/*
* 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 java.io.IOException;
import java.util.List;
import ucar.ma2.Array;
import ucar.ma2.ArrayDouble;
import ucar.ma2.ArrayDouble.D1;
import ucar.ma2.Index;
import ucar.ma2.InvalidRangeException;
import ucar.nc2.Dimension;
import ucar.nc2.NetcdfFile;
import ucar.nc2.Variable;
import ucar.nc2.constants.CDM;
import ucar.nc2.units.SimpleUnit;
import ucar.unidata.util.Parameter;
/**
* Create a 3D height(z,y,x) array using the CF formula for
* "atmospheric sigma vertical coordinate".
* <p><strong>pressure(x,y,z) = ptop + sigma(z)*surfacePressure(x,y)</strong>
*
* @author caron
* @see <a href="http://cf-pcmdi.llnl.gov/">http://cf-pcmdi.llnl.gov/</a>
*/
public class AtmosSigma extends VerticalTransformImpl {
/**
* P-naught identifier
*/
public static final String PTOP = "PressureTop_variableName";
/**
* Surface pressure name identifier
*/
public static final String PS = "SurfacePressure_variableName";
/**
* The "depth" variable name identifier
*/
public static final String SIGMA = "Sigma_variableName";
/**
* The ps, sigma variables
*/
private Variable psVar;
/**
* The sigma array, function of z
*/
private double[] sigma;
/**
* Top of the model
*/
private double ptop;
/**
* Create a new vertical transform for Ocean S coordinates
*
* @param ds dataset
* @param timeDim time dimension
* @param params list of transformation Parameters
*/
public AtmosSigma(NetcdfFile ds, Dimension timeDim, List<Parameter> params) {
super(timeDim);
String psName = getParameterStringValue(params, PS);
psVar = ds.findVariable(psName);
String ptopName = getParameterStringValue(params, PTOP);
Variable ptopVar = ds.findVariable(ptopName);
try {
this.ptop = ptopVar.readScalarDouble();
} catch (IOException e) {
throw new IllegalArgumentException("AtmosSigma failed to read "
+ ptopVar + " err= " + e.getMessage());
}
String sigmaName = getParameterStringValue(params, SIGMA);
Variable sigmaVar = ds.findVariable(sigmaName);
try {
Array data = sigmaVar.read();
sigma = (double[]) data.get1DJavaArray(double.class);
} catch (IOException e) {
throw new IllegalArgumentException("AtmosSigma failed to read "
+ sigmaName + " err= " + e.getMessage());
}
units = ds.findAttValueIgnoreCase(psVar, CDM.UNITS, "none");
String ptopUnitStr = ds.findAttValueIgnoreCase(ptopVar, CDM.UNITS, "none");
if (!units.equalsIgnoreCase(ptopUnitStr)) {
// Convert ptopVar to units of psVar
SimpleUnit psUnit = SimpleUnit.factory(units);
SimpleUnit ptopUnit = SimpleUnit.factory(ptopUnitStr);
double factor = ptopUnit.convertTo(1.0, psUnit);
this.ptop = this.ptop * factor;
}
}
/**
* 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 ps = readArray(psVar, timeIndex);
Index psIndex = ps.getIndex();
int nz = sigma.length;
int[] shape2D = ps.getShape();
int ny = shape2D[0];
int nx = shape2D[1];
ArrayDouble.D3 result = new ArrayDouble.D3(nz, ny, nx);
for (int y = 0; y < ny; y++) {
for (int x = 0; x < nx; x++) {
double psVal = ps.getDouble(psIndex.set(y, x));
for (int z = 0; z < nz; z++) {
result.set(z, y, x, ptop + sigma[z] * (psVal - ptop));
}
}
}
return result;
}
/**
* Get the 1D vertical coordinate array for this time step and point
*
* (needds test!!!)
*
* @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 ps = readArray(psVar, timeIndex);
Index psIndex = ps.getIndex();
int nz = sigma.length;
ArrayDouble.D1 result = new ArrayDouble.D1(nz);
double psVal = ps.getDouble(psIndex.set(yIndex, xIndex));
for (int z = 0; z < nz; z++) {
result.set(z, ptop + sigma[z] * (psVal - ptop));
}
return result;
}
}