Merge branch 'histogram-stuff'

algorithms/core/src/main/java/net/imglib2/algorithm/histogram/BinMapper1d.java

@@ -0,0 +1,104 @@
+/*
+ * #%L
+ * ImgLib2: a general-purpose, multidimensional image processing library.
+ * %%
+ * Copyright (C) 2009 - 2013 Stephan Preibisch, Tobias Pietzsch, Barry DeZonia,
+ * Stephan Saalfeld, Albert Cardona, Curtis Rueden, Christian Dietz, Jean-Yves
+ * Tinevez, Johannes Schindelin, Lee Kamentsky, Larry Lindsey, Grant Harris,
+ * Mark Hiner, Aivar Grislis, Martin Horn, Nick Perry, Michael Zinsmaier,
+ * Steffen Jaensch, Jan Funke, Mark Longair, and Dimiter Prodanov.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * 
+ * The views and conclusions contained in the software and documentation are
+ * those of the authors and should not be interpreted as representing official
+ * policies, either expressed or implied, of any organization.
+ * #L%
+ */
+
+package net.imglib2.algorithm.histogram;
+
+
+/**
+ * @author Barry DeZonia
+ */
+public interface BinMapper1d<T> {
+
+	/**
+	 * Returns true if this bin mapping has bins on the ends of the distribution
+	 * that count out of bounds values.
+	 */
+	boolean hasTails();
+
+	/**
+	 * Returns the number of bins within this bin mapping distribution.
+	 */
+	long getBinCount();
+
+	/**
+	 * Converts a data value to a long index within the bin distribution.
+	 */
+	long map(T value);
+
+	/**
+	 * Gets the data value associated with the center of a bin.
+	 * 
+	 * @param binPos
+	 * @param value Output to contain center data value
+	 */
+	void getCenterValue(long binPos, T value);
+
+	/**
+	 * Gets the data value associated with the left edge of a bin.
+	 * 
+	 * @param binPos Bin number of interest
+	 * @param value Output to contain left edge data value
+	 */
+	void getLowerBound(long binPos, T value);
+
+	/**
+	 * Gets the data value associated with the right edge of a bin.
+	 * 
+	 * @param binPos Bin number of interest
+	 * @param value Output to contain right edge data value
+	 */
+	void getUpperBound(long binPos, T value);
+
+	/**
+	 * Returns true if values matching the right edge data value for a given bin
+	 * are counted in the distribution. Basically is this bin interval closed on
+	 * the right or not.
+	 * 
+	 * @param binPos Bin number of interest
+	 */
+	boolean includesUpperBound(long binPos);
+
+	/**
+	 * Returns true if values matching the left edge data value for a given bin
+	 * are counted in the distribution. Basically is this bin interval closed on
+	 * the left or not.
+	 * 
+	 * @param binPos Bin number of interest
+	 */
+	boolean includesLowerBound(long binPos);
+
+}

algorithms/core/src/main/java/net/imglib2/algorithm/histogram/DiscreteFrequencyDistribution.java

@@ -0,0 +1,288 @@
+/*
+ * #%L
+ * ImgLib2: a general-purpose, multidimensional image processing library.
+ * %%
+ * Copyright (C) 2009 - 2013 Stephan Preibisch, Tobias Pietzsch, Barry DeZonia,
+ * Stephan Saalfeld, Albert Cardona, Curtis Rueden, Christian Dietz, Jean-Yves
+ * Tinevez, Johannes Schindelin, Lee Kamentsky, Larry Lindsey, Grant Harris,
+ * Mark Hiner, Aivar Grislis, Martin Horn, Nick Perry, Michael Zinsmaier,
+ * Steffen Jaensch, Jan Funke, Mark Longair, and Dimiter Prodanov.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * 
+ * The views and conclusions contained in the software and documentation are
+ * those of the authors and should not be interpreted as representing official
+ * policies, either expressed or implied, of any organization.
+ * #L%
+ */
+
+package net.imglib2.algorithm.histogram;
+
+import java.util.Iterator;
+
+import net.imglib2.Cursor;
+import net.imglib2.Interval;
+import net.imglib2.IterableRealInterval;
+import net.imglib2.Positionable;
+import net.imglib2.RandomAccess;
+import net.imglib2.RealPositionable;
+import net.imglib2.img.Img;
+import net.imglib2.img.ImgFactory;
+import net.imglib2.img.array.ArrayImgFactory;
+import net.imglib2.type.numeric.integer.LongType;
+
+/**
+ * This class represents an n-dimensional set of counters. Histogram
+ * implementations use these for tracking value counts.
+ * 
+ * @author Barry DeZonia
+ */
+public class DiscreteFrequencyDistribution implements Img<LongType> {
+
+	// -- instance variables --
+
+	private final Img<LongType> counts;
+	private final RandomAccess<LongType> accessor;
+	private long totalValues;
+
+	// -- public api --
+
+	/**
+	 * Construct an n-dimensional counter with the given number of bins
+	 */
+	public DiscreteFrequencyDistribution(long[] binCounts) {
+		// check inputs for issues
+
+		for (int i = 0; i < binCounts.length; i++) {
+			if (binCounts[i] <= 0) {
+				throw new IllegalArgumentException("invalid bin count (<= 0)");
+			}
+		}
+
+		// then build object
+
+		counts = new ArrayImgFactory<LongType>().create(binCounts, new LongType());
+
+		accessor = counts.randomAccess();
+
+		totalValues = 0;
+	}
+
+	/**
+	 * Construct an n-dimensional counter using a provided Img<LongType> to store
+	 * counts.
+	 */
+	public DiscreteFrequencyDistribution(Img<LongType> img) {
+		counts = img;
+		accessor = counts.randomAccess();
+		resetCounters();
+	}
+
+	/**
+	 * Resets all frequency counts to zero.
+	 */
+	public void resetCounters() {
+		Cursor<LongType> cursor = counts.cursor();
+		while (cursor.hasNext()) {
+			cursor.next().setZero();
+		}
+		totalValues = 0;
+	}
+
+	/**
+	 * Returns the frequency count associated with a given bin.
+	 */
+	public long frequency(long[] binPos) {
+		for (int i = 0; i < accessor.numDimensions(); i++) {
+			if (binPos[i] < 0 || binPos[i] >= dimension(i)) return 0;
+		}
+		accessor.setPosition(binPos);
+		return accessor.get().get();
+	}
+
+	/**
+	 * Returns the relative frequency (0 <= f <= 1) associated with a given bin.
+	 */
+	public double relativeFrequency(long[] binPos) {
+		if (totalValues == 0) return 0;
+		return 1.0 * frequency(binPos) / totalValues;
+	}
+
+	/**
+	 * Increments the frequency count of a specified bin.
+	 */
+	public void increment(long[] binPos) {
+		accessor.setPosition(binPos);
+		accessor.get().inc();
+		totalValues++;
+	}
+
+	/**
+	 * Decrements the frequency count of a specified bin.
+	 */
+	public void decrement(long[] binPos) {
+		accessor.setPosition(binPos);
+		accessor.get().dec();
+		totalValues--;
+	}
+
+	/**
+	 * Returns the total number of values counted by this distribution.
+	 */
+	public long totalValues() {
+		return totalValues;
+	}
+
+	// -- Img methods --
+
+	@Override
+	public RandomAccess<LongType> randomAccess() {
+		return counts.randomAccess();
+	}
+
+	@Override
+	public RandomAccess<LongType> randomAccess(Interval interval) {
+		return counts.randomAccess(interval);
+	}
+
+	@Override
+	public int numDimensions() {
+		return counts.numDimensions();
+	}
+
+	@Override
+	public long min(int d) {
+		return counts.min(d);
+	}
+
+	@Override
+	public void min(long[] min) {
+		counts.min(min);
+	}
+
+	@Override
+	public void min(Positionable min) {
+		counts.min(min);
+	}
+
+	@Override
+	public long max(int d) {
+		return counts.max(d);
+	}
+
+	@Override
+	public void max(long[] max) {
+		counts.max(max);
+	}
+
+	@Override
+	public void max(Positionable max) {
+		counts.max(max);
+	}
+
+	@Override
+	public double realMin(int d) {
+		return counts.realMin(d);
+	}
+
+	@Override
+	public void realMin(double[] min) {
+		counts.realMin(min);
+	}
+
+	@Override
+	public void realMin(RealPositionable min) {
+		counts.realMin(min);
+	}
+
+	@Override
+	public double realMax(int d) {
+		return counts.realMax(d);
+	}
+
+	@Override
+	public void realMax(double[] max) {
+		counts.realMax(max);
+	}
+
+	@Override
+	public void realMax(RealPositionable max) {
+		counts.realMax(max);
+	}
+
+	@Override
+	public void dimensions(long[] dimensions) {
+		counts.dimensions(dimensions);
+	}
+
+	@Override
+	public long dimension(int d) {
+		return counts.dimension(d);
+	}
+
+	@Override
+	public Cursor<LongType> cursor() {
+		return counts.cursor();
+	}
+
+	@Override
+	public Cursor<LongType> localizingCursor() {
+		return counts.localizingCursor();
+	}
+
+	@Override
+	public long size() {
+		return counts.size();
+	}
+
+	@Override
+	public LongType firstElement() {
+		return counts.firstElement();
+	}
+
+	@Override
+	public Object iterationOrder() {
+		return counts.iterationOrder();
+	}
+
+	@Override
+	@Deprecated
+	public boolean equalIterationOrder(IterableRealInterval<?> f) {
+		return counts.equalIterationOrder(f);
+	}
+
+	@Override
+	public Iterator<LongType> iterator() {
+		return counts.iterator();
+	}
+
+	@Override
+	public ImgFactory<LongType> factory() {
+		return counts.factory();
+	}
+
+	@Override
+	public DiscreteFrequencyDistribution copy() {
+		return new DiscreteFrequencyDistribution(counts.copy());
+	}
+
+}