Examples of com.thoughtworks.xstream.io.binary.ReaderDepthState$Attribute

Package com.thoughtworks.xstream.io.binary

Examples of com.thoughtworks.xstream.io.binary.ReaderDepthState$Attribute

ucar.nc2.Attribute
Maintains the state of a pull reader at various states in the document depth. Used by the {@link BinaryStreamReader} @author Joe Walnes @since 1.2

  public Nimbus() {
    this.conventionName = "NCAR-RAF/nimbus";
  }


  public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
    ds.addAttribute(null, new Attribute("cdm_data_type", ucar.nc2.constants.FeatureType.TRAJECTORY.name()));


    if (!setAxisType(ds, "LATC", AxisType.Lat))
      if (!setAxisType(ds, "LAT", AxisType.Lat))
        setAxisType(ds, "GGLAT", AxisType.Lat);


    if (!setAxisType(ds, "LONC", AxisType.Lon))
      if (!setAxisType(ds, "LON", AxisType.Lon))
        setAxisType(ds, "GGLON", AxisType.Lon);


    if (!setAxisType(ds, "PALT", AxisType.Height))
      setAxisType(ds, "GGALT", AxisType.Height);


    boolean hasTime = setAxisType(ds, "Time", AxisType.Time);
    if (!hasTime)
      hasTime = setAxisType(ds, "time", AxisType.Time);


    // do we need to version this ?
    // String version =  ds.findAttValueIgnoreCase(null, "version", null);


    if (!hasTime) {
      Variable time = ds.findVariable("time_offset");
      if (time != null) {
        Variable base = ds.findVariable("base_time");
        int base_time = base.readScalarInt();
        try {
          DateUnit dunit = new DateUnit("seconds since 1970-01-01 00:00");
          String time_units = "seconds since " + dunit.makeStandardDateString(base_time);
          time.addAttribute(new Attribute("units", time_units));
          time.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.name()));
        } catch (Exception e) {
          e.printStackTrace();
        }
      }
    }


    // look for coordinates
    String coordinates = ds.findAttValueIgnoreCase(null, "coordinates", null);
    if (coordinates != null) {
      String[] vars = coordinates.split(" ");
      for (String vname : vars) {
        Variable v = ds.findVariable(vname);
        if (v != null) {
          AxisType atype = getAxisType(ds, (VariableEnhanced) v);
          if (atype != null)
            v.addAttribute(new Attribute(_Coordinate.AxisType, atype.name()));
        }
      }
    }


  }

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  private boolean setAxisType(NetcdfDataset ds, String varName, AxisType atype) {
    Variable v = ds.findVariable(varName);
    if (v == null) return false;


    v.addAttribute(new Attribute(_Coordinate.AxisType, atype.toString()));
    return true;
  }

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   * @param attname name of variable
   * @param defValue default value if attribute is not found
   * @return attribute value as a double, else NaN if not found
   */
  protected double readAttributeDouble(Variable v, String attname, double defValue) {
    Attribute att = v.findAttributeIgnoreCase(attname);
    if (att == null) return defValue;
    if (att.isString())
      return Double.parseDouble(att.getStringValue());
    else
      return att.getNumericValue().doubleValue();
  }

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  public CoordinateTransform makeCoordinateTransform(NetcdfDataset ds, Variable ctv) {
    int zone = (int) readAttributeDouble( ctv, "utm_zone_number", Double.NaN);
    boolean isNorth = zone > 0;
    zone = Math.abs(zone);


    Attribute a;
    double axis = 0.0, f = 0.0;
    if (null != (a = ctv.findAttribute( "semimajor_axis")))
      axis = a.getNumericValue().doubleValue();
    if (null != (a = ctv.findAttribute( "inverse_flattening")))
      f = a.getNumericValue().doubleValue();


    // double a, double f, int zone, boolean isNorth
    UtmProjection proj = (axis != 0.0) ? new UtmProjection(axis, f, zone, isNorth) : new UtmProjection(zone, isNorth);
    return new ProjectionCT(ctv.getShortName(), "FGDC", proj);
  }

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    addAxisType( v, a);
    return true;
  }


  private void addAxisType(Variable v, AxisType a) {
    v.addAttribute( new Attribute(_Coordinate.AxisType, a.toString()));
  }

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  static public VariableDS makeDummyTransformVariable(NetcdfDataset ds, CoordinateTransform ct) {
    VariableDS v = new VariableDS( ds, null, null, ct.getName(), DataType.CHAR, "", null, null);
    List<Parameter> params = ct.getParameters();
    for (Parameter p : params) {
      if (p.isString())
        v.addAttribute(new Attribute(p.getName(), p.getStringValue()));
      else {
        double[] data = p.getNumericValues();
        Array dataA = Array.factory(double.class, new int[]{data.length}, data);
        v.addAttribute(new Attribute(p.getName(), dataA));
      }
    }
    v.addAttribute( new Attribute(_Coordinate.TransformType, ct.getTransformType().toString()));


    // fake data
    Array data = Array.factory(DataType.CHAR.getPrimitiveClassType(), new int[] {}, new char[] {' '});
    v.setCachedData(data, true);

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            makeVariable( ncfile, ray0.getDatatypeName(key),ray0.getDatatypeName(key) , key, group);
        }






        ncfile.addAttribute(null, new Attribute("Conventions", _Coordinate.Convention));
        ncfile.addAttribute(null, new Attribute("format", headerParser.getDataFormat()));
        ncfile.addAttribute(null, new Attribute("cdm_data_type", FeatureType.RADIAL.toString()));
        //Date d = Cinrad2Record.getDate(volScan.getTitleJulianDays(), volScan.getTitleMsecs());
        //ncfile.addAttribute(null, new Attribute("base_date", formatter.toDateOnlyString(d)));
        ncfile.addAttribute(null, new Attribute("StationLatitude", new Double(headerParser.getStationLatitude())));
        ncfile.addAttribute(null, new Attribute("StationLongitude", new Double(headerParser.getStationLongitude())));
        ncfile.addAttribute(null, new Attribute("StationElevationInMeters", new Double(headerParser.getStationElevation())));
        ncfile.addAttribute(null, new Attribute("time_coverage_start", formatter.toDateTimeStringISO(headerParser.getStartDate())));; //.toDateTimeStringISO(d)));
        ncfile.addAttribute(null, new Attribute("time_coverage_end", formatter.toDateTimeStringISO(headerParser.getEndDate())));
        double latRadiusDegrees = Math.toDegrees( radarRadius / ucar.unidata.geoloc.Earth.getRadius());
        ncfile.addAttribute(null, new Attribute("geospatial_lat_min", new Double(headerParser.getStationLatitude() - latRadiusDegrees)));
        ncfile.addAttribute(null, new Attribute("geospatial_lat_max", new Double(headerParser.getStationLatitude() + latRadiusDegrees)));
        double cosLat = Math.cos( Math.toRadians(headerParser.getStationLatitude()));
        double lonRadiusDegrees = Math.toDegrees( radarRadius / cosLat / ucar.unidata.geoloc.Earth.getRadius());
        ncfile.addAttribute(null, new Attribute("geospatial_lon_min", new Double(headerParser.getStationLongitude() - lonRadiusDegrees)));
        ncfile.addAttribute(null, new Attribute("geospatial_lon_max", new Double(headerParser.getStationLongitude() + lonRadiusDegrees)));
        ncfile.addAttribute(null, new Attribute("history", "Direct read of Nexrad Level 2 file into NetCDF-Java 2.2 API"));
        ncfile.addAttribute(null, new Attribute("DataType", "Radial"));


        ncfile.addAttribute(null, new Attribute("Title", "Nexrad Level 2 Station "+headerParser.getStationId()+" from "+
            formatter.toDateTimeStringISO(headerParser.getStartDate()) + " to " +
            formatter.toDateTimeStringISO(headerParser.getEndDate())));


        ncfile.addAttribute(null, new Attribute("Summary", "Weather Surveillance Radar-1988 Doppler (WSR-88D) "+
            "Level II data are the three meteorological base data quantities: reflectivity, mean radial velocity, and "+
            "spectrum width."));


        ncfile.addAttribute(null, new Attribute("keywords", "WSR-88D; NEXRAD; Radar Level II; reflectivity; mean radial velocity; spectrum width"));
        ncfile.addAttribute(null, new Attribute("SweepMode", new Short(headerParser.getSweepMode())));


       // ncfile.addAttribute(null, new Attribute("VolumeCoveragePattern", new Integer(headerParser.getVCP())));
       // ncfile.addAttribute(null, new Attribute("HorizonatalBeamWidthInDegrees", new Double(headerParser.getHorizontalBeamWidth(abbrev))));


        ncfile.finish();

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        Variable v = new Variable(ncfile, null, null, shortName+abbrev);
        v.setDataType(DataType.SHORT);
        v.setDimensions(dims);
        ncfile.addVariable(null, v);


        v.addAttribute( new Attribute("units", firstRay.getDatatypeUnits(abbrev)));
        v.addAttribute( new Attribute("long_name", longName));
        v.addAttribute( new Attribute("abbrev", abbrev));
        v.addAttribute( new Attribute("missing_value", firstRay.getMissingData()));
        v.addAttribute( new Attribute("signal_below_threshold", firstRay.getDatatypeRangeFoldingThreshhold(abbrev)));
        v.addAttribute( new Attribute("scale_factor", firstRay.getDatatypeScaleFactor(abbrev)));
        v.addAttribute( new Attribute("add_offset", firstRay.getDatatypeAddOffset(abbrev)));
       // v.addAttribute( new Attribute("_Unsigned", "false"));


        v.addAttribute( new Attribute("range_folding_threshold" ,firstRay.getDatatypeRangeFoldingThreshhold(abbrev)));


        List<Dimension> dim2 = new ArrayList<Dimension>();
        dim2.add( scanDim);
        dim2.add( radialDim);


        // add time coordinate variable
        String timeCoordName = "time"+abbrev;
        Variable timeVar = new Variable(ncfile, null, null, timeCoordName);
        timeVar.setDataType(DataType.INT);
        timeVar.setDimensions(dim2);
        ncfile.addVariable(null, timeVar);




        // int julianDays = volScan.getTitleJulianDays();
        // Date d = Level2Record.getDate( julianDays, 0);
        Date d = firstRay.getDate();
        String units = "msecs since "+formatter.toDateTimeStringISO(d);


        timeVar.addAttribute( new Attribute("long_name", "time since base date"));
        timeVar.addAttribute( new Attribute("units", units));
        timeVar.addAttribute( new Attribute("missing_value", firstRay.getMissingData()));
        timeVar.addAttribute( new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));


        // add elevation coordinate variable
        String elevCoordName = "elevation"+abbrev;
        Variable elevVar = new Variable(ncfile, null, null, elevCoordName);
        elevVar.setDataType(DataType.FLOAT);
        elevVar.setDimensions(dim2);
        ncfile.addVariable(null, elevVar);


        elevVar.addAttribute( new Attribute("units", "degrees"));
        elevVar.addAttribute( new Attribute("long_name", "elevation angle in degres: 0 = parallel to pedestal base, 90 = perpendicular"));
        elevVar.addAttribute( new Attribute("missing_value", firstRay.getMissingData()));
        elevVar.addAttribute( new Attribute(_Coordinate.AxisType, AxisType.RadialElevation.toString()));


        // add azimuth coordinate variable
        String aziCoordName = "azimuth"+abbrev;
        Variable aziVar = new Variable(ncfile, null, null, aziCoordName);
        aziVar.setDataType(DataType.FLOAT);
        aziVar.setDimensions(dim2);
        ncfile.addVariable(null, aziVar);


        aziVar.addAttribute( new Attribute("units", "degrees"));
        aziVar.addAttribute( new Attribute("long_name", "azimuth angle in degrees: 0 = true north, 90 = east"));
        aziVar.addAttribute( new Attribute("missing_value", firstRay.getMissingData()));
        aziVar.addAttribute( new Attribute(_Coordinate.AxisType, AxisType.RadialAzimuth.toString()));


        // add gate coordinate variable
        String gateCoordName = "distance"+abbrev;
        Variable gateVar = new Variable(ncfile, null, null, gateCoordName);
        gateVar.setDataType(DataType.FLOAT);
        gateVar.setDimensions(gateDimName);
        Array data = Array.makeArray( DataType.FLOAT, ngates,
            (double) firstRay.getGateStart(abbrev), (double) firstRay.getGateSize(abbrev));
        gateVar.setCachedData( data, false);
        ncfile.addVariable(null, gateVar);
  //      radarRadius = firstRay.getGateStart(datatype) + ngates * firstRay.getGateSize(datatype);


        gateVar.addAttribute( new Attribute("units", "m"));
        gateVar.addAttribute( new Attribute("long_name", "radial distance to start of gate"));
        gateVar.addAttribute( new Attribute(_Coordinate.AxisType, AxisType.RadialDistance.toString()));


        // add number of radials variable
        String nradialsName = "numRadials"+abbrev;
        Variable nradialsVar = new Variable(ncfile, null, null, nradialsName);
        nradialsVar.setDataType(DataType.INT);
        nradialsVar.setDimensions(scanDim.getName());
        nradialsVar.addAttribute( new Attribute("long_name", "number of valid radials in this scan"));
        ncfile.addVariable(null, nradialsVar);


        // add number of gates variable
        String ngateName = "numGates"+abbrev;
        Variable ngateVar = new Variable(ncfile, null, null, ngateName);
        ngateVar.setDataType(DataType.INT);
        ngateVar.setDimensions(scanDim.getName());
        ngateVar.addAttribute( new Attribute("long_name", "number of valid gates in this scan"));
        ncfile.addVariable(null, ngateVar);


        makeCoordinateDataWithMissing(abbrev, timeVar, elevVar, aziVar, nradialsVar, ngateVar, groups);


        // back to the data variable
        String coordinates = timeCoordName+" "+elevCoordName +" "+ aziCoordName+" "+gateCoordName;
        v.addAttribute( new Attribute(_Coordinate.Axes, coordinates));


        // make the ray map
        int nradials = radialDim.getLength();
        Ray[][] map = new Ray[nscans][nradials];
        for (int i = 0; i < groups.size(); i++) {

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        String   timeCoordName = "time";
        Variable taxis         = new Variable(ncfile, null, null, timeCoordName);


        taxis.setDataType(DataType.DOUBLE);
        taxis.setDimensions("time");
        taxis.addAttribute(new Attribute("long_name", "time since base date"));
        taxis.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));


        double[] tdata = new double[1];


        tdata[0] = dd.getTime();


        Array dataT = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { 1 }, tdata);


        taxis.setCachedData(dataT, false);


        DateFormatter formatter = new DateFormatter();


        taxis.addAttribute(new Attribute("units", "msecs since " + formatter.toDateTimeStringISO(new Date(0))));
        ncfile.addVariable(null, taxis);
        dims.add(dimT);


        Dimension jDim = new Dimension("y", numY, true, false, false);
        Dimension iDim = new Dimension("x", numX, true, false, false);


        dims.add(jDim);
        dims.add(iDim);
        ncfile.addDimension(null, iDim);
        ncfile.addDimension(null, jDim);
        ncfile.addAttribute(null, new Attribute("cdm_data_type", FeatureType.GRID.toString()));


        String   coordinates = "time y x";
        Variable v           = new Variable(ncfile, null, null, cname);


        v.setDataType(DataType.BYTE);
        v.setDimensions(dims);
        ncfile.addVariable(null, v);
        v.addAttribute(new Attribute("long_name", ctitle));
        v.addAttribute(new Attribute("units", cunit));
        v.setSPobject(new Vinfo(numX, numY, hoff, false));
        v.addAttribute(new Attribute(_Coordinate.Axes, coordinates));


        // create coordinate variables
        Variable xaxis = new Variable(ncfile, null, null, "x");


        xaxis.setDataType(DataType.DOUBLE);
        xaxis.setDimensions("x");
        xaxis.addAttribute(new Attribute("standard_name", "projection x coordinate"));
        xaxis.addAttribute(new Attribute("units", "km"));
        xaxis.addAttribute(new Attribute(_Coordinate.AxisType, "GeoX"));


        double[]       data1      = new double[numX];
        ProjectionImpl projection = new LambertConformal(clat, clon, lat1, lat2);
        double ullat = 51.8294;
        double ullon = -135.8736;
        double lrlat = 17.2454;
        double lrlon = -70.1154;


        ProjectionPointImpl ptul = (ProjectionPointImpl) projection.latLonToProj(new LatLonPointImpl(ullat, ullon));
        ProjectionPointImpl ptlr = (ProjectionPointImpl) projection.latLonToProj(new LatLonPointImpl(lrlat, lrlon));
        ProjectionPointImpl ptc = (ProjectionPointImpl) projection.latLonToProj(new LatLonPointImpl(clat, clon));
        double startX = ptul.getX();
        double startY = ptlr.getY();
        double dx = (ptlr.getX() - ptul.getX())/(numX-1);
        for (int i = 0; i < numX; i++) {
            data1[i] = startX + i*dx;
        }


        Array dataA = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { numX }, data1);


        xaxis.setCachedData(dataA, false);
        ncfile.addVariable(null, xaxis);


        Variable yaxis = new Variable(ncfile, null, null, "y");


        yaxis.setDataType(DataType.DOUBLE);
        yaxis.setDimensions("y");
        yaxis.addAttribute(new Attribute("standard_name", "projection y coordinate"));
        yaxis.addAttribute(new Attribute("units", "km"));
        yaxis.addAttribute(new Attribute(_Coordinate.AxisType, "GeoY"));
        data1 = new double[numY];
        double dy = (ptul.getY() - ptlr.getY())/(numY-1);


        for (int i = 0; i < numY; i++) {
            data1[i] = startY + i*dy;
        }


        dataA = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { numY }, data1);
        yaxis.setCachedData(dataA, false);
        ncfile.addVariable(null, yaxis);


        // projection
        // lower left and upper right corner lat/lons
        // modified cylind. equidistant or  CED with lat/lon ration != 1
        Variable ct = new Variable(ncfile, null, null, projection.getClassName());


        ct.setDataType(DataType.CHAR);
        ct.setDimensions("");


        List params = projection.getProjectionParameters();


        for (int i = 0; i < params.size(); i++) {
            Parameter p = (Parameter) params.get(i);


            ct.addAttribute(new Attribute(p));
        }


        ct.addAttribute(new Attribute(_Coordinate.TransformType, "Projection"));
        //ct.addAttribute(new Attribute(_Coordinate.Axes, "lat lon"));
        ct.addAttribute( new Attribute(_Coordinate.Axes, "x y "));
        // fake data
        dataA = Array.factory(DataType.CHAR.getPrimitiveClassType(), new int[] {});
        dataA.setChar(dataA.getIndex(), ' ');
        ct.setCachedData(dataA, false);
        ncfile.addVariable(null, ct);

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        String   timeCoordName = "time";
        Variable taxis         = new Variable(ncfile, null, null, timeCoordName);


        taxis.setDataType(DataType.DOUBLE);
        taxis.setDimensions("time");
        taxis.addAttribute(new Attribute("long_name", "time since base date"));
        taxis.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));


        double[] tdata = new double[1];


        tdata[0] = dd.getTime();


        Array dataT = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { 1 }, tdata);


        taxis.setCachedData(dataT, false);


        DateFormatter formatter = new DateFormatter();


        taxis.addAttribute(new Attribute("units", "msecs since " + formatter.toDateTimeStringISO(new Date(0))));
        ncfile.addVariable(null, taxis);
        dims.add(dimT);


        Dimension jDim = new Dimension("lat", numY, true, false, false);
        Dimension iDim = new Dimension("lon", numX, true, false, false);


        dims.add(jDim);
        dims.add(iDim);
        ncfile.addDimension(null, iDim);
        ncfile.addDimension(null, jDim);
        ncfile.addAttribute(null, new Attribute("cdm_data_type", FeatureType.GRID.toString()));


        String   coordinates = "time lat lon";
        Variable v           = new Variable(ncfile, null, null, cname);


        v.setDataType(DataType.BYTE);
        v.setDimensions(dims);
        ncfile.addVariable(null, v);
        v.addAttribute(new Attribute("long_name", ctitle));
        v.addAttribute(new Attribute("units", cunit));
        v.setSPobject(new Vinfo(numX, numY, hoff, false));
        v.addAttribute(new Attribute(_Coordinate.Axes, coordinates));


        // create coordinate variables
        Variable xaxis = new Variable(ncfile, null, null, "lon");
        xaxis.setDataType(DataType.DOUBLE);
        xaxis.setDimensions("lon");
        xaxis.addAttribute(new Attribute("long_name", "longitude"));
        xaxis.addAttribute(new Attribute("units", "degree"));
        xaxis.addAttribute(new Attribute(_Coordinate.AxisType, "Lon"));


        double[] data1 = new double[numX];


        for (int i = 0; i < numX; i++) {
            data1[i] = (double) (rlon1 + i * dlon);
        }


        Array dataA = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { numX }, data1);


        xaxis.setCachedData(dataA, false);
        ncfile.addVariable(null, xaxis);


        Variable yaxis = new Variable(ncfile, null, null, "lat");
        yaxis.setDataType(DataType.DOUBLE);
        yaxis.setDimensions("lat");
        yaxis.addAttribute(new Attribute("long_name", "latitude"));
        yaxis.addAttribute(new Attribute("units", "degree"));
        yaxis.addAttribute(new Attribute(_Coordinate.AxisType, "Lat"));
        data1 = new double[numY];


        for (int i = 0; i < numY; i++) {
            data1[i] = rlat1 + i * dlat;
        }

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