/*
* 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.ncml;
import ucar.nc2.*;
import ucar.nc2.Attribute;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants.CF;
import ucar.nc2.dataset.*;
import ucar.ma2.*;
import org.jdom2.*;
import org.jdom2.output.XMLOutputter;
import org.jdom2.output.Format;
import java.io.*;
import java.util.*;
import ucar.unidata.util.Parameter;
/**
* Helper class to write NcML-G.
*
* @see ucar.nc2.NetcdfFile
* @see <a href="http://zeus.pin.unifi.it/projectsSites/galeon2-ncml-gml/">http://zeus.pin.unifi.it/projectsSites/galeon2-ncml-gml/</a>
* @author caron
*/
public class NcMLGWriter {
protected static final String schemaLocation = "http://www.unidata.ucar.edu/schemas/netcdf-cs.xsd";
/**
* Write a NetcdfDataset as an NcML-G document to the specified stream.
*
* @param ncd write this dataset; should have opened with "add coordinates".
* @param os write to this OutputStream
* @param showCoords show 1D coordinate values
* @param uri use this url, if null use getLocation()
* @throws IOException on io error
*/
public void writeXML(NetcdfDataset ncd, OutputStream os, boolean showCoords, String uri) throws IOException {
// Output the document, use standard formatter
//XMLOutputter fmt = new XMLOutputter(" ", true);
//fmt.setLineSeparator("\n");
XMLOutputter fmt = new XMLOutputter( Format.getPrettyFormat());
fmt.output(makeDocument(ncd, showCoords, uri), os);
}
Document makeDocument(NetcdfDataset ncd, boolean showCoords, String uri) {
Element rootElem = new Element("netcdf", thredds.client.catalog.Catalog.ncmlNS);
Document doc = new Document(rootElem);
// namespaces
rootElem.addNamespaceDeclaration(thredds.client.catalog.Catalog.ncmlNS);
rootElem.addNamespaceDeclaration(thredds.client.catalog.Catalog.xsiNS);
rootElem.setAttribute("schemaLocation", thredds.client.catalog.Catalog.ncmlNS.getURI()+" "+schemaLocation, thredds.client.catalog.Catalog.xsiNS);
if (null != ncd.getId())
rootElem.setAttribute("id", ncd.getId());
if (null != uri)
rootElem.setAttribute("url", uri);
else
rootElem.setAttribute("url", ncd.getLocation());
// dimensions
for (Dimension dim : ncd.getDimensions()) {
rootElem.addContent(makeDim(dim));
}
// attributes
for (Attribute att : ncd.getGlobalAttributes()) {
rootElem.addContent(makeAttribute(att, "attribute"));
}
// coordinate axes
for (Variable var : ncd.getVariables()) {
if (var instanceof CoordinateAxis)
rootElem.addContent(makeCoordinateAxis((CoordinateAxis) var, showCoords));
}
// regular variables
for (Variable var : ncd.getVariables()) {
if (!(var instanceof CoordinateAxis))
rootElem.addContent(makeVariable( (VariableDS) var));
}
///////////////////////////////////////////////////////////
// reference systems
// find common coordinate transforms
/* ReferenceSystem rs = cs.getReferenceSystem();
int idx = commonRS.indexOf(rs);
if (idx >= 0) {
cs.setReferenceSystem( (ReferenceSystem) commonRS.get(idx)); // point to common one
continue;
}
for (int j=i+1; j<csys.size(); j++) {
CoordinateSystem cs2 = (CoordinateSystem) csys.get(j);
ReferenceSystem rs2 = cs2.getReferenceSystem();
if (rs.equals(rs2)) { // used more than once
commonRS.add( rs);
break;
}
}
}
/* find common reference systems
ArrayList commonRS = new ArrayList();
List csys = ncd.getCoordinateSystems();
for (int i=0; i<csys.size(); i++) {
CoordinateSystem cs = (CoordinateSystem) csys.get(i);
ReferenceSystem rs = cs.getReferenceSystem();
int idx = commonRS.indexOf(rs);
if (idx >= 0) {
cs.setReferenceSystem( (ReferenceSystem) commonRS.get(idx)); // point to common one
continue;
}
for (int j=i+1; j<csys.size(); j++) {
CoordinateSystem cs2 = (CoordinateSystem) csys.get(j);
ReferenceSystem rs2 = cs2.getReferenceSystem();
if (rs.equals(rs2)) { // used more than once
commonRS.add( rs);
break;
}
}
}
// find common horiz reference systems
ArrayList commonHRS = new ArrayList();
csys = ncd.getCoordinateSystems();
for (int i=0; i<csys.size(); i++) {
CoordinateSystem cs = (CoordinateSystem) csys.get(i);
ReferenceSystem rs = cs.getReferenceSystem();
ReferenceSystem.Horiz hrs = rs.getHoriz();
int idx = commonHRS.indexOf(hrs);
if (idx >= 0) {
rs.setHoriz( (ReferenceSystem.Horiz) commonHRS.get(idx)); // point to common one
continue;
}
for (int j=i+1; j<csys.size(); j++) {
CoordinateSystem cs2 = (CoordinateSystem) csys.get(j);
ReferenceSystem rs2 = cs2.getReferenceSystem();
ReferenceSystem.Horiz hrs2 = rs2.getHoriz();
if (hrs.equals(hrs2)) { // used more than once
commonHRS.add( hrs);
hrs.setId( hrs.getProjectionName()); // wrong
break;
}
}
} */
// coordinate systems
for (CoordinateSystem cs : ncd.getCoordinateSystems()) {
rootElem.addContent(makeCoordSys(cs));
}
// look for coordinate transforms, ref systems
List<CoordinateTransform> coordTrans = new ArrayList<CoordinateTransform>();
for (CoordinateSystem cs : ncd.getCoordinateSystems()) {
List<CoordinateTransform> ctList = cs.getCoordinateTransforms();
if (ctList != null) {
for (CoordinateTransform ct : ctList) {
if (!coordTrans.contains(ct))
coordTrans.add(ct);
}
}
}
// coordinate transforms
for (CoordinateTransform coordTran : coordTrans)
rootElem.addContent(makeCoordTransform(coordTran));
return doc;
}
private Element makeAttribute( ucar.nc2.Attribute att, String elementName) {
Element attElem = new Element(elementName, thredds.client.catalog.Catalog.ncmlNS);
attElem.setAttribute("name", att.getShortName());
DataType dt = att.getDataType();
if (dt != null)
attElem.setAttribute("type", dt.toString());
if (att.isString()) {
String value = att.getStringValue();
String err = org.jdom2.Verifier.checkCharacterData(value);
if (err != null) {
value = "NcMLWriter invalid attribute value, err= "+err;
System.out.println(value);
}
attElem.setAttribute("value", value);
} else {
StringBuffer buff = new StringBuffer();
for (int i=0; i<att.getLength(); i++) {
Number val = att.getNumericValue(i);
if (i > 0) buff.append( " ");
buff.append( val.toString());
}
attElem.setAttribute("value", buff.toString());
}
return attElem;
}
private Element makeAttribute( ucar.unidata.util.Parameter att, String elementName) {
Element attElem = new Element(elementName, thredds.client.catalog.Catalog.ncmlNS);
attElem.setAttribute("name", att.getName());
if (att.isString()) {
String value = att.getStringValue();
String err = org.jdom2.Verifier.checkCharacterData(value);
if (err != null) {
value = "NcMLWriter invalid attribute value, err= "+err;
System.out.println(value);
}
attElem.setAttribute("value", value);
} else {
attElem.setAttribute("type", "double");
StringBuffer buff = new StringBuffer();
for (int i=0; i<att.getLength(); i++) {
double val = att.getNumericValue(i);
if (i > 0) buff.append( " ");
buff.append( Double.toString( val));
}
attElem.setAttribute("value", buff.toString());
}
return attElem;
}
private Element makeCoordinateAxis( CoordinateAxis var, boolean showCoords) {
Element varElem = new Element("coordinateAxis", thredds.client.catalog.Catalog.ncmlNS);
varElem.setAttribute("name", var.getFullName());
StringBuffer buff = new StringBuffer();
List dims = var.getDimensions();
for (int i=0; i<dims.size(); i++) {
Dimension dim = (Dimension) dims.get(i);
if (i > 0) buff.append( " ");
buff.append( dim.getShortName());
}
if (buff.length() > 0)
varElem.setAttribute("shape", buff.toString());
DataType dt = var.getDataType();
varElem.setAttribute("type", dt.toString());
// attributes
for (Attribute att : var.getAttributes()) {
varElem.addContent(makeAttribute(att, "attribute"));
}
if (var.isMetadata() || (showCoords && var.getRank() <= 1))
varElem.addContent( makeValues( var));
// coordinate axis
varElem.setAttribute(CDM.UNITS, var.getUnitsString());
if (var.getAxisType() != null)
varElem.setAttribute("axisType", var.getAxisType().toString());
String positive = var.getPositive();
if (positive != null)
varElem.setAttribute(CF.POSITIVE, positive);
String boundaryRef = var.getBoundaryRef();
if (boundaryRef != null)
varElem.setAttribute("boundaryRef", boundaryRef);
// coordinate systems
List csys = var.getCoordinateSystems();
if (csys.size() > 0) {
buff.setLength(0);
for (int i=0; i<csys.size(); i++) {
CoordinateSystem cs = (CoordinateSystem) csys.get(i);
if (i>0) buff.append(" ");
buff.append( cs.getName());
}
varElem.setAttribute("coordinateSystems", buff.toString());
}
return varElem;
}
private Element makeCoordSys( CoordinateSystem cs) {
Element csElem = new Element("coordinateSystem", thredds.client.catalog.Catalog.ncmlNS);
csElem.setAttribute("name", cs.getName());
for (CoordinateAxis axis : cs.getCoordinateAxes()) {
Element axisElem = new Element("coordinateAxisRef", thredds.client.catalog.Catalog.ncmlNS);
axisElem.setAttribute("ref", axis.getFullName());
csElem.addContent(axisElem);
}
List<CoordinateTransform> transforms = cs.getCoordinateTransforms();
if (transforms != null)
for (CoordinateTransform ct : transforms) {
if (ct == null) continue;
Element tElem = new Element("coordinateTransformRef", thredds.client.catalog.Catalog.ncmlNS);
tElem.setAttribute("ref", ct.getName());
csElem.addContent(tElem);
}
return csElem;
}
private Element makeCoordTransform( CoordinateTransform coordTransform) {
Element elem = new Element("coordinateTransform", thredds.client.catalog.Catalog.ncmlNS);
elem.setAttribute("name", coordTransform.getName());
elem.setAttribute("authority", coordTransform.getAuthority());
if (coordTransform.getTransformType() != null)
elem.setAttribute("transformType", coordTransform.getTransformType().toString());
List<Parameter> params = coordTransform.getParameters();
for (Parameter p : params) {
elem.addContent(makeAttribute(p, "parameter"));
}
return elem;
}
private Element makeDim( Dimension dim) {
Element dimElem = new Element("dimension", thredds.client.catalog.Catalog.ncmlNS);
dimElem.setAttribute("name", dim.getShortName());
dimElem.setAttribute("length", Integer.toString(dim.getLength()));
if (dim.isUnlimited())
dimElem.setAttribute("isUnlimited", "true");
return dimElem;
}
/* private Element makeReferenceSys( ReferenceSystem referenceSystem) {
Element elem = new Element("referenceCoordinateSystem", thredds.client.catalog.Catalog.ncmlNS);
elem.setAttribute("name", referenceSystem.getName());
elem.setAttribute("authority", referenceSystem.getAuthority());
if (referenceSystem.getReferenceType() != null)
elem.setAttribute("type", referenceSystem.getReferenceType().toString());
ArrayList params = referenceSystem.getParameters();
for (int i=0; i<params.size(); i++) {
ucar.nc2.Attribute att = (ucar.nc2.Attribute) params.get(i);
elem.addContent( makeAttribute(att, "parameter"));
}
return elem;
} */
private Element makeVariable( VariableDS var) {
Element varElem = new Element("variable", thredds.client.catalog.Catalog.ncmlNS);
varElem.setAttribute("name", var.getFullName());
StringBuffer buff = new StringBuffer();
List dims = var.getDimensions();
for (int i=0; i<dims.size(); i++) {
Dimension dim = (Dimension) dims.get(i);
if (i > 0) buff.append( " ");
buff.append( dim.getShortName());
}
if (buff.length() > 0)
varElem.setAttribute("shape", buff.toString());
DataType dt = var.getDataType();
if (dt != null)
varElem.setAttribute("type", dt.toString());
// attributes
for (Attribute att : var.getAttributes()) {
varElem.addContent(makeAttribute(att, "attribute"));
}
if (var.isMetadata())
varElem.addContent( makeValues( var));
// coordinate systems
List csys = var.getCoordinateSystems();
if (csys.size() > 0) {
buff.setLength(0);
for (int i=0; i<csys.size(); i++) {
CoordinateSystem cs = (CoordinateSystem) csys.get(i);
if (i>0) buff.append(" ");
buff.append( cs.getName());
}
varElem.setAttribute("coordinateSystems", buff.toString());
}
return varElem;
}
private Element makeValues( VariableDS v) {
Element elem = new Element("values", thredds.client.catalog.Catalog.ncmlNS);
StringBuffer buff = new StringBuffer();
Array a;
try {
a = v.read();
} catch (IOException ioe) {
return elem;
}
if (a instanceof ArrayChar) {
//strings
ArrayChar dataC = (ArrayChar) a;
for (int i=0; i<dataC.getShape()[0]; i++) {
if (i > 0) buff.append(" ");
buff.append("\"").append(dataC.getString(i)).append("\"");
}
elem.setText(buff.toString());
} else {
// numbers
if (v instanceof CoordinateAxis1D && ((CoordinateAxis1D)v).isRegular()) {
CoordinateAxis1D axis = (CoordinateAxis1D) v;
elem.setAttribute("start", Double.toString(axis.getStart()));
elem.setAttribute("increment", Double.toString(axis.getIncrement()));
elem.setAttribute("npts", Long.toString(v.getSize()));
} else {
// numbers
boolean isDouble = (v.getDataType() == DataType.DOUBLE);
boolean isFloat = (v.getDataType() == DataType.FLOAT);
IndexIterator iter = a.getIndexIterator();
while (iter.hasNext()) {
if (isDouble)
buff.append(iter.getDoubleNext());
else if (isFloat)
buff.append(iter.getFloatNext());
else
buff.append(iter.getIntNext());
buff.append(" ");
}
elem.setText(buff.toString());
} // not regular
} // not string
return elem;
}
public static void main( String arg[]){
//String urls = "C:/data/conventions/coards/cldc.mean.nc";
String urls = "C:/data/galeon/RUC.nc";
try {
NetcdfDataset df = NetcdfDataset.openDataset(urls);
NcMLGWriter ncFactory = new NcMLGWriter();
System.out.println("NetcdfDataset = "+urls+"\n"+df);
System.out.println("-----------");
ncFactory.writeXML( df, System.out, true, null);
} catch (Exception ioe) {
System.out.println("error = "+urls);
ioe.printStackTrace();
}
}
}