Merge remote-tracking branch 'imglib/master' into hough-circle-transform

Author: tinevez

.travis/build.sh

@@ -1,7 +1,10 @@
 #!/bin/sh
 dir="$(dirname "$0")"
-test "$TRAVIS_SECURE_ENV_VARS" = true \
+if [ "$TRAVIS_SECURE_ENV_VARS" = true \
   -a "$TRAVIS_PULL_REQUEST" = false \
-  -a "$TRAVIS_BRANCH" = master &&
-  mvn -Pdeploy-to-imagej deploy --settings "$dir/settings.xml" ||
+  -a "$TRAVIS_BRANCH" = master ]
+then
+  mvn -Pdeploy-to-imagej deploy --settings "$dir/settings.xml"
+else
   mvn install
+fi

pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>imglib2-algorithm</artifactId>
-	<version>0.6.4-SNAPSHOT</version>
+	<version>0.8.2-SNAPSHOT</version>
 
 	<name>ImgLib2 Algorithms</name>
 	<description>Useful image processing algorithms.</description>
@@ -188,13 +188,16 @@ 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.</license.copyrightOwners>
+
+		<imglib2-realtransform.version>2.0.0-beta-38</imglib2-realtransform.version>
+		<jitk-tps.version>3.0.0</jitk-tps.version>
 	</properties>
 
 	<repositories>
 		<!-- NB: for SciJava dependencies -->
 		<repository>
 			<id>imagej.public</id>
-			<url>http://maven.imagej.net/content/groups/public</url>
+			<url>https://maven.imagej.net/content/groups/public</url>
 		</repository>
 	</repositories>
 
@@ -229,6 +232,11 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 			<artifactId>trove4j</artifactId>
 			<version>3.0.3</version>
 		</dependency>
+		<dependency>
+			<groupId>org.ojalgo</groupId>
+			<artifactId>ojalgo</artifactId>
+			<version>43.0</version>
+		</dependency>
 
 		<!-- Test dependencies -->
 		<dependency>
@@ -237,4 +245,15 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 			<scope>test</scope>
 		</dependency>
 	</dependencies>
+
+	<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>
+		</plugins>
+	</build>
 </project>

src/main/java/net/imglib2/algorithm/OutputAlgorithm.java

@@ -35,7 +35,8 @@
 package net.imglib2.algorithm;
 
 /**
- * TODO This interface should be empty and extend Callable<F>, Algorithm.
+ * TODO This interface should be empty and extend {@code Callable<F>},
+ * {@link Algorithm}.
  * 
  * @author Stephan Preibisch
  * @author Stephan Saalfeld

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

@@ -64,8 +64,8 @@ public class Thresholder
 	 * @param threshold
 	 *            the threshold.
 	 * @param above
-	 *            if <code>true</code>, the target value will be true for source
-	 *            values above the threshold, <code>false</code> otherwise.
+	 *            if {@code true}, the target value will be true for source
+	 *            values above the threshold, {@code false} otherwise.
 	 * @param numThreads
 	 *            the number of threads to use for thresholding.
 	 * @return a new {@link Img} of type {@link BitType} and of same dimension

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

@@ -52,20 +52,21 @@
 
 /**
  * Build the component tree of an image. This is an implementation of the
- * algorithm described by D. Nister and H. Stewenius in
- * "Linear Time Maximally Stable Extremal Regions" (ECCV 2008).
- * 
- * The input to the algorithm is a RandomAccessibleInterval< T >. Further, a
- * Comparator<T> and a {@link PartialComponent.Generator} to instantiate new
- * components are required. Pixel locations are aggregated in
+ * algorithm described by D. Nister and H. Stewenius in "Linear Time Maximally
+ * Stable Extremal Regions" (ECCV 2008).
+ * <p>
+ * The input to the algorithm is a {@code RandomAccessibleInterval< T >}.
+ * Further, a {@code Comparator<T>} and a {@link PartialComponent.Generator} to
+ * instantiate new components are required. Pixel locations are aggregated in
  * {@link PartialComponent}s which are passed to a
  * {@link PartialComponent.Handler} whenever a connected component for a
  * specific threshold is completed.
- * 
+ * </p>
+ * <p>
  * Building up a tree structure out of the completed components should happen in
  * the {@link PartialComponent.Handler} implementation. See
  * {@link PixelListComponentTree} for an example.
- * 
+ * </p>
  * <p>
  * <strong>TODO</strong> Add support for non-zero-min RandomAccessibleIntervals.
  * (Currently, we assume that the input image is a <em>zero-min</em> interval.)

src/main/java/net/imglib2/algorithm/componenttree/mser/ComputeDelta.java

@@ -37,8 +37,10 @@
 /**
  * For a given threshold value compute the threshold value delta steps down the
  * component tree. This might mean addition or subtraction, depending on whether
- * it's a dark-to-bright or bright-to-dark pass. {@see ComputeDeltaBrightToDark}
- * {@see ComputeDeltaDarkToBright}
+ * it's a dark-to-bright or bright-to-dark pass.
+ * 
+ * @see ComputeDeltaBrightToDark
+ * @see ComputeDeltaDarkToBright
  * 
  * @param <T>
  *            value type of the input image.

src/main/java/net/imglib2/algorithm/componenttree/mser/MserTree.java

@@ -65,23 +65,10 @@
  * Maximally Stable Extremal Regions (MSER) are selected from the component tree
  * as follows. For each component, an instability score is computed as
  * <!-- |R_i - R_{i-\Delta}| / |R_i| -->
- * <math style="display:block">
- * <mi>s</mi><mfenced><msub><mi>R</mi><mi>i</mi></msub></mfenced>
- * <mo>=</mo>
- * <mfrac>
- *   <mfenced open="|" close="|">
- *     <mrow><msub><mi>R</mi><mi>i</mi></msub>
- *   	   <mo lspace=mediummathspace rspace=mediummathspace>\</mo>
- *         <msub><mi>R</mi><mrow><mi>i</mi><mo>-</mo><mi>&Delta;</mi></mrow></msub>
- *     </mrow>
- *   </mfenced>
- *   <mfenced open="|" close="|">
- *     <msub><mi>R</mi><mi>i</mi></msub>
- *   </mfenced>
- * </mfrac>
- * </math>
  * </p>
- * 
+ * <blockquote>
+ * \[\frac{|R_i - R_{i-\Delta}|}{|R_i|}\]
+ * </blockquote>
  * <p>
  * Regions whose score is a local minimum are selected as MSER candidates.
  * </p>
@@ -96,20 +83,10 @@
  * A tree is build of the remaining candidates. Finally, candidates are pruned
  * from the tree, if they are too similar to their parent: Let <em>A</em>,
  * <em>B</em> be a region and its parent. Then <em>A</em> is discarded if
- * <!-- |B - A| / |B| <= minDiversity -->
- * <math style="display:block">
- * <mfrac>
- *   <mfenced open="|" close="|"><mrow>
- *     <mi>B</mi>
- *     <mo lspace=mediummathspace rspace=mediummathspace>\</mo>
- *     <mi>A</mi>
- *   </mrow></mfenced>
- *   <mfenced open="|" close="|"><mi>B</mi></mfenced>
- * </mfrac>
- * <mo>&le;</mo><mi>minDiversity</mi>
- * </math>
  * </p>
- * 
+ * <blockquote>
+ * \[\frac{|B - A|}{|B|} \leq minDiversity\]
+ * </blockquote>
  * <p>
  * <strong>TODO</strong> Add support for non-zero-min RandomAccessibleIntervals.
  * (Currently, we assume that the input image is a <em>zero-min</em> interval.)

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

@@ -97,8 +97,8 @@ public static < T extends RealType< T > > PixelListComponentTree< T > buildCompo
 	 * @param type
 	 *            a variable of the input image type.
 	 * @param imgFactory
-	 *            used for creating the {@link PixelList} image {@see
-	 *            PixelListComponentGenerator}.
+	 *            used for creating the {@link PixelList} image (see
+	 *            {@link PixelListPartialComponentGenerator}).
 	 * @param darkToBright
 	 *            whether to apply thresholds from dark to bright (true) or
 	 *            bright to dark (false)
@@ -146,8 +146,8 @@ public static < T extends Type< T > > PixelListComponentTree< T > buildComponent
 	 * @param comparator
 	 *            determines ordering of threshold values.
 	 * @param imgFactory
-	 *            used for creating the {@link PixelList} image {@see
-	 *            PixelListComponentGenerator}.
+	 *            used for creating the {@link PixelList} image
+	 *            {@link PixelListPartialComponentGenerator}.
 	 * @return component tree of the image.
 	 */
 	public static < T extends Type< T > > PixelListComponentTree< T > buildComponentTree( final RandomAccessibleInterval< T > input, final T maxValue, final Comparator< T > comparator, final ImgFactory< LongType > imgFactory )

src/main/java/net/imglib2/algorithm/dog/DifferenceOfGaussian.java

@@ -63,11 +63,12 @@ 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 sigmaLarger > sigmaSmaller).
-	 *
+	 * of sigmaLarger (where {@code sigmaLarger > sigmaSmaller}).
 	 * <p>
 	 * Creates an appropriate temporary image and calls
-	 * {@link #DoG(double[], double[], RandomAccessible, RandomAccessible, RandomAccessibleInterval, int)}.
+	 * {@link #DoG(double[], double[], RandomAccessible, RandomAccessible, RandomAccessibleInterval, ExecutorService)}
+	 * .
+	 * </p>
 	 *
 	 * @param sigmaSmaller
 	 *            stddev (in every dimension) of smaller Gaussian.
@@ -99,7 +100,7 @@ public static < I extends NumericType< I >, T extends NumericType< T > & NativeT
 	/**
 	 * 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 > sigmaSmaller).
+	 * of sigmaLarger (where sigmaLarger &gt; sigmaSmaller).
 	 *
 	 * @param sigmaSmaller
 	 *            stddev (in every dimension) of smaller Gaussian.
@@ -200,7 +201,7 @@ public Void call()
 
 	/**
 	 * Helper function to compute per-dimension sigmas in pixel coordinates. The
-	 * parameters <code>sigma1</code> and <code>sigma2</code> specify desired
+	 * parameters {@code sigma1} and {@code sigma2} specify desired
 	 * sigmas (scale) in image coordinates. Taking into account the sigma of the
 	 * input image as well as the image calibration, the resulting sigma arrays
 	 * specifiy the smoothing that has to be applied to achieve the desired
@@ -209,15 +210,15 @@ public Void call()
 	 * @param imageSigma
 	 *            estimated sigma of the input image, in pixel coordinates.
 	 * @param minf
-	 *            multiple of the <code>imageSigma</code> that smoothing with
+	 *            multiple of the {@code imageSigma} that smoothing with
 	 *            the resulting sigma must at least achieve.
 	 * @param pixelSize
 	 *            calibration. Dimensions of a pixel in image units.
 	 * @param sigma1
 	 *            desired sigma in image coordinates.
 	 * @param sigma2
 	 *            desired sigma in image coordinates.
-	 * @return <code>double[2][numDimensions]</code>, array of two arrays
+	 * @return {@code double[2][numDimensions]}, array of two arrays
 	 *         contains resulting sigmas for sigma1, sigma2.
 	 */
 	public static double[][] computeSigmas( final double imageSigma, final double minf, final double[] pixelSize, final double sigma1, final double sigma2 )

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

@@ -84,9 +84,9 @@ public class FloodFill
 	 *            written into. Returns false if target pixel has been visited
 	 *            or source pixel is not part of the same connected component.
 	 * @param <T>
-	 *            T implements {@link Type<U>}.
+	 *            T implements {@code Type<U>}.
 	 * @param <U>
-	 *            U implements {@link Type<U>}.
+	 *            U implements {@code Type<U>}.
 	 */
 	public static < T extends Type< T >, U extends Type< U > > void fill( final RandomAccessible< T > source, final RandomAccessible< U > target, final Localizable seed, final U fillLabel, final Shape shape, final Filter< Pair< T, U >, Pair< T, U > > filter )
 	{
@@ -125,7 +125,7 @@ public static < T extends Type< T >, U extends Type< U > > void fill( final Rand
 	 * @param <T>
 	 *            No restrictions on {@link T}.
 	 * @param <U>
-	 *            {@link U} implements {@link Type<U>}.
+	 *            {@link U} implements {@code Type<U>}.
 	 */
 	public static < T, U extends Type< U > > void fill( final RandomAccessible< T > source, final RandomAccessible< U > target, final Localizable seed, final T seedLabel, final U fillLabel, final Shape shape, final Filter< Pair< T, U >, Pair< T, U > > filter )
 	{