Fixes MAHOUT-1202.

https://issues.apache.org/jira/browse/MAHOUT-1202 This issue relates to the design document at https://docs.google.com/document/d/1g1PjUuvjyh2LBdq2_rKLIcUiDbeOORA1sCJiSsz-JVU/edit#heading=h.koi571fvwha3jj git-svn-id: https://svn.apache.org/repos/asf/mahout/trunk@1478958 13f79535-47bb-0310-9956-ffa450edef68
apache · May 3, 2013 · 221b595 · 221b595
1 parent bf82164
commit 221b595
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Showing 29 changed files with 2,462 additions and 614 deletions.
diff --git a/core/src/main/java/org/apache/mahout/common/distance/ChebyshevDistanceMeasure.java b/core/src/main/java/org/apache/mahout/common/distance/ChebyshevDistanceMeasure.java
@@ -19,12 +19,12 @@
 
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Iterator;
 
 import org.apache.hadoop.conf.Configuration;
 import org.apache.mahout.common.parameters.Parameter;
 import org.apache.mahout.math.CardinalityException;
 import org.apache.mahout.math.Vector;
+import org.apache.mahout.math.function.Functions;
 
 /**
  * This class implements a "Chebyshev distance" metric by finding the maximum difference
@@ -52,17 +52,7 @@ public double distance(Vector v1, Vector v2) {
     if (v1.size() != v2.size()) {
       throw new CardinalityException(v1.size(), v2.size());
     }
-    double result = 0.0;
-    Vector vector = v1.minus(v2);
-    Iterator<Vector.Element> iter = vector.iterateNonZero(); 
-    while (iter.hasNext()) {
-      Vector.Element e = iter.next();
-      double d = Math.abs(e.get());
-      if (d > result) {
-        result = d;
-      }
-    }
-    return result;
+    return v1.aggregate(v2, Functions.MAX_ABS, Functions.MINUS);
   }
 
   @Override

diff --git a/core/src/main/java/org/apache/mahout/common/distance/ManhattanDistanceMeasure.java b/core/src/main/java/org/apache/mahout/common/distance/ManhattanDistanceMeasure.java
@@ -19,12 +19,12 @@
 
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Iterator;
 
 import org.apache.hadoop.conf.Configuration;
 import org.apache.mahout.common.parameters.Parameter;
 import org.apache.mahout.math.CardinalityException;
 import org.apache.mahout.math.Vector;
+import org.apache.mahout.math.function.Functions;
 
 /**
  * This class implements a "manhattan distance" metric by summing the absolute values of the difference
@@ -60,15 +60,7 @@ public double distance(Vector v1, Vector v2) {
     if (v1.size() != v2.size()) {
       throw new CardinalityException(v1.size(), v2.size());
     }
-    double result = 0;
-    Vector vector = v1.minus(v2);
-    Iterator<Vector.Element> iter = vector.iterateNonZero();
-    // this contains all non zero elements between the two
-    while (iter.hasNext()) {
-      Vector.Element e = iter.next();
-      result += Math.abs(e.get());
-    }
-    return result;
+    return v1.aggregate(v2, Functions.PLUS, Functions.MINUS_ABS);
   }
 
   @Override

diff --git a/core/src/main/java/org/apache/mahout/common/distance/MinkowskiDistanceMeasure.java b/core/src/main/java/org/apache/mahout/common/distance/MinkowskiDistanceMeasure.java
@@ -18,15 +18,14 @@
 package org.apache.mahout.common.distance;
 
 import java.util.Collection;
-import java.util.Iterator;
 import java.util.List;
 
 import com.google.common.collect.Lists;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.mahout.common.parameters.DoubleParameter;
 import org.apache.mahout.common.parameters.Parameter;
 import org.apache.mahout.math.Vector;
-import org.apache.mahout.math.Vector.Element;
+import org.apache.mahout.math.function.Functions;
 
 /** 
  * Implement Minkowski distance, a real-valued generalization of the 
@@ -82,14 +81,7 @@ public void setExponent(double exponent) {
    */
   @Override
   public double distance(Vector v1, Vector v2) {
-    Vector distVector = v1.minus(v2);
-    double sum = 0.0;
-    Iterator<Element> it = distVector.iterateNonZero();
-    while (it.hasNext()) {
-      Element e = it.next();
-      sum += Math.pow(Math.abs(e.get()), exponent);
-    }
-    return Math.pow(sum, 1.0 / exponent);
+    return Math.pow(v1.aggregate(v2, Functions.PLUS, Functions.minusAbsPow(exponent)), 1.0 / exponent);
   }
 
   // TODO: how?

diff --git a/core/src/main/java/org/apache/mahout/common/distance/TanimotoDistanceMeasure.java b/core/src/main/java/org/apache/mahout/common/distance/TanimotoDistanceMeasure.java
@@ -17,9 +17,8 @@
 
 package org.apache.mahout.common.distance;
 
-import java.util.Iterator;
-
 import org.apache.mahout.math.Vector;
+import org.apache.mahout.math.function.Functions;
 
 /**
  * Tanimoto coefficient implementation.
@@ -42,8 +41,10 @@ public double distance(Vector a, Vector b) {
     double ab;
     double denominator;
     if (getWeights() != null) {
-      ab = dot(b, a); // b is SequentialAccess
-      denominator = dot(a, a) + dot(b, b) - ab;
+      ab = a.times(b).aggregate(getWeights(), Functions.PLUS, Functions.MULT);
+      denominator = a.aggregate(getWeights(), Functions.PLUS, Functions.MULT_SQUARE_LEFT)
+          + b.aggregate(getWeights(), Functions.PLUS, Functions.MULT_SQUARE_LEFT)
+          - ab;
     } else {
       ab = b.dot(a); // b is SequentialAccess
       denominator = a.getLengthSquared() + b.getLengthSquared() - ab;
@@ -53,28 +54,13 @@ public double distance(Vector a, Vector b) {
       denominator = ab;
     }
     if (denominator > 0) {
-      // denom == 0 only when dot(a,a) == dot(b,b) == dot(a,b) == 0
+      // denominator == 0 only when dot(a,a) == dot(b,b) == dot(a,b) == 0
       return 1.0 - ab / denominator;
     } else {
       return 0.0;
     }
   }
-
-  public double dot(Vector a, Vector b) {
-    boolean sameVector = a == b;
-    Iterator<Vector.Element> it = a.iterateNonZero();
-    Vector.Element el;
-    Vector weights = getWeights();
-    double dot = 0.0;
-    while (it.hasNext() && (el = it.next()) != null) {
-      double elementValue = el.get();
-      double value = elementValue * (sameVector ? elementValue : b.getQuick(el.index()));
-      value *= weights.getQuick(el.index());  
-      dot += value;
-    }
-    return dot;
-  }
-
+
   @Override
   public double distance(double centroidLengthSquare, Vector centroid, Vector v) {
     return distance(centroid, v); // TODO

diff --git a/core/src/main/java/org/apache/mahout/math/hadoop/stochasticsvd/qr/GivensThinSolver.java b/core/src/main/java/org/apache/mahout/math/hadoop/stochasticsvd/qr/GivensThinSolver.java
@@ -25,6 +25,7 @@
 import org.apache.mahout.math.AbstractVector;
 import org.apache.mahout.math.DenseVector;
 import org.apache.mahout.math.Matrix;
+import org.apache.mahout.math.OrderedIntDoubleMapping;
 import org.apache.mahout.math.Vector;
 import org.apache.mahout.math.hadoop.stochasticsvd.UpperTriangular;
 
@@ -595,11 +596,43 @@ public int getNumNondefaultElements() {
       throw new UnsupportedOperationException();
     }
 
+    @Override
+    public double getLookupCost() {
+      return 1;
+    }
+
+    @Override
+    public double getIteratorAdvanceCost() {
+      return 1;
+    }
+
+    @Override
+    public boolean isAddConstantTime() {
+      return true;
+    }
+
     @Override
     public Matrix matrixLike(int rows, int columns) {
       throw new UnsupportedOperationException();
     }
 
+    /**
+     * Used internally by assign() to update multiple indices and values at once.
+     * Only really useful for sparse vectors (especially SequentialAccessSparseVector).
+     * <p/>
+     * If someone ever adds a new type of sparse vectors, this method must merge (index, value) pairs into the vector.
+     *
+     * @param updates a mapping of indices to values to merge in the vector.
+     */
+    @Override
+    public void mergeUpdates(OrderedIntDoubleMapping updates) {
+      int indices[] = updates.getIndices();
+      double values[] = updates.getValues();
+      for (int i = 0; i < updates.getNumMappings(); ++i) {
+        viewed.setQuick(rowNum, indices[i], values[i]);
+      }
+    }
+
   }
 
 }
diff --git a/math/pom.xml b/math/pom.xml
@@ -172,5 +172,12 @@
       <artifactId>junit</artifactId>
       <scope>test</scope>
     </dependency>
+
+    <dependency>
+      <groupId>org.easymock</groupId>
+      <artifactId>easymock</artifactId>
+      <version>3.1</version>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
 </project>
diff --git a/math/src/main/java/org/apache/mahout/math/AbstractMatrix.java b/math/src/main/java/org/apache/mahout/math/AbstractMatrix.java
@@ -379,6 +379,7 @@ public double determinant() {
 
   }
 
+  @SuppressWarnings("CloneDoesntDeclareCloneNotSupportedException")
   @Override
   public Matrix clone() {
     AbstractMatrix clone;
@@ -617,6 +618,7 @@ protected TransposeViewVector(Matrix m, int offset, boolean rowToColumn) {
       numCols = rowToColumn ? m.numCols() : m.numRows();
     }
 
+    @SuppressWarnings("CloneDoesntCallSuperClone")
     @Override
     public Vector clone() {
       Vector v = new DenseVector(size());
@@ -683,6 +685,19 @@ public void set(double value) {
       };
     }
 
+    /**
+     * Used internally by assign() to update multiple indices and values at once.
+     * Only really useful for sparse vectors (especially SequentialAccessSparseVector).
+     * <p/>
+     * If someone ever adds a new type of sparse vectors, this method must merge (index, value) pairs into the vector.
+     *
+     * @param updates a mapping of indices to values to merge in the vector.
+     */
+    @Override
+    public void mergeUpdates(OrderedIntDoubleMapping updates) {
+      throw new UnsupportedOperationException("Cannot mutate TransposeViewVector");
+    }
+
     @Override
     public double getQuick(int index) {
       Vector v = rowToColumn ? matrix.viewColumn(index) : matrix.viewRow(index);
@@ -725,6 +740,21 @@ public Vector like(int cardinality) {
     public int getNumNondefaultElements() {
       return size();
     }
+
+    @Override
+    public double getLookupCost() {
+      return (rowToColumn ? matrix.viewColumn(0) : matrix.viewRow(0)).getLookupCost();
+    }
+
+    @Override
+    public double getIteratorAdvanceCost() {
+      return (rowToColumn ? matrix.viewColumn(0) : matrix.viewRow(0)).getIteratorAdvanceCost();
+    }
+
+    @Override
+    public boolean isAddConstantTime() {
+      return (rowToColumn ? matrix.viewColumn(0) : matrix.viewRow(0)).isAddConstantTime();
+    }
   }
 
   @Override