Java Code Examples for ucar.nc2.dataset.NetcdfDataset#finish()

public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) {
  String start_date = ds.findAttValueIgnoreCase(null, "start_date", null);
  if (start_date == null)
    return;

  SimpleDateFormat df = new SimpleDateFormat("yyyy.DDD.HH.mm.ss"); // "2006.105.00.00.00"
  DateFormatter dfo = new DateFormatter();

  Date start;
  try {
    start = df.parse(start_date);
  } catch (ParseException e) {
    throw new RuntimeException("Cant read start_date=" + start_date);
  }

  Variable v = ds.findVariable("time_offset");
  v.addAttribute(new Attribute(CDM.UNITS, "seconds since " + dfo.toDateTimeString(start)));

  Group root = ds.getRootGroup();
  root.addAttribute(new Attribute(CDM.CONVENTIONS, "Suomi-Station-CDM"));
  ds.finish();
}
 

public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) {
  for (Variable v : ds.getVariables()) {
    switch (v.getShortName()) {
      case "staName":
        v.addAttribute(new Attribute("standard_name", "station_name"));
        break;
      case "staLat":
        v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
        break;
      case "staLon":
        v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
        break;
      case "staElev":
      case "levels":
        v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Height.toString()));
        break;
      case "timeObs":
        v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
        break;
    }
  }
  ds.finish();
}
 

/**
 *
 */
private void augmentDataset3(NetcdfDataset ds) {
  Group grids = ds.findGroup("/HDFEOS/GRIDS");
  if (grids == null) {
    return;
  }
  for (Group g2 : grids.getGroups()) {
    Attribute gctp = g2.findAttribute("GCTPProjectionCode");

    if (gctp == null || !gctp.getNumericValue().equals(0)) {
      continue;
    }

    Attribute nlon = g2.findAttribute("NumberOfLongitudesInGrid");
    Attribute nlat = g2.findAttribute("NumberOfLatitudesInGrid");

    if (nlon == null || nlon.isString()) {
      continue;
    }
    if (nlat == null || nlat.isString()) {
      continue;
    }

    ds.addCoordinateAxis(makeLonCoordAxis(ds, g2, nlon.getNumericValue().intValue(), "XDim"));
    ds.addCoordinateAxis(makeLatCoordAxis(ds, g2, nlat.getNumericValue().intValue(), "YDim"));

    for (Group g3 : g2.getGroups()) {
      for (Variable v : g3.getVariables()) {
        v.addAttribute(new Attribute(_Coordinate.Axes, "lat lon"));
      }
    }
  }

  ds.finish();
}
 

public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
  if (null != ds.findVariable("xCoord"))
    return; // check if its already been done - aggregating enhanced datasets.

  parseInfo.format("IFPS augmentDataset %n");

  // Figure out projection info. Assume the same for all variables
  VariableDS lonVar = (VariableDS) ds.findVariable("longitude");
  lonVar.setUnitsString(CDM.LON_UNITS);
  lonVar.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
  VariableDS latVar = (VariableDS) ds.findVariable("latitude");
  latVar.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
  latVar.setUnitsString(CDM.LAT_UNITS);

  projVar = latVar;
  String projName = ds.findAttValueIgnoreCase(projVar, "projectionType", null);
  if ("LAMBERT_CONFORMAL".equals(projName)) {
    Projection proj = makeLCProjection(ds);
    makeXYcoords(ds, proj, latVar, lonVar);
  }

  // figure out the time coordinate for each data variable
  // LOOK : always seperate; could try to discover if they are the same
  List<Variable> vars = ds.getVariables();
  for (Variable ncvar : vars) {
    // variables that are used but not displayable or have no data have DIM_0, also don't want history, since those
    // are just how the person edited the grids
    if ((!ncvar.getDimension(0).getShortName().equals("DIM_0")) && !ncvar.getShortName().endsWith("History")
        && (ncvar.getRank() > 2) && !ncvar.getShortName().startsWith("Tool")) {
      createTimeCoordinate(ds, ncvar);
    } else if (ncvar.getShortName().equals("Topo")) {
      // Deal with Topography variable
      ncvar.addAttribute(new Attribute(CDM.LONG_NAME, "Topography"));
      ncvar.addAttribute(new Attribute(CDM.UNITS, "ft"));
    }
  }

  ds.finish();
}
 

/**
 * Add information from the InvDataset to the NetcdfDataset.
 *
 * @param ds get info from here
 * @param ncDataset add to here
 */
public static void annotate(InvDataset ds, NetcdfDataset ncDataset) {
  ncDataset.setTitle(ds.getName());
  ncDataset.setId(ds.getID());

  // add properties as global attributes
  for (InvProperty p : ds.getProperties()) {
    String name = p.getName();
    if (null == ncDataset.findGlobalAttribute(name)) {
      ncDataset.addAttribute(null, new Attribute(name, p.getValue()));
    }
  }

  /*
   * ThreddsMetadata.GeospatialCoverage geoCoverage = ds.getGeospatialCoverage();
   * if (geoCoverage != null) {
   * if ( null != geoCoverage.getNorthSouthRange()) {
   * ncDataset.addAttribute(null, new Attribute("geospatial_lat_min", new Double(geoCoverage.getLatSouth())));
   * ncDataset.addAttribute(null, new Attribute("geospatial_lat_max", new Double(geoCoverage.getLatNorth())));
   * }
   * if ( null != geoCoverage.getEastWestRange()) {
   * ncDataset.addAttribute(null, new Attribute("geospatial_lon_min", new Double(geoCoverage.getLonWest())));
   * ncDataset.addAttribute(null, new Attribute("geospatial_lon_max", new Double(geoCoverage.getLonEast())));
   * }
   * if ( null != geoCoverage.getUpDownRange()) {
   * ncDataset.addAttribute(null, new Attribute("geospatial_vertical_min", new Double(geoCoverage.getHeightStart())));
   * ncDataset.addAttribute(null, new Attribute("geospatial_vertical_max", new Double(geoCoverage.getHeightStart() +
   * geoCoverage.getHeightExtent())));
   * }
   * }
   * 
   * DateRange timeCoverage = ds.getTimeCoverage();
   * if (timeCoverage != null) {
   * ncDataset.addAttribute(null, new Attribute("time_coverage_start",
   * timeCoverage.getStart().toDateTimeStringISO()));
   * ncDataset.addAttribute(null, new Attribute("time_coverage_end", timeCoverage.getEnd().toDateTimeStringISO()));
   * }
   */

  ncDataset.finish();
}
 

/**
 * Add information from the Dataset to the NetcdfDataset.
 *
 * @param ds get info from here
 * @param ncDataset add to here
 */
public static void annotate(Dataset ds, NetcdfDataset ncDataset) {
  ncDataset.setTitle(ds.getName());
  ncDataset.setId(ds.getId());

  // add properties as global attributes
  for (Property p : ds.getProperties()) {
    String name = p.getName();
    if (null == ncDataset.findGlobalAttribute(name)) {
      ncDataset.addAttribute(null, new Attribute(name, p.getValue()));
    }
  }

  /*
   * ThreddsMetadata.GeospatialCoverage geoCoverage = ds.getGeospatialCoverage();
   * if (geoCoverage != null) {
   * if ( null != geoCoverage.getNorthSouthRange()) {
   * ncDataset.addAttribute(null, new Attribute("geospatial_lat_min", new Double(geoCoverage.getLatSouth())));
   * ncDataset.addAttribute(null, new Attribute("geospatial_lat_max", new Double(geoCoverage.getLatNorth())));
   * }
   * if ( null != geoCoverage.getEastWestRange()) {
   * ncDataset.addAttribute(null, new Attribute("geospatial_lon_min", new Double(geoCoverage.getLonWest())));
   * ncDataset.addAttribute(null, new Attribute("geospatial_lon_max", new Double(geoCoverage.getLonEast())));
   * }
   * if ( null != geoCoverage.getUpDownRange()) {
   * ncDataset.addAttribute(null, new Attribute("geospatial_vertical_min", new Double(geoCoverage.getHeightStart())));
   * ncDataset.addAttribute(null, new Attribute("geospatial_vertical_max", new Double(geoCoverage.getHeightStart() +
   * geoCoverage.getHeightExtent())));
   * }
   * }
   * 
   * DateRange timeCoverage = ds.getTimeCoverage();
   * if (timeCoverage != null) {
   * ncDataset.addAttribute(null, new Attribute("time_coverage_start",
   * timeCoverage.getStart().toDateTimeStringISO()));
   * ncDataset.addAttribute(null, new Attribute("time_coverage_end", timeCoverage.getEnd().toDateTimeStringISO()));
   * }
   */

  ncDataset.finish();
}
 

protected TableConfig getStationAsPointConfig(NetcdfDataset ds, Formatter errlog) {
  boolean needFinish = false;

  // find lat coord
  Variable lat = CoordSysEvaluator.findCoordByType(ds, AxisType.Lat);
  if (lat == null) {
    errlog.format("GempakCdm: Must have a Latitude coordinate");
    return null;
  }

  // find lon coord
  Variable lon = CoordSysEvaluator.findCoordByType(ds, AxisType.Lon);
  if (lon == null) {
    errlog.format("GempakCdm: Must have a Longitude coordinate");
    return null;
  }

  if (lat.getRank() != lon.getRank()) {
    errlog.format("GempakCdm: Lat and Lon coordinate must have same rank");
    return null;
  }

  // check dimensions
  boolean stnIsScalar = (lat.getRank() == 0);
  boolean stnIsSingle = (lat.getRank() == 1) && (lat.getSize() == 1);
  Dimension stationDim = null;

  if (!stnIsScalar) {
    if (lat.getDimension(0) != lon.getDimension(0)) {
      errlog.format("Lat and Lon coordinate must have same size");
      return null;
    }
    stationDim = lat.getDimension(0);
  }

  // optional alt coord
  Variable alt = CoordSysEvaluator.findCoordByType(ds, AxisType.Height);

  // obs table
  VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
  if (time == null) {
    errlog.format("GempakCdm: Must have a Time coordinate");
    return null;
  }
  Dimension obsDim = time.getDimension(time.getRank() - 1); // may be time(time) or time(stn, obs)

  Table.Type obsTableType = Table.Type.Structure;
  Structure multidimStruct = Evaluator.findStructureWithDimensions(ds, stationDim, obsDim);

  if (multidimStruct == null) {
    errlog.format("GempakCdm: Cannot figure out StationAsPoint table structure");
    return null;
  }

  TableConfig obs = new TableConfig(obsTableType, obsDim.getShortName());
  obs.dimName = obsDim.getShortName();
  obs.structName = multidimStruct.getFullName();
  obs.structureType = TableConfig.StructureType.Structure;
  obs.featureType = FeatureType.POINT;

  obs.lat = lat.getFullName();
  obs.lon = lon.getFullName();
  obs.time = time.getFullName();
  if (alt != null)
    obs.elev = alt.getFullName();

  List<String> vars = new ArrayList<>(30);
  for (Variable v : ds.getVariables()) {
    if ((v.getDimension(0) == stationDim)
        && ((v.getRank() == 1) || ((v.getRank() == 2) && (v.getDataType() == DataType.CHAR))))
      vars.add(v.getShortName());
  }

  StructureDS s = new StructurePseudoDS(ds, null, "stnStruct", vars, stationDim);
  obs.addJoin(new JoinMuiltdimStructure(s, obsDim.getLength()));
  obs.addJoin(new JoinArray(time, JoinArray.Type.modulo, obsDim.getLength()));

  if (needFinish)
    ds.finish();
  return obs;
}