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Merged
ctrueden merged 31 commits into from
Nov 20, 2021
Merged

Enforce package hierarchy #39

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fb69b99
Add package cycle enforcer to incubator
gselzer Jun 28, 2021
71796e3
Move Op to org.scijava.ops
gselzer Jun 28, 2021
c9c2659
Move OpCollection to org.scijava.ops
gselzer Jun 28, 2021
d3121a0
Move OpBuilder to org.scijava.ops
gselzer Jun 28, 2021
078f56a
Move Hints/OpHints to org.scijava.ops
gselzer Jun 28, 2021
eb53ac4
Extract OpService interface
gselzer Jun 29, 2021
a0b69e6
Extract OpRef interface
gselzer Jun 29, 2021
3c29298
OpMatchingException: Extend RuntimeException
gselzer Jun 29, 2021
487f192
Move OpCandidate to org.scijava.ops
gselzer Jun 29, 2021
1e6c35b
Move util tests from org.scijava.ops to util package
gselzer Jun 29, 2021
e04e63f
Move OpWrapper to org.scijava.ops package
gselzer Jun 29, 2021
1992e36
Remove HashMaps from FifaceUtils classes
gselzer Jun 29, 2021
e227db9
Move fiface utility methods to OpBuilder
gselzer Jun 29, 2021
921c6ff
Remove match methods from fiface util classes
gselzer Jun 30, 2021
ce7a982
Export MatchingUtils methods to scijava-types
gselzer Jun 30, 2021
ab8a892
Remove Parameter annotation
gselzer Jun 30, 2021
1b7514b
Switch to MemberParser paradigm
gselzer Jun 30, 2021
870375c
Remove org.scijava.param package
gselzer Jul 1, 2021
852886b
Move ValidityException to org.scijava.ops
gselzer Jul 2, 2021
75cbd21
Extract matcher impl details to impl subpackage
gselzer Jul 2, 2021
1ac0b49
Prevent cycle: org.scijava.ops.simplify/struct
gselzer Jul 2, 2021
049506e
Prevent cycle: org.scijava.ops.util/org.scijava.ops.struct
gselzer Jul 2, 2021
ddfe944
Fix ExceptionUtils
gselzer Jul 2, 2021
f0f487f
Resolve package cycle: geom tests
gselzer Jul 2, 2021
34a38ed
Fix package cycle: Persist tests
gselzer Jul 2, 2021
d59cb34
Use new scijava-maven-plugin NoPackageCycles rule
gselzer Jul 12, 2021
b293068
Consolidate create packages
gselzer Jul 13, 2021
4c3dbe4
Absorb zernike helper into zernike package
gselzer Jul 13, 2021
2180d19
Absorb net.imagej.ops2.geom.geom3d.mesh
gselzer Jul 13, 2021
620dcf8
Add subpackage dependency prevention rule
gselzer Jul 13, 2021
90b38f0
Resolve provenance package cycle
gselzer Aug 5, 2021
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4 changes: 0 additions & 4 deletions imagej/imagej-ops2/src/main/java/module-info.java
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Expand Up @@ -13,8 +13,6 @@
opens net.imagej.ops2.convert.copy to org.scijava, org.scijava.ops;
opens net.imagej.ops2.copy to org.scijava, org.scijava.ops;
opens net.imagej.ops2.create to org.scijava, org.scijava.ops;
opens net.imagej.ops2.create.img to org.scijava, org.scijava.ops;
opens net.imagej.ops2.create.kernel to org.scijava, org.scijava.ops;
opens net.imagej.ops2.deconvolve to org.scijava, org.scijava.ops;
opens net.imagej.ops2.deconvolve.accelerate to org.scijava, org.scijava.ops;
opens net.imagej.ops2.eval to org.scijava, org.scijava.ops;
Expand All @@ -24,7 +22,6 @@
opens net.imagej.ops2.features.lbp2d to org.scijava, org.scijava.ops;
opens net.imagej.ops2.features.tamura2d to org.scijava, org.scijava.ops;
opens net.imagej.ops2.features.zernike to org.scijava, org.scijava.ops;
opens net.imagej.ops2.features.zernike.helper to org.scijava, org.scijava.ops;
opens net.imagej.ops2.filter to org.scijava, org.scijava.ops;
opens net.imagej.ops2.filter.addNoise to org.scijava, org.scijava.ops;
opens net.imagej.ops2.filter.bilateral to org.scijava, org.scijava.ops;
Expand All @@ -51,7 +48,6 @@
opens net.imagej.ops2.geom to org.scijava, org.scijava.ops;
opens net.imagej.ops2.geom.geom2d to org.scijava, org.scijava.ops;
opens net.imagej.ops2.geom.geom3d to org.scijava, org.scijava.ops;
opens net.imagej.ops2.geom.geom3d.mesh to org.scijava, org.scijava.ops;
opens net.imagej.ops2.identity to org.scijava, org.scijava.ops;
opens net.imagej.ops2.image.ascii to org.scijava, org.scijava.ops;
opens net.imagej.ops2.image.cooccurrenceMatrix to org.scijava, org.scijava.ops;
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java
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Expand Up @@ -38,8 +38,8 @@

import org.scijava.function.Computers;
import org.scijava.function.Functions;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.plugin.Plugin;

/**
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java
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import net.imglib2.util.IterablePair;
import net.imglib2.util.Pair;

import org.scijava.ops.core.Op;
import org.scijava.ops.Op;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java
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Expand Up @@ -49,9 +49,8 @@

import org.scijava.function.Computers;
import org.scijava.function.Functions;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.util.IntArray;

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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java
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import net.imglib2.view.Views;

import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java
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Expand Up @@ -35,7 +35,7 @@
import net.imglib2.util.IterablePair;
import net.imglib2.util.Pair;

import org.scijava.ops.core.Op;
import org.scijava.ops.Op;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/ConvertTypes.java
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import net.imglib2.type.numeric.real.FloatType;

import org.scijava.function.Computers;
import org.scijava.ops.OpCollection;
import org.scijava.ops.OpField;
import org.scijava.ops.core.OpCollection;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/Converters.java
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import net.imglib2.type.Type;

import org.scijava.function.Functions;
import org.scijava.ops.OpCollection;
import org.scijava.ops.OpField;
import org.scijava.ops.core.OpCollection;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

@Plugin(type = OpCollection.class)
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/clip/ClipRealTypes.java
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import net.imglib2.type.numeric.RealType;

import org.scijava.function.Computers;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.ops.Op;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/copy/CopyRealTypes.java
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import net.imglib2.type.numeric.RealType;

import org.scijava.function.Computers;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.ops.Op;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyArrayImg.java
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Expand Up @@ -39,9 +39,8 @@

import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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2 changes: 1 addition & 1 deletion imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyII.java
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Expand Up @@ -36,8 +36,8 @@
import net.imglib2.IterableInterval;

import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.ops.util.Maps;
import org.scijava.plugin.Plugin;

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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImg.java
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Expand Up @@ -35,9 +35,8 @@
import net.imglib2.type.NativeType;

import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImgLabeling.java
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Expand Up @@ -38,9 +38,8 @@
import net.imglib2.util.Util;

import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyLabelingMapping.java
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Expand Up @@ -37,8 +37,7 @@

import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.ops.Op;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyRAI.java
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Expand Up @@ -35,9 +35,8 @@
import net.imglib2.view.Views;

import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyType.java
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Expand Up @@ -32,8 +32,7 @@
import net.imglib2.type.Type;

import org.scijava.function.Computers;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.ops.Op;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/CreateTypes.java
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Expand Up @@ -19,9 +19,8 @@
import net.imglib2.type.numeric.real.FloatType;

import org.scijava.function.Producer;
import org.scijava.ops.OpCollection;
import org.scijava.ops.OpField;
import org.scijava.ops.core.OpCollection;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

@Plugin(type = OpCollection.class)
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10 changes: 1 addition & 9 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/Creators.java
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Expand Up @@ -6,14 +6,6 @@

import net.imagej.ImgPlus;
import net.imagej.ImgPlusMetadata;
import net.imagej.ops2.create.img.Imgs;
import net.imagej.ops2.create.kernel.DefaultCreateKernel2ndDerivBiGauss;
import net.imagej.ops2.create.kernel.DefaultCreateKernelBiGauss;
import net.imagej.ops2.create.kernel.DefaultCreateKernelGabor;
import net.imagej.ops2.create.kernel.DefaultCreateKernelGauss;
import net.imagej.ops2.create.kernel.DefaultCreateKernelGibsonLanni;
import net.imagej.ops2.create.kernel.DefaultCreateKernelLog;
import net.imagej.ops2.create.kernel.DefaultCreateKernelSobel;
import net.imglib2.Cursor;
import net.imglib2.Dimensions;
import net.imglib2.FinalDimensions;
Expand Down Expand Up @@ -50,8 +42,8 @@
import org.scijava.Priority;
import org.scijava.function.Functions;
import org.scijava.function.Producer;
import org.scijava.ops.OpCollection;
import org.scijava.ops.OpField;
import org.scijava.ops.core.OpCollection;
import org.scijava.plugin.Plugin;

@Plugin(type = OpCollection.class)
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2 changes: 1 addition & 1 deletion ...l/DefaultCreateKernel2ndDerivBiGauss.java → ...e/DefaultCreateKernel2ndDerivBiGauss.java
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Expand Up @@ -27,7 +27,7 @@
* #L%
*/

package net.imagej.ops2.create.kernel;
package net.imagej.ops2.create;

import java.util.function.BiFunction;

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2 changes: 1 addition & 1 deletion ...te/kernel/DefaultCreateKernelBiGauss.java → ...s2/create/DefaultCreateKernelBiGauss.java
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* #L%
*/

package net.imagej.ops2.create.kernel;
package net.imagej.ops2.create;

import java.util.function.BiFunction;

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2 changes: 1 addition & 1 deletion ...eate/kernel/DefaultCreateKernelGabor.java → ...ops2/create/DefaultCreateKernelGabor.java
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* #L%
*/

package net.imagej.ops2.create.kernel;
package net.imagej.ops2.create;

import java.util.function.BiFunction;

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2 changes: 1 addition & 1 deletion ...eate/kernel/DefaultCreateKernelGauss.java → ...ops2/create/DefaultCreateKernelGauss.java
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* #L%
*/

package net.imagej.ops2.create.kernel;
package net.imagej.ops2.create;

import java.util.function.BiFunction;

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2 changes: 1 addition & 1 deletion ...ernel/DefaultCreateKernelGibsonLanni.java → ...reate/DefaultCreateKernelGibsonLanni.java
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* #L%
*/

package net.imagej.ops2.create.kernel;
package net.imagej.ops2.create;

import java.util.function.BiFunction;

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2 changes: 1 addition & 1 deletion ...create/kernel/DefaultCreateKernelLog.java → ...j/ops2/create/DefaultCreateKernelLog.java
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Expand Up @@ -27,7 +27,7 @@
* #L%
*/

package net.imagej.ops2.create.kernel;
package net.imagej.ops2.create;

import java.util.function.BiFunction;

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2 changes: 1 addition & 1 deletion ...eate/kernel/DefaultCreateKernelSobel.java → ...ops2/create/DefaultCreateKernelSobel.java
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Expand Up @@ -26,7 +26,7 @@
* #L%
*/

package net.imagej.ops2.create.kernel;
package net.imagej.ops2.create;

import java.util.function.BiFunction;

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2 changes: 1 addition & 1 deletion ...java/net/imagej/ops2/create/img/Imgs.java → ...ain/java/net/imagej/ops2/create/Imgs.java
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Expand Up @@ -26,7 +26,7 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package net.imagej.ops2.create.img;
package net.imagej.ops2.create;

import net.imglib2.Dimensions;
import net.imglib2.Interval;
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantFirstGuess.java
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Expand Up @@ -42,9 +42,8 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.function.Functions;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions ...imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantNormalizationFactor.java
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Expand Up @@ -50,9 +50,8 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.function.Inplaces;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyC.java
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Expand Up @@ -45,9 +45,8 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.function.Inplaces;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyCorrection.java
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Expand Up @@ -44,9 +44,8 @@

import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyF.java
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Expand Up @@ -47,9 +47,8 @@
import org.scijava.function.Computers;
import org.scijava.function.Functions;
import org.scijava.function.Inplaces;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyTVF.java
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Expand Up @@ -48,9 +48,8 @@
import org.scijava.function.Computers;
import org.scijava.function.Functions;
import org.scijava.function.Inplaces;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyTVUpdate.java
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import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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3 changes: 1 addition & 2 deletions imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyUpdate.java
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Expand Up @@ -34,9 +34,8 @@

import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.param.Parameter;
import org.scijava.plugin.Plugin;

/**
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2 changes: 1 addition & 1 deletion ...ej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/accelerate/VectorAccelerator.java
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import org.scijava.Priority;
import org.scijava.function.Functions;
import org.scijava.function.Inplaces;
import org.scijava.ops.Op;
import org.scijava.ops.OpDependency;
import org.scijava.ops.core.Op;
import org.scijava.ops.util.Adapt;
import org.scijava.plugin.Plugin;

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