Java Code Examples for ucar.nc2.ft.FeatureDatasetPoint#getDataVariables()

public static ThreddsMetadata.Variables extractVariables(FeatureDatasetPoint fd) {
  ThreddsMetadata.Variables vars = new ThreddsMetadata.Variables("CF-1.5");
  List<VariableSimpleIF> dataVars = fd.getDataVariables();
  if (dataVars == null)
    return vars;

  for (VariableSimpleIF v : dataVars) {
    ThreddsMetadata.Variable tv = new ThreddsMetadata.Variable();
    vars.addVariable(tv);

    tv.setName(v.getShortName());
    tv.setDescription(v.getDescription());
    tv.setUnits(v.getUnitsString());

    ucar.nc2.Attribute att = v.findAttributeIgnoreCase("standard_name");
    if (att != null)
      tv.setVocabularyName(att.getStringValue());
  }
  vars.sort();
  return vars;
}
 

private static int writePointFeatureCollection(FeatureDatasetPoint fdpoint, PointFeatureCollection pfc,
    String fileOut, CFPointWriterConfig config) throws IOException {

  try (WriterCFPointCollection pointWriter = new WriterCFPointCollection(fileOut, fdpoint.attributes(),
      fdpoint.getDataVariables(), pfc.getTimeUnit(), pfc.getAltUnits(), config)) {

    pointWriter.setExtraVariables(pfc.getExtraVariables());

    int count = 0;
    for (PointFeature pf : pfc) {
      if (count == 0)
        pointWriter.writeHeader(pf);

      pointWriter.writeRecord(pf, pf.getFeatureData());
      count++;
      if (debug && count % 100 == 0)
        System.out.printf("%d ", count);
      if (debug && count % 1000 == 0)
        System.out.printf("%n ");
    }

    pointWriter.finish();
    return count;
  }
}
 

public ThreddsMetadata.VariableGroup extractVariables(FeatureDatasetPoint fd) {
  List<ThreddsMetadata.Variable> vars = new ArrayList<>();

  List<VariableSimpleIF> dataVars = fd.getDataVariables();
  if (dataVars == null)
    return null;

  for (VariableSimpleIF v : dataVars) {
    String name = v.getShortName();
    String desc = v.getDescription();
    String units = v.getUnitsString();
    String vname = null;
    String id = null;

    ucar.nc2.Attribute att = v.attributes().findAttributeIgnoreCase("standard_name");
    if (att != null)
      vname = att.getStringValue();
    vars.add(new ThreddsMetadata.Variable(name, desc, vname, units, id));
  }

  Collections.sort(vars);
  // String vocab, String vocabHref, URI vocabUri, URI mapUri, List<Variable> variables
  return new ThreddsMetadata.VariableGroup("CF-1.0", null, null, vars);
}
 

private static int writeStationFeatureCollection(FeatureDatasetPoint dataset, StationTimeSeriesFeatureCollection fc,
    String fileOut, CFPointWriterConfig config) throws IOException {

  try (WriterCFStationCollection cfWriter = new WriterCFStationCollection(fileOut, dataset.attributes(),
      dataset.getDataVariables(), fc.getTimeUnit(), fc.getAltUnits(), config)) {

    cfWriter.setExtraVariables(fc.getExtraVariables());

    // write all data, but no need to sort by station
    PointFeatureCollection pfc = fc.flatten(null, null, null);

    int count = 0;
    for (PointFeature pf : pfc) {
      StationPointFeature spf = (StationPointFeature) pf;
      if (count == 0)
        cfWriter.writeHeader(fc.getStationFeatures(), spf);

      cfWriter.writeRecord(spf.getStation(), pf, pf.getFeatureData());
      count++;
      if (debug && count % 100 == 0)
        System.out.printf("%d ", count);
      if (debug && count % 1000 == 0)
        System.out.printf("%n ");
    }

    cfWriter.finish();
    return count;
  }
}
 

public static List<VariableSimpleIF> getWantedVariables(FeatureDatasetPoint fdPoint, SubsetParams ncssParams)
    throws VariableNotContainedInDatasetException {
  List<String> vars = ncssParams.getVariables();
  if (vars.size() == 1 && vars.get(0).equals("all")) {
    return fdPoint.getDataVariables(); // Return all variables.
  }

  // restrict to these variables
  Map<String, VariableSimpleIF> dataVarsMap = new HashMap<>();
  for (VariableSimpleIF dataVar : fdPoint.getDataVariables()) {
    dataVarsMap.put(dataVar.getShortName(), dataVar);
  }

  List<String> allVarNames = new ArrayList<>(dataVarsMap.keySet());
  List<VariableSimpleIF> wantedVars = new ArrayList<>();

  for (String varName : vars) {
    if (allVarNames.contains(varName)) {
      VariableSimpleIF var = dataVarsMap.get(varName);
      wantedVars.add(var);
    } else {
      throw new VariableNotContainedInDatasetException(
          "Variable: " + varName + " is not contained in the requested dataset");
    }
  }

  return wantedVars;
}
 

/**
 * Write a ucar.nc2.ft.PointFeatureCollection in CF point format.
 *
 * @param pfDataset find the first PointFeatureCollection, and write all data from it
 * @param fileOut write to this netcdf-3 file
 * @return number of records written
 * @throws IOException on read/write error, or if no PointFeatureCollection in pfDataset
 */
public static int writePointFeatureCollection(FeatureDatasetPoint pfDataset, String fileOut) throws IOException {
  // extract the PointFeatureCollection
  PointFeatureCollection pointFeatureCollection = null;
  List<DsgFeatureCollection> featureCollectionList = pfDataset.getPointFeatureCollectionList();
  for (DsgFeatureCollection featureCollection : featureCollectionList) {
    if (featureCollection instanceof PointFeatureCollection)
      pointFeatureCollection = (PointFeatureCollection) featureCollection;
  }
  if (null == pointFeatureCollection)
    throw new IOException("There is no PointFeatureCollection in  " + pfDataset.getLocation());

  long start = System.currentTimeMillis();

  FileOutputStream fos = new FileOutputStream(fileOut);
  DataOutputStream out = new DataOutputStream(new BufferedOutputStream(fos, 10000));
  WriterCFPointDataset writer = null;

  // LOOK BAD
  List<VariableSimpleIF> dataVars = new ArrayList<VariableSimpleIF>();
  ucar.nc2.NetcdfFile ncfile = pfDataset.getNetcdfFile();
  if ((ncfile == null) || !(ncfile instanceof NetcdfDataset)) {
    dataVars.addAll(pfDataset.getDataVariables());
  } else {
    NetcdfDataset ncd = (NetcdfDataset) ncfile;
    for (VariableSimpleIF vs : pfDataset.getDataVariables()) {
      if (ncd.findCoordinateAxis(vs.getShortName()) == null)
        dataVars.add(vs);
    }
  }

  int count = 0;
  for (PointFeature pointFeature : pointFeatureCollection) {
    StructureData data = pointFeature.getDataAll();
    if (count == 0) {
      EarthLocation loc = pointFeature.getLocation(); // LOOK we dont know this until we see the obs
      String altUnits = Double.isNaN(loc.getAltitude()) ? null : "meters"; // LOOK units may be wrong
      writer = new WriterCFPointDataset(out, pfDataset.getGlobalAttributes(), altUnits);
      writer.writeHeader(dataVars, -1);
    }
    writer.writeRecord(pointFeature, data);
    count++;
  }

  writer.finish();
  out.flush();
  out.close();

  long took = System.currentTimeMillis() - start;
  System.out.printf("Write %d records from %s to %s took %d msecs %n", count, pfDataset.getLocation(), fileOut, took);
  return count;
}