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gselzergselzer
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Modernize added code
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-53
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3 files changed

+32
-53
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‎imagej/imagej-ops2/src/main/java/module-info.java‎

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

‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/transform/realTransform/DefaultTransformView.java‎ renamed to ‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/transform/DefaultTransformView.java‎

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@@ -27,7 +27,10 @@
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* #L%
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*/
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package net.imagej.ops2.transform.realTransform;
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package net.imagej.ops2.transform;
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import org.scijava.function.Functions;
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import org.scijava.ops.spi.Optional;
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import net.imglib2.FinalInterval;
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import net.imglib2.Interval;
@@ -39,30 +42,16 @@
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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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* @implNote op names="transform.realTransform", priority="101.0"
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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>>
@@ -72,7 +61,7 @@ public class DefaultTransformView<T extends NumericType<T> & RealType<T>>
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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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* {@link Functions.Arity4}
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*
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* @param input the input
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* @param transform the transform to apply
@@ -82,10 +71,12 @@ public class DefaultTransformView<T extends NumericType<T> & RealType<T>>
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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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public RandomAccessibleInterval<T> apply( //
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RandomAccessibleInterval<T> input, //
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InvertibleRealTransform transform, //
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@Optional Interval outputInterval, //
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@Optional 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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}
@@ -94,11 +85,11 @@ public RandomAccessibleInterval<T> apply(RandomAccessibleInterval<T> input,
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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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var extended = Views.extendZero(input);
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var interpolated = Views.interpolate(extended, interpolator);
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var transformed = RealViews.transformReal(interpolated, transform);
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var rasterized = Views.raster(transformed);
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return Views.interval(rasterized, outputInterval);
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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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@@ -27,56 +27,43 @@ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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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 static org.junit.jupiter.api.Assertions.assertEquals;
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import org.junit.jupiter.api.Test;
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import org.scijava.types.Nil;
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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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55-
final Img<UnsignedByteType> image = openUnsignedByteType(getClass(),
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final Img<UnsignedByteType> image = openRelativeUnsignedByteImg(getClass(),
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"lowresbridge.tif");
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final Img<UnsignedByteType> expectedOutput = openUnsignedByteType(
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final Img<UnsignedByteType> expectedOutput = openRelativeUnsignedByteImg(
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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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double translation = ((double) image.dimension(0) / 2);
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transform.translate(-translation, -translation);
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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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transform.translate(translation, translation);
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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<>()
74-
{};
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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,
77-
intervalNil, factoryNil).outType(imgNil).function();
78-
final RandomAccessibleInterval<UnsignedByteType> actualOutput = f.apply(
79-
image, transform, null, null);
62+
var outType = new Nil<RandomAccessibleInterval<UnsignedByteType>>() {};
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var actualOutput = ops.op("transform.realTransform").arity2() //
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.input(image, transform) //
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.outType(outType) //
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.apply();
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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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