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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 1998-2009 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.nc2.dataset.conv;
import ucar.ma2.Array;
import ucar.ma2.ArrayObject;
import ucar.ma2.DataType;
import ucar.ma2.InvalidRangeException;
import ucar.nc2.*;
import ucar.nc2.constants.CF;
import ucar.nc2.dataset.*;
import ucar.nc2.time.CalendarDate;
import ucar.nc2.time.CalendarDateUnit;
import ucar.nc2.units.DateUnit;
import ucar.nc2.util.CancelTask;
import ucar.nc2.constants.AxisType;
import ucar.nc2.constants._Coordinate;
import ucar.nc2.units.SimpleUnit;
import ucar.unidata.geoloc.ProjectionImpl;
import ucar.unidata.geoloc.projection.LambertConformal;
import ucar.unidata.geoloc.projection.TransverseMercator;
import ucar.unidata.geoloc.projection.Stereographic;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.StringTokenizer;
/**
* Default Coordinate Conventions.
* Split from GDV.
* @author caron
* @since Dec 17, 2008
*/
public class DefaultConvention extends CoordSysBuilder {
protected ProjectionCT projCT = null;
public DefaultConvention() {
this.conventionName = "Default";
}
public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) {
projCT = makeProjectionCT(ds);
if (projCT != null) {
VariableDS v = makeCoordinateTransformVariable(ds, projCT);
ds.addVariable(null, v);
String xname = findCoordinateName(ds, AxisType.GeoX);
String yname = findCoordinateName(ds, AxisType.GeoY);
if (xname != null && yname != null)
v.addAttribute(new Attribute(_Coordinate.Axes, xname + " " + yname));
}
ds.finish();
}
@Override
protected void findCoordinateAxes(NetcdfDataset ds) {
for (VarProcess vp : varList) {
if (vp.isCoordinateVariable) continue;
Variable ncvar = vp.v;
if (!(ncvar instanceof VariableDS)) continue; // cant be a structure
String dimName = findAlias(ds, ncvar);
if (dimName.length() == 0) // none
continue;
Dimension dim = ds.findDimension(dimName);
if (null != dim) {
vp.isCoordinateAxis = true;
parseInfo.format(" Coordinate Axis added (alias) = %s for dimension %s\n", vp.v.getFullName(), dimName);
}
}
// coordinates is an alias for _CoordinateAxes
for (VarProcess vp : varList) {
if (vp.coordAxes == null) { // dont override if already set
String coordsString = ds.findAttValueIgnoreCase(vp.v, CF.COORDINATES, null);
if (coordsString != null) {
vp.coordinates = coordsString;
}
}
}
super.findCoordinateAxes(ds);
/////////////////////////
// now we start forcing
HashMap map = new HashMap();
// find existing axes, so we dont duplicate
for (VarProcess vp : varList) {
if (vp.isCoordinateAxis) {
AxisType atype = getAxisType(ds, (VariableEnhanced) vp.v);
if (atype != null)
map.put(atype, vp);
}
}
// look for time axes based on units
if (map.get(AxisType.Time) == null) {
for (VarProcess vp : varList) {
Variable ncvar = vp.v;
if (!(ncvar instanceof VariableDS)) continue; // cant be a structure
String unit = ncvar.getUnitsString();
if (unit != null && SimpleUnit.isDateUnit(unit)) {
vp.isCoordinateAxis = true;
map.put(AxisType.Time, vp);
parseInfo.format(" Time Coordinate Axis added (unit) = %s from unit %s\n", vp.v.getFullName(), unit);
//break; // allow multiple time coords
}
}
}
// look for missing axes by using name hueristics
for (VarProcess vp : varList) {
if (vp.isCoordinateVariable) continue;
Variable ncvar = vp.v;
if (!(ncvar instanceof VariableDS)) continue; // cant be a structure
AxisType atype = getAxisType(ds, (VariableEnhanced) vp.v);
if (atype != null) {
if (map.get(atype) == null) {
vp.isCoordinateAxis = true;
parseInfo.format(" Coordinate Axis added (Default forced) = %s for axis %s\n", vp.v.getFullName(), atype);
map.put(atype, vp);
}
}
}
}
/**
* look for aliases.
*
* @param ds containing dataset
* @param axisType look for this axis type
* @return name of axis of that type
*/
private String findCoordinateName(NetcdfDataset ds, AxisType axisType) {
List vlist = ds.getVariables();
for (Variable aVlist : vlist) {
VariableEnhanced ve = (VariableEnhanced) aVlist;
if (axisType == getAxisType(ds, ve)) {
return ve.getFullName();
}
}
return null;
}
protected void makeCoordinateTransforms(NetcdfDataset ds) {
if (projCT != null) {
VarProcess vp = findVarProcess(projCT.getName());
if (vp != null)
vp.ct = projCT;
}
super.makeCoordinateTransforms(ds);
}
protected AxisType getAxisType(NetcdfDataset ds, VariableEnhanced ve) {
AxisType result = getAxisTypeCoards(ds, ve);
if (result != null) return result;
Variable v = (Variable) ve;
String vname = v.getShortName();
if (vname == null)
return null;
String unit = v.getUnitsString();
if (unit == null) unit = "";
String desc = v.getDescription();
if (desc == null) desc = "";
if (vname.equalsIgnoreCase("x") || findAlias(ds, v).equalsIgnoreCase("x"))
return AxisType.GeoX;
if (vname.equalsIgnoreCase("lon") || vname.equalsIgnoreCase("longitude") || findAlias(ds, v).equalsIgnoreCase("lon"))
return AxisType.Lon;
if (vname.equalsIgnoreCase("y") || findAlias(ds, v).equalsIgnoreCase("y"))
return AxisType.GeoY;
if (vname.equalsIgnoreCase("lat") || vname.equalsIgnoreCase("latitude") || findAlias(ds, v).equalsIgnoreCase("lat"))
return AxisType.Lat;
if (vname.equalsIgnoreCase("lev") || findAlias(ds, v).equalsIgnoreCase("lev") ||
(vname.equalsIgnoreCase("level") || findAlias(ds, v).equalsIgnoreCase("level")))
return AxisType.GeoZ;
if (vname.equalsIgnoreCase("z") || findAlias(ds, v).equalsIgnoreCase("z") ||
vname.equalsIgnoreCase("altitude") || desc.contains("altitude") || vname.equalsIgnoreCase("depth") ||
vname.equalsIgnoreCase("elev") || vname.equalsIgnoreCase("elevation")) {
if ((unit != null) && SimpleUnit.isCompatible("m", unit)) // units of meters
return AxisType.Height;
}
if (vname.equalsIgnoreCase("time") || findAlias(ds, v).equalsIgnoreCase("time")) {
if (SimpleUnit.isDateUnit(unit))
return AxisType.Time;
}
if (vname.equalsIgnoreCase("time") && v.getDataType() == DataType.STRING) {
try {
Array firstValue = v.read("0");
// System.out.printf("%s%n", NCdumpW.printArray(firstValue, "firstValue", null));
if (firstValue instanceof ArrayObject.D1) {
ArrayObject.D1 sarry = (ArrayObject.D1) firstValue;
String firstStringValue = (String) sarry.get(0);
if (CalendarDate.parseISOformat(null, firstStringValue) != null) // valid iso date string
return AxisType.Time;
}
} catch (Exception e) {
}
}
return null;
}
// look for an coord_axis or coord_alias attribute
private String findAlias(NetcdfDataset ds, Variable v) {
String alias = ds.findAttValueIgnoreCase(v, "coord_axis", null);
if (alias == null)
alias = ds.findAttValueIgnoreCase(v, "coord_alias", "");
if (alias == null) alias = "";
return alias;
}
// replicated from COARDS, but we need to diverge from COARDS
// we assume that coordinate axes get identified by being coordinate variables
private AxisType getAxisTypeCoards( NetcdfDataset ncDataset, VariableEnhanced v) {
String unit = v.getUnitsString();
if (unit == null)
return null;
if( unit.equalsIgnoreCase("degrees_east") ||
unit.equalsIgnoreCase("degrees_E") ||
unit.equalsIgnoreCase("degreesE") ||
unit.equalsIgnoreCase("degree_east") ||
unit.equalsIgnoreCase("degree_E") ||
unit.equalsIgnoreCase("degreeE"))
return AxisType.Lon;
if ( unit.equalsIgnoreCase("degrees_north") ||
unit.equalsIgnoreCase("degrees_N") ||
unit.equalsIgnoreCase("degreesN") ||
unit.equalsIgnoreCase("degree_north") ||
unit.equalsIgnoreCase("degree_N") ||
unit.equalsIgnoreCase("degreeN"))
return AxisType.Lat;
if (SimpleUnit.isDateUnit(unit)) // || SimpleUnit.isTimeUnit(unit)) removed dec 18, 2008
return AxisType.Time;
// look for other z coordinate
//if (SimpleUnit.isCompatible("m", unit))
// return AxisType.Height;
if (SimpleUnit.isCompatible("mbar", unit))
return AxisType.Pressure;
if (unit.equalsIgnoreCase("level") || unit.equalsIgnoreCase("layer") || unit.equalsIgnoreCase("sigma_level"))
return AxisType.GeoZ;
String positive = ncDataset.findAttValueIgnoreCase((Variable) v, "positive", null);
if (positive != null) {
if (SimpleUnit.isCompatible("m", unit))
return AxisType.Height;
else
return AxisType.GeoZ;
}
return null;
}
private ProjectionCT makeProjectionCT(NetcdfDataset ds) {
// look for projection in global attribute
String projection = ds.findAttValueIgnoreCase(null, "projection", null);
if (null == projection) {
parseInfo.format("Default Conventions error: NO projection name found \n");
return null;
}
String params = ds.findAttValueIgnoreCase(null, "projection_params", null);
if (null == params) params = ds.findAttValueIgnoreCase(null, "proj_params", null);
if (null == params) {
parseInfo.format("Default Conventions error: NO projection parameters found \n");
return null;
}
// parse the parameters
int count = 0;
double[] p = new double[4];
try {
// new way : just the parameters
StringTokenizer stoke = new StringTokenizer(params, " ,");
while (stoke.hasMoreTokens() && (count < 4)) {
p[count++] = Double.parseDouble(stoke.nextToken());
}
} catch (NumberFormatException e) {
// old way : every other one
StringTokenizer stoke = new StringTokenizer(params, " ,");
while (stoke.hasMoreTokens() && (count < 4)) {
stoke.nextToken(); // skip
p[count++] = Double.parseDouble(stoke.nextToken());
}
}
parseInfo.format("Default Conventions projection %s params = %f %f %f %f\n", projection, p[0],p[1],p[2],p[3]);
ProjectionImpl proj;
if (projection.equalsIgnoreCase("LambertConformal"))
proj = new LambertConformal(p[0], p[1], p[2], p[3]);
else if (projection.equalsIgnoreCase("TransverseMercator"))
proj = new TransverseMercator(p[0], p[1], p[2]);
else if (projection.equalsIgnoreCase("Stereographic") || projection.equalsIgnoreCase("Oblique_Stereographic"))
proj = new Stereographic(p[0], p[1], p[2]);
else {
parseInfo.format("Default Conventions error: Unknown projection %s\n",projection);
return null;
}
return new ProjectionCT(proj.getClassName(), "FGDC", proj);
}
}