// @todo Make sure units are meters
 public Array getElevation(Range range) throws IOException, InvalidRangeException {
   List section = new ArrayList(1);
   section.add(range);
   Array a = elevVar.read(section);
   if (elevVarUnitsConversionFactor == 1.0) return (a);
   for (IndexIterator it = a.getIndexIterator(); it.hasNext(); ) {
     if (elevVar.getDataType() == DataType.DOUBLE) {
       double val = it.getDoubleNext();
       it.setDoubleCurrent(val * elevVarUnitsConversionFactor);
     } else if (elevVar.getDataType() == DataType.FLOAT) {
       float val = it.getFloatNext();
       it.setFloatCurrent((float) (val * elevVarUnitsConversionFactor));
     } else if (elevVar.getDataType() == DataType.INT) {
       int val = it.getIntNext();
       it.setIntCurrent((int) (val * elevVarUnitsConversionFactor));
     } else if (elevVar.getDataType() == DataType.LONG) {
       long val = it.getLongNext();
       it.setLongCurrent((long) (val * elevVarUnitsConversionFactor));
     } else {
       throw new IllegalStateException(
           "Elevation variable type <"
               + elevVar.getDataType().toString()
               + "> not double, float, int, or long.");
     }
   }
   return (a);
 }
  private void createProfiles(int nprofiles) throws IOException {
    this.nprofiles = nprofiles;

    // add the dimensions
    Dimension profileDim = ncfile.addDimension(profileDimName, nprofiles);
    profileDims.add(profileDim);

    Variable v = ncfile.addVariable(numObsName, DataType.INT, profileDimName);
    ncfile.addVariableAttribute(
        v, new Attribute("long_name", "number of children in linked list for this profile"));

    v = ncfile.addVariable(numProfilesTotalName, DataType.INT, "");
    ncfile.addVariableAttribute(v, new Attribute("long_name", "number of valid profiles"));

    v = ncfile.addVariable(firstObsName, DataType.INT, profileDimName);
    ncfile.addVariableAttribute(
        v,
        new Attribute("long_name", "record number of first obs in linked list for this profile"));

    // time variable
    Variable timeVar = ncfile.addStringVariable(timeName, profileDims, 20);
    ncfile.addVariableAttribute(
        timeVar, new Attribute("long_name", "ISO-8601 Date - time of observation"));

    v = ncfile.addVariable(parentStationIndex, DataType.INT, profileDimName);
    ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent station"));

    v = ncfile.addVariable(nextProfileName, DataType.INT, profileDimName);
    ncfile.addVariableAttribute(
        v, new Attribute("long_name", "index of next profile in linked list for this station"));
  }
  /**
   * Create a new GridVertCoord for a layer
   *
   * @param record layer record
   * @param levelName name of this level
   * @param lookup lookup table
   * @param level1 level 1
   * @param level2 level 2
   */
  GridVertCoord(
      GridRecord record,
      String levelName,
      GridTableLookup lookup,
      double[] level1,
      double[] level2) {
    this.typicalRecord = record;
    this.levelName = levelName;
    this.lookup = lookup;

    // dontUseVertical    = !lookup.isVerticalCoordinate(record);
    positive = lookup.isPositiveUp(record) ? "up" : "down";
    units = lookup.getLevelUnit(record);
    usesBounds = lookup.isLayer(this.typicalRecord);

    levels = new ArrayList<LevelCoord>(level1.length);
    for (int i = 0; i < level1.length; i++) {
      levels.add(new LevelCoord(level1[i], (level2 == null) ? 0.0 : level2[i]));
    }

    Collections.sort(levels);
    if (positive.equals("down")) {
      Collections.reverse(levels);
    }
    dontUseVertical = (levels.size() == 1);
  }
 public Array getData(Range range, String parameterName)
     throws IOException, InvalidRangeException {
   Variable variable = ncfile.getRootGroup().findVariable(parameterName);
   int varRank = variable.getRank();
   int[] varShape = variable.getShape();
   List section = new ArrayList(varRank);
   section.add(range);
   for (int i = 1; i < varRank; i++) {
     section.add(new Range(0, varShape[i] - 1));
   }
   Array array = variable.read(section);
   if (array.getShape()[0] == 1) {
     return (array.reduce(0));
   } else {
     return (array);
   }
   // return( array.getShape()[0] == 1 ? array.reduce( 0 ) : array);
 }
Example #5
0
  /**
   * Constructor.
   *
   * @param dataset belongs to this dataset
   * @param dsvar wraps this Variable
   * @param gcs has this grid coordinate system
   */
  public GeoGrid(GridDataset dataset, VariableDS dsvar, GridCoordSys gcs) {
    this.dataset = dataset;
    this.vs = dsvar;
    this.gcs = gcs;

    CoordinateAxis xaxis = gcs.getXHorizAxis();
    if (xaxis instanceof CoordinateAxis1D) {
      xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0));
      yDimOrgIndex = findDimension(gcs.getYHorizAxis().getDimension(0));

    } else { // 2D case
      yDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0));
      xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(1));
    }

    if (gcs.getVerticalAxis() != null)
      zDimOrgIndex = findDimension(gcs.getVerticalAxis().getDimension(0));
    if (gcs.getTimeAxis() != null) {
      if (gcs.getTimeAxis1D() != null)
        tDimOrgIndex = findDimension(gcs.getTimeAxis1D().getDimension(0));
      else tDimOrgIndex = findDimension(gcs.getTimeAxis().getDimension(1));
    }
    if (gcs.getEnsembleAxis() != null)
      eDimOrgIndex = findDimension(gcs.getEnsembleAxis().getDimension(0));
    if (gcs.getRunTimeAxis() != null)
      rtDimOrgIndex = findDimension(gcs.getRunTimeAxis().getDimension(0));

    // construct canonical dimension list
    int count = 0;
    this.mydims = new ArrayList<Dimension>();
    if ((rtDimOrgIndex >= 0) && (rtDimOrgIndex != tDimOrgIndex)) {
      mydims.add(dsvar.getDimension(rtDimOrgIndex));
      rtDimNewIndex = count++;
    }
    if (eDimOrgIndex >= 0) {
      mydims.add(dsvar.getDimension(eDimOrgIndex));
      eDimNewIndex = count++;
    }
    if (tDimOrgIndex >= 0) {
      mydims.add(dsvar.getDimension(tDimOrgIndex));
      tDimNewIndex = count++;
    }
    if (zDimOrgIndex >= 0) {
      mydims.add(dsvar.getDimension(zDimOrgIndex));
      zDimNewIndex = count++;
    }
    if (yDimOrgIndex >= 0) {
      mydims.add(dsvar.getDimension(yDimOrgIndex));
      yDimNewIndex = count++;
    }
    if (xDimOrgIndex >= 0) {
      mydims.add(dsvar.getDimension(xDimOrgIndex));
      xDimNewIndex = count;
    }
  }
  /**
   * Match levels
   *
   * @param records records to match
   * @return true if they have the same levels
   */
  boolean matchLevels(List<GridRecord> records) {

    // first create a new list
    List<LevelCoord> levelList = new ArrayList<LevelCoord>(records.size());
    for (GridRecord record : records) {
      LevelCoord lc = new LevelCoord(record.getLevel1(), record.getLevel2());
      if (!levelList.contains(lc)) {
        levelList.add(lc);
      }
    }

    Collections.sort(levelList);
    if (positive.equals("down")) {
      Collections.reverse(levelList);
    }

    // gotta equal existing list
    return levelList.equals(levels);
  }
  private void writeHeader(ProfileFeature profile, PointFeature obs) throws IOException {

    Formatter coordNames = new Formatter().format("%s %s %s", profileTimeName, latName, lonName);
    List<VariableSimpleIF> 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<VariableSimpleIF> 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);
    }
  }
  /**
   * Add levels
   *
   * @param records GridRecords, one for each level
   */
  void addLevels(List<GridRecord> records) {
    for (int i = 0; i < records.size(); i++) {
      GridRecord record = records.get(i);

      if (coordIndex(record) < 0) {
        levels.add(new LevelCoord(record.getLevel1(), record.getLevel2()));
        if (dontUseVertical && (levels.size() > 1)) {
          if (GridServiceProvider.debugVert) {
            logger.warn(
                "GribCoordSys: unused level coordinate has > 1 levels = "
                    + levelName
                    + " "
                    + record.getLevelType1()
                    + " "
                    + levels.size());
          }
        }
      }
    }
    Collections.sort(levels);
    if (positive.equals("down")) {
      Collections.reverse(levels);
    }
  }
  public static void main(String args[]) throws Exception {
    long start = System.currentTimeMillis();
    Map<String, ucar.unidata.geoloc.Station> staHash =
        new HashMap<String, ucar.unidata.geoloc.Station>();

    String location = "R:/testdata/sounding/netcdf/Upperair_20070401_0000.nc";
    NetcdfDataset ncfile = NetcdfDataset.openDataset(location);
    ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);

    // look through record varibles, for those that have "manLevel" dimension
    // make a StructureData object for those
    StructureMembers sm = new StructureMembers("manLevel");
    Dimension manDim = ncfile.findDimension("manLevel");
    Structure record = (Structure) ncfile.findVariable("record");
    List<Variable> allList = record.getVariables();
    List<VariableSimpleIF> varList = new ArrayList<VariableSimpleIF>();
    for (Variable v : allList) {
      if ((v.getRank() == 1) && v.getDimension(0).equals(manDim)) {
        // public VariableDS(NetcdfDataset ds, Group group, Structure parentStructure, String
        // shortName, DataType dataType,
        // String dims, String units, String desc) {
        varList.add(
            new VariableDS(
                ncfile,
                null,
                null,
                v.getShortName(),
                v.getDataType(),
                "",
                v.getUnitsString(),
                v.getDescription()));
        // (String name, String desc, String units, DataType dtype, int []shape)
        sm.addMember(
            v.getShortName(),
            v.getDescription(),
            v.getUnitsString(),
            v.getDataType(),
            new int[0]); // scalar
      }
    }

    ArrayStructureMA manAS = new ArrayStructureMA(sm, new int[] {manDim.getLength()});

    // need the date units
    Variable time = ncfile.findVariable("synTime");
    String timeUnits = ncfile.findAttValueIgnoreCase(time, "units", null);
    timeUnits = StringUtil.remove(timeUnits, '('); // crappy fsl'ism
    timeUnits = StringUtil.remove(timeUnits, ')');
    DateUnit timeUnit = new DateUnit(timeUnits);

    // extract stations
    int nrecs = 0;
    StructureDataIterator iter = record.getStructureIterator();
    while (iter.hasNext()) {
      StructureData sdata = iter.next();
      String name = sdata.getScalarString("staName");
      ucar.unidata.geoloc.Station s = staHash.get(name);
      if (s == null) {
        float lat = sdata.convertScalarFloat("staLat");
        float lon = sdata.convertScalarFloat("staLon");
        float elev = sdata.convertScalarFloat("staElev");
        s = new StationImpl(name, "", lat, lon, elev);
        staHash.put(name, s);
      }
      nrecs++;
    }
    List<ucar.unidata.geoloc.Station> stnList =
        Arrays.asList(staHash.values().toArray(new ucar.unidata.geoloc.Station[staHash.size()]));
    Collections.sort(stnList);

    // create the writer
    WriterProfileObsDataset writer =
        new WriterProfileObsDataset(location + ".out", "rewrite " + location);
    writer.writeHeader(stnList, varList, nrecs, "prMan");

    // extract records
    iter = record.getStructureIterator();
    while (iter.hasNext()) {
      StructureData sdata = iter.next();
      String name = sdata.getScalarString("staName");
      double timeValue = sdata.convertScalarDouble("synTime");
      Date date = timeUnit.makeDate(timeValue);

      // transfer to the ArrayStructure
      List<String> names = sm.getMemberNames();
      for (String mname : names) {
        manAS.setMemberArray(mname, sdata.getArray(mname));
      }

      // each level is weritten as a seperate structure
      int numMand = sdata.getScalarInt("numMand");
      if (numMand >= manDim.getLength()) continue;

      for (int i = 0; i < numMand; i++) {
        StructureData useData = manAS.getStructureData(i);
        writer.writeRecord(name, date, useData);
      }
    }

    writer.finish();

    long took = System.currentTimeMillis() - start;
    System.out.println("That took = " + took);
  }
  private void createStations(List<ucar.unidata.geoloc.Station> stnList) throws IOException {
    int nstns = stnList.size();

    // see if there's altitude, wmoId for any stations
    for (int i = 0; i < nstns; i++) {
      ucar.unidata.geoloc.Station stn = stnList.get(i);

      // if (!Double.isNaN(stn.getAltitude()))
      //  useAlt = true;
      if ((stn.getWmoId() != null) && (stn.getWmoId().trim().length() > 0)) useWmoId = true;
    }

    /* if (useAlt)
    ncfile.addGlobalAttribute("altitude_coordinate", altName); */

    // find string lengths
    for (int i = 0; i < nstns; i++) {
      ucar.unidata.geoloc.Station station = stnList.get(i);
      name_strlen = Math.max(name_strlen, station.getName().length());
      desc_strlen = Math.max(desc_strlen, station.getDescription().length());
      if (useWmoId) wmo_strlen = Math.max(wmo_strlen, station.getName().length());
    }

    LatLonRect llbb = getBoundingBox(stnList);
    ncfile.addGlobalAttribute(
        "geospatial_lat_min", Double.toString(llbb.getLowerLeftPoint().getLatitude()));
    ncfile.addGlobalAttribute(
        "geospatial_lat_max", Double.toString(llbb.getUpperRightPoint().getLatitude()));
    ncfile.addGlobalAttribute(
        "geospatial_lon_min", Double.toString(llbb.getLowerLeftPoint().getLongitude()));
    ncfile.addGlobalAttribute(
        "geospatial_lon_max", Double.toString(llbb.getUpperRightPoint().getLongitude()));

    // add the dimensions
    Dimension recordDim = ncfile.addUnlimitedDimension(recordDimName);
    recordDims.add(recordDim);

    Dimension stationDim = ncfile.addDimension(stationDimName, nstns);
    stationDims.add(stationDim);

    // add the station Variables using the station dimension
    Variable v = ncfile.addVariable(latName, DataType.DOUBLE, stationDimName);
    ncfile.addVariableAttribute(v, new Attribute("units", "degrees_north"));
    ncfile.addVariableAttribute(v, new Attribute("long_name", "station latitude"));

    v = ncfile.addVariable(lonName, DataType.DOUBLE, stationDimName);
    ncfile.addVariableAttribute(v, new Attribute("units", "degrees_east"));
    ncfile.addVariableAttribute(v, new Attribute("long_name", "station longitude"));

    if (useAlt) {
      v = ncfile.addVariable(altName, DataType.DOUBLE, stationDimName);
      ncfile.addVariableAttribute(v, new Attribute("units", "meters"));
      ncfile.addVariableAttribute(v, new Attribute("long_name", "station altitude"));
    }

    v = ncfile.addStringVariable(idName, stationDims, name_strlen);
    ncfile.addVariableAttribute(v, new Attribute("long_name", "station identifier"));

    v = ncfile.addStringVariable(descName, stationDims, desc_strlen);
    ncfile.addVariableAttribute(v, new Attribute("long_name", "station description"));

    if (useWmoId) {
      v = ncfile.addStringVariable(wmoName, stationDims, wmo_strlen);
      ncfile.addVariableAttribute(v, new Attribute("long_name", "station WMO id"));
    }

    v = ncfile.addVariable(numProfilesName, DataType.INT, stationDimName);
    ncfile.addVariableAttribute(
        v, new Attribute("long_name", "number of profiles in linked list for this station"));

    v = ncfile.addVariable(firstProfileName, DataType.INT, stationDimName);
    ncfile.addVariableAttribute(
        v, new Attribute("long_name", "index of first profile in linked list for this station"));
  }
 // @todo Make sure units are degrees_east
 public Array getLongitude(Range range) throws IOException, InvalidRangeException {
   List section = new ArrayList(1);
   section.add(range);
   return (lonVar.read(section));
 }
 public List getTrajectories() // throws IOException;
     {
   List l = new ArrayList();
   l.add(trajectory);
   return (l);
 }
 public List getTrajectoryIds() {
   List l = new ArrayList();
   l.add(trajectoryId);
   return (l);
 }