Modularize imglib2-imagej

Author: gselzer

pom.xml

@@ -159,6 +159,21 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
+
+		<!--
+		NB: Older versions of OpenJDK 11 have a bug in the javadoc tool,
+		which causes errors like:
+
+		[ERROR] javadoc: error - The code being documented uses packages
+		in the unnamed module, but the packages defined in
+		https://github.com/scijava/scijava/apidocs/ are in named modules.
+
+		The most recent version of OpenJDK 11 known to have this problem
+		is 11.0.8; the oldest version known to have fixed it is 11.0.17.
+		Therefore, we set the minimum build JDK version to 11.0.17 here.
+		-->
+		<scijava.jvm.build.version>[11.0.17,)</scijava.jvm.build.version>
+		<scijava.jvm.version>11</scijava.jvm.version>
 	</properties>
 
 	<repositories>
@@ -192,12 +207,6 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>net.imglib2</groupId>
-			<artifactId>imglib2</artifactId>
-			<classifier>tests</classifier>
-			<scope>test</scope>
-		</dependency>
 		<dependency>
 			<groupId>org.openjdk.jmh</groupId>
 			<artifactId>jmh-core</artifactId>

src/main/java/module-info.java

@@ -0,0 +1,7 @@
+module net.imglib2.imagej {
+    requires net.imglib2;
+    requires ij;
+    requires net.imglib2.cache;
+    requires java.desktop;
+    exports net.imglib2.imagej;
+}

src/test/java/net/imglib2/imagej/imageplus/ImagePlusImgTest.java

@@ -38,7 +38,6 @@
 
 import net.imglib2.img.array.ArrayImgFactory;
 import net.imglib2.type.numeric.real.FloatType;
-import net.imglib2.util.ImgTestHelper;
 import net.imglib2.util.Util;
 
 import org.junit.Test;

src/test/java/net/imglib2/imagej/imageplus/ImgTestHelper.java

@@ -0,0 +1,283 @@
+/*
+ * #%L
+ * ImgLib2: a general-purpose, multidimensional image processing library.
+ * %%
+ * Copyright (C) 2009 - 2025 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
+ * John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
+ * Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
+ * Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
+ * Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
+ * Jean-Yves Tinevez and Michael Zinsmaier.
+ * %%
+ * 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.imglib2.imagej.imageplus;
+
+import java.util.Random;
+import java.util.function.Function;
+
+import net.imglib2.exception.InvalidDimensionsException;
+import net.imglib2.util.Util;
+import org.junit.Assert;
+import net.imglib2.Cursor;
+import net.imglib2.RandomAccess;
+import net.imglib2.img.Img;
+import net.imglib2.img.ImgFactory;
+import net.imglib2.outofbounds.OutOfBoundsPeriodicFactory;
+import net.imglib2.type.numeric.real.FloatType;
+import net.imglib2.view.ExtendedRandomAccessibleInterval;
+
+/**
+ * Helper class for {@link Img} subclass unit tests.
+ * 
+ * @author Stephan Preibisch
+ * @author Stephan Saalfeld
+ * @author Curtis Rueden
+ * @author Philipp Hanslovsky
+ */
+public class ImgTestHelper
+{
+	// which dimensions to test
+	private static final long[][] DIM =
+			new long[][] {
+					{ 127 },
+					{ 288 },
+					{ 135, 111 },
+					{ 172, 131 },
+					{ 15, 13, 33 },
+					{ 110, 38, 30 },
+					{ 109, 34, 111 },
+					{ 12, 43, 92, 10 },
+					{ 21, 34, 29, 13 },
+					{ 5, 12, 30, 4, 21 },
+					{ 14, 21, 13, 9, 12 }
+			};
+
+	public static long[][] dims()
+	{
+		return DIM.clone();
+	}
+
+	private static final long[][] INVALID_DIM = {
+			{ -127 },
+			{ 0 },
+			{ -1, 0 },
+			{ -1, 1 },
+			{ -3, -2 },
+			{ 0, 0, 0 },
+			{ -1, 2, 3 },
+			{ 4, -2, 100 },
+			{ 3151, -235, 8341 },
+			{ 34, 5135, 35163, 0 },
+			{ 35135, 3531, -2, 1 },
+	};
+
+	public static void assertInvalidDims( final ImgFactory< ? > factory )
+	{
+		assertInvalidDims( factory::create );
+	}
+
+	public static void assertInvalidDims( final Function< long[], Img< ? > > factory )
+	{
+		for ( final long[] dims : INVALID_DIM )
+			assertInvalidDims( dims, factory );
+	}
+
+	private static void assertInvalidDims( final long[] dims, final Function< long[], Img< ? > > factory )
+	{
+		try
+		{
+			factory.apply( dims );
+		}
+		catch ( final InvalidDimensionsException exception )
+		{
+			Assert.assertArrayEquals( dims, exception.getDimenionsCopy() );
+			return;
+		}
+		catch ( final Throwable exception )
+		{
+
+			Assert.fail( String.format(
+					"Expected exception of type %s but %s was thrown.",
+					InvalidDimensionsException.class.getName(),
+					exception.getClass().getName() ) );
+		}
+
+		Assert.fail( String.format(
+				"Expected exception of type %s but no exception was thrown.",
+				InvalidDimensionsException.class.getName() ) );
+	}
+
+	public static boolean testImg( final long[] size, final ImgFactory< FloatType > factory1, final ImgFactory< FloatType > factory2 )
+	{
+		// create the image
+		final Img< FloatType > img1 = factory1.create( size );
+		final Img< FloatType > img2 = factory2.create( size );
+
+		final int numDimensions = img1.numDimensions();
+
+		// get a reference to compare to
+		final float[] reference = createReference( img1 );
+
+		// copy into a second image using simple cursors
+		final Cursor< FloatType > cursor1 = img1.cursor();
+		final Cursor< FloatType > cursor2 = img2.cursor();
+
+		while ( cursor1.hasNext() )
+		{
+			cursor1.fwd();
+			cursor2.fwd();
+
+			cursor2.get().set( cursor1.get() );
+		}
+
+		cursor1.reset();
+		cursor2.reset();
+
+		// and copy right back
+		while ( cursor2.hasNext() )
+		{
+			cursor1.fwd();
+			cursor2.fwd();
+
+			cursor1.get().set( cursor2.get() );
+		}
+
+		// copy back into a second image using localizable and positionable
+		// cursors
+		final Cursor< FloatType > localizableCursor1 = img1.localizingCursor();
+		final RandomAccess< FloatType > positionable2 = img2.randomAccess();
+
+		int i = 0;
+
+		while ( localizableCursor1.hasNext() )
+		{
+			localizableCursor1.fwd();
+			++i;
+
+			if ( i % 2 == 0 )
+				positionable2.setPosition( localizableCursor1 );
+			else
+				positionable2.setPosition( localizableCursor1 );
+
+			final FloatType t2 = positionable2.get();
+			final FloatType t1 = localizableCursor1.get();
+//			float f1 = t1.getRealFloat();
+//			float f2 = t2.getRealFloat();
+			t2.set( t1 );
+//			positionable2.get().set( localizableCursor1.get() );
+		}
+
+		// copy again to the first image using a LocalizableByDimOutsideCursor
+		// and a LocalizableByDimCursor
+		final ExtendedRandomAccessibleInterval< FloatType, Img< FloatType > > extendedImg2 = new ExtendedRandomAccessibleInterval< FloatType, Img< FloatType > >( img2, new OutOfBoundsPeriodicFactory< FloatType, Img< FloatType > >() );
+		final RandomAccess< FloatType > outsideCursor2 = extendedImg2.randomAccess();
+		localizableCursor1.reset();
+
+		final int[] pos = new int[ numDimensions ];
+		i = 0;
+		int direction = 1;
+
+		try
+		{
+			while ( localizableCursor1.hasNext() )
+			{
+				localizableCursor1.fwd();
+				localizableCursor1.localize( pos );
+				++i;
+
+				// how many times far away from the original image do we grab
+				// the pixel
+				final int distance = i % 5;
+				direction *= -1;
+
+				pos[ i % numDimensions ] += img1.dimension( i % numDimensions ) * distance * direction;
+
+				if ( i % 7 == 0 )
+					outsideCursor2.setPosition( pos );
+				else
+					outsideCursor2.setPosition( pos );
+
+				final FloatType t1 = localizableCursor1.get();
+				final FloatType t2 = outsideCursor2.get();
+
+//				final float f1 = t1.getRealFloat();
+//				final float f2 = t2.getRealFloat();
+
+				t1.set( t2 );
+
+			}
+		}
+		catch ( final ArrayIndexOutOfBoundsException e )
+		{
+			System.err.println( ( i % 7 == 0 ? "setPosition() " : "moveTo() " ) + Util.printCoordinates( pos ) );
+			e.printStackTrace();
+			System.exit( 1 );
+		}
+
+		final boolean success = test( img1, reference );
+
+		return success;
+	}
+
+	private static float[] createReference( final Img< FloatType > img )
+	{
+		// use a random number generator
+		final Random rnd = new Random( 1241234 );
+
+		// create reference array
+		final float[] reference = new float[ ( int ) img.size() ];
+
+		// iterate over image and reference array and fill with data
+		final Cursor< FloatType > cursor = img.cursor();
+		int i = 0;
+
+		while ( cursor.hasNext() )
+		{
+			cursor.fwd();
+
+			final float value = rnd.nextFloat();
+			reference[ i++ ] = value;
+			cursor.get().set( value );
+		}
+
+		return reference;
+	}
+
+	private static boolean test( final Img< FloatType > img, final float[] reference )
+	{
+		boolean allEqual = true;
+
+		final Cursor< FloatType > cursor = img.cursor();
+		int i = 0;
+
+		while ( cursor.hasNext() )
+		{
+			cursor.fwd();
+			allEqual &= cursor.get().get() == reference[ i++ ];
+		}
+
+		return allEqual;
+	}
+}