Rename Ops

imglib · Dec 21, 2023 · fc7f865 · fc7f865
1 parent d09eb8b
commit fc7f865
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Showing 50 changed files with 298 additions and 286 deletions.
diff --git a/pom.xml b/pom.xml
@@ -293,8 +293,8 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 					<fork>true</fork>
 					<showWarnings>true</showWarnings>
 					<compilerArgs>
-						<arg>-Aparse.ops="${scijava.parse.ops}"</arg>
-						<arg>-Aop.version="${project.version}"</arg>
+						<arg>-Aparse.ops=${scijava.parse.ops}</arg>
+						<arg>-Aop.version=${project.version}</arg>
 					</compilerArgs>
 				</configuration>
 			</plugin>

diff --git a/src/main/java/net/imglib2/algorithm/binary/Thresholder.java b/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=Function
+	 * @implNote op name='binary.threshold',type=Function
 	 * @param source
 	 *            the image to threshold.
 	 * @param threshold

diff --git a/src/main/java/net/imglib2/algorithm/componenttree/BuildComponentTree.java b/src/main/java/net/imglib2/algorithm/componenttree/BuildComponentTree.java
@@ -87,7 +87,7 @@ 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=Function
+	 * @implNote op name='componenttree.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=Function
+	 * @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='buildMserTree',type=Function
+	 * @implNote op name='componenttree.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=Function
+	 * @implNote op name='componenttree.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=Function
+	 * @implNote op name='componenttree.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=Function
+	 * @implNote op name='componenttree.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=Function
+	 * @implNote op name='componenttree.buildMserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param computeDelta

diff --git a/src/main/java/net/imglib2/algorithm/componenttree/pixellist/PixelListComponentTree.java b/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=Function
+	 * @implNote op name='componenttree.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=Function
+	 * @implNote op name='componenttree.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=Function
+	 * @implNote op name='componenttree.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=Function
+	 * @implNote op name='componenttree.buildPixelListComponentTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param maxValue

diff --git a/src/main/java/net/imglib2/algorithm/convolution/fast_gauss/FastGauss.java b/src/main/java/net/imglib2/algorithm/convolution/fast_gauss/FastGauss.java
@@ -79,31 +79,31 @@ public class FastGauss
 	}
 
 	/**
-	 * @implNote op name='convolveFastGauss',type=Function
+	 * @implNote op name='convolve.fastGauss',type=Function
 	 */
 	public static Convolution< RealType< ? > > convolution( final double sigma )
 	{
 		return new MultiDimensionConvolution<>( k -> convolution( nCopies( k, sigma ) ) );
 	}
 
 	/**
-	 * @implNote op name='convolveFastGauss',type=Function
+	 * @implNote op name='convolve.fastGauss',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=Computer
+	 * @implNote op name='convolve.fastGauss',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=Computer
+	 * @implNote op name='convolve.fastGauss',type=Computer
 	 */
 	public static void convolve( final double sigma, final RandomAccessible< ? extends RealType< ? > > input, final RandomAccessibleInterval< ? extends RealType< ? > > output )
 	{

diff --git a/src/main/java/net/imglib2/algorithm/dog/DifferenceOfGaussian.java b/src/main/java/net/imglib2/algorithm/dog/DifferenceOfGaussian.java
@@ -74,7 +74,7 @@ public class DifferenceOfGaussian
 	 * only in that its parameter order is tailored to an Op. The output comes
 	 * last, and the primary input (the input image) comes first.
 	 *
-	 * @implNote op name="DoG", type="org.scijava.function.Computers.Arity4"
+	 * @implNote op name="filter.DoG", type="org.scijava.function.Computers.Arity4"
 	 * @param input
 	 *            the input image extended to infinity (or at least covering the
 	 *            same interval as the dog result image, plus borders for
@@ -145,7 +145,7 @@ public static < I extends NumericType< I >, T extends NumericType< T > & NativeT
 	 * only in that its parameter order is tailored to an Op. The output comes
 	 * last, and the primary input (the input image) comes first.
 	 *
-	 * @implNote op name="DoG", type="org.scijava.function.Computers.Arity5"
+	 * @implNote op name="filter.DoG", type="org.scijava.function.Computers.Arity5"
 	 * @param input
 	 *            the input image extended to infinity (or at least covering the
 	 *            same interval as the dog result image, plus borders for

diff --git a/src/main/java/net/imglib2/algorithm/edge/SubpixelEdgelDetection.java b/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=Function
+	 * @implNote op name='edge.subpixelEdgels', type=Function
 	 * @param input
 	 *            input image
 	 * @param factory

diff --git a/src/main/java/net/imglib2/algorithm/fill/FloodFill.java b/src/main/java/net/imglib2/algorithm/fill/FloodFill.java
@@ -34,13 +34,15 @@
 
 package net.imglib2.algorithm.fill;
 
-import java.util.concurrent.ExecutorService;
 import java.util.function.BiPredicate;
 import java.util.function.Consumer;
 
 import gnu.trove.list.TLongList;
 import gnu.trove.list.array.TLongArrayList;
-import net.imglib2.*;
+import net.imglib2.Cursor;
+import net.imglib2.Localizable;
+import net.imglib2.RandomAccess;
+import net.imglib2.RandomAccessible;
 import net.imglib2.algorithm.neighborhood.Neighborhood;
 import net.imglib2.algorithm.neighborhood.Shape;
 import net.imglib2.type.Type;
@@ -120,7 +122,7 @@ 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=Computer
+	 * @implNote op name='fill.flood', type=Computer
 	 * @param source
 	 *            input
 	 * @param seed
@@ -212,7 +214,7 @@ 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=Computer
+	 * @implNote op name='fill.flood', type=Computer
 	 * @param source
 	 *            input
 	 * @param seed
@@ -347,7 +349,7 @@ public static < T, U > void fill(
 	 * last, and the primary input (the input image) comes first.
 	 * </p>
 	 *
-	 * @implNote op name='floodFill', type=Computer
+	 * @implNote op name='fill.flood', type=Computer
 	 * @param source
 	 *            input
 	 * @param seed

diff --git a/src/main/java/net/imglib2/algorithm/gauss3/Gauss3.java b/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=Computer
+	 * @implNote op name='filter.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=Computer
+	 * @implNote op name='filter.gauss', type=Computer
 	 * @param sigma
 	 *            standard deviation in every dimension.
 	 * @param source

diff --git a/src/main/java/net/imglib2/algorithm/gradient/PartialDerivative.java b/src/main/java/net/imglib2/algorithm/gradient/PartialDerivative.java
@@ -40,11 +40,11 @@
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Future;
-import java.util.function.BiPredicate;
-import java.util.function.Consumer;
 
-import net.imglib2.*;
-import net.imglib2.algorithm.neighborhood.Shape;
+import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
+import net.imglib2.RandomAccessible;
+import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.loops.LoopBuilder;
 import net.imglib2.type.numeric.NumericType;
 import net.imglib2.util.Intervals;
@@ -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=Computer
+	 * @implNote op name='filter.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=Computer
+	 * @implNote op name='filter.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=Computer
+	 * @implNote op name='filter.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=Computer
+	 * @implNote op name='filter.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=Computer
+	 * @implNote op name='filter.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