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Diffstat (limited to 'src/main/java/org/apache/commons/math3/linear/OpenMapRealVector.java')
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1 files changed, 799 insertions, 0 deletions
diff --git a/src/main/java/org/apache/commons/math3/linear/OpenMapRealVector.java b/src/main/java/org/apache/commons/math3/linear/OpenMapRealVector.java new file mode 100644 index 0000000..d13e47e --- /dev/null +++ b/src/main/java/org/apache/commons/math3/linear/OpenMapRealVector.java @@ -0,0 +1,799 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.apache.commons.math3.linear; + +import org.apache.commons.math3.exception.DimensionMismatchException; +import org.apache.commons.math3.exception.MathArithmeticException; +import org.apache.commons.math3.exception.NotPositiveException; +import org.apache.commons.math3.exception.OutOfRangeException; +import org.apache.commons.math3.exception.util.LocalizedFormats; +import org.apache.commons.math3.util.FastMath; +import org.apache.commons.math3.util.OpenIntToDoubleHashMap; +import org.apache.commons.math3.util.OpenIntToDoubleHashMap.Iterator; + +import java.io.Serializable; + +/** + * This class implements the {@link RealVector} interface with a {@link OpenIntToDoubleHashMap} + * backing store. + * + * <p>Caveat: This implementation assumes that, for any {@code x}, the equality {@code x * 0d == 0d} + * holds. But it is is not true for {@code NaN}. Moreover, zero entries will lose their sign. Some + * operations (that involve {@code NaN} and/or infinities) may thus give incorrect results, like + * multiplications, divisions or functions mapping. + * + * @since 2.0 + */ +public class OpenMapRealVector extends SparseRealVector implements Serializable { + /** Default Tolerance for having a value considered zero. */ + public static final double DEFAULT_ZERO_TOLERANCE = 1.0e-12; + + /** Serializable version identifier. */ + private static final long serialVersionUID = 8772222695580707260L; + + /** Entries of the vector. */ + private final OpenIntToDoubleHashMap entries; + + /** Dimension of the vector. */ + private final int virtualSize; + + /** Tolerance for having a value considered zero. */ + private final double epsilon; + + /** + * Build a 0-length vector. Zero-length vectors may be used to initialized construction of + * vectors by data gathering. We start with zero-length and use either the {@link + * #OpenMapRealVector(OpenMapRealVector, int)} constructor or one of the {@code append} method + * ({@link #append(double)}, {@link #append(RealVector)}) to gather data into this vector. + */ + public OpenMapRealVector() { + this(0, DEFAULT_ZERO_TOLERANCE); + } + + /** + * Construct a vector of zeroes. + * + * @param dimension Size of the vector. + */ + public OpenMapRealVector(int dimension) { + this(dimension, DEFAULT_ZERO_TOLERANCE); + } + + /** + * Construct a vector of zeroes, specifying zero tolerance. + * + * @param dimension Size of the vector. + * @param epsilon Tolerance below which a value considered zero. + */ + public OpenMapRealVector(int dimension, double epsilon) { + virtualSize = dimension; + entries = new OpenIntToDoubleHashMap(0.0); + this.epsilon = epsilon; + } + + /** + * Build a resized vector, for use with append. + * + * @param v Original vector. + * @param resize Amount to add. + */ + protected OpenMapRealVector(OpenMapRealVector v, int resize) { + virtualSize = v.getDimension() + resize; + entries = new OpenIntToDoubleHashMap(v.entries); + epsilon = v.epsilon; + } + + /** + * Build a vector with known the sparseness (for advanced use only). + * + * @param dimension Size of the vector. + * @param expectedSize The expected number of non-zero entries. + */ + public OpenMapRealVector(int dimension, int expectedSize) { + this(dimension, expectedSize, DEFAULT_ZERO_TOLERANCE); + } + + /** + * Build a vector with known the sparseness and zero tolerance setting (for advanced use only). + * + * @param dimension Size of the vector. + * @param expectedSize Expected number of non-zero entries. + * @param epsilon Tolerance below which a value is considered zero. + */ + public OpenMapRealVector(int dimension, int expectedSize, double epsilon) { + virtualSize = dimension; + entries = new OpenIntToDoubleHashMap(expectedSize, 0.0); + this.epsilon = epsilon; + } + + /** + * Create from an array. Only non-zero entries will be stored. + * + * @param values Set of values to create from. + */ + public OpenMapRealVector(double[] values) { + this(values, DEFAULT_ZERO_TOLERANCE); + } + + /** + * Create from an array, specifying zero tolerance. Only non-zero entries will be stored. + * + * @param values Set of values to create from. + * @param epsilon Tolerance below which a value is considered zero. + */ + public OpenMapRealVector(double[] values, double epsilon) { + virtualSize = values.length; + entries = new OpenIntToDoubleHashMap(0.0); + this.epsilon = epsilon; + for (int key = 0; key < values.length; key++) { + double value = values[key]; + if (!isDefaultValue(value)) { + entries.put(key, value); + } + } + } + + /** + * Create from an array. Only non-zero entries will be stored. + * + * @param values The set of values to create from + */ + public OpenMapRealVector(Double[] values) { + this(values, DEFAULT_ZERO_TOLERANCE); + } + + /** + * Create from an array. Only non-zero entries will be stored. + * + * @param values Set of values to create from. + * @param epsilon Tolerance below which a value is considered zero. + */ + public OpenMapRealVector(Double[] values, double epsilon) { + virtualSize = values.length; + entries = new OpenIntToDoubleHashMap(0.0); + this.epsilon = epsilon; + for (int key = 0; key < values.length; key++) { + double value = values[key].doubleValue(); + if (!isDefaultValue(value)) { + entries.put(key, value); + } + } + } + + /** + * Copy constructor. + * + * @param v Instance to copy from. + */ + public OpenMapRealVector(OpenMapRealVector v) { + virtualSize = v.getDimension(); + entries = new OpenIntToDoubleHashMap(v.getEntries()); + epsilon = v.epsilon; + } + + /** + * Generic copy constructor. + * + * @param v Instance to copy from. + */ + public OpenMapRealVector(RealVector v) { + virtualSize = v.getDimension(); + entries = new OpenIntToDoubleHashMap(0.0); + epsilon = DEFAULT_ZERO_TOLERANCE; + for (int key = 0; key < virtualSize; key++) { + double value = v.getEntry(key); + if (!isDefaultValue(value)) { + entries.put(key, value); + } + } + } + + /** + * Get the entries of this instance. + * + * @return the entries of this instance. + */ + private OpenIntToDoubleHashMap getEntries() { + return entries; + } + + /** + * Determine if this value is within epsilon of zero. + * + * @param value Value to test + * @return {@code true} if this value is within epsilon to zero, {@code false} otherwise. + * @since 2.1 + */ + protected boolean isDefaultValue(double value) { + return FastMath.abs(value) < epsilon; + } + + /** {@inheritDoc} */ + @Override + public RealVector add(RealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + if (v instanceof OpenMapRealVector) { + return add((OpenMapRealVector) v); + } else { + return super.add(v); + } + } + + /** + * Optimized method to add two OpenMapRealVectors. It copies the larger vector, then iterates + * over the smaller. + * + * @param v Vector to add. + * @return the sum of {@code this} and {@code v}. + * @throws DimensionMismatchException if the dimensions do not match. + */ + public OpenMapRealVector add(OpenMapRealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + boolean copyThis = entries.size() > v.entries.size(); + OpenMapRealVector res = copyThis ? this.copy() : v.copy(); + Iterator iter = copyThis ? v.entries.iterator() : entries.iterator(); + OpenIntToDoubleHashMap randomAccess = copyThis ? entries : v.entries; + while (iter.hasNext()) { + iter.advance(); + int key = iter.key(); + if (randomAccess.containsKey(key)) { + res.setEntry(key, randomAccess.get(key) + iter.value()); + } else { + res.setEntry(key, iter.value()); + } + } + return res; + } + + /** + * Optimized method to append a OpenMapRealVector. + * + * @param v vector to append + * @return The result of appending {@code v} to self + */ + public OpenMapRealVector append(OpenMapRealVector v) { + OpenMapRealVector res = new OpenMapRealVector(this, v.getDimension()); + Iterator iter = v.entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + res.setEntry(iter.key() + virtualSize, iter.value()); + } + return res; + } + + /** {@inheritDoc} */ + @Override + public OpenMapRealVector append(RealVector v) { + if (v instanceof OpenMapRealVector) { + return append((OpenMapRealVector) v); + } else { + final OpenMapRealVector res = new OpenMapRealVector(this, v.getDimension()); + for (int i = 0; i < v.getDimension(); i++) { + res.setEntry(i + virtualSize, v.getEntry(i)); + } + return res; + } + } + + /** {@inheritDoc} */ + @Override + public OpenMapRealVector append(double d) { + OpenMapRealVector res = new OpenMapRealVector(this, 1); + res.setEntry(virtualSize, d); + return res; + } + + /** + * {@inheritDoc} + * + * @since 2.1 + */ + @Override + public OpenMapRealVector copy() { + return new OpenMapRealVector(this); + } + + /** + * Computes the dot product. Note that the computation is now performed in the parent class: no + * performance improvement is to be expected from this overloaded method. The previous + * implementation was buggy and cannot be easily fixed (see MATH-795). + * + * @param v Vector. + * @return the dot product of this vector with {@code v}. + * @throws DimensionMismatchException if {@code v} is not the same size as {@code this} vector. + * @deprecated as of 3.1 (to be removed in 4.0). The computation is performed by the parent + * class. The method must be kept to maintain backwards compatibility. + */ + @Deprecated + public double dotProduct(OpenMapRealVector v) throws DimensionMismatchException { + return dotProduct((RealVector) v); + } + + /** {@inheritDoc} */ + @Override + public OpenMapRealVector ebeDivide(RealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + OpenMapRealVector res = new OpenMapRealVector(this); + /* + * MATH-803: it is not sufficient to loop through non zero entries of + * this only. Indeed, if this[i] = 0d and v[i] = 0d, then + * this[i] / v[i] = NaN, and not 0d. + */ + final int n = getDimension(); + for (int i = 0; i < n; i++) { + res.setEntry(i, this.getEntry(i) / v.getEntry(i)); + } + return res; + } + + /** {@inheritDoc} */ + @Override + public OpenMapRealVector ebeMultiply(RealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + OpenMapRealVector res = new OpenMapRealVector(this); + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + res.setEntry(iter.key(), iter.value() * v.getEntry(iter.key())); + } + return res; + } + + /** {@inheritDoc} */ + @Override + public OpenMapRealVector getSubVector(int index, int n) + throws NotPositiveException, OutOfRangeException { + checkIndex(index); + if (n < 0) { + throw new NotPositiveException( + LocalizedFormats.NUMBER_OF_ELEMENTS_SHOULD_BE_POSITIVE, n); + } + checkIndex(index + n - 1); + OpenMapRealVector res = new OpenMapRealVector(n); + int end = index + n; + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + int key = iter.key(); + if (key >= index && key < end) { + res.setEntry(key - index, iter.value()); + } + } + return res; + } + + /** {@inheritDoc} */ + @Override + public int getDimension() { + return virtualSize; + } + + /** + * Optimized method to compute distance. + * + * @param v Vector to compute distance to. + * @return the distance from {@code this} and {@code v}. + * @throws DimensionMismatchException if the dimensions do not match. + */ + public double getDistance(OpenMapRealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + Iterator iter = entries.iterator(); + double res = 0; + while (iter.hasNext()) { + iter.advance(); + int key = iter.key(); + double delta; + delta = iter.value() - v.getEntry(key); + res += delta * delta; + } + iter = v.getEntries().iterator(); + while (iter.hasNext()) { + iter.advance(); + int key = iter.key(); + if (!entries.containsKey(key)) { + final double value = iter.value(); + res += value * value; + } + } + return FastMath.sqrt(res); + } + + /** {@inheritDoc} */ + @Override + public double getDistance(RealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + if (v instanceof OpenMapRealVector) { + return getDistance((OpenMapRealVector) v); + } else { + return super.getDistance(v); + } + } + + /** {@inheritDoc} */ + @Override + public double getEntry(int index) throws OutOfRangeException { + checkIndex(index); + return entries.get(index); + } + + /** + * Distance between two vectors. This method computes the distance consistent with L<sub>1</sub> + * norm, i.e. the sum of the absolute values of elements differences. + * + * @param v Vector to which distance is requested. + * @return distance between this vector and {@code v}. + * @throws DimensionMismatchException if the dimensions do not match. + */ + public double getL1Distance(OpenMapRealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + double max = 0; + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + double delta = FastMath.abs(iter.value() - v.getEntry(iter.key())); + max += delta; + } + iter = v.getEntries().iterator(); + while (iter.hasNext()) { + iter.advance(); + int key = iter.key(); + if (!entries.containsKey(key)) { + double delta = FastMath.abs(iter.value()); + max += FastMath.abs(delta); + } + } + return max; + } + + /** {@inheritDoc} */ + @Override + public double getL1Distance(RealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + if (v instanceof OpenMapRealVector) { + return getL1Distance((OpenMapRealVector) v); + } else { + return super.getL1Distance(v); + } + } + + /** + * Optimized method to compute LInfDistance. + * + * @param v Vector to compute distance from. + * @return the LInfDistance. + * @throws DimensionMismatchException if the dimensions do not match. + */ + private double getLInfDistance(OpenMapRealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + double max = 0; + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + double delta = FastMath.abs(iter.value() - v.getEntry(iter.key())); + if (delta > max) { + max = delta; + } + } + iter = v.getEntries().iterator(); + while (iter.hasNext()) { + iter.advance(); + int key = iter.key(); + if (!entries.containsKey(key) && iter.value() > max) { + max = iter.value(); + } + } + return max; + } + + /** {@inheritDoc} */ + @Override + public double getLInfDistance(RealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + if (v instanceof OpenMapRealVector) { + return getLInfDistance((OpenMapRealVector) v); + } else { + return super.getLInfDistance(v); + } + } + + /** {@inheritDoc} */ + @Override + public boolean isInfinite() { + boolean infiniteFound = false; + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + final double value = iter.value(); + if (Double.isNaN(value)) { + return false; + } + if (Double.isInfinite(value)) { + infiniteFound = true; + } + } + return infiniteFound; + } + + /** {@inheritDoc} */ + @Override + public boolean isNaN() { + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + if (Double.isNaN(iter.value())) { + return true; + } + } + return false; + } + + /** {@inheritDoc} */ + @Override + public OpenMapRealVector mapAdd(double d) { + return copy().mapAddToSelf(d); + } + + /** {@inheritDoc} */ + @Override + public OpenMapRealVector mapAddToSelf(double d) { + for (int i = 0; i < virtualSize; i++) { + setEntry(i, getEntry(i) + d); + } + return this; + } + + /** {@inheritDoc} */ + @Override + public void setEntry(int index, double value) throws OutOfRangeException { + checkIndex(index); + if (!isDefaultValue(value)) { + entries.put(index, value); + } else if (entries.containsKey(index)) { + entries.remove(index); + } + } + + /** {@inheritDoc} */ + @Override + public void setSubVector(int index, RealVector v) throws OutOfRangeException { + checkIndex(index); + checkIndex(index + v.getDimension() - 1); + for (int i = 0; i < v.getDimension(); i++) { + setEntry(i + index, v.getEntry(i)); + } + } + + /** {@inheritDoc} */ + @Override + public void set(double value) { + for (int i = 0; i < virtualSize; i++) { + setEntry(i, value); + } + } + + /** + * Optimized method to subtract OpenMapRealVectors. + * + * @param v Vector to subtract from {@code this}. + * @return the difference of {@code this} and {@code v}. + * @throws DimensionMismatchException if the dimensions do not match. + */ + public OpenMapRealVector subtract(OpenMapRealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + OpenMapRealVector res = copy(); + Iterator iter = v.getEntries().iterator(); + while (iter.hasNext()) { + iter.advance(); + int key = iter.key(); + if (entries.containsKey(key)) { + res.setEntry(key, entries.get(key) - iter.value()); + } else { + res.setEntry(key, -iter.value()); + } + } + return res; + } + + /** {@inheritDoc} */ + @Override + public RealVector subtract(RealVector v) throws DimensionMismatchException { + checkVectorDimensions(v.getDimension()); + if (v instanceof OpenMapRealVector) { + return subtract((OpenMapRealVector) v); + } else { + return super.subtract(v); + } + } + + /** {@inheritDoc} */ + @Override + public OpenMapRealVector unitVector() throws MathArithmeticException { + OpenMapRealVector res = copy(); + res.unitize(); + return res; + } + + /** {@inheritDoc} */ + @Override + public void unitize() throws MathArithmeticException { + double norm = getNorm(); + if (isDefaultValue(norm)) { + throw new MathArithmeticException(LocalizedFormats.ZERO_NORM); + } + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + entries.put(iter.key(), iter.value() / norm); + } + } + + /** {@inheritDoc} */ + @Override + public double[] toArray() { + double[] res = new double[virtualSize]; + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + res[iter.key()] = iter.value(); + } + return res; + } + + /** + * {@inheritDoc} Implementation Note: This works on exact values, and as a result it is possible + * for {@code a.subtract(b)} to be the zero vector, while {@code a.hashCode() != b.hashCode()}. + */ + @Override + public int hashCode() { + final int prime = 31; + int result = 1; + long temp; + temp = Double.doubleToLongBits(epsilon); + result = prime * result + (int) (temp ^ (temp >>> 32)); + result = prime * result + virtualSize; + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + temp = Double.doubleToLongBits(iter.value()); + result = prime * result + (int) (temp ^ (temp >> 32)); + } + return result; + } + + /** + * {@inheritDoc} Implementation Note: This performs an exact comparison, and as a result it is + * possible for {@code a.subtract(b}} to be the zero vector, while {@code a.equals(b) == false}. + */ + @Override + public boolean equals(Object obj) { + if (this == obj) { + return true; + } + if (!(obj instanceof OpenMapRealVector)) { + return false; + } + OpenMapRealVector other = (OpenMapRealVector) obj; + if (virtualSize != other.virtualSize) { + return false; + } + if (Double.doubleToLongBits(epsilon) != Double.doubleToLongBits(other.epsilon)) { + return false; + } + Iterator iter = entries.iterator(); + while (iter.hasNext()) { + iter.advance(); + double test = other.getEntry(iter.key()); + if (Double.doubleToLongBits(test) != Double.doubleToLongBits(iter.value())) { + return false; + } + } + iter = other.getEntries().iterator(); + while (iter.hasNext()) { + iter.advance(); + double test = iter.value(); + if (Double.doubleToLongBits(test) != Double.doubleToLongBits(getEntry(iter.key()))) { + return false; + } + } + return true; + } + + /** + * @return the percentage of none zero elements as a decimal percent. + * @since 2.2 + */ + public double getSparsity() { + return (double) entries.size() / (double) getDimension(); + } + + /** {@inheritDoc} */ + @Override + public java.util.Iterator<Entry> sparseIterator() { + return new OpenMapSparseIterator(); + } + + /** + * Implementation of {@code Entry} optimized for OpenMap. This implementation does not allow + * arbitrary calls to {@code setIndex} since the order in which entries are returned is + * undefined. + */ + protected class OpenMapEntry extends Entry { + /** Iterator pointing to the entry. */ + private final Iterator iter; + + /** + * Build an entry from an iterator point to an element. + * + * @param iter Iterator pointing to the entry. + */ + protected OpenMapEntry(Iterator iter) { + this.iter = iter; + } + + /** {@inheritDoc} */ + @Override + public double getValue() { + return iter.value(); + } + + /** {@inheritDoc} */ + @Override + public void setValue(double value) { + entries.put(iter.key(), value); + } + + /** {@inheritDoc} */ + @Override + public int getIndex() { + return iter.key(); + } + } + + /** + * Iterator class to do iteration over just the non-zero elements. This implementation is + * fail-fast, so cannot be used to modify any zero element. + */ + protected class OpenMapSparseIterator implements java.util.Iterator<Entry> { + /** Underlying iterator. */ + private final Iterator iter; + + /** Current entry. */ + private final Entry current; + + /** Simple constructor. */ + protected OpenMapSparseIterator() { + iter = entries.iterator(); + current = new OpenMapEntry(iter); + } + + /** {@inheritDoc} */ + public boolean hasNext() { + return iter.hasNext(); + } + + /** {@inheritDoc} */ + public Entry next() { + iter.advance(); + return current; + } + + /** {@inheritDoc} */ + public void remove() { + throw new UnsupportedOperationException("Not supported"); + } + } +} |