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gselzer
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wiedenm
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WIP: Port features namespace
TODO: Port ops that this namespace depends on (the main one is filter.mean?)
1 parent 39e5b7b commit 76b27fd

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‎src/main/java/net/imagej/ops/features/haralick/AbstractHaralickFeature.java‎

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/*
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2018 ImageJ developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package net.imagej.ops.features.haralick;
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import net.imagej.ops.image.cooccurrenceMatrix.CooccurrenceMatrix2D;
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import net.imagej.ops.image.cooccurrenceMatrix.MatrixOrientation;
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import net.imglib2.IterableInterval;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.function.Function4;
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/**
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* Abstract class for HaralickFeatures.
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*
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* @author Christian Dietz (University of Konstanz)
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* @param <T>
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*/
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public abstract class AbstractHaralickFeature<T extends RealType<T>>
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implements Function4<IterableInterval<T>, Integer, Integer, MatrixOrientation, DoubleType> {
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@OpDependency(name = "image.cooccurrenceMatrix")
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private Function4<IterableInterval<T>, Integer, Integer, MatrixOrientation, double[][]> coocFunc;
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/**
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* Creates {@link CooccurrenceMatrix2D} from {@link IterableInterval} on demand,
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* given the specified parameters. No caching!
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*
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* @return the {@link CooccurrenceMatrix2D}
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*/
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protected double[][] getCooccurrenceMatrix(final IterableInterval<T> input, final Integer numGreyLevels,
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final Integer distance, final MatrixOrientation matrixOrientation) {
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if (matrixOrientation.numDims() != input.numDimensions())
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throw new IllegalArgumentException("MatrixOrientation must be of the same dimensions as the input!");
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return coocFunc.apply(input, numGreyLevels, distance, matrixOrientation);
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}
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}

‎src/main/java/net/imagej/ops/features/haralick/DefaultASM.java‎

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/*
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2018 ImageJ developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package net.imagej.ops.features.haralick;
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import net.imagej.ops.image.cooccurrenceMatrix.MatrixOrientation;
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import net.imglib2.IterableInterval;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.core.Op;
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import org.scijava.param.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.struct.ItemIO;
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/**
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*
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* Implementation of Angular Second Moment Haralick Feature
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*
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* @author Andreas Graumann (University of Konstanz)
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* @author Christian Dietz (University of Konstanz)
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*
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*/
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@Plugin(type = Op.class, name = "features.haralick.asm")
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@Parameter(key = "input")
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@Parameter(key = "numGreyLevels")
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@Parameter(key = "distance")
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@Parameter(key = "matrixOrientation")
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@Parameter(key = "output", type = ItemIO.OUTPUT)
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public class DefaultASM<T extends RealType<T>> extends AbstractHaralickFeature<T> {
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@Override
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public DoubleType apply(final IterableInterval<T> input, final Integer numGreyLevels, final Integer distance,
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final MatrixOrientation orientation) {
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final double[][] matrix = getCooccurrenceMatrix(input, numGreyLevels, distance, orientation);
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final int nrGrayLevels = matrix.length;
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double res = 0;
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for (int i = 0; i < nrGrayLevels; i++) {
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for (int j = 0; j < nrGrayLevels; j++) {
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res += matrix[i][j] * matrix[i][j];
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}
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}
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DoubleType output = new DoubleType();
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output.setReal(res);
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return output;
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}
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}

‎src/main/java/net/imagej/ops/features/haralick/DefaultClusterPromenence.java‎

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/*
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2018 ImageJ developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package net.imagej.ops.features.haralick;
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import java.util.function.Function;
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import net.imagej.ops.image.cooccurrenceMatrix.MatrixOrientation;
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import net.imglib2.IterableInterval;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.Op;
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import org.scijava.param.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.struct.ItemIO;
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/**
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*
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* Implementation of Cluster Promenence Haralick Feature
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*
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* @author Andreas Graumann (University of Konstanz)
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* @author Christian Dietz (University of Konstanz)
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*
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*/
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@Plugin(type = Op.class, name = "features.haralick.clusterPromenence")
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@Parameter(key = "input")
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@Parameter(key = "numGreyLevels")
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@Parameter(key = "distance")
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@Parameter(key = "matrixOrientation")
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@Parameter(key = "output", type = ItemIO.OUTPUT)
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public class DefaultClusterPromenence<T extends RealType<T>> extends AbstractHaralickFeature<T> {
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@OpDependency(name = "features.haralick.coocMeanX")
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private Function<double[][], DoubleType> coocMeanXFunc;
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@OpDependency(name = "features.haralick.coocMeanY")
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private Function<double[][], DoubleType> coocMeanYFunc;
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@Override
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public DoubleType apply(final IterableInterval<T> input, final Integer numGreyLevels, final Integer distance,
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final MatrixOrientation orientation) {
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final double[][] matrix = getCooccurrenceMatrix(input, numGreyLevels, distance, orientation);
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final int nrGrayLevels = matrix.length;
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final double mux = coocMeanXFunc.apply(matrix).getRealDouble();
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final double muy = coocMeanYFunc.apply(matrix).getRealDouble();
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double res = 0;
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for (int i = 0; i < nrGrayLevels; i++) {
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for (int j = 0; j < nrGrayLevels; j++) {
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res += Math.pow(i + j - mux - muy, 4) * matrix[i][j];
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}
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}
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DoubleType output = new DoubleType();
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output.setReal(res);
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return output;
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}
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}

‎src/main/java/net/imagej/ops/features/haralick/DefaultClusterShade.java‎

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/*
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2018 ImageJ developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package net.imagej.ops.features.haralick;
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import java.util.function.Function;
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import net.imagej.ops.image.cooccurrenceMatrix.MatrixOrientation;
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import net.imglib2.IterableInterval;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.Op;
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import org.scijava.param.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.struct.ItemIO;
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/**
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* Implementation of Cluster Shade Haralick Feature
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*
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* @author Andreas Graumann (University of Konstanz)
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* @author Christian Dietz (University of Konstanz)
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*
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*/
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@Plugin(type = Op.class, name = "features.haralick.clusterShade")
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@Parameter(key = "input")
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@Parameter(key = "numGreyLevels")
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@Parameter(key = "distance")
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@Parameter(key = "matrixOrientation")
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@Parameter(key = "output", type = ItemIO.OUTPUT)
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public class DefaultClusterShade<T extends RealType<T>> extends AbstractHaralickFeature<T> {
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@OpDependency(name = "features.haralick.coocMeanX")
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private Function<double[][], DoubleType> coocMeanXFunc;
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@OpDependency(name = "features.haralick.coocMeanY")
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private Function<double[][], DoubleType> coocMeanYFunc;
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@Override
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public DoubleType apply(final IterableInterval<T> input, final Integer numGreyLevels, final Integer distance,
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final MatrixOrientation orientation) {
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final double[][] matrix = getCooccurrenceMatrix(input, numGreyLevels, distance, orientation);
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final double mux = coocMeanXFunc.apply(matrix).getRealDouble();
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final double muy = coocMeanYFunc.apply(matrix).getRealDouble();
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double res = 0;
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for (int j = 0; j < matrix.length; j++) {
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for (int i = 0; i < matrix.length; i++) {
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res += Math.pow(i + j - mux - muy, 3) * matrix[j][i];
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}
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}
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DoubleType output = new DoubleType();
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output.setReal(res);
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return output;
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}
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}

‎src/main/java/net/imagej/ops/features/haralick/DefaultContrast.java‎

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/*
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* #%L
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* ImageJ software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2018 ImageJ developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package net.imagej.ops.features.haralick;
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import java.util.function.Function;
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import net.imagej.ops.image.cooccurrenceMatrix.MatrixOrientation;
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import net.imglib2.IterableInterval;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.ops.OpDependency;
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import org.scijava.ops.core.Op;
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import org.scijava.param.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.struct.ItemIO;
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/**
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*
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* Implementation of texture contrast haralick feature.
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*
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* @author Andreas Graumann (University of Konstanz)
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* @author Christian Dietz (University of Konstanz)
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*
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*/
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@Plugin(type = Op.class, name = "features.haralick.contrast")
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@Parameter(key = "input")
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@Parameter(key = "numGreyLevels")
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@Parameter(key = "distance")
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@Parameter(key = "matrixOrientation")
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@Parameter(key = "output", type = ItemIO.OUTPUT)
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public class DefaultContrast<T extends RealType<T>> extends AbstractHaralickFeature<T> {
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@OpDependency(name = "features.haralick.coocPXMinusY")
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private Function<double[][], double[]> coocPXMinusYFunc;
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@Override
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public DoubleType apply(final IterableInterval<T> input, final Integer numGreyLevels, final Integer distance,
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final MatrixOrientation orientation) {
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final double[][] matrix = getCooccurrenceMatrix(input, numGreyLevels, distance, orientation);
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final double[] pxminusxy = coocPXMinusYFunc.apply(matrix);
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double res = 0;
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for (int k = 0; k <= matrix.length - 1; k++) {
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res += k * k * pxminusxy[k];
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}
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DoubleType output = new DoubleType();
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output.set(res);
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return output;
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}
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}

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