstractImageMomentOp<I extends RealType<I>, O extends RealType`
`46`	`46`	`extends Computers.Arity1<RandomAccessibleInterval<I>, O>`
`47`	`47`	`{`
`48`	`48`
`49`		`- public void computeMoment(RandomAccessibleInterval<I> input, O output);`
	`49`	`+ void computeMoment(RandomAccessibleInterval<I> input, O output);`
`50`	`50`
`51`	`51`	`/**`
`52`	`52`	`* TODO`
Original file line number	Diff line number	Diff line change
`@@ -219,7 +219,7 @@ private void assertResults(final RandomAccessibleInterval<FloatType> in,`
`219`	`219`	`// count labels`
`220`	`220`	`Set<Integer> labelSet = new HashSet<>();`
`221`	`221`	`for (LabelingType<Integer> pixel : Regions.sample(`
`222`		`- (IterableInterval<Void>) regions, out))`
	`222`	`+ regions.inside(), out))`
`223`	`223`	`{`
`224`	`224`	`labelSet.addAll(pixel);`
`225`	`225`	`}`
Original file line number	Diff line number	Diff line change
`@@ -220,7 +220,7 @@ private void assertResults(final RandomAccessibleInterval<FloatType> in,`
`220`	`220`	`// count labels`
`221`	`221`	`Set<Integer> labelSet = new HashSet<>();`
`222`	`222`	`for (LabelingType<Integer> pixel : Regions.sample(`
`223`		`- (IterableInterval<Void>) regions, out))`
	`223`	`+ regions.inside(), out))`
`224`	`224`	`{`
`225`	`225`	`labelSet.addAll(pixel);`
`226`	`226`	`}`