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Merge pull request #219 from maarzt/add-unit-test-utils
Asserts And Radomized Images for JUnit Tests with ImgLib2
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‎src/main/java/net/imglib2/test/ImgLib2Assert.java‎

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/*
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* #%L
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* ImgLib2: a general-purpose, multidimensional image processing library.
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* %%
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* Copyright (C) 2009 - 2018 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
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* John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
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* Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
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* Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
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* Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
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* Jean-Yves Tinevez and Michael Zinsmaier.
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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.imglib2.test;
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import net.imglib2.Cursor;
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import net.imglib2.Interval;
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import net.imglib2.Localizable;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.type.numeric.IntegerType;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.type.operators.ValueEquals;
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import net.imglib2.util.Intervals;
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import net.imglib2.util.Pair;
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import net.imglib2.view.IntervalView;
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import net.imglib2.view.Views;
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import java.util.Arrays;
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import java.util.StringJoiner;
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import java.util.function.BiPredicate;
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public class ImgLib2Assert
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{
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private ImgLib2Assert()
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{
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// prevent from instantiation
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}
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/**
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* Throws an AssertionError, if the content or intervals of the two images differ.
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* Comparision is done pixel wise using {@link ValueEquals#valueEquals(Object)}.
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*/
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public static < A extends ValueEquals< B >, B >
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void assertImageEquals( final RandomAccessibleInterval< ? extends A > actual, final RandomAccessibleInterval< ? extends B > expected )
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{
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assertImageEquals( actual, expected, ValueEquals::valueEquals );
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}
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/**
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* Throws an AssertionError, if the content or intervals of the two images differ.
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* Comparision is done pixel wise. Two pixels are considered equal, if the values
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* returned by {@link RealType#getRealDouble()} differ by less than "tolerance".
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*/
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public static void assertImageEqualsRealType( final RandomAccessibleInterval< ? extends RealType< ? > > actual, final RandomAccessibleInterval< ? extends RealType< ? > > expected, double tolerance )
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{
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assertImageEquals( actual, expected, ( a, e ) -> Math.abs( a.getRealDouble() - e.getRealDouble() ) <= tolerance );
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}
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/**
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* Throws an AssertionError, if the content or intervals of the two images differ.
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* Comparision is done pixel wise. Two pixels are considered equal, if the values
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* returned by {@link IntegerType#getIntegerLong()} are equal.
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*/
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public static void assertImageEqualsIntegerType( final RandomAccessibleInterval< ? extends IntegerType< ? > > actual, final RandomAccessibleInterval< ? extends IntegerType< ? > > expected )
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{
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assertImageEquals( actual, expected, ( a, e ) -> a.getIntegerLong() == e.getIntegerLong() );
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}
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/**
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* Throws an AssertionError, if the content or intervals of the two images differ.
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* Comparision is done pixel wise. Two pixels are considered equal, if the give
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* predicate returns true.
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*/
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public static < A, B >
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void assertImageEquals( final RandomAccessibleInterval< ? extends A > a, final RandomAccessibleInterval< ? extends B > b, BiPredicate< A, B > equals )
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{
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assertIntervalEquals( a, b );
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IntervalView< ? extends Pair< ? extends A, ? extends B > > pairs = Views.interval( Views.pair( a, b ), b );
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Cursor< ? extends Pair< ? extends A, ? extends B > > cursor = pairs.cursor();
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while ( cursor.hasNext() )
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{
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Pair< ? extends A, ? extends B > p = cursor.next();
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if ( !equals.test( p.getA(), p.getB() ) )
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fail( "Pixel values differ on coordinate " +
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positionToString( cursor ) + ", expected: "
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+ p.getA() + " actual: " + p.getB() );
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}
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}
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/**
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* Throws an AssertionError, if the two Intervals differ.
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*/
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public static void assertIntervalEquals( Interval a, Interval b )
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{
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if ( !Intervals.equals( a, b ) )
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fail( "Intervals are different, expected: " + intervalToString( a ) + ", actual: " + intervalToString( b ) );
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}
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// -- Helper methods --
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private static String positionToString( Localizable localizable )
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{
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StringJoiner joiner = new StringJoiner( ", " );
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for ( int i = 0, n = localizable.numDimensions(); i < n; i++ )
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joiner.add( String.valueOf( localizable.getIntPosition( i ) ) );
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return "(" + joiner + ")";
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}
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static String intervalToString( Interval a )
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{
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return "{min=" + Arrays.toString( Intervals.minAsLongArray( a ) ) +
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", max=" + Arrays.toString( Intervals.maxAsLongArray( a ) ) + "}";
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}
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private static void fail( String message )
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{
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throw new AssertionError( message );
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}
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}

‎src/main/java/net/imglib2/test/RandomImgs.java‎

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/*
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* #%L
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* ImgLib2: a general-purpose, multidimensional image processing library.
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* %%
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* Copyright (C) 2009 - 2018 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
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* John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
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* Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
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* Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
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* Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
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* Jean-Yves Tinevez and Michael Zinsmaier.
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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
27+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
28+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
29+
* 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.imglib2.test;
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import net.imglib2.Interval;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.img.Img;
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import net.imglib2.img.array.ArrayImgFactory;
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import net.imglib2.type.NativeType;
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import net.imglib2.type.numeric.ARGBType;
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import net.imglib2.type.numeric.IntegerType;
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import net.imglib2.type.numeric.integer.AbstractIntegerBitType;
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import net.imglib2.type.numeric.integer.ByteType;
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import net.imglib2.type.numeric.integer.IntType;
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import net.imglib2.type.numeric.integer.LongType;
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import net.imglib2.type.numeric.integer.ShortType;
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import net.imglib2.type.numeric.integer.UnsignedByteType;
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import net.imglib2.type.numeric.integer.UnsignedIntType;
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import net.imglib2.type.numeric.integer.UnsignedLongType;
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import net.imglib2.type.numeric.integer.UnsignedShortType;
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import net.imglib2.type.numeric.integer.UnsignedVariableBitLengthType;
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import net.imglib2.type.numeric.real.DoubleType;
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import net.imglib2.type.numeric.real.FloatType;
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import net.imglib2.util.Intervals;
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import net.imglib2.util.Util;
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import net.imglib2.view.Views;
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import java.util.Random;
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import java.util.function.Consumer;
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public class RandomImgs
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{
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private final Random random;
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public static RandomImgs seed( int seed )
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{
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return new RandomImgs( seed );
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}
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private RandomImgs( int seed )
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{
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this.random = new Random( seed );
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}
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/**
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* Creates an image with randomized content.
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* @param type Pixel type
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* @param interval Interval
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*/
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public < T extends NativeType< T > > RandomAccessibleInterval< T > nextImage( final T type, Interval interval )
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{
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long[] sizes = Intervals.dimensionsAsLongArray( interval );
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long[] min = Intervals.minAsLongArray( interval );
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return Views.translate( nextImage( type, sizes ), min );
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}
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/**
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* Creates an image with randomized content
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* @param type Pixel type
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* @param dims Dimensions
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*/
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public < T extends NativeType< T > > Img< T > nextImage( final T type, final long... dims )
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{
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final Img< T > result = new ArrayImgFactory<>( type ).create( dims );
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return randomize( result );
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}
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/**
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* Randomizes the content of the given image.
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* @return Reference to the given image
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*/
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public < I extends RandomAccessibleInterval< T >, T >
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I randomize( final I image )
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{
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final T type = Util.getTypeFromInterval( image );
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Views.iterable( image ).forEach( randomSetter( type ) );
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return image;
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}
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private < T > Consumer< T > randomSetter( final T type )
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{
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if ( ( type instanceof UnsignedByteType )
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|| ( type instanceof ByteType )
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|| ( type instanceof ShortType )
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|| ( type instanceof UnsignedShortType )
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|| ( type instanceof IntType ) )
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return b -> ( ( IntegerType< ? > ) b ).setInteger( random.nextInt() );
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if ( ( type instanceof UnsignedLongType )
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|| ( type instanceof UnsignedIntType )
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|| ( type instanceof AbstractIntegerBitType )
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|| ( type instanceof UnsignedVariableBitLengthType )
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|| ( type instanceof LongType ) )
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return b -> ( ( IntegerType< ? > ) b ).setInteger( random.nextLong() );
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if ( type instanceof ARGBType )
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return b -> ( ( ARGBType ) b ).set( random.nextInt() );
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if ( type instanceof FloatType )
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return b -> ( ( FloatType ) b ).setReal( random.nextFloat() );
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if ( type instanceof DoubleType )
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return b -> ( ( DoubleType ) b ).setReal( random.nextDouble() );
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throw new UnsupportedOperationException( "Randomization of type: " + type.getClass() + " is not supported." );
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}
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}

‎src/main/java/net/imglib2/util/Util.java‎

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package net.imglib2.util;
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37-
import java.util.List;
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import net.imglib2.Dimensions;
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import net.imglib2.Interval;
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import net.imglib2.IterableInterval;
@@ -47,13 +45,21 @@
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import net.imglib2.RealLocalizable;
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import net.imglib2.RealRandomAccess;
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import net.imglib2.RealRandomAccessible;
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import net.imglib2.img.Img;
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import net.imglib2.img.ImgFactory;
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import net.imglib2.img.array.ArrayImg;
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import net.imglib2.img.array.ArrayImgFactory;
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import net.imglib2.img.cell.CellImgFactory;
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import net.imglib2.img.list.ListImgFactory;
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import net.imglib2.type.NativeType;
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import net.imglib2.type.Type;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.type.operators.ValueEquals;
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import net.imglib2.view.Views;
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import java.util.List;
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import java.util.function.BiPredicate;
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import java.util.stream.StreamSupport;
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/**
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* A collection of general-purpose utility methods for working with ImgLib2 data
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return true;
954960
}
955961

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/**
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* Checks if both images have equal intervals and content.
964+
*/
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public static < T extends ValueEquals< U >, U > boolean imagesEqual( final RandomAccessibleInterval< ? extends T > a, final RandomAccessibleInterval< ? extends U > b )
966+
{
967+
return imagesEqual( a, b, ValueEquals::valueEquals );
968+
}
969+
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/**
971+
* Checks if both images have equal intervals and content.
972+
* A predicate must be given to check if two pixels are equal.
973+
*/
974+
public static < T, U > boolean imagesEqual( final RandomAccessibleInterval< ? extends T > a, final RandomAccessibleInterval< ? extends U > b, BiPredicate< T, U > pixelEquals )
975+
{
976+
if ( !Intervals.equals( a, b ) )
977+
return false;
978+
for ( Pair< ? extends T, ? extends U > pair : Views.interval( Views.pair( a, b ), b ) )
979+
if ( !pixelEquals.test( pair.getA(), pair.getB() ) )
980+
return false;
981+
return true;
982+
}
983+
956984
/**
957985
* Writes min(a,b) into a
958986
*
@@ -978,4 +1006,30 @@ final static public void max( final double[] a, final double[] b )
9781006
if ( b[ i ] > a[ i ] )
9791007
a[ i ] = b[ i ];
9801008
}
1009+
1010+
/**
1011+
* Returns the content of {@code Iterable<RealType>} as array of doubles.
1012+
*/
1013+
public static double[] asDoubleArray( Iterable< ? extends RealType< ? > > iterable )
1014+
{
1015+
return StreamSupport.stream( iterable.spliterator(), false ).mapToDouble( RealType::getRealDouble ).toArray();
1016+
}
1017+
1018+
/**
1019+
* Returns the pixels of an RandomAccessibleInterval of RealType as array of doubles.
1020+
* The pixels are sorted in flat iteration order.
1021+
*/
1022+
public static double[] asDoubleArray( RandomAccessibleInterval< ? extends RealType< ? > > rai )
1023+
{
1024+
return asDoubleArray( Views.flatIterable( rai ) );
1025+
}
1026+
1027+
/**
1028+
* Returns the pixels of an image of RealType as array of doubles.
1029+
* The pixels are sorted in flat iteration order.
1030+
*/
1031+
public static double[] asDoubleArray( Img< ? extends RealType< ? > > image )
1032+
{
1033+
return asDoubleArray( ( RandomAccessibleInterval< ? extends RealType< ? > > ) image );
1034+
}
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}

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