Opify ImgLib2 Algorithm

imglib · Aug 26, 2024 · 678df37 · 678df37
1 parent 53a2a06
commit 678df37
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diff --git a/.github/workflows/build-main.yml b/.github/workflows/build-main.yml
@@ -16,7 +16,7 @@ jobs:
       - name: Set up Java
         uses: actions/setup-java@v3
         with:
-          java-version: '8'
+          java-version: '11'
           distribution: 'zulu'
           cache: 'maven'
       - name: Set up CI environment

diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml
@@ -14,7 +14,7 @@ jobs:
       - name: Set up Java
         uses: actions/setup-java@v3
         with:
-          java-version: '8'
+          java-version: '11'
           distribution: 'zulu'
           cache: 'maven'
       - name: Set up CI environment

diff --git a/pom.xml b/pom.xml
@@ -206,6 +206,22 @@ 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>
 
 	<repositories>
@@ -281,4 +297,39 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 			<scope>test</scope>
 		</dependency>
 	</dependencies>
+
+	<!-- TODO: Remove relevant sections once upstream -->
+	<build>
+		<plugins>
+			<plugin>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<configuration>
+					<annotationProcessorPaths>
+						<path>
+							<groupId>org.scijava</groupId>
+							<artifactId>scijava-ops-indexer</artifactId>
+							<version>1.0.0</version>
+						</path>
+					</annotationProcessorPaths>
+					<fork>true</fork>
+					<compilerArgs>
+						<arg>-Ascijava.ops.parse=${scijava.parse.ops}</arg>
+						<arg>-Ascijava.ops.opVersion=${project.version}</arg>
+					</compilerArgs>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-javadoc-plugin</artifactId>
+				<configuration>
+					<tags>
+						<tag>
+							<name>implNote</name>
+							<placement>a</placement>
+							<head>Implementation Note:</head>
+						</tag>
+					</tags>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
 </project>
diff --git a/src/main/java/net/imglib2/algorithm/binary/Thresholder.java b/src/main/java/net/imglib2/algorithm/binary/Thresholder.java
@@ -70,6 +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.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/mser/MserTree.java b/src/main/java/net/imglib2/algorithm/componenttree/mser/MserTree.java
@@ -105,7 +105,8 @@ public final class MserTree< T extends Type< T > > implements ComponentForest< M
 	 * {@link #buildMserTree(RandomAccessibleInterval, RealType, long, long, double, double, ImgFactory, boolean)}
 	 * using an {@link ArrayImgFactory} or {@link CellImgFactory} depending on
 	 * input image size.
-	 * 
+	 *
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param delta
@@ -133,7 +134,8 @@ public static < T extends RealType< T > > MserTree< T > buildMserTree( final Ran
 	 * {@link #buildMserTree(RandomAccessibleInterval, RealType, long, long, double, double, ImgFactory, boolean)}
 	 * using an {@link ArrayImgFactory} or {@link CellImgFactory} depending on
 	 * input image size.
-	 * 
+	 *
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param delta
@@ -159,7 +161,8 @@ public static < T extends RealType< T > > MserTree< T > buildMserTree( final Ran
 
 	/**
 	 * Build a MSER tree from an input image.
-	 * 
+	 *
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param delta
@@ -198,7 +201,8 @@ public static < T extends RealType< T > > MserTree< T > buildMserTree( final Ran
 	 * {@link #buildMserTree(RandomAccessibleInterval, ComputeDelta, long, long, double, double, ImgFactory, Type, Comparator)}
 	 * using an {@link ArrayImgFactory} or {@link CellImgFactory} depending on
 	 * input image size.
-	 * 
+	 *
+	 * @implNote op name='create.mserTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param computeDelta
@@ -226,7 +230,8 @@ public static < T extends Type< T > > MserTree< T > buildMserTree( final RandomA
 
 	/**
 	 * Build a MSER tree from an input image.
-	 * 
+	 *
+	 * @implNote op name='create.mserTree',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
@@ -74,6 +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='create.pixelListComponentTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param type
@@ -92,6 +93,7 @@ public static < T extends RealType< T > > PixelListComponentTree< T > buildCompo
 	/**
 	 * Build a component tree from an input image.
 	 *
+	 * @implNote op name='create.pixelListComponentTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param type
@@ -120,6 +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='create.pixelListComponentTree',type=Function
 	 * @param input
 	 *            the input image.
 	 * @param maxValue
@@ -138,6 +141,7 @@ public static < T extends Type< T > > PixelListComponentTree< T > buildComponent
 	/**
 	 * Build a component tree from an input image.
 	 *
+	 * @implNote op name='create.pixelListComponentTree',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
@@ -88,11 +88,23 @@ public class FastGauss
 		return new LineConvolution<>( new FastGaussConvolverRealType( sigma ), direction );
 	}
 
+	/**
+	 * @param sigmas the standard deviations of the Gaussian blur (in each dimension)
+	 * @param input the input data to blur
+	 * @param output the preallocated output buffer
+	 * @implNote op name='filter.gauss', type=Computer
+	 */
 	public static void convolve( final double[] sigmas, final RandomAccessible< ? extends RealType< ? > > input, final RandomAccessibleInterval< ? extends RealType< ? > > output )
 	{
 		convolution( sigmas ).process( input, output );
 	}
 
+	/**
+	 * @param sigma the standard deviation of the Gaussian blur (in all dimensions)
+	 * @param input the input data to blur
+	 * @param output the preallocated output buffer
+	 * @implNote op name='filter.gauss', type=Computer
+	 */
 	public static void convolve( final double sigma, final RandomAccessible< ? extends RealType< ? > > input, final RandomAccessibleInterval< ? extends RealType< ? > > output )
 	{
 		convolution( sigma ).process( input, output );

diff --git a/src/main/java/net/imglib2/algorithm/convolution/kernel/Kernel1D.java b/src/main/java/net/imglib2/algorithm/convolution/kernel/Kernel1D.java
@@ -56,6 +56,8 @@ public class Kernel1D
 	 * @param halfKernel
 	 *            the upper half (starting at the center pixel) of the symmetric
 	 *            convolution kernel.
+	 * @return a {@link Kernel1D} used for one dimensional convolutions
+	 * @implNote op name='create.kernel1DSymmetric'
 	 */
 	public static Kernel1D symmetric( final double... halfKernel )
 	{
@@ -68,6 +70,9 @@ public static Kernel1D symmetric( final double... halfKernel )
 	/**
 	 * Similar to {@link #symmetric(double[])} but creates an array of
 	 * one-dimensional convolution kernels.
+	 * @param halfKernels the upper halves (starting at the center pixel) of the symmetric convolution kernels
+	 * @return an array of {@link Kernel1D}s used for one dimensional convolutions
+	 * @implNote op name='create.kernel1DSymmetric'
 	 */
 	public static Kernel1D[] symmetric( final double[][] halfKernels )
 	{
@@ -82,6 +87,8 @@ public static Kernel1D[] symmetric( final double[][] halfKernels )
 	 * @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
+	 * @implNote op name='create.kernel1DAsymmetric'
 	 */
 	public static Kernel1D asymmetric( final double[] fullKernel, final int originIndex )
 	{
@@ -94,6 +101,9 @@ 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.
+	 * @param kernel the raw data of the symmetric convolution kernel
+	 * @return a {@link Kernel1D} used for one dimensional convolutions
+	 * @implNote op name='create.kernel1DCentralAsymmetric'
 	 */
 	public static Kernel1D centralAsymmetric( final double... kernel )
 	{
@@ -103,6 +113,13 @@ public static Kernel1D centralAsymmetric( final double... kernel )
 	/**
 	 * Similar to {@link #asymmetric(double[], int)} but creates an array of
 	 * one-dimensional convolution kernels.
+	 * @param fullKernels
+	 *            arrays containing the values of each kernel
+	 * @param originIndices
+	 *            the indices of the array elements at the origin of each
+	 *            kernel
+	 * @return an array of {@link Kernel1D}s used for one dimensional convolutions
+	 * @implNote op name='create.kernel1DAsymmetric'
 	 */
 	public static Kernel1D[] asymmetric( final double[][] fullKernels, final int[] originIndices )
 	{
@@ -113,6 +130,9 @@ public static Kernel1D[] asymmetric( final double[][] fullKernels, final int[] o
 	/**
 	 * Similar to {@link #centralAsymmetric(double...)} but creates an array of
 	 * one-dimensional convolution kernels.
+	 * @param kernels the upper halves (starting at the center pixel) of the symmetric convolution kernels
+	 * @return an array of {@link Kernel1D}s used for one dimensional convolutions
+	 * @implNote op name='create.kernel1DCentralAsymmetric'
 	 */
 	public static Kernel1D[] centralAsymmetric( final double[][] kernels )
 	{

diff --git a/src/main/java/net/imglib2/algorithm/convolution/kernel/SeparableKernelConvolution.java b/src/main/java/net/imglib2/algorithm/convolution/kernel/SeparableKernelConvolution.java
@@ -114,6 +114,7 @@ public class SeparableKernelConvolution
 	 *            the required source interval.
 	 * @param target
 	 *            target image.
+	 * @implNote op name='filter.convolve', type=Computer
 	 */
 	public static void convolve( final Kernel1D[] kernels,
 			final RandomAccessible< ? extends NumericType< ? > > source,

diff --git a/src/main/java/net/imglib2/algorithm/dog/DifferenceOfGaussian.java b/src/main/java/net/imglib2/algorithm/dog/DifferenceOfGaussian.java
@@ -60,6 +60,44 @@
  */
 public class DifferenceOfGaussian
 {
+	/**
+	 * Compute the difference of Gaussian for the input. Input convolved with
+	 * Gaussian of sigmaSmaller is subtracted from input convolved with Gaussian
+	 * of sigmaLarger (where {@code sigmaLarger > sigmaSmaller}).
+	 * <p>
+	 * Creates an appropriate temporary image and calls
+	 * {@link #DoG(double[], double[], RandomAccessible, RandomAccessible, RandomAccessibleInterval, ExecutorService)}
+	 * .
+	 * </p>
+	 * This method differs from
+	 * {@link #DoG(double[], double[], RandomAccessible, RandomAccessibleInterval, ExecutorService)}
+	 * 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="filter.DoG", type=Computer
+	 * @param input
+	 *            the input image extended to infinity (or at least covering the
+	 *            same interval as the dog result image, plus borders for
+	 *            convolution).
+	 * @param sigmaSmaller
+	 *            stddev (in every dimension) of smaller Gaussian.
+	 * @param sigmaLarger
+	 *            stddev (in every dimension) of larger Gaussian.
+	 * @param service
+	 *            service providing threads for multi-threading
+	 * @param dog
+	 *            the Difference-of-Gaussian result image.
+	 */
+	public static < I extends NumericType< I >, T extends NumericType< T > & NativeType< T > > void DoG(
+			final RandomAccessible< I > input,
+			final double[] sigmaSmaller,
+			final double[] sigmaLarger,
+			final ExecutorService service,
+			final RandomAccessibleInterval< T > dog)
+	{
+		DoG( sigmaSmaller, sigmaLarger, input, dog, service );
+	}
+
 	/**
 	 * Compute the difference of Gaussian for the input. Input convolved with
 	 * Gaussian of sigmaSmaller is subtracted from input convolved with Gaussian
@@ -97,6 +135,44 @@ public static < I extends NumericType< I >, T extends NumericType< T > & NativeT
 		DoG( sigmaSmaller, sigmaLarger, input, Views.translate( g1, translation ), dog, service );
 	}
 
+	/**
+	 * Compute the difference of Gaussian for the input. Input convolved with
+	 * Gaussian of sigmaSmaller is subtracted from input convolved with Gaussian
+	 * of sigmaLarger (where sigmaLarger &gt; sigmaSmaller).
+	 * </p>
+	 * This method differs from
+	 * {@link #DoG(double[], double[], RandomAccessible, RandomAccessible, RandomAccessibleInterval, ExecutorService)}
+	 * 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="filter.DoG", type=Computer
+	 * @param input
+	 *            the input image extended to infinity (or at least covering the
+	 *            same interval as the dog result image, plus borders for
+	 *            convolution).
+	 * @param sigmaSmaller
+	 *            stddev (in every dimension) of smaller Gaussian.
+	 * @param sigmaLarger
+	 *            stddev (in every dimension) of larger Gaussian.
+	 * @param tmp
+	 *            temporary image, must at least cover the same interval as the
+	 *            dog result image.
+	 * @param service
+	 *            how many threads to use for the computation.
+	 * @param dog
+	 *            the Difference-of-Gaussian result image.
+	 */
+	public static < I extends NumericType< I >, T extends NumericType< T > & NativeType< T > > void DoG(
+			final RandomAccessible< I > input,
+			final double[] sigmaSmaller,
+			final double[] sigmaLarger,
+			final RandomAccessible< T > tmp,
+			final ExecutorService service,
+			final RandomAccessibleInterval< T > dog)
+	{
+		DoG(sigmaSmaller, sigmaLarger, input, tmp, dog, service);
+	}
+
 	/**
 	 * Compute the difference of Gaussian for the input. Input convolved with
 	 * Gaussian of sigmaSmaller is subtracted from input convolved with Gaussian

diff --git a/src/main/java/net/imglib2/algorithm/edge/SubpixelEdgelDetection.java b/src/main/java/net/imglib2/algorithm/edge/SubpixelEdgelDetection.java
@@ -73,7 +73,8 @@ public class SubpixelEdgelDetection
 	 * <p>
 	 * Note: The input image type must be a signed type! Otherwise gradient
 	 * computation will not work.
-	 * 
+	 *
+	 * @implNote op name='image.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
@@ -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,
@@ -138,6 +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,
@@ -180,6 +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,