WIP: Update to scijava-ops-indexer

pom.xml

@@ -201,7 +201,7 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 		<net.imglib2.imglib2.version>6.2.0</net.imglib2.imglib2.version>
-		<therapi.packages/>
+		<scijava.parse.ops>true</scijava.parse.ops>
 	</properties>
 
 	<repositories>
@@ -280,29 +280,30 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 
 	<build>
 		<plugins>
-			<plugin>
-				<artifactId>maven-javadoc-plugin</artifactId>
-				<configuration>
-					<additionalparam>--allow-script-in-comments -header '&lt;script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"&gt;&lt;/script&gt;'</additionalparam>
-				</configuration>
-			</plugin>
-			<!-- TODO: Remove once version handled by pom-scijava-base -->
 			<plugin>
 				<artifactId>maven-compiler-plugin</artifactId>
 				<configuration>
 					<annotationProcessorPaths>
 						<path>
-							<groupId>com.github.therapi</groupId>
-							<artifactId>therapi-runtime-javadoc-scribe</artifactId>
-							<version>0.12.0</version>
+							<groupId>org.scijava</groupId>
+							<artifactId>scijava-ops-indexer</artifactId>
+							<version>0-SNAPSHOT</version>
 						</path>
 					</annotationProcessorPaths>
 					<fork>true</fork>
+					<showWarnings>true</showWarnings>
 					<compilerArgs>
-						<arg>-Ajavadoc.packages=${therapi.packages}</arg>
+						<arg>-Aparse.ops="${scijava.parse.ops}"</arg>
+						<arg>-Aop.version="${project.version}"</arg>
 					</compilerArgs>
 				</configuration>
 			</plugin>
+			<plugin>
+				<artifactId>maven-javadoc-plugin</artifactId>
+				<configuration>
+					<additionalparam>--allow-script-in-comments -header '&lt;script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"&gt;&lt;/script&gt;'</additionalparam>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 </project>

src/main/java/net/imglib2/algorithm/binary/Thresholder.java

@@ -59,7 +59,7 @@ public class Thresholder
 	 * Returns a new boolean {@link Img} generated by thresholding the values of
 	 * the source image.
 	 *
-	 * @implNote op name='threshold',type='org.scijava.function.Functions.Arity4'
+	 * @implNote op name='threshold',type=Function
 	 * @param source
 	 *            the image to threshold.
 	 * @param threshold

src/main/java/net/imglib2/algorithm/componenttree/BuildComponentTree.java

@@ -87,7 +87,7 @@ 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='buildComponentTree',type='org.scijava.function.Functions.Arity4'
+	 * @implNote op name='buildComponentTree',type=Function
 	 * @param input
 	 *            input image.
 	 * @param componentGenerator
@@ -112,7 +112,7 @@ public static < T extends Type< T >, C extends PartialComponent< T, C > > void b
 	 * tree structure. An implementations of {@link PartialComponent.Handler} is
 	 * provided for example by {@link PixelListComponentTree}.
 	 *
-	 * @implNote op name='buildComponentTree',type='org.scijava.function.Functions.Arity4'
+	 * @implNote op name='buildComponentTree',type=Function
 	 * @param input
 	 *            input image of a comparable value type.
 	 * @param componentGenerator

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='buildMserTree',type='org.scijava.function.Functions.Arity7'
+	 * @implNote op name='buildMserTree',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='buildMserTree',type='org.scijava.function.Functions.Arity7'
+	 * @implNote op name='buildMserTree',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='buildMserTree',type='org.scijava.function.Functions.Arity8'
+	 * @implNote op name='buildMserTree',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='buildMserTree',type='org.scijava.function.Functions.Arity8'
+	 * @implNote op name='buildMserTree',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='buildMserTree',type='org.scijava.function.Functions.Arity9'
+	 * @implNote op name='buildMserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param computeDelta

src/main/java/net/imglib2/algorithm/componenttree/pixellist/PixelListComponentTree.java

@@ -74,7 +74,7 @@ public final class PixelListComponentTree< T extends Type< T > > implements Comp
 	 * using an {@link ArrayImgFactory} or {@link CellImgFactory} depending on
 	 * input image size.
 	 *
-	 * @implNote op name='buildPixelListComponentTree',type='org.scijava.function.Functions.Arity3'
+	 * @implNote op name='buildPixelListComponentTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param type
@@ -93,7 +93,7 @@ public static < T extends RealType< T > > PixelListComponentTree< T > buildCompo
 	/**
 	 * Build a component tree from an input image.
 	 *
-	 * @implNote op name='buildPixelListComponentTree',type='org.scijava.function.Functions.Arity4'
+	 * @implNote op name='buildPixelListComponentTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param type
@@ -122,7 +122,7 @@ public static < T extends RealType< T > > PixelListComponentTree< T > buildCompo
 	 * using an {@link ArrayImgFactory} or {@link CellImgFactory} depending on
 	 * input image size.
 	 *
-	 * @implNote op name='buildPixelListComponentTree',type='org.scijava.function.Functions.Arity3'
+	 * @implNote op name='buildPixelListComponentTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param maxValue
@@ -141,7 +141,7 @@ public static < T extends Type< T > > PixelListComponentTree< T > buildComponent
 	/**
 	 * Build a component tree from an input image.
 	 *
-	 * @implNote op name='buildPixelListComponentTree',type='org.scijava.function.Functions.Arity4'
+	 * @implNote op name='buildPixelListComponentTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param maxValue

src/main/java/net/imglib2/algorithm/convolution/fast_gauss/FastGauss.java

@@ -79,31 +79,31 @@ public class FastGauss
 	}
 
 	/**
-	 * @implNote op name='convolveFastGauss',type='java.util.function.Function'
+	 * @implNote op name='convolveFastGauss',type=Function
 	 */
 	public static Convolution< RealType< ? > > convolution( final double sigma )
 	{
 		return new MultiDimensionConvolution<>( k -> convolution( nCopies( k, sigma ) ) );
 	}
 
 	/**
-	 * @implNote op name='convolveFastGauss',type='java.util.function.BiFunction'
+	 * @implNote op name='convolveFastGauss',type=Function
 	 */
 	public static Convolution< RealType< ? > > convolution1d( final double sigma, final int direction )
 	{
 		return new LineConvolution<>( new FastGaussConvolverRealType( sigma ), direction );
 	}
 
 	/**
-	 * @implNote op name='convolveFastGauss',type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='convolveFastGauss',type=Computer
 	 */
 	public static void convolve( final double[] sigmas, final RandomAccessible< ? extends RealType< ? > > input, final RandomAccessibleInterval< ? extends RealType< ? > > output )
 	{
 		convolution( sigmas ).process( input, output );
 	}
 
 	/**
-	 * @implNote op name='convolveFastGauss',type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='convolveFastGauss',type=Computer
 	 */
 	public static void convolve( final double sigma, final RandomAccessible< ? extends RealType< ? > > input, final RandomAccessibleInterval< ? extends RealType< ? > > output )
 	{

src/main/java/net/imglib2/algorithm/convolution/kernel/Kernel1D.java

@@ -53,10 +53,11 @@ public class Kernel1D
 	/**
 	 * Creates a one-dimensional symmetric convolution kernel.
 	 *
-	 * @implNote op name='create.kernel1DSymmetric',type='java.util.function.Function'
+	 * @implNote op name='create.kernel1DSymmetric',type=Function
 	 * @param halfKernel
 	 *            the upper half (starting at the center pixel) of the symmetric
 	 *            convolution kernel.
+	 * @return a {@link Kernel1D} used for one dimensional convolutions
 	 */
 	public static Kernel1D symmetric( final double... halfKernel )
 	{
@@ -69,7 +70,7 @@ public static Kernel1D symmetric( final double... halfKernel )
 	/**
 	 * Similar to {@link #symmetric(double[])} but creates an array of
 	 * one-dimensional convolution kernels.
-	 * @implNote op name='create.kernel1DSymmetric',type='java.util.function.Function'
+	 * @implNote op name='create.kernel1DSymmetric',type=Function
 	 */
 	public static Kernel1D[] symmetric( final double[][] halfKernels )
 	{
@@ -79,12 +80,13 @@ public static Kernel1D[] symmetric( final double[][] halfKernels )
 	/**
 	 * Creates a one-dimensional asymmetric convolution kernel.
 	 *
-	 * @implNote op name='create.kernel1DAsymmetric',type='java.util.function.BiFunction'
+	 * @implNote op name='create.kernel1DAsymmetric',type=Function
 	 * @param fullKernel
 	 *            an array containing the values of the kernel
 	 * @param originIndex
 	 *            the index of the array element which is the origin of the
 	 *            kernel
+	 * @return an asymmetric {@link Kernel1D} used for one dimensional convolutions
 	 */
 	public static Kernel1D asymmetric( final double[] fullKernel, final int originIndex )
 	{
@@ -97,7 +99,7 @@ public static Kernel1D asymmetric( final double[] fullKernel, final int originIn
 	/**
 	 * Creates a one-dimensional asymmetric convolution kernel, where the origin
 	 * of the kernel is in the middle.
-	 * @implNote op name='create.kernel1DCentralAsymmetric',type='java.util.function.Function'
+	 * @implNote op name='create.kernel1DCentralAsymmetric',type=Function
 	 */
 	public static Kernel1D centralAsymmetric( final double... kernel )
 	{
@@ -107,7 +109,7 @@ public static Kernel1D centralAsymmetric( final double... kernel )
 	/**
 	 * Similar to {@link #asymmetric(double[], int)} but creates an array of
 	 * one-dimensional convolution kernels.
-	 * @implNote op name='create.kernel1DAsymmetric',type='java.util.function.BiFunction'
+	 * @implNote op name='create.kernel1DAsymmetric',type=Function
 	 */
 	public static Kernel1D[] asymmetric( final double[][] fullKernels, final int[] originIndices )
 	{
@@ -118,7 +120,7 @@ public static Kernel1D[] asymmetric( final double[][] fullKernels, final int[] o
 	/**
 	 * Similar to {@link #centralAsymmetric(double...)} but creates an array of
 	 * one-dimensional convolution kernels.
-	 * @implNote op name='create.kernel1DCentralAsymmetric',type='java.util.function.Function'
+	 * @implNote op name='create.kernel1DCentralAsymmetric',type=Function
 	 */
 	public static Kernel1D[] centralAsymmetric( final double[][] kernels )
 	{

src/main/java/net/imglib2/algorithm/convolution/kernel/SeparableKernelConvolution.java

@@ -68,7 +68,9 @@ public class SeparableKernelConvolution
 	 * }
 	 * </pre>
 	 *
-	 * @implNote op name='filter.convolveSeparable',type='java.util.function.Function'
+	 * @param kernels the kernel(s) to use in the convolution
+	 * @return a {@link Convolution} object that can convolve an image
+	 * @implNote op name='filter.convolveSeparable',type=Function
 	 * @see Convolution
 	 */
 	public static Convolution< NumericType< ? > > convolution( final Kernel1D... kernels )
@@ -90,7 +92,10 @@ public class SeparableKernelConvolution
 	 * }
 	 * </pre>
 	 *
-	 * @implNote op name='filter.convolveSeparable',type='java.util.function.BiFunction'
+	 * @param kernel the kernel to use in the convolution
+	 * @param direction the direction to use in the convolution
+	 * @return a {@link Convolution} object that can convolve an image
+	 * @implNote op name='filter.convolveSeparable',type=Function
 	 * @see Convolution
 	 */
 	public static Convolution< NumericType< ? > > convolution1d( final Kernel1D kernel, final int direction )
@@ -108,7 +113,7 @@ public class SeparableKernelConvolution
 	 * in their own precision. The source type S and target type T are either
 	 * both {@link RealType RealTypes} or both the same type.
 	 *
-	 * @implNote op name='filter.convolveSeparable',type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='filter.convolveSeparable',type=Computer
 	 * @param kernels
 	 *            an array containing kernels for every dimension.
 	 * @param source

src/main/java/net/imglib2/algorithm/edge/SubpixelEdgelDetection.java

@@ -74,7 +74,7 @@ public class SubpixelEdgelDetection
 	 * Note: The input image type must be a signed type! Otherwise gradient
 	 * computation will not work.
 	 *
-	 * @implNote op name='subpixelEdgels', type='org.scijava.function.Functions.Arity3'
+	 * @implNote op name='subpixelEdgels', type=Function
 	 * @param input
 	 *            input image
 	 * @param factory

src/main/java/net/imglib2/algorithm/fill/FloodFill.java

@@ -120,7 +120,7 @@ public static < T extends Type< T >, U extends Type< U > > void fill(
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='floodFill', type='org.scijava.function.Computers.Arity4'
+	 * @implNote op name='floodFill', type=Computer
 	 * @param source
 	 *            input
 	 * @param seed
@@ -212,7 +212,7 @@ public static < T, U extends Type< U > > void fill(
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='floodFill', type='org.scijava.function.Computers.Arity5'
+	 * @implNote op name='floodFill', type=Computer
 	 * @param source
 	 *            input
 	 * @param seed
@@ -347,7 +347,7 @@ public static < T, U > void fill(
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='floodFill', type='org.scijava.function.Computers.Arity5'
+	 * @implNote op name='floodFill', type=Computer
 	 * @param source
 	 *            input
 	 * @param seed

src/main/java/net/imglib2/algorithm/gauss3/Gauss3.java

@@ -74,7 +74,7 @@ public final class Gauss3
 	 * {@link Parallelization} context. (By default, it will use the
 	 * {@link ForkJoinPool#commonPool() common ForkJoinPool})
 	 *
-	 * @implNote op name='gauss', type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='gauss', type=Computer
 	 * @param sigma
 	 *            standard deviation of isotropic Gaussian.
 	 * @param source
@@ -117,7 +117,7 @@ public static < S extends NumericType< S >, T extends NumericType< T > > void ga
 	 * {@link Parallelization} context. (By default, it will use the
 	 * {@link ForkJoinPool#commonPool() common ForkJoinPool})
 	 *
-	 * @implNote op name='gauss', type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='gauss', type=Computer
 	 * @param sigma
 	 *            standard deviation in every dimension.
 	 * @param source

src/main/java/net/imglib2/algorithm/gradient/PartialDerivative.java

@@ -100,7 +100,7 @@ public static < T extends NumericType< T > > void gradientCentralDifference2( fi
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='gradientCentralDifference2', type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='gradientCentralDifference2', type=Computer
 	 * @param source
 	 *            source image, has to provide valid data in the interval of the
 	 *            gradient image plus a one pixel border in dimension.
@@ -201,7 +201,7 @@ public static < T extends NumericType< T > > void gradientCentralDifferenceParal
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='gradientCentralDifferenceParallel', type='org.scijava.function.Computers.Arity4'
+	 * @implNote op name='gradientCentralDifferenceParallel', type=Computer
 	 * @param source
 	 *            source image, has to provide valid data in the interval of the
 	 *            gradient image plus a one pixel border in dimension.
@@ -265,7 +265,7 @@ public static < T extends NumericType< T > > void gradientCentralDifference( fin
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='gradientCentralDifference', type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='gradientCentralDifference', type=Computer
 	 * @param source
 	 *            source image, has to provide valid data in the interval of the
 	 *            gradient image plus a one pixel border in dimension.
@@ -313,7 +313,7 @@ public static < T extends NumericType< T > > void gradientBackwardDifference( fi
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='gradientBackwardDifference', type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='gradientBackwardDifference', type=Computer
 	 * @param source source image, has to provide valid data in the interval of
 	 *            the gradient image plus a one pixel border in dimension.
 	 * @param dimension along which dimension the partial derivatives are computed
@@ -358,7 +358,7 @@ public static < T extends NumericType< T > > void gradientForwardDifference( fin
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='gradientForwardDifference', type='org.scijava.function.Computers.Arity2'
+	 * @implNote op name='gradientForwardDifference', type=Computer
 	 * @param source source image, has to provide valid data in the interval of
 	 *            the gradient image plus a one pixel border in dimension.
 	 * @param dimension along which dimension the partial derivatives are computed