From 68952f0ce0ce30180d5f6c5cf7a3c98c07d55e94 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Sat, 4 Feb 2012 13:55:28 +0000
Subject: [PATCH] Make MDAbstractArray an Iterable<ArrayEntry>. Add methods
computeReverseIndex(), numberOfHyperRows(). Add methods getAsObject(int) and
setToObject(T, int) (1D, i.e.linear index). Make computeIndex() methods
public.
SVN: 24341
---
.../cisd/base/mdarray/MDAbstractArray.java | 127 +++++++++++++++--
.../systemsx/cisd/base/mdarray/MDArray.java | 12 ++
.../cisd/base/mdarray/MDByteArray.java | 12 ++
.../cisd/base/mdarray/MDDoubleArray.java | 12 ++
.../cisd/base/mdarray/MDFloatArray.java | 12 ++
.../cisd/base/mdarray/MDIntArray.java | 12 ++
.../cisd/base/mdarray/MDLongArray.java | 12 ++
.../cisd/base/mdarray/MDShortArray.java | 12 ++
.../cisd/base/mdarray/MDArrayTests.java | 133 ++++++++----------
9 files changed, 258 insertions(+), 86 deletions(-)
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java
index 6986d7a4930..4c11abfe31b 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDAbstractArray.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.base.mdarray;
import java.io.Serializable;
+import java.util.Iterator;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.ClassUtils;
@@ -30,9 +31,9 @@ import org.apache.commons.lang.ClassUtils;
*
* @author Bernd Rinn
*/
-public abstract class MDAbstractArray<T> implements Serializable
+public abstract class MDAbstractArray<T> implements Serializable,
+ Iterable<MDAbstractArray<T>.ArrayEntry>
{
-
private static final long serialVersionUID = 1L;
protected final int[] dimensions;
@@ -40,9 +41,46 @@ public abstract class MDAbstractArray<T> implements Serializable
protected int hyperRowLength;
protected int capacityHyperRows;
-
+
protected int size;
+ /**
+ * A class to represent an entry (index and value) of a {@link MDArray}, used for iteration.
+ */
+ public class ArrayEntry
+ {
+ private final int linearIndex;
+
+ ArrayEntry(int linearIndex)
+ {
+ this.linearIndex = linearIndex;
+ }
+
+ /**
+ * The multi-dimensional index of this entry.
+ */
+ public int[] getIndex()
+ {
+ return computeReverseIndex(linearIndex);
+ }
+
+ /**
+ * The linear index of this entry.
+ */
+ public int getLinearIndex()
+ {
+ return linearIndex;
+ }
+
+ /**
+ * The value of this entry.
+ */
+ public T getValue()
+ {
+ return getAsObject(linearIndex);
+ }
+ }
+
protected MDAbstractArray(int[] dimensions, int arrayLength, int capacityHyperRows)
{
assert dimensions != null;
@@ -61,8 +99,8 @@ public abstract class MDAbstractArray<T> implements Serializable
+ " does not match hyper-row length " + hyperRowLength + ".");
}
this.capacityHyperRows =
- (capacityHyperRows > 0) ? capacityHyperRows : Math.max(dimensions[0], arrayLength
- / hyperRowLength);
+ (capacityHyperRows > 0) ? capacityHyperRows : Math.max(dimensions[0],
+ arrayLength / hyperRowLength);
this.size = dimensions[0] * hyperRowLength;
}
}
@@ -124,6 +162,23 @@ public abstract class MDAbstractArray<T> implements Serializable
{
return size;
}
+
+ /**
+ * Returns the current number of hyper rows of of this array.
+ */
+ public int numberOfHyperRows()
+ {
+ return numberOfHyperRows();
+ }
+
+ /**
+ * Return an object which has the same value as the element of the array specified by
+ * <var>linearIndex</var>.
+ *
+ * @param linearIndex The index in the linear array returned by {@link #getAsFlatArray()}.
+ * @return The value at the specified index.
+ */
+ public abstract T getAsObject(int linearIndex);
/**
* Return an object which has the same value as the element of the array specified by
@@ -137,6 +192,15 @@ public abstract class MDAbstractArray<T> implements Serializable
*/
public abstract void setToObject(T value, int... indices);
+ /**
+ * Sets the element of the array specified by <var>linearIndex</var> to the particular
+ * <var>value</var>.
+ *
+ * @param value The new value to set.
+ * @param linearIndex The index in the linear array returned by {@link #getAsFlatArray()}.
+ */
+ public abstract void setToObject(T value, int linearIndex);
+
/**
* Returns the array in flattened form. Changes to the returned object will change the
* multi-dimensional array directly.
@@ -188,7 +252,7 @@ public abstract class MDAbstractArray<T> implements Serializable
/**
* Computes the linear index for the multi-dimensional <var>indices</var> provided.
*/
- protected int computeIndex(int... indices)
+ public int computeIndex(int... indices)
{
assert indices != null;
assert indices.length == dimensions.length;
@@ -201,10 +265,27 @@ public abstract class MDAbstractArray<T> implements Serializable
return index;
}
+ /**
+ * Computes the multi-dimensional index from the <var>linearIndex</var>.
+ */
+ public int[] computeReverseIndex(int linearIndex)
+ {
+ final int[] index = new int[dimensions.length];
+ int workIndex = linearIndex;
+ int blockSize = size;
+ for (int i = 0; i < dimensions.length; ++i)
+ {
+ blockSize /= dimensions[i];
+ index[i] = workIndex / blockSize;
+ workIndex = workIndex - index[i] * blockSize;
+ }
+ return index;
+ }
+
/**
* Computes the linear index for the two-dimensional (<var>indexX, indexY</var>) provided.
*/
- protected int computeIndex(int indexX, int indexY)
+ public int computeIndex(int indexX, int indexY)
{
assert 2 == dimensions.length;
@@ -215,7 +296,7 @@ public abstract class MDAbstractArray<T> implements Serializable
* Computes the linear index for the three-dimensional (<var>indexX, indexY, indexZ</var>)
* provided.
*/
- protected int computeIndex(int indexX, int indexY, int indexZ)
+ public int computeIndex(int indexX, int indexY, int indexZ)
{
assert 3 == dimensions.length;
@@ -335,6 +416,36 @@ public abstract class MDAbstractArray<T> implements Serializable
return intLength;
}
+ //
+ // Iterable
+ //
+
+ public Iterator<ArrayEntry> iterator()
+ {
+ return new Iterator<ArrayEntry>()
+ {
+ int linearIndex = 0;
+
+ public boolean hasNext()
+ {
+ return linearIndex < size;
+ }
+
+ public ArrayEntry next()
+ {
+ final ArrayEntry next = new ArrayEntry(linearIndex);
+ ++linearIndex;
+ return next;
+ }
+
+ public void remove()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ };
+ }
+
//
// Object
//
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDArray.java
index 861acd77b9d..1a4a2360b77 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDArray.java
@@ -149,6 +149,18 @@ public class MDArray<T> extends MDAbstractArray<T>
set(value, indices);
}
+ @Override
+ public T getAsObject(int linearIndex)
+ {
+ return get(linearIndex);
+ }
+
+ @Override
+ public void setToObject(T value, int linearIndex)
+ {
+ set(value, linearIndex);
+ }
+
@Override
public T[] getAsFlatArray()
{
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java
index b724d6fce00..4bb36ad7d58 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDByteArray.java
@@ -179,6 +179,18 @@ public final class MDByteArray extends MDAbstractArray<Byte>
set(value, indices);
}
+ @Override
+ public Byte getAsObject(int linearIndex)
+ {
+ return get(linearIndex);
+ }
+
+ @Override
+ public void setToObject(Byte value, int linearIndex)
+ {
+ set(value, linearIndex);
+ }
+
@Override
public byte[] getAsFlatArray()
{
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java
index 40c60fef379..8a755f442ab 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDDoubleArray.java
@@ -179,6 +179,18 @@ public final class MDDoubleArray extends MDAbstractArray<Double>
set(value, indices);
}
+ @Override
+ public Double getAsObject(int linearIndex)
+ {
+ return get(linearIndex);
+ }
+
+ @Override
+ public void setToObject(Double value, int linearIndex)
+ {
+ set(value, linearIndex);
+ }
+
@Override
public double[] getAsFlatArray()
{
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java
index 69e7e076d2f..4b10fb8da65 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDFloatArray.java
@@ -179,6 +179,18 @@ public final class MDFloatArray extends MDAbstractArray<Float>
set(value, indices);
}
+ @Override
+ public Float getAsObject(int linearIndex)
+ {
+ return get(linearIndex);
+ }
+
+ @Override
+ public void setToObject(Float value, int linearIndex)
+ {
+ set(value, linearIndex);
+ }
+
@Override
public float[] getAsFlatArray()
{
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java
index 7fea30fdd8b..76cbcd144e3 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDIntArray.java
@@ -179,6 +179,18 @@ public final class MDIntArray extends MDAbstractArray<Integer>
set(value, indices);
}
+ @Override
+ public Integer getAsObject(int linearIndex)
+ {
+ return get(linearIndex);
+ }
+
+ @Override
+ public void setToObject(Integer value, int linearIndex)
+ {
+ set(value, linearIndex);
+ }
+
@Override
public int[] getAsFlatArray()
{
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java
index 085caffb57d..3b927b131fe 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDLongArray.java
@@ -179,6 +179,18 @@ public final class MDLongArray extends MDAbstractArray<Long>
set(value, indices);
}
+ @Override
+ public Long getAsObject(int linearIndex)
+ {
+ return get(linearIndex);
+ }
+
+ @Override
+ public void setToObject(Long value, int linearIndex)
+ {
+ set(value, linearIndex);
+ }
+
@Override
public long[] getAsFlatArray()
{
diff --git a/base/source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java b/base/source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java
index 122213b07fb..eefb0b8459f 100644
--- a/base/source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java
+++ b/base/source/java/ch/systemsx/cisd/base/mdarray/MDShortArray.java
@@ -179,6 +179,18 @@ public final class MDShortArray extends MDAbstractArray<Short>
set(value, indices);
}
+ @Override
+ public Short getAsObject(int linearIndex)
+ {
+ return get(linearIndex);
+ }
+
+ @Override
+ public void setToObject(Short value, int linearIndex)
+ {
+ set(value, linearIndex);
+ }
+
@Override
public short[] getAsFlatArray()
{
diff --git a/base/sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java b/base/sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java
index a20b743dd87..38a91820966 100644
--- a/base/sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java
+++ b/base/sourceTest/java/ch/systemsx/cisd/base/mdarray/MDArrayTests.java
@@ -34,57 +34,6 @@ import ch.systemsx.cisd.base.BuildAndEnvironmentInfo;
*/
public class MDArrayTests
{
-
- static class TestMDArray extends MDAbstractArray<Void>
- {
- private static final long serialVersionUID = 1L;
-
- protected TestMDArray(int[] shape)
- {
- super(shape, 0, 0);
- }
-
- @Override
- public Void getAsObject(int... indices)
- {
- return null;
- }
-
- @Override
- public void setToObject(Void value, int... indices)
- {
- }
-
- @Override
- public int size()
- {
- return 0;
- }
-
- @Override
- public int capacity()
- {
- return 0;
- }
-
- @Override
- public Object getAsFlatArray()
- {
- return null;
- }
-
- @Override
- public Object getCopyAsFlatArray()
- {
- return null;
- }
-
- @Override
- protected void adaptCapacityHyperRows()
- {
- }
- }
-
@Test
public void testGetLength()
{
@@ -93,21 +42,21 @@ public class MDArrayTests
assertEquals(1, MDAbstractArray.getLength(new int[]
{ 1 }, 0));
assertEquals(2, MDAbstractArray.getLength(new int[]
- { 1 }, 2));
+ { 1 }, 2));
assertEquals(15, MDAbstractArray.getLength(new int[]
{ 5, 3 }, 0));
assertEquals(21, MDAbstractArray.getLength(new int[]
- { 5, 3 }, 7));
+ { 5, 3 }, 7));
assertEquals(15, MDAbstractArray.getLength(new int[]
- { 5, 3 }, 3));
+ { 5, 3 }, 3));
assertEquals(1, MDAbstractArray.getLength(new int[]
{ 1, 1, 1 }, 0));
assertEquals(3, MDAbstractArray.getLength(new int[]
- { 1, 1, 1 }, 3));
+ { 1, 1, 1 }, 3));
assertEquals(8, MDAbstractArray.getLength(new int[]
{ 2, 2, 2 }, 0));
assertEquals(20, MDAbstractArray.getLength(new int[]
- { 2, 2, 2 }, 5));
+ { 2, 2, 2 }, 5));
assertEquals(2, MDAbstractArray.getLength(new int[]
{ 1, 1, 2 }, 0));
assertEquals(2, MDAbstractArray.getLength(new int[]
@@ -132,32 +81,40 @@ public class MDArrayTests
@Test
public void testComputeIndex()
{
- TestMDArray array;
- array = new TestMDArray(new int[]
+ MDArray<Object> array;
+ array = new MDArray<Object>(Object.class, new int[]
{ 33 });
assertEquals(17, array.computeIndex(new int[]
{ 17 }));
- array = new TestMDArray(new int[]
+ assertTrue(Arrays.toString(array.computeReverseIndex(17)), Arrays.equals(new int[]
+ { 17 }, array.computeReverseIndex(17)));
+ array = new MDArray<Object>(Object.class, new int[]
{ 100, 10 });
- assertEquals(10 * 42 + 17, array.computeIndex(new int[]
- { 42, 17 }));
- array = new TestMDArray(new int[]
+ assertEquals(10 * 42 + 8, array.computeIndex(new int[]
+ { 42, 8 }));
+ assertTrue(Arrays.toString(array.computeReverseIndex(10 * 42 + 8)),
+ Arrays.equals(new int[]
+ { 42, 8 }, array.computeReverseIndex(10 * 42 + 8)));
+ array = new MDArray<Object>(Object.class, new int[]
{ 2, 7, 3 });
- assertEquals(3 * 7 * 1 + 3 * 2 + 3, array.computeIndex(new int[]
- { 1, 2, 3 }));
+ assertEquals(3 * 7 * 1 + 3 * 3 + 2, array.computeIndex(new int[]
+ { 1, 3, 2 }));
+ assertTrue(Arrays.toString(array.computeReverseIndex(3 * 7 * 1 + 3 * 3 + 2)),
+ Arrays.equals(new int[]
+ { 1, 3, 2 }, array.computeReverseIndex(3 * 7 * 1 + 3 * 3 + 2)));
}
@Test
public void testComputeIndex2D()
{
- TestMDArray array;
- array = new TestMDArray(new int[]
+ MDArray<Object> array;
+ array = new MDArray<Object>(Object.class, new int[]
{ 100, 10 });
assertEquals(array.computeIndex(new int[]
{ 5, 8, }), array.computeIndex(5, 8));
assertEquals(array.computeIndex(new int[]
{ 9, 1, }), array.computeIndex(9, 1));
- array = new TestMDArray(new int[]
+ array = new MDArray<Object>(Object.class, new int[]
{ 101, 11 });
assertEquals(array.computeIndex(new int[]
{ 5, 8, }), array.computeIndex(5, 8));
@@ -168,14 +125,14 @@ public class MDArrayTests
@Test
public void testComputeIndex3()
{
- TestMDArray array;
- array = new TestMDArray(new int[]
+ MDArray<Object> array;
+ array = new MDArray<Object>(Object.class, new int[]
{ 100, 10, 17 });
assertEquals(array.computeIndex(new int[]
{ 5, 8, 16 }), array.computeIndex(5, 8, 16));
assertEquals(array.computeIndex(new int[]
{ 9, 1, 5 }), array.computeIndex(9, 1, 5));
- array = new TestMDArray(new int[]
+ array = new MDArray<Object>(Object.class, new int[]
{ 101, 11, 3 });
assertEquals(array.computeIndex(new int[]
{ 5, 8, 0 }), array.computeIndex(5, 8, 0));
@@ -190,11 +147,12 @@ public class MDArrayTests
assertEquals(0, arr.dimensions()[0]);
assertEquals(0, arr.dimensions()[1]);
}
-
+
@Test
public void testChangeHyperRowCountIntArray()
{
- final MDIntArray arr = new MDIntArray(new int[] { 2, 2 }, 3);
+ final MDIntArray arr = new MDIntArray(new int[]
+ { 2, 2 }, 3);
assertEquals(2, arr.dimensions[0]);
assertEquals(2, arr.dimensions[1]);
arr.set(1, 0, 0);
@@ -204,7 +162,7 @@ public class MDArrayTests
final MDIntArray arr2 = new MDIntArray(arr.getCopyAsFlatArray(), arr.dimensions());
assertTrue(arr2.equals(arr));
-
+
arr.incNumberOfHyperRows(1);
assertEquals(3, arr.dimensions[0]);
assertEquals(1, arr.get(0, 0));
@@ -234,11 +192,12 @@ public class MDArrayTests
assertEquals(7, arr.get(3, 0));
assertEquals(8, arr.get(3, 1));
}
-
+
@Test
public void testChangeHyperRowCountIntArrayFromZero()
{
- final MDIntArray arr = new MDIntArray(new int[] { 0 });
+ final MDIntArray arr = new MDIntArray(new int[]
+ { 0 });
assertEquals(0, arr.size(0));
arr.incNumberOfHyperRows(1);
assertEquals(1, arr.size(0));
@@ -248,11 +207,12 @@ public class MDArrayTests
arr.incNumberOfHyperRows(1);
assertEquals(3, arr.size());
}
-
+
@Test
public void testChangeHyperRowCountTArray()
{
- final MDArray<Integer> arr = new MDArray<Integer>(Integer.class, new int[] { 2, 2 }, 3);
+ final MDArray<Integer> arr = new MDArray<Integer>(Integer.class, new int[]
+ { 2, 2 }, 3);
assertEquals(2, arr.dimensions[0]);
assertEquals(2, arr.dimensions[1]);
arr.set(1, 0, 0);
@@ -288,7 +248,24 @@ public class MDArrayTests
assertEquals(7, (int) arr.get(3, 0));
assertEquals(8, (int) arr.get(3, 1));
}
-
+
+ @Test
+ public void testMDIntArrayIterator()
+ {
+ final int[] linArray = new int[120];
+ for (int i = 0; i < linArray.length; ++i)
+ {
+ linArray[i] = i;
+ }
+ final MDIntArray array = new MDIntArray(linArray, new int[]
+ { 2, 3, 4, 5 });
+ for (MDIntArray.ArrayEntry e : array)
+ {
+ assertEquals(e.getLinearIndex(), e.getValue().intValue());
+ assertEquals(e.getLinearIndex(), array.computeIndex(e.getIndex()));
+ }
+ }
+
@Test
public void testMDFloatArrayMatrix()
{
--
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