Real transform

src/main/java/net/imagej/ops/transform/TransformNamespace.java

@@ -50,6 +50,7 @@
 import net.imglib2.img.array.ArrayImg;
 import net.imglib2.interpolation.InterpolatorFactory;
 import net.imglib2.outofbounds.OutOfBoundsFactory;
+import net.imglib2.realtransform.InvertibleRealTransform;
 import net.imglib2.transform.integer.shear.InverseShearTransform;
 import net.imglib2.transform.integer.shear.ShearTransform;
 import net.imglib2.type.Type;
@@ -173,7 +174,8 @@ public <T> MixedTransformView<T> addDimensionView(
 	@OpMethod(
 		op = net.imagej.ops.transform.collapseNumericView.DefaultCollapseNumeric2CompositeView.class)
 	public <N extends NumericType<N>> CompositeView<N, NumericComposite<N>>
-		collapseNumericView(final RandomAccessible<N> input, final int numChannels)
+		collapseNumericView(final RandomAccessible<N> input,
+			final int numChannels)
 	{
 		return (CompositeView<N, NumericComposite<N>>) ops().run(
 			Ops.Transform.CollapseNumericView.class, input, numChannels);
@@ -335,7 +337,8 @@ ExtendedRandomAccessibleInterval<T, F> extendBorderView(final F input)
 	@OpMethod(
 		op = net.imagej.ops.transform.extendMirrorDoubleView.DefaultExtendMirrorDoubleView.class)
 	public <T, F extends RandomAccessibleInterval<T>>
-		ExtendedRandomAccessibleInterval<T, F> extendMirrorDoubleView(final F input)
+		ExtendedRandomAccessibleInterval<T, F> extendMirrorDoubleView(
+			final F input)
 	{
 		return (ExtendedRandomAccessibleInterval<T, F>) ops().run(
 			Ops.Transform.ExtendMirrorDoubleView.class, input);
@@ -354,7 +357,8 @@ ExtendedRandomAccessibleInterval<T, F> extendMirrorDoubleView(final F input)
 	@OpMethod(
 		op = net.imagej.ops.transform.extendMirrorSingleView.DefaultExtendMirrorSingleView.class)
 	public <T extends Type<T>, F extends RandomAccessibleInterval<T>>
-		ExtendedRandomAccessibleInterval<T, F> extendMirrorSingleView(final F input)
+		ExtendedRandomAccessibleInterval<T, F> extendMirrorSingleView(
+			final F input)
 	{
 		return (ExtendedRandomAccessibleInterval<T, F>) ops().run(
 			Ops.Transform.ExtendMirrorSingleView.class, input);
@@ -1203,4 +1207,46 @@ public <T extends Type<T>> RandomAccessibleInterval<T> concatenateView(
 			ConcatenateViewWithAccessMode.class, source, concatenationAxis, mode);
 	}
 
+	@OpMethod(
+		op = net.imagej.ops.transform.realTransform.DefaultTransformView.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> realTransform(
+		final RandomAccessibleInterval<T> in,
+		final InvertibleRealTransform transform)
+	{
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(
+				Ops.Transform.RealTransform.class, in,
+				transform);
+		return result;
+	}
+
+	@OpMethod(
+		op = net.imagej.ops.transform.realTransform.DefaultTransformView.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> realTransform(
+		final RandomAccessibleInterval<T> in,
+		final InvertibleRealTransform transform, final Interval outputInterval)
+	{
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(
+				Ops.Transform.RealTransform.class, in,
+				transform, outputInterval);
+		return result;
+	}
+
+	@OpMethod(
+		op = net.imagej.ops.transform.realTransform.DefaultTransformView.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> realTransform(
+		final RandomAccessibleInterval<T> in,
+		final InvertibleRealTransform transform, final Interval outputInterval,
+		final InterpolatorFactory<T, RandomAccessible<T>> interpolator)
+	{
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(
+				Ops.Transform.RealTransform.class, in,
+				transform, outputInterval, interpolator);
+		return result;
+	}
+
+
+
 }

src/main/java/net/imagej/ops/transform/realTransform/DefaultTransformView.java

@@ -0,0 +1,99 @@
+/*
+ * #%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.ops.transform.realTransform;
+
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.function.AbstractUnaryFunctionOp;
+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.outofbounds.OutOfBoundsFactory;
+import net.imglib2.outofbounds.OutOfBoundsMirrorFactory;
+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.IntervalView;
+import net.imglib2.view.Views;
+
+import org.scijava.Priority;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+/**
+ * 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)
+ */
+@Plugin(type = Ops.Transform.RealTransform.class, priority = Priority.HIGH + 1)
+public class DefaultTransformView<T extends NumericType<T> & RealType<T>>
+	extends
+	AbstractUnaryFunctionOp<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>>
+	implements Ops.Transform.RealTransform
+{
+
+	/**
+	 * The transform to apply
+	 */
+	@Parameter
+	InvertibleRealTransform transform;
+
+	@Parameter(required = false)
+	private Interval outputInterval;
+
+	@Parameter(required = false)
+	private InterpolatorFactory<T, RandomAccessible<T>> interpolator;
+
+	@Override
+	public RandomAccessibleInterval<T> calculate(
+		final RandomAccessibleInterval<T> input)
+	{
+
+		if (outputInterval == null) {
+			outputInterval = new FinalInterval(input);
+		}
+
+		if (interpolator == null) {
+			interpolator = new LanczosInterpolatorFactory<>();
+		}
+
+		final IntervalView<T> interval = Views.interval(Views.raster(RealViews
+			.transformReal(Views.interpolate(Views.extendZero(input), interpolator),
+				transform)), outputInterval);
+
+		return interval;
+	}
+
+}

src/main/templates/net/imagej/ops/Ops.list

@@ -448,6 +448,7 @@ namespaces = ```
 		[name: "translateView",                  iface: "TranslateView"],
 		[name: "unshearView",                    iface: "UnshearView"],
 		[name: "zeroMinView",                    iface: "ZeroMinView"],
+		[name: "realTransform",                  iface: "RealTransform"],
 	]],
 	[name: "zernike", iface: "Zernike", ops: [
 		[name: "magnitude",                      iface: "Magnitude"],

src/test/java/net/imagej/ops/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.ops.transform.realTransform;
+
+import static org.junit.Assert.assertEquals;
+
+import net.imagej.ops.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;
+
+import org.junit.Test;
+
+public class RealTransformTest extends AbstractOpTest {
+
+	@Test
+	public void regressionTest() throws Exception {
+
+		final Img<UnsignedByteType> image = openUnsignedByteType(getClass(),
+			"lowresbridge.tif");
+		final Img<UnsignedByteType> expectedOutput = openUnsignedByteType(
+			getClass(), "rotatedscaledcenter.tif");
+
+		final AffineTransform2D transform = new AffineTransform2D();
+
+		transform.translate(-image.dimension(0) / 2, -image.dimension(0) / 2);
+		transform.rotate(1);
+		transform.scale(0.5);
+		transform.translate(image.dimension(0) / 2, image.dimension(0) / 2);
+
+		@SuppressWarnings("unchecked")
+		final RandomAccessibleInterval<UnsignedByteType> actualOutput =
+			(RandomAccessibleInterval<UnsignedByteType>) ops.run(
+				net.imagej.ops.transform.realTransform.DefaultTransformView.class,
+				image, transform);
+
+		// 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);
+		}
+
+	}
+
+}