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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 (c) 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.ft.point.writer;

import java.io.IOException;
import java.util.*;

import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants.CF;
import ucar.nc2.dataset.conv.CF1Convention;
import ucar.nc2.ft.PointFeature;
import ucar.nc2.ft.ProfileFeature;
import ucar.nc2.time.CalendarDate;
import ucar.nc2.units.DateUnit;

/**
 * Write a CF "Discrete Sample" profile collection file.
 * Example H.3.5. Contiguous ragged array representation of profiles, H.3.4
 *
 * 
 * 
 *   writeHeader()
 *   iterate { writeRecord() }
 *   finish()
 * 
 *
 * @see "http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8372832"
 * @author caron
 * @since April, 2012
 */
public class WriterCFProfileCollection extends CFPointWriter {

  ///////////////////////////////////////////////////
  // private Formatter coordNames = new Formatter();
  protected Structure profileStruct;  // used for netcdf4 extended
  private Map featureVarMap = new HashMap<>();
  private boolean headerDone = false;

  public WriterCFProfileCollection(String fileOut, List globalAtts, List dataVars, List extra,
                                   DateUnit timeUnit, String altUnits, CFPointWriterConfig config) throws IOException {
    super(fileOut, globalAtts, dataVars, extra, timeUnit, altUnits, config);
    writer.addGroupAttribute(null, new Attribute(CF.FEATURE_TYPE, CF.FeatureType.profile.name()));
  }

  public int writeProfile (ProfileFeature profile) throws IOException {
    profile.resetIteration();
    int count = 0;
    while (profile.hasNext()) {
      PointFeature pf = profile.next();
      if (!headerDone) {
        if (id_strlen == 0) id_strlen = profile.getName().length() * 2;
        writeHeader(profile, pf);
        headerDone = true;
      }
      writeObsData(pf);
      count++;
    }

    writeProfileData(profile, count);
    return count;
  }

  private void writeHeader(ProfileFeature profile, PointFeature obs) throws IOException {

    Formatter coordNames = new Formatter().format("%s %s %s", profileTimeName, latName, lonName);
    List coords = new ArrayList<>();
    if (useAlt) {
      coords.add( VariableSimpleImpl.makeScalar(altitudeCoordinateName, "obs altitude", altUnits, DataType.DOUBLE)
              .add(new Attribute(CF.STANDARD_NAME, "altitude"))
              .add(new Attribute(CF.POSITIVE, CF1Convention.getZisPositive(altitudeCoordinateName, altUnits))));
      coordNames.format(" %s", altitudeCoordinateName);
    }

    super.writeHeader(coords, profile.getFeatureData(), obs.getFeatureData(), coordNames.toString());
  }

  protected void makeFeatureVariables(StructureData featureData, boolean isExtended) throws IOException {

    // LOOK why not unlimited here ?
    Dimension profileDim = writer.addDimension(null, profileDimName, nfeatures);
    // Dimension profileDim = isExtendedModel ?  writer.addUnlimitedDimension(profileDimName) : writer.addDimension(null, profileDimName, nprofiles);

    // add the profile Variables using the profile dimension
    List profileVars = new ArrayList<>();
    profileVars.add(VariableSimpleImpl.makeScalar(latName, "profile latitude", CDM.LAT_UNITS, DataType.DOUBLE));
    profileVars.add(VariableSimpleImpl.makeScalar(lonName, "profile longitude", CDM.LON_UNITS, DataType.DOUBLE));
    profileVars.add(VariableSimpleImpl.makeString(profileIdName, "profile identifier", null, id_strlen)
            .add(new Attribute(CF.CF_ROLE, CF.PROFILE_ID)));         // profileId:cf_role = "profile_id";

    profileVars.add(VariableSimpleImpl.makeScalar(numberOfObsName, "number of obs for this profile", null, DataType.INT)
            .add(new Attribute(CF.SAMPLE_DIMENSION, recordDimName)));         // rowSize:sample_dimension = "obs"

    profileVars.add(VariableSimpleImpl.makeScalar(profileTimeName, "nominal time of profile", timeUnit.getUnitsString(), DataType.DOUBLE));

    for (StructureMembers.Member m : featureData.getMembers()) {
      VariableSimpleIF dv = getDataVar(m.getName());
      if (dv != null)
        profileVars.add(dv);
    }

    if (isExtended) {
      profileStruct = (Structure) writer.addVariable(null, profileStructName, DataType.STRUCTURE, profileDimName);
      addCoordinatesExtended(profileStruct, profileVars);
    } else {
      addCoordinatesClassic(profileDim, profileVars, featureVarMap);
    }
  }

  private int profileRecno = 0;
  public void writeProfileData(ProfileFeature profile, int nobs) throws IOException {
    trackBB(profile.getLatLon(), CalendarDate.of(profile.getTime()));

    StructureDataScalar profileCoords = new StructureDataScalar("Coords");
    profileCoords.addMember(latName, null, null, DataType.DOUBLE, false, profile.getLatLon().getLatitude());
    profileCoords.addMember(lonName, null, null, DataType.DOUBLE, false, profile.getLatLon().getLongitude());
    if (profile.getTime() != null)
      profileCoords.addMember(profileTimeName, null, null, DataType.DOUBLE, false,  timeUnit.makeValue(profile.getTime()));  // LOOK time not always part of profile
    profileCoords.addMemberString(profileIdName, null, null, profile.getName().trim(), id_strlen);
    profileCoords.addMember(numberOfObsName, null, null, DataType.INT, false, nobs);

    StructureData profileData = profile.getFeatureData();
    StructureDataComposite sdall = new StructureDataComposite();
    sdall.add(profileCoords); // coords first so it takes precedence
    sdall.add(profileData);

    profileRecno = super.writeStructureData(profileRecno, profileStruct, sdall, featureVarMap);
  }


  private int obsRecno = 0;
  public void writeObsData(PointFeature pf) throws IOException {

    StructureDataScalar coords = new StructureDataScalar("Coords");
    if (useAlt) coords.addMember(altitudeCoordinateName, null, null, DataType.DOUBLE, false, pf.getLocation().getAltitude());

    StructureDataComposite sdall = new StructureDataComposite();
    sdall.add(coords); // coords first so it takes precedence
    sdall.add(pf.getFeatureData());

    obsRecno = super.writeStructureData(obsRecno, record, sdall, dataMap);
  }

}