/*
   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");
  }
  private void init() throws IOException {
    members = new StructureMembers("stationObs");

    // used to convert from adde format
    calendar = new GregorianCalendar();
    calendar.setTimeZone(TimeZone.getTimeZone("GMT"));

    // time unit
    timeUnit = DateUnit.getUnixDateUnit();

    try {
      AddePointDataReader reader = callAdde(addeURL);

      String[] params = reader.getParams();
      String[] units = reader.getUnits();
      int[] scales = reader.getScales();
      scaleFactor = new double[params.length];

      if (debugHead) System.out.println(" Param  Unit Scale");
      for (int paramNo = 0; paramNo < params.length; paramNo++) {
        // memberNames.add( params[i]);

        if (debugHead)
          System.out.println(" " + params[paramNo] + " " + units[paramNo] + " " + scales[paramNo]);
        if (scales[paramNo] != 0)
          scaleFactor[paramNo] = 1.0 / Math.pow(10.0, (double) scales[paramNo]);

        DataType dt = null;
        if ("CHAR".equals(units[paramNo])) dt = DataType.STRING;
        else if (scaleFactor[paramNo] == 0) dt = DataType.INT;
        else dt = DataType.DOUBLE;

        String unitString = null;
        if ((units[paramNo] != null) && (units[paramNo].length() > 0))
          unitString = visad.jmet.MetUnits.makeSymbol(units[paramNo]);

        AddeTypedDataVariable tdv = new AddeTypedDataVariable(params[paramNo], unitString, dt);
        dataVariables.add(tdv);
        StructureMembers.Member m =
            members.addMember(
                tdv.getShortName(),
                tdv.getDescription(),
                tdv.getUnitsString(),
                tdv.getDataType(),
                tdv.getShape());
        m.setDataParam(paramNo);
        members.addMember(m);
      }

    } catch (AddeException e) {
      e.printStackTrace();
      throw new IOException(e.getMessage());
    }
  }
  private double getTime(StructureMembers.Member timeVar, StructureData sdata) {
    if (timeVar == null) return 0.0;

    if ((timeVar.getDataType() == DataType.CHAR) || (timeVar.getDataType() == DataType.STRING)) {
      String time = sdata.getScalarString(timeVar);
      CalendarDate date = CalendarDateFormatter.isoStringToCalendarDate(null, time);
      if (date == null) {
        log.error("Cant parse date - not ISO formatted, = " + time);
        return 0.0;
      }
      return date.getMillis() / 1000.0;

    } else {
      return sdata.convertScalarDouble(timeVar);
    }
  }
  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);
    }
  }
  @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");
  }
Example #6
0
  public boolean compareStructureData(
      StructureData sdata1, StructureData sdata2, double tol, boolean justOne) {
    boolean ok = true;

    StructureMembers sm1 = sdata1.getStructureMembers();
    StructureMembers sm2 = sdata2.getStructureMembers();
    if (sm1.getMembers().size() != sm2.getMembers().size()) {
      f.format(" size %d !== %d%n", sm1.getMembers().size(), sm2.getMembers().size());
      ok = false;
    }

    for (StructureMembers.Member m1 : sm1.getMembers()) {
      if (m1.getName().equals("time")) continue;
      StructureMembers.Member m2 = sm2.findMember(m1.getName());
      Array data1 = sdata1.getArray(m1);
      Array data2 = sdata2.getArray(m2);
      ok &= compareData(m1.getName(), data1, data2, tol, justOne);
    }

    return ok;
  }
Example #7
0
  private double copyVarData(NetcdfFileWriteable ncfile, Structure recordStruct)
      throws IOException, InvalidRangeException {
    int nrecs = (int) recordStruct.getSize();
    int sdataSize = recordStruct.getElementSize();

    double total = 0;
    double totalRecordBytes = 0;
    for (int count = 0; count < nrecs; count++) {

      StructureData recordData = recordStruct.readStructure(count);
      for (StructureMembers.Member m : recordData.getMembers()) {

        if (m.getDataType() == DataType.STRUCTURE) {
          int countLevel = 0;
          ArrayStructure seq1 = recordData.getArrayStructure(m);
          StructureDataIterator iter = seq1.getStructureDataIterator();
          try {
            while (iter.hasNext()) {
              StructureData seqData = iter.next();
              for (StructureMembers.Member seqm : seqData.getMembers()) {
                Array data = seqData.getArray(seqm);
                int[] shape = data.getShape();
                int[] newShape = new int[data.getRank() + 2];
                newShape[0] = 1;
                newShape[1] = 1;
                for (int i = 0; i < data.getRank(); i++) newShape[i + 1] = shape[i];

                int[] origin = new int[data.getRank() + 2];
                origin[0] = count;
                origin[1] = countLevel;

                String mname = seqm.getName() + "-" + m.getName();
                if (debug && (count == 0) && (countLevel == 0))
                  System.out.println("write to = " + mname);
                ncfile.write(mname, origin, data.reshape(newShape));
              }
              countLevel++;
            }
          } finally {
            iter.finish();
          }
        } else {

          Array data = recordData.getArray(m);
          int[] shape = data.getShape();
          int[] newShape = new int[data.getRank() + 1];
          newShape[0] = 1;
          for (int i = 0; i < data.getRank(); i++) newShape[i + 1] = shape[i];

          int[] origin = new int[data.getRank() + 1];
          origin[0] = count;

          if (debug && (count == 0)) System.out.println("write to = " + m.getName());
          ncfile.write(m.getName(), origin, data.reshape(newShape));
        }
      }
      totalRecordBytes += sdataSize;
    }

    total += totalRecordBytes;
    totalRecordBytes /= 1000 * 1000;
    if (debug)
      System.out.println(
          "write record var; total = " + totalRecordBytes + " Mbytes # recs=" + nrecs);

    return total;
  }