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Merge pull request #49 from scijava/imagej/imagej-ops2/plugin-purging
Use Therapi Discovery in ImageJ Ops2
2 parents 883acc7 + 8a62ad7 commit c893de5

487 files changed

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‎imagej/imagej-ops2/pom.xml‎

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<!-- NB: Deploy releases to the ImageJ Maven repository. -->
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<releaseProfiles>deploy-to-imagej</releaseProfiles>
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<therapi.packages></therapi.packages>
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</properties>
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<build>

‎imagej/imagej-ops2/src/main/java/module-info.java‎

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‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java‎

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import org.scijava.function.Computers;
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import org.scijava.function.Functions;
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import org.scijava.ops.spi.Op;
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import org.scijava.ops.spi.OpDependency;
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import org.scijava.plugin.Plugin;
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/**
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* This algorithm calculates Li et al.'s ICQ (intensity correlation quotient).
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* Type of the first image
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* @param <U>
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* Type of the second image
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*@implNote op names='coloc.icq'
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*/
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@Plugin(type = Op.class, name = "coloc.icq")
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public class LiICQ<T extends RealType<T>, U extends RealType<U>, V extends RealType<V>>
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implements Functions.Arity4<Iterable<T>, Iterable<U>, DoubleType, DoubleType, Double> {
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}
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@Plugin(type = Op.class, name = "coloc.icq")
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/**
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*@implNote op names='coloc.icq'
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*/
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class LiICQSimple<T extends RealType<T>, U extends RealType<U>, V extends RealType<V>>
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implements BiFunction<Iterable<T>, Iterable<U>, Double> {
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‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java‎

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import net.imglib2.util.IterablePair;
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import net.imglib2.util.Pair;
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import org.scijava.ops.spi.Op;
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import org.scijava.plugin.Plugin;
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/**
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* This algorithm calculates Kendall's Tau-b rank correlation coefficient
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* <p>
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* @author Johannes Schindelin
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* @author Ellen T Arena
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* @param <T>
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*@implNote op names='coloc.kendallTau'
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*/
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@Plugin(type = Op.class, name = "coloc.kendallTau")
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public class KendallTauBRank<T extends RealType<T>, U extends RealType<U>>
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/* extends Algorithm<T> */ implements BiFunction<Iterable<T>, Iterable<U>, Double> {
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‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java‎

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import org.scijava.function.Computers;
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import org.scijava.function.Functions;
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import org.scijava.ops.spi.Op;
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import org.scijava.ops.spi.OpDependency;
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import org.scijava.plugin.Plugin;
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import org.scijava.util.IntArray;
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/**
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* @author Ellen T Arena
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* @author Shulei Wang
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* @author Curtis Rueden
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*@implNote op names='coloc.maxTKendallTau'
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*/
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@Plugin(type = Op.class, name = "coloc.maxTKendallTau")
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public class MTKT<T extends RealType<T>, U extends RealType<U>>
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implements Functions.Arity3<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Long, Double>
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{
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}
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@Plugin(type = Op.class, name = "coloc.maxTKendallTau")
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/**
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*@implNote op names='coloc.maxTKendallTau'
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*/
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class MTKTSimple<T extends RealType<T>, U extends RealType<U>>
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implements BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>
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{

‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java‎

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import net.imglib2.view.Views;
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import org.scijava.function.Computers;
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import org.scijava.ops.spi.Op;
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import org.scijava.ops.spi.OpDependency;
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import org.scijava.plugin.Plugin;
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/**
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* This algorithm repeatedly executes a colocalization algorithm, computing a
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* p-value. It is based on a new statistical framework published by Wang et al
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* (2017) IEEE Signal Processing "Automated and Robust Quantification of
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* Colocalization in Dual-Color Fluorescence Microscopy: A Nonparametric
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* Statistical Approach".
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*@implNote op names='coloc.pValue'
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*/
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@Plugin(type = Op.class, name = "coloc.pValue")
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public class DefaultPValue<T extends RealType<T>, U extends RealType<U>> implements
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Computers.Arity7<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, Dimensions, Long, ExecutorService, PValueResult> {
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}
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}
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@Plugin(type = Op.class, name = "coloc.pValue")
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/**
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*@implNote op names='coloc.pValue'
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*/
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class PValueSimpleWithRandomizations<T extends RealType<T>, U extends RealType<U>> implements
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Computers.Arity5<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, Integer, ExecutorService, PValueResult> {
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}
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@Plugin(type = Op.class, name = "coloc.pValue")
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/**
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*@implNote op names='coloc.pValue'
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*/
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class PValueSimple<T extends RealType<T>, U extends RealType<U>> implements
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Computers.Arity4<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, BiFunction<RandomAccessibleInterval<T>, RandomAccessibleInterval<U>, Double>, ExecutorService, PValueResult> {
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‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java‎

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import net.imglib2.util.IterablePair;
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import net.imglib2.util.Pair;
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import org.scijava.ops.spi.Op;
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import org.scijava.plugin.Plugin;
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/**
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* A class that represents the mean calculation of the two source images in the
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* data container. It implements the FAST calculation for Pearson's Correlation.
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*
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* @author Ellen T Arena
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*@implNote op names='coloc.pearsons'
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*/
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@Plugin(type = Op.class, name = "coloc.pearsons")
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public class DefaultPearsons<T extends RealType<T>, U extends RealType<U>> implements
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BiFunction<Iterable<T>, Iterable<U>, Double>
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{

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