Examples of ucar.nc2.Dimension

ucar.nc2.Dimension
A Dimension is used to define the array shape of a Variable. It may be shared among Variables, which provides a simple yet powerful way of associating Variables. When a Dimension is shared, it has a unique name within its Group. It may have a coordinate Variable, which gives each index a coordinate value. A private Dimension cannot have a coordinate Variable, so use shared dimensions with coordinates when possible. The Dimension length must be > 0, except for an unlimited dimension which may have length = 0, and a vlen Dimension has length = -1.
Immutable if setImmutable() was called, except for an Unlimited Dimension, whose size can change. @author caron


    Table.Type stationTableType = Table.Type.Structure;
    if (info.encoding == Encoding.single) stationTableType = Table.Type.Top;
    if (info.encoding == Encoding.flat) stationTableType = Table.Type.Construct;


    Dimension stationDim = (info.encoding == Encoding.flat) ? info.childDim : info.parentDim;
    String name = (stationDim == null) ? " single" : stationDim.getName();
    TableConfig stnTable = new TableConfig(stationTableType, name);
    stnTable.featureType = ftype;
    stnTable.stnId = findNameVariableWithStandardNameAndDimension(ds, CF.STATION_ID, stationDim, errlog);
    stnTable.stnDesc = findNameVariableWithStandardNameAndDimension(ds, CF.STATION_DESC, stationDim, errlog);
    stnTable.stnWmoId = findNameVariableWithStandardNameAndDimension(ds, CF.STATION_WMOID, stationDim, errlog);
    stnTable.stnAlt = findNameVariableWithStandardNameAndDimension(ds, CF.STATION_ALTITUDE, stationDim, errlog);
    stnTable.lat = lat.getFullName();
    stnTable.lon = lon.getFullName();


    // station id
    if (stnTable.stnId == null) {
      errlog.format("Must have a Station id variable with standard name station_id%n");
      return null;
    }


    if (info.encoding != Encoding.single) {
      // set up structure
      boolean hasStruct = Evaluator.hasRecordStructure(ds) && stationDim.isUnlimited();
      stnTable.structureType = hasStruct ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;
      stnTable.dimName = stationDim.getName();
      stnTable.structName = hasStruct ? "record" : stationDim.getName();
    }


    // LOOK probably need a standard name here
    // optional alt coord - detect if its a station height or actually associated with the obs, eg for a profile
    if (stnTable.stnAlt == null) {

View Full Code Here

  }


  // the inner table of Structure(outer, inner) and middle table of Structure(outer, middle, inner)


  private TableConfig makeMultidimInner(NetcdfDataset ds, TableConfig parentTable, Dimension obsDim, Formatter errlog) throws IOException {
    Dimension parentDim = ds.findDimension(parentTable.dimName);


    Table.Type obsTableType = (parentTable.structureType == TableConfig.StructureType.PsuedoStructure) ? Table.Type.MultidimInnerPsuedo : Table.Type.MultidimInner;
    TableConfig obsTable = new TableConfig(obsTableType, obsDim.getName());


    obsTable.lat = matchAxisTypeAndDimension(ds, AxisType.Lat, parentDim, obsDim);
    obsTable.lon = matchAxisTypeAndDimension(ds, AxisType.Lon, parentDim, obsDim);
    obsTable.elev = matchAxisTypeAndDimension(ds, AxisType.Height, parentDim, obsDim);
    obsTable.time = matchAxisTypeAndDimension(ds, AxisType.Time, parentDim, obsDim);


    // divide up the variables between the parent and the obs
    List<String> obsVars = null;
    List<Variable> vars = ds.getVariables();
    List<String> parentVars = new ArrayList<String>(vars.size());
    obsVars = new ArrayList<String>(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(obsDim))
            obsVars.add(orgV.getShortName());
        }
      }
    }
    parentTable.vars = parentVars;

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  }


  // the inner table of Structure(outer, middle, inner)


  private TableConfig makeMultidimInner3D(NetcdfDataset ds, TableConfig outerTable, TableConfig middleTable, Dimension innerDim, Formatter errlog) throws IOException {
    Dimension outerDim = ds.findDimension(outerTable.dimName);
    Dimension middleDim = ds.findDimension(middleTable.innerName);


    Table.Type obsTableType = (outerTable.structureType == TableConfig.StructureType.PsuedoStructure) ? Table.Type.MultidimInnerPsuedo3D : Table.Type.MultidimInner3D;
    TableConfig obsTable = new TableConfig(obsTableType, innerDim.getName());
    obsTable.structureType = TableConfig.StructureType.PsuedoStructure2D;
    obsTable.dimName = outerTable.dimName;
    obsTable.outerName = middleTable.innerName;
    obsTable.innerName = innerDim.getName();
    obsTable.structName = innerDim.getName();


    obsTable.lat = matchAxisTypeAndDimension(ds, AxisType.Lat, outerDim, middleDim, innerDim);
    obsTable.lon = matchAxisTypeAndDimension(ds, AxisType.Lon, outerDim, middleDim, innerDim);
    obsTable.elev = matchAxisTypeAndDimension(ds, AxisType.Height, outerDim, middleDim, innerDim);
    obsTable.time = matchAxisTypeAndDimension(ds, AxisType.Time, outerDim, middleDim, innerDim);


    // divide up the variables between the 3 tables
    List<Variable> vars = ds.getVariables();
    List<String> outerVars = new ArrayList<String>(vars.size());
    List<String> middleVars = new ArrayList<String>(vars.size());
    List<String> innerVars = new ArrayList<String>(vars.size());
    for (Variable orgV : vars) {
      if (orgV instanceof Structure) continue;


      if ((orgV.getRank() == 1) || ((orgV.getRank() == 2) && orgV.getDataType() == DataType.CHAR)) {
        if (outerDim.equals(orgV.getDimension(0)))
          outerVars.add(orgV.getShortName());


      } else if (orgV.getRank() == 2) {
        if (outerDim.equals(orgV.getDimension(0)) && middleDim.equals(orgV.getDimension(1)))
          middleVars.add(orgV.getShortName());


      } else if (orgV.getRank() == 3) {
        if (outerDim.equals(orgV.getDimension(0)) && middleDim.equals(orgV.getDimension(1)) && innerDim.equals(orgV.getDimension(2)))
          innerVars.add(orgV.getShortName());
      }
    }
    outerTable.vars = outerVars;
    middleTable.vars = middleVars;

View Full Code Here

    CoordinateAxis coordAxis = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (coordAxis == null) {
      errlog.format("Cant find a time coordinate");
      return null;
    }
    Dimension innerDim = coordAxis.getDimension(0);
    boolean obsIsStruct = Evaluator.hasRecordStructure(ds) && innerDim.isUnlimited();


    TableConfig obsTable = new TableConfig(Table.Type.Structure, innerDim.getName());
    obsTable.dimName = innerDim.getName();
    obsTable.time = coordAxis.getFullName();
    obsTable.structName = obsIsStruct ? "record" : innerDim.getName();
    obsTable.structureType = obsIsStruct ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;
    CoordSysEvaluator.findCoordWithDimension(obsTable, ds, innerDim); 


    topTable.addChild(obsTable);
    return topTable;

View Full Code Here

      makeMultidimInner(ds, tc, inner, inner.outerName, inner.innerName);
    return tc;
  }


  private void makeMultidimInner(NetcdfDataset ds, TableConfig parentTable, TableConfig childTable, String outerDin, String innerDim) {
    Dimension parentDim = ds.findDimension(outerDin);
    Dimension childDim = ds.findDimension(innerDim);


    // divide up the variables between the parent and the child
    List<String> obsVars = null;
    List<Variable> vars = ds.getVariables();
    List<String> parentVars = new ArrayList<String>(vars.size());
    obsVars = new ArrayList<String>(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;

View Full Code Here

    </table>
  </stationFeature>
   */


   public TableConfig getConfig(FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog) {
    Dimension obsDim = ds.getUnlimitedDimension();
    if (obsDim == null) {
      CoordinateAxis axis = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
      if ((axis != null) && axis.isScalar())
        obsDim = axis.getDimension(0);
    }


    if (obsDim == null) {
      errlog.format("Must have an Observation dimension: unlimited dimension, or from Time Coordinate");
      return null;
    }
     boolean hasStruct = Evaluator.hasRecordStructure(ds);


    // wants a Point
    if ((wantFeatureType == FeatureType.POINT)) {
      TableConfig nt = new TableConfig(Table.Type.Structure, hasStruct ? "record" : obsDim.getName() );
      nt.structName = "record";
      nt.structureType = hasStruct ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;      
      nt.featureType = FeatureType.POINT;
      CoordSysEvaluator.findCoords(nt, ds);
      return nt;
    }


    // otherwise, make it a Station
    TableConfig nt = new TableConfig(Table.Type.Top, "station");
    nt.featureType = FeatureType.STATION;


    nt.lat = CoordSysEvaluator.findCoordNameByType(ds, AxisType.Lat);
    nt.lon = CoordSysEvaluator.findCoordNameByType(ds, AxisType.Lon);


    nt.stnId = ds.findAttValueIgnoreCase(null, "station", null);
    nt.stnDesc = ds.findAttValueIgnoreCase(null, "description", null);
    if (nt.stnDesc == null)
      nt.stnDesc = ds.findAttValueIgnoreCase(null, "comment", null);


    TableConfig obs = new TableConfig(Table.Type.Structure, hasStruct ? "record" : obsDim.getName());
    obs.structName = "record";
    obs.structureType = hasStruct ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;
    obs.dimName = obsDim.getName();
    obs.time = CoordSysEvaluator.findCoordNameByType(ds, AxisType.Time);
    nt.addChild(obs);


    return nt;
  }

View Full Code Here

      makeMultidimInner(ds, tc, inner, inner.outerName, inner.innerName);
    return tc;
  }


  private void makeMultidimInner(NetcdfDataset ds, TableConfig parentTable, TableConfig childTable, String outerDin, String innerDim) {
    Dimension parentDim = ds.findDimension(outerDin);
    Dimension childDim = ds.findDimension(innerDim);


    // divide up the variables between the parent and the child
    List<String> obsVars = null;
    List<Variable> vars = ds.getVariables();
    List<String> parentVars = new ArrayList<String>(vars.size());
    obsVars = new ArrayList<String>(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;

View Full Code Here

    return false;
  }


  public TableConfig getConfig(FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog) {


    Dimension obsDim = UnidataPointDatasetHelper.findObsDimension(ds);
    if (obsDim == null) {
      errlog.format("Must have an Observation dimension: named by global attribute 'observationDimension', or unlimited dimension");
      return null;
    }
    boolean hasStruct = Evaluator.hasRecordStructure(ds);


    FeatureType ft = Evaluator.getFeatureType(ds, ":cdm_datatype", null);
    if (ft == null )
      ft = Evaluator.getFeatureType(ds, ":cdm_data_type", null);


    // its really a point
    if (ft == FeatureType.POINT) {
      TableConfig obsTable = new TableConfig(Table.Type.Structure, hasStruct ? "record" : obsDim.getName());
      obsTable.structureType = hasStruct ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;
      obsTable.featureType = FeatureType.POINT;
      obsTable.structName = "record";


      obsTable.time = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Time, obsDim);
      obsTable.lat = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lat, obsDim);
      obsTable.lon = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lon, obsDim);
      obsTable.elev = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Height, obsDim);


      obsTable.dimName = obsDim.getName();
      return obsTable;
    }


    //  we want a point dataset, but its really a station
    // iterate over obs struct, in file order
    // extra join on station structure
    if ((ft == FeatureType.STATION) && (wantFeatureType == FeatureType.POINT)) {
      TableConfig obsTable = new TableConfig(Table.Type.Structure, hasStruct ? "record" : obsDim.getName() );
      obsTable.structureType = hasStruct ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;
      obsTable.featureType = FeatureType.POINT;
      obsTable.dimName = obsDim.getName();
      obsTable.structName = "record";


      obsTable.time = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Time, obsDim);
      obsTable.lat = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lat, obsDim);
      obsTable.lon = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lon, obsDim);
      obsTable.stnAlt = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Height, obsDim);


      // if they have lat and lon in the obs, then use it
      if ((obsTable.lat != null) && (obsTable.lon != null)) {
        return obsTable;
      }


      // otherwise join it to the station with a parent_index
      String parentIndexVar = UnidataPointDatasetHelper.findVariableName(ds, "parent_index");
      if (parentIndexVar == null)  {
        errlog.format("Must have a parent_index variable");
        return null;
      }


      Dimension stationDim = UnidataPointDatasetHelper.findDimension(ds, "station");
      if (stationDim == null) {
        errlog.format("Must have a station dimension");
        return null;
      }


      // TableConfig stationTable = new TableConfig(Table.Type.Structure, "station");
      //stationTable.isPsuedoStructure = true;
      //stationTable.dim = stationDim;
      obsTable.lat = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lat, stationDim);
      obsTable.lon = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lon, stationDim);
      obsTable.elev = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Height, stationDim);


      StructureDS stns = new StructurePseudoDS(ds, null, "stationPsuedoStructure", null, stationDim);
      obsTable.addJoin( new JoinParentIndex(stns, parentIndexVar));


      return obsTable;
    }




    // its really a trajectory
    if (ft == FeatureType.TRAJECTORY) {
      TableConfig obsTable = new TableConfig(Table.Type.Structure, hasStruct ? "record" : obsDim.getName());
      obsTable.structureType = hasStruct ? TableConfig.StructureType.Structure : TableConfig.StructureType.PsuedoStructure;
      obsTable.featureType = FeatureType.TRAJECTORY;


      obsTable.time = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Time, obsDim);
      obsTable.lat = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lat, obsDim);
      obsTable.lon = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lon, obsDim);
      obsTable.elev = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Height, obsDim);
      obsTable.dimName = obsDim.getName();


      Dimension trajDim = UnidataPointDatasetHelper.findDimension(ds, "trajectory");
      if (trajDim != null) {
        log.error("Ignoring trajectory structure "+ds.getLocation());
      }


      return obsTable;
    }


    // otherwise its a Station
    Dimension stationDim = UnidataPointDatasetHelper.findDimension(ds, "station");
    if (stationDim == null) {
      errlog.format("Must have a dimension named station, or named by global attribute 'stationDimension'");
      return null;
    }


    String lastVar = UnidataPointDatasetHelper.findVariableName(ds, "lastChild");
    String prevVar = UnidataPointDatasetHelper.findVariableName(ds, "prevChild");
    String firstVar = UnidataPointDatasetHelper.findVariableName(ds, "firstChild");
    String nextVar = UnidataPointDatasetHelper.findVariableName(ds, "nextChild");
    String numChildrenVar = UnidataPointDatasetHelper.findVariableName(ds, "numChildren");


    boolean isForwardLinkedList = (firstVar != null) && (nextVar != null);
    boolean isBackwardLinkedList = (lastVar != null) && (prevVar != null);
    boolean isContiguousList = !isForwardLinkedList && !isBackwardLinkedList && (firstVar != null) && (numChildrenVar != null);
    boolean isMultiDim = !isForwardLinkedList && !isBackwardLinkedList && !isContiguousList;


    // station table
    TableConfig stationTable = new TableConfig(Table.Type.Structure, "station");
    stationTable.structureType = TableConfig.StructureType.PsuedoStructure;
    stationTable.featureType = FeatureType.STATION;
    stationTable.dimName = stationDim.getName();
    stationTable.limit = Evaluator.getVariableName(ds, "number_stations", null);


    stationTable.stnId = Evaluator.getVariableName(ds, "station_id", null);
    stationTable.stnDesc = Evaluator.getVariableName(ds, "station_description", null);
    stationTable.stnWmoId = Evaluator.getVariableName(ds, "wmo_id", null);


    stationTable.lat = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lat);
    stationTable.lon = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Lon);
    stationTable.stnAlt = UnidataPointDatasetHelper.getCoordinateName(ds, AxisType.Height);


    // obs table
    TableConfig obsTable;
    if (isMultiDim) {
      obsTable = new TableConfig(Table.Type.MultidimInner, "obs");
      obsTable.outerName = stationDim.getName();
      obsTable.innerName = obsDim.getName();
      obsTable.dimName = obsDim.getName();


    } else {

View Full Code Here

   */
  public static double[][] readNetCdfFile(String pathname) throws IOException {
    double[][] array = null;
    try {
      NetcdfFile dataFile = NetcdfFile.open(pathname);
      Dimension data_dim_time = dataFile.getRootGroup().findDimension(
          "data_dim_time");
      Dimension data_dim_z = dataFile.getRootGroup().findDimension(
          "data_dim_z");
      Dimension data_dim_x = dataFile.getRootGroup().findDimension(
          "data_dim_x");
      Dimension data_dim_y = dataFile.getRootGroup().findDimension(
          "data_dim_y");
      if (data_dim_time == null || data_dim_z == null
          || data_dim_x == null || data_dim_y == null) {
        System.err
            .println("This netCDF file is not compatible to the PivNet 2 standard:");
        System.err
            .println("http://www.meol.cnrs.fr/LML/EuroPIV2/Pages/netcdf.htm");
        ncView(pathname);
        throw (new IOException());
      } else if (data_dim_time.getLength() != 1
          || data_dim_z.getLength() != 1) {
        System.err
            .println("This netCDF file contains a time series and/or volumetric data.");
        System.err
            .println("The visualization of multi dimensional data is not implemented, yet.");
        ncView(pathname);
        throw (new IOException());
      } else {
        int dim_x = data_dim_x.getLength();
        int dim_y = data_dim_y.getLength();
        ArrayFloat.D1 grid_x = (ArrayFloat.D1) dataFile.read("grid_x",
            true);
        ArrayFloat.D1 grid_y = (ArrayFloat.D1) dataFile.read("grid_y",
            true);
        ArrayFloat.D4 disp_x = (ArrayFloat.D4) dataFile.read("disp_x",

View Full Code Here

    private Number getVerticalValueByIndex(Variable variable, final int zIndex,
            final CoordinateSystem cs ) {
        double ve = Double.NaN;
        if (cs != null && cs.hasVerticalAxis()) {
            final int rank = variable.getRank();
            final Dimension verticalDimension = variable.getDimension(rank - NetCDFUtilities.Z_DIMENSION);
            return (Number) reader.coordinatesVariables.get(verticalDimension.getFullName()).read(zIndex);
        }
        return ve;
    }

View Full Code Here

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