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‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/transform/realTransform/DefaultTransformView.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.ops2.transform.realTransform;
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import net.imglib2.FinalInterval;
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import net.imglib2.Interval;
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import net.imglib2.RandomAccessible;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.interpolation.InterpolatorFactory;
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import net.imglib2.interpolation.randomaccess.LanczosInterpolatorFactory;
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import net.imglib2.realtransform.InvertibleRealTransform;
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import net.imglib2.realtransform.RealViews;
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import net.imglib2.type.numeric.NumericType;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.view.IntervalView;
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import net.imglib2.view.Views;
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import org.scijava.Priority;
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import org.scijava.ops.core.Op;
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import org.scijava.ops.function.Functions;
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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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* Applies an Affine transform to a {@link RandomAccessibleInterval}
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*
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* @author Brian Northan (True North Intelligent Algorithms)
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* @author Martin Horn (University of Konstanz)
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* @author Stefan Helfrich (University of Konstanz)
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*/
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@Plugin(type = Op.class, name = "transform.realTransform",
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priority = Priority.HIGH + 1)
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@Parameter(key = "input")
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@Parameter(key = "transform")
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@Parameter(key = "outputInterval")
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@Parameter(key = "interpolator")
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@Parameter(key = "output", itemIO = ItemIO.OUTPUT)
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public class DefaultTransformView<T extends NumericType<T> & RealType<T>>
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implements
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Functions.Arity4<RandomAccessibleInterval<T>, InvertibleRealTransform, Interval, InterpolatorFactory<T, RandomAccessible<T>>, RandomAccessibleInterval<T>>
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{
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/**
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* TODO: declare {@code outputInterval}, {@code interpolator} as optional once
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* <a href=https://github.com/scijava/incubator/pull/32>this issue</a> has
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* been resolved. Until then, this op <b>must</b> be called as a
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* {@link org.scijava.ops.function.Functions.Arity4}
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*
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* @param input the input
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* @param transform the transform to apply
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* @param outputInterval the output interval
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* @param interpolator the {@link InterpolatorFactory} delegated to for
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* interpolation
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* @return the output
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*/
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@Override
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public RandomAccessibleInterval<T> apply(RandomAccessibleInterval<T> input,
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InvertibleRealTransform transform, Interval outputInterval,
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InterpolatorFactory<T, RandomAccessible<T>> interpolator)
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{
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if (outputInterval == null) {
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outputInterval = new FinalInterval(input);
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}
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if (interpolator == null) {
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interpolator = new LanczosInterpolatorFactory<>();
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}
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final IntervalView<T> interval = Views.interval(Views.raster(RealViews
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.transformReal(Views.interpolate(Views.extendZero(input), interpolator),
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transform)), outputInterval);
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return interval;
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}
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}

‎imagej/imagej-ops2/src/test/java/net/imagej/ops2/transform/realTransform/RealTransformTest.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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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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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.ops2.transform.realTransform;
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import static org.junit.Assert.assertEquals;
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import net.imagej.ops2.AbstractOpTest;
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import net.imglib2.Cursor;
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import net.imglib2.Interval;
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import net.imglib2.RandomAccess;
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import net.imglib2.RandomAccessible;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.img.Img;
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import net.imglib2.interpolation.InterpolatorFactory;
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import net.imglib2.realtransform.AffineTransform2D;
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import net.imglib2.realtransform.InvertibleRealTransform;
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import net.imglib2.type.numeric.integer.UnsignedByteType;
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import net.imglib2.view.Views;
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import org.junit.jupiter.api.Test;
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import org.scijava.ops.function.Functions;
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import org.scijava.types.Nil;
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public class RealTransformTest extends AbstractOpTest {
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@Test
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public void regressionTest() throws Exception {
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final Img<UnsignedByteType> image = openUnsignedByteType(getClass(),
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"lowresbridge.tif");
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final Img<UnsignedByteType> expectedOutput = openUnsignedByteType(
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getClass(), "rotatedscaledcenter.tif");
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final AffineTransform2D transform = new AffineTransform2D();
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transform.translate(-image.dimension(0) / 2, -image.dimension(0) / 2);
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transform.rotate(1);
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transform.scale(0.5);
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transform.translate(image.dimension(0) / 2, image.dimension(0) / 2);
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// TODO: make the op call simpler once incubator PR 32 has been merged
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Nil<RandomAccessibleInterval<UnsignedByteType>> imgNil = new Nil<>() {};
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Nil<InvertibleRealTransform> transformNil = Nil.of(
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InvertibleRealTransform.class);
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Nil<Interval> intervalNil = Nil.of(Interval.class);
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Nil<InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>> factoryNil =
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new Nil<>()
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{};
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final Functions.Arity4<RandomAccessibleInterval<UnsignedByteType>, InvertibleRealTransform, Interval, InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, RandomAccessibleInterval<UnsignedByteType>> f =
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ops.op("transform.realTransform").inType(imgNil, transformNil,
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intervalNil, factoryNil).outType(imgNil).function();
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final RandomAccessibleInterval<UnsignedByteType> actualOutput = f.apply(
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image, transform, null, null);
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// compare the output image data to that stored in the file.
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final Cursor<UnsignedByteType> cursor = Views.iterable(actualOutput)
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.localizingCursor();
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final RandomAccess<UnsignedByteType> actualRA = actualOutput.randomAccess();
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final RandomAccess<UnsignedByteType> expectedRA = expectedOutput
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.randomAccess();
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while (cursor.hasNext()) {
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cursor.fwd();
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actualRA.setPosition(cursor);
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expectedRA.setPosition(cursor);
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assertEquals(expectedRA.get().get(), actualRA.get().get(), 0);
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}
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}
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}

‎imagej/imagej-ops2/src/test/resources/net/imagej/ops2/transform/realTransform/lowresbridge.tif

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‎imagej/imagej-ops2/src/test/resources/net/imagej/ops2/transform/realTransform/rotatedscaledcenter.tif

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