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Performance optimization of multidimensional array access #535

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Performance optimization of multidimensional array access #535

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1c220c7
array optimization - part 1 - remove duplicate and unused code
jan-zajic Feb 5, 2018
6c12248
array optimization - part 2 - replace Array.get
jan-zajic Feb 5, 2018
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24 changes: 1 addition & 23 deletions src/main/java/org/numenta/nupic/util/AbstractFlatMatrix.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
package org.numenta.nupic.util;

import java.io.Serializable;
import java.lang.reflect.Array;
import java.util.Arrays;

/**
Expand Down Expand Up @@ -112,7 +111,7 @@ protected void checkDims(int[] index) {
for(int i = 0;i < index.length - 1;i++) {
if(index[i] >= dimensions[i]) {
throw new IllegalArgumentException("Specified coordinates exceed the configured array dimensions " +
print1DArray(index) + " > " + print1DArray(dimensions));
Arrays.toString(index) + " > " + Arrays.toString(dimensions));
}
}
}
Expand Down Expand Up @@ -179,27 +178,6 @@ public static int[] reverse(int[] input) {
return retVal;
}

/**
* Prints the specified array to a returned String.
*
* @param aObject the array object to print.
* @return the array in string form suitable for display.
*/
public static String print1DArray(Object aObject) {
if (aObject.getClass().isArray()) {
if (aObject instanceof Object[]) // can we cast to Object[]
return Arrays.toString((Object[]) aObject);
else { // we can't cast to Object[] - case of primitive arrays
int length = Array.getLength(aObject);
Object[] objArr = new Object[length];
for (int i=0; i<length; i++)
objArr[i] = Array.get(aObject, i);
return Arrays.toString(objArr);
}
}
return "[]";
}

@Override
public abstract T get(int index);

Expand Down
167 changes: 79 additions & 88 deletions src/main/java/org/numenta/nupic/util/ArrayUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ public static int product(int[] dims) {

return retVal;
}

/**
* Returns an array containing the successive elements of each
* argument array as in [ first[0], second[0], first[1], second[1], ... ].
Expand All @@ -100,16 +100,16 @@ public static <F, S> Object[] interleave(F first, S second) {
Object[] retVal = new Object[(flen = Array.getLength(first)) + (slen = Array.getLength(second))];
for(int i = 0, j = 0, k = 0;i < flen || j < slen;) {
if(i < flen) {
retVal[k++] = Array.get(first, i++);
retVal[k++] = getValue(first, i++);
}
if(j < slen) {
retVal[k++] = Array.get(second, j++);
retVal[k++] = getValue(second, j++);
}
}

return retVal;
}

/**
* <p>
* Return a new double[] containing the difference of each element and its
Expand Down Expand Up @@ -340,60 +340,6 @@ public static int[] unravel(int[][] array) {
return result;
}

/**
* Takes a two-dimensional array of r rows and c columns and reshapes it to
* have (r*c)/n by n columns. The value in location [i][j] of the input array
* is copied into location [j][i] of the new array.
*
* @param array The array of values to be reshaped.
* @param n The number of columns in the created array.
* @return The new (r*c)/n by n array.
* @throws IllegalArgumentException If r*c is not evenly divisible by n.
*/
public static int[][] reshape(int[][] array, int n) throws IllegalArgumentException {
int r = array.length;
if (r == 0) {
return new int[0][0]; // Special case: zero-length array
}
if ((array.length * array[0].length) % n != 0) {
int size = array.length * array[0].length;
throw new IllegalArgumentException(size + " is not evenly divisible by " + n);
}
int c = array[0].length;
int[][] result = new int[(r * c) / n][n];
int ii = 0;
int jj = 0;

for (int i = 0; i < r; i++) {
for (int j = 0; j < c; j++) {
result[ii][jj] = array[i][j];
jj++;
if (jj == n) {
jj = 0;
ii++;
}
}
}
return result;
}

/**
* Returns an int[] with the dimensions of the input.
* @param inputArray
* @return
*/
public static int[] shape(Object inputArray) {
int nr = 1 + inputArray.getClass().getName().lastIndexOf('[');
Object oa = inputArray;
int[] l = new int[nr];
for(int i = 0;i < nr;i++) {
int len = l[i] = Array.getLength(oa);
if (0 < len) { oa = Array.get(oa, 0); }
}

return l;
}

/**
* Sorts the array, then returns an array containing the indexes of
* those sorted items in the original array.
Expand Down Expand Up @@ -1143,28 +1089,6 @@ public static int[] sparseBinaryOr(int[] arg1, int[] arg2) {
return unique(t.toArray());
}

/**
* Prints the specified array to a returned String.
*
* @param aObject the array object to print.
* @return the array in string form suitable for display.
*/
public static String print1DArray(Object aObject) {
if (aObject.getClass().isArray()) {
if (aObject instanceof Object[]) // can we cast to Object[]
{
return Arrays.toString((Object[])aObject);
} else { // we can't cast to Object[] - case of primitive arrays
int length = Array.getLength(aObject);
Object[] objArr = new Object[length];
for (int i = 0; i < length; i++)
objArr[i] = Array.get(aObject, i);
return Arrays.toString(objArr);
}
}
return "[]";
}

/**
* Another utility to account for the difference between Python and Java.
* Here the modulo operator is defined differently.
Expand Down Expand Up @@ -2122,28 +2046,95 @@ public static int[] tail(int[] original) {
* @param indexes
*/
public static void setValue(Object array, int value, int... indexes) {
if (indexes.length == 1) {
if(indexes.length == 1) {
((int[])array)[indexes[0]] = value;
} else {
setValue(Array.get(array, indexes[0]), value, tail(indexes));
setValue(ArrayUtils.getSlice(array, indexes[0]), value, tail(indexes));
}
}

/**
* Get <tt>value</tt> for <tt>array</tt> at specified position <tt>indexes</tt>
*
* @param array
* @param indexes
*/
public static int getIntValue(Object array, int... indexes) {
Object slice = array;
if(indexes.length > 1) {
for(int i = 0;i < indexes.length - 1;i++) {
slice = ((Object[])slice)[indexes[i]];
}
}
return ((int[])slice)[indexes[indexes.length - 1]];
}

public static Object getValue(Object array, int... indexes) {
Object slice = array;
for(int i = 0;i < indexes.length;i++) {
slice = Array.get(slice, indexes[i]);
if(indexes.length > 1) {
for(int i = 0;i < indexes.length - 1;i++) {
slice = get(slice, i);
}
}
return get(slice, indexes[indexes.length - 1]);
}

/**
* Get <tt>slice</tt> for <tt>array</tt> at specified position
* <tt>indexes</tt>
*
* @param array
* @param indexes
*/
public static Object getSlice(Object array, int... indexes) {
Object slice = array;
if(indexes.length > 1) {
for(int i = 0;i < indexes.length - 1;i++) {
slice = ((Object[])slice)[indexes[i]];
}
}

return slice;
return ((Object[])slice)[indexes[indexes.length - 1]];
}

/**
* Gets an element of an array. Primitive elements will be wrapped in the
* corresponding class type.
*
* @param array
* the array to access
* @param index
* the array index to access
* @return the element at <code>array[index]</code>
* @throws IllegalArgumentException
* if <code>array</code> is not an array
* @throws NullPointerException
* if <code>array</code> is null
* @throws ArrayIndexOutOfBoundsException
* if <code>index</code> is out of bounds
*/
public static Object get(Object array, int index) {
if(array instanceof Object[])
return ((Object[])array)[index];
if(array instanceof boolean[])
return ((boolean[])array)[index] ? Boolean.TRUE : Boolean.FALSE;
if(array instanceof byte[])
return new Byte(((byte[])array)[index]);
if(array instanceof char[])
return new Character(((char[])array)[index]);
if(array instanceof short[])
return new Short(((short[])array)[index]);
if(array instanceof int[])
return new Integer(((int[])array)[index]);
if(array instanceof long[])
return new Long(((long[])array)[index]);
if(array instanceof float[])
return new Float(((float[])array)[index]);
if(array instanceof double[])
return new Double(((double[])array)[index]);
if(array == null)
throw new NullPointerException();
throw new IllegalArgumentException();
}

/**
*Assigns the specified int value to each element of the specified any dimensional array
Expand Down
26 changes: 1 addition & 25 deletions src/main/java/org/numenta/nupic/util/NamedTuple.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,13 +22,13 @@

package org.numenta.nupic.util;

import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;

import org.numenta.nupic.model.Persistable;
import static org.numenta.nupic.util.ArrayUtils.interleave;

/**
* Immutable tuple which adds associative lookup functionality.
Expand Down Expand Up @@ -408,28 +408,4 @@ public boolean equals(Object obj) {
}
}

/**
* Returns an array containing the successive elements of each
* argument array as in [ first[0], second[0], first[1], second[1], ... ].
*
* Arrays may be of zero length, and may be of different sizes, but may not be null.
*
* @param first the first array
* @param second the second array
* @return
*/
static <F, S> Object[] interleave(F first, S second) {
int flen, slen;
Object[] retVal = new Object[(flen = Array.getLength(first)) + (slen = Array.getLength(second))];
for(int i = 0, j = 0, k = 0;i < flen || j < slen;) {
if(i < flen) {
retVal[k++] = Array.get(first, i++);
}
if(j < slen) {
retVal[k++] = Array.get(second, j++);
}
}

return retVal;
}
}
20 changes: 10 additions & 10 deletions src/main/java/org/numenta/nupic/util/SparseBinaryMatrix.java
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Original file line number Diff line number Diff line change
Expand Up @@ -83,18 +83,18 @@ private void back(int val, int... coordinates) {
*
* @param coordinates the coordinates which specify the returned array
* @return the array specified
* @throws IllegalArgumentException if the specified coordinates address
* an actual value instead of the array holding it.
* @throws IllegalArgumentException if the specified coordinates address
* an actual value instead of the array holding it.
*/
@Override
public Object getSlice(int... coordinates) {
Object slice = ArrayUtils.getValue(this.backingArray, coordinates);
//Ensure return value is of type Array
if(!slice.getClass().isArray()) {
sliceError(coordinates);
try {
return ArrayUtils.getSlice(this.backingArray, coordinates);
} catch(ClassCastException e) {
throw new IllegalArgumentException(
"This method only returns the array holding the specified maximum index: " +
Arrays.toString(dimensions));
}

return slice;
}

/**
Expand Down Expand Up @@ -177,7 +177,7 @@ public AbstractSparseBinaryMatrix set(int[] indexes, int[] values) {
*/
public void clearStatistics(int row) {
this.setTrueCount(row, 0);
int[] slice = (int[])Array.get(backingArray, row);
int[] slice = (int[])ArrayUtils.getSlice(backingArray, row);
Arrays.fill(slice, 0);
}

Expand All @@ -194,7 +194,7 @@ public Integer get(int index) {
return Array.getInt(this.backingArray, index);
}

else return (Integer) ArrayUtils.getValue(this.backingArray, coordinates);
else return (Integer) ArrayUtils.getIntValue(this.backingArray, coordinates);
}

@Override
Expand Down
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