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Addition of getType() API #654

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merged 5 commits into from
Aug 29, 2024
Merged

Addition of getType() API #654

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ccb600e
WIP: Update to ImgLib2 v7
tpietzsch Apr 5, 2024
07c65b9
Fix remaining compile error (related to imglib/imglib2-roi#71)
tpietzsch Aug 28, 2024
142aac2
POM: Bump parent to pom-scijava-38.0.1
tpietzsch Aug 28, 2024
9fc76dc
POM: Bump dependency versions: imglib2 -> 7.1.0
tpietzsch Aug 28, 2024
bd43d4f
POM: update imagej-common to 2.1.1
ctrueden Aug 28, 2024
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8 changes: 6 additions & 2 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>37.0.0</version>
<version>38.0.1</version>
<relativePath />
</parent>

Expand Down Expand Up @@ -256,7 +256,11 @@
<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

<scijava-common.version>2.98.0</scijava-common.version>
<imglib2.version>7.1.0</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</imagej-common.version>
</properties>

<repositories>
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6 changes: 6 additions & 0 deletions src/main/java/net/imagej/ops/coloc/ShuffledView.java
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Expand Up @@ -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;
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4 changes: 2 additions & 2 deletions src/main/java/net/imagej/ops/geom/geom3d/DefaultInertiaTensor3D.java
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Expand Up @@ -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);
Expand All @@ -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);
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2 changes: 1 addition & 1 deletion src/main/java/net/imagej/ops/image/watershed/Watershed.java
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Expand Up @@ -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));
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2 changes: 1 addition & 1 deletion src/main/java/net/imagej/ops/labeling/MergeLabeling.java
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Expand Up @@ -92,7 +92,7 @@ public void compute(final ImgLabeling<L, I> input1,
{
if (mask != null) {
final IterableRegion iterable = Regions.iterable(mask);
final IterableInterval<LabelingType<L>> sample = Regions.sample(iterable,
final IterableInterval<LabelingType<L>> sample = Regions.sample(iterable.inside(),
output);
final RandomAccess<LabelingType<L>> randomAccess = input1.randomAccess();
final RandomAccess<LabelingType<L>> randomAccess2 = input2.randomAccess();
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