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Merged
gselzer merged 3 commits into from
Jan 16, 2025
Merged

Scijava ops image/feature rai get type #280

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5f588b3
Update code to ImgLib2 7.x
ctrueden Apr 2, 2024
45b98ea
Remove conflicting create Op for imglib 7
elevans Jan 14, 2025
83054c6
Get the remaining tests working
gselzer Jan 15, 2025
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5 changes: 5 additions & 0 deletions scijava-ops-image/pom.xml
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Expand Up @@ -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>
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5 changes: 5 additions & 0 deletions scijava-ops-image/src/main/java/org/scijava/ops/image/coloc/ShuffledView.java
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Expand Up @@ -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();
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8 changes: 2 additions & 6 deletions scijava-ops-image/src/main/java/org/scijava/ops/image/coloc/pValue/DefaultPValue.java
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Expand Up @@ -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;
Expand All @@ -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;
Expand All @@ -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>
{

/**
Expand All @@ -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, //
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8 changes: 0 additions & 8 deletions scijava-ops-image/src/main/java/org/scijava/ops/image/create/Creators.java
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions ...ava-ops-image/src/main/java/org/scijava/ops/image/geom/geom3d/DefaultInertiaTensor3D.java
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Expand Up @@ -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);
Expand All @@ -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);
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2 changes: 1 addition & 1 deletion scijava-ops-image/src/main/java/org/scijava/ops/image/image/watershed/Watershed.java
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Expand Up @@ -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));
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3 changes: 1 addition & 2 deletions scijava-ops-image/src/main/java/org/scijava/ops/image/image/watershed/WatershedSeeded.java
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Expand Up @@ -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();

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2 changes: 1 addition & 1 deletion ...ava-ops-image/src/main/java/org/scijava/ops/image/imagemoments/AbstractImageMomentOp.java
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Expand Up @@ -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
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15 changes: 4 additions & 11 deletions scijava-ops-image/src/main/java/org/scijava/ops/image/labeling/MergeLabeling.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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();
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2 changes: 1 addition & 1 deletion scijava-ops-image/src/test/java/org/scijava/ops/image/OpRegressionTest.java
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Expand Up @@ -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);
}
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2 changes: 1 addition & 1 deletion ...va-ops-image/src/test/java/org/scijava/ops/image/image/watershed/WatershedSeededTest.java
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Expand Up @@ -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);
}
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2 changes: 1 addition & 1 deletion scijava-ops-image/src/test/java/org/scijava/ops/image/image/watershed/WatershedTest.java
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Expand Up @@ -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);
}
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