ucar.nc2.ncml.NcMLGWriter Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of cdm Show documentation
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 1998-2009 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 thredds.catalog.XMLEntityResolver;
import ucar.unidata.util.Parameter;

/**
 * Helper class to write NcML-G.
 *
 * @see ucar.nc2.NetcdfFile
 * @see http://zeus.pin.unifi.it/projectsSites/galeon2-ncml-gml/
 * @author caron
 */

public class NcMLGWriter {
  protected static final Namespace ncNS = Namespace.getNamespace("http://www.ucar.edu/schemas/netcdf");
  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", ncNS);
    Document doc = new Document(rootElem);

      // namespaces
    rootElem.addNamespaceDeclaration(ncNS);
    rootElem.addNamespaceDeclaration(XMLEntityResolver.xsiNS);
    rootElem.setAttribute("schemaLocation", ncNS.getURI()+" "+schemaLocation, XMLEntityResolver.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= 0) {
        cs.setReferenceSystem( (ReferenceSystem) commonRS.get(idx)); // point to common one
        continue;
      }
      for (int j=i+1; j= 0) {
        rs.setHoriz( (ReferenceSystem.Horiz) commonHRS.get(idx)); // point to common one
        continue;
      }
      for (int j=i+1; j coordTrans = new ArrayList();
    for (CoordinateSystem cs : ncd.getCoordinateSystems()) {
      List 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, ncNS);
    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 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, ncNS);
    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 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", ncNS);
    varElem.setAttribute("name", var.getFullName());

    StringBuffer buff = new StringBuffer();
    List dims = var.getDimensions();
    for (int i=0; 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; i0) buff.append(" ");
        buff.append( cs.getName());
      }
      varElem.setAttribute("coordinateSystems", buff.toString());
    }

    return varElem;
  }

  private Element makeCoordSys( CoordinateSystem cs) {
    Element csElem = new Element("coordinateSystem", ncNS);
    csElem.setAttribute("name", cs.getName());

    for (CoordinateAxis axis : cs.getCoordinateAxes()) {
      Element axisElem = new Element("coordinateAxisRef", ncNS);
      axisElem.setAttribute("ref", axis.getFullName());
      csElem.addContent(axisElem);
    }

    List transforms = cs.getCoordinateTransforms();
    if (transforms != null)
      for (CoordinateTransform ct : transforms) {
        if (ct == null) continue;
        Element tElem = new Element("coordinateTransformRef", ncNS);
        tElem.setAttribute("ref", ct.getName());
        csElem.addContent(tElem);
      }
    return csElem;
  }

  private Element makeCoordTransform( CoordinateTransform coordTransform) {
    Element elem = new Element("coordinateTransform", ncNS);
    elem.setAttribute("name", coordTransform.getName());
    elem.setAttribute("authority", coordTransform.getAuthority());
    if (coordTransform.getTransformType() != null)
      elem.setAttribute("transformType", coordTransform.getTransformType().toString());

    List params = coordTransform.getParameters();
    for (Parameter p : params) {
      elem.addContent(makeAttribute(p, "parameter"));
    }
    return elem;
  }

  private Element makeDim( Dimension dim) {
    Element dimElem = new Element("dimension", ncNS);
    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", 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( " ");
      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; i0) buff.append(" ");
        buff.append( cs.getName());
      }
      varElem.setAttribute("coordinateSystems", buff.toString());
    }

    return varElem;
  }

  private Element makeValues( VariableDS v) {
    Element elem = new Element("values", ncNS);

    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 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();
    }
  }

}