Java Code Examples for ucar.nc2.dataset.CoordinateAxis1D#Builder

@Nullable
private CoordinateAxis.Builder makeLonCoordAxis(int n, String xname) {
  double min = findAttributeDouble("xMin");
  double max = findAttributeDouble("xMax");
  double d = findAttributeDouble("dx");
  if (Double.isNaN(min) || Double.isNaN(max) || Double.isNaN(d))
    return null;

  CoordinateAxis1D.Builder v = CoordinateAxis1D.builder().setName(xname).setDataType(DataType.DOUBLE)
      .setParentGroupBuilder(rootGroup).setDimensionsByName(xname).setUnits(CDM.LON_UNITS).setDesc("longitude");
  v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
  v.setAutoGen(min, d);

  double maxCalc = min + d * n;
  parseInfo.format("Created Lon Coordinate Axis (max calc= %f should be = %f)%n", maxCalc, max);
  return v;
}
 

private CoordinateAxis.Builder makeLatCoordAxis(int n, String name) {
  double min = findAttributeDouble("yMin");
  double max = findAttributeDouble("yMax");
  double d = findAttributeDouble("dy");
  if (Double.isNaN(min) || Double.isNaN(max) || Double.isNaN(d))
    return null;

  CoordinateAxis1D.Builder v = CoordinateAxis1D.builder().setName(name).setDataType(DataType.DOUBLE)
      .setParentGroupBuilder(rootGroup).setDimensionsByName(name).setUnits(CDM.LAT_UNITS).setDesc("latitude");
  v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
  v.setAutoGen(min, d);

  double maxCalc = min + d * n;
  parseInfo.format("Created Lat Coordinate Axis (max calc= %f should be = %f)%n", maxCalc, max);
  return v;
}
 

private CoordinateAxis.Builder makeLonCoordAxis(String xname) {
  CoordinateAxis1D.Builder v = CoordinateAxis1D.builder().setName(xname).setDataType(DataType.DOUBLE)
      .setParentGroupBuilder(rootGroup).setDimensionsByName(xname).setUnits(CDM.LON_UNITS).setDesc("longitude");
  v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
  v.setAutoGen(startx, dx);

  parseInfo.format("Created Lon Coordinate Axis = %s%n", xname);
  return v;
}
 

private CoordinateAxis.Builder makeLatCoordAxis(String yname) {
  CoordinateAxis1D.Builder v = CoordinateAxis1D.builder().setName(yname).setDataType(DataType.DOUBLE)
      .setParentGroupBuilder(rootGroup).setDimensionsByName(yname).setUnits(CDM.LAT_UNITS).setDesc("latitude");
  v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
  v.setAutoGen(starty, dy);
  parseInfo.format("Created Lat Coordinate Axis = %s%n", yname);
  return v;
}
 

CoordinateAxis.Builder makeXCoordAxis(String xname) {
  CoordinateAxis1D.Builder v = CoordinateAxis1D.builder().setName(xname).setDataType(DataType.DOUBLE)
      .setParentGroupBuilder(rootGroup).setDimensionsByName(xname).setUnits("km").setDesc("x on projection");
  v.setAutoGen(startx, dx);

  parseInfo.format("Created X Coordinate Axis = %s%n", xname);
  return v;
}
 

CoordinateAxis.Builder makeYCoordAxis(String yname) {
  CoordinateAxis1D.Builder v = CoordinateAxis1D.builder().setName(yname).setDataType(DataType.DOUBLE)
      .setParentGroupBuilder(rootGroup).setDimensionsByName(yname).setUnits("km").setDesc("y on projection");
  v.setAutoGen(starty, dy);

  parseInfo.format("Created Y Coordinate Axis = %s%n", yname);
  return v;
}
 

@Nullable
private CoordinateAxis.Builder makeTimeCoordAxisFromReference(Array vals) {
  if (!rootGroup.findVariableLocal("reftime").isPresent())
    return null;
  VariableDS.Builder refVar = (VariableDS.Builder) rootGroup.findVariableLocal("reftime").get();

  double refValue;
  try {
    Array refArray = refVar.orgVar.read();
    refValue = refArray.getDouble(refArray.getIndex()); // get the first value
  } catch (IOException ioe) {
    return null;
  }
  if (refValue == N3iosp.NC_FILL_DOUBLE) // why?
    return null;

  // construct the values array - make it a double to be safe
  Array dvals = Array.factory(DataType.DOUBLE, vals.getShape());
  IndexIterator diter = dvals.getIndexIterator();
  IndexIterator iiter = vals.getIndexIterator();
  while (iiter.hasNext())
    diter.setDoubleNext(iiter.getDoubleNext() + refValue); // add reftime to each of the values

  String name = "timeCoord";
  String units = refVar.getAttributeContainer().findAttributeString(CDM.UNITS, "seconds since 1970-1-1 00:00:00");
  units = normalize(units);
  String desc = "synthesized time coordinate from reftime, valtimeMINUSreftime";
  CoordinateAxis1D.Builder timeCoord =
      CoordinateAxis1D.builder().setName(name).setDataType(DataType.DOUBLE).setParentGroupBuilder(rootGroup)
          .setDimensionsByName("record").setUnits(units).setDesc(desc).setCachedData(dvals, true);

  parseInfo.format("Created Time Coordinate Axis From reftime Variable%n");
  return timeCoord;
}
 

private CoordinateAxis.Builder makeTimeCoordAxis() {
  VariableDS.Builder timeVar = (VariableDS.Builder) rootGroup.findVariableLocal("valtimeMINUSreftime")
      .orElseThrow(() -> new RuntimeException("must have varible 'valtimeMINUSreftime'"));

  Dimension recordDim =
      rootGroup.findDimension("record").orElseThrow(() -> new RuntimeException("must have dimension 'record'"));

  Array vals;
  try {
    vals = timeVar.orgVar.read();
  } catch (IOException ioe) {
    return null;
  }

  // it seems that the record dimension does not always match valtimeMINUSreftime dimension!!
  // HAHAHAHAHAHAHAHA !
  int recLen = recordDim.getLength();
  int valLen = (int) vals.getSize();
  if (recLen != valLen) {
    try {
      vals = vals.sectionNoReduce(new int[] {0}, new int[] {recordDim.getLength()}, null);
      parseInfo.format(" corrected the TimeCoordAxis length%n");
    } catch (InvalidRangeException e) {
      parseInfo.format("makeTimeCoordAxis InvalidRangeException%n");
    }
  }

  // create the units out of the filename if possible
  String units = makeTimeUnitFromFilename(datasetBuilder.location);
  if (units == null) // ok that didnt work, try something else
    return makeTimeCoordAxisFromReference(vals);

  // create the coord axis
  String name = "timeCoord";
  String desc = "synthesized time coordinate from valtimeMINUSreftime and filename YYYYMMDD_HHMM";
  CoordinateAxis1D.Builder timeCoord =
      CoordinateAxis1D.builder().setName(name).setDataType(DataType.INT).setParentGroupBuilder(rootGroup)
          .setDimensionsByName("record").setUnits(units).setDesc(desc).setCachedData(vals, true);

  parseInfo.format("Created Time Coordinate Axis = %s%n", name);
  return timeCoord;
}
 

private void makeTimeCoordAxis(String timeName) {
  int start_date = findAttributeInt("SDATE");
  int start_time = findAttributeInt("STIME");
  int time_step = findAttributeInt("TSTEP");

  int year = start_date / 1000;
  int doy = start_date % 1000;
  int hour = start_time / 10000;
  start_time = start_time % 10000;
  int min = start_time / 100;
  int sec = start_time % 100;

  Calendar cal = new GregorianCalendar(new SimpleTimeZone(0, "GMT"));
  cal.clear();
  cal.set(Calendar.YEAR, year);
  cal.set(Calendar.DAY_OF_YEAR, doy);
  cal.set(Calendar.HOUR_OF_DAY, hour);
  cal.set(Calendar.MINUTE, min);
  cal.set(Calendar.SECOND, sec);

  java.text.SimpleDateFormat dateFormatOut = new java.text.SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
  dateFormatOut.setTimeZone(TimeZone.getTimeZone("GMT"));

  String units = "seconds since " + dateFormatOut.format(cal.getTime()) + " UTC";

  // parse the time step
  hour = time_step / 10000;
  time_step = time_step % 10000;
  min = time_step / 100;
  sec = time_step % 100;
  time_step = hour * 3600 + min * 60 + sec;

  // create the coord axis
  CoordinateAxis1D.Builder timeCoord = CoordinateAxis1D.builder().setName("time").setDataType(DataType.INT)
      .setParentGroupBuilder(rootGroup).setDimensionsByName(timeName).setUnits(units)
      .setDesc("synthesized time coordinate from SDATE, STIME, STEP global attributes");
  timeCoord.setAutoGen(0, time_step);
  timeCoord.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));

  datasetBuilder.replaceCoordinateAxis(rootGroup, timeCoord);
}
 

private void createTimeCoordinate(VariableDS.Builder<?> ncVar) {
  // Time coordinate is stored in the attribute validTimes
  // One caveat is that the times have two bounds an upper and a lower

  // get the times values
  Attribute timesAtt = ncVar.getAttributeContainer().findAttribute("validTimes");
  if (timesAtt == null)
    return;
  Array timesArray = timesAtt.getValues();

  // get every other one LOOK this is awkward
  try {
    int n = (int) timesArray.getSize();
    List<Range> list = new ArrayList<>();
    list.add(new Range(0, n - 1, 2));
    timesArray = timesArray.section(list);
  } catch (InvalidRangeException e) {
    throw new IllegalStateException(e);
  }

  // make sure it matches the dimension
  DataType dtype = DataType.getType(timesArray);
  int nTimesAtt = (int) timesArray.getSize();

  // create a special dimension and coordinate variable
  Dimension dimTime = ncVar.orgVar.getDimension(0);
  int nTimesDim = dimTime.getLength();
  if (nTimesDim != nTimesAtt) {
    parseInfo.format(" **error ntimes in attribute (%d) doesnt match dimension length (%d) for variable %s%n",
        nTimesAtt, nTimesDim, ncVar.getFullName());
    return;
  }

  // add the dimension
  String dimName = ncVar.shortName + "_timeCoord";
  Dimension newDim = new Dimension(dimName, nTimesDim);
  rootGroup.addDimension(newDim);

  // add the coordinate variable
  String units = "seconds since 1970-1-1 00:00:00";
  String desc = "time coordinate for " + ncVar.shortName;

  CoordinateAxis1D.Builder timeCoord = CoordinateAxis1D.builder().setName(dimName).setDataType(dtype)
      .setParentGroupBuilder(rootGroup).setDimensionsByName(dimName).setUnits(units).setDesc(desc);
  timeCoord.setCachedData(timesArray, true);
  timeCoord.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
  datasetBuilder.replaceCoordinateAxis(rootGroup, timeCoord);

  parseInfo.format(" added coordinate variable %s%n", dimName);

  // now make the original variable use the new dimension
  ArrayList<Dimension> newDims = new ArrayList<>(ncVar.getDimensions());
  newDims.set(0, newDim);
  ncVar.setDimensions(newDims);

  // better to explicitly set the coordinate system
  ncVar.addAttribute(new Attribute(_Coordinate.Axes, dimName + " yCoord xCoord"));

  // fix the attributes
  Attribute att = ncVar.getAttributeContainer().findAttribute("fillValue");
  if (att != null)
    ncVar.addAttribute(new Attribute(CDM.FILL_VALUE, att.getNumericValue()));
  att = ncVar.getAttributeContainer().findAttribute("descriptiveName");
  if (null != att)
    ncVar.addAttribute(new Attribute(CDM.LONG_NAME, att.getStringValue()));
}