scijava · gselzer · Mar 25, 2021 · Jul 21, 2020 · Mar 5, 2021 · May 20, 2021
diff --git a/.travis/build.sh b/.travis/build.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+(cd scijava/scijava-taglets && mvn install)
+curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/master/travis-build.sh
+sh travis-build.sh $encrypted_844f7d2110b9_key $encrypted_844f7d2110b9_iv
diff --git a/imagej/imagej-ops2/pom.xml b/imagej/imagej-ops2/pom.xml
@@ -12,8 +12,8 @@
 	<groupId>net.imagej</groupId>
 	<artifactId>imagej-ops2</artifactId>
 
-	<name>ImageJ Ops</name>
-	<description>ImageJ Operations: a framework for reusable algorithms.</description>
+	<name>ImageJ Ops 2</name>
+	<description>ImageJ Operations 2: a framework for reusable algorithms.</description>
 	<url>http://imagej.net/ImageJ_Ops</url>
 	<inceptionYear>2014</inceptionYear>
 	<organization>
@@ -210,7 +210,8 @@
 		<license.projectName>ImageJ software for multidimensional image processing and analysis.</license.projectName>
 
 		<!-- NB While we depend on old scijava-common -->
-		<allowedDuplicateClasses>org.scijava.*</allowedDuplicateClasses>
+		<imagej-ops2.allowedDuplicateClasses>${scijava.allowedDuplicateClasses}, org.scijava.*,com.github.therapi.runtimejavadoc.repack.com.eclipsesource.json.*</imagej-ops2.allowedDuplicateClasses>
+		<allowedDuplicateClasses>${imagej-ops2.allowedDuplicateClasses}</allowedDuplicateClasses>
 
 		<!-- NB: Deploy releases to the ImageJ Maven repository. -->
 		<releaseProfiles>deploy-to-imagej</releaseProfiles>
@@ -272,7 +273,17 @@
 		</dependency>
 		<dependency>
 			<groupId>org.scijava</groupId>
-			<artifactId>scijava-ops</artifactId>
+			<artifactId>scijava-ops-api</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>scijava-ops-spi</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>scijava-ops-engine</artifactId>
 			<version>${project.version}</version>
 		</dependency>
 		<dependency>
@@ -297,10 +308,6 @@
 		</dependency>
 
 		<!-- Third party dependencies -->
-		<dependency>
-			<groupId>com.google.guava</groupId>
-			<artifactId>guava</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-math3</artifactId>
@@ -320,18 +327,13 @@
 
 		<!-- Test scope dependencies -->
 		<dependency>
-			<groupId>org.junit.jupiter</groupId>
-			<artifactId>junit-jupiter-api</artifactId>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.junit.jupiter</groupId>
-			<artifactId>junit-jupiter-engine</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.junit.vintage</groupId>
-			<artifactId>junit-vintage-engine</artifactId>
+			<artifactId>junit-jupiter-api</artifactId>
 			<scope>test</scope>
 		</dependency>
 		<dependency>

diff --git a/imagej/imagej-ops2/src/main/java/module-info.java b/imagej/imagej-ops2/src/main/java/module-info.java
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java
@@ -38,11 +38,9 @@
 
 import org.scijava.function.Computers;
 import org.scijava.function.Functions;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
 import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
 
 /**
  * This algorithm calculates Li et al.'s ICQ (intensity correlation quotient).
@@ -53,11 +51,6 @@
  *            Type of the second image
  */
 @Plugin(type = Op.class, name = "coloc.icq")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "mean1")
-@Parameter(key = "mean2")
-@Parameter(key = "output")
 public class LiICQ<T extends RealType<T>, U extends RealType<U>, V extends RealType<V>>
 		implements Functions.Arity4<Iterable<T>, Iterable<U>, DoubleType, DoubleType, Double> {
 
@@ -66,6 +59,15 @@ public class LiICQ<T extends RealType<T>, U extends RealType<U>, V extends RealT
 	@OpDependency(name = "stats.mean")
 	private Computers.Arity1<Iterable<U>, DoubleType> meanUOp;
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @param mean1
+	 * @param mean2
+	 * @return the output
+	 */
 	@Override
 	public Double apply(final Iterable<T> image1, final Iterable<U> image2, final DoubleType mean1, final DoubleType mean2) {
 
@@ -120,15 +122,19 @@ private double computeMeanUOf(final Iterable<U> in) {
 }
 
 @Plugin(type = Op.class, name = "coloc.icq")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "output")
 class LiICQSimple<T extends RealType<T>, U extends RealType<U>, V extends RealType<V>>
 		implements BiFunction<Iterable<T>, Iterable<U>, Double> {
 
 	@OpDependency(name = "coloc.icq")
 	private Functions.Arity4<Iterable<T>, Iterable<U>, DoubleType, DoubleType, Double> colocOp;
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @return the output
+	 */
 	@Override
 	public Double apply(Iterable<T> image1, Iterable<U> image2) {
 		return colocOp.apply(image1, image2, null, null);

diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java
@@ -38,10 +38,8 @@
 import net.imglib2.util.IterablePair;
 import net.imglib2.util.Pair;
 
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
 import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
 
 /**
  * This algorithm calculates Kendall's Tau-b rank correlation coefficient
@@ -76,12 +74,16 @@
  * @param <T>
  */
 @Plugin(type = Op.class, name = "coloc.kendallTau")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "output")
 public class KendallTauBRank<T extends RealType<T>, U extends RealType<U>>
 		/* extends Algorithm<T> */ implements BiFunction<Iterable<T>, Iterable<U>, Double> {
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @return the output
+	 */
 	@Override
 	public Double apply(Iterable<T> image1, Iterable<U> image2) {
 		if (!ColocUtil.sameIterationOrder(image1, image2))

diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java
@@ -49,11 +49,9 @@
 
 import org.scijava.function.Computers;
 import org.scijava.function.Functions;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
 import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
 import org.scijava.util.IntArray;
 
 /**
@@ -68,10 +66,6 @@
  * @author Curtis Rueden
  */
 @Plugin(type = Op.class, name = "coloc.maxTKendallTau")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "seed")
-@Parameter(key = "output")
 public class MTKT<T extends RealType<T>, U extends RealType<U>>
 	implements Functions.Arity3<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Long, Double> 
 {
@@ -86,6 +80,14 @@ public class MTKT<T extends RealType<T>, U extends RealType<U>>
 	@OpDependency(name = "threshold.otsu")
 	private Computers.Arity1<Histogram1d<U>, U> thresholdOpU;
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @param seed
+	 * @return the output
+	 */
 	@Override
 	public Double apply(final RandomAccessibleInterval<T> image1, final RandomAccessibleInterval<U> image2, final Long seed) {
 		// check image sizes
@@ -248,9 +250,6 @@ static double calculateKendallTau(final double[][] rank,
 }
 
 @Plugin(type = Op.class, name = "coloc.maxTKendallTau")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "output")
 class MTKTSimple<T extends RealType<T>, U extends RealType<U>>
 	implements BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double> 
 {
@@ -260,6 +259,13 @@ class MTKTSimple<T extends RealType<T>, U extends RealType<U>>
 
 	private long seed = 0x89302341;
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @return the output
+	 */
 	@Override
 	public Double apply(RandomAccessibleInterval<T> image1, RandomAccessibleInterval<U> image2) {
 		return colocOp.apply(image1, image2, seed);

diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java
@@ -48,11 +48,9 @@
 import net.imglib2.view.Views;
 
 import org.scijava.function.Computers;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
 import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
 
 /**
  * This algorithm repeatedly executes a colocalization algorithm, computing a
@@ -62,17 +60,21 @@
  * Statistical Approach".
  */
 @Plugin(type = Op.class, name = "coloc.pValue")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "op")
-@Parameter(key = "nrRandomizations")
-@Parameter(key = "psfSize")
-@Parameter(key = "seed")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
 public class DefaultPValue<T extends RealType<T>, U extends RealType<U>> implements
 		Computers.Arity7<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, Dimensions, Long, ExecutorService, PValueResult> {
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @param op
+	 * @param nrRandomizations
+	 * @param psfSize
+	 * @param seed
+	 * @param executorService
+	 * @param output
+	 */
 	@Override
 	public void compute(final RandomAccessibleInterval<T> image1, final RandomAccessibleInterval<U> image2,
 			final BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double> op,
@@ -191,18 +193,22 @@ private static <V> RandomAccessibleInterval<V> trim(final RandomAccessibleInterv
 }
 
 @Plugin(type = Op.class, name = "coloc.pValue")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "op")
-@Parameter(key = "nrRandomizations")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
 class PValueSimpleWithRandomizations<T extends RealType<T>, U extends RealType<U>> implements
 		Computers.Arity5<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, ExecutorService, PValueResult> {
 
 	@OpDependency(name = "coloc.pValue")
 	private Computers.Arity7<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, Dimensions, Long, ExecutorService, PValueResult> pValueOp;
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @param op
+	 * @param nrRandomizations
+	 * @param executorService
+	 * @param output
+	 */
 	@Override
 	public void compute(RandomAccessibleInterval<T> in1, RandomAccessibleInterval<U> in2,
 			BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double> in3, Integer in4,
@@ -214,17 +220,21 @@ public void compute(RandomAccessibleInterval<T> in1, RandomAccessibleInterval<U>
 }
 
 @Plugin(type = Op.class, name = "coloc.pValue")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "op")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
 class PValueSimple<T extends RealType<T>, U extends RealType<U>> implements
 		Computers.Arity4<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, ExecutorService, PValueResult> {
 
 	@OpDependency(name = "coloc.pValue")
 	private Computers.Arity5<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, ExecutorService, PValueResult> pValueOp;
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @param op
+	 * @param executorService
+	 * @param output
+	 */
 	@Override
 	public void compute(RandomAccessibleInterval<T> in1, RandomAccessibleInterval<U> in2,
 			BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double> in3, ExecutorService in4,

diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java
@@ -35,10 +35,8 @@
 import net.imglib2.util.IterablePair;
 import net.imglib2.util.Pair;
 
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
 import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
 
 /**
  * A class that represents the mean calculation of the two source images in the
@@ -47,13 +45,17 @@
  * @author Ellen T Arena
  */
 @Plugin(type = Op.class, name = "coloc.pearsons")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "output")
 public class DefaultPearsons<T extends RealType<T>, U extends RealType<U>> implements
 	BiFunction<Iterable<T>, Iterable<U>, Double> 
 {
 
+	/**
+	 * TODO
+	 *
+	 * @param image1
+	 * @param image2
+	 * @return the output
+	 */
 	@Override
 	public Double apply(final Iterable<T> image1,
 		final Iterable<U> image2)

diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/ConvertTypes.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/ConvertTypes.java
@@ -52,11 +52,9 @@
 import net.imglib2.type.numeric.real.FloatType;
 
 import org.scijava.function.Computers;
-import org.scijava.ops.OpField;
-import org.scijava.ops.core.OpCollection;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.OpCollection;
+import org.scijava.ops.spi.OpField;
 import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
 
 /**
  * Converters for converting between Complex types

diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/Converters.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/Converters.java
@@ -6,11 +6,9 @@
 import net.imglib2.type.Type;
 
 import org.scijava.function.Functions;
-import org.scijava.ops.OpField;
-import org.scijava.ops.core.OpCollection;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.OpCollection;
+import org.scijava.ops.spi.OpField;
 import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
 
 @Plugin(type = OpCollection.class)
 public class Converters<I, O extends Type<O>> {