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);
      }
    }
  }
  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"));
  }
Exemple #4
0
  public void testWritePermute() throws Exception {
    NetcdfFileWriteable ncfile = new NetcdfFileWriteable();
    ncfile.setName(TestLocal.cdmTestDataDir + "permuteTest.nc");

    // define dimensions
    Dimension xDim = ncfile.addDimension("x", 3);
    Dimension yDim = ncfile.addDimension("y", 5);
    Dimension zDim = ncfile.addDimension("z", 4);
    Dimension tDim = ncfile.addDimension("time", 2);

    // define Variables
    ncfile.addVariable("time", double.class, new Dimension[] {tDim});
    ncfile.addVariableAttribute("time", "units", "secs since 1-1-1 00:00");

    ncfile.addVariable("z", double.class, new Dimension[] {zDim});
    ncfile.addVariableAttribute("z", "units", "meters");
    ncfile.addVariableAttribute("z", "positive", "up");

    ncfile.addVariable("y", double.class, new Dimension[] {yDim});
    ncfile.addVariableAttribute("y", "units", "degrees_north");

    ncfile.addVariable("x", double.class, new Dimension[] {xDim});
    ncfile.addVariableAttribute("x", "units", "degrees_east");

    ncfile.addVariable("tzyx", double.class, new Dimension[] {tDim, zDim, yDim, xDim});
    ncfile.addVariableAttribute("tzyx", "units", "K");

    ncfile.addVariable("tzxy", double.class, new Dimension[] {tDim, zDim, xDim, yDim});
    ncfile.addVariableAttribute("tzxy", "units", "K");

    ncfile.addVariable("tyxz", double.class, new Dimension[] {tDim, yDim, xDim, zDim});
    ncfile.addVariableAttribute("tyxz", "units", "K");

    ncfile.addVariable("txyz", double.class, new Dimension[] {tDim, xDim, yDim, zDim});
    ncfile.addVariableAttribute("txyz", "units", "K");

    ncfile.addVariable("zyxt", double.class, new Dimension[] {zDim, yDim, xDim, tDim});
    ncfile.addVariableAttribute("zyxt", "units", "K");

    ncfile.addVariable("zxyt", double.class, new Dimension[] {zDim, xDim, yDim, tDim});
    ncfile.addVariableAttribute("zxyt", "units", "K");

    ncfile.addVariable("yxzt", double.class, new Dimension[] {yDim, xDim, zDim, tDim});
    ncfile.addVariableAttribute("yxzt", "units", "K");

    ncfile.addVariable("xyzt", double.class, new Dimension[] {xDim, yDim, zDim, tDim});
    ncfile.addVariableAttribute("xyzt", "units", "K");

    // missing one dimension
    ncfile.addVariable("zyx", double.class, new Dimension[] {zDim, yDim, xDim});
    ncfile.addVariable("txy", double.class, new Dimension[] {tDim, xDim, yDim});
    ncfile.addVariable("yxz", double.class, new Dimension[] {yDim, xDim, zDim});
    ncfile.addVariable("xzy", double.class, new Dimension[] {xDim, zDim, yDim});
    ncfile.addVariable("yxt", double.class, new Dimension[] {yDim, xDim, tDim});
    ncfile.addVariable("xyt", double.class, new Dimension[] {xDim, yDim, tDim});
    ncfile.addVariable("xyz", double.class, new Dimension[] {xDim, yDim, zDim});

    // missing two dimension
    ncfile.addVariable("yx", double.class, new Dimension[] {yDim, xDim});
    ncfile.addVariable("xy", double.class, new Dimension[] {xDim, yDim});
    ncfile.addVariable("yz", double.class, new Dimension[] {yDim, zDim});
    ncfile.addVariable("xz", double.class, new Dimension[] {xDim, zDim});
    ncfile.addVariable("yt", double.class, new Dimension[] {yDim, tDim});
    ncfile.addVariable("xt", double.class, new Dimension[] {xDim, tDim});
    ncfile.addVariable("ty", double.class, new Dimension[] {tDim, yDim});
    ncfile.addVariable("tx", double.class, new Dimension[] {tDim, xDim});

    // add global attributes
    ncfile.addGlobalAttribute("Convention", "COARDS");

    // create the file
    try {
      ncfile.create();
    } catch (IOException e) {
      System.err.println("ERROR creating file");
      assert (false);
    }

    // write time data
    int len = tDim.getLength();
    ArrayDouble A = new ArrayDouble.D1(len);
    Index ima = A.getIndex();
    for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3600));
    int[] origin = new int[1];
    try {
      ncfile.write("time", origin, A);
    } catch (IOException e) {
      System.err.println("ERROR writing time");
      assert (false);
    }

    // write z data
    len = zDim.getLength();
    A = new ArrayDouble.D1(len);
    ima = A.getIndex();
    for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 10));
    try {
      ncfile.write("z", origin, A);
    } catch (IOException e) {
      System.err.println("ERROR writing z");
      assert (false);
    }

    // write y data
    len = yDim.getLength();
    A = new ArrayDouble.D1(len);
    ima = A.getIndex();
    for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3));
    try {
      ncfile.write("y", origin, A);
    } catch (IOException e) {
      System.err.println("ERROR writing y");
      assert (false);
    }

    // write x data
    len = xDim.getLength();
    A = new ArrayDouble.D1(len);
    ima = A.getIndex();
    for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 5));
    try {
      ncfile.write("x", origin, A);
    } catch (IOException e) {
      System.err.println("ERROR writing x");
      assert (false);
    }

    // write tzyx data
    doWrite4(ncfile, "tzyx");
    doWrite4(ncfile, "tzxy");
    doWrite4(ncfile, "txyz");
    doWrite4(ncfile, "tyxz");
    doWrite4(ncfile, "zyxt");
    doWrite4(ncfile, "zxyt");
    doWrite4(ncfile, "xyzt");
    doWrite4(ncfile, "yxzt");

    doWrite3(ncfile, "zyx");
    doWrite3(ncfile, "txy");
    doWrite3(ncfile, "yxz");
    doWrite3(ncfile, "xzy");
    doWrite3(ncfile, "yxt");
    doWrite3(ncfile, "xyt");
    doWrite3(ncfile, "yxt");
    doWrite3(ncfile, "xyz");

    doWrite2(ncfile, "yx");
    doWrite2(ncfile, "xy");
    doWrite2(ncfile, "yz");
    doWrite2(ncfile, "xz");
    doWrite2(ncfile, "yt");
    doWrite2(ncfile, "xt");
    doWrite2(ncfile, "ty");
    doWrite2(ncfile, "tx");

    if (show) System.out.println("ncfile = " + ncfile);

    // all done
    try {
      ncfile.close();
    } catch (IOException e) {
      System.err.println("ERROR writing file");
      assert (false);
    }

    System.out.println("*****************Test Write done");
  }
Exemple #5
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  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");
  }
Exemple #6
0
  Write2ncRect(NetcdfFile bufr, String fileOutName, boolean fill)
      throws IOException, InvalidRangeException {

    NetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(fileOutName, fill);
    if (debug) {
      System.out.println("FileWriter write " + bufr.getLocation() + " to " + fileOutName);
    }

    // global attributes
    List<Attribute> glist = bufr.getGlobalAttributes();
    for (Attribute att : glist) {
      String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
      Attribute useAtt;
      if (att.isArray()) useAtt = ncfile.addGlobalAttribute(useName, att.getValues());
      else if (att.isString()) useAtt = ncfile.addGlobalAttribute(useName, att.getStringValue());
      else useAtt = ncfile.addGlobalAttribute(useName, att.getNumericValue());
      if (debug) System.out.println("add gatt= " + useAtt);
    }

    // global dimensions
    Dimension recordDim = null;
    Map<String, Dimension> dimHash = new HashMap<String, Dimension>();
    for (Dimension oldD : bufr.getDimensions()) {
      String useName = N3iosp.makeValidNetcdfObjectName(oldD.getName());
      boolean isRecord = useName.equals("record");
      Dimension newD = ncfile.addDimension(useName, oldD.getLength(), true, false, false);
      dimHash.put(newD.getName(), newD);
      if (isRecord) recordDim = newD;
      if (debug) System.out.println("add dim= " + newD);
    }

    // Variables
    Structure recordStruct = (Structure) bufr.findVariable(BufrIosp.obsRecord);
    for (Variable oldVar : recordStruct.getVariables()) {
      if (oldVar.getDataType() == DataType.STRUCTURE) continue;

      String varName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());
      DataType newType = oldVar.getDataType();

      List<Dimension> newDims = new ArrayList<Dimension>();
      newDims.add(recordDim);
      for (Dimension dim : oldVar.getDimensions()) {
        newDims.add(ncfile.addDimension(oldVar.getShortName() + "_strlen", dim.getLength()));
      }

      Variable newVar = ncfile.addVariable(varName, newType, newDims);
      if (debug) System.out.println("add var= " + newVar);

      // attributes
      List<Attribute> attList = oldVar.getAttributes();
      for (Attribute att : attList) {
        String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
        if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
        else if (att.isString())
          ncfile.addVariableAttribute(varName, useName, att.getStringValue());
        else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
      }
    }

    // int max_seq = countSeq(recordStruct);
    // Dimension seqD = ncfile.addDimension("level", max_seq);

    for (Variable v : recordStruct.getVariables()) {
      if (v.getDataType() != DataType.STRUCTURE) continue;
      String structName = N3iosp.makeValidNetcdfObjectName(v.getShortName());
      int shape[] = v.getShape();

      Dimension structDim = ncfile.addDimension(structName, shape[0]);

      Structure struct = (Structure) v;
      for (Variable seqVar : struct.getVariables()) {
        String varName = N3iosp.makeValidNetcdfObjectName(seqVar.getShortName() + "-" + structName);
        DataType newType = seqVar.getDataType();

        List<Dimension> newDims = new ArrayList<Dimension>();
        newDims.add(recordDim);
        newDims.add(structDim);
        for (Dimension dim : seqVar.getDimensions()) {
          newDims.add(ncfile.addDimension(seqVar.getShortName() + "_strlen", dim.getLength()));
        }

        Variable newVar = ncfile.addVariable(varName, newType, newDims);
        if (debug) System.out.println("add var= " + newVar);

        // attributes
        List<Attribute> attList = seqVar.getAttributes();
        for (Attribute att : attList) {
          String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
          if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
          else if (att.isString())
            ncfile.addVariableAttribute(varName, useName, att.getStringValue());
          else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
        }
      }
    }

    // create the file
    ncfile.create();
    if (debug) System.out.println("File Out= " + ncfile.toString());

    // boolean ok = (Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);

    double total = copyVarData(ncfile, recordStruct);
    ncfile.flush();
    System.out.println("FileWriter done total bytes = " + total);
    ncfile.close();
  }