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DefaultGaussRAI.java
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DefaultGaussRAI.java
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/*
* #%L
* ImageJ2 software for multidimensional image processing and analysis.
* %%
* Copyright (C) 2014 - 2024 ImageJ2 developers.
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package net.imagej.ops.filter.gauss;
import net.imagej.ops.Ops;
import net.imagej.ops.special.hybrid.AbstractUnaryHybridCF;
import net.imglib2.RandomAccessible;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.algorithm.gauss3.Gauss3;
import net.imglib2.algorithm.gauss3.SeparableSymmetricConvolution;
import net.imglib2.exception.IncompatibleTypeException;
import net.imglib2.outofbounds.OutOfBoundsFactory;
import net.imglib2.outofbounds.OutOfBoundsMirrorFactory;
import net.imglib2.outofbounds.OutOfBoundsMirrorFactory.Boundary;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.NumericType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.view.Views;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.thread.ThreadService;
/**
* Gaussian filter, wrapping {@link Gauss3} of imglib2-algorithms.
*
* @author Christian Dietz (University of Konstanz)
* @author Stephan Saalfeld
* @param <T> type of input and output
*/
@SuppressWarnings({ "unchecked", "rawtypes" })
@Plugin(type = Ops.Filter.Gauss.class, priority = 1.0)
public class DefaultGaussRAI<T extends NumericType<T> & NativeType<T>> extends
AbstractUnaryHybridCF<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>>
implements Ops.Filter.Gauss
{
@Parameter
private ThreadService threads;
@Parameter
private double[] sigmas;
@Parameter(required = false)
private OutOfBoundsFactory<T, RandomAccessibleInterval<T>> outOfBounds;
@Override
public void compute(final RandomAccessibleInterval<T> input,
final RandomAccessibleInterval<T> output)
{
if (outOfBounds == null) {
outOfBounds = new OutOfBoundsMirrorFactory<>(Boundary.SINGLE);
}
final RandomAccessible<FloatType> eIn = //
(RandomAccessible) Views.extend(input, outOfBounds);
try {
SeparableSymmetricConvolution.convolve(Gauss3.halfkernels(sigmas), eIn,
output, threads.getExecutorService());
}
catch (final IncompatibleTypeException e) {
throw new RuntimeException(e);
}
}
@Override
public RandomAccessibleInterval<T> createOutput(
final RandomAccessibleInterval<T> input)
{
return ops().create().img(input);
}
}