public void writeHeader(
      List<ucar.unidata.geoloc.Station> stns,
      List<VariableSimpleIF> vars,
      int nprofiles,
      String altVarName)
      throws IOException {
    createGlobalAttributes();
    createStations(stns);
    createProfiles(nprofiles);

    // dummys, update in finish()
    ncfile.addGlobalAttribute("zaxis_coordinate", altVarName);
    ncfile.addGlobalAttribute("time_coverage_start", dateFormatter.toDateTimeStringISO(new Date()));
    ncfile.addGlobalAttribute("time_coverage_end", dateFormatter.toDateTimeStringISO(new Date()));

    createDataVariables(vars);

    ncfile.create(); // done with define mode

    writeStationData(stns); // write out the station info

    // now write the observations
    if (!(Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE))
      throw new IllegalStateException("can't add record variable");
  }
  public void writeRecord(String stnName, Date obsDate, StructureData sdata) throws IOException {
    StationTracker stnTracker = stationMap.get(stnName);
    ProfileTracker proTracker = stnTracker.profileMap.get(obsDate);

    if (proTracker == null) {
      proTracker = new ProfileTracker(profileIndex);
      stnTracker.profileMap.put(obsDate, proTracker);

      stnTracker.link.add(profileIndex);
      stnTracker.lastChild = profileIndex;
      stnTracker.numChildren++;

      try {
        originTime[0] = profileIndex; // 2d index
        timeArray.set(0, dateFormatter.toDateTimeStringISO(obsDate));
        parentArray.set(0, stnTracker.parent_index);
        ncfile.writeStringData(timeName, originTime, timeArray);
        ncfile.write(parentStationIndex, originTime, parentArray);
      } catch (InvalidRangeException e) {
        e.printStackTrace();
        throw new IllegalStateException(e);
      }

      profileIndex++;
    }

    // needs to be wrapped as an ArrayStructure, even though we are only writing one at a time.
    ArrayStructureW sArray = new ArrayStructureW(sdata.getStructureMembers(), new int[] {1});
    sArray.setStructureData(sdata, 0);

    // track the min and max date
    if ((minDate == null) || minDate.after(obsDate)) minDate = obsDate;
    if ((maxDate == null) || maxDate.before(obsDate)) maxDate = obsDate;

    timeArray.set(0, dateFormatter.toDateTimeStringISO(obsDate));
    parentArray.set(0, proTracker.parent_index);

    proTracker.link.add(recno);
    proTracker.lastChild = recno; // not currently used
    proTracker.numChildren++;

    // write the recno record
    origin[0] = recno; // 1d index
    originTime[0] = recno; // 2d index
    try {
      ncfile.write("record", origin, sArray);
      ncfile.write(parentProfileIndex, originTime, parentArray);
    } catch (InvalidRangeException e) {
      e.printStackTrace();
      throw new IllegalStateException(e);
    }

    recno++;
  }
 private void createGlobalAttributes() {
   ncfile.addGlobalAttribute("Conventions", "Unidata Observation Dataset v1.0");
   ncfile.addGlobalAttribute("cdm_datatype", "Profile");
   ncfile.addGlobalAttribute("title", title);
   ncfile.addGlobalAttribute("desc", "Extracted by THREDDS/Netcdf Subset Service");
   /* ncfile.addGlobalAttribute("observationDimension", recordDimName);
   ncfile.addGlobalAttribute("stationDimension", stationDimName);
   ncfile.addGlobalAttribute("latitude_coordinate", latName);
   ncfile.addGlobalAttribute("longitude_coordinate", lonName);
   ncfile.addGlobalAttribute("time_coordinate", timeName); */
 }
  private void writeStationData(List<ucar.unidata.geoloc.Station> stnList) throws IOException {
    this.stnList = stnList;
    int nstns = stnList.size();
    stationMap = new HashMap<String, StationTracker>(2 * nstns);
    if (debug) System.out.println("stationMap created");

    // now write the station data
    ArrayDouble.D1 latArray = new ArrayDouble.D1(nstns);
    ArrayDouble.D1 lonArray = new ArrayDouble.D1(nstns);
    ArrayDouble.D1 altArray = new ArrayDouble.D1(nstns);
    ArrayObject.D1 idArray = new ArrayObject.D1(String.class, nstns);
    ArrayObject.D1 descArray = new ArrayObject.D1(String.class, nstns);
    ArrayObject.D1 wmoArray = new ArrayObject.D1(String.class, nstns);

    for (int i = 0; i < stnList.size(); i++) {
      ucar.unidata.geoloc.Station stn = stnList.get(i);
      stationMap.put(stn.getName(), new StationTracker(i));

      latArray.set(i, stn.getLatitude());
      lonArray.set(i, stn.getLongitude());
      if (useAlt) altArray.set(i, stn.getAltitude());

      idArray.set(i, stn.getName());
      descArray.set(i, stn.getDescription());
      if (useWmoId) wmoArray.set(i, stn.getWmoId());
    }

    try {
      ncfile.write(latName, latArray);
      ncfile.write(lonName, lonArray);
      if (useAlt) ncfile.write(altName, altArray);
      ncfile.writeStringData(idName, idArray);
      ncfile.writeStringData(descName, descArray);
      if (useWmoId) ncfile.writeStringData(wmoName, wmoArray);

    } catch (InvalidRangeException e) {
      e.printStackTrace();
      throw new IllegalStateException(e);
    }
  }
  private void createDataVariables(List<VariableSimpleIF> dataVars) throws IOException {

    /* height variable
    Variable heightVar = ncfile.addStringVariable(altName, recordDims, 20);
    ncfile.addVariableAttribute(heightVar, new Attribute("long_name", "height of observation"));
    ncfile.addVariableAttribute(heightVar, new Attribute("units", altUnits));  */

    Variable v = ncfile.addVariable(parentProfileIndex, DataType.INT, recordDimName);
    ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent profile"));

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

    // find all dimensions needed by the data variables
    for (VariableSimpleIF var : dataVars) {
      List<Dimension> dims = var.getDimensions();
      dimSet.addAll(dims);
    }

    // add them
    for (Dimension d : dimSet) {
      if (!d.isUnlimited())
        ncfile.addDimension(d.getName(), d.getLength(), d.isShared(), false, d.isVariableLength());
    }

    // add the data variables all using the record dimension
    for (VariableSimpleIF oldVar : dataVars) {
      List<Dimension> dims = oldVar.getDimensions();
      StringBuffer dimNames = new StringBuffer(recordDimName);
      for (Dimension d : dims) {
        if (!d.isUnlimited()) dimNames.append(" ").append(d.getName());
      }
      Variable newVar =
          ncfile.addVariable(oldVar.getName(), oldVar.getDataType(), dimNames.toString());

      List<Attribute> atts = oldVar.getAttributes();
      for (Attribute att : atts) {
        ncfile.addVariableAttribute(newVar, att);
      }
    }
  }
 public void finish() throws IOException {
   writeDataFinish();
   ncfile.close();
 }
  private void writeDataFinish() throws IOException {
    // finish global variables
    ArrayInt.D0 totalArray = new ArrayInt.D0();
    totalArray.set(profileIndex);
    try {
      ncfile.write(numProfilesTotalName, totalArray);
    } catch (InvalidRangeException e) {
      e.printStackTrace();
      throw new IllegalStateException(e);
    }

    // finish the station data
    int nstns = stnList.size();
    ArrayInt.D1 firstProfileArray = new ArrayInt.D1(nstns);
    ArrayInt.D1 numProfileArray = new ArrayInt.D1(nstns);
    ArrayInt.D1 nextProfileArray = new ArrayInt.D1(nprofiles);

    for (int i = 0; i < stnList.size(); i++) {
      ucar.unidata.geoloc.Station stn = stnList.get(i);
      StationTracker tracker = stationMap.get(stn.getName());

      numProfileArray.set(i, tracker.numChildren);

      int first = (tracker.link.size() > 0) ? tracker.link.get(0) : -1;
      firstProfileArray.set(i, first);

      if (tracker.link.size() > 0) {
        // construct forward link
        List<Integer> nextList = tracker.link;
        for (int j = 0; j < nextList.size() - 1; j++) {
          Integer curr = nextList.get(j);
          Integer next = nextList.get(j + 1);
          nextProfileArray.set(curr, next);
        }
        Integer curr = nextList.get(nextList.size() - 1);
        nextProfileArray.set(curr, -1);
      }
    }

    try {
      ncfile.write(firstProfileName, firstProfileArray);
      ncfile.write(numProfilesName, numProfileArray);
      ncfile.write(nextProfileName, nextProfileArray);

    } catch (InvalidRangeException e) {
      e.printStackTrace();
      throw new IllegalStateException(e);
    }

    // finish the profile data
    ArrayInt.D1 nextObsArray = new ArrayInt.D1(recno);
    ArrayInt.D1 firstObsArray = new ArrayInt.D1(nprofiles);
    ArrayInt.D1 numObsArray = new ArrayInt.D1(nprofiles);

    for (int i = 0; i < stnList.size(); i++) {
      ucar.unidata.geoloc.Station stn = stnList.get(i);
      StationTracker stnTracker = stationMap.get(stn.getName());

      Set<Date> dates = stnTracker.profileMap.keySet();
      for (Date date : dates) {
        ProfileTracker proTracker = stnTracker.profileMap.get(date);
        int trackerIndex = proTracker.parent_index;
        numObsArray.set(trackerIndex, proTracker.numChildren);

        int first = (proTracker.link.size() > 0) ? proTracker.link.get(0) : -1;
        firstObsArray.set(trackerIndex, first);

        if (proTracker.link.size() > 0) {
          // construct forward link
          List<Integer> nextList = proTracker.link;
          for (int j = 0; j < nextList.size() - 1; j++) {
            Integer curr = nextList.get(j);
            Integer next = nextList.get(j + 1);
            nextObsArray.set(curr, next);
          }
          Integer curr = nextList.get(nextList.size() - 1);
          nextObsArray.set(curr, -1);
        }
      }
    }

    try {
      ncfile.write(firstObsName, firstObsArray);
      ncfile.write(numObsName, numObsArray);
      ncfile.write(nextObsName, nextObsArray);

    } catch (InvalidRangeException e) {
      e.printStackTrace();
      throw new IllegalStateException(e);
    }

    // finish the obs data

    ncfile.updateAttribute(
        null, new Attribute("time_coverage_start", dateFormatter.toDateTimeStringISO(minDate)));
    ncfile.updateAttribute(
        null, new Attribute("time_coverage_end", dateFormatter.toDateTimeStringISO(maxDate)));
  }
  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"));
  }
  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"));
  }
 public void setLength(long size) {
   ncfile.setLength(size);
 }
 public WriterProfileObsDataset(String fileOut, String title) throws IOException {
   ncfile = NetcdfFileWriteable.createNew(fileOut, false);
   ncfile.setFill(false);
   this.title = title;
 }
Beispiel #12
0
  public void testWriteStandardVar() throws Exception {
    NetcdfFileWriteable ncfile = new NetcdfFileWriteable(filename, false);

    // define dimensions
    Dimension latDim = ncfile.addDimension("lat", 2);
    Dimension lonDim = ncfile.addDimension("lon", 3);

    ArrayList dims = new ArrayList();
    dims.add(latDim);
    dims.add(lonDim);

    // case 1
    ncfile.addVariable("t1", DataType.DOUBLE, dims);
    ncfile.addVariableAttribute("t1", CDM.SCALE_FACTOR, new Double(2.0));
    ncfile.addVariableAttribute("t1", "add_offset", new Double(77.0));

    // case 2
    ncfile.addVariable("t2", DataType.BYTE, dims);
    ncfile.addVariableAttribute("t2", CDM.SCALE_FACTOR, new Short((short) 2));
    ncfile.addVariableAttribute("t2", "add_offset", new Short((short) 77));

    // case 3
    ncfile.addVariable("t3", DataType.BYTE, dims);
    ncfile.addVariableAttribute("t3", "_FillValue", new Byte((byte) 255));

    // case 4
    ncfile.addVariable("t4", DataType.SHORT, dims);
    ncfile.addVariableAttribute("t4", CDM.MISSING_VALUE, new Short((short) -9999));

    // case 5
    ncfile.addVariable("t5", DataType.SHORT, dims);
    ncfile.addVariableAttribute("t5", CDM.MISSING_VALUE, new Short((short) -9999));
    ncfile.addVariableAttribute("t5", CDM.SCALE_FACTOR, new Short((short) 2));
    ncfile.addVariableAttribute("t5", "add_offset", new Short((short) 77));

    // case 1
    ncfile.addVariable("m1", DataType.DOUBLE, dims);
    ncfile.addVariableAttribute("m1", CDM.MISSING_VALUE, -999.99);

    // create the file
    ncfile.create();

    // write t1
    ArrayDouble A = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
    int i, j;
    Index ima = A.getIndex();
    // write
    for (i = 0; i < latDim.getLength(); i++)
      for (j = 0; j < lonDim.getLength(); j++) A.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
    int[] origin = new int[2];
    ncfile.write("t1", origin, A);

    // write t2
    ArrayByte Ab = new ArrayByte.D2(latDim.getLength(), lonDim.getLength());
    ima = Ab.getIndex();
    for (i = 0; i < latDim.getLength(); i++)
      for (j = 0; j < lonDim.getLength(); j++) Ab.setByte(ima.set(i, j), (byte) (i * 10 + j));
    ncfile.write("t2", origin, Ab);

    // write t3
    ncfile.write("t3", origin, Ab);

    // write t4
    Array As = new ArrayShort.D2(latDim.getLength(), lonDim.getLength());
    ima = As.getIndex();
    for (i = 0; i < latDim.getLength(); i++)
      for (j = 0; j < lonDim.getLength(); j++) As.setShort(ima.set(i, j), (short) (i * 10 + j));
    ncfile.write("t4", origin, As);

    As.setShort(ima.set(0, 0), (short) -9999);
    ncfile.write("t5", origin, As);

    // write m1
    ArrayDouble.D2 Ad = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
    for (i = 0; i < latDim.getLength(); i++)
      for (j = 0; j < lonDim.getLength(); j++) Ad.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
    Ad.set(1, 1, -999.99);
    ncfile.write("m1", new int[2], Ad);

    // all done
    ncfile.close();

    System.out.println("**************TestStandardVar Write done");
  }