コード例 #1
0
  private void makeMultidimInner(
      NetcdfDataset ds, TableConfig parentTable, TableConfig childTable) {
    Dimension parentDim = ds.findDimension(parentTable.dimName);
    Dimension childDim = ds.findDimension(childTable.innerName);

    // divide up the variables between the parent and the child
    List<String> obsVars;
    List<Variable> vars = ds.getVariables();
    List<String> parentVars = new ArrayList<>(vars.size());
    obsVars = new ArrayList<>(vars.size());
    for (Variable orgV : vars) {
      if (orgV instanceof Structure) continue;

      Dimension dim0 = orgV.getDimension(0);
      if ((dim0 != null) && dim0.equals(parentDim)) {
        if ((orgV.getRank() == 1)
            || ((orgV.getRank() == 2) && orgV.getDataType() == DataType.CHAR)) {
          parentVars.add(orgV.getShortName());
        } else {
          Dimension dim1 = orgV.getDimension(1);
          if ((dim1 != null) && dim1.equals(childDim)) obsVars.add(orgV.getShortName());
        }
      }
    }
    parentTable.vars = parentVars;
    childTable.vars = obsVars;
  }
コード例 #2
0
  public void testAggCoordVar2(NetcdfFile ncfile) {

    Variable time = ncfile.findVariable("time");
    assert null != time;
    assert time.getShortName().equals("time");
    assert time.getRank() == 1 : time.getRank();
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.INT;

    assert time.getDimension(0) == ncfile.findDimension("time");

    try {
      Array data = time.read();

      assert (data instanceof ArrayInt);
      IndexIterator dataI = data.getIndexIterator();
      assert dataI.getIntNext() == 0 : dataI.getIntCurrent();
      assert dataI.getIntNext() == 1 : dataI.getIntCurrent();
      assert dataI.getIntNext() == 2 : dataI.getIntCurrent();

    } catch (IOException io) {
      io.printStackTrace();
      assert false;
    }
  }
コード例 #3
0
  public void testAggCoordVar(NetcdfFile ncfile) {

    Variable time = ncfile.findVariable("time");
    assert null != time;
    assert time.getShortName().equals("time");
    assert time.getRank() == 1 : time.getRank();
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.INT;

    assert time.getDimension(0) == ncfile.findDimension("time");

    try {
      Array data = time.read();

      assert (data instanceof ArrayInt.D1) : data.getClass().getName();
      ArrayInt.D1 dataI = (ArrayInt.D1) data;
      assert dataI.get(0) == 0;
      assert dataI.get(1) == 10;
      assert dataI.get(2) == 99;

    } catch (IOException io) {
      io.printStackTrace();
      assert false;
    }
  }
コード例 #4
0
  private void check(NetcdfFile ncfile, int n) throws IOException, InvalidRangeException {
    Variable v = ncfile.findVariable("time");
    assert v != null;
    System.out.printf(" time= %s%n", v.getNameAndDimensions());
    assert v.getSize() == n : v.getSize();

    v = ncfile.findVariable("eta");
    assert v != null;
    assert v.getRank() == 3 : v.getRank();
  }
コード例 #5
0
ファイル: Write2ncRect.java プロジェクト: nbald/thredds
  private void copySome(NetcdfFileWriteable ncfile, Variable oldVar, int nelems)
      throws IOException {
    String newName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());

    int[] shape = oldVar.getShape();
    int[] origin = new int[oldVar.getRank()];
    int size = shape[0];

    for (int i = 0; i < size; i += nelems) {
      origin[0] = i;
      int left = size - i;
      shape[0] = Math.min(nelems, left);

      Array data;
      try {
        data = oldVar.read(origin, shape);
        if (oldVar.getDataType() == DataType.STRING) {
          data = convertToChar(ncfile.findVariable(newName), data);
        }
        if (data.getSize() > 0) { // zero when record dimension = 0
          ncfile.write(newName, origin, data);
          if (debug) System.out.println("write " + data.getSize() + " bytes");
        }

      } catch (InvalidRangeException e) {
        e.printStackTrace();
        throw new IOException(e.getMessage());
      }
    }
  }
コード例 #6
0
  public void testAggCoordVar(NetcdfFile ncfile) {
    Variable time = ncfile.findVariable("time");
    assert null != time;

    assert time.getShortName().equals("time");
    assert time.getRank() == 1;
    assert time.getSize() == 3;
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.DOUBLE;

    assert time.getDimension(0) == ncfile.findDimension("time");

    try {
      Array data = time.read();
      assert data.getRank() == 1;
      assert data.getSize() == 3;
      assert data.getShape()[0] == 3;
      assert data.getElementType() == double.class;

      int count = 0;
      IndexIterator dataI = data.getIndexIterator();
      while (dataI.hasNext()) {
        assert Misc.closeEnough(dataI.getDoubleNext(), result[count]);
        count++;
      }

    } catch (IOException io) {
      io.printStackTrace();
      assert false;
    }
  }
コード例 #7
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 #8
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 #9
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 #10
0
 void CheckInt16(Variable v) throws IOException {
   // int16
   // assert(null != (v = dodsfile.findVariable("types.integers.i16")));
   // assert v.getName().equals("types.integers.i16");
   assert v.getRank() == 0;
   assert v.getSize() == 1;
   assert v.getDataType() == DataType.SHORT;
   CheckInt16Value(v.read());
 }
コード例 #11
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 #12
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 #13
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 #14
0
  public void testAggCoordVar3(NetcdfFile ncfile) throws IOException {
    Variable time = ncfile.findVariable("time");
    assert null != time;
    assert time.getShortName().equals("time");
    assert time.getRank() == 1 : time.getRank();
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.DOUBLE : time.getDataType();

    assert time.getDimension(0) == ncfile.findDimension("time");

    Array data = time.read();

    assert (data instanceof ArrayDouble);
    IndexIterator dataI = data.getIndexIterator();
    double val = dataI.getDoubleNext();
    assert Misc.closeEnough(val, 0.0) : val;
    assert Misc.closeEnough(dataI.getDoubleNext(), 10.0) : dataI.getDoubleCurrent();
    assert Misc.closeEnough(dataI.getDoubleNext(), 99.0) : dataI.getDoubleCurrent();
  }
コード例 #15
0
  public void testAggCoordVarScan(NetcdfFile ncfile) throws IOException {
    Variable time = ncfile.findVariable("time");
    assert null != time;
    assert time.getShortName().equals("time");
    assert time.getRank() == 1 : time.getRank();
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.INT : time.getDataType();

    assert time.getDimension(0) == ncfile.findDimension("time");

    int count = 0;
    Array data = time.read();
    assert (data instanceof ArrayInt);
    while (data.hasNext()) {
      int val = data.nextInt();
      assert val == count * 10 : val + "!=" + count * 10;
      count++;
    }
  }
コード例 #16
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 #17
0
ファイル: NcDAS.java プロジェクト: blazetopher/THREDDS
  private int addAttributes(opendap.dap.AttributeTable table, Variable v, Iterator iter) {
    int count = 0;

    // add attribute table for this variable
    while (iter.hasNext()) {
      Attribute att = (Attribute) iter.next();
      int dods_type = DODSNetcdfFile.convertToDODSType(att.getDataType(), false);

      try {
        String attName = NcDDS.escapeName(att.getName());
        if (att.isString()) {
          /* FIX String value = escapeAttributeStringValues(att.getStringValue());
          table.appendAttribute(attName, dods_type, "\""+value+"\"");
          */
          table.appendAttribute(attName, dods_type, att.getStringValue());
        } else {
          // cant send signed bytes
          if (att.getDataType() == DataType.BYTE) {
            boolean signed = false;
            for (int i = 0; i < att.getLength(); i++) {
              if (att.getNumericValue(i).byteValue() < 0) signed = true;
            }
            if (signed) // promote to signed short
            dods_type = opendap.dap.Attribute.INT16;
          }

          for (int i = 0; i < att.getLength(); i++)
            table.appendAttribute(attName, dods_type, att.getNumericValue(i).toString());
        }
        count++;

      } catch (Exception e) {
        log.error(
            "Error appending attribute " + att.getName() + " = " + att.getStringValue() + "\n" + e);
      }
    } // loop over variable attributes

    // kludgy thing to map char arrays to DODS Strings
    if ((v != null) && (v.getDataType().getPrimitiveClassType() == char.class)) {
      int rank = v.getRank();
      int strlen = (rank == 0) ? 0 : v.getShape(rank - 1);
      Dimension dim = (rank == 0) ? null : v.getDimension(rank - 1);
      try {
        opendap.dap.AttributeTable dodsTable = table.appendContainer("DODS");
        dodsTable.appendAttribute("strlen", opendap.dap.Attribute.INT32, Integer.toString(strlen));
        if ((dim != null) && dim.isShared())
          dodsTable.appendAttribute("dimName", opendap.dap.Attribute.STRING, dim.getName());
        count++;
      } catch (Exception e) {
        log.error("Error appending attribute strlen\n" + e);
      }
    }

    return count;
  }
コード例 #18
0
  public void testAggCoordVarNoCoordsDir(NetcdfFile ncfile) throws IOException {
    Variable time = ncfile.findVariable("time");
    assert null != time;
    assert time.getShortName().equals("time");
    assert time.getRank() == 1 : time.getRank();
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.STRING : time.getDataType();

    assert time.getDimension(0) == ncfile.findDimension("time");

    Array data = time.read();

    assert (data instanceof ArrayObject);
    IndexIterator dataI = data.getIndexIterator();
    String coordName = (String) dataI.getObjectNext();
    assert coordName.equals("time0Dir.nc") : coordName;
    coordName = (String) dataI.getObjectNext();
    assert coordName.equals("time1Dir.nc") : coordName;
    coordName = (String) dataI.getObjectNext();
    assert coordName.equals("time2Dir.nc") : coordName;
  }
コード例 #19
0
ファイル: TestWritePermute.java プロジェクト: nbald/thredds
  private int[] getWeights(Variable v) {
    int rank = v.getRank();
    int[] w = new int[rank];

    for (int n = 0; n < rank; n++) {
      Dimension dim = v.getDimension(n);
      String dimName = dim.getName();
      if (dimName.equals("time")) w[n] = 1000;
      if (dimName.equals("z")) w[n] = 100;
      if (dimName.equals("y")) w[n] = 10;
      if (dimName.equals("x")) w[n] = 1;
    }

    return w;
  }
コード例 #20
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 #21
0
 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);
 }
コード例 #22
0
ファイル: SeadasFileReader.java プロジェクト: bcdev/seadas
  protected Band addNewBand(Product product, Variable variable) {
    final int sceneRasterWidth = product.getSceneRasterWidth();
    final int sceneRasterHeight = product.getSceneRasterHeight();
    Band band = null;

    int variableRank = variable.getRank();
    if (variableRank == 2) {
      final int[] dimensions = variable.getShape();
      final int height = dimensions[0] - leadLineSkip - tailLineSkip;
      final int width = dimensions[1];
      if (height == sceneRasterHeight && width == sceneRasterWidth) {
        final String name = variable.getShortName();
        final int dataType = getProductDataType(variable);
        band = new Band(name, dataType, width, height);
        final String validExpression = bandInfoMap.get(name);
        if (validExpression != null && !validExpression.equals("")) {
          band.setValidPixelExpression(validExpression);
        }
        product.addBand(band);

        try {
          band.setNoDataValue(
              (double) variable.findAttribute("bad_value_scaled").getNumericValue().floatValue());
          band.setNoDataValueUsed(true);
        } catch (Exception ignored) {
        }

        final List<Attribute> list = variable.getAttributes();
        for (Attribute hdfAttribute : list) {
          final String attribName = hdfAttribute.getShortName();
          if ("units".equals(attribName)) {
            band.setUnit(hdfAttribute.getStringValue());
          } else if ("long_name".equals(attribName)) {
            band.setDescription(hdfAttribute.getStringValue());
          } else if ("slope".equals(attribName)) {
            band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
          } else if ("intercept".equals(attribName)) {
            band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
          }
        }
      }
    }
    return band;
  }
コード例 #23
0
  /**
   * Sets the name of the lookup variable for the East-West position
   *
   * @param name
   */
  public void setXLookup(String name) {
    lonVar = uFile.findVariable(lonName);
    if (lonVar == null) {
      System.out.println(
          "Incorrect variable match:\n\nVariables in local config file: " + lonName + ".");
      System.out.println("Velocity file variables: " + uFile.getVariables().toString() + "\n");
    }

    int dim = 0;

    if (lonVar.getRank() > 1) {
      dim = 1;
    }

    xloc = new IndexLookup_Nearest(lonVar, dim); // dimension 1 because
    // slices
    // have 2D lat/lon
    bounds[3][0] = xloc.getMinVal();
    bounds[3][1] = xloc.getMaxVal();
  }
コード例 #24
0
  public void testAggCoordVarSubsetDefeatLocalCache(NetcdfFile ncfile)
      throws InvalidRangeException, IOException {
    Variable time = ncfile.findVariable("time");
    assert null != time;

    assert time.getShortName().equals("time");
    assert time.getRank() == 1;
    assert time.getSize() == 3;
    assert time.getShape()[0] == 3;
    assert time.getDataType() == DataType.DOUBLE;

    assert time.getDimension(0) == ncfile.findDimension("time");

    time.setCachedData(null, false);
    Array data = time.read("1:2");
    assert data.getRank() == 1;
    assert data.getSize() == 2;
    assert data.getShape()[0] == 2;
    assert data.getElementType() == double.class;

    int count = 0;
    IndexIterator dataI = data.getIndexIterator();
    while (dataI.hasNext()) {
      assert Misc.closeEnough(dataI.getDoubleNext(), result[count + 1]);
      count++;
    }

    time.setCachedData(null, false);
    data = time.read("0:2:2");
    assert data.getRank() == 1;
    assert data.getSize() == 2;
    assert data.getShape()[0] == 2;
    assert data.getElementType() == double.class;

    count = 0;
    dataI = data.getIndexIterator();
    while (dataI.hasNext()) {
      assert Misc.closeEnough(dataI.getDoubleNext(), result[count * 2]);
      count++;
    }
  }
コード例 #25
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 #26
0
  public void testReadData(NetcdfFile ncfile, String name) throws IOException {

    Variable v = ncfile.findVariable(name);
    assert null != v;
    assert v.getShortName().equals(name);
    assert v.getRank() == 3;
    assert v.getSize() == 36 : v.getSize();
    assert v.getShape()[0] == 3;
    assert v.getShape()[1] == 3;
    assert v.getShape()[2] == 4;
    assert v.getDataType() == DataType.DOUBLE;

    assert !v.isCoordinateVariable();

    assert v.getDimension(0) == ncfile.findDimension("time");
    assert v.getDimension(1) == ncfile.findDimension("lat");
    assert v.getDimension(2) == ncfile.findDimension("lon");

    Array data = v.read();
    assert data.getRank() == 3;
    assert data.getSize() == 36;
    assert data.getShape()[0] == 3;
    assert data.getShape()[1] == 3;
    assert data.getShape()[2] == 4;
    assert data.getElementType() == double.class;

    int[] shape = data.getShape();
    Index tIndex = data.getIndex();
    for (int i = 0; i < shape[0]; i++)
      for (int j = 0; j < shape[1]; j++)
        for (int k = 0; k < shape[2]; k++) {
          double val = data.getDouble(tIndex.set(i, j, k));
          // System.out.println(" "+val);
          assert TestUtils.close(val, 100 * i + 10 * j + k) : val;
        }
  }
コード例 #27
0
  public void testCoordVar(NetcdfFile ncfile) {

    Variable lat = ncfile.findVariable("lat");
    assert null != lat;
    assert lat.getShortName().equals("lat");
    assert lat.getRank() == 1;
    assert lat.getSize() == 3;
    assert lat.getShape()[0] == 3;
    assert lat.getDataType() == DataType.FLOAT;

    assert !lat.isUnlimited();
    assert lat.getDimension(0).equals(ncfile.findDimension("lat"));

    Attribute att = lat.findAttribute("units");
    assert null != att;
    assert !att.isArray();
    assert att.isString();
    assert att.getDataType() == DataType.STRING;
    assert att.getStringValue().equals("degrees_north");
    assert att.getNumericValue() == null;
    assert att.getNumericValue(3) == null;

    try {
      Array data = lat.read();
      assert data.getRank() == 1;
      assert data.getSize() == 3;
      assert data.getShape()[0] == 3;
      assert data.getElementType() == float.class;

      IndexIterator dataI = data.getIndexIterator();
      assert TestUtils.close(dataI.getDoubleNext(), 41.0);
      assert TestUtils.close(dataI.getDoubleNext(), 40.0);
      assert TestUtils.close(dataI.getDoubleNext(), 39.0);
    } catch (IOException io) {
    }
  }
コード例 #28
0
  /**
   * Generates an empty template for a block
   *
   * @param files
   * @param outputFile
   * @return
   */
  private NetcdfFileWriteable makeTemplate(TreeMap<Long, NetcdfFile> files, String outputFile) {

    NetcdfFileWriteable ncf_out = null;
    if (!(new File(outputDir).exists())) {
      throw new IllegalArgumentException("Directory " + outputDir + " does not exist.");
    }

    try {
      ncf_in = files.get((new ArrayList<Long>(files.keySet())).get(0));

      Variable time = ncf_in.findVariable(inTimeName);
      if (time == null) {
        List<Variable> var = ncf_in.getVariables();
        System.out.println(
            "WARNING: Variable "
                + inTimeName
                + " was not found.  File variables are:\n"
                + Arrays.toString(var.toArray()));
      }

      Variable depth = ncf_in.findVariable(inDepthName);

      if (depth == null && ncf_in.getDimensions().size() > 3) {
        List<Variable> var = ncf_in.getVariables();
        System.out.println(
            "WARNING: Depth variable "
                + inDepthName
                + " not found, and the number of dimensions is greater than 3."
                + "  File variables are:\n"
                + Arrays.toString(var.toArray()));
      }

      Variable lat = ncf_in.findVariable(inLatName);
      if (lat == null) {
        List<Variable> var = ncf_in.getVariables();
        System.out.println(
            "WARNING: Variable "
                + inLatName
                + " was not found.  File variables are:\n"
                + Arrays.toString(var.toArray()));
      }

      Variable lon = ncf_in.findVariable(inLonName);
      if (lon == null) {
        List<Variable> var = ncf_in.getVariables();
        System.out.println(
            "WARNING: Variable "
                + inLonName
                + " was not found.  File variables are:\n"
                + Arrays.toString(var.toArray()));
      }

      int latidx = lat.findDimensionIndex(inVerticalDim);
      int lonidx = lon.findDimensionIndex(inHorizontalDim);
      int latlen = lat.getDimension(latidx).getLength();
      int lonlen = lon.getDimension(lonidx).getLength();

      Long[] la = files.keySet().toArray(new Long[files.size()]);
      timeArr = Array.factory(DataType.DOUBLE, new int[] {files.size()});

      for (int i = 0; i < la.length; i++) {
        timeArr.setDouble(i, TimeConvert.millisToHYCOM(la[i]));
      }

      if (depth != null) {
        depthArr = depth.read();
        if (reverseDepth) {
          for (int i = 0; i < depthArr.getShape()[0]; i++) {
            if (i != 0) {
              depthArr.setDouble(i, -depthArr.getDouble(i));
            } else {
              depthArr.setDouble(i, 0);
            }
          }
        }
      }

      int[] latshape = ones(lat.getRank());
      latshape[latidx] = latlen;
      latArr = (lat.read(new int[lat.getRank()], latshape)).reduce();

      int[] lonshape = ones(lon.getRank());
      lonshape[lonidx] = lonlen;
      lonArr = (lon.read(new int[lon.getRank()], lonshape)).reduce();

      ncf_out = NetcdfFileWriteable.createNew(outputFile, false);

      // Add Dimensions
      Dimension timeDim = new Dimension(outTimeName, timeArr.getShape()[0]);
      Dimension depthDim = null;

      if (depthArr != null) {
        depthDim = new Dimension(outDepthName, depthArr.getShape()[0]);
      }

      Dimension latDim = new Dimension(outLatName, latArr.getShape()[0]);
      Dimension lonDim = new Dimension(outLonName, lonArr.getShape()[0]);

      ncf_out.addDimension(null, timeDim);
      if (depthDim != null) {
        ncf_out.addDimension(null, depthDim);
      }
      ncf_out.addDimension(null, latDim);
      ncf_out.addDimension(null, lonDim);

      // Add Variables
      ncf_out.addVariable(outTimeName, DataType.DOUBLE, new Dimension[] {timeDim});

      if (depthDim != null) {
        ncf_out.addVariable(outDepthName, DataType.DOUBLE, new Dimension[] {depthDim});
      }

      ncf_out.addVariable(outLatName, DataType.DOUBLE, new Dimension[] {latDim});
      ncf_out.addVariable(outLonName, DataType.DOUBLE, new Dimension[] {lonDim});

      Dimension[] dims = null;

      if (depthDim == null) {
        dims = new Dimension[] {timeDim, latDim, lonDim};
      } else {
        dims = new Dimension[] {timeDim, depthDim, latDim, lonDim};
      }

      ncf_out.addVariable(outVarName, DataType.FLOAT, dims);

      // Add attribute information (cloned from source)

      cloneAttributes(ncf_in, inTimeName, ncf_out, outTimeName);
      cloneAttributes(ncf_in, inDepthName, ncf_out, outDepthName);
      cloneAttributes(ncf_in, inLatName, ncf_out, outLatName);
      cloneAttributes(ncf_in, inLonName, ncf_out, outLonName);
      cloneAttributes(ncf_in, inVarName, ncf_out, outVarName);

      ncf_out.create();
    } catch (IOException e) {
      e.printStackTrace();
    } catch (InvalidRangeException e) {
      e.printStackTrace();
    }

    return ncf_out;
  }
コード例 #29
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 #30
0
  @Override
  public Product createProduct() throws ProductIOException {

    int[] dims;
    int sceneHeight = 0;
    int sceneWidth = 0;
    Group geodata = ncFile.findGroup("geophysical_data");
    if (productReader.getProductType() == SeadasProductReader.ProductType.OISST) {
      dims = ncFile.getVariables().get(4).getShape();
      sceneHeight = dims[2];
      sceneWidth = dims[3];
      mustFlipY = true;
    } else if (productReader.getProductType() == SeadasProductReader.ProductType.ANCCLIM) {
      List<Variable> vars = ncFile.getVariables();
      for (Variable v : vars) {
        if (v.getRank() == 2) {
          dims = v.getShape();
          sceneHeight = dims[0];
          sceneWidth = dims[1];
        }
      }
    } else {
      if (geodata != null) {
        dims = geodata.getVariables().get(0).getShape();
        sceneHeight = dims[0];
        sceneWidth = dims[1];
      } else {
        ucar.nc2.Dimension latdim = ncFile.findDimension("lat");
        ucar.nc2.Dimension londim = ncFile.findDimension("lon");
        if (latdim != null) {
          sceneHeight = latdim.getLength();
          sceneWidth = londim.getLength();
        } else {
          dims = ncFile.getVariables().get(0).getShape();
          sceneHeight = dims[0];
          sceneWidth = dims[1];
        }
      }
    }

    String productName = productReader.getInputFile().getName();
    try {
      productName = getStringAttribute("Product_Name");
    } catch (Exception ignored) {

    }

    SeadasProductReader.ProductType productType = productReader.getProductType();

    Product product = new Product(productName, productType.toString(), sceneWidth, sceneHeight);
    product.setDescription(productName);

    product.setFileLocation(productReader.getInputFile());
    product.setProductReader(productReader);

    addGlobalMetadata(product);
    addSmiMetadata(product);
    //        variableMap = addBands(product, ncFile.getVariables());
    variableMap = addSmiBands(product, ncFile.getVariables());
    try {
      addGeocoding(product);
    } catch (Exception ignored) {
    }
    addFlagsAndMasks(product);
    if (productReader.getProductType() == SeadasProductReader.ProductType.Bathy) {
      mustFlipY = true;
      Dimension tileSize = new Dimension(640, 320);
      product.setPreferredTileSize(tileSize);
    }
    return product;
  }