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The NetCDF-Java Library is a Java interface to NetCDF files,
as well as to many other types of scientific data formats.
The newest version!
/*
* Copyright 1998-2014 University Corporation for Atmospheric Research/Unidata
*
* Portions of this software were developed by the Unidata Program at the
* University Corporation for Atmospheric Research.
*
* Access and use of this software shall impose the following obligations
* and understandings on the user. The user is granted the right, without
* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
* documentation for any purpose whatsoever, provided that this entire
* notice appears in all copies of the software, derivative works and
* supporting documentation. Further, UCAR requests that the user credit
* UCAR/Unidata in any publications that result from the use of this
* software or in any product that includes this software. The names UCAR
* and/or Unidata, however, may not be used in any advertising or publicity
* to endorse or promote any products or commercial entity unless specific
* written permission is obtained from UCAR/Unidata. The user also
* understands that UCAR/Unidata is not obligated to provide the user with
* any support, consulting, training or assistance of any kind with regard
* to the use, operation and performance of this software nor to provide
* the user with any updates, revisions, new versions or "bug fixes."
*
* THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
* INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
* FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
* NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
* WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
*/
package ucar.ma2;
import java.math.BigInteger;
import java.util.Arrays;
import java.util.List;
import java.util.ArrayList;
import java.nio.*;
/**
* Superclass for implementations of multidimensional arrays. An Array has a classType which gives
* the Class of its elements, and a shape which describes the number of elements in each index.
* The rank is the number of indices. A scalar Array has rank = 0. An
* Array may have arbitrary rank. The Array size is the total number of elements, which must be less than
* 2^31 (about 2x10^9).
*
* Actual data storage is done with Java 1D arrays and stride index calculations.
* This makes our Arrays rectangular, i.e. no "ragged arrays" where different elements
* can have different lengths as in Java multidimensional arrays, which are arrays of arrays.
*
* Each primitive Java type (boolean, byte, char, short, int, long, float, double) has a corresponding concrete
* implementation, e.g. ArrayBoolean, ArrayDouble. Reference types are all implemented using the ArrayObject class,
* with the exceptions of the reference types that correspond to the primitive types, eg Double.class is mapped to
* double.class.
*
* For efficiency, each Array type implementation has concrete subclasses for ranks 0-7, eg ArrayDouble.D0 is a double
* array of rank 0, ArrayDouble.D1 is a double array of rank 1, etc. These type and rank specific classes are convenient
* to work with when you know the type and rank of the Array. Ranks greater than 7 are handled by the type-specific
* superclass e.g. ArrayDouble. The Array class itself is used for fully general handling of any type and rank array.
* Use the Array.factory() methods to create Arrays in a general way.
*
* The stride index calculations allow logical views to be efficiently implemented, eg subset, transpose, slice, etc.
* These views use the same data storage as the original Array they are derived from. The index stride calculations are
* equally efficient for any composition of logical views.
*
* The type, shape and backing storage of an Array are immutable.
* The data itself is read or written using an Index or an IndexIterator, which stores any needed state information
* for efficient traversal. This makes use of Arrays thread-safe (as long as you dont share the Index or IndexIterator)
* except for the possibility of non-atomic read/write on long/doubles. If this is the case, you should probably
* synchronize your calls. Presumably 64-bit CPUs will make those operations atomic also.
*
* @author caron
* @see Index
* @see IndexIterator
*/
public abstract class Array {
/* implementation notes.
Could create interface for Ranges, ScatterIndex and pass array of that (?)
*/
/**
* Generate new Array with given type and shape and zeroed storage.
*
* @param dataType instance of DataType.
* @param shape shape of the array.
* @return new Array or Array.D if 0 <= rank <= 7.
*/
static public Array factory(DataType dataType, int[] shape) {
Index index = Index.factory(shape);
return factory(dataType.getPrimitiveClassType(), index);
}
/**
* Generate new Array with given type and shape and zeroed storage.
*
* @param classType element Class type, eg double.class.
* @param shape shape of the array.
* @return new Array or Array.D if 0 <= rank <= 7.
*/
static public Array factory(Class classType, int[] shape) {
Index index = Index.factory(shape);
return factory(classType, index);
}
/* generate new Array with given type and shape and zeroed storage */
static private Array factory(Class classType, Index index) {
if ((classType == double.class) || (classType == Double.class))
return ArrayDouble.factory(index);
else if ((classType == float.class) || (classType == Float.class))
return ArrayFloat.factory(index);
else if ((classType == long.class) || (classType == Long.class))
return ArrayLong.factory(index);
else if ((classType == int.class) || (classType == Integer.class))
return ArrayInt.factory(index);
else if ((classType == short.class) || (classType == Short.class))
return ArrayShort.factory(index);
else if ((classType == byte.class) || (classType == Byte.class))
return ArrayByte.factory(index);
else if ((classType == char.class) || (classType == Character.class))
return ArrayChar.factory(index);
else if ((classType == boolean.class) || (classType == Boolean.class))
return ArrayBoolean.factory(index);
else
return ArrayObject.factory(classType, index);
}
/**
* /** Generate new Array with given type, shape, storage.
*
* @param dataType DataType, eg DataType.DOUBLE.
* @param shape shape of the array.
* @param storage primitive array of correct type
* @return new Array or Array.D if 0 <= rank <= 7.
*/
static public Array factory(DataType dataType, int[] shape, Object storage) {
return factory(dataType.getPrimitiveClassType(), shape, storage);
}
/**
* Generate new Array with given type, shape, storage.
* This should be package private, but is exposed for efficiency.
* Normally use factory( Class classType, int [] shape) instead.
* storage must be 1D array of type classType.
* storage.length must equal product of shapes
* storage data needs to be in canonical order
*
* @param classType element class type, eg double.class. Corresponding Object types like Double.class are
* mapped to double.class. Any reference types use ArrayObject.
* @param shape array shape
* @param storage 1D java array of type classType, except object types like Double.class are mapped to
* their corresponding primitive type, eg double.class.
* @return Array of given type, shape and storage
* @throws IllegalArgumentException storage.length != product of shapes
* @throws ClassCastException wrong storage type
*/
static public Array factory(Class classType, int[] shape, Object storage) {
Index indexCalc = Index.factory(shape);
return factory(classType, indexCalc, storage);
}
static private Array factory(Class classType, Index indexCalc, Object storage) {
if ((classType == double.class) || (classType == Double.class))
return ArrayDouble.factory(indexCalc, (double[]) storage);
else if ((classType == float.class) || (classType == Float.class))
return ArrayFloat.factory(indexCalc, (float[]) storage);
else if ((classType == long.class) || (classType == Long.class))
return ArrayLong.factory(indexCalc, (long[]) storage);
else if ((classType == int.class) || (classType == Integer.class))
return ArrayInt.factory(indexCalc, (int[]) storage);
else if ((classType == short.class) || (classType == Short.class))
return ArrayShort.factory(indexCalc, (short[]) storage);
else if ((classType == byte.class) || (classType == Byte.class))
return ArrayByte.factory(indexCalc, (byte[]) storage);
else if ((classType == char.class) || (classType == Character.class))
return ArrayChar.factory(indexCalc, (char[]) storage);
else if ((classType == boolean.class) || (classType == Boolean.class))
return ArrayBoolean.factory(indexCalc, (boolean[]) storage);
else
return ArrayObject.factory(classType, indexCalc, (Object[]) storage);
}
/**
* Generate new Array with given type and shape and an Index that always return 0.
*
* @param classType element Class type, eg double.class.
* @param shape shape of the array.
* @param storage primitive array of correct type of length 1
* @return new Array or Array.D if 0 <= rank <= 7.
*/
static public Array factoryConstant(Class classType, int[] shape, Object storage) {
Index index = new IndexConstant(shape);
if ((classType == double.class) || (classType == Double.class))
return new ArrayDouble(index, (double[]) storage);
else if ((classType == float.class) || (classType == Float.class))
return new ArrayFloat(index, (float[]) storage);
else if ((classType == long.class) || (classType == Long.class))
return new ArrayLong(index, (long[]) storage);
else if ((classType == int.class) || (classType == Integer.class))
return new ArrayInt(index, (int[]) storage);
else if ((classType == short.class) || (classType == Short.class))
return new ArrayShort(index, (short[]) storage);
else if ((classType == byte.class) || (classType == Byte.class))
return new ArrayByte(index, (byte[]) storage);
else if ((classType == char.class) || (classType == Character.class))
return new ArrayChar(index, (char[]) storage);
else if ((classType == boolean.class) || (classType == Boolean.class))
return new ArrayBoolean(index, (boolean[]) storage);
else
return new ArrayObject(classType, index, (Object[]) storage);
}
/**
* Generate a new Array from a java array of any rank and type.
* This makes a COPY of the data values of javaArray.
* LOOK: not sure this works for reference types.
*
* @param javaArray scalar Object or a java array of any rank and type
* @return Array of the appropriate rank and type, with the data copied from javaArray.
*/
static public Array factory(Object javaArray) {
// get the rank and type
int rank_ = 0;
Class componentType = javaArray.getClass();
while (componentType.isArray()) {
rank_++;
componentType = componentType.getComponentType();
}
/* if( rank_ == 0)
throw new IllegalArgumentException("Array.factory: not an array");
if( !componentType.isPrimitive())
throw new UnsupportedOperationException("Array.factory: not a primitive array"); */
// get the shape
int count = 0;
int[] shape = new int[rank_];
Object jArray = javaArray;
Class cType = jArray.getClass();
while (cType.isArray()) {
shape[count++] = java.lang.reflect.Array.getLength(jArray);
jArray = java.lang.reflect.Array.get(jArray, 0);
cType = jArray.getClass();
}
// create the Array
Array aa = factory(componentType, shape);
// copy the original array
IndexIterator aaIter = aa.getIndexIterator();
reflectArrayCopyIn(javaArray, aa, aaIter);
return aa;
}
static private void reflectArrayCopyIn(Object jArray, Array aa, IndexIterator aaIter) {
Class cType = jArray.getClass().getComponentType();
if (cType.isPrimitive()) {
aa.copyFrom1DJavaArray(aaIter, jArray); // subclass does type-specific copy
} else {
for (int i = 0; i < java.lang.reflect.Array.getLength(jArray); i++) // recurse
reflectArrayCopyIn(java.lang.reflect.Array.get(jArray, i), aa, aaIter);
}
}
static private void reflectArrayCopyOut(Object jArray, Array aa, IndexIterator aaIter) {
Class cType = jArray.getClass().getComponentType();
//if (cType.isPrimitive()) { // Rob Weingruber May 11, 2011
if (!cType.isArray()) {
aa.copyTo1DJavaArray(aaIter, jArray); // subclass does type-specific copy
} else {
for (int i = 0; i < java.lang.reflect.Array.getLength(jArray); i++) // recurse
reflectArrayCopyOut(java.lang.reflect.Array.get(jArray, i), aa, aaIter);
}
}
/**
* Cover for System.arraycopy(). Works with the underlying data arrays.
* ArraySrc and ArrayDst must be the same primitive type.
* Exposed for efficiency; use at your own risk.
*
* @param arraySrc copy from here : if not in canonical order, an extra copy will be done
* @param srcPos starting at
* @param arrayDst copy to here : must be in canonical order
* @param dstPos starting at
* @param len number of elements to copy
*/
static public void arraycopy(Array arraySrc, int srcPos, Array arrayDst, int dstPos, int len) {
// deal with special case
if (arraySrc.isConstant()) {
double d = arraySrc.getDouble(0);
for (int i = dstPos; i < dstPos + len; i++)
arrayDst.setDouble(i, d);
return;
}
Object src = arraySrc.get1DJavaArray(arraySrc.getElementType()); // ensure canonical order
Object dst = arrayDst.getStorage();
System.arraycopy(src, srcPos, dst, dstPos, len);
}
/**
* Make a 1D array from a start and inccr.
*
* @param dtype data type of result. must be convertible to double.
* @param npts number of points
* @param start starting values
* @param incr increment
* @return 1D array
*/
static public Array makeArray(DataType dtype, int npts, double start, double incr) {
Array result = Array.factory(dtype.getPrimitiveClassType(), new int[]{npts});
IndexIterator dataI = result.getIndexIterator();
for (int i = 0; i < npts; i++) {
double val = start + i * incr;
dataI.setDoubleNext(val);
}
return result;
}
/**
* Make an 1D array from a list of strings.
*
* @param dtype data type of the array.
* @param isUnsigned may be unsigned (byte, short, int, long)
* @param stringValues list of strings.
* @return resulting 1D array.
* @throws NumberFormatException if string values not parseable to specified data type
*/
static public Array makeArray(DataType dtype, boolean isUnsigned, List stringValues) throws NumberFormatException {
Array result = Array.factory(dtype.getPrimitiveClassType(), new int[]{stringValues.size()});
IndexIterator dataI = result.getIndexIterator();
for (String s : stringValues) {
if (dtype == DataType.STRING) {
dataI.setObjectNext(s);
} else if (dtype == DataType.LONG) {
if (isUnsigned) {
BigInteger biggy = new BigInteger(s);
long convert = biggy.longValue(); // > 63 bits will become "negetive".
System.out.printf("%s == %d%n", biggy, convert);
dataI.setLongNext(biggy.longValue());
} else {
long val = Long.parseLong(s);
dataI.setLongNext(val);
}
} else {
double val = Double.parseDouble(s);
dataI.setDoubleNext(val);
}
}
return result;
}
/**
* Make an 1D array from a list of strings.
*
* @param dtype data type of the array. Assumed unsigned
* @param stringValues list of strings.
* @return resulting 1D array.
* @throws NumberFormatException if string values not parseable to specified data type
*/
static public Array makeArray(DataType dtype, List stringValues) throws NumberFormatException {
return makeArray(dtype, false, stringValues);
}
/**
* Make an 1D array from an array of strings.
*
* @param dtype data type of the array. Assumed unsigned
* @param stringValues list of strings.
* @return resulting 1D array.
* @throws NumberFormatException if string values not parseable to specified data type
*/
static public Array makeArray(DataType dtype, String[] stringValues) throws NumberFormatException {
return makeArray(dtype, Arrays.asList(stringValues));
}
/**
* Add extra dimension with len = 1.
*
* @param org original array
* @return rank1 array of rank + 1
*/
static public Array makeArrayRankPlusOne(Array org) {
int[] shape = new int[org.getRank()+1];
System.arraycopy(org.getShape(), 0, shape, 1, org.getRank());
shape[0] = 1;
return factory(org.getDataType(), shape, org.getStorage());
}
/////////////////////////////////////////////////////
protected final Index indexCalc;
protected final int rank;
protected boolean unsigned;
private IndexIterator ii; // local iterator
private DataType datatype;
// for subclasses only
protected Array(int[] shape) {
rank = shape.length;
indexCalc = Index.factory(shape);
this.datatype = computesort();
}
protected Array(Index index) {
rank = index.getRank();
indexCalc = index;
this.datatype = computesort();
}
/**
* Compute the datatype sort
*/
DataType
computesort() {
if (this instanceof ArrayBoolean)
return DataType.BOOLEAN;
if (this instanceof ArrayByte)
return DataType.BYTE;
if (this instanceof ArrayChar)
return DataType.CHAR;
if (this instanceof ArrayShort)
return DataType.SHORT;
if (this instanceof ArrayInt)
return DataType.INT;
if (this instanceof ArrayLong)
return DataType.LONG;
if (this instanceof ArrayFloat)
return DataType.FLOAT;
if (this instanceof ArrayDouble)
return DataType.DOUBLE;
if (this instanceof ArrayString)
return DataType.STRING;
if (this instanceof ArrayObject)
return DataType.OBJECT;
if (this instanceof ArraySequence)
return DataType.SEQUENCE;
if (this instanceof ArrayStructure)
return DataType.STRUCTURE;
return null;
}
/**
* Return the computed datatype for this array
*
* @return the data type
*/
public DataType getDataType() {
return this.datatype;
}
/**
* Get an Index object used for indexed access of this Array.
*
* @return an Index for this Array
* @see Index
*/
public Index getIndex() {
return (Index) indexCalc.clone();
}
/**
* Get an Index object used for indexed access of this Array.
*
* @return an Index for this Array
*/
public Index getIndexPrivate() {
return indexCalc;
}
/**
* Get an index iterator for traversing the array in canonical order.
*
* @return an IndexIterator for this Array
* @see IndexIterator
*/
public IndexIterator getIndexIterator() {
return indexCalc.getIndexIterator(this);
}
/**
* Get the number of dimensions of the array.
*
* @return number of dimensions of the array
*/
public int getRank() {
return rank;
}
/**
* Get the shape: length of array in each dimension.
*
* @return array whose length is the rank of this
* Array and whose elements represent the length of each of its indices.
*/
public int[] getShape() {
return indexCalc.getShape();
}
/**
* Get the total number of elements in the array.
*
* @return total number of elements in the array
*/
public long getSize() {
return indexCalc.getSize();
}
/**
* Get the total number of bytes in the array.
*
* @return total number of bytes in the array
*/
public long getSizeBytes() {
DataType dtype = DataType.getType(getElementType());
return indexCalc.getSize() * dtype.getSize();
}
/**
* Get an index iterator for traversing a section of the array in canonical order.
* This is equivalent to Array.section(ranges).getIterator();
*
* @param ranges list of Ranges that specify the array subset.
* Must be same rank as original Array.
* A particular Range: 1) may be a subset, or 2) may be null, meaning use entire Range.
* @return an IndexIterator over the named range.
* @throws InvalidRangeException if ranges is invalid
*/
public IndexIterator getRangeIterator(List ranges) throws InvalidRangeException {
return section(ranges).getIndexIterator();
}
/**
* Get an index iterator for traversing the array in arbitrary order.
* Use this if you dont care what order the elements are returned, eg if you are summing an Array.
* To get an iteration in order, use getIndexIterator(), which returns a fast iterator if possible.
*
* @return an IndexIterator for traversing the array in arbitrary order.
* @deprecated use getIndexIterator
*/
public IndexIterator getIndexIteratorFast() {
return indexCalc.getIndexIteratorFast(this);
}
/**
* Get the element class type of this Array
*
* @return the class of the element
*/
public abstract Class getElementType();
/**
* Get underlying primitive array storage.
* Exposed for efficiency, use at your own risk.
*
* @return underlying primitive array storage
*/
public abstract Object getStorage();
// So it turns out that non-public, non-protected abstract
// methods cannot be overridden in classes in other packages.
// If the methods are declared protected, however, they
// can be overridden; just one of those Java things.
//
// So, modify the following methods to be protected:
// copyFrom1DJavaArray, copyTo1DJavaArray, and createView.
//
// This has consequences all over ucar.ma2.
// used to create Array from java array
abstract protected void copyFrom1DJavaArray(IndexIterator iter, Object javaArray);
abstract protected void copyTo1DJavaArray(IndexIterator iter, Object javaArray);
/**
* create new Array with given Index and the same backing store
*
* @param index use this Index
* @return a view of the Array using the given Index
*/
abstract protected Array createView(Index index);
/**
* Create a new Array as a subsection of this Array, with rank reduction.
* No data is moved, so the new Array references the same backing store as the original.
*
* @param ranges list of Ranges that specify the array subset.
* Must be same rank as original Array.
* A particular Range: 1) may be a subset, or 2) may be null, meaning use entire Range.
* If Range[dim].length == 1, then the rank of the resulting Array is reduced at that dimension.
* @return the new Array
* @throws InvalidRangeException if ranges is invalid
*/
public Array section(List ranges) throws InvalidRangeException {
return createView(indexCalc.section(ranges));
}
/**
* Create a new Array as a subsection of this Array, with rank reduction.
* No data is moved, so the new Array references the same backing store as the original.
*
*
* @param origin int array specifying the starting index. Must be same rank as original Array.
* @param shape int array specifying the extents in each dimension.
* This becomes the shape of the returned Array. Must be same rank as original Array.
* If shape[dim] == 1, then the rank of the resulting Array is reduced at that dimension.
* @return the new Array
* @throws InvalidRangeException if ranges is invalid
*/
public Array section(int[] origin, int[] shape) throws InvalidRangeException {
return section(origin, shape, null);
}
/**
* Create a new Array as a subsection of this Array, with rank reduction.
* No data is moved, so the new Array references the same backing store as the original.
*
*
* @param origin int array specifying the starting index. Must be same rank as original Array.
* @param shape int array specifying the extents in each dimension.
* This becomes the shape of the returned Array. Must be same rank as original Array.
* If shape[dim] == 1, then the rank of the resulting Array is reduced at that dimension.
* @param stride int array specifying the strides in each dimension. If null, assume all ones.
* @return the new Array
* @throws InvalidRangeException if ranges is invalid
*/
public Array section(int[] origin, int[] shape, int[] stride) throws InvalidRangeException {
List ranges = new ArrayList<>(origin.length);
if (stride == null) {
stride = new int[origin.length];
for (int i = 0; i < stride.length; i++) stride[i] = 1;
}
for (int i = 0; i < origin.length; i++)
ranges.add(new Range(origin[i], origin[i] + stride[i] * shape[i] - 1, stride[i]));
return createView(indexCalc.section(ranges));
}
/**
* Create a new Array as a subsection of this Array, without rank reduction.
* No data is moved, so the new Array references the same backing store as the original.
* Vlen is transferred over unchanged.
*
* @param ranges list of Ranges that specify the array subset.
* Must be same rank as original Array.
* A particular Range: 1) may be a subset, or 2) may be null, meaning use entire Range.
* @return the new Array
* @throws InvalidRangeException if ranges is invalid
*/
public Array sectionNoReduce(List ranges) throws InvalidRangeException {
return createView(indexCalc.sectionNoReduce(ranges));
}
/**
* Create a new Array as a subsection of this Array, without rank reduction.
* No data is moved, so the new Array references the same backing store as the original.
*
* @param origin int array specifying the starting index. Must be same rank as original Array.
* @param shape int array specifying the extents in each dimension.
* This becomes the shape of the returned Array. Must be same rank as original Array.
* @param stride int array specifying the strides in each dimension. If null, assume all ones.
* @return the new Array
* @throws InvalidRangeException if ranges is invalid
*/
public Array sectionNoReduce(int[] origin, int[] shape, int[] stride) throws InvalidRangeException {
List ranges = new ArrayList<>(origin.length);
if (stride == null) {
stride = new int[origin.length];
for (int i = 0; i < stride.length; i++) stride[i] = 1;
}
for (int i = 0; i < origin.length; i++) {
if (shape[i] < 0) // VLEN
ranges.add(Range.VLEN);
else
ranges.add(new Range(origin[i], origin[i] + stride[i] * shape[i] - 1, stride[i]));
}
return createView(indexCalc.sectionNoReduce(ranges));
}
/**
* Create a new Array using same backing store as this Array, by
* fixing the specified dimension at the specified index value. This reduces rank by 1.
*
* @param dim which dimension to fix
* @param value at what index value
* @return a new Array
*/
public Array slice(int dim, int value) {
int[] origin = new int[rank];
int[] shape = getShape();
origin[dim] = value;
shape[dim] = 1;
try {
return sectionNoReduce(origin, shape, null).reduce(dim); // preserve other dim 1
} catch (InvalidRangeException e) {
throw new IllegalArgumentException();
}
}
/**
* Create a copy of this Array, copying the data so that physical order is the same as
* logical order
*
* @return the new Array
*/
public Array copy() {
Array newA = factory(getElementType(), getShape());
MAMath.copy(newA, this);
newA.setUnsigned(isUnsigned());
return newA;
}
/**
* This gets the equivalent java array of the wanted type, in correct order.
* It avoids copying if possible.
*
* @param wantType returned object will be an array of this type. This must be convertible to it.
* @return java array of type want
*/
public Object get1DJavaArray(Class wantType) {
if (wantType == getElementType()) {
if (indexCalc.isFastIterator())
return getStorage(); // already in order
else return copyTo1DJavaArray(); // gotta copy
}
// gotta convert to new type
Array newA = factory(wantType, getShape());
MAMath.copy(newA, this);
return newA.getStorage();
}
/**
* This gets the data as a ByteBuffer, in correct order.
* It avoids copying if possible.
* Only for numeric types (byte, short, int, long, double, float)
*
* @return equivilent data in a ByteBuffer
*/
public ByteBuffer getDataAsByteBuffer() {
throw new UnsupportedOperationException();
}
/**
* Create an Array from a ByteBuffer
*
* @param dtype type of data
* @param shape shape of data; if null, then use int[]{bb.limit()}
* @param bb data is in here
* @return equivilent Array
*/
public static Array factory(DataType dtype, int[] shape, ByteBuffer bb) {
int size;
Array result;
switch (dtype) {
case ENUM1:
case BYTE:
if (shape == null) shape = new int[]{bb.limit()};
return factory(dtype, shape, bb.array());
case CHAR:
size = bb.limit();
if (shape == null) shape = new int[]{size};
result = factory(dtype, shape);
for (int i = 0; i < size; i++)
result.setChar(i, (char) bb.get(i));
return result;
case ENUM2:
case SHORT:
ShortBuffer sb = bb.asShortBuffer();
size = sb.limit();
if (shape == null) shape = new int[]{size};
result = factory(dtype, shape);
for (int i = 0; i < size; i++)
result.setShort(i, sb.get(i));
return result;
case ENUM4:
case INT:
IntBuffer ib = bb.asIntBuffer();
size = ib.limit();
if (shape == null) shape = new int[]{size};
result = factory(dtype, shape);
for (int i = 0; i < size; i++)
result.setInt(i, ib.get(i));
return result;
case LONG:
LongBuffer lb = bb.asLongBuffer();
size = lb.limit();
if (shape == null) shape = new int[]{size};
result = factory(dtype, shape);
for (int i = 0; i < size; i++)
result.setLong(i, lb.get(i));
return result;
case FLOAT:
FloatBuffer ffb = bb.asFloatBuffer();
size = ffb.limit();
if (shape == null) shape = new int[]{size};
result = factory(dtype, shape);
for (int i = 0; i < size; i++)
result.setFloat(i, ffb.get(i));
return result;
case DOUBLE:
DoubleBuffer db = bb.asDoubleBuffer();
size = db.limit();
if (shape == null) shape = new int[]{size};
result = factory(dtype, shape);
for (int i = 0; i < size; i++)
result.setDouble(i, db.get(i));
return result;
}
throw new UnsupportedOperationException("" + dtype);
}
/**
* Copy this array to a 1D Java primitive array of type getElementType(), with the physical order
* of the result the same as logical order.
*
* @return a Java 1D array of type getElementType().
*/
public Object copyTo1DJavaArray() {
Array newA = copy();
return newA.getStorage();
}
/**
* Copy this array to a n-Dimensional Java primitive array of type getElementType()
* and rank getRank(). Makes a copy of the data.
*
* @return a Java ND array of type getElementType().
*/
public Object copyToNDJavaArray() {
Object javaArray;
try {
javaArray = java.lang.reflect.Array.newInstance(getElementType(), getShape());
} catch (Exception e) {
throw new IllegalArgumentException(e);
}
// copy data
IndexIterator iter = getIndexIterator();
reflectArrayCopyOut(javaArray, this, iter);
return javaArray;
}
/**
* Create a new Array using same backing store as this Array, by
* flipping the index so that it runs from shape[index]-1 to 0.
*
* @param dim dimension to flip
* @return the new Array
*/
public Array flip(int dim) {
return createView(indexCalc.flip(dim));
}
/**
* Create a new Array using same backing store as this Array, by
* transposing two of the indices.
*
* @param dim1 transpose these two indices
* @param dim2 transpose these two indices
* @return the new Array
*/
public Array transpose(int dim1, int dim2) {
return createView(indexCalc.transpose(dim1, dim2));
}
/**
* Create a new Array using same backing store as this Array, by
* permuting the indices.
*
* @param dims the old index dims[k] becomes the new kth index.
* @return the new Array
* @throws IllegalArgumentException: wrong rank or dim[k] not valid
*/
public Array permute(int[] dims) {
return createView(indexCalc.permute(dims));
}
/**
* Create a new Array by copying this Array to a new one with given shape
*
* @param shape the new shape
* @return the new Array
* @throws IllegalArgumentException new shape is not conformable
*/
public Array reshape(int[] shape) {
Array result = factory(this.getElementType(), shape);
if (result.getSize() != getSize())
throw new IllegalArgumentException("reshape arrays must have same total size");
result.setUnsigned(isUnsigned());
Array.arraycopy(this, 0, result, 0, (int) getSize());
return result;
}
/**
* Reshape this array without copying data
*
* @param shape the new shape
* @return the new Array, using same backing object
* @throws IllegalArgumentException new shape is not conformable
*/
public Array reshapeNoCopy(int[] shape) {
Array result = factory(this.getElementType(), shape, getStorage());
if (result.getSize() != getSize())
throw new IllegalArgumentException("reshape arrays must have same total size");
return result;
}
/**
* Create a new Array using same backing store as this Array, by
* eliminating any dimensions with length one.
*
* @return the new Array, or the same array if no reduction was done
*/
public Array reduce() {
Index ri = indexCalc.reduce();
if (ri == indexCalc) return this;
return createView(ri);
}
/**
* Create a new Array using same backing store as this Array, by
* eliminating the specified dimension.
*
* @param dim dimension to eliminate: must be of length one, else IllegalArgumentException
* @return the new Array
*/
public Array reduce(int dim) {
return createView(indexCalc.reduce(dim));
}
//////////////////////////////////////////////////////////////
/**
* Find whether the underlying data should be interpreted as unsigned.
* Only affects byte, short, and int.
* When true, conversions to wider types are handled correctly.
*
* @return true if the data is unsigned integer type.
*/
public boolean isUnsigned() {
return unsigned;
}
/**
* If this is a constant array
*
* @return If this is a constant array
*/
public boolean isConstant() {
return indexCalc instanceof IndexConstant;
}
/**
* Set whether the data should be interpreted as unsigned.
* Only valid for byte, short, int, and long.
* When true, conversions to wider types are handled correctly.
*
* @param unsigned true if unsigned
*/
public void setUnsigned(boolean unsigned) {
this.unsigned = unsigned;
}
/*
* Set the name of one of the indices.
* @param dim which index?
* @param indexName name of index
*
public void setIndexName( int dim, String indexName) {
indexCalc.setIndexName( dim, indexName);
}
/*
* Get the name of one of the indices.
* @param dim which index?
* @return name of index, or null if none.
*
public String getIndexName( int dim) {
return indexCalc.getIndexName( dim);
} */
///////////////////////////////////////////////////
/* these are the type-specific element accessors */
///////////////////////////////////////////////////
/**
* Get the array element at the current element of ima, as a double.
*
* @param ima Index with current element set
* @return value at index cast to double if necessary.
*/
public abstract double getDouble(Index ima);
/**
* Set the array element at the current element of ima.
*
* @param ima Index with current element set
* @param value the new value; cast to underlying data type if necessary.
*/
public abstract void setDouble(Index ima, double value);
/**
* Get the array element at the current element of ima, as a float.
*
* @param ima Index with current element set
* @return value at index cast to float if necessary.
*/
public abstract float getFloat(Index ima);
/**
* Set the array element at the current element of ima.
*
* @param ima Index with current element set
* @param value the new value; cast to underlying data type if necessary.
*/
public abstract void setFloat(Index ima, float value);
/**
* Get the array element at the current element of ima, as a long.
*
* @param ima Index with current element set
* @return value at index cast to long if necessary.
*/
public abstract long getLong(Index ima);
/**
* Set the array element at the current element of ima.
*
* @param ima Index with current element set
* @param value the new value; cast to underlying data type if necessary.
*/
public abstract void setLong(Index ima, long value);
/**
* Get the array element at the current element of ima, as a int.
*
* @param ima Index with current element set
* @return value at index cast to int if necessary.
*/
public abstract int getInt(Index ima);
/**
* Set the array element at the current element of ima.
*
* @param ima Index with current element set
* @param value the new value; cast to underlying data type if necessary.
*/
public abstract void setInt(Index ima, int value);
/**
* Get the array element at the current element of ima, as a short.
*
* @param ima Index with current element set
* @return value at index cast to short if necessary.
*/
public abstract short getShort(Index ima);
/**
* Set the array element at the current element of ima.
*
* @param ima Index with current element set
* @param value the new value; cast to underlying data type if necessary.
*/
public abstract void setShort(Index ima, short value);
/**
* Get the array element at the current element of ima, as a byte.
*
* @param ima Index with current element set
* @return value at index cast to float if necessary.
*/
public abstract byte getByte(Index ima);
/**
* Set the array element at the current element of ima.
*
* @param ima Index with current element set
* @param value the new value; cast to underlying data type if necessary.
*/
public abstract void setByte(Index ima, byte value);
/**
* Get the array element at the current element of ima, as a char.
*
* @param ima Index with current element set
* @return value at index cast to char if necessary.
*/
public abstract char getChar(Index ima);
/**
* Set the array element at the current element of ima.
*
* @param ima Index with current element set
* @param value the new value; cast to underlying data type if necessary.
*/
public abstract void setChar(Index ima, char value);
/**
* Get the array element at the current element of ima, as a boolean.
*
* @param ima Index with current element set
* @return value at index cast to boolean if necessary.
* @throws ForbiddenConversionException if underlying array not boolean
*/
public abstract boolean getBoolean(Index ima);
/**
* Set the array element at the current element of ima.
*
* @param ima Index with current element set
* @param value the new value; cast to underlying data type if necessary.
* @throws ForbiddenConversionException if underlying array not boolean
*/
public abstract void setBoolean(Index ima, boolean value);
/**
* Get the array element at index as an Object.
* The returned value is wrapped in an object, eg Double for double
*
* @param ima element Index
* @return Object value at index
* @throws ArrayIndexOutOfBoundsException if index incorrect rank or out of bounds
*/
public abstract Object getObject(Index ima);
/**
* Set the array element at index to the specified value.
* the value must be passed wrapped in the appropriate Object (eg Double for double)
*
* @param ima Index with current element set
* @param value the new value.
* @throws ArrayIndexOutOfBoundsException if index incorrect rank or out of bounds
* @throws ClassCastException if Object is incorrect type
*/
abstract public void setObject(Index ima, Object value);
//// these are for optimized access with no need to check index values
//// elem is the index into the backing data
abstract public double getDouble(int elem);
abstract public void setDouble(int elem, double val);
abstract public float getFloat(int elem);
abstract public void setFloat(int elem, float val);
abstract public long getLong(int elem);
abstract public void setLong(int elem, long value);
abstract public int getInt(int elem);
abstract public void setInt(int elem, int value);
abstract public short getShort(int elem);
abstract public void setShort(int elem, short value);
abstract public byte getByte(int elem);
abstract public void setByte(int elem, byte value);
abstract public char getChar(int elem);
abstract public void setChar(int elem, char value);
abstract public boolean getBoolean(int elem);
abstract public void setBoolean(int elem, boolean value);
abstract public Object getObject(int elem);
abstract public void setObject(int elem, Object value);
public String toString() {
StringBuilder sbuff = new StringBuilder();
IndexIterator ii = getIndexIterator();
while (ii.hasNext()) {
Object data = ii.getObjectNext();
sbuff.append(data);
sbuff.append(" ");
}
return sbuff.toString();
}
/**
* Create a string representation of the shape of this Array.
*
* @return string representation of the shape
*/
public String shapeToString() {
int[] shape = getShape();
if (shape.length == 0) return "";
StringBuilder sb = new StringBuilder();
sb.append('(');
for (int i = 0; i < shape.length; i++) {
int s = shape[i];
if (i > 0) sb.append(",");
sb.append(s);
}
sb.append(')');
return sb.toString();
}
/**
* Check if more elements in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
* You cannot call any of the array.nextXXX() methods without calling hasNext() first.
* If you are not sure of the state of the iterator, you must reset it before use. Example:
*
* arr.resetLocalIterator();
* while (arr.hasNext()) {
* double val = mdata.nextDouble();
* ..
* }
* <.pre>
*
* @return true if there are more elements in the iteration
*/
public boolean hasNext() {
if (null == ii) ii = getIndexIterator();
return ii.hasNext();
}
/**
* Return the next object in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as an Object, same as IndexIterator.getObjectNext().
*/
public Object next() {
return ii.getObjectNext();
}
/**
* Return the next double in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as a double, same as IndexIterator.getDoubleNext().
*/
public double nextDouble() {
return ii.getDoubleNext();
}
/**
* Return the next float in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as a float, same as IndexIterator.getFloatNext().
*/
public float nextFloat() {
return ii.getFloatNext();
}
/**
* Return the next byte in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as a byte, same as IndexIterator.getByteNext().
*/
public byte nextByte() {
return ii.getByteNext();
}
/**
* Return the next short in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as a short, same as IndexIterator.getShortNext().
*/
public short nextShort() {
return ii.getShortNext();
}
/**
* Return the next int in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as a int, same as IndexIterator.getIntNext().
*/
public int nextInt() {
return ii.getIntNext();
}
/**
* Return the next long in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as a long, same as IndexIterator.getLongNext().
*/
public long nextLong() {
return ii.getLongNext();
}
/**
* Return the next char in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as a char, same as IndexIterator.getCharNext().
*/
public char nextChar() {
return ii.getCharNext();
}
/**
* Return the next boolean in the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*
* @return next element as a boolean, same as IndexIterator.getBooleanNext().
*/
public boolean nextBoolean() {
return ii.getBooleanNext();
}
/**
* Reset the local iterator.
* Uses the local iterator, which is not thread-safe. Use getIndexIterator if you need thread-safety.
*/
public void resetLocalIterator() {
ii = null;
}
}
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