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The following commit(s) were added to refs/heads/LicenseSwap2 by this push:
new 00ddab0 Code cleanup.
00ddab0 is described below
commit 00ddab0ce372a535d853cd31e34e77ab0cc249e0
Author: Lee Rhodes <[email protected]>
AuthorDate: Thu Oct 17 13:59:07 2019 -0700
Code cleanup.
---
.../apache/datasketches/vector/MatrixFamily.java | 5 +++-
.../vector/decomposition/MatrixOps.java | 28 +++++++++++++++++++---
.../vector/decomposition/MatrixOpsImplOjAlgo.java | 17 +++++++------
.../datasketches/vector/decomposition/SVDAlgo.java | 23 ++++++++++++++++++
.../apache/datasketches/vector/matrix/Matrix.java | 8 +++++--
.../datasketches/vector/matrix/MatrixBuilder.java | 3 +++
.../vector/matrix/MatrixImplOjAlgo.java | 3 +++
.../datasketches/vector/matrix/MatrixType.java | 14 +++++++++++
.../decomposition/FrequentDirectionsTest.java | 8 ++++---
.../vector/decomposition/MatrixOpsTest.java | 7 +++---
.../vector/matrix/MatrixBuilderTest.java | 1 +
.../vector/matrix/MatrixImplOjAlgoTest.java | 2 ++
.../datasketches/vector/matrix/MatrixTest.java | 1 +
13 files changed, 99 insertions(+), 21 deletions(-)
diff --git a/src/main/java/org/apache/datasketches/vector/MatrixFamily.java
b/src/main/java/org/apache/datasketches/vector/MatrixFamily.java
index dec7952..9c1d141 100644
--- a/src/main/java/org/apache/datasketches/vector/MatrixFamily.java
+++ b/src/main/java/org/apache/datasketches/vector/MatrixFamily.java
@@ -41,6 +41,9 @@ public enum MatrixFamily {
* matrix.
*/
MATRIX(128, "Matrix", 2, 3),
+ /**
+ * Select Frequent Directions Family
+ */
FREQUENTDIRECTIONS(129, "FrequentDirections", 2, 4);
@@ -80,7 +83,7 @@ public enum MatrixFamily {
public void checkFamilyID(final int id) {
if (id != id_) {
throw new IllegalArgumentException(
- "Possible Corruption: This Family " + this.toString()
+ "Possible Corruption: This Family " + toString()
+ " does not match the ID of the given Family: " +
idToFamily(id).toString());
}
}
diff --git
a/src/main/java/org/apache/datasketches/vector/decomposition/MatrixOps.java
b/src/main/java/org/apache/datasketches/vector/decomposition/MatrixOps.java
index 845ad46..7c5e57c 100644
--- a/src/main/java/org/apache/datasketches/vector/decomposition/MatrixOps.java
+++ b/src/main/java/org/apache/datasketches/vector/decomposition/MatrixOps.java
@@ -17,15 +17,37 @@
* under the License.
*/
+//License header from the SVD.java file:
+/*
+ * Copyright (C) 2003-2006 Bjørn-Ove Heimsund
+ *
+ * This file is part of MTJ.
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by the
+ * Free Software Foundation; either version 2.1 of the License, or (at your
+ * option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation,
+ * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+
package org.apache.datasketches.vector.decomposition;
import org.apache.datasketches.vector.matrix.Matrix;
/**
- * Computes singular value decompositions and related Matrix operations needed
by Frequent Directions. May
- * return as many singular values as exist, but other operations will limit
output to k dimensions.
+ * Computes singular value decompositions and related Matrix operations needed
by Frequent Directions.
+ * May return as many singular values as exist, but other operations will
limit output to k dimensions.
*/
-// Directly derived from LGPL'd Matrix Toolkit for Java:
+// Directly derived from LGPL'd Matrix Toolkit for Java (MTL):
//
https://github.com/fommil/matrix-toolkits-java/blob/master/src/main/java/no/uib/cipr/matrix/SVD.java
abstract class MatrixOps {
diff --git
a/src/main/java/org/apache/datasketches/vector/decomposition/MatrixOpsImplOjAlgo.java
b/src/main/java/org/apache/datasketches/vector/decomposition/MatrixOpsImplOjAlgo.java
index 401d00b..4c1f8d1 100644
---
a/src/main/java/org/apache/datasketches/vector/decomposition/MatrixOpsImplOjAlgo.java
+++
b/src/main/java/org/apache/datasketches/vector/decomposition/MatrixOpsImplOjAlgo.java
@@ -30,7 +30,6 @@ import org.ojalgo.matrix.store.SparseStore;
import org.ojalgo.random.Normal;
import org.apache.datasketches.vector.matrix.Matrix;
-import org.apache.datasketches.vector.matrix.MatrixImplOjAlgo;
import org.apache.datasketches.vector.matrix.MatrixType;
class MatrixOpsImplOjAlgo extends MatrixOps {
@@ -44,7 +43,7 @@ class MatrixOpsImplOjAlgo extends MatrixOps {
// work objects for Symmetric EVD
private Eigenvalue<Double> evd_;
-
+
// work object for full SVD
private SingularValue<Double> svd_;
@@ -68,7 +67,7 @@ class MatrixOpsImplOjAlgo extends MatrixOps {
throw new IllegalArgumentException("A.numColumns() != d_");
}
- if (computeVectors && Vt_ == null) {
+ if (computeVectors && (Vt_ == null)) {
Vt_ = PrimitiveDenseStore.FACTORY.makeZero(n_, d_);
S_ = SparseStore.makePrimitive(sv_.length, sv_.length);
}
@@ -98,7 +97,7 @@ class MatrixOpsImplOjAlgo extends MatrixOps {
@Override
Matrix getVt() {
- return MatrixImplOjAlgo.wrap(Vt_);
+ return Matrix.wrap(Vt_);
}
@Override
@@ -111,9 +110,9 @@ class MatrixOpsImplOjAlgo extends MatrixOps {
double medianSVSq = sv_[k_ - 1]; // (l_/2)th item, not yet squared
medianSVSq *= medianSVSq;
svAdjustment += medianSVSq; // always track, even if not using
compensative mode
- for (int i = 0; i < k_ - 1; ++i) {
+ for (int i = 0; i < (k_ - 1); ++i) {
final double val = sv_[i];
- final double adjSqSV = val * val - medianSVSq;
+ final double adjSqSV = (val * val) - medianSVSq;
S_.set(i, i, adjSqSV < 0 ? 0.0 : Math.sqrt(adjSqSV)); // just to be
safe
}
for (int i = k_ - 1; i < S_.countColumns(); ++i) {
@@ -144,9 +143,9 @@ class MatrixOpsImplOjAlgo extends MatrixOps {
= PrimitiveDenseStore.FACTORY.copy((PrimitiveDenseStore)
A.getRawObject());
svd(Matrix.wrap(result), true);
- for (int i = 0; i < k_ - 1; ++i) {
+ for (int i = 0; i < (k_ - 1); ++i) {
final double val = sv_[i];
- final double adjSV = Math.sqrt(val * val + svAdjustment);
+ final double adjSV = Math.sqrt((val * val) + svAdjustment);
S_.set(i, i, adjSV);
}
for (int i = k_ - 1; i < S_.countColumns(); ++i) {
@@ -223,7 +222,7 @@ class MatrixOpsImplOjAlgo extends MatrixOps {
for (int i = 0; i < ev.length; ++i) {
final double val = Math.sqrt(ev[i]);
sv_[i] = val;
- if (computeVectors && val > 0) { S_.set(i, i, 1 / val); }
+ if (computeVectors && (val > 0)) { S_.set(i, i, 1 / val); }
}
if (computeVectors) {
diff --git
a/src/main/java/org/apache/datasketches/vector/decomposition/SVDAlgo.java
b/src/main/java/org/apache/datasketches/vector/decomposition/SVDAlgo.java
index 87d2bd2..25db3c6 100644
--- a/src/main/java/org/apache/datasketches/vector/decomposition/SVDAlgo.java
+++ b/src/main/java/org/apache/datasketches/vector/decomposition/SVDAlgo.java
@@ -31,8 +31,23 @@ package org.apache.datasketches.vector.decomposition;
* </ul>
*/
public enum SVDAlgo {
+
+ /**
+ * The matrix library's default SVD implementation.
+ */
FULL(1, "Full"),
+
+ /**
+ * Simultaneous iteration, an approximate method likely to be more efficient
only with sparse
+ * matrices or when <em>k</em> is significantly smaller than the number of
rows in the sketch.
+ */
SISVD(2, "SISVD"),
+
+ /**
+ * Takes advantage of matrix dimensionality, first computing eigenvalues of
AA^T, then computes
+ * intended results. Squaring A alters condition number and may cause
numeric stability issues,
+ * but unlikely an issue for Frequent Directions since discarding the
smaller singular values/vectors.
+ */
SYM(3, "Symmetrized");
private int id_;
@@ -43,8 +58,16 @@ public enum SVDAlgo {
name_ = name;
}
+ /**
+ * Returns the ID.
+ * @return the ID.
+ */
public int getId() { return id_; }
+ /**
+ * Gets the name
+ * @return the name
+ */
public String getName() { return name_; }
@Override
diff --git a/src/main/java/org/apache/datasketches/vector/matrix/Matrix.java
b/src/main/java/org/apache/datasketches/vector/matrix/Matrix.java
index 947bb1e..284eee6 100644
--- a/src/main/java/org/apache/datasketches/vector/matrix/Matrix.java
+++ b/src/main/java/org/apache/datasketches/vector/matrix/Matrix.java
@@ -177,9 +177,9 @@ public abstract class Matrix {
final int nRows = Math.min(rows, numRows_);
final int nCols = Math.min(cols, numCols_);
- if (nRows < 1 || nCols < 1) {
+ if ((nRows < 1) || (nCols < 1)) {
return MatrixFamily.MATRIX.getMinPreLongs() * Long.BYTES;
- } else if (nRows == numRows_ && nCols == numCols_) {
+ } else if ((nRows == numRows_) && (nCols == numCols_)) {
return getSizeBytes();
}
@@ -226,5 +226,9 @@ public abstract class Matrix {
return sb.toString();
}
+ /**
+ * Gets the matrix type
+ * @return the matrix type
+ */
public abstract MatrixType getMatrixType();
}
diff --git
a/src/main/java/org/apache/datasketches/vector/matrix/MatrixBuilder.java
b/src/main/java/org/apache/datasketches/vector/matrix/MatrixBuilder.java
index 059fc91..a9ada47 100644
--- a/src/main/java/org/apache/datasketches/vector/matrix/MatrixBuilder.java
+++ b/src/main/java/org/apache/datasketches/vector/matrix/MatrixBuilder.java
@@ -26,6 +26,9 @@ public class MatrixBuilder {
private MatrixType type_ = MatrixType.OJALGO; // default type
+ /**
+ * Default no-op constructor.
+ */
public MatrixBuilder() {}
/**
diff --git
a/src/main/java/org/apache/datasketches/vector/matrix/MatrixImplOjAlgo.java
b/src/main/java/org/apache/datasketches/vector/matrix/MatrixImplOjAlgo.java
index 4bcc8f1..590ddcb 100644
--- a/src/main/java/org/apache/datasketches/vector/matrix/MatrixImplOjAlgo.java
+++ b/src/main/java/org/apache/datasketches/vector/matrix/MatrixImplOjAlgo.java
@@ -35,6 +35,9 @@ import org.apache.datasketches.memory.Memory;
import org.apache.datasketches.memory.WritableMemory;
import org.apache.datasketches.vector.MatrixFamily;
+/**
+ * Implements the OJ-Algo Matrix operations.
+ */
public final class MatrixImplOjAlgo extends Matrix {
private PrimitiveDenseStore mtx_;
diff --git
a/src/main/java/org/apache/datasketches/vector/matrix/MatrixType.java
b/src/main/java/org/apache/datasketches/vector/matrix/MatrixType.java
index f24acfa..8f2564e 100644
--- a/src/main/java/org/apache/datasketches/vector/matrix/MatrixType.java
+++ b/src/main/java/org/apache/datasketches/vector/matrix/MatrixType.java
@@ -19,7 +19,13 @@
package org.apache.datasketches.vector.matrix;
+/**
+ * The MatrixType enum
+ */
public enum MatrixType {
+ /**
+ * Select the ojAlgo
+ */
OJALGO(1, "ojAlgo");
private int id_;
@@ -30,8 +36,16 @@ public enum MatrixType {
name_ = name;
}
+ /**
+ * Gets the ID
+ * @return the ID
+ */
public int getId() { return id_; }
+ /**
+ * Gets the name
+ * @return the name
+ */
public String getName() { return name_; }
@Override
diff --git
a/src/test/java/org/apache/datasketches/vector/decomposition/FrequentDirectionsTest.java
b/src/test/java/org/apache/datasketches/vector/decomposition/FrequentDirectionsTest.java
index df4e6d5..e14e757 100644
---
a/src/test/java/org/apache/datasketches/vector/decomposition/FrequentDirectionsTest.java
+++
b/src/test/java/org/apache/datasketches/vector/decomposition/FrequentDirectionsTest.java
@@ -34,7 +34,9 @@ import org.apache.datasketches.memory.WritableMemory;
import org.apache.datasketches.vector.MatrixFamily;
import org.apache.datasketches.vector.matrix.Matrix;
+@SuppressWarnings("javadoc")
public class FrequentDirectionsTest {
+
@Test
public void instantiateFD() {
final int k = 32;
@@ -94,7 +96,7 @@ public class FrequentDirectionsTest {
runUpdateTest(fd);
}
- private void runUpdateTest(final FrequentDirections fd) {
+ private static void runUpdateTest(final FrequentDirections fd) {
final int k = fd.getK();
final int d = fd.getD();
@@ -165,7 +167,7 @@ public class FrequentDirectionsTest {
assertEquals(fd2.getN(), initialRows);
fd1.update(fd2);
- final int expectedRows = ((2 * initialRows) % k) + k - 1; // assumes 2 *
initialRows > k
+ final int expectedRows = (((2 * initialRows) % k) + k) - 1; // assumes 2 *
initialRows > k
assertEquals(fd1.getNumRows(), expectedRows);
assertEquals(fd1.getN(), 2 * initialRows);
@@ -196,7 +198,7 @@ public class FrequentDirectionsTest {
runCompensativeResultTest(fd);
}
- private void runCompensativeResultTest(final FrequentDirections fd) {
+ private static void runCompensativeResultTest(final FrequentDirections fd) {
final int d = fd.getD();
final int k = fd.getK();
diff --git
a/src/test/java/org/apache/datasketches/vector/decomposition/MatrixOpsTest.java
b/src/test/java/org/apache/datasketches/vector/decomposition/MatrixOpsTest.java
index d438d5c..2288c07 100644
---
a/src/test/java/org/apache/datasketches/vector/decomposition/MatrixOpsTest.java
+++
b/src/test/java/org/apache/datasketches/vector/decomposition/MatrixOpsTest.java
@@ -28,6 +28,7 @@ import org.apache.datasketches.vector.matrix.Matrix;
import org.apache.datasketches.vector.matrix.MatrixBuilder;
import org.apache.datasketches.vector.matrix.MatrixType;
+@SuppressWarnings("javadoc")
public class MatrixOpsTest {
@Test
@@ -70,7 +71,7 @@ public class MatrixOpsTest {
final Matrix A = generateIncreasingEye(d, 2 * k);
final MatrixOps mo = MatrixOps.newInstance(A, SVDAlgo.FULL, k);
- Matrix B = generateIncreasingEye(d, 2 * k + 1);
+ Matrix B = generateIncreasingEye(d, (2 * k) + 1);
try {
mo.svd(B, true);
fail();
@@ -88,7 +89,7 @@ public class MatrixOpsTest {
}
- private void compareSingularValues(final double[] A, final double[] B, final
int n) {
+ private static void compareSingularValues(final double[] A, final double[]
B, final int n) {
assertEquals(A.length, B.length);
for (int i = 0; i < n; ++i) {
@@ -97,7 +98,7 @@ public class MatrixOpsTest {
}
- private void compareMatrixElementMagnitudes(final Matrix A, final Matrix B,
final int n) {
+ private static void compareMatrixElementMagnitudes(final Matrix A, final
Matrix B, final int n) {
assertEquals(A.getNumColumns(), B.getNumColumns());
assertEquals(A.getNumRows(), B.getNumRows());
diff --git
a/src/test/java/org/apache/datasketches/vector/matrix/MatrixBuilderTest.java
b/src/test/java/org/apache/datasketches/vector/matrix/MatrixBuilderTest.java
index 24feb17..2de3326 100644
--- a/src/test/java/org/apache/datasketches/vector/matrix/MatrixBuilderTest.java
+++ b/src/test/java/org/apache/datasketches/vector/matrix/MatrixBuilderTest.java
@@ -24,6 +24,7 @@ import static org.testng.Assert.assertNotNull;
import org.testng.annotations.Test;
+@SuppressWarnings("javadoc")
public class MatrixBuilderTest {
@Test
public void checkBuild() {
diff --git
a/src/test/java/org/apache/datasketches/vector/matrix/MatrixImplOjAlgoTest.java
b/src/test/java/org/apache/datasketches/vector/matrix/MatrixImplOjAlgoTest.java
index c1310d3..ab76ea5 100644
---
a/src/test/java/org/apache/datasketches/vector/matrix/MatrixImplOjAlgoTest.java
+++
b/src/test/java/org/apache/datasketches/vector/matrix/MatrixImplOjAlgoTest.java
@@ -28,7 +28,9 @@ import org.testng.annotations.Test;
import org.apache.datasketches.memory.Memory;
import org.apache.datasketches.memory.WritableMemory;
+@SuppressWarnings("javadoc")
public class MatrixImplOjAlgoTest {
+
@Test
public void checkInstantiation() {
final int nRows = 10;
diff --git
a/src/test/java/org/apache/datasketches/vector/matrix/MatrixTest.java
b/src/test/java/org/apache/datasketches/vector/matrix/MatrixTest.java
index ca34bc0..3943ab7 100644
--- a/src/test/java/org/apache/datasketches/vector/matrix/MatrixTest.java
+++ b/src/test/java/org/apache/datasketches/vector/matrix/MatrixTest.java
@@ -31,6 +31,7 @@ import org.apache.datasketches.memory.Memory;
import org.apache.datasketches.memory.WritableMemory;
import org.apache.datasketches.vector.MatrixFamily;
+@SuppressWarnings("javadoc")
public class MatrixTest {
@Test
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