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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.
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/*
* 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.unidata.geoloc.vertical;
import ucar.ma2.*;
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 s vertical coordinate g2".
* standard name: ocean_s_coordinate_g2
*
* @author Sachin ([email protected])
* @see http://cf-pcmdi.llnl.gov/
* @see https://www.myroms.org/wiki/index.php/Vertical_S-coordinate#Metadata_Considerations
*/
public class OceanSG2 extends VerticalTransformImpl {
/**
* The eta variable name identifier
*/
public static final String ETA = "Eta_variableName";
/**
* The "s" variable name identifier
*/
public static final String S = "S_variableName";
/**
* The "depth" variable name identifier
*/
public static final String DEPTH = "Depth_variableName";
/**
* The "depth c" variable name identifier
*/
public static final String DEPTH_C = "Depth_c_variableName";
/**
* The "C" variable name identifier
*/
public static final String C = "c_variableName";
/**
* the values of depth_c
*/
private double depth_c;
/**
* The eta, s, C and depth variables
*/
private Variable etaVar, sVar, depthVar, cVar, depthCVar;
/**
* Create a new vertical transform for Ocean_S_coordinate_g2
*
* @param ds dataset
* @param timeDim time dimension
* @param params list of transformation Parameters
*/
public OceanSG2(NetcdfFile ds, Dimension timeDim, List params) {
super(timeDim);
String etaName = getParameterStringValue(params, ETA);
String sName = getParameterStringValue(params, S);
String depthName = getParameterStringValue(params, DEPTH);
String depthCName = getParameterStringValue(params, DEPTH_C);
String cName = getParameterStringValue(params, C);
etaVar = ds.findVariable(etaName);
sVar = ds.findVariable(sName);
depthVar = ds.findVariable(depthName);
depthCVar = ds.findVariable(depthCName);
cVar = ds.findVariable(cName);
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 java.io.IOException problem reading data
* @throws ucar.ma2.InvalidRangeException _more_
*/
public ArrayDouble.D3 getCoordinateArray(int timeIndex)
throws IOException, InvalidRangeException {
Array etaArray = readArray(etaVar, timeIndex);
Array sArray = readArray(sVar, timeIndex);
Array depthArray = readArray(depthVar, timeIndex);
Array cArray = readArray(cVar, timeIndex);
depth_c = depthCVar.readScalarDouble();
return makeHeight(etaArray, sArray, depthArray, cArray, depth_c);
}
/** Add new method for retrieving 1D Z values for specified indices for lat/lon. */
/**
* Get the 1D vertical coordinate array for this time step and
* the specified X,Y index for Lat-Lon 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 ArrayDouble.D1 getCoordinateArray1D(int timeIndex, int xIndex, int yIndex)
throws IOException, InvalidRangeException {
Array etaArray = readArray(etaVar, timeIndex);
Array sArray = readArray(sVar, timeIndex);
Array depthArray = readArray(depthVar, timeIndex);
Array cArray = readArray(cVar, timeIndex);
depth_c = depthCVar.readScalarDouble();
return makeHeight1D(etaArray, sArray, depthArray, cArray, depth_c, xIndex, yIndex);
}
/**
* Make height from the given data.
*
*
* height(x,y,z) = eta(x,y) + ( eta(x,y) + depth([n],x,y) ) * S(x,y,z)
*
* where,
* S(x,y,z) = (depth_c*s(z) + (depth([n],x,y) * C(z)) / (depth_c + depth([n],x,y))
* /
*
* @param eta eta Array
* @param s s Array
* @param depth depth Array
* @param c c Array
* @param depth_c value of depth_c
* @return height data
*/
private ArrayDouble.D3 makeHeight(Array eta, Array s, Array depth,
Array c, double depth_c) {
int nz = (int) s.getSize();
Index sIndex = s.getIndex();
Index cIndex = c.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 sz = s.getDouble(sIndex.set(z));
double cz = c.getDouble(cIndex.set(z));
double term1 = depth_c * sz;
for (int y = 0; y < ny; y++) {
for (int x = 0; x < nx; x++) {
double fac1 = depth.getDouble(depthIndex.set(y, x));
double term2 = fac1 * cz;
double Sterm = (term1 + term2)/(depth_c + fac1);
double term3 = eta.getDouble(etaIndex.set(y, x));
double term4 = (term3 + fac1) * Sterm;
double hterm = term3 + term4;
height.set(z, y, x,hterm);
}
}
}
return height;
}
private ArrayDouble.D1 makeHeight1D(Array eta, Array s, Array depth,
Array c, double depth_c, int x_index, int y_index) {
int nz = (int) s.getSize();
Index sIndex = s.getIndex();
Index cIndex = c.getIndex();
Index etaIndex = eta.getIndex();
Index depthIndex = depth.getIndex();
ArrayDouble.D1 height = new ArrayDouble.D1(nz);
for (int z = 0; z < nz; z++) {
double sz = s.getDouble(sIndex.set(z));
double cz = c.getDouble(cIndex.set(z));
double term1 = depth_c * sz;
double fac1 = depth.getDouble(depthIndex.set(y_index, x_index));
double term2 = fac1 * cz;
double Sterm = (term1 + term2)/(depth_c + fac1);
double term3 = eta.getDouble(etaIndex.set(y_index, x_index));
double term4 = (term3 + fac1) * Sterm;
double hterm = term3 + term4;
height.set(z,hterm);
}
return height;
}
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