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Merged
ctrueden merged 19 commits into from
Jul 1, 2022
Merged

Revisions on the Revisions of the Data Provenance branch #53

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3ea7201
Remove javadoc about hints construction
gselzer Jan 7, 2022
9109009
Remove cacheOp method
gselzer Jan 7, 2022
7076ff7
Move wrapViaCache lower in OpEnvironment
gselzer Jan 7, 2022
8c8afb0
Change {@code opCache} to {@link #opCache}
gselzer Jan 7, 2022
5f65b44
Reference Op using "an Op"
gselzer Jan 7, 2022
e2647a1
Refactor ManualOpCandidate into constructor
gselzer Jan 7, 2022
6d78f59
Clean Hints javadoc
gselzer Jan 7, 2022
797e32e
instantation to instantiation
gselzer Jan 7, 2022
4b20ae9
Add OpInfo constructors to generate version
gselzer Jan 7, 2022
880eca1
Provide some javadoc to OpMetadata
gselzer Jan 7, 2022
2a680de
Close out list elements
gselzer Jan 7, 2022
8fad709
Add javadoc to InfoChain
gselzer Jan 7, 2022
a0dfaa9
Remove SJC dep in SciJava Ops SPI
gselzer Jan 14, 2022
c40a4f1
More InfoChain javadoc
gselzer Jan 14, 2022
68eda09
Add more javadoc
gselzer Jan 14, 2022
c361aa8
Rename InstanceChain.op()
gselzer Jan 14, 2022
6f01deb
Rename OpInfo.IMPL_DECLARATION
gselzer Jan 14, 2022
2624254
Fix ProvenanceTest typo
gselzer Jan 14, 2022
d2f2aba
Identify expected behavior in empty catch block
gselzer Jan 14, 2022
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2 changes: 1 addition & 1 deletion ...imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantNormalizationFactor.java
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Expand Up @@ -94,7 +94,7 @@ public class NonCirculantNormalizationFactor<I extends RealType<I>, O extends Re
@OpDependency(name = "filter.correlate")
private Computers.Arity7<RandomAccessibleInterval<O>, RandomAccessibleInterval<K>, RandomAccessibleInterval<C>, RandomAccessibleInterval<C>, Boolean, Boolean, ExecutorService, RandomAccessibleInterval<O>> correlater;

// @OpDependency(name = "math.divide") TODO: match an op here?
// @OpDependency(name = "math.divide") TODO: match an Op here?
private BiConsumer<RandomAccessibleInterval<O>, RandomAccessibleInterval<O>> divide = (numerResult, denom) -> {
final O tmp = Util.getTypeFromInterval(numerResult).createVariable();
LoopBuilder.setImages(numerResult, denom).forEachPixel((n, d) -> {
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyCorrection.java
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Expand Up @@ -73,7 +73,7 @@ public class RichardsonLucyCorrection<I extends RealType<I>, O extends RealType<
@OpDependency(name = "copy.rai")
private Function<RandomAccessibleInterval<O>, RandomAccessibleInterval<O>> copy;

// @OpDependency(name = "math.divide") TODO: match an op here?
// @OpDependency(name = "math.divide") TODO: match an Op here?
private BiConsumer<RandomAccessibleInterval<O>, RandomAccessibleInterval<I>> divide = (denomResult, numer) -> {
final O tmp = Util.getTypeFromInterval(denomResult).createVariable();
LoopBuilder.setImages(denomResult, numer).forEachPixel((d, n) -> {
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/eval/OpEvaluator.java
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Expand Up @@ -48,7 +48,7 @@
import org.scijava.types.Nil;

/**
* A Parsington {@link Evaluator} using available {@link Op}s.
* A Parsington {@link Evaluator} using available Ops.
*
* @author Curtis Rueden
*/
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10 changes: 5 additions & 5 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/filter/tubeness/DefaultTubeness.java
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Expand Up @@ -65,17 +65,17 @@
* the large eigenvalue is negative, we return its absolute value and otherwise
* return 0.
* <ul>
* <li>Source image is filtered first by a gaussian with 𝜎 that sets its scale.
* <li>The the Hessian matrix is calculated for each pixel.
* <li>Source image is filtered first by a gaussian with 𝜎 that sets its scale.</li>
* <li>The the Hessian matrix is calculated for each pixel.</li>
* <li>We yield the eigenvalues of the Hessian matrix. The output of the
* tubeness filter is a combination of these eigenvalues:
* tubeness filter is a combination of these eigenvalues:</li>
* <ul>
* <li>in 2D where <code>λ₂</code> is the largest eigenvalue:
* <code>out = 𝜎 × 𝜎 × |λ₂|</code> if <code>λ₂</code> is negative, 0
* otherwise.
* otherwise.</li>
* <li>in 3D where <code>λ₂</code> and <code>λ₃</code> are the largest
* eigenvalues:, <code>out = 𝜎 × 𝜎 × sqrt( λ₂ * λ₃ )</code> if <code>λ₂</code>
* and <code>λ₃</code> are negative, 0 otherwise.
* and <code>λ₃</code> are negative, 0 otherwise.</li>
* </ul>
* </ul>
* This results in enhancing filaments of roughly <code>𝜎 / sqrt(d)</code>
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/geom/CentroidII.java
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Expand Up @@ -39,7 +39,7 @@
import org.scijava.ops.spi.Op;

/**
* This {@link Op} computes the centroid of a {@link IterableRegion} (Label).
* This Op computes the centroid of a {@link IterableRegion} (Label).
*
* @author Tim-Oliver Buchholz (University of Konstanz)
* @implNote op names='geom.centroid', priority='1'
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/geom/CentroidLabelRegion.java
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Expand Up @@ -39,7 +39,7 @@
import org.scijava.ops.spi.Op;

/**
* This {@link Op} computes the centroid of a {@link IterableRegion} (Label).
* This Op computes the centroid of a {@link IterableRegion} (Label).
*
* @author Tim-Oliver Buchholz (University of Konstanz)
* @implNote op names='geom.centroid', priority='2'
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/geom/DefaultCenterOfGravity.java
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Expand Up @@ -41,7 +41,7 @@
import org.scijava.ops.spi.Op;

/**
* This {@link Op} computes the center of gravity of a {@link IterableRegion}
* This Op computes the center of gravity of a {@link IterableRegion}
* (Label).
*
* @author Daniel Seebacher (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/geom/geom3d/DefaultInertiaTensor3D.java
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Expand Up @@ -42,7 +42,7 @@
import org.scijava.ops.spi.OpDependency;

/**
* This {@link Op} computes the 2nd multi variate of a {@link IterableRegion}
* This Op computes the 2nd multi variate of a {@link IterableRegion}
* (Label).
*
* @author Tim-Oliver Buchholz (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/geom/geom3d/DefaultInertiaTensor3DMesh.java
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Expand Up @@ -42,7 +42,7 @@
import org.scijava.ops.spi.OpDependency;

/**
* This {@link Op} computes the 2nd multi variate of a {@link Mesh} (Label).
* This Op computes the 2nd multi variate of a {@link Mesh} (Label).
*
* @author Tim-Oliver Buchholz (University of Konstanz)
*@implNote op names='geom.secondMoment'
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4 changes: 2 additions & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/image/invert/InvertIIInteger.java
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Expand Up @@ -78,7 +78,7 @@
// }
//
// public static <T extends RealType<T>> T minValue(T type) {
// // TODO: Consider making minValue an op.
// // TODO: Consider making minValue an Op.
// final T min = type.createVariable();
// if (type instanceof UnboundedIntegerType) min.setReal(0);
// else min.setReal(min.getMinValue());
Expand All @@ -87,7 +87,7 @@
// }
//
// public static <T extends RealType<T>> T maxValue(T type) {
// // TODO: Consider making maxValue an op.
// // TODO: Consider making maxValue an Op.
// final T max = type.createVariable();
// if (max instanceof Unsigned128BitType) {
// final Unsigned128BitType t = (Unsigned128BitType) max;
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4 changes: 2 additions & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/image/invert/Inverters.java
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Expand Up @@ -118,7 +118,7 @@ private void setBigInteger(T out, BigInteger bi) {
}

public static <T extends RealType<T>> T minValue(T type) {
// TODO: Consider making minValue an op.
// TODO: Consider making minValue an Op.
final T min = type.createVariable();
if (type instanceof UnboundedIntegerType)
min.setReal(0);
Expand All @@ -129,7 +129,7 @@ public static <T extends RealType<T>> T minValue(T type) {
}

public static <T extends RealType<T>> T maxValue(T type) {
// TODO: Consider making maxValue an op.
// TODO: Consider making maxValue an Op.
final T max = type.createVariable();
if (max instanceof Unsigned128BitType) {
final Unsigned128BitType t = (Unsigned128BitType) max;
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment00.java
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Expand Up @@ -38,7 +38,7 @@
import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment00}.
* Op to calculate the {@code imageMoments.centralMoment00}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment01.java
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Expand Up @@ -36,7 +36,7 @@
import org.scijava.ops.spi.Op;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment01} directly.
* Op to calculate the {@code imageMoments.centralMoment01} directly.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment02.java
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Expand Up @@ -42,7 +42,7 @@
import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment02}.
* Op to calculate the {@code imageMoments.centralMoment02}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment03.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment03} using
* Op to calculate the {@code imageMoments.centralMoment03} using
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment10.java
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import org.scijava.ops.spi.Op;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment10} directly.
* Op to calculate the {@code imageMoments.centralMoment10} directly.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment11.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment11}.
* Op to calculate the {@code imageMoments.centralMoment11}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment12.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment12}.
* Op to calculate the {@code imageMoments.centralMoment12}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment20.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment20}.
* Op to calculate the {@code imageMoments.centralMoment20}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment21.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment21}.
* Op to calculate the {@code imageMoments.centralMoment21}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...ps2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/DefaultCentralMoment30.java
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Expand Up @@ -42,7 +42,7 @@
import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment30}.
* Op to calculate the {@code imageMoments.centralMoment30}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...s2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/IterableCentralMoment00.java
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Expand Up @@ -37,7 +37,7 @@
import org.scijava.ops.spi.Op;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment00} directly.
* Op to calculate the {@code imageMoments.centralMoment00} directly.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...s2/src/main/java/net/imagej/ops2/imagemoments/centralmoments/IterableCentralMoment11.java
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import org.scijava.ops.spi.Op;

/**
* {@link Op} to calculate the {@code imageMoments.centralMoment11} directly.
* Op to calculate the {@code imageMoments.centralMoment11} directly.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/hu/DefaultHuMoment1.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.huMoment1}.
* Op to calculate the {@code imageMoments.huMoment1}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/hu/DefaultHuMoment2.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.huMoment2}.
* Op to calculate the {@code imageMoments.huMoment2}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/hu/DefaultHuMoment3.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.huMoment3}.
* Op to calculate the {@code imageMoments.huMoment3}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/hu/DefaultHuMoment4.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.huMoment4}.
* Op to calculate the {@code imageMoments.huMoment4}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/hu/DefaultHuMoment5.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.huMoment5}.
* Op to calculate the {@code imageMoments.huMoment5}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/hu/DefaultHuMoment6.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.huMoment6}.
* Op to calculate the {@code imageMoments.huMoment6}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
Expand Down
2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/hu/DefaultHuMoment7.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.huMoment7}.
* Op to calculate the {@code imageMoments.huMoment7}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/moments/DefaultMoment00.java
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import org.scijava.ops.spi.Op;

/**
* {@link Op} to calculate the {@code imageMoments.moment00}.
* Op to calculate the {@code imageMoments.moment00}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
Expand Down
2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/moments/DefaultMoment01.java
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import org.scijava.ops.spi.Op;

/**
* {@link Op} to calculate the {@code imageMoments.moment01}.
* Op to calculate the {@code imageMoments.moment01}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
Expand Down
2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/moments/DefaultMoment10.java
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import org.scijava.ops.spi.Op;

/**
* {@link Op} to calculate the {@code imageMoments.moment10}.
* Op to calculate the {@code imageMoments.moment10}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
Expand Down
2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/imagemoments/moments/DefaultMoment11.java
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import org.scijava.ops.spi.Op;

/**
* {@link Op} to calculate the {@code imageMoments.moment11}.
* Op to calculate the {@code imageMoments.moment11}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...t/imagej/ops2/imagemoments/normalizedcentralmoments/DefaultNormalizedCentralMoment02.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.normalizedCentralMoment02}.
* Op to calculate the {@code imageMoments.normalizedCentralMoment02}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...t/imagej/ops2/imagemoments/normalizedcentralmoments/DefaultNormalizedCentralMoment03.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.normalizedCentralMoment03}.
* Op to calculate the {@code imageMoments.normalizedCentralMoment03}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...t/imagej/ops2/imagemoments/normalizedcentralmoments/DefaultNormalizedCentralMoment11.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.normalizedCentralMoment11}.
* Op to calculate the {@code imageMoments.normalizedCentralMoment11}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...t/imagej/ops2/imagemoments/normalizedcentralmoments/DefaultNormalizedCentralMoment12.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.normalizedCentralMoment12}.
* Op to calculate the {@code imageMoments.normalizedCentralMoment12}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...t/imagej/ops2/imagemoments/normalizedcentralmoments/DefaultNormalizedCentralMoment20.java
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import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.normalizedCentralMoment20}.
* Op to calculate the {@code imageMoments.normalizedCentralMoment20}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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2 changes: 1 addition & 1 deletion ...t/imagej/ops2/imagemoments/normalizedcentralmoments/DefaultNormalizedCentralMoment21.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
import org.scijava.ops.spi.OpDependency;

/**
* {@link Op} to calculate the {@code imageMoments.normalizedCentralMoment21}.
* Op to calculate the {@code imageMoments.normalizedCentralMoment21}.
*
* @author Daniel Seebacher (University of Konstanz)
* @author Christian Dietz (University of Konstanz)
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