/*
* 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
* this software, and any derivative works thereof, and its supporting
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package ucar.unidata.geoloc.vertical;
import ucar.ma2.*;
import ucar.ma2.ArrayDouble.D1;
import ucar.nc2.*;
import ucar.nc2.constants.CDM;
import ucar.unidata.util.Parameter;
import java.io.IOException;
import java.util.List;
/**
* Create a 3D height(z,y,x) array using the CF formula for
* "ocean sigma vertical coordinate".
*
* @author caron
* @see <a href="http://cf-pcmdi.llnl.gov/">http://cf-pcmdi.llnl.gov/</a>
*/
public class OceanSigma extends VerticalTransformImpl {
/**
* The eta variable name identifier
*/
public static final String ETA = "Eta_variableName";
/**
* The "s" variable name identifier
*/
public static final String SIGMA = "Sigma_variableName";
/**
* The "depth" variable name identifier
*/
public static final String DEPTH = "Depth_variableName";
/**
* The eta, s and depth variables
*/
private Variable etaVar, sVar, depthVar;
/**
* Create a new vertical transform for Ocean S coordinates
*
* @param ds dataset
* @param timeDim time dimension
* @param params list of transformation Parameters
*/
public OceanSigma(NetcdfFile ds, Dimension timeDim, List<Parameter> params) {
super(timeDim);
String etaName = getParameterStringValue(params, ETA);
String sName = getParameterStringValue(params, SIGMA);
String depthName = getParameterStringValue(params, DEPTH);
etaVar = ds.findVariable(etaName);
sVar = ds.findVariable(sName);
depthVar = ds.findVariable(depthName);
units = ds.findAttValueIgnoreCase(depthVar, CDM.UNITS, "none");
}
/**
* 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
* @throws InvalidRangeException _more_
*/
public ArrayDouble.D3 getCoordinateArray(int timeIndex)
throws IOException, InvalidRangeException {
Array eta = readArray(etaVar, timeIndex);
Array sigma = readArray(sVar, timeIndex);
Array depth = readArray(depthVar, timeIndex);
int nz = (int) sigma.getSize();
Index sIndex = sigma.getIndex();
int[] shape2D = eta.getShape();
int ny = shape2D[0];
int nx = shape2D[1];
Index etaIndex = eta.getIndex();
Index depthIndex = depth.getIndex();
ArrayDouble.D3 height = new ArrayDouble.D3(nz, ny, nx);
for (int z = 0; z < nz; z++) {
double sigmaVal = sigma.getDouble(sIndex.set(z));
for (int y = 0; y < ny; y++) {
for (int x = 0; x < nx; x++) {
double etaVal = eta.getDouble(etaIndex.set(y, x));
double depthVal = depth.getDouble(depthIndex.set(y, x));
height.set(z, y, x,
etaVal + sigmaVal * (depthVal + etaVal));
}
}
}
return height;
}
/**
* 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 {
Array eta = readArray(etaVar, timeIndex);
Array sigma = readArray(sVar, timeIndex);
Array depth = readArray(depthVar, timeIndex);
int nz = (int) sigma.getSize();
Index sIndex = sigma.getIndex();
Index etaIndex = eta.getIndex();
Index depthIndex = depth.getIndex();
ArrayDouble.D1 height = new ArrayDouble.D1(nz);
for (int z = 0; z < nz; z++) {
double sigmaVal = sigma.getDouble(sIndex.set(z));
double etaVal = eta.getDouble(etaIndex.set(yIndex, xIndex));
double depthVal = depth.getDouble(depthIndex.set(yIndex, xIndex));
height.set(z, etaVal + sigmaVal * (depthVal + etaVal));
}
return height;
}
}