WIP: More reorganizing

imglib · Aug 26, 2024 · d73c239 · d73c239
1 parent 75f2f35
commit d73c239
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Showing 20 changed files with 110 additions and 2,490 deletions.
diff --git a/pom.xml b/pom.xml
@@ -206,6 +206,21 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 		<imglib2-roi.version>0.15.0</imglib2-roi.version>
 		<imglib2-cache.version>1.0.0-beta-18</imglib2-cache.version>
 		<sc.fiji.bigdataviewer-core.version>10.4.16</sc.fiji.bigdataviewer-core.version>
+
+		<!--
+		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>8</scijava.jvm.version>
 		<scijava.parse.ops>true</scijava.parse.ops>
 	</properties>
 
@@ -292,7 +307,7 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 						<path>
 							<groupId>org.scijava</groupId>
 							<artifactId>scijava-ops-indexer</artifactId>
-							<version>1.0.1-SNAPSHOT</version>
+							<version>1.0.0</version>
 						</path>
 					</annotationProcessorPaths>
 					<fork>true</fork>

diff --git a/src/main/java/net/imglib2/algorithm/binary/Thresholder.java b/src/main/java/net/imglib2/algorithm/binary/Thresholder.java
@@ -70,7 +70,7 @@ public class Thresholder
 	 *            the number of threads to use for thresholding.
 	 * @return a new {@link Img} of type {@link BitType} and of same dimension
 	 *         that the source image.
-	 * @implNote op name='threshold.value'
+	 * @implNote op name='threshold.apply'
 	 */
 	public static final < T extends Type< T > & Comparable< T >> Img< BitType > threshold( final Img< T > source, final T threshold, final boolean above, final int numThreads )
 	{

diff --git a/src/main/java/net/imglib2/algorithm/componenttree/BuildComponentTree.java b/src/main/java/net/imglib2/algorithm/componenttree/BuildComponentTree.java
@@ -87,7 +87,6 @@ public final class BuildComponentTree< T extends Type< T >, C extends PartialCom
 	 * tree structure. An implementations of {@link PartialComponent.Handler} is
 	 * provided for example by {@link PixelListComponentTree}.
 	 *
-	 * @implNote op name='componenttree.buildComponentTree',type=Function
 	 * @param input
 	 *            input image.
 	 * @param componentGenerator
@@ -111,8 +110,7 @@ public static < T extends Type< T >, C extends PartialComponent< T, C > > void b
 	 * {@link PartialComponent.Handler} which is responsible for building up the
 	 * tree structure. An implementations of {@link PartialComponent.Handler} is
 	 * provided for example by {@link PixelListComponentTree}.
-	 *
-	 * @implNote op name='componenttree.buildComponentTree',type=Function
+	 * 
 	 * @param input
 	 *            input image of a comparable value type.
 	 * @param componentGenerator

diff --git a/src/main/java/net/imglib2/algorithm/componenttree/mser/MserTree.java b/src/main/java/net/imglib2/algorithm/componenttree/mser/MserTree.java
@@ -106,7 +106,7 @@ public final class MserTree< T extends Type< T > > implements ComponentForest< M
 	 * using an {@link ArrayImgFactory} or {@link CellImgFactory} depending on
 	 * input image size.
 	 *
-	 * @implNote op name='componenttree.buildMserTree',type=Function
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param delta
@@ -135,7 +135,7 @@ public static < T extends RealType< T > > MserTree< T > buildMserTree( final Ran
 	 * using an {@link ArrayImgFactory} or {@link CellImgFactory} depending on
 	 * input image size.
 	 *
-	 * @implNote op name='componenttree.buildMserTree',type=Function
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param delta
@@ -162,7 +162,7 @@ public static < T extends RealType< T > > MserTree< T > buildMserTree( final Ran
 	/**
 	 * Build a MSER tree from an input image.
 	 *
-	 * @implNote op name='componenttree.buildMserTree',type=Function
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param delta
@@ -202,7 +202,7 @@ public static < T extends RealType< T > > MserTree< T > buildMserTree( final Ran
 	 * using an {@link ArrayImgFactory} or {@link CellImgFactory} depending on
 	 * input image size.
 	 *
-	 * @implNote op name='componenttree.buildMserTree',type=Function
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param computeDelta
@@ -231,7 +231,7 @@ public static < T extends Type< T > > MserTree< T > buildMserTree( final RandomA
 	/**
 	 * Build a MSER tree from an input image.
 	 *
-	 * @implNote op name='componenttree.buildMserTree',type=Function
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param computeDelta

diff --git a/src/main/java/net/imglib2/algorithm/fill/FloodFill.java b/src/main/java/net/imglib2/algorithm/fill/FloodFill.java
@@ -90,6 +90,7 @@ public class FloodFill
 	 *            input pixel type
 	 * @param <U>
 	 *            fill label type
+	 * @implNote op name='image.floodFill', type=Computer2
 	 */
 	public static < T extends Type< T >, U extends Type< U > > void fill(
 			final RandomAccessible< T > source,
@@ -105,53 +106,6 @@ public static < T extends Type< T >, U extends Type< U > > void fill(
 		fill( source, target, seed, fillLabel, shape, filter );
 	}
 
-	/**
-	 * Iterative n-dimensional flood fill for arbitrary neighborhoods: Starting
-	 * at seed location, write fillLabel into target at current location and
-	 * continue for each pixel in neighborhood defined by shape if neighborhood
-	 * pixel is in the same connected component and fillLabel has not been
-	 * written into that location yet.
-	 *
-	 * Convenience call to
-	 * {@link #fill(RandomAccessible, RandomAccessible, Localizable, Type, Shape, BiPredicate)}.
-	 * seedLabel is extracted from source at seed location.
-	 * <p>
-	 * This method differs from
-	 * {@link #fill(RandomAccessible, RandomAccessible, Localizable, Type, Shape)}
-	 * only in that its parameter order is tailored to an Op. The output comes
-	 * last, and the primary input (the input image) comes first.
-	 * </p>
-	 *
-	 * @implNote op name='image.floodFill', type=Computer
-	 * @param source
-	 *            input
-	 * @param seed
-	 *            Start flood fill at this location.
-	 * @param fillLabel
-	 *            Immutable. Value to be written into valid flood fill
-	 *            locations.
-	 * @param shape
-	 *            Defines neighborhood that is considered for connected
-	 *            components, e.g.
-	 *            {@link net.imglib2.algorithm.neighborhood.DiamondShape}
-	 * @param target
-	 *            {@link RandomAccessible} to be written into. May be the same
-	 *            as input.
-	 * @param <T>
-	 *            input pixel type
-	 * @param <U>
-	 *            fill label type
-	 */
-	public static < T extends Type< T >, U extends Type< U > > void fill(
-			final RandomAccessible< T > source,
-			final Localizable seed,
-			final U fillLabel,
-			final Shape shape,
-			final RandomAccessible< U > target)
-	{
-		fill(source, target, seed, fillLabel, shape);
-	}
-
 	/**
 	 * Iterative n-dimensional flood fill for arbitrary neighborhoods: Starting
 	 * at seed location, write fillLabel into target at current location and
@@ -185,6 +139,7 @@ public static < T extends Type< T >, U extends Type< U > > void fill(
 	 *            input pixel type
 	 * @param <U>
 	 *            fill label type
+	 * @implNote op name='image.floodFill', type=Computer2
 	 */
 	public static < T, U extends Type< U > > void fill(
 			final RandomAccessible< T > source,
@@ -197,58 +152,6 @@ public static < T, U extends Type< U > > void fill(
 		fill( source, target, seed, shape, filter, targetPixel -> targetPixel.set( fillLabel ) );
 	}
 
-	/**
-	 * Iterative n-dimensional flood fill for arbitrary neighborhoods: Starting
-	 * at seed location, write fillLabel into target at current location and
-	 * continue for each pixel in neighborhood defined by shape if neighborhood
-	 * pixel is in the same connected component and fillLabel has not been
-	 * written into that location yet.
-	 *
-	 * Convenience call to
-	 * {@link FloodFill#fill(RandomAccessible, RandomAccessible, Localizable, Shape, BiPredicate, Consumer)}
-	 * with {@link Type#set} as writer.
-	 * <p>
-	 * This method differs from
-	 * {@link #fill(RandomAccessible, RandomAccessible, Localizable, Type, Shape, BiPredicate)}
-	 * only in that its parameter order is tailored to an Op. The output comes
-	 * last, and the primary input (the input image) comes first.
-	 * </p>
-	 *
-	 * @implNote op name='image.floodFill', type=Computer
-	 * @param source
-	 *            input
-	 * @param seed
-	 *            Start flood fill at this location.
-	 * @param fillLabel
-	 *            Immutable. Value to be written into valid flood fill
-	 *            locations.
-	 * @param shape
-	 *            Defines neighborhood that is considered for connected
-	 *            components, e.g.
-	 *            {@link net.imglib2.algorithm.neighborhood.DiamondShape}
-	 * @param filter
-	 *            Returns true if pixel has not been visited yet and should be
-	 *            written into. Returns false if target pixel has been visited
-	 *            or source pixel is not part of the same connected component.
-	 * @param target
-	 *            {@link RandomAccessible} to be written into. May be the same
-	 *            as input.
-	 * @param <T>
-	 *            input pixel type
-	 * @param <U>
-	 *            fill label type
-	 */
-	public static < T, U extends Type< U > > void fill(
-			final RandomAccessible< T > source,
-			final Localizable seed,
-			final U fillLabel,
-			final Shape shape,
-			final BiPredicate< T, U > filter,
-			final RandomAccessible< U > target)
-	{
-		fill( source, target, seed, shape, filter, targetPixel -> targetPixel.set( fillLabel ) );
-	}
-
 	/**
 	 *
 	 * Iterative n-dimensional flood fill for arbitrary neighborhoods: Starting
@@ -279,6 +182,7 @@ public static < T, U extends Type< U > > void fill(
 	 *            input pixel type
 	 * @param <U>
 	 *            fill label type
+	 * @implNote op name='image.floodFill', type=Computer2
 	 */
 	public static < T, U > void fill(
 			final RandomAccessible< T > source,
@@ -335,54 +239,6 @@ public static < T, U > void fill(
 		}
 
 	}
-	/**
-	 *
-	 * Iterative n-dimensional flood fill for arbitrary neighborhoods: Starting
-	 * at seed location, write fillLabel into target at current location and
-	 * continue for each pixel in neighborhood defined by shape if neighborhood
-	 * pixel is in the same connected component and fillLabel has not been
-	 * written into that location yet.
-	 * <p>
-	 * This method differs from
-	 * {@link #fill(RandomAccessible, RandomAccessible, Localizable, Shape, BiPredicate, Consumer)}
-	 * only in that its parameter order is tailored to an Op. The output comes
-	 * last, and the primary input (the input image) comes first.
-	 * </p>
-	 *
-	 * @implNote op name='image.floodFill', type=Computer
-	 * @param source
-	 *            input
-	 * @param seed
-	 *            Start flood fill at this location.
-	 * @param shape
-	 *            Defines neighborhood that is considered for connected
-	 *            components, e.g.
-	 *            {@link net.imglib2.algorithm.neighborhood.DiamondShape}
-	 * @param filter
-	 *            Returns true if pixel has not been visited yet and should be
-	 *            written into. Returns false if target pixel has been visited
-	 *            or source pixel is not part of the same connected component.
-	 * @param writer
-	 *            Defines how fill label is written into target at current
-	 *            location.
-	 * @param target
-	 *            {@link RandomAccessible} to be written into. May be the same
-	 *            as input.
-	 * @param <T>
-	 *            input pixel type
-	 * @param <U>
-	 *            fill label type
-	 */
-	public static < T, U > void fill(
-			final RandomAccessible< T > source,
-			final Localizable seed,
-			final Shape shape,
-			final BiPredicate< T, U > filter,
-			final Consumer< U > writer,
-			final RandomAccessible< U > target )
-	{
-		fill(source, target, seed, shape, filter, writer);
-	}
 
 	/**
 	 * Iterative n-dimensional flood fill for arbitrary neighborhoods: Starting