Java Code Examples for ucar.ma2.Array#makeArray()

private boolean addTimeCoordinate(NetcdfDataset ds) {
  // add time coordinate
  CalendarDate cd = parseFilenameForDate(ds.getLocation());
  if (cd == null)
    return false;

  ds.addAttribute(ds.getRootGroup(), new Attribute("_MODIS_Date", cd.toString()));

  // add the time dimension
  int nTimesDim = 1;
  Dimension newDim = new Dimension(TIME_NAME, nTimesDim);
  ds.addDimension(null, newDim);

  // add the coordinate variable
  String units = "seconds since " + cd;
  String desc = "time coordinate";

  Array data = Array.makeArray(DataType.DOUBLE, 1, 0.0, 0.0);

  CoordinateAxis1D timeCoord = new CoordinateAxis1D(ds, null, TIME_NAME, DataType.DOUBLE, "", units, desc);
  timeCoord.setCachedData(data, true);
  timeCoord.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
  ds.addCoordinateAxis(timeCoord);

  return true;
}
 

/**
 * Set the data values from a list of Strings.
 *
 * @param v for this variable
 * @param values list of Strings
 * @throws IllegalArgumentException if values array not correct size, or values wont parse to the correct type
 * @deprecated use Variable.setValues()
 */
@Deprecated
public void setValues(Variable v, List<String> values) throws IllegalArgumentException {
  Array data = Array.makeArray(v.getDataType(), values);

  if (data.getSize() != v.getSize())
    throw new IllegalArgumentException("Incorrect number of values specified for the Variable " + v.getFullName()
        + " needed= " + v.getSize() + " given=" + data.getSize());

  if (v.getRank() != 1) // dont have to reshape for rank 1
    data = data.reshape(v.getShape());

  v.setCachedData(data, true);
}
 

TimeStringParsing() throws IOException {

    String filename = "file:C:\\Documents and Settings\\caron\\.unidata\\cachePersist\\fileD-godas-singleAgg.ncml";
    Element aggElem = ucar.nc2.util.xml.Parse.readRootElement(filename);

    List<Element> ncList = aggElem.getChildren("netcdf", thredds.client.catalog.Catalog.ncmlNS);
    for (Element netcdfElemNested : ncList) {
      String location = netcdfElemNested.getAttributeValue("location");

      List<Element> cacheElemList = netcdfElemNested.getChildren("cache", thredds.client.catalog.Catalog.ncmlNS);
      for (Element cacheElemNested : cacheElemList) {
        String varName = cacheElemNested.getAttributeValue("varName");
        String sdata = cacheElemNested.getText();
        System.out.println("text size = " + sdata.length());

        long start = System.nanoTime();
        String[] vals = sdata.split(" ");
        double took = .001 * .001 * .001 * (System.nanoTime() - start);
        System.out.println(" split took = " + took + " sec; ");

        start = System.nanoTime();
        Array data = Array.makeArray(DataType.DOUBLE, vals);
        took = .001 * .001 * .001 * (System.nanoTime() - start);
        System.out.println(" makeArray took = " + took + " sec; ");
      }
    }

  }
 

/**
 * Parse the values element
 *
 * @param s JDOM element to parse
 * @return Array with parsed values
 * @throws IllegalArgumentException if string values not parsable to specified data type
 */
public static ucar.ma2.Array readAttributeValues(Element s) throws IllegalArgumentException {
  String valString = s.getAttributeValue("value");

  // can also be element text
  if (valString == null) {
    valString = s.getTextNormalize();
  }

  // no value specified hmm technically this is not illegal !!
  if (valString == null)
    throw new IllegalArgumentException("No value specified");

  String type = s.getAttributeValue("type");
  DataType dtype = (type == null) ? DataType.STRING : DataType.getType(type);
  if (dtype == DataType.CHAR)
    dtype = DataType.STRING;

  // backwards compatibility with deprecated isUnsigned attribute
  String unS = s.getAttributeValue("isUnsigned");
  boolean isUnsignedSet = "true".equalsIgnoreCase(unS);
  if (isUnsignedSet && dtype.isIntegral() && !dtype.isUnsigned()) {
    dtype = dtype.withSignedness(DataType.Signedness.UNSIGNED);
  }

  String sep = s.getAttributeValue("separator");
  if ((sep == null) && (dtype == DataType.STRING)) {
    List<String> list = new ArrayList<>();
    list.add(valString);
    return Array.makeArray(dtype, list);
  }

  if (sep == null)
    sep = " "; // default whitespace separated

  List<String> stringValues = new ArrayList<>();
  StringTokenizer tokn = new StringTokenizer(valString, sep);
  while (tokn.hasMoreTokens())
    stringValues.add(tokn.nextToken());

  return Array.makeArray(dtype, stringValues);
}
 

/**
 * Parse the values element
 *
 * @param s JDOM element to parse
 * @return Array with parsed values
 * @throws IllegalArgumentException if string values not parsable to specified data type
 */
private static ucar.ma2.Array readAttributeValues(Element s) throws IllegalArgumentException {
  String valString = s.getAttributeValue("value");

  // can also be element text
  if (valString == null) {
    valString = s.getTextNormalize();
  }

  // no value specified hmm technically this is not illegal !!
  if (valString == null) {
    throw new IllegalArgumentException("No value specified");
  }

  String type = s.getAttributeValue("type");
  DataType dtype = (type == null) ? DataType.STRING : DataType.getType(type);
  if (dtype == DataType.CHAR) {
    dtype = DataType.STRING;
  }

  // backwards compatibility with deprecated isUnsigned attribute
  String unS = s.getAttributeValue("isUnsigned");
  boolean isUnsignedSet = "true".equalsIgnoreCase(unS);
  if (isUnsignedSet && dtype.isIntegral() && !dtype.isUnsigned()) {
    dtype = dtype.withSignedness(DataType.Signedness.UNSIGNED);
  }

  String sep = s.getAttributeValue("separator");
  if ((sep == null) && (dtype == DataType.STRING)) {
    List<String> list = new ArrayList<>();
    list.add(valString);
    return Array.makeArray(dtype, list);
  }

  if (sep == null) {
    sep = " "; // default whitespace separated
  }

  List<String> stringValues = new ArrayList<>();
  StringTokenizer tokn = new StringTokenizer(valString, sep);
  while (tokn.hasMoreTokens()) {
    stringValues.add(tokn.nextToken());
  }

  return Array.makeArray(dtype, stringValues);
}
 

@Test
public void testArrayConstructor() {
  Array data = Array.makeArray(DataType.FLOAT, ImmutableList.of("3.14", ".0015"));
  Attribute att = Attribute.builder().setName("name").setValues(data).build();
  assertThat(att).isEqualTo(new Attribute("name", data));
}
 

@Test
public void testUnsignedAttribute() throws IOException, InvalidRangeException {
  String filename = tempFolder.newFile().getAbsolutePath();

  NetcdfFormatWriter.Builder writerb = NetcdfFormatWriter.createNewNetcdf3(filename);
  writerb.addUnlimitedDimension("time");

  writerb.addVariable("time", DataType.BYTE, "time").addAttribute(new Attribute(CDM.UNSIGNED, "true"))
      .addAttribute(new Attribute(CDM.SCALE_FACTOR, 10.0))
      .addAttribute(new Attribute(CDM.VALID_RANGE, ImmutableList.of(10, 240), false));

  /*
   * byte Band1(y, x);
   * > Band1:_Unsigned = "true";
   * > Band1:_FillValue = -1b; // byte
   */
  writerb.addVariable("Band1", DataType.BYTE, "time").addAttribute(new Attribute(CDM.UNSIGNED, "true"))
      .addAttribute(new Attribute(CDM.FILL_VALUE, (byte) -1)).addAttribute(new Attribute(CDM.SCALE_FACTOR, 1.0));

  /*
   * byte Band2(y, x);
   * > Band2:_Unsigned = "true";
   * > Band2:valid_range = 0s, 254s; // short
   */
  writerb.addVariable("Band2", DataType.BYTE, "time").addAttribute(new Attribute(CDM.UNSIGNED, "true"))
      .addAttribute(new Attribute(CDM.SCALE_FACTOR, 1.0))
      .addAttribute(new Attribute(CDM.VALID_RANGE, ImmutableList.of((short) 0, (short) 254)));

  try (NetcdfFormatWriter writer = writerb.build()) {
    Array timeData = Array.factory(DataType.BYTE, new int[] {1});
    int[] time_origin = new int[] {0};

    for (int time = 0; time < 256; time++) {
      timeData.setInt(timeData.getIndex(), time);
      time_origin[0] = time;
      writer.write("time", time_origin, timeData);
      writer.write("Band1", time_origin, timeData);
      writer.write("Band2", time_origin, timeData);
    }
  }

  Array expected = Array.makeArray(DataType.BYTE, 256, 0, 1);
  try (NetcdfFile ncFile = NetcdfFiles.open(filename)) {
    Array result2 = ncFile.readSection("time");
    CompareNetcdf2.compareData("time", expected, result2);
  }
}
 

/**
 * Generate the list of values from a starting value and an increment.
 * Will reshape to variable if needed.
 *
 * @param v for this variable
 * @param npts number of values, must = v.getSize()
 * @param start starting value
 * @param incr increment
 * @deprecated use Variable.setValues()
 */
@Deprecated
public void setValues(Variable v, int npts, double start, double incr) {
  if (npts != v.getSize())
    throw new IllegalArgumentException("bad npts = " + npts + " should be " + v.getSize());
  Array data = Array.makeArray(v.getDataType(), npts, start, incr);
  if (v.getRank() != 1)
    data = data.reshape(v.getShape());
  v.setCachedData(data, true);
}
 

/**
 * Make a 1D array from a list of strings.
 *
 * @param dtype data type of the array.
 * @param stringValues list of strings.
 * @return resulting 1D array.
 * @throws NumberFormatException if string values not parssable to specified data type
 * @deprecated use Array#makeArray directly
 */
@Deprecated
public static Array makeArray(DataType dtype, List<String> stringValues) throws NumberFormatException {
  return Array.makeArray(dtype, stringValues);
}