Merge pull request #36 from scijava/imagej/imagej-ops2/real-transform

RealTransform

Author: ctrueden

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

@@ -167,6 +167,7 @@
 	requires ojalgo;
 	requires jama;
 	requires mines.jtk;
+	requires net.imglib2.realtransform;
 
 	provides org.scijava.types.TypeExtractor with
 			net.imagej.ops2.types.ImgFactoryTypeExtractor,

imagej/imagej-ops2/src/main/java/net/imagej/ops2/transform/DefaultTransformView.java

@@ -0,0 +1,95 @@
+/*
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2018 ImageJ 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.ops2.transform;
+
+import org.scijava.function.Functions;
+import org.scijava.ops.spi.Optional;
+
+import net.imglib2.FinalInterval;
+import net.imglib2.Interval;
+import net.imglib2.RandomAccessible;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.interpolation.InterpolatorFactory;
+import net.imglib2.interpolation.randomaccess.LanczosInterpolatorFactory;
+import net.imglib2.realtransform.InvertibleRealTransform;
+import net.imglib2.realtransform.RealViews;
+import net.imglib2.type.numeric.NumericType;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.view.Views;
+
+/**
+ * Applies an Affine transform to a {@link RandomAccessibleInterval}
+ *
+ * @author Brian Northan (True North Intelligent Algorithms)
+ * @author Martin Horn (University of Konstanz)
+ * @author Stefan Helfrich (University of Konstanz)
+ * @implNote op names="transform.realTransform", priority="101.0"
+ */
+public class DefaultTransformView<T extends NumericType<T> & RealType<T>>
+	implements
+	Functions.Arity4<RandomAccessibleInterval<T>, InvertibleRealTransform, Interval, InterpolatorFactory<T, RandomAccessible<T>>, RandomAccessibleInterval<T>>
+{
+
+	/**
+	 * TODO: declare {@code outputInterval}, {@code interpolator} as optional once
+	 * <a href=https://github.com/scijava/incubator/pull/32>this issue</a> has
+	 * been resolved. Until then, this op <b>must</b> be called as a
+	 * {@link Functions.Arity4}
+	 * 
+	 * @param input the input
+	 * @param transform the transform to apply
+	 * @param outputInterval the output interval
+	 * @param interpolator the {@link InterpolatorFactory} delegated to for
+	 *          interpolation
+	 * @return the output
+	 */
+	@Override
+	public RandomAccessibleInterval<T> apply( //
+		RandomAccessibleInterval<T> input, //
+		InvertibleRealTransform transform, //
+		@Optional Interval outputInterval, //
+		@Optional InterpolatorFactory<T, RandomAccessible<T>> interpolator //
+	) {
+		if (outputInterval == null) {
+			outputInterval = new FinalInterval(input);
+		}
+
+		if (interpolator == null) {
+			interpolator = new LanczosInterpolatorFactory<>();
+		}
+
+		var extended = Views.extendZero(input);
+		var interpolated = Views.interpolate(extended, interpolator);
+		var transformed = RealViews.transformReal(interpolated, transform);
+		var rasterized = Views.raster(transformed);
+		return Views.interval(rasterized, outputInterval);
+	}
+
+}

imagej/imagej-ops2/src/test/java/net/imagej/ops2/OpRegressionTest.java

@@ -39,7 +39,7 @@ public class OpRegressionTest extends AbstractOpTest {
 
 	@Test
 	public void opDiscoveryRegressionIT() {
-		long expected = 1457;
+		long expected = 1460;
 		long actual = StreamSupport.stream(ops.infos().spliterator(), false).count();
 		assertEquals(expected, actual);
 	}

imagej/imagej-ops2/src/test/java/net/imagej/ops2/transform/realTransform/RealTransformTest.java

@@ -0,0 +1,84 @@
+/*-
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2018 ImageJ 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.ops2.transform.realTransform;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.Test;
+import org.scijava.types.Nil;
+
+import net.imagej.ops2.AbstractOpTest;
+import net.imglib2.Cursor;
+import net.imglib2.RandomAccess;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.Img;
+import net.imglib2.realtransform.AffineTransform2D;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.view.Views;
+
+public class RealTransformTest extends AbstractOpTest {
+
+	@Test
+	public void regressionTest() {
+
+		final Img<UnsignedByteType> image = openRelativeUnsignedByteImg(getClass(),
+			"lowresbridge.tif");
+		final Img<UnsignedByteType> expectedOutput = openRelativeUnsignedByteImg(
+			getClass(), "rotatedscaledcenter.tif");
+
+		final AffineTransform2D transform = new AffineTransform2D();
+
+		double translation = ((double) image.dimension(0) / 2);
+		transform.translate(-translation, -translation);
+		transform.rotate(1);
+		transform.scale(0.5);
+		transform.translate(translation, translation);
+
+		var outType = new Nil<RandomAccessibleInterval<UnsignedByteType>>() {};
+		var actualOutput = ops.op("transform.realTransform").arity2() //
+			.input(image, transform) //
+			.outType(outType) //
+			.apply();
+
+		// compare the output image data to that stored in the file.
+		final Cursor<UnsignedByteType> cursor = Views.iterable(actualOutput)
+			.localizingCursor();
+		final RandomAccess<UnsignedByteType> actualRA = actualOutput.randomAccess();
+		final RandomAccess<UnsignedByteType> expectedRA = expectedOutput
+			.randomAccess();
+
+		while (cursor.hasNext()) {
+			cursor.fwd();
+			actualRA.setPosition(cursor);
+			expectedRA.setPosition(cursor);
+			assertEquals(expectedRA.get().get(), actualRA.get().get(), 0);
+		}
+
+	}
+
+}