コード例 #1
1
ファイル: DatasetViewer.java プロジェクト: mazl123321/thredds
    // create from a dataset
    public VariableBean(Variable vs) {
      this.vs = vs;
      // vs = (v instanceof VariableEnhanced) ? (VariableEnhanced) v : new VariableStandardized( v);

      setName(vs.getShortName());
      setDescription(vs.getDescription());
      setUnits(vs.getUnitsString());
      setDataType(vs.getDataType().toString());

      // Attribute csAtt = vs.findAttribute("_coordSystems");
      // if (csAtt != null)
      //  setCoordSys( csAtt.getStringValue());

      // collect dimensions
      StringBuilder lens = new StringBuilder();
      StringBuilder names = new StringBuilder();
      java.util.List dims = vs.getDimensions();
      for (int j = 0; j < dims.size(); j++) {
        ucar.nc2.Dimension dim = (ucar.nc2.Dimension) dims.get(j);
        if (j > 0) {
          lens.append(",");
          names.append(",");
        }
        String name = dim.isShared() ? dim.getName() : "anon";
        names.append(name);
        lens.append(dim.getLength());
      }
      setDimensions(names.toString());
      setShape(lens.toString());
    }
コード例 #2
0
  void CheckS(Variable v) throws IOException {

    // string
    // assert(null != (v = dodsfile.findVariable("types.strings.s")));
    // assert v.getName().equals("types.strings.s");
    assert v.getRank() == 0;
    assert v.getDataType() == DataType.STRING : v.getDataType();
    CheckSValue(v.read());
  }
コード例 #3
0
  void CheckUint16(Variable v) throws IOException {

    // uint16
    // assert(null != (v = dodsfile.findVariable("types.integers.ui16")));
    // assert v.getName().equals("types.integers.ui16");
    assert v.getRank() == 0;
    assert v.getSize() == 1;
    assert v.getDataType() == DataType.SHORT : v.getDataType();
    CheckUInt16Value(v.read());
  }
コード例 #4
0
  void CheckUrl(Variable v) throws IOException {

    // url
    // assert(null != (v = dodsfile.findVariable("types.strings.u")));
    // assert v.getName().equals("types.strings.u");
    assert v.getRank() == 0;
    assert v.getDataType() == DataType.STRING : v.getDataType();
    String str = v.readScalarString();
    assert str.equals("http://www.opendap.org") || str.equals("http://www.dods.org") : str;
  }
コード例 #5
0
  void CheckD(Variable v) throws IOException {

    // double
    // assert(null != (v = dodsfile.findVariable("types.floats.f64")));
    // assert v.getName().equals("types.floats.f64");
    assert v.getRank() == 0;
    assert v.getSize() == 1;
    assert v.getDataType() == DataType.DOUBLE : v.getDataType();
    CheckDValue(v.read());
  }
コード例 #6
0
  void CheckF(Variable v) throws IOException {

    // float
    // assert(null != (v = dodsfile.findVariable("types.floats.f32")));
    // assert v.getName().equals("types.floats.f32");
    assert v.getRank() == 0;
    assert v.getSize() == 1;
    assert v.getDataType() == DataType.FLOAT : v.getDataType();
    CheckFValue(v.read());
  }
コード例 #7
0
  void CheckLong32(Variable v) throws IOException {

    // uint32
    // assert(null != (v = dodsfile.findVariable("types.integers.ui32")));
    // assert v.getName().equals("types.integers.ui32");
    assert v.getRank() == 0;
    assert v.getSize() == 1;
    assert v.getDataType() == DataType.LONG : v.getDataType();
    CheckLongValue(v.read());
  }
コード例 #8
0
  /* Structure {
      int LAT[0];
      ...
      int LAT[149];
  } IMAGE_LAT_ARRAY(3600);
     type = Layout(8);  type= 2 (chunked) storageSize = (1,600) dataSize=0 dataAddress=2548046
  */
  @Test
  public void testReadOneAtATime() throws java.io.IOException, InvalidRangeException {
    try (NetcdfFile ncfile = TestH5.openH5("IASI/IASI.h5")) {

      Variable dset = ncfile.findVariable("U-MARF/EPS/IASI_xxx_1C/DATA/IMAGE_LAT_ARRAY");
      assert (null != dset);
      assert (dset.getDataType() == DataType.STRUCTURE);
      assert (dset.getRank() == 1);
      assert (dset.getSize() == 3600);

      Dimension d = dset.getDimension(0);
      assert (d.getLength() == 3600);

      Structure s = (Structure) dset;

      // read last one - chunked
      StructureData sd = s.readStructure(3599);
      assert sd.getScalarInt("LAT[0]") == 70862722;
      assert sd.getScalarInt("LAT[149]") == 85302263;

      // read one at a time
      for (int i = 3590; i < d.getLength(); i++) {
        s.readStructure(i);
        System.out.println(" read structure " + i);
      }
    }
    System.out.println("*** testReadIASI ok");
  }
コード例 #9
0
  /*
   Structure {
    int a_name;
    byte b_name(3);
    byte c_name(3);
    short d_name(3);
    int e_name(3);
    long f_name(3);
    int g_name(3);
    short h_name(3);
    int i_name(3);
    long j_name(3);
    float k_name(3);
    double l_name(3);
  } CompoundNative(15);
      type = Layout(8);  type= 1 (contiguous) storageSize = (15,144) dataSize=0 dataAddress=2048
  */
  @Test
  public void testReadH5StructureArrayMembers() throws java.io.IOException {
    try (NetcdfFile ncfile = TestH5.openH5("complex/compound_native.h5")) {

      Variable dset = ncfile.findVariable("CompoundNative");
      assert (null != dset);
      assert (dset.getDataType() == DataType.STRUCTURE);
      assert (dset.getRank() == 1);
      assert (dset.getSize() == 15);

      Dimension d = dset.getDimension(0);
      assert (d.getLength() == 15);

      Structure s = (Structure) dset;

      // read all with the iterator
      StructureDataIterator iter = s.getStructureIterator();
      while (iter.hasNext()) {
        StructureData sd = iter.next();

        for (StructureMembers.Member m : sd.getMembers()) {
          Array data = sd.getArray(m);
          NCdumpW.printArray(data, m.getName(), out, null);
        }
      }
    }
    System.out.println("*** testReadH5StructureArrayMembers ok");
  }
コード例 #10
0
  /**
   * Set extra information used by station obs datasets. Use stnIdVName or stnIndexVName.
   *
   * @param stnIdVName the obs variable that is used to find the station in the stnHash; may be type
   *     int or a String (char).
   * @param stnDescVName optional station var containing station description
   */
  public void setStationInfo(
      String stnIdVName, String stnDescVName, String stnIndexVName, StationHelper stationHelper) {
    this.stnIdVName = stnIdVName;
    this.stnDescVName = stnDescVName;
    this.stnIndexVName = stnIndexVName;
    this.stationHelper = stationHelper;

    if (stnIdVName != null) {
      Variable stationVar = ncfile.findVariable(stnIdVName);
      stationIdType = stationVar.getDataType();
    }
  }
コード例 #11
0
ファイル: TestWritePermute.java プロジェクト: nbald/thredds
  private void doWrite2(NetcdfFileWriteable ncfile, String varName) throws Exception {
    Variable v = ncfile.findVariable(varName);
    int[] w = getWeights(v);

    int[] shape = v.getShape();
    Array aa = Array.factory(v.getDataType().getPrimitiveClassType(), shape);
    Index ima = aa.getIndex();
    for (int i = 0; i < shape[0]; i++) {
      for (int j = 0; j < shape[1]; j++) {
        aa.setDouble(ima.set(i, j), (double) (i * w[0] + j * w[1]));
      }
    }

    ncfile.write(varName, aa);
  }
コード例 #12
0
  @Test
  public void testH5StructureDS() throws java.io.IOException {
    int a_name = 0;
    String[] b_name =
        new String[] {
          "A fight is a contract that takes two people to honor.",
          "A combative stance means that you've accepted the contract.",
          "In which case, you deserve what you get.",
          "  --  Professor Cheng Man-ch'ing"
        };
    String c_name = "Hello!";

    // H5header.setDebugFlags(new ucar.nc2.util.DebugFlagsImpl("H5header/header"));
    try (NetcdfDataset ncfile =
        NetcdfDataset.openDataset(TestH5.testDir + "complex/compound_complex.h5")) {

      Variable dset = ncfile.findVariable("CompoundComplex");
      assert (null != dset);
      assert (dset.getDataType() == DataType.STRUCTURE);
      assert (dset.getRank() == 1);
      assert (dset.getSize() == 6);

      Dimension d = dset.getDimension(0);
      assert (d.getLength() == 6);

      Structure s = (Structure) dset;

      // read all with the iterator
      StructureDataIterator iter = s.getStructureIterator();
      while (iter.hasNext()) {
        StructureData sd = iter.next();
        assert sd.getScalarInt("a_name") == a_name;
        a_name++;
        assert sd.getScalarString("c_name").equals(c_name);
        String[] results = sd.getJavaArrayString(sd.findMember("b_name"));
        assert results.length == b_name.length;
        int count = 0;
        for (String r : results) assert r.equals(b_name[count++]);

        for (StructureMembers.Member m : sd.getMembers()) {
          Array data = sd.getArray(m);
          NCdumpW.printArray(data, m.getName(), out, null);
        }
      }
    }
    System.out.println("*** testH5StructureDS ok");
  }
コード例 #13
0
  /*  Structure {
    char EntryName(64);
    char Definition(1024);
    char Unit(1024);
    char Scale Factor(1024);
  } TIME_DESCR(60);
     type = Layout(8);  type= 2 (chunked) storageSize = (1,3136) dataSize=0 dataAddress=684294
  */
  @Test
  public void testReadManyAtATime() throws java.io.IOException, InvalidRangeException {
    try (NetcdfFile ncfile = TestH5.openH5("IASI/IASI.h5")) {

      Variable dset = ncfile.findVariable("U-MARF/EPS/IASI_xxx_1C/DATA/TIME_DESCR");
      assert (null != dset);
      assert (dset.getDataType() == DataType.STRUCTURE);
      assert (dset.getRank() == 1);
      assert (dset.getSize() == 60);

      Dimension d = dset.getDimension(0);
      assert (d.getLength() == 60);

      ArrayStructure data = (ArrayStructure) dset.read();
      StructureMembers.Member m = data.getStructureMembers().findMember("EntryName");
      assert m != null;
      for (int i = 0; i < dset.getSize(); i++) {
        String r = data.getScalarString(i, m);
        if (i % 2 == 0) assert r.equals("TIME[" + i / 2 + "]-days") : r + " at " + i;
        else assert r.equals("TIME[" + i / 2 + "]-milliseconds") : r + " at " + i;
      }
    }
    System.out.println("*** testReadManyAtATime ok");
  }
コード例 #14
0
  @Test
  public void testArraySubset() throws IOException {
    DODSNetcdfFile dodsfile = TestDODSRead.open("test.02?i32[1:10],f64[2:2:10]");

    Variable v = null;
    Array a = null;

    // int32
    assert (null != (v = dodsfile.findVariable("i32")));
    assert v.getFullName().equals("i32");
    assert v.getRank() == 1;
    assert v.getSize() == 10;
    assert v.getDataType() == DataType.INT;
    a = v.read();
    assert a.getRank() == 1;
    assert a.getSize() == 25;
    assert a.getElementType() == int.class;
    assert a instanceof ArrayInt.D1;

    ArrayInt.D1 ai = (ArrayInt.D1) a;
    for (int i = 0; i < 10; i++) {
      int val = ai.get(i);
      assert (val == i * 2048) : val + " != " + (i * 2048);
    }

    // uint16
    assert null == (v = dodsfile.findVariable("ui16"));
    assert null == (v = dodsfile.findVariable("ui32"));

    // double
    assert (null != (v = dodsfile.findVariable("f64")));
    assert v.getFullName().equals("f64");
    assert v.getRank() == 1;
    assert v.getSize() == 5;
    assert v.getDataType() == DataType.DOUBLE : v.getDataType();
    a = v.read();
    assert a.getRank() == 1;
    assert a.getSize() == 25;
    assert a.getElementType() == double.class;
    assert a instanceof ArrayDouble.D1;
    ArrayDouble.D1 ad = (ArrayDouble.D1) a;
    double[] tFloat64 =
        new double[] {
          1.0,
          0.9999500004166653,
          0.9998000066665778,
          0.9995500337489875,
          0.9992001066609779,
          0.9987502603949663,
          0.9982005399352042,
          0.9975510002532796,
          0.9968017063026194,
          0.9959527330119943,
          0.9950041652780257,
          0.9939560979566968,
          0.9928086358538663,
          0.9915618937147881,
          0.9902159962126371,
          0.9887710779360422,
          0.9872272833756269,
          0.9855847669095608,
          0.9838436927881214,
          0.9820042351172703,
          0.9800665778412416,
          0.9780309147241483,
          0.9758974493306055,
          0.9736663950053749,
          0.9713379748520297
        };

    for (int i = 0; i < 5; i++) {
      double val = ad.get(i);
      assert Misc.closeEnough(val, tFloat64[i], 1.0e-9);
    }

    dodsfile.close();
  }
コード例 #15
0
    // create from a dataset
    public ObsBean(Structure obs, StructureData sdata) {
      // first choice
      for (Variable v : obs.getVariables()) {
        Attribute att = v.findAttribute("BUFR:TableB_descriptor");
        if (att == null) continue;
        String val = att.getStringValue();
        if (val.equals("0-5-1") && Double.isNaN(lat)) {
          lat = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-6-1") && Double.isNaN(lon)) {
          lon = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-7-30") && Double.isNaN(alt)) {

          alt = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-4-1") && (year < 0)) {
          year = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-2") && (month < 0)) {
          month = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-3") && (day < 0)) {
          day = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-4") && (hour < 0)) {
          hour = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-5") && (minute < 0)) {
          minute = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-4-6") && (sec < 0)) {
          sec = sdata.convertScalarInt(v.getShortName());

        } else if (val.equals("0-1-1") && (wmo_block < 0)) {
          wmo_block = sdata.convertScalarInt(v.getShortName());
        } else if (val.equals("0-1-2") && (wmo_id < 0)) {
          wmo_id = sdata.convertScalarInt(v.getShortName());

        } else if ((stn == null)
            && (val.equals("0-1-7")
                || val.equals("0-1-194")
                || val.equals("0-1-11")
                || val.equals("0-1-18"))) {
          if (v.getDataType().isString()) stn = sdata.getScalarString(v.getShortName());
          else stn = Integer.toString(sdata.convertScalarInt(v.getShortName()));
        }
      }

      // second choice
      for (Variable v : obs.getVariables()) {
        Attribute att = v.findAttribute("BUFR:TableB_descriptor");
        if (att == null) continue;
        String val = att.getStringValue();
        if (val.equals("0-5-2") && Double.isNaN(lat)) {
          lat = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-6-2") && Double.isNaN(lon)) {
          lon = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-7-1") && Double.isNaN(alt)) {
          alt = sdata.convertScalarDouble(v.getShortName());
        } else if ((val.equals("0-4-7")) && (sec < 0)) {
          sec = sdata.convertScalarInt(v.getShortName());
        }
      }

      // third choice
      for (Variable v : obs.getVariables()) {
        Attribute att = v.findAttribute("BUFR:TableB_descriptor");
        if (att == null) continue;
        String val = att.getStringValue();
        if (val.equals("0-7-10") && Double.isNaN(alt)) {
          alt = sdata.convertScalarDouble(v.getShortName());
        } else if (val.equals("0-7-2") && Double.isNaN(alt)) {
          alt = sdata.convertScalarDouble(v.getShortName());
        }
      }
    }
コード例 #16
0
  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);
  }
コード例 #17
0
 void CheckByte(Variable v) throws IOException {
   assert v.getRank() == 0;
   assert v.getSize() == 1;
   assert v.getDataType() == DataType.BYTE;
   CheckByteValue(v.read());
 }