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Merged
ctrueden merged 1 commit into from
Aug 9, 2024
Merged

Add ERAI type extractor #259

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1 change: 1 addition & 0 deletions scijava-ops-image/src/main/java/module-info.java
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Expand Up @@ -57,6 +57,7 @@
requires net.imglib2.realtransform;

provides org.scijava.types.extract.TypeExtractor with
org.scijava.ops.image.types.ExtendedRAITypeExtractor,
org.scijava.ops.image.types.Histogram1dTypeExtractor,
org.scijava.ops.image.types.ImgFactoryTypeExtractor,
org.scijava.ops.image.types.ImgLabelingTypeExtractor,
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17 changes: 3 additions & 14 deletions scijava-ops-image/src/main/java/org/scijava/ops/image/convert/ConvertImages.java
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Expand Up @@ -29,32 +29,21 @@

package org.scijava.ops.image.convert;

import java.util.function.BiFunction;

import net.imglib2.Dimensions;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.loops.LoopBuilder;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.ComplexType;
import net.imglib2.type.numeric.complex.ComplexDoubleType;
import net.imglib2.type.numeric.complex.ComplexFloatType;
import net.imglib2.type.numeric.integer.ByteType;
import net.imglib2.type.numeric.integer.IntType;
import net.imglib2.type.numeric.integer.LongType;
import net.imglib2.type.numeric.integer.ShortType;
import net.imglib2.type.numeric.integer.Unsigned128BitType;
import net.imglib2.type.numeric.integer.Unsigned12BitType;
import net.imglib2.type.numeric.integer.Unsigned2BitType;
import net.imglib2.type.numeric.integer.Unsigned4BitType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.integer.UnsignedIntType;
import net.imglib2.type.numeric.integer.UnsignedLongType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.integer.*;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.type.numeric.real.FloatType;
import org.scijava.function.Computers;
import org.scijava.ops.spi.OpDependency;

import java.util.function.BiFunction;

/**
* Converters for converting between images of Complex types
*
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72 changes: 72 additions & 0 deletions scijava-ops-image/src/main/java/org/scijava/ops/image/types/ExtendedRAITypeExtractor.java
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/*
* #%L
* Image processing operations for SciJava Ops.
* %%
* Copyright (C) 2014 - 2024 SciJava 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 org.scijava.ops.image.types;

import net.imglib2.util.Util;
import net.imglib2.view.ExtendedRandomAccessibleInterval;
import org.scijava.priority.Priority;
import org.scijava.types.extract.SubTypeExtractor;
import org.scijava.types.extract.TypeExtractor;
import org.scijava.types.extract.TypeReifier;

import java.lang.reflect.Type;

/**
* {@link TypeExtractor} plugin which operates on
* {@link ExtendedRandomAccessibleInterval} objects.
*
* @author Gabriel Selzer
*/
public class ExtendedRAITypeExtractor extends
SubTypeExtractor<ExtendedRandomAccessibleInterval<?, ?>>
{

@Override
public double priority() {
return Priority.HIGH;
}

@Override
public Class<?> baseClass() {
return ExtendedRandomAccessibleInterval.class;
}

@Override
protected Type[] getTypeParameters( //
TypeReifier r, //
ExtendedRandomAccessibleInterval<?, ?> object //
) {
return new Type[] { //
r.reify(Util.getTypeFromInterval(object.getSource())), //
r.reify(object.getSource()) //
};
}

}
1 change: 1 addition & 0 deletions ...va-ops-image/src/main/resources/META-INF/services/org.scijava.types.extract.TypeExtractor
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# -- DO NOT EDIT -- This file is autogenerated
# Instead, modify and re-run <basedir>/bin/generate-meta-inf.sh from the top-level
org.scijava.ops.image.types.ExtendedRAITypeExtractor
org.scijava.ops.image.types.Histogram1dTypeExtractor
org.scijava.ops.image.types.ImgFactoryTypeExtractor
org.scijava.ops.image.types.ImgLabelingTypeExtractor
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58 changes: 40 additions & 18 deletions scijava-ops-image/src/test/java/org/scijava/ops/image/types/TypeExtractorTests.java
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Expand Up @@ -40,6 +40,8 @@
import net.imglib2.outofbounds.OutOfBoundsRandomValueFactory;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.view.ExtendedRandomAccessibleInterval;
import net.imglib2.view.Views;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.scijava.ops.image.AbstractOpTest;
Expand All @@ -56,6 +58,44 @@
*/
public class TypeExtractorTests extends AbstractOpTest {

@Test
public void testExtendedRAITypeExtractor() {
Img<DoubleType> data = ArrayImgs.doubles(20, 20);
// Use an Op to get a histogram
var eRAI = Views.extendZero(data);
// Get the generic type (indirectly using the Type reification system through ops)
Type objType = ops.genericType(eRAI);
Assertions.assertInstanceOf(ParameterizedType.class, objType);
ParameterizedType pType = (ParameterizedType) objType;
// Assert raw type
Assertions.assertEquals(ExtendedRandomAccessibleInterval.class, pType.getRawType());
// Assert first type parameter
Assertions.assertEquals(DoubleType.class, pType.getActualTypeArguments()[0]);
// Assert second type parameter
ParameterizedType secondArgType = (ParameterizedType) pType.getActualTypeArguments()[1];
Assertions.assertEquals(ArrayImg.class, secondArgType.getRawType());
Assertions.assertEquals(DoubleType.class, secondArgType.getActualTypeArguments()[0]);
Assertions.assertEquals(DoubleArray.class, secondArgType.getActualTypeArguments()[1]);
}

@Test
public void testHistogram1dTypeExtractor() {
Img<DoubleType> data = ArrayImgs.doubles(20, 20);
// Use an Op to get a histogram
Histogram1d<DoubleType> doubles = ops.op("image.histogram") //
.input(data) //
.outType(new Nil<Histogram1d<DoubleType>>() {}) //
.apply();
// Get the generic type (indirectly using the Type reification system through ops)
Type objType = ops.genericType(doubles);
Assertions.assertInstanceOf(ParameterizedType.class, objType);
ParameterizedType pType = (ParameterizedType) objType;
// Assert raw type
Assertions.assertEquals(Histogram1d.class, pType.getRawType());
// Assert first type parameter
Assertions.assertArrayEquals(new Type[] {DoubleType.class}, pType.getActualTypeArguments());
}

@Test
public void testOutOfBoundsConstantValueFactoryTypeExtractors() {
OutOfBoundsFactory<UnsignedByteType, RandomAccessibleInterval<UnsignedByteType>> oobf =
Expand Down Expand Up @@ -107,22 +147,4 @@ public void testRAITypeExtractor() {
pType.getActualTypeArguments() //
);
}

@Test
public void testHistogram1dTypeExtractor() {
Img<DoubleType> data = ArrayImgs.doubles(20, 20);
// Use an Op to get a histogram
Histogram1d<DoubleType> doubles = ops.op("image.histogram") //
.input(data) //
.outType(new Nil<Histogram1d<DoubleType>>() {}) //
.apply();
// Get the generic type (indirectly using the Type reification system through ops)
Type objType = ops.genericType(doubles);
Assertions.assertInstanceOf(ParameterizedType.class, objType);
ParameterizedType pType = (ParameterizedType) objType;
// Assert raw type
Assertions.assertEquals(Histogram1d.class, pType.getRawType());
// Assert first type parameter
Assertions.assertArrayEquals(new Type[] {DoubleType.class}, pType.getActualTypeArguments());
}
}