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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.
The newest version!
/*
* 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.nc2.ncml;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.Attribute;
import ucar.nc2.util.URLnaming;
import ucar.nc2.dataset.*;
import thredds.catalog.XMLEntityResolver;
import org.jdom2.*;
import org.jdom2.output.XMLOutputter;
import org.jdom2.output.Format;
import ucar.nc2.util.xml.Parse;
import java.io.*;
import java.util.*;
/**
* Helper class to write NcML.
*
* @author caron
* @see ucar.nc2.NetcdfFile
* @see http://www.unidata.ucar.edu/software/netcdf/ncml/
*/
public class NcMLWriter {
protected static final Namespace ncNS = Namespace.getNamespace(XMLEntityResolver.NJ22_NAMESPACE);
protected static final Namespace xsiNS = Namespace.getNamespace("xsi", XMLEntityResolver.W3C_XML_NAMESPACE);
static private org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(NcMLWriter.class);
private NetcdfDataset ncd;
private XMLOutputter fmt;
private Variable aggCoord;
/**
* Write NcML from specified NetcdfFile to a String.
*
* @param ncfile NcML for this NetcdfFile
* @return the NcML in a String
* @throws IOException on io error
*/
public String writeXML(NetcdfFile ncfile) throws IOException {
if (ncfile instanceof NetcdfDataset)
ncd = (NetcdfDataset) ncfile;
else
ncd = new NetcdfDataset(ncfile, false);
// Output the document, use standard formatter
//fmt = new XMLOutputter(" ", true);
//fmt.setLineSeparator("\n");
fmt = new XMLOutputter(Format.getPrettyFormat());
return fmt.outputString(makeDocument( null));
}
public String writeXML(Variable v) throws IOException {
// Output the document, use standard formatter
//fmt = new XMLOutputter(" ", true);
//fmt.setLineSeparator("\n");
fmt = new XMLOutputter(Format.getPrettyFormat());
return fmt.outputString(makeDocument( null));
}
/**
* Write a NetcdfFile as an XML document to the specified file.
*
* @param ncfile NcML for this NetcdfFile
* @param filenameOut write NcML to this location
* @throws IOException on io error
*/
public void writeXML(NetcdfFile ncfile, String filenameOut) throws IOException {
OutputStream out = new BufferedOutputStream(new FileOutputStream(filenameOut, false));
writeXML(ncfile, out, null);
out.close();
}
/**
* Write a NetcdfFile as an XML document to the specified stream.
*
* @param ncfile NcML for this NetcdfFile
* @param os write to this OutputStream
* @param location normally null, meaning use ncd.getLocation(); otherwise put this into the NcML location
* @throws IOException on io error
*/
public void writeXML(NetcdfFile ncfile, OutputStream os, String location) throws IOException {
if (ncfile instanceof NetcdfDataset)
ncd = (NetcdfDataset) ncfile;
else
ncd = new NetcdfDataset(ncfile, false);
fmt = new XMLOutputter(Format.getPrettyFormat());
fmt.output(makeDocument(location), os);
}
public void writeXMLexplicit(NetcdfFile ncfile, OutputStream os, String location) throws IOException {
if (ncfile instanceof NetcdfDataset)
ncd = (NetcdfDataset) ncfile;
else
ncd = new NetcdfDataset(ncfile, false);
fmt = new XMLOutputter(Format.getPrettyFormat());
Document doc = makeDocument(location);
Element root = doc.getRootElement();
root.addContent( new Element("explicit", ncNS));
fmt.output(doc, os);
}
private Document makeDocument(String location) throws IOException {
Element rootElem = new Element("netcdf", ncNS);
Document doc = new Document(rootElem);
// namespaces
rootElem.addNamespaceDeclaration(ncNS);
/* rootElem.addNamespaceDeclaration(xsiNS);
if (ncfile instanceof NetcdfDataset)
rootElem.setAttribute("schemaLocation",
"http://www.ucar.edu/schemas/netcdf-2.2 http://www.unidata.ucar.edu/schemas/netcdfCS-2.2.xsd", xsiNS);
else
rootElem.setAttribute("schemaLocation",
"http://www.ucar.edu/schemas/netcdf-2.2 http://www.unidata.ucar.edu/schemas/netcdf-2.2.xsd", xsiNS);
*/
if (null == location)
location = ncd.getLocation();
if (null != location) {
rootElem.setAttribute("location", URLnaming.canonicalizeWrite(location));
}
if (null != ncd.getId())
rootElem.setAttribute("id", ncd.getId());
if (null != ncd.getTitle())
rootElem.setAttribute("title", ncd.getTitle());
//if (ncd.getEnhanceMode() != NetcdfDataset.EnhanceMode.None)
// rootElem.setAttribute("enhance", ncd.getEnhanceMode().toString());
Aggregation agg = ncd.getAggregation();
if (agg != null) {
String aggDimensionName = agg.getDimensionName();
aggCoord = ncd.findVariable(aggDimensionName);
//System.out.println("isMetadata="+aggCoord.isMetadata());
}
Group rootGroup = ncd.getRootGroup();
/* if (ncd.getCoordSysWereAdded()) {
String conv = ncd.findAttValueIgnoreCase(null, "Conventions", null);
if (conv == null)
rootGroup.addAttribute(new Attribute("Conventions", _Coordinate.Convention));
else
rootGroup.addAttribute(new Attribute("Conventions", conv + ", " + _Coordinate.Convention));
} */
writeGroup(rootElem, rootGroup);
//if (agg != null) { LOOK ncml3
// rootElem.addContent(writeAggregation(agg));
//}
return doc;
}
/* private Element writeAggregation(AggregationIF agg) throws IOException {
Element aggElem = new Element("aggregation", ncNS);
Aggregation.Type type = agg.getType();
aggElem.setAttribute("type", type.toString());
String dimName = agg.getDimensionName();
if (dimName != null)
aggElem.setAttribute("dimName", dimName);
List varList = agg.getVariables();
for (String s : varList) {
Element e = new Element("variableAgg", ncNS);
e.setAttribute("name", s);
aggElem.addContent(e);
}
List dsList = agg.getNestedDatasets();
for (Aggregation.Dataset ds : dsList) {
Element e = new Element("netcdf", ncNS);
e.setAttribute("location", ds.getLocation());
//if (type == Aggregation.Type.JOIN_EXISTING)
e.setAttribute("ncoords", Integer.toString(ds.getNcoords(null)));
if (null != ds.getCoordValueString())
e.setAttribute("coordValue", ds.getCoordValueString());
aggElem.addContent(e);
}
if (agg.getType() == Aggregation.Type.UNION) {
List unionList = ((AggregationUnion) agg).getUnionDatasets();
for (NetcdfDataset ds : unionList) {
Element e = new Element("netcdf", ncNS);
e.setAttribute("location", ds.getLocation());
aggElem.addContent(e);
}
}
return aggElem;
} LOOK ncml3 */
public static Element writeAttribute(ucar.nc2.Attribute att, String elementName, Namespace ns) {
Element attElem = new Element(elementName, ns);
attElem.setAttribute("name", att.getShortName());
DataType dt = att.getDataType();
if ((dt != null) && (dt != DataType.STRING))
attElem.setAttribute("type", dt.toString());
if (att.getLength() == 0) {
if (att.isUnsigned())
attElem.setAttribute("isUnsigned", "true");
return attElem;
}
if (att.isString()) {
StringBuilder buff = new StringBuilder();
for (int i = 0; i < att.getLength(); i++) {
String sval = att.getStringValue(i);
if (i > 0) buff.append(",");
buff.append(sval);
}
attElem.setAttribute("value", Parse.cleanCharacterData(buff.toString()));
if (att.getLength() > 1)
attElem.setAttribute("separator", ",");
} else {
StringBuilder buff = new StringBuilder();
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());
if (att.isUnsigned())
attElem.setAttribute("isUnsigned", "true");
}
return attElem;
}
// shared dimensions
public static Element writeDimension(Dimension dim, Namespace ns) {
Element dimElem = new Element("dimension", ns);
dimElem.setAttribute("name", dim.getShortName());
if (dim.isVariableLength())
dimElem.setAttribute("length", "*");
else
dimElem.setAttribute("length", Integer.toString(dim.getLength()));
if (dim.isUnlimited())
dimElem.setAttribute("isUnlimited", "true");
if (dim.isVariableLength())
dimElem.setAttribute("isVariableLength", "true");
return dimElem;
}
// enum Typedef
public static Element writeEnumTypedef(EnumTypedef etd, Namespace ns) {
Element typeElem = new Element("enumTypedef", ns);
typeElem.setAttribute("name", etd.getShortName());
typeElem.setAttribute("type", etd.getBaseType().toString());
Map map = etd.getMap();
for (Map.Entry entry : map.entrySet()) {
typeElem.addContent(new Element("enum", ns)
.setAttribute("key", Integer.toString(entry.getKey()))
.addContent(entry.getValue()));
}
return typeElem;
}
private Element writeGroup(Element elem, Group group) {
// enumTypeDef
for (EnumTypedef etd : group.getEnumTypedefs()) {
elem.addContent(writeEnumTypedef(etd, ncNS));
}
// dimensions
for (Dimension dim : group.getDimensions()) {
elem.addContent(writeDimension(dim, ncNS));
}
// attributes
for (Attribute att : group.getAttributes()) {
elem.addContent(writeAttribute(att, "attribute", ncNS));
}
/* if (addCoords) {
// coordinate axes
Iterator vars = group.getVariables().iterator();
while ( vars.hasNext()) {
VariableEnhanced var = (VariableEnhanced) vars.next();
if (var instanceof CoordinateAxis)
elem.addContent( makeCoordinateAxis( (CoordinateAxis) var));
}
} */
// regular variables
for (Variable var : group.getVariables()) {
try {
elem.addContent(writeVariable((VariableEnhanced) var));
} catch (ClassCastException e) {
log.error("var not instanceof VariableEnhanced = " + var.getFullName(), e);
}
}
// nested groups
for (Group g : group.getGroups()) {
Element groupElem = new Element("group", ncNS);
groupElem.setAttribute("name", g.getShortName());
elem.addContent(writeGroup(groupElem, g));
}
return elem;
}
/* private Element makeParameter( ucar.unidata.util.Parameter p, String elementName) {
Element attElem = new Element(elementName, ncNS);
attElem.setAttribute("name", p.getName());
attElem.setAttribute("type", p.isString() ? "String" : "double");
if (p.isString()) {
String value = p.getStringValue();
String err = org.jdom.Verifier.checkCharacterData(value);
if (err != null) {
value = "NcMLWriter invalid attribute value, err= "+err;
System.out.println(value);
}
attElem.setAttribute("value", value);
} else {
StringBuilder buff = new StringBuilder();
for (int i=0; i 0) buff.append( " ");
buff.append( val);
}
attElem.setAttribute("value", buff.toString());
}
return attElem;
} */
/* private Element makeReferenceSys( ReferenceSystem referenceSystem) {
Element elem = new Element("referenceCoordinateSystem", ncNS);
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 0) buff.append(" ");
if (dim.isShared())
buff.append(dim.getShortName());
else if (dim.isVariableLength())
buff.append("*");
else
buff.append(dim.getLength());
}
//if (buff.length() > 0)
varElem.setAttribute("shape", buff.toString());
DataType dt = var.getDataType();
if (dt != null) {
varElem.setAttribute("type", dt.toString());
if (dt.isEnum())
varElem.setAttribute("typedef", var.getEnumTypedef().getShortName());
}
// attributes
for (Attribute att : var.getAttributes()) {
varElem.addContent(writeAttribute(att, "attribute", ncNS));
}
if (var.isMetadata() || (var == aggCoord))
varElem.addContent(writeValues(var, ncNS, true));
if (isStructure) {
Structure s = (Structure) var;
for (Variable variable : s.getVariables()) {
VariableEnhanced nestedV = (VariableEnhanced) variable;
varElem.addContent(writeVariable(nestedV));
}
}
return varElem;
}
/* private Element makeCoordinateAxis( CoordinateAxis var) {
var.addAttribute( new Attribute(CDM.UNITS, var.getUnitsString()));
if (var.getAxisType() != null)
var.addAttribute( new Attribute(_Coordinate.AxisType", var.getAxisType().toString()));
if (var.getPositive() != null)
var.addAttribute( new Attribute(_Coordinate.ZisPositive", var.getPositive()));
return makeVariable(var);
} */
public static Element writeValues(VariableEnhanced v, Namespace ns, boolean allowRegular) {
Element elem = new Element("values", ns);
StringBuilder buff = new StringBuilder();
Array a;
try {
a = v.read();
} catch (IOException ioe) {
return elem;
}
if (v.getDataType() == DataType.CHAR) {
char[] data = (char[]) a.getStorage();
elem.setText(new String(data));
} else if (v.getDataType() == DataType.STRING) { // use seperate elements??
IndexIterator iter = a.getIndexIterator();
int count = 0;
while (iter.hasNext()) {
String s = (String) iter.getObjectNext();
if (count++ > 0) buff.append(" ");
buff.append("\"").append(s).append("\"");
}
elem.setText(buff.toString());
} else {
//check to see if regular
if (allowRegular && (a.getRank() == 1) && (a.getSize() > 2)) {
Index ima = a.getIndex();
double start = a.getDouble(ima.set(0));
double incr = a.getDouble(ima.set(1)) - start;
boolean isRegular = true;
for (int i = 2; i < a.getSize(); i++) {
double v1 = a.getDouble(ima.set(i));
double v0 = a.getDouble(ima.set(i - 1));
if (!ucar.nc2.util.Misc.closeEnough(v1 - v0, incr))
isRegular = false;
}
if (isRegular) {
elem.setAttribute("start", Double.toString(start));
elem.setAttribute("increment", Double.toString(incr));
elem.setAttribute("npts", Long.toString(v.getSize()));
return elem;
}
}
// not regular
boolean isRealType = (v.getDataType() == DataType.DOUBLE) || (v.getDataType() == DataType.FLOAT);
IndexIterator iter = a.getIndexIterator();
buff.append(isRealType ? iter.getDoubleNext() : iter.getIntNext());
while (iter.hasNext()) {
buff.append(" ");
buff.append(isRealType ? iter.getDoubleNext() : iter.getIntNext());
}
elem.setText(buff.toString());
} // not string
return elem;
}
public static void main(String arg[]) {
//String urls = "C:/data/conventions/coards/cldc.mean.nc";
String test = "http://testbedapps.sura.org/thredds/dodsC/shelf_hypoxia_scan/noaa/NGOM/GOMUD-2009.3.182.3D.nc";
String urls = (arg.length == 0) ? test : arg[0];
try {
NetcdfDataset df = NetcdfDataset.openDataset(urls);
NcMLWriter writer = new NcMLWriter();
System.out.println("NetcdfDataset = " + urls + "\n" + df);
System.out.println("-----------");
writer.writeXML(df, System.out, null);
} catch (Exception ioe) {
System.out.println("error = " + urls);
ioe.printStackTrace();
}
}
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