ucar.ma2.MAMath Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of cdm Show documentation
Show all versions of cdm Show documentation
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 ucar.nc2.ft.grid.IsMissingEvaluator;
import ucar.nc2.util.Misc;
/**
* Element by element algebra on Arrays
*
* @author caron
* @see Index
*/
public class MAMath {
/**
* Add elements of two arrays together, allocating the result array.
* The result type and the operation type are taken from the type of a.
*
* @param a add values from here
* @param b add values from here
* @return result = a + b
* @throws IllegalArgumentException a and b are not conformable
* @throws UnsupportedOperationException dont support this data type yet
*/
public static Array add(Array a, Array b) throws IllegalArgumentException {
Array result = Array.factory(a.getElementType(), a.getShape());
if (a.getElementType() == double.class) {
addDouble(result, a, b);
} else
throw new UnsupportedOperationException();
return result;
}
/**
* Add elements of two arrays together as doubles, place sum in the result array.
* The values from the arrays a and b are converted to double (if needed),
* and the sum is converted to the type of result (if needed).
*
* @param result result array
* @param a operand
* @param b operand
* @throws IllegalArgumentException a,b,and result are not conformable
*/
public static void addDouble(Array result, Array a, Array b)
throws IllegalArgumentException {
if (!conformable(result, a) || !conformable(a, b))
throw new IllegalArgumentException();
IndexIterator iterR = result.getIndexIterator();
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterB = b.getIndexIterator();
while (iterA.hasNext())
iterR.setDoubleNext(iterA.getDoubleNext() + iterB.getDoubleNext());
}
/**
* Check that two arrays are conformable.
*
* @param a operand
* @param b operand
* @return true if conformable
*/
public static boolean conformable(Array a, Array b) {
return conformable(a.getShape(), b.getShape());
}
/**
* Check that two array shapes are conformable.
* The shapes must match exactly, except that dimensions of length 1 are ignored.
*
* @param shapeA shape of array 1
* @param shapeB shape of array 2
* @return true if conformable
*/
public static boolean conformable(int[] shapeA, int[] shapeB) {
if (reducedRank(shapeA) != reducedRank(shapeB))
return false;
int rankB = shapeB.length;
int dimB = 0;
for (int aShapeA : shapeA) {
//System.out.println(dimA + " "+ dimB);
//skip length 1 dimensions
if (aShapeA == 1)
continue;
while (dimB < rankB)
if (shapeB[dimB] == 1) dimB++;
else break;
// test same shape (NB dimB cant be > rankB due to first test)
if (aShapeA != shapeB[dimB])
return false;
dimB++;
}
return true;
}
/**
* Convert unsigned data to signed data of a wider type.
*
* @param unsigned must be of type byte, short or int
* @return converted data of type short, int, or long
*/
public static Array convertUnsigned( Array unsigned) {
if (unsigned.getElementType().equals(byte.class)) {
Array result = Array.factory(DataType.SHORT, unsigned.getShape());
IndexIterator ii = result.getIndexIterator();
unsigned.resetLocalIterator();
while (unsigned.hasNext())
ii.setShortNext( DataType.unsignedByteToShort(unsigned.nextByte()));
return result;
} else if (unsigned.getElementType().equals(short.class)) {
Array result = Array.factory(DataType.INT, unsigned.getShape());
IndexIterator ii = result.getIndexIterator();
unsigned.resetLocalIterator();
while (unsigned.hasNext())
ii.setIntNext( DataType.unsignedShortToInt(unsigned.nextShort()));
return result;
} else if (unsigned.getElementType().equals(int.class)) {
Array result = Array.factory(DataType.LONG, unsigned.getShape());
IndexIterator ii = result.getIndexIterator();
unsigned.resetLocalIterator();
while (unsigned.hasNext())
ii.setLongNext( DataType.unsignedIntToLong(unsigned.nextInt()));
return result;
}
throw new IllegalArgumentException("Cant convertUnsigned type= "+unsigned.getElementType());
}
/**
* Convert original array to desired type
*
* @param org original array
* @param wantType desired type
* @return converted data of desired type, or original array if it is already
*/
public static Array convert( Array org, DataType wantType) {
if (org == null) return null;
Class wantClass = wantType.getPrimitiveClassType();
if (org.getElementType().equals(wantClass))
return org;
Array result = Array.factory(wantType, org.getShape());
copy(wantType, org.getIndexIterator(), result.getIndexIterator());
return result;
}
/**
* Copy using iterators. Will copy until !from.hasNext().
*
* @param dataType use this operation type (eg DataType.DOUBLE uses getDoubleNext())
* @param from copy from here
* @param to copy to here
* @throws IllegalArgumentException a and b are not conformable
* @throws UnsupportedOperationException dont support this data type
*/
public static void copy(DataType dataType, IndexIterator from, IndexIterator to) throws IllegalArgumentException {
if (dataType == DataType.DOUBLE) {
while (from.hasNext())
to.setDoubleNext(from.getDoubleNext());
} else if (dataType == DataType.FLOAT) {
while (from.hasNext())
to.setFloatNext(from.getFloatNext());
} else if (dataType == DataType.LONG) {
while (from.hasNext())
to.setLongNext(from.getLongNext());
} else if ((dataType == DataType.INT) || (dataType == DataType.ENUM4)) {
while (from.hasNext())
to.setIntNext(from.getIntNext());
} else if ((dataType == DataType.SHORT) || (dataType == DataType.ENUM2)) {
while (from.hasNext())
to.setShortNext(from.getShortNext());
} else if (dataType == DataType.CHAR) {
while (from.hasNext())
to.setCharNext(from.getCharNext());
} else if ((dataType == DataType.BYTE) || (dataType == DataType.ENUM1)) {
while (from.hasNext())
to.setByteNext(from.getByteNext());
} else if (dataType == DataType.BOOLEAN) {
while (from.hasNext())
to.setBooleanNext(from.getBooleanNext());
} else {
while (from.hasNext())
to.setObjectNext(from.getObjectNext());
}
}
/**
* Copy array a to array result, the result array will be in canonical order
* The operation type is taken from the type of a.
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and b are not conformable
* @throws UnsupportedOperationException dont support this data type yet
*/
public static void copy(Array result, Array a) throws IllegalArgumentException {
Class classType = a.getElementType();
if (classType == double.class) {
copyDouble(result, a);
} else if (classType == float.class) {
copyFloat(result, a);
} else if (classType == long.class) {
copyLong(result, a);
} else if (classType == int.class) {
copyInt(result, a);
} else if (classType == short.class) {
copyShort(result, a);
} else if (classType == char.class) {
copyChar(result, a);
} else if (classType == byte.class) {
copyByte(result, a);
} else if (classType == boolean.class) {
copyBoolean(result, a);
} else
copyObject(result, a);
}
/**
* copy array a to array result as doubles
* The values from the arrays a are converted to double (if needed),
* and then converted to the type of result (if needed).
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyDouble(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setDoubleNext(iterA.getDoubleNext());
}
/**
* copy array a to array result as floats
* The values from the arrays a are converted to float (if needed),
* and then converted to the type of result (if needed).
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyFloat(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setFloatNext(iterA.getFloatNext());
}
/**
* copy array a to array result as longs
* The values from the array a are converted to long (if needed),
* and then converted to the type of result (if needed).
* @param result copy to here
* @param a copy from here
*
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyLong(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setLongNext(iterA.getLongNext());
}
/**
* copy array a to array result as integers
* The values from the arrays a are converted to integer (if needed),
* and then converted to the type of result (if needed).
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyInt(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setIntNext(iterA.getIntNext());
}
/**
* copy array a to array result as shorts
* The values from the array a are converted to short (if needed),
* and then converted to the type of result (if needed).
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyShort(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setShortNext(iterA.getShortNext());
}
/**
* copy array a to array result as char
* The values from the array a are converted to char (if needed),
* and then converted to the type of result (if needed).
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyChar(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setCharNext(iterA.getCharNext());
}
/**
* copy array a to array result as bytes
* The values from the array a are converted to byte (if needed),
* and then converted to the type of result (if needed).
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyByte(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setByteNext(iterA.getByteNext());
}
/**
* copy array a to array result as bytes
* The array a and result must be type boolean
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyBoolean(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setBooleanNext(iterA.getBooleanNext());
}
/**
* copy array a to array result as an Object
* The array a and result must be type object
*
* @param result copy to here
* @param a copy from here
*
* @throws IllegalArgumentException a and result are not conformable
*/
public static void copyObject(Array result, Array a) throws IllegalArgumentException {
if (!conformable(a, result))
throw new IllegalArgumentException("copy arrays are not conformable");
IndexIterator iterA = a.getIndexIterator();
IndexIterator iterR = result.getIndexIterator();
while (iterA.hasNext())
iterR.setObjectNext(iterA.getObjectNext());
}
/**
* Calculate the reduced rank of this shape, by subtracting dimensions with length 1
* @param shape shape of the array
* @return rank without dimensions of length 1
*/
public static int reducedRank(int[] shape) {
int rank = 0;
for (int aShape : shape) {
if (aShape > 1)
rank++;
}
return rank;
}
public static double getMinimum(Array a) {
IndexIterator iter = a.getIndexIterator();
double min = Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if (Double.isNaN(val)) continue;
if (val < min)
min = val;
}
return min;
}
public static double getMaximum(Array a) {
IndexIterator iter = a.getIndexIterator();
double max = -Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if (Double.isNaN(val)) continue;
if (val > max)
max = val;
}
return max;
}
/**
* Find min and max value in this array, getting values as doubles. Skip Double.NaN.
*
* @param a the array.
* @return MinMax
*/
public static MAMath.MinMax getMinMax(Array a) {
IndexIterator iter = a.getIndexIterator();
double max = -Double.MAX_VALUE;
double min = Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if (Double.isNaN(val)) continue;
if (val > max)
max = val;
if (val < min)
min = val;
}
return new MinMax(min, max);
}
public static MAMath.MinMax getMinMaxSkipMissingData(Array a, IsMissingEvaluator eval) {
if (!eval.hasMissing())
return MAMath.getMinMax(a);
IndexIterator iter = a.getIndexIterator();
double max = -Double.MAX_VALUE;
double min = Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if (eval.isMissing(val))
continue;
if (val > max)
max = val;
if (val < min)
min = val;
}
return new MAMath.MinMax(min, max);
}
public static double getMinimumSkipMissingData(Array a, double missingValue) {
IndexIterator iter = a.getIndexIterator();
double min = Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if ((val != missingValue) && (val < min))
min = val;
}
return min;
}
public static double getMaximumSkipMissingData(Array a, double missingValue) {
IndexIterator iter = a.getIndexIterator();
double max = -Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if ((val != missingValue) && (val > max))
max = val;
}
return max;
}
public static MAMath.MinMax getMinMaxSkipMissingData(Array a, double missingValue) {
IndexIterator iter = a.getIndexIterator();
double max = -Double.MAX_VALUE;
double min = Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if (val == missingValue)
continue;
if (val > max)
max = val;
if (val < min)
min = val;
}
return new MinMax(min, max);
}
/**
* Set all the elements of this array to the given double value.
* The value is converted to the element type of the array, if needed.
*
* @param result change this Array
* @param val set all elements to this value
*/
public static void setDouble(Array result, double val) {
IndexIterator iter = result.getIndexIterator();
while (iter.hasNext()) {
iter.setDoubleNext(val);
}
}
/**
* sum all of the elements of array a as doubles.
* The values from the array a are converted to double (if needed).
* @param a read values from this Array
* @return sum of elements
*/
public static double sumDouble(Array a) {
double sum = 0;
IndexIterator iterA = a.getIndexIterator();
while (iterA.hasNext()) {
sum += iterA.getDoubleNext();
}
return sum;
}
/**
* sum all of the elements of array a as doubles.
* The values from the array a are converted to double (if needed).
* @param a read values from this Array
* @param missingValue skip values equal to this, or which are NaNs
* @return sum of elements
*/
public static double sumDoubleSkipMissingData(Array a, double missingValue) {
double sum = 0;
IndexIterator iterA = a.getIndexIterator();
while (iterA.hasNext()) {
double val = iterA.getDoubleNext();
if ((val == missingValue) || Double.isNaN(val))
continue;
sum += val;
}
return sum;
}
/**
* Holds a minimum and maximum value.
*/
public static class MinMax {
public double min, max;
public MinMax(double min, double max) {
this.min = min;
this.max = max;
}
@Override
public String toString() {
return "MinMax{" +
"min=" + min +
", max=" + max +
'}';
}
}
/**
* Calculate the scale/offset for an array of numbers.
*
* If signed:
* then
* max value unpacked = 2^(n-1) - 1 packed
* min value unpacked = -(2^(n-1) - 1) packed
* note that -2^(n-1) is unused, and a good place to map missing values
* by solving 2 eq in 2 unknowns, we get:
* scale = (max - min) / (2^n - 2)
* offset = (max + min) / 2
* If unsigned then
* max value unpacked = 2^n - 1 packed
* min value unpacked = 0 packed
* and:
* scale = (max - min) / (2^n - 1)
* offset = min
* One could modify this to allow a holder for missing values.
*
* @param a array to convert (not changed)
* @param missingValue skip these
* @param nbits map into this many bits
* @param isUnsigned use signed or unsigned packed values
* @return ScaleOffset, calculated as above.
*/
public static MAMath.ScaleOffset calcScaleOffsetSkipMissingData(Array a, double missingValue, int nbits, boolean isUnsigned) {
MAMath.MinMax minmax = getMinMaxSkipMissingData(a, missingValue);
if (isUnsigned) {
long size = (1L << nbits) - 1;
double offset = minmax.min;
double scale =(minmax.max - minmax.min) / size;
return new ScaleOffset(scale, offset);
} else {
long size = (1L << nbits) - 2;
double offset = (minmax.max + minmax.min) / 2;
double scale =(minmax.max - minmax.min) / size;
return new ScaleOffset(scale, offset);
}
}
public static Array convert2packed(Array unpacked, double missingValue, int nbits, boolean isUnsigned, DataType packedType) {
MAMath.ScaleOffset scaleOffset = calcScaleOffsetSkipMissingData(unpacked, missingValue, nbits, isUnsigned);
Array result = Array.factory(packedType, unpacked.getShape());
IndexIterator riter = result.getIndexIterator();
while (unpacked.hasNext()) {
double uv = unpacked.nextDouble();
double pv = (uv - scaleOffset.offset) / scaleOffset.scale;
riter.setDoubleNext( pv);
}
return result;
}
public static Array convert2Unpacked(Array packed, ScaleOffset scaleOffset) {
//boolean isUnsigned = packed.isUnsigned();
Array result = Array.factory(DataType.DOUBLE, packed.getShape());
IndexIterator riter = result.getIndexIterator();
while (packed.hasNext()) {
riter.setDoubleNext( packed.nextDouble() * scaleOffset.scale + scaleOffset.offset);
}
return result;
}
/**
* Holds a scale and offset.
*/
public static class ScaleOffset {
public double scale, offset;
public ScaleOffset(double scale, double offset) {
this.scale = scale;
this.offset = offset;
}
}
public static boolean isEqual(Array data1, Array data2) {
if (data1.getSize() != data2.getSize()) return false;
DataType dt = DataType.getType(data1.getElementType());
IndexIterator iter1 = data1.getIndexIterator();
IndexIterator iter2 = data2.getIndexIterator();
if (dt == DataType.DOUBLE) {
while (iter1.hasNext() && iter2.hasNext()) {
double v1 = iter1.getDoubleNext();
double v2 = iter2.getDoubleNext();
if (!Double.isNaN(v1) || !Double.isNaN(v2))
if (!Misc.closeEnough(v1, v2, 1.0e-8))
return false;
}
} else if (dt == DataType.FLOAT) {
while (iter1.hasNext() && iter2.hasNext()) {
float v1 = iter1.getFloatNext();
float v2 = iter2.getFloatNext();
if (!Float.isNaN(v1) || !Float.isNaN(v2))
if (!Misc.closeEnough(v1, v2, 1.0e-5))
return false;
}
} else if (dt == DataType.INT) {
while (iter1.hasNext() && iter2.hasNext()) {
int v1 = iter1.getIntNext();
int v2 = iter2.getIntNext();
if (v1 != v2) return false;
}
} else if (dt == DataType.SHORT) {
while (iter1.hasNext() && iter2.hasNext()) {
short v1 = iter1.getShortNext();
short v2 = iter2.getShortNext();
if (v1 != v2) return false;
}
} else if (dt == DataType.BYTE) {
while (iter1.hasNext() && iter2.hasNext()) {
byte v1 = iter1.getByteNext();
byte v2 = iter2.getByteNext();
if (v1 != v2) return false;
}
} else if (dt == DataType.LONG) {
while (iter1.hasNext() && iter2.hasNext()) {
long v1 = iter1.getLongNext();
long v2 = iter2.getLongNext();
if (v1 != v2) return false;
}
}
return true;
}
}
© 2015 - 2024 Weber Informatics LLC | Privacy Policy