Java Code Examples for ucar.nc2.Variable#getUnitsString()

private Variable hasUnits(NetcdfDataset ds, String unitList) {
  List<Variable> varList = ds.getVariables();
  StringTokenizer stoker = new StringTokenizer(unitList, ",");
  while (stoker.hasMoreTokens()) {
    String unit = stoker.nextToken();

    for (Variable ve : varList) {
      String hasUnit = ve.getUnitsString();
      if (hasUnit == null)
        continue;
      if (hasUnit.equalsIgnoreCase(unit))
        return ve;
    }
  }
  return null;
}
 

@Test
public void testSimpleGeometryBuildCS() throws IOException, InvalidRangeException {
  NetcdfDataset data =
      NetcdfDataset.openDataset(TestDir.cdmLocalTestDataDir + "dataset/SimpleGeos/hru_soil_moist_3hru_5timestep.nc");
  List<CoordinateSystem> csl = data.getCoordinateSystems();
  SimpleGeometryCSBuilder builder = new SimpleGeometryCSBuilder(data, csl.get(0), null);
  Variable hru_test = data.findVariable("hru_soil_moist");

  SimpleGeometryFeature sgc =
      new SimpleGeometryFeature(hru_test.getFullNameEscaped(), hru_test.getDataType(), hru_test.attributes(),
          csl.get(0).getName(), hru_test.getUnitsString(), hru_test.getDescription(), null, GeometryType.POLYGON);
  sgc.setCoordSys(builder.makeCoordSys());

  // Test retrieval of axis
  Assert.assertEquals("catchments_x", sgc.getXAxis().getFullNameEscaped());
  Assert.assertEquals("catchments_y", sgc.getYAxis().getFullNameEscaped());
  Assert.assertEquals("hruid", sgc.getIDAxis().getFullNameEscaped());
  Assert.assertEquals(null, sgc.getZAxis());

  // Now test reading a geometry.
  SimpleGeometry testGeometry = sgc.readGeometry(0);
  boolean testInstancePolygon = false;

  if (testGeometry instanceof Polygon)
    testInstancePolygon = true;
  Assert.assertEquals(true, testInstancePolygon);

  Polygon polygonTestGeometry = (Polygon) testGeometry;
  Assert.assertEquals(6233, polygonTestGeometry.getPoints().size());
}
 

/**
 * Creates and returns an IGeometryInfo object for the given variable in the given netcdfFile.
 * If no geometry info available, then returns null.
 *
 * @param variable
 * @param netcdfFile
 * @return geometryInfo or null.
 */
public static IArrayGeometryInfo createGeometryInfo(Variable variable, NetcdfFile netcdfFile) {

	Variable latitudeVariable = findLatitudeVariableForVariable(variable, netcdfFile);
	Variable longitudeVariable = findLongitudeVariableForVariable(variable, netcdfFile);
	//currently only 2D grids are supported.
	if (latitudeVariable == null || longitudeVariable == null) {//if data does not depend on space.
		return null;
	}

	//if 2D grid.
	IQuantityInfo latitudeQuantityInfo = new QuantityInfo(LATITUDE_STANDARD_NAME, latitudeVariable.getUnitsString());
	IQuantityInfo longitudeQuantityInfo = new QuantityInfo(LONGITUDE_STANDARD_NAME, longitudeVariable.getUnitsString());
	List<Dimension> latitudeVariableDimensions = latitudeVariable.getDimensions();
	int[] latitudeValueIndices = new int[latitudeVariableDimensions.size()];
	for (int n = 0; n < latitudeValueIndices.length; n++) {
		latitudeValueIndices[n] = variable.findDimensionIndex(latitudeVariableDimensions.get(n).getShortName());
	}
	List<Dimension> longitudeVariableDimensions = longitudeVariable.getDimensions();
	int[] longitudeValueIndices = new int[longitudeVariableDimensions.size()];
	for (int n = 0; n < longitudeValueIndices.length; n++) {
		longitudeValueIndices[n] = variable.findDimensionIndex(longitudeVariableDimensions.get(n).getShortName());
	}
	IArray latitudeArray = (IArray) readData(latitudeVariable);
	IArray longitudeArray = (IArray) readData(longitudeVariable);
       //the latitude and longitude coordinates are stored in the same order as in the netcdf file.
	ArrayGeometryInfo geometryInfo = new ArrayGeometryInfo(latitudeArray, latitudeValueIndices,
			latitudeQuantityInfo, longitudeArray, longitudeValueIndices, longitudeQuantityInfo,null,null,null);
	return geometryInfo;
}
 

/**
 * Returns true if the given variable is a valid time (coordinate) variable.
 *
 * @param variable
 * @return whether the given variable is a valid time (coordinate) variable.
 */
public static boolean isTimeVariable(Variable variable) {
	//check if axis is "T".
	if ("T".equalsIgnoreCase(getAttributeStringValue(variable, AXIS_ATTRIBUTE_NAME))) {
		return true;
	}

	// check if the variable is frequency (the unit is Hz); if so, return false.
	// This is explicitly written here because getDateUnitFromDimension(variable) does not give null
	// for frequency, as if frequency is a time coordinate variable.
	if ("Hz".equalsIgnoreCase(variable.getUnitsString())){
		return false;
	}

	//check if unit of time.
	//according to the CF-convention (see http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.5/cf-conventions.html#time-coordinate):
	//"A time coordinate is identifiable from its units string alone.
	//The Udunits routines utScan() and utIsTime() can be used to make this determination."
	//TODO use Udunits routines utScan() and utIsTime() instead of ucar.nc2.units.DateUnit. AK
	if (variable.getUnitsString() != null && !variable.getUnitsString().isEmpty()
			&& getDateUnitFromDimension(variable) != null) {
		//if variable has a valid unit of time.
		return true;
	}

	return false;
}
 

/**
 * @param var
 * @return DateUnit converted unit for this <code>var</code>
 *		 null if conversion to DateUnit throws an exception
 */
private static DateUnit getDateUnitFromDimension(Variable var) {
	try {
		String unitString = var.getUnitsString();
		DateUnit unit = new DateUnit(unitString);
		return unit;
	} catch (Exception e) {
		//if the given variable does not have a valid unit of time.
		return null;
	}
}
 

/**
 * Returns true if the given variable is a valid latitude variable.
 *
 * @param variable
 * @return whether the given variable is a valid latitude variable.
 */
private static boolean isLatitudeVariable(Variable variable) {
	//check if axis is "Y".
	String axisAttributeStringValue = getAttributeStringValue(variable, AXIS_ATTRIBUTE_NAME);
	if ("Y".equalsIgnoreCase(axisAttributeStringValue)) {
		return true;
	}

	//check if axis is "N".
	if ("N".equalsIgnoreCase(axisAttributeStringValue)) {
		return true;
	}

	//check if standard name is "latitude".
	String standardNameAttributeStringValue = getAttributeStringValue(variable, STANDARD_NAME_ATTRIBUTE_NAME);
	if (LATITUDE_STANDARD_NAME.equalsIgnoreCase(standardNameAttributeStringValue)) {
		return true;
	}

	//check if standard name is "projection_y_coordinate".
	if (LATITUDE_STANDARD_NAME_2.equalsIgnoreCase(standardNameAttributeStringValue)) {
		return true;
	}

	//check if unit of latitude.
	//according to the CF-convention (see http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.5/cf-conventions.html#latitude-coordinate):
	//"The recommended unit of latitude is degrees_north.
	//Also acceptable are degree_north, degree_N, degrees_N, degreeN, and degreesN."
	String unitsString = variable.getUnitsString();
	if (unitsString != null && (unitsString.equalsIgnoreCase("degrees_north") || unitsString.equalsIgnoreCase("degree_north")
								|| unitsString.equalsIgnoreCase("degree_N") || unitsString.equalsIgnoreCase("degrees_N")
								|| unitsString.equalsIgnoreCase("degreeN") || unitsString.equalsIgnoreCase("degreesN"))) {
		//if variable has a valid unit of latitude.
		return true;
	}

	return false;
}
 

/**
 * Returns true if the given variable is a valid longitude variable.
 *
 * @param variable
 * @return whether the given variable is a valid longitude variable.
 */
private static boolean isLongitudeVariable(Variable variable) {
	//check if axis is "X".
	if ("X".equalsIgnoreCase(getAttributeStringValue(variable, AXIS_ATTRIBUTE_NAME))) {
		return true;
	}

	//check if axis is "N".
	if ("N".equalsIgnoreCase(getAttributeStringValue(variable, AXIS_ATTRIBUTE_NAME))) {
		return true;
	}

	//check if standard name is "longitude".
	if (LONGITUDE_STANDARD_NAME.equalsIgnoreCase(getAttributeStringValue(variable, STANDARD_NAME_ATTRIBUTE_NAME))) {
		return true;
	}

	//check if standard name is "projection_x_coordinate".
	if (LONGITUDE_STANDARD_NAME_2.equalsIgnoreCase(getAttributeStringValue(variable, STANDARD_NAME_ATTRIBUTE_NAME))) {
		return true;
	}

	//check if unit of longitude.
	//according to the CF-convention (see http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.5/cf-conventions.html#longitude-coordinate):
	//"The recommended unit of longitude is degrees_east.
	//Also acceptable are degree_east, degree_E, degrees_E, degreeE, and degreesE."
	String unitsString = variable.getUnitsString();
	if (unitsString != null && (unitsString.equalsIgnoreCase("degrees_east") || unitsString.equalsIgnoreCase("degree_east")
								|| unitsString.equalsIgnoreCase("degree_E") || unitsString.equalsIgnoreCase("degrees_N")
								|| unitsString.equalsIgnoreCase("degreeE") || unitsString.equalsIgnoreCase("degreesE"))) {
		//if variable has a valid unit of longitude.
		return true;
	}

	return false;
}
 

protected void setTimeUnits() throws Exception {
  Variable t = ds.findVariable("time");
  String ut = t.getUnitsString();
  dateUnits = new DateUnit(ut);
  calDateUnits = CalendarDateUnit.of(null, ut);
}
 

private void transferGroup(Group srcGroup, Group targetGroup, NetcdfDataset target) throws IOException {
  // group attributes
  DatasetConstructor.transferGroupAttributes(srcGroup, targetGroup);

  // dimensions
  for (Dimension d : srcGroup.getDimensions()) {
    if (null == targetGroup.findDimensionLocal(d.getShortName())) {
      Dimension newd =
          new Dimension(d.getShortName(), d.getLength(), d.isShared(), d.isUnlimited(), d.isVariableLength());
      targetGroup.addDimension(newd);
    }
  }

  // transfer variables - eliminate any references to component files
  for (Variable v : srcGroup.getVariables()) {
    Variable targetV = targetGroup.findVariableLocal(v.getShortName());

    if (null == targetV) { // add it
      if (v instanceof Structure) {
        targetV = new StructureDS(target, targetGroup, null, v.getShortName(), v.getDimensionsString(),
            v.getUnitsString(), v.getDescription());
        // LOOK - not adding the members here - what to do ??

      } else {
        targetV = new VariableDS(target, targetGroup, null, v.getShortName(), v.getDataType(),
            v.getDimensionsString(), v.getUnitsString(), v.getDescription());
      }

      DatasetConstructor.transferVariableAttributes(v, targetV);
      VariableDS vds = (VariableDS) v;
      targetV.setSPobject(vds); // temporary, for non-agg variables when proto is made
      if (vds.hasCachedDataRecurse()) {
        if (vds.getSize() > 1000 * 1000) {
          boolean wtf = vds.hasCachedDataRecurse();
        }
        targetV.setCachedData(vds.read()); //
      }
      targetGroup.addVariable(targetV);
    }
  }

  // nested groups - check if target already has it
  for (Group srcNested : srcGroup.getGroups()) {
    Group nested = targetGroup.findGroupLocal(srcNested.getShortName());
    if (null == nested) {
      nested = new Group(target, targetGroup, srcNested.getShortName());
      targetGroup.addGroup(nested);
      for (EnumTypedef et : srcNested.getEnumTypedefs()) {
        targetGroup.addEnumeration(et);
      }
    }
    transferGroup(srcNested, nested, target);
  }
}