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elevanselevans
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Add SACA PValue heatmatp op
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‎scijava-ops-image/src/main/java/org/scijava/ops/image/coloc/saca/PNorm.java‎

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/*-
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* #%L
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* ImageJ2 software for multidimensional image processing and analysis.
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* %%
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* Copyright (C) 2014 - 2024 ImageJ2 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 org.scijava.ops.image.coloc.saca;
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import net.imglib2.loops.LoopBuilder;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.apache.commons.math3.distribution.NormalDistribution;
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/**
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* Helper class for Spatially Adaptive Colocalization Analysis (SACA) op.
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*
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* @author Edward Evans
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*/
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public final class PNorm {
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private PNorm() {}
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public static void compute(RandomAccessibleInterval<DoubleType> input,
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boolean lowerTail, RandomAccessibleInterval<DoubleType> output)
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{
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// compute normal distribution over the image
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NormalDistribution normalDistribution = new NormalDistribution();
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LoopBuilder.setImages(input, output).multiThreaded().forEachPixel((i, o) -> {
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double normDistValue = normalDistribution.cumulativeProbability(i.get());
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if (!lowerTail) {
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normDistValue = 1 - normDistValue;
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}
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o.set(normDistValue);
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});
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}
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}

‎scijava-ops-image/src/main/java/org/scijava/ops/image/coloc/saca/SACAHeatmapPValue.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 - 2024 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 org.scijava.ops.image.coloc.saca;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.function.Computers;
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import org.scijava.ops.spi.Nullable;
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/**
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* Spatially Adaptive Colocalization Analysis (SACA) Adapted from Shulei's
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* original Java code for AdaptiveSmoothedKendallTau from his RKColocal R
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* package.
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* (https://github.com/lakerwsl/RKColocal/blob/master/RKColocal_0.0.1.0000.tar.gz)
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*
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* @author Shulei Wang
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* @author Curtis Rueden
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* @author Ellen TA Dobson
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* @author Edward Evans
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* @implNote op names='coloc.saca.heatmapPValue', priority='100.'
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*/
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public class SACAHeatmapPValue implements
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Computers.Arity2<RandomAccessibleInterval<DoubleType>, Boolean, RandomAccessibleInterval<DoubleType>>
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{
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/**
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* Spatially Adaptive Colocalization Analysis (SACA) P Value heatmap
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*
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* @param heatmap input heatmap returned from 'coloc.saca.heatmapZScore'
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* @param lowerTail lower tail (default=false)
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* @param result P value heatmap output
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*/
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@Override
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public void compute(final RandomAccessibleInterval<DoubleType> heatmap,
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@Nullable Boolean lowerTail, RandomAccessibleInterval<DoubleType> result)
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{
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// set lowerTail if necessary
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if (lowerTail == null) lowerTail = true;
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// compute the normal distribution
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PNorm.compute(heatmap, lowerTail, result);
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}
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}

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