Merge pull request #280 from scijava/scijava-ops-image/feature-rai-getType

gselzer · web-flow · commit 943971ee1939 · 2025-01-16T08:56:26.000-06:00
Scijava ops image/feature rai get type
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>0.15.2</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/coloc/pValue/DefaultPValue.java b/scijava-ops-image/src/main/java/org/scijava/ops/image/coloc/pValue/DefaultPValue.java
@@ -29,7 +29,6 @@
 
 package org.scijava.ops.image.coloc.pValue;
 
-import java.util.List;
 import java.util.Random;
 import java.util.function.BiFunction;
 import java.util.function.Consumer;
@@ -39,12 +38,9 @@
 import org.scijava.concurrent.Parallelization;
 import org.scijava.function.Computers;
 import org.scijava.ops.spi.Nullable;
-import org.scijava.ops.spi.OpDependency;
 
 import org.scijava.ops.image.coloc.ShuffledView;
-import net.imglib2.Cursor;
 import net.imglib2.Dimensions;
-import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
 import net.imglib2.type.numeric.RealType;
@@ -63,7 +59,7 @@
  */
 public class DefaultPValue<T extends RealType<T>, U extends RealType<U>>
 	implements
-	Computers.Arity6<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, Dimensions, Long, PValueResult>
+	Computers.Arity6<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<? super RandomAccessibleInterval<T>, ? super RandomAccessibleInterval<U>, Double>, Integer, Dimensions, Long, PValueResult>
 {
 
 	/**
@@ -81,7 +77,7 @@ public class DefaultPValue<T extends RealType<T>, U extends RealType<U>>
 	public void compute( //
 		final RandomAccessibleInterval<T> image1, //
 		final RandomAccessibleInterval<U> image2, //
-		final BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double> op, //
+		final BiFunction<? super RandomAccessibleInterval<T>, ? super RandomAccessibleInterval<U>, Double> op, //
 		@Nullable Integer nrRandomizations, //
 		@Nullable Dimensions psfSize, //
 		@Nullable Long seed, //
diff --git a/scijava-ops-image/src/main/java/org/scijava/ops/image/create/Creators.java b/scijava-ops-image/src/main/java/org/scijava/ops/image/create/Creators.java
@@ -207,14 +207,6 @@ public class Creators<N extends NativeType<N>, L, I extends IntegerType<I>, T ex
 			type);
 	};
 
-	/**
-	 * @input rai
-	 * @output img
-	 * @implNote op names='create.img, engine.create', priority='0.'
-	 */
-	public final Function<RandomAccessibleInterval<T>, Img<T>> imgFromRAI = (
-		rai) -> imgFromDimsAndType.apply(rai, Util.getTypeFromInterval(rai));
-
 	/**
 	 * @input arrayImg
 	 * @output img
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/OpRegressionTest.java b/scijava-ops-image/src/test/java/org/scijava/ops/image/OpRegressionTest.java
@@ -42,7 +42,7 @@ public class OpRegressionTest {
 
 	@Test
 	public void testOpDiscoveryRegression() {
-		long expected = 1941;
+		long expected = 1940;
 		long actual = ops.infos().size();
 		assertEquals(expected, actual);
 	}
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
`@@ -42,7 +42,7 @@ public class OpRegressionTest {`
`42`	`42`
`43`	`43`	`@Test`
`44`	`44`	`public void testOpDiscoveryRegression() {`
`45`		`- long expected = 1941;`
	`45`	`+ long expected = 1940;`
`46`	`46`	`long actual = ops.infos().size();`
`47`	`47`	`assertEquals(expected, actual);`
`48`	`48`	`}`