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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,
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 *   WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
 */

package ucar.nc2.dataset.transform;

import ucar.nc2.dataset.*;
import ucar.nc2.Variable;
import ucar.nc2.Dimension;
import ucar.unidata.geoloc.vertical.OceanS;
import ucar.unidata.util.Parameter;

/**
 * Create a ocean_s_coordinate Vertical Transform from the information in the Coordinate Transform Variable.
 *
 * @author caron
 */
public class VOceanS extends AbstractCoordTransBuilder {
  private String s = "", eta = "", depth = "", a = "", b = "", depth_c = "";

  public String getTransformName() {
    return "ocean_s_coordinate";
  }

  public TransformType getTransformType() {
    return TransformType.Vertical;
  }

  public CoordinateTransform makeCoordinateTransform(NetcdfDataset ds, Variable ctv) {
    String formula_terms = getFormula(ds, ctv);
    if (null == formula_terms) return null;

     // parse the formula string
    String[] values = parseFormula(formula_terms, "s eta depth a b depth_c");
    if (values == null) return null;

    s = values[0];
    eta = values[1];
    depth = values[2];
    a = values[3];
    b = values[4];
    depth_c = values[5];

    CoordinateTransform rs = new VerticalCT("OceanS_Transform_"+ctv.getShortName(), getTransformName(), VerticalCT.Type.OceanS, this);
    rs.addParameter(new Parameter("standard_name", getTransformName()));
    rs.addParameter(new Parameter("formula_terms", formula_terms));
   // rs.addParameter((new Parameter("height_formula", "height(x,y,z) = eta(x,y)*(1+s(z)) + depth_c*s(z) + (depth(x,y)-depth_c)*C(z)")));
     //-sachin 03/25/09 modify formula according to Hernan Arango
    rs.addParameter((new Parameter("height_formula", "height(x,y,z) = depth_c*s(z) + (depth(x,y)-depth_c)*C(z) + eta(x,y) * (1 + (depth_c*s(z) + (depth(x,y)-depth_c)*C(z))/depth(x,y) ")));
    rs.addParameter((new Parameter("C_formula", "C(z) = (1-b)*sinh(a*s(z))/sinh(a) + b*(tanh(a*(s(z)+0.5))/(2*tanh(0.5*a))-0.5)")));

    if (!addParameter(rs, OceanS.ETA, ds, eta)) return null;
    if (!addParameter(rs, OceanS.S, ds, s)) return null;
    if (!addParameter(rs, OceanS.DEPTH, ds, depth)) return null;

    if (!addParameter(rs, OceanS.DEPTH_C, ds, depth_c)) return null;
    if (!addParameter(rs, OceanS.A, ds, a)) return null;
    if (!addParameter(rs, OceanS.B, ds, b)) return null;

    return rs;
  }

  public String toString() {
    return "OceanS:" + " s:"+s + " eta:"+eta + " depth:"+depth + " a:"+a + " b:"+b+" depth_c:"+depth_c;    

  }

  public ucar.unidata.geoloc.vertical.VerticalTransform makeMathTransform(NetcdfDataset ds, Dimension timeDim, VerticalCT vCT) {
    return new OceanS(ds, timeDim, vCT.getParameters());
  }
}