Examples of ucar.nc2.dataset.VariableDS

ucar.nc2.dods.DODSNetcdfFile
An wrapper around a Variable, creating an "enhanced" Variable. The original Variable is used for the I/O. There are several distinct uses:
1. 1) handle scale/offset/missing values/enum conversion; this can change DataType and data values
2. 2) container for coordinate system information
3. 3) NcML modifications to underlying Variable
@see NetcdfDataset @author caron


  private TableConfig getSectionConfig(NetcdfDataset ds, Formatter errlog) throws IOException {
    EncodingInfo info = identifyEncodingSection(ds, CF.FeatureType.trajectoryProfile, errlog);
    if (info == null) return null;


    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time.getRank() == 0) {
      errlog.format("section cannot have a scalar time coordinate%n");
      return null;
    }


    /* if (info.encoding == Encoding.single) {
      Dimension profileDim = time.getDimension(0); // may be time(profile) or time(profile, z)
      Variable parentId = identifyParent(ds, CF.FeatureType.trajectoryProfile);
      if ((parentId != null) && (parentId.getRank() == 1) && (parentId.getDimension(0).equals(profileDim))) {
        info = new EncodingInfo(Encoding.flat, parentId);
      }
    } */


    TableConfig parentTable = makeStructTable(ds, FeatureType.SECTION, info, errlog);
    if (parentTable == null) return null;
    parentTable.feature_id = identifyParentId(ds, CF.FeatureType.trajectoryProfile);
    if (parentTable.feature_id == null) {
      errlog.format("getSectionConfig cant find a section id %n");
    }


    //Dimension sectionDim = ds.findDimension(parentTable.dimName);
    //Dimension profileDim = null;
    //Dimension zDim = null;


    // find the non-station altitude
    VariableDS z = findZAxisNotStationAlt(ds);
    if (z == null) {
      errlog.format("section must have a z coordinate%n");
      return null;
    }
    if (z.getRank() == 0) {
      errlog.format("section cannot have a scalar z coordinate%n");
      return null;
    }


    switch (info.encoding) {
      case single: {
        assert ((time.getRank() >= 1) && (time.getRank() <= 2)) : "time must be rank 1 or 2";
        assert ((z.getRank() >= 1) && (z.getRank() <= 2)) : "z must be rank 1 or 2";


        if (time.getRank() == 2) {
          if (z.getRank() == 2)  // 2d time, 2d z
            assert time.getDimensions().equals(z.getDimensions()) : "rank-2 time and z dimensions must be the same";
          else  // 2d time, 1d z
            assert time.getDimension(1).equals(z.getDimension(0)) : "rank-2 time must have z inner dimension";
          //profileDim = time.getDimension(0);
          //zDim = time.getDimension(1);


        } else { // 1d time
          if (z.getRank() == 2) { // 1d time, 2d z
            assert z.getDimension(0).equals(time.getDimension(0)) : "rank-2 z must have time outer dimension";
            //profileDim = z.getDimension(0);
            //zDim = z.getDimension(1);
          } else { // 1d time, 1d z
            assert !time.getDimension(0).equals(z.getDimension(0)) : "time and z dimensions must be different";
            //profileDim = time.getDimension(0);
            //zDim = z.getDimension(0);
          }
        }
        // make profile table
        TableConfig profileTable = makeStructTable(ds, FeatureType.PROFILE, new EncodingInfo(Encoding.multidim, info.childDim), errlog);
        if (profileTable == null) return null;
        if (time.getRank() == 1) // join time(time)
          profileTable.addJoin(new JoinArray(time, JoinArray.Type.raw, 0));
        parentTable.addChild(profileTable);


        // make the inner (z) table
        TableConfig zTable = makeMultidimInner(ds, profileTable, info.grandChildDim, errlog);
        if (z.getRank() == 1) // join z(z)
          zTable.addJoin(new JoinArray(z, JoinArray.Type.raw, 0));
        profileTable.addChild(zTable);


        break;
      }


      case multidim: {
        assert ((time.getRank() >= 2) && (time.getRank() <= 3)) : "time must be rank 2 or 3";
        assert ((z.getRank() == 1) || (z.getRank() == 3)) : "z must be rank 1 or 3";


        if (time.getRank() == 3) {
          if (z.getRank() == 3)  // 3d time, 3d z
            assert time.getDimensions().equals(z.getDimensions()) : "rank-3 time and z dimensions must be the same";
          else  // 3d time, 1d z
            assert time.getDimension(2).equals(z.getDimension(0)) : "rank-3 time must have z inner dimension";
          //profileDim = time.getDimension(1);
          //zDim = time.getDimension(2);


        } else { // 2d time
          if (z.getRank() == 3) { // 2d time, 3d z
            assert z.getDimension(1).equals(time.getDimension(1)) : "rank-2 time must have time inner dimension";
           // profileDim = z.getDimension(1);
            //zDim = z.getDimension(2);
          } else { // 2d time, 1d z
            assert !time.getDimension(0).equals(z.getDimension(0)) : "time and z dimensions must be different";
            assert !time.getDimension(1).equals(z.getDimension(0)) : "time and z dimensions must be different";
            //profileDim = time.getDimension(1);
            //zDim = z.getDimension(0);
          }
        }


        // make profile table
        //   private TableConfig makeMultidimInner(NetcdfDataset ds, TableConfig parentTable, Dimension obsDim, Formatter errlog) throws IOException {


        TableConfig profileTable = makeMultidimInner(ds, parentTable, info.childDim, errlog);
        if (profileTable == null) return null;
        profileTable.feature_id = identifyParentId(ds, CF.FeatureType.profile);
        parentTable.addChild(profileTable);


        // make the inner (z) table
        TableConfig zTable = makeMultidimInner3D(ds, parentTable, profileTable, info.grandChildDim, errlog);
        if (z.getRank() == 1) // join z(z)
          zTable.addJoin(new JoinArray(z, JoinArray.Type.raw, 0));
        profileTable.addChild(zTable);
        break;
      }

View Full Code Here


  // given the feature type, figure out the encoding


  private EncodingInfo identifyEncodingStation(NetcdfDataset ds, CF.FeatureType ftype, Formatter errlog) {
    // find the obs dimension
    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time == null) {
      errlog.format("Must have a Time coordinate%n");
      return null;
    }
    Dimension obsDim = null;
    if (time.getRank() > 0)
      obsDim = time.getDimension(time.getRank() - 1); // may be time(time) or time(stn, obs)
    else if (time.getParentStructure() != null) {
      Structure parent = time.getParentStructure(); // if time axis is a structure member, try pulling dimension out of parent structure
      obsDim = parent.getDimension(parent.getRank() - 1);
    }
    if (obsDim == null) {
      errlog.format("Must have a non-scalar Time coordinate%n");
      return null;

View Full Code Here

    return null;
  }


  private EncodingInfo identifyEncodingTraj(NetcdfDataset ds, CF.FeatureType ftype, Formatter errlog) {
    // find the obs dimension
    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time == null) {
      errlog.format("Must have a Time coordinate%n");
      return null;
    }
    Dimension obsDim = null;
    if (time.getRank() > 0)
      obsDim = time.getDimension(time.getRank() - 1); // may be time(time) or time(traj, obs)
    else if (time.getParentStructure() != null) {
      Structure parent = time.getParentStructure(); // if time axis is a structure member, try pulling dimension out of parent structure
      obsDim = parent.getDimension(parent.getRank() - 1);
    }
    if (obsDim == null) {
      errlog.format("Must have a non-scalar Time coordinate%n");
      return null;
    }


    // parent dimension
    Dimension parentDim = null;
    if (time.getRank() > 1) {
      parentDim = time.getDimension(0);
      return new EncodingInfo(Encoding.multidim, parentDim, obsDim);
    }


    // the raggeds
    String dimName = Evaluator.getVariableAttributeValue(ds, CF.RAGGED_PARENTINDEX);
    if (dimName != null) {
      parentDim = ds.findDimension(dimName);
      if (parentDim != null)
        return new EncodingInfo(Encoding.raggedIndex, parentDim, obsDim);
      else {
        errlog.format("CFpointObs %s ragged_parent_index must name parent dimension%n", ftype);
        return null;
      }
    }


    Variable ragged_rowSize = Evaluator.getVariableWithAttributeValue(ds, CF.RAGGED_ROWSIZE, obsDim.getName());
    if (ragged_rowSize != null) {
      parentDim = ragged_rowSize.getDimension(0);
      return new EncodingInfo(Encoding.raggedContiguous, parentDim, obsDim);
    }


    VariableDS lat = CoordSysEvaluator.findCoordByType(ds, AxisType.Lat);
    if (lat == null) {
      errlog.format("Must have a Lat coordinate%n");
      return null;
    }
    if (lat.getRank() > 0) { // multidim case
      for (Dimension d : lat.getDimensions()) {
         if (!d.equals(obsDim)) {
            return new EncodingInfo(Encoding.multidim, d, obsDim);
         }
      }
    }

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    return new EncodingInfo(Encoding.single, null, obsDim);
  }


  private EncodingInfo identifyEncodingProfile(NetcdfDataset ds, CF.FeatureType ftype, Formatter errlog) {
    // find the obs dimension
    VariableDS z = CoordSysEvaluator.findCoordByType(ds, AxisType.Height);
    if (z == null) {
      errlog.format("Must have a Height coordinate%n");
      return null;
    }
    Dimension obsDim = null;
    if (z.getRank() > 0)
      obsDim = z.getDimension(z.getRank() - 1); // may be z(z) or alt(profile, z)
    else if (z.getParentStructure() != null) {
      Structure parent = z.getParentStructure(); // if time axis is a structure member, try pulling dimension out of parent structure
      obsDim = parent.getDimension(parent.getRank() - 1);
    }
    if (obsDim == null) {
      errlog.format("Must have a non-scalar Height coordinate%n");
      return null;
    }


    // parent dimension
    Dimension parentDim = null;
    if (z.getRank() > 1) {
      parentDim = z.getDimension(0);
      return new EncodingInfo(Encoding.multidim, parentDim, obsDim);
    }


    // the raggeds
    String dimName = Evaluator.getVariableAttributeValue(ds, CF.RAGGED_PARENTINDEX);
    if (dimName != null) {
      parentDim = ds.findDimension(dimName);
      if (parentDim != null)
        return new EncodingInfo(Encoding.raggedIndex, parentDim, obsDim);
      else {
        errlog.format("CFpointObs %s ragged_parent_index must name parent dimension%n", ftype);
        return null;
      }
    }


    Variable ragged_rowSize = Evaluator.getVariableWithAttributeValue(ds, CF.RAGGED_ROWSIZE, obsDim.getName());
    if (ragged_rowSize != null) {
      parentDim = ragged_rowSize.getDimension(0);
      return new EncodingInfo(Encoding.raggedContiguous, parentDim, obsDim);
    }


    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time == null) {
      errlog.format("Must have a Time coordinate%n");
      return null;
    }
    if ((time.getRank() == 0) || (time.getDimension(0) == obsDim))
      return new EncodingInfo(Encoding.single, null, obsDim);


    parentDim = time.getDimension(0);
    return new EncodingInfo(Encoding.multidim, parentDim, obsDim);
  }

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    return new EncodingInfo(Encoding.multidim, parentDim, obsDim);
  }


  private EncodingInfo identifyEncodingSection(NetcdfDataset ds, CF.FeatureType ftype, Formatter errlog) {
    // find the z dimension
    VariableDS z = CoordSysEvaluator.findCoordByType(ds, AxisType.Height);
    if (z == null) {
      errlog.format("Must have a Height coordinate%n");
      return null;
    }
    Dimension obsDim = null;
    if (z.getRank() > 0)
      obsDim = z.getDimension(z.getRank() - 1); // may be z(z) or alt(profile, z)
    else if (z.getParentStructure() != null) {
      Structure parent = z.getParentStructure(); // if time axis is a structure member, try pulling dimension out of parent structure
      obsDim = parent.getDimension(parent.getRank() - 1);
    }
    if (obsDim == null) {
      errlog.format("Must have a non-scalar Height coordinate%n");
      return null;
    }


    // parent dimension
    Dimension trajDim = null;
    Dimension profileDim = null;
    if (z.getRank() > 2) {
      trajDim = z.getDimension(0);
      profileDim = z.getDimension(1);
      return new EncodingInfo(Encoding.multidim, trajDim, profileDim, obsDim);
    }


    // ragged
    String dimName = Evaluator.getVariableAttributeValue(ds, CF.RAGGED_PARENTINDEX);
    if (dimName != null) {
      trajDim = ds.findDimension(dimName);
      if (trajDim != null) {
        Variable ragged_rowSize = Evaluator.getVariableWithAttributeValue(ds, CF.RAGGED_ROWSIZE, obsDim.getName());
        if (ragged_rowSize != null) {
          profileDim = ragged_rowSize.getDimension(0);
          return new EncodingInfo(Encoding.raggedIndex, trajDim, profileDim, obsDim);
        } else {
          errlog.format("CFpointObs %s ragged_row_count must name obs dimension%n", ftype);
          return null;
        }
      } else {
        errlog.format("CFpointObs %s ragged_parent_index must name station dimension%n", ftype);
        return null;
      }
    }


    VariableDS lat = CoordSysEvaluator.findCoordByType(ds, AxisType.Lat);
    if (lat == null) {
      errlog.format("Must have a Lat coordinate%n");
      return null;
    }
    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time == null) {
      errlog.format("Must have a Time coordinate%n");
      return null;
    }
    if (lat.getRank() == 0) {
      errlog.format("CFpointObs %s may not have scalar lat/lon%n", ftype);
      return null;
    }


    if (time.getRank() > 2) {
      trajDim = time.getDimension(0);
      profileDim = time.getDimension(1);
      return new EncodingInfo(Encoding.multidim, trajDim, profileDim, obsDim);
    }


    if (lat.getRank() == 1) {
      profileDim = lat.getDimension(0);

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    return null;
  }


  private EncodingInfo identifyEncodingTimeSeriesProfile(NetcdfDataset ds, CF.FeatureType ftype, Formatter errlog) {
    // find the non-station altitude
    VariableDS z = findZAxisNotStationAlt(ds);
    if (z == null) {
      errlog.format("timeSeriesProfile must have a z coordinate, not the station altitude%n");
      return null;
    }
    if (z.getRank() == 0) {
      errlog.format("timeSeriesProfile cannot have a scalar z coordinate%n");
      return null;
    }


    Dimension obsDim = z.getDimension(z.getRank() - 1); // may be z(z) or alt(profile, z)


    // parent dimension
    Dimension stnDim = null;
    Dimension profileDim = null;
    if (z.getRank() > 2) {
      stnDim = z.getDimension(0);
      profileDim = z.getDimension(1);
      return new EncodingInfo(Encoding.multidim, stnDim, profileDim, obsDim);
    }


    // ragged
    String dimName = Evaluator.getVariableAttributeValue(ds, CF.RAGGED_PARENTINDEX);
    if (dimName != null) {
      stnDim = ds.findDimension(dimName);
      if (stnDim != null) {
        Variable ragged_rowSize = Evaluator.getVariableWithAttributeValue(ds, CF.RAGGED_ROWSIZE, obsDim.getName());
        if (ragged_rowSize != null) {
          profileDim = ragged_rowSize.getDimension(0);
          return new EncodingInfo(Encoding.raggedIndex, stnDim, profileDim, obsDim);
        } else {
          errlog.format("CFpointObs %s ragged_row_count must name obs dimension%n", ftype);
          return null;
        }
      } else {
        errlog.format("CFpointObs %s ragged_parent_index must name station dimension%n", ftype);
        return null;
      }
    }


    VariableDS lat = CoordSysEvaluator.findCoordByType(ds, AxisType.Lat);
    if (lat == null) {
      errlog.format("Must have a Lat coordinate%n");
      return null;
    }
    VariableDS time = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
    if (time == null) {
      errlog.format("Must have a Time coordinate%n");
      return null;
    }
    if (lat.getRank() == 0) {
      profileDim = time.getDimension(0); // may be time(profile) or time(profile, z)
      return new EncodingInfo(Encoding.single, null, profileDim, obsDim);
    }


    if ((time.getRank() == 1) || (time.getRank() == 2 && time.getDimension(1) == obsDim)) {
      profileDim = time.getDimension(0); // may be time(profile) or time(profile, z)
      return new EncodingInfo(Encoding.flat, null, profileDim, obsDim);
    }


    if (time.getRank() > 1) {
      stnDim = time.getDimension(0); // may be time(station, profile) or time(station, profile, z)
      profileDim = time.getDimension(1);
      return new EncodingInfo(Encoding.multidim, stnDim, profileDim, obsDim);
    }


    errlog.format("CFpointObs %s unrecognized form%n", ftype);
    return null;

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            if (variables != null) {


                // cycle on all variables to get parse them
                for (final Variable var_ : variables) {
                    if (var_ != null && var_ instanceof VariableDS) {
                        final VariableDS variable= (VariableDS) var_;
                        
                        // get the name
                        // check if it is filtered or not
                        String varName = variable.getFullName();
                        if (!ancillaryFileManager.acceptsVariable(varName)) {
                            continue;
                        }


                        // is it acceptable?

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     * @return The data type, or {@link DataBuffer#TYPE_UNDEFINED} if unknown.
     * 
     * @see NetcdfImageReader#getRawDataType
     */
    public static int getRawDataType(final VariableIF variable) {
        VariableDS ds = (VariableDS) variable;
        final DataType type = ds.getOriginalDataType();
        return transcodeNetCDFDataType(type,variable.isUnsigned());
    }

View Full Code Here

  private VerticalCT makeWRFEtaVerticalCoordinateTransform(NetcdfDataset ds, CoordinateSystem cs) {
    if ((null == ds.findVariable("PH")) || (null == ds.findVariable("PHB")) ||
        (null == ds.findVariable("P")) || (null == ds.findVariable("PB")))
      return null;


    WRFEtaTransformBuilder builder = new WRFEtaTransformBuilder(cs);
    return (VerticalCT) builder.makeCoordinateTransform(ds, null);
  }

View Full Code Here

  }
*/


  static private NetcdfFile acquireDODS(FileCache cache, FileFactory factory, Object hashKey,
                                        String location, int buffer_size, ucar.nc2.util.CancelTask cancelTask, Object spiObject) throws IOException {
    if (cache == null) return new DODSNetcdfFile(location, cancelTask);


    if (factory == null) factory = new DodsFactory();
    return (NetcdfFile) cache.acquire(factory, hashKey, location, buffer_size, cancelTask, spiObject);
  }

View Full Code Here

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