Update code to ImgLib2 7.x

ctrueden · ctrueden · commit 39c0fe7f84e6 · 2024-05-07T20:17:06.000-05:00
And fix backwards incompatibilities due to the new getType() method.
diff --git a/scijava-ops-image/pom.xml b/scijava-ops-image/pom.xml
@@ -264,6 +264,11 @@
 
 		<license.licenseName>bsd_2</license.licenseName>
 		<license.copyrightOwners>SciJava developers.</license.copyrightOwners>
+
+		<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>
 
 	<repositories>
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 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.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 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));
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
@@ -207,7 +207,7 @@ public void compute( //
 		// Only iterate seeds that are not excluded by the mask
 		final IterableRegion<B> maskRegions = Regions.iterable(mask);
 		final IterableInterval<LabelingType<Integer>> seedsMasked = Regions.sample(
-			(IterableInterval<Void>) maskRegions, seeds);
+			maskRegions.inside(), seeds);
 		final Cursor<LabelingType<Integer>> cursorSeeds = seedsMasked
 			.localizingCursor();
 
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
@@ -87,8 +87,8 @@ public ImgLabeling<L, I> apply( //
 			.iterable(input1.getSource()).firstElement());
 		if (mask != null) {
 			final IterableRegion iterable = Regions.iterable(mask);
-			final IterableInterval<LabelingType<L>> sample = Regions.sample(
-				(IterableInterval<Void>) iterable, output);
+			final IterableInterval<LabelingType<L>> sample = //
+				Regions.sample(iterable.inside(), output);
 			final RandomAccess<LabelingType<L>> randomAccess = input1.randomAccess();
 			final RandomAccess<LabelingType<L>> randomAccess2 = input2.randomAccess();
 			final Cursor<LabelingType<L>> 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
`@@ -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`	`}`