Java Code Examples for ucar.nc2.constants.AxisType#Pressure

/**
 * Turn the variable into a coordinate axis, if not already. Add to the dataset, replacing variable if needed.
 *
 * @return variable as a coordinate axis
 */
public CoordinateAxis makeIntoCoordinateAxis() {
  if (axis != null)
    return axis;

  // if not a CoordinateAxis, will turn into one
  v = axis = ds.addCoordinateAxis((VariableDS) v);

  if (axisType != null) {
    axis.setAxisType(axisType);
    axis.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));

    if (((axisType == AxisType.Height) || (axisType == AxisType.Pressure) || (axisType == AxisType.GeoZ))
        && (positive != null)) {
      axis.setPositive(positive);
      axis.addAttribute(new Attribute(_Coordinate.ZisPositive, positive));
    }
  }
  return axis;
}
 

public CoverageCoordAxis getZAxis() {
  for (String axisName : getAxisNames()) {
    CoverageCoordAxis axis = dataset.findCoordAxis(axisName);
    if (axis == null)
      throw new IllegalStateException("Cant find axis with name " + axisName);
    if (axis.getAxisType() == AxisType.GeoZ || axis.getAxisType() == AxisType.Height
        || axis.getAxisType() == AxisType.Pressure)
      return axis;
  }
  return null;
}
 

public static AxisType convertAxisType(CdmrFeatureProto.AxisType dtype) {
  switch (dtype) {
    case RunTime:
      return AxisType.RunTime;
    case Ensemble:
      return AxisType.Ensemble;
    case Time:
      return AxisType.Time;
    case GeoX:
      return AxisType.GeoX;
    case GeoY:
      return AxisType.GeoY;
    case GeoZ:
      return AxisType.GeoZ;
    case Lat:
      return AxisType.Lat;
    case Lon:
      return AxisType.Lon;
    case Height:
      return AxisType.Height;
    case Pressure:
      return AxisType.Pressure;
    case RadialAzimuth:
      return AxisType.RadialAzimuth;
    case RadialDistance:
      return AxisType.RadialDistance;
    case RadialElevation:
      return AxisType.RadialElevation;
    case Spectral:
      return AxisType.Spectral;
    case TimeOffset:
      return AxisType.TimeOffset;
  }
  throw new IllegalStateException("illegal data type " + dtype);
}
 

/**
 * true if increasing z coordinate values means "up" in altitude
 */
@Override
public boolean isZPositive() {
  if (vertZaxis == null)
    return false;
  if (vertZaxis.getPositive() != null) {
    return vertZaxis.getPositive().equalsIgnoreCase(ucar.nc2.constants.CF.POSITIVE_UP);
  }
  if (vertZaxis.getAxisType() == AxisType.Height)
    return true;
  return vertZaxis.getAxisType() != AxisType.Pressure;
}
 

@Override
protected AxisType getAxisType(VariableDS.Builder vb) {
  String vname = vb.shortName;

  if (vname.equalsIgnoreCase("x") || vname.equalsIgnoreCase("x_stag"))
    return AxisType.GeoX;

  if (vname.equalsIgnoreCase("lon"))
    return AxisType.Lon;

  if (vname.equalsIgnoreCase("y") || vname.equalsIgnoreCase("y_stag"))
    return AxisType.GeoY;

  if (vname.equalsIgnoreCase("lat"))
    return AxisType.Lat;

  if (vname.equalsIgnoreCase("z") || vname.equalsIgnoreCase("z_stag"))
    return AxisType.GeoZ;

  if (vname.equalsIgnoreCase("Z"))
    return AxisType.Height;

  if (vname.equalsIgnoreCase("time"))
    return AxisType.Time;

  String unit = vb.getUnits();
  if (unit != null) {
    if (SimpleUnit.isCompatible("millibar", unit))
      return AxisType.Pressure;

    if (SimpleUnit.isCompatible("m", unit))
      return AxisType.Height;
  }


  return null;
}
 

@Override
@Nullable
protected AxisType getAxisType(VariableDS.Builder v) {
  String vname = v.shortName;

  if (vname.equalsIgnoreCase("x"))
    return AxisType.GeoX;
  if (vname.equalsIgnoreCase("lon"))
    return AxisType.Lon;
  if (vname.equalsIgnoreCase("y"))
    return AxisType.GeoY;
  if (vname.equalsIgnoreCase("lat"))
    return AxisType.Lat;
  if (vname.equalsIgnoreCase("record"))
    return AxisType.Time;

  String dimName = v.getFirstDimensionName();
  if ((dimName != null) && dimName.equalsIgnoreCase("record"))
    return AxisType.Time;

  String unit = v.getUnits();
  if (unit != null) {
    if (SimpleUnit.isCompatible("millibar", unit))
      return AxisType.Pressure;
    if (SimpleUnit.isCompatible("m", unit))
      return AxisType.Height;
  }
  // otherwise guess
  return AxisType.GeoZ;
}
 

@Override
@Nullable
protected AxisType getAxisType(VariableDS.Builder v) {
  String vname = v.shortName;

  if (vname.equalsIgnoreCase("x") || vname.equalsIgnoreCase("x_stag"))
    return AxisType.GeoX;

  if (vname.equalsIgnoreCase("lon"))
    return AxisType.Lon;

  if (vname.equalsIgnoreCase("y") || vname.equalsIgnoreCase("y_stag"))
    return AxisType.GeoY;

  if (vname.equalsIgnoreCase("lat"))
    return AxisType.Lat;

  if (vname.equalsIgnoreCase("z") || vname.equalsIgnoreCase("z_stag"))
    return AxisType.GeoZ;

  if (vname.equalsIgnoreCase("Z"))
    return AxisType.Height;

  if (vname.equalsIgnoreCase("time") || vname.equalsIgnoreCase("times"))
    return AxisType.Time;

  String unit = v.getUnits();
  if (unit != null) {
    if (SimpleUnit.isCompatible("millibar", unit))
      return AxisType.Pressure;

    if (SimpleUnit.isCompatible("m", unit))
      return AxisType.Height;
  }


  return null;
}
 

protected AxisType getAxisType(NetcdfDataset ds, VariableEnhanced ve) {
  Variable v = (Variable) ve;
  String vname = v.getShortName();

  if (vname.equalsIgnoreCase("x") || vname.equalsIgnoreCase("x_stag"))
    return AxisType.GeoX;

  if (vname.equalsIgnoreCase("lon"))
    return AxisType.Lon;

  if (vname.equalsIgnoreCase("y") || vname.equalsIgnoreCase("y_stag"))
    return AxisType.GeoY;

  if (vname.equalsIgnoreCase("lat"))
    return AxisType.Lat;

  if (vname.equalsIgnoreCase("z") || vname.equalsIgnoreCase("z_stag"))
    return AxisType.GeoZ;

  if (vname.equalsIgnoreCase("Z"))
    return AxisType.Height;

  if (vname.equalsIgnoreCase("time") || vname.equalsIgnoreCase("times"))
    return AxisType.Time;

  String unit = ve.getUnitsString();
  if (unit != null) {
    if (SimpleUnit.isCompatible("millibar", unit))
      return AxisType.Pressure;

    if (SimpleUnit.isCompatible("m", unit))
      return AxisType.Height;
  }


  return null;
}
 

protected AxisType getAxisType(NetcdfDataset ds, VariableEnhanced ve) {
  Variable v = (Variable) ve;
  String vname = v.getShortName();

  if (vname.equalsIgnoreCase("x"))
    return AxisType.GeoX;

  if (vname.equalsIgnoreCase("lon"))
    return AxisType.Lon;

  if (vname.equalsIgnoreCase("y"))
    return AxisType.GeoY;

  if (vname.equalsIgnoreCase("lat"))
    return AxisType.Lat;

  if (vname.equalsIgnoreCase("record"))
    return AxisType.Time;
  Dimension dim = v.getDimension(0);
  if ((dim != null) && dim.getShortName().equalsIgnoreCase("record"))
    return AxisType.Time;

  String unit = ve.getUnitsString();
  if (unit != null) {
    if (SimpleUnit.isCompatible("millibar", unit))
      return AxisType.Pressure;

    if (SimpleUnit.isCompatible("m", unit))
      return AxisType.Height;
  }


  return AxisType.GeoZ;
}
 

/**
 * Turn the variable into a coordinate axis.
 * Add to the dataset, replacing variable if needed.
 *
 * @return coordinate axis
 */
protected CoordinateAxis.Builder makeIntoCoordinateAxis() {
  if (axis != null) {
    return axis;
  }

  if (vb instanceof CoordinateAxis.Builder) {
    axis = (CoordinateAxis.Builder) vb;
  } else {
    // Create a CoordinateAxis out of this variable.
    vb = axis = CoordinateAxis.fromVariableDS(vb);
  }

  if (axisType != null) {
    axis.setAxisType(axisType);
    axis.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));

    if (((axisType == AxisType.Height) || (axisType == AxisType.Pressure) || (axisType == AxisType.GeoZ))
        && (positive != null)) {
      axis.setPositive(positive);
      axis.addAttribute(new Attribute(_Coordinate.ZisPositive, positive));
    }
  }
  coords.replaceCoordinateAxis(axis);
  if (axis.getParentStructureBuilder() != null) {
    axis.getParentStructureBuilder().replaceMemberVariable(axis);
  } else {
    gb.replaceVariable(axis);
  }
  return axis;
}
 

protected AxisType getAxisType(NetcdfDataset ds, VariableEnhanced ve) {
  Variable v = (Variable) ve;
  String vname = v.getShortName();

  if (vname.equalsIgnoreCase("x") || vname.equalsIgnoreCase("x_stag"))
    return AxisType.GeoX;

  if (vname.equalsIgnoreCase("lon"))
    return AxisType.Lon;

  if (vname.equalsIgnoreCase("y") || vname.equalsIgnoreCase("y_stag"))
    return AxisType.GeoY;

  if (vname.equalsIgnoreCase("lat"))
    return AxisType.Lat;

  if (vname.equalsIgnoreCase("z") || vname.equalsIgnoreCase("z_stag"))
    return AxisType.GeoZ;

  if (vname.equalsIgnoreCase("Z"))
    return AxisType.Height;

  if (vname.equalsIgnoreCase("time"))
    return AxisType.Time;

  String unit = ve.getUnitsString();
  if (unit != null) {
    if (SimpleUnit.isCompatible("millibar", unit))
      return AxisType.Pressure;

    if (SimpleUnit.isCompatible("m", unit))
      return AxisType.Height;
  }


  return null;
}
 

protected AxisType getAxisType(NetcdfDataset ds, VariableEnhanced ve) {
  Variable v = (Variable) ve;
  String vname = v.getShortName();

  if (vname.equalsIgnoreCase("lat"))
    return AxisType.Lat;

  if (vname.equalsIgnoreCase("lon"))
    return AxisType.Lon;

  if (vname.equalsIgnoreCase(xaxisName))
    return AxisType.GeoX;

  if (vname.equalsIgnoreCase(yaxisName))
    return AxisType.GeoY;

  if (vname.equalsIgnoreCase("record"))
    return AxisType.Time;
  Dimension dim = v.getDimension(0);
  if ((dim != null) && dim.getShortName().equalsIgnoreCase("record")) { // wow thats bad!
    return AxisType.Time;
  }

  String unit = ve.getUnitsString();
  if (unit != null) {
    if (SimpleUnit.isCompatible("millibar", unit))
      return AxisType.Pressure;

    if (SimpleUnit.isCompatible("m", unit))
      return AxisType.Height;

    if (SimpleUnit.isCompatible("sec", unit))
      return null;
  }

  return AxisType.GeoZ; // AxisType.GeoZ;
}
 

@Nullable
private AxisType getAxisTypeCoards(VariableDS.Builder vb) {
  String unit = vb.getUnits();
  if (unit == null) {
    return null;
  }

  if (unit.equalsIgnoreCase("degrees_east") || unit.equalsIgnoreCase("degrees_E") || unit.equalsIgnoreCase("degreesE")
      || unit.equalsIgnoreCase("degree_east") || unit.equalsIgnoreCase("degree_E")
      || unit.equalsIgnoreCase("degreeE")) {
    return AxisType.Lon;
  }

  if (unit.equalsIgnoreCase("degrees_north") || unit.equalsIgnoreCase("degrees_N")
      || unit.equalsIgnoreCase("degreesN") || unit.equalsIgnoreCase("degree_north")
      || unit.equalsIgnoreCase("degree_N") || unit.equalsIgnoreCase("degreeN")) {
    return AxisType.Lat;
  }

  if (SimpleUnit.isDateUnit(unit)) // || SimpleUnit.isTimeUnit(unit)) removed dec 18, 2008
  {
    return AxisType.Time;
  }

  // look for other z coordinate
  // if (SimpleUnit.isCompatible("m", unit))
  // return AxisType.Height;
  if (SimpleUnit.isCompatible("mbar", unit)) {
    return AxisType.Pressure;
  }
  if (unit.equalsIgnoreCase("level") || unit.equalsIgnoreCase("layer") || unit.equalsIgnoreCase("sigma_level")) {
    return AxisType.GeoZ;
  }

  String positive = vb.getAttributeContainer().findAttributeString("positive", null);
  if (positive != null) {
    if (SimpleUnit.isCompatible("m", unit)) {
      return AxisType.Height;
    } else {
      return AxisType.GeoZ;
    }
  }
  return null;
}
 

/**
 * Create a vertical dimension variable based on the info. Based on
 * visad.data.vis5d.Vis5DVerticalSystem.
 *
 * @param vert_sys the vertical system id
 * @param n_levels the number of levels
 * @param vert_args the vertical system arguments
 * @return the vertical dimesion variable
 * @throws IOException problem reading the file or creating the data
 */
private Variable makeVerticalVariable(int vert_sys, int n_levels, float[] vert_args) throws IOException {

  String vert_unit;
  String vert_type;
  ArrayFloat.D1 data = new ArrayFloat.D1(n_levels);
  AxisType axisType = null;

  switch (vert_sys) {

    case (0):
      vert_unit = null;
      vert_type = "height";
      break;

    case (1):
    case (2):
      vert_unit = "km";
      vert_type = "altitude";
      axisType = AxisType.Height;
      break;

    case (3):
      vert_unit = "mbar";
      vert_type = "pressure";
      axisType = AxisType.Pressure;
      break;

    default:
      throw new IOException("vert_sys unknown");
  }

  Variable vertVar = new Variable(ncfile, null, null, vert_type);
  vertVar.setDimensions(LEVEL);
  vertVar.setDataType(DataType.FLOAT);
  if (vert_unit != null) {
    vertVar.addAttribute(new Attribute(CDM.UNITS, vert_unit));
  }
  if (axisType != null) {
    vertVar.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));
  }

  switch (vert_sys) {

    case (0):
    case (1):
      for (int i = 0; i < n_levels; i++) {
        data.set(i, vert_args[0] + vert_args[1] * i);
      }
      break;

    case (2): // Altitude in km - non-linear
      for (int i = 0; i < n_levels; i++) {
        data.set(i, vert_args[i]);
      }
      break;

    case (3): // heights of pressure surfaces in km - non-linear
      try {
        Vis5DVerticalSystem.Vis5DVerticalCoordinateSystem vert_cs =
            new Vis5DVerticalSystem.Vis5DVerticalCoordinateSystem();
        float[][] pressures = new float[1][n_levels];
        System.arraycopy(vert_args, 0, pressures[0], 0, n_levels);
        for (int i = 0; i < n_levels; i++) {
          pressures[0][i] *= 1000; // km->m
        }
        pressures = vert_cs.fromReference(pressures); // convert to pressures
        for (int i = 0; i < n_levels; i++) {
          data.set(i, pressures[0][i]);
        }
      } catch (VisADException ve) {
        throw new IOException("unable to make vertical system");
      }
      break;
  }
  vertVar.setCachedData(data, false);
  return vertVar;
}
 

protected AxisType getAxisType(NetcdfDataset ds, VariableEnhanced ve) {
  Variable v = (Variable) ve;
  String vname = v.getShortName();
  String units = v.getUnitsString();

  if (units.equalsIgnoreCase(CDM.LON_UNITS))
    return AxisType.Lon;

  if (units.equalsIgnoreCase(CDM.LAT_UNITS))
    return AxisType.Lat;


  if (vname.equalsIgnoreCase("x"))
    return AxisType.GeoX;

  if (vname.equalsIgnoreCase("lon"))
    return AxisType.Lon;

  if (vname.equalsIgnoreCase("y"))
    return AxisType.GeoY;

  if (vname.equalsIgnoreCase("lat"))
    return AxisType.Lat;

  if (vname.equalsIgnoreCase("record"))
    return AxisType.Time;
  Dimension dim = v.getDimension(0);
  if ((dim != null) && dim.getShortName().equalsIgnoreCase("record"))
    return AxisType.Time;

  String unit = ve.getUnitsString();
  if (unit != null) {
    if (SimpleUnit.isCompatible("millibar", unit))
      return AxisType.Pressure;

    if (SimpleUnit.isCompatible("m", unit))
      return AxisType.Height;
  }

  return AxisType.GeoZ;
}
 

@Override
@Nullable
protected AxisType getAxisType(VariableDS.Builder vb) {
  String unit = vb.getUnits();
  if (unit == null) {
    return null;
  }
  unit = unit.trim();

  if (unit.equalsIgnoreCase("degrees_east") || unit.equalsIgnoreCase("degrees_E") || unit.equalsIgnoreCase("degreesE")
      || unit.equalsIgnoreCase("degree_east") || unit.equalsIgnoreCase("degree_E")
      || unit.equalsIgnoreCase("degreeE")) {
    return AxisType.Lon;
  }

  if (unit.equalsIgnoreCase("degrees_north") || unit.equalsIgnoreCase("degrees_N")
      || unit.equalsIgnoreCase("degreesN") || unit.equalsIgnoreCase("degree_north")
      || unit.equalsIgnoreCase("degree_N") || unit.equalsIgnoreCase("degreeN")) {
    return AxisType.Lat;
  }

  if (SimpleUnit.isDateUnit(unit)) {
    return AxisType.Time;
  }
  // look for other z coordinate
  if (SimpleUnit.isCompatible("mbar", unit)) {
    return AxisType.Pressure;
  }
  if (unit.equalsIgnoreCase("level") || unit.equalsIgnoreCase("layer") || unit.equalsIgnoreCase("sigma_level")) {
    return AxisType.GeoZ;
  }

  String positive = vb.getAttributeContainer().findAttributeString(CF.POSITIVE, null);
  if (positive != null) {
    if (SimpleUnit.isCompatible("m", unit)) {
      return AxisType.Height;
    } else {
      return AxisType.GeoZ;
    }
  }

  // a bad idea, but CDC SST relies on it :
  // :Source = "NOAA/National Climatic Data Center";
  // :Contact = "Dick Reynolds, email: [email protected] & Chunying Liu, email: [email protected]";
  // :netcdf_Convention = "COARDS";
  // if (checkForMeter && SimpleUnit.isCompatible("m", unit))
  // return AxisType.Height;

  return null;
}
 

private AxisType addAxisType(Variable.Builder v) {
  String name = v.shortName;
  if (name.equalsIgnoreCase("Latitude") || name.equalsIgnoreCase("GeodeticLatitude")) {
    v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
    v.addAttribute(new Attribute(CDM.UNITS, CDM.LAT_UNITS));
    return AxisType.Lat;

  } else if (name.equalsIgnoreCase("Longitude")) {
    v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
    v.addAttribute(new Attribute(CDM.UNITS, CDM.LON_UNITS));
    return AxisType.Lon;

  } else if (name.equalsIgnoreCase("Time")) {
    v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
    if (v.getAttributeContainer().findAttribute(CDM.UNITS) == null) {
      /*
       * from http://newsroom.gsfc.nasa.gov/sdptoolkit/hdfeosfaq.html
       * HDF-EOS uses the TAI93 (International Atomic Time) format. This means that time is stored as the number of
       * elapsed seconds since January 1, 1993 (negative values represent times prior to this date).
       * An 8 byte floating point number is used, producing microsecond accuracy from 1963 (when leap second records
       * became available electronically) to 2100. The SDP Toolkit provides conversions from other date formats to and
       * from TAI93. Other representations of time can be entered as ancillary data, if desired.
       * For lists and descriptions of other supported time formats, consult the Toolkit documentation or write to
       * [email protected].
       */
      v.addAttribute(new Attribute(CDM.UNITS, "seconds since 1993-01-01T00:00:00Z"));
      v.addAttribute(new Attribute(CF.CALENDAR, "TAI"));
      /*
       * String tit = ncfile.findAttValueIgnoreCase(v, "Title", null);
       * if (tit != null && tit.contains("TAI93")) {
       * // Time is given in the TAI-93 format, i.e. the number of seconds passed since 01-01-1993, 00:00 UTC.
       * v.addAttribute(new Attribute(CDM.UNITS, "seconds since 1993-01-01T00:00:00Z"));
       * v.addAttribute(new Attribute(CF.CALENDAR, "TAI"));
       * } else { // who the hell knows ??
       * v.addAttribute(new Attribute(CDM.UNITS, "seconds since 1970-01-01T00:00:00Z"));
       * }
       */
    }
    return AxisType.Time;

  } else if (name.equalsIgnoreCase("Pressure")) {
    v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Pressure.toString()));
    return AxisType.Pressure;

  } else if (name.equalsIgnoreCase("Altitude")) {
    v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Height.toString()));
    v.addAttribute(new Attribute(CF.POSITIVE, CF.POSITIVE_UP)); // probably
    return AxisType.Height;
  }

  return null;
}
 

protected CoordinateSystem(Builder<?> builder, NetcdfDataset ncd, List<CoordinateAxis> axes,
    List<CoordinateTransform> allTransforms) {
  this.ds = ncd;
  this.isImplicit = builder.isImplicit;

  // find referenced coordinate axes
  List<CoordinateAxis> axesList = new ArrayList<>();
  StringTokenizer stoker = new StringTokenizer(builder.coordAxesNames);
  while (stoker.hasMoreTokens()) {
    String vname = stoker.nextToken();
    for (CoordinateAxis a : axes) {
      String aname = a.getFullName();
      if (aname.equals(vname)) {
        axesList.add(a);
      }
    }
  }
  this.coordAxes = axesList;

  // calculated
  this.name = makeName(coordAxes);

  for (CoordinateAxis axis : this.coordAxes) {
    // look for AxisType
    AxisType axisType = axis.getAxisType();
    if (axisType != null) {
      if (axisType == AxisType.GeoX)
        xAxis = lesserRank(xAxis, axis);
      if (axisType == AxisType.GeoY)
        yAxis = lesserRank(yAxis, axis);
      if (axisType == AxisType.GeoZ)
        zAxis = lesserRank(zAxis, axis);
      if (axisType == AxisType.Time)
        tAxis = lesserRank(tAxis, axis);
      if (axisType == AxisType.Lat)
        latAxis = lesserRank(latAxis, axis);
      if (axisType == AxisType.Lon)
        lonAxis = lesserRank(lonAxis, axis);
      if (axisType == AxisType.Height)
        hAxis = lesserRank(hAxis, axis);
      if (axisType == AxisType.Pressure)
        pAxis = lesserRank(pAxis, axis);
      if (axisType == AxisType.Ensemble)
        ensAxis = lesserRank(ensAxis, axis);

      if (axisType == AxisType.RadialAzimuth)
        aziAxis = lesserRank(aziAxis, axis);
      if (axisType == AxisType.RadialDistance)
        radialAxis = lesserRank(radialAxis, axis);
      if (axisType == AxisType.RadialElevation)
        elevAxis = lesserRank(elevAxis, axis);
    }
    // collect dimensions
    List<Dimension> dims = axis.getDimensionsAll();
    domain.addAll(dims);
  }

  // Find the named coordinate transforms in allTransforms.
  for (String wantTransName : builder.transNames) {
    CoordinateTransform got = allTransforms.stream()
        .filter(ct -> (wantTransName.equals(ct.getName())
            || ct.getAttributeContainer() != null && wantTransName.equals(ct.getAttributeContainer().getName())))
        .findFirst().orElse(null);
    if (got != null) {
      coordTrans.add(got);
    }

  }
}
 

/**
 * Constructor.
 * 
 * @param ds the containing dataset
 * @param axes Collection of type CoordinateAxis, must be at least one.
 * @param coordTrans Collection of type CoordinateTransform, may be empty or null.
 * @deprecated Use CoordinateSystem.builder()
 */
@Deprecated
public CoordinateSystem(NetcdfDataset ds, Collection<CoordinateAxis> axes,
    Collection<CoordinateTransform> coordTrans) {
  this.ds = ds;
  this.coordAxes = new ArrayList<>(axes);
  this.name = makeName(coordAxes);

  if (coordTrans != null)
    this.coordTrans = new ArrayList<>(coordTrans);

  for (CoordinateAxis axis : coordAxes) {
    // look for AxisType
    AxisType axisType = axis.getAxisType();
    if (axisType != null) {
      if (axisType == AxisType.GeoX)
        xAxis = lesserRank(xAxis, axis);
      if (axisType == AxisType.GeoY)
        yAxis = lesserRank(yAxis, axis);
      if (axisType == AxisType.GeoZ)
        zAxis = lesserRank(zAxis, axis);
      if (axisType == AxisType.Time)
        tAxis = lesserRank(tAxis, axis);
      if (axisType == AxisType.Lat)
        latAxis = lesserRank(latAxis, axis);
      if (axisType == AxisType.Lon)
        lonAxis = lesserRank(lonAxis, axis);
      if (axisType == AxisType.Height)
        hAxis = lesserRank(hAxis, axis);
      if (axisType == AxisType.Pressure)
        pAxis = lesserRank(pAxis, axis);
      if (axisType == AxisType.Ensemble)
        ensAxis = lesserRank(ensAxis, axis);

      if (axisType == AxisType.RadialAzimuth)
        aziAxis = lesserRank(aziAxis, axis);
      if (axisType == AxisType.RadialDistance)
        radialAxis = lesserRank(radialAxis, axis);
      if (axisType == AxisType.RadialElevation)
        elevAxis = lesserRank(elevAxis, axis);
    }

    // collect dimensions
    List<Dimension> dims = axis.getDimensionsAll();
    domain.addAll(dims);
  }
}
 

/**
 * Add this coordinate system to the netCDF file
 *
 * @param ncfile the netCDF file
 * @param g the group to add to
 */
void addToNetcdfFile(NetcdfFile ncfile, Group g) {
  if (dontUseVertical) {
    return;
  }

  if (g == null) {
    g = ncfile.getRootGroup();
  }

  String dims = "time";
  if (!dontUseVertical) {
    dims = dims + " " + verticalName;
  }
  if (hcs.isLatLon()) {
    dims = dims + " lat lon";
  } else {
    dims = dims + " y x";
  }

  // Collections.sort( levels);
  int nlevs = levels.size();
  // ncfile.addDimension(g, new Dimension(verticalName, nlevs, true));

  // coordinate axis and coordinate system Variable
  Variable v = new Variable(ncfile, g, null, verticalName);
  v.setDataType(DataType.DOUBLE);

  v.addAttribute(new Attribute("long_name", lookup.getLevelDescription(record)));
  v.addAttribute(new Attribute("units", lookup.getLevelUnit(record)));

  // positive attribute needed for CF-1 Height and Pressure
  if (positive != null) {
    v.addAttribute(new Attribute("positive", positive));
  }

  if (units != null) {
    AxisType axisType;
    if (SimpleUnit.isCompatible("millibar", units)) {
      axisType = AxisType.Pressure;
    } else if (SimpleUnit.isCompatible("m", units)) {
      axisType = AxisType.Height;
    } else {
      axisType = AxisType.GeoZ;
    }

    v.addAttribute(new Attribute("grid_level_type", Integer.toString(record.getLevelType1())));

    v.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));
    v.addAttribute(new Attribute(_Coordinate.Axes, dims));
    if (!hcs.isLatLon()) {
      v.addAttribute(new Attribute(_Coordinate.Transforms, hcs.getGridName()));
    }
  }

  double[] data = new double[nlevs];
  for (int i = 0; i < levels.size(); i++) {
    Double d = levels.get(i);
    data[i] = d;
  }
  Array dataArray = Array.factory(DataType.DOUBLE, new int[] {nlevs}, data);

  v.setDimensions(verticalName);
  v.setCachedData(dataArray, false);

  ncfile.addVariable(g, v);

  // look for vertical transforms
  if (record.getLevelType1() == 109) {
    findCoordinateTransform(g, "Pressure", record.getLevelType1());
  }
}