/*
* 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.
*
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* any fee or cost, to use, copy, modify, alter, enhance and distribute
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package ucar.unidata.geoloc.vertical;
import ucar.ma2.Array;
import ucar.ma2.ArrayDouble;
import ucar.ma2.Index;
import ucar.ma2.IndexIterator;
import ucar.ma2.InvalidRangeException;
import ucar.ma2.ArrayDouble.D1;
import ucar.nc2.Dimension;
import ucar.nc2.Variable;
import ucar.nc2.NetcdfFile;
import ucar.unidata.util.Parameter;
import java.io.IOException;
import java.util.List;
/**
* Models the vertical coordinate for the Weather Research and Forecast
* (WRF) model's vertical Eta coordinate
*
* @author IDV Development Team
*/
public class WRFEta extends VerticalTransformImpl {
public static final String BasePressureVariable = "base_presure";
public static final String PerturbationPressureVariable = "perturbation_presure";
public static final String BaseGeopotentialVariable = "base_geopotential";
public static final String PerturbationGeopotentialVariable = "perturbation_geopotential";
public static final String IsStaggeredX = "staggered_x";
public static final String IsStaggeredY = "staggered_y";
public static final String IsStaggeredZ = "staggered_z";
/**
* perturbation variable
*/
private Variable pertVar;
/**
* base variable
*/
private Variable baseVar;
/**
* some boolean flags
*/
private boolean isXStag, isYStag, isZStag;
/**
* Construct a vertical coordinate for the Weather Research and Forecast
* (WRF) model's vertical Eta coordinate
*
* @param ds netCDF dataset
* @param timeDim time dimension
* @param params list of transformation Parameters
*/
public WRFEta(NetcdfFile ds, Dimension timeDim, List<Parameter> params) {
super(timeDim);
isXStag = getParameterBooleanValue(params, IsStaggeredX);
isYStag = getParameterBooleanValue(params, IsStaggeredY);
isZStag = getParameterBooleanValue(params, IsStaggeredZ);
String pertVarName;
String baseVarName;
if (isZStag) {
//Geopotential is provided on the staggered z grid
//so we'll transform like grids to height levels
pertVarName = getParameterStringValue(params, PerturbationGeopotentialVariable);
baseVarName = getParameterStringValue(params, BaseGeopotentialVariable);
units = "m"; //PH and PHB are in m^2/s^2, so dividing by g=9.81 m/s^2 results in meters
} else {
//Pressure is provided on the non-staggered z grid
//so we'll transform like grids to pressure levels
pertVarName = getParameterStringValue(params, PerturbationPressureVariable);
baseVarName = getParameterStringValue(params, BasePressureVariable);
units = "Pa"; //P and PB are in Pascals //ADD:safe assumption? grab unit attribute?
}
pertVar = ds.findVariable(pertVarName);
baseVar = ds.findVariable(baseVarName);
if (pertVar == null) {
throw new RuntimeException(
"Cant find perturbation pressure variable= " + pertVarName
+ " in WRF file");
}
if (baseVar == null) {
throw new RuntimeException(
"Cant find base state pressure variable= " + baseVarName
+ " in WRF file");
}
}
/**
* Get the 3D vertical coordinate array for this time step.
*
* @param timeIndex the time index. Ignored if !isTimeDependent().
* @return vertical coordinate array
* @throws IOException problem reading data
*/
public ArrayDouble.D3 getCoordinateArray(int timeIndex)
throws IOException {
ArrayDouble.D3 array;
Array pertArray = getTimeSlice(pertVar, timeIndex);
Array baseArray = getTimeSlice(baseVar, timeIndex);
//ADD: use MAMath?
//ADD: use IndexIterator from getIndexIteratorFast?
int[] shape = pertArray.getShape();
//ADD: assert that rank = 3
//ADD: assert that both arrays are same shape
int ni = shape[0];
int nj = shape[1];
int nk = shape[2];
array = new ArrayDouble.D3(ni, nj, nk);
Index index = array.getIndex();
for (int i = 0; i < ni; i++) {
for (int j = 0; j < nj; j++) {
for (int k = 0; k < nk; k++) {
index.set(i, j, k);
double d = pertArray.getDouble(index) + baseArray.getDouble(index);
if (isZStag) {
d = d / 9.81; //convert geopotential to height
}
array.setDouble(index, d);
}
}
}
if (isXStag) {
array = addStagger(array, 2); //assuming x dim index is 2
}
if (isYStag) {
array = addStagger(array, 1); //assuming y dim index is 1
}
return array;
}
/**
* Get the 1D vertical coordinate array for this time step and point
*
* @param timeIndex the time index. Ignored if !isTimeDependent().
* @param xIndex the x index
* @param yIndex the y index
* @return vertical coordinate array
* @throws java.io.IOException problem reading data
* @throws ucar.ma2.InvalidRangeException _more_
*/
public D1 getCoordinateArray1D(int timeIndex, int xIndex, int yIndex)
throws IOException, InvalidRangeException {
ArrayDouble.D3 data = getCoordinateArray(timeIndex);
int[] origin = new int[3];
int[] shape = new int[3];
origin[0]=0;
origin[1]=yIndex;
origin[2]=xIndex;
shape[0] = data.getShape()[0];
shape[1] =1;
shape[2] =1;
Array tmp = data.section(origin, shape);
return (ArrayDouble.D1)tmp.reduce();
}
/**
* Add 1 to the size of the array for the given dimension.
* Use linear average and interpolation to fill in the values.
*
* @param array use this array
* @param dimIndex use this dimension
* @return new array with stagger
*/
private ArrayDouble.D3 addStagger(ArrayDouble.D3 array, int dimIndex) {
//ADD: assert 0<=dimIndex<=2
int[] shape = array.getShape();
int[] newShape = new int[3];
System.arraycopy(shape, 0, newShape, 0, 3);
newShape[dimIndex]++;
int ni = newShape[0];
int nj = newShape[1];
int nk = newShape[2];
ArrayDouble.D3 newArray = new ArrayDouble.D3(ni, nj, nk);
//Index newIndex = newArray.getIndex();
//extract 1d array to be extended
int n = shape[dimIndex]; //length of extracted array
double[] d = new double[n]; //tmp array to hold extracted values
int[] eshape = new int[3]; //shape of extracted array
int[] neweshape = new int[3]; //shape of new array slice to write into
for (int i = 0; i < 3; i++) {
eshape[i] = (i == dimIndex)
? n
: 1;
neweshape[i] = (i == dimIndex)
? n + 1
: 1;
}
int[] origin = new int[3];
try {
//loop through the other 2 dimensions and "extrapinterpolate" the other
for (int i = 0; i < ((dimIndex == 0)
? 1
: ni); i++) {
for (int j = 0; j < ((dimIndex == 1)
? 1
: nj); j++) {
for (int k = 0; k < ((dimIndex == 2)
? 1
: nk); k++) {
origin[0] = i;
origin[1] = j;
origin[2] = k;
IndexIterator it = array.section(origin,
eshape).getIndexIterator();
for (int l = 0; l < n; l++) {
d[l] = it.getDoubleNext(); //get the original values
}
double[] d2 = extrapinterpolate(d); //compute new values
//define slice of new array to write into
IndexIterator newit =
newArray.section(origin,
neweshape).getIndexIterator();
for (int l = 0; l < n + 1; l++) {
newit.setDoubleNext(d2[l]);
}
}
}
}
} catch (InvalidRangeException e) {
//ADD: report error?
return null;
}
return newArray;
}
/**
* Add one element to the array by linear interpolation
* and extrapolation at the ends.
*
* @param array input array
* @return extrapolated/interpolated array
*/
private double[] extrapinterpolate(double[] array) {
int n = array.length;
double[] d = new double[n + 1];
//end points from linear extrapolation
//equations confirmed by Christopher Lindholm
d[0] = 1.5 * array[0] - 0.5 * array[1];
d[n] = 1.5 * array[n - 1] - 0.5 * array[n - 2];
//inner points from simple average
for (int i = 1; i < n; i++) {
d[i] = 0.5 * (array[i - 1] + array[i]);
}
return d;
}
/**
* Extract an Array (with rank reduced by one) from the Variable
* for the given time index.
*
* @param v variable to extract from
* @param timeIndex time index
* @return Array of data
* @throws IOException problem getting Array
*/
private Array getTimeSlice(Variable v, int timeIndex) throws IOException {
//ADD: this would make a good utility method
//ADD: use Array.slice?
int[] shape = v.getShape();
int[] origin = new int[v.getRank()];
if (getTimeDimension() != null) {
int dimIndex = v.findDimensionIndex(getTimeDimension().getShortName());
if (dimIndex >= 0) {
shape[dimIndex] = 1;
origin[dimIndex] = timeIndex;
}
}
try {
return v.read(origin, shape).reduce();
} catch (InvalidRangeException e) {
throw new IOException(e);
}
}
}