Examples of ucar.nc2.dataset.NetcdfDataset

ucar.nc2.dataset.NetcdfDataset
NetcdfDataset extends the netCDF API, adding standard attribute parsing such as scale and offset, and explicit support for Coordinate Systems. A NetcdfDataset wraps a NetcdfFile, or is defined by an NcML document.

Be sure to close the dataset when done, best practice is to enclose in a try/finally block:
```
 NetcdfDataset ncd = null; try { ncd = NetcdfDataset.openDataset(fileName); ... } finally { ncd.close(); } 
```
By default NetcdfDataset is opened with all enhancements turned on. The default "enhance mode" can be set through setDefaultEnhanceMode(). One can also explicitly set the enhancements you want in the dataset factory methods. The enhancements are:
- ScaleMissing : process scale/offset/missing attributes, and automatically convert the data.
- ScaleMissingDefer : process scale/offset/missing attributes, but dont automatically convert the data. You can call VariableEnhanced.convertScaleOffsetMissing() on the data manually.
- CoordSystem : extract CoordinateSystem using the CoordSysBuilder plug-in mechanism
- ConvertEnums : automaticlly convert enum values to their corresponding Strings. If you want to do this manually, you can call Variable.lookupEnumString() manually.
Automatic ScaleMissing processing has some overhead, and if you need maximum performance, but still want to use scale/offset/missing value handling, open the NetcdfDataset with ScaleMissingDefer. The VariableDS data type is not promoted, and the data is not converted on a read, but you can call the convertScaleOffsetMissing() routines which will do the conversion on a point-by-point basis. @author caron @see ucar.nc2.NetcdfFile

                                  (String) headerInfo.get( HeaderInfoTitle.DATA_SET_ID.toString() ) );
    recordSizeInBytes = Integer.parseInt( (String) headerInfo.get( HeaderInfoTitle.RECORD_BYTES.toString() ) );
    numRecords = Integer.parseInt( (String) headerInfo.get( HeaderInfoTitle.NUM_RECORDS.toString() ) );
    numHeaderRecords = Integer.parseInt( (String) headerInfo.get( HeaderInfoTitle.NUM_HEADER_RECORDS.toString() ) );
    numDataRecords = Integer.parseInt( (String) headerInfo.get( HeaderInfoTitle.NUM_DATA_RECORDS.toString() ) );
    numDataRecordsDim = new Dimension( this.numDataRecordsDimName,
                                       numDataRecords, true, true, false );
    numArtificialDataRecords = Integer.parseInt( (String) headerInfo.get( HeaderInfoTitle.NUM_ARTIFICIAL_DATA_RECORDS.toString() ) );
    if ( numHeaderRecords + numDataRecordsDim.getLength() + numArtificialDataRecords != numRecords )
    {
      throw new IOException( "Invalid DMSP file: the number of header records <" + this.numHeaderRecords + ">, data records <" + this.numDataRecordsDim.getLength() + ">, and artificial data records <" + this.numArtificialDataRecords + "> is not equal to total records <" + this.numRecords + ">." );

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   * Parse the sensor information from the header.
   */
  private void handleSensorInformation()
  {
    numSamplesPerBand = Integer.parseInt( (String) headerInfo.get( HeaderInfoTitle.SAMPLES_PER_BAND.toString()) );
    numSamplesPerBandDim = new Dimension(
            this.numSamplesPerBandDimName,
            numSamplesPerBand);


    // Read nominal resolution information
    nominalResolutionAtt = new Attribute( nominalResolutionAttName,

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        int                        numZ  = 0;
        HashMap<String, Dimension> zDims = new HashMap<String, Dimension>();
        for (GradsDimension dim : dims) {
            String    name  = getVarName(dim);
            int       size  = dim.getSize();
            Dimension ncDim = new Dimension(name, size, true);
            ncFile.addDimension(null, ncDim);
            if (name.equals(ENS_VAR)) {
                v = new Variable(ncFile, null, null, name, DataType.STRING,
                                 name);
                v.addAttribute(new Attribute("standard_name", "ensemble"));
                v.addAttribute(new Attribute(_Coordinate.AxisType,
                                             AxisType.Ensemble.toString()));
                List<String> names =
                    gradsDDF.getEnsembleDimension().getEnsembleNames();
                String[] nameArray = new String[names.size()];
                for (int i = 0; i < nameArray.length; i++) {
                    nameArray[i] = names.get(i);
                }
                Array dataArray = Array.factory(DataType.STRING,
                                      new int[] { nameArray.length },
                                      nameArray);
                v.setCachedData(dataArray, false);
            } else {
                double[] vals = dim.getValues();
                v = new Variable(ncFile, null, null, name, DataType.DOUBLE,
                                 name);
                v.addAttribute(new Attribute("units", dim.getUnit()));
                if (name.equals(Y_VAR)) {
                    v.addAttribute(new Attribute("long_name", "latitude"));
                    v.addAttribute(new Attribute("standard_name",
                            "latitude"));
                    v.addAttribute(new Attribute("axis", "Y"));
                    sizeY = dim.getSize();
                    v.addAttribute(new Attribute(_Coordinate.AxisType,
                            AxisType.Lat.toString()));
                } else if (name.equals(X_VAR)) {
                    v.addAttribute(new Attribute("long_name", "longitude"));
                    v.addAttribute(new Attribute("standard_name",
                            "longitude"));
                    v.addAttribute(new Attribute("axis", "X"));
                    v.addAttribute(new Attribute(_Coordinate.AxisType,
                            AxisType.Lon.toString()));
                    sizeX = dim.getSize();
                } else if (name.equals(Z_VAR)) {
                    numZ = size;
                    zDims.put(name, ncDim);
                    v.addAttribute(new Attribute("long_name", "level"));
                    addZAttributes(dim, v);
                } else if (name.equals(TIME_VAR)) {
                    v.addAttribute(new Attribute("long_name", "time"));
                    v.addAttribute(new Attribute(_Coordinate.AxisType,
                            AxisType.Time.toString()));
                }
                ArrayDouble.D1 varArray = new ArrayDouble.D1(size);
                for (int i = 0; i < vals.length; i++) {
                    varArray.set(i, vals[i]);
                }
                v.setCachedData(varArray, false);
            }
            ncFile.addVariable(null, v);
        }
        if (numZ > 0) {
            GradsDimension zDim = gradsDDF.getZDimension();
            double[]       vals = zDim.getValues();
            for (GradsVariable var : vars) {
                int nl = var.getNumLevels();
                if ((nl > 0) && (nl != numZ)) {
                    String name = Z_VAR + nl;
                    if (zDims.get(name) == null) {
                        Dimension ncDim = new Dimension(name, nl, true);
                        ncFile.addDimension(null, ncDim);
                        Variable vz = new Variable(ncFile, null, null, name,
                                          DataType.DOUBLE, name);
                        vz.addAttribute(new Attribute("long_name", name));
                        vz.addAttribute(new Attribute("units",

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    }


    Variable v = ds.findVariable("time_offset");
    v.addAttribute(new Attribute( "units", "seconds since "+dfo.toDateTimeString(start)));


    Group root = ds.getRootGroup();
    root.addAttribute(new Attribute( "Convention", "Suomi-Station-CDM"));    
    ds.finish();
  }

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        List<GradsVariable>  vars  = gradsDDF.getVariables();
        List<GradsAttribute> attrs = gradsDDF.getAttributes();
        //TODO: ensembles
        List<GradsDimension>       dims = gradsDDF.getDimensions();
        Variable                   v;
        int                        numZ  = 0;
        HashMap<String, Dimension> zDims = new HashMap<String, Dimension>();
        for (GradsDimension dim : dims) {
            String    name  = getVarName(dim);
            int       size  = dim.getSize();
            Dimension ncDim = new Dimension(name, size, true);
            ncFile.addDimension(null, ncDim);
            if (name.equals(ENS_VAR)) {
                v = new Variable(ncFile, null, null, name, DataType.STRING,
                                 name);
                v.addAttribute(new Attribute("standard_name", "ensemble"));
                v.addAttribute(new Attribute(_Coordinate.AxisType,
                                             AxisType.Ensemble.toString()));
                List<String> names =
                    gradsDDF.getEnsembleDimension().getEnsembleNames();
                String[] nameArray = new String[names.size()];
                for (int i = 0; i < nameArray.length; i++) {
                    nameArray[i] = names.get(i);
                }
                Array dataArray = Array.factory(DataType.STRING,
                                      new int[] { nameArray.length },
                                      nameArray);
                v.setCachedData(dataArray, false);
            } else {
                double[] vals = dim.getValues();
                v = new Variable(ncFile, null, null, name, DataType.DOUBLE,
                                 name);
                v.addAttribute(new Attribute("units", dim.getUnit()));
                if (name.equals(Y_VAR)) {
                    v.addAttribute(new Attribute("long_name", "latitude"));
                    v.addAttribute(new Attribute("standard_name",
                            "latitude"));
                    v.addAttribute(new Attribute("axis", "Y"));
                    sizeY = dim.getSize();
                    v.addAttribute(new Attribute(_Coordinate.AxisType,
                            AxisType.Lat.toString()));
                } else if (name.equals(X_VAR)) {
                    v.addAttribute(new Attribute("long_name", "longitude"));
                    v.addAttribute(new Attribute("standard_name",
                            "longitude"));
                    v.addAttribute(new Attribute("axis", "X"));
                    v.addAttribute(new Attribute(_Coordinate.AxisType,
                            AxisType.Lon.toString()));
                    sizeX = dim.getSize();
                } else if (name.equals(Z_VAR)) {
                    numZ = size;
                    zDims.put(name, ncDim);
                    v.addAttribute(new Attribute("long_name", "level"));
                    addZAttributes(dim, v);
                } else if (name.equals(TIME_VAR)) {
                    v.addAttribute(new Attribute("long_name", "time"));
                    v.addAttribute(new Attribute(_Coordinate.AxisType,
                            AxisType.Time.toString()));
                }
                ArrayDouble.D1 varArray = new ArrayDouble.D1(size);
                for (int i = 0; i < vals.length; i++) {
                    varArray.set(i, vals[i]);
                }
                v.setCachedData(varArray, false);
            }
            ncFile.addVariable(null, v);
        }
        if (numZ > 0) {
            GradsDimension zDim = gradsDDF.getZDimension();
            double[]       vals = zDim.getValues();
            for (GradsVariable var : vars) {
                int nl = var.getNumLevels();
                if ((nl > 0) && (nl != numZ)) {
                    String name = Z_VAR + nl;
                    if (zDims.get(name) == null) {
                        Dimension ncDim = new Dimension(name, nl, true);
                        ncFile.addDimension(null, ncDim);
                        Variable vz = new Variable(ncFile, null, null, name,
                                          DataType.DOUBLE, name);
                        vz.addAttribute(new Attribute("long_name", name));
                        vz.addAttribute(new Attribute("units",
                                zDim.getUnit()));
                        addZAttributes(zDim, vz);
                        ArrayDouble.D1 varArray = new ArrayDouble.D1(nl);
                        for (int i = 0; i < nl; i++) {
                            varArray.set(i, vals[i]);
                        }
                        vz.setCachedData(varArray, false);
                        ncFile.addVariable(null, vz);
                        zDims.put(name, ncDim);
                    }
                }
            }
        }
        zDims = null;
        for (GradsVariable var : vars) {
            String coords = "latitude longitude";
            int    nl     = var.getNumLevels();
            if (nl > 0) {
                if (nl == numZ) {
                    coords = "level " + coords;
                } else {
                    coords = Z_VAR + nl + " " + coords;
                }
            }
            coords = "time " + coords;
            if (gradsDDF.getEnsembleDimension() != null) {
                coords = "ensemble " + coords;
            }
            v = new Variable(ncFile, null, null, var.getName(),
                             DataType.FLOAT, coords);
            v.addAttribute(new Attribute("long_name", var.getDescription()));
            if (var.getUnitName() != null) {
                v.addAttribute(new Attribute("units", var.getUnitName()));
            }

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   * @param ncfile the NetcdfFile to test
   * @return true if we think this is a Zebra file.
   */
  public static boolean isMine(NetcdfFile ncfile) {


    Variable v = ncfile.findVariable("time_offset");
    if (v == null || !v.isCoordinateVariable()) return false;
    String desc = v.getDescription();
    if (desc == null || !desc.equals("Time delta from start_time")) return false;


    if (null == ncfile.findGlobalAttribute( "start_date")) return false;
    if (null == ncfile.findGlobalAttribute( "start_time")) return false;

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      start = df.parse(start_date);
    } catch (ParseException e) {
      throw new RuntimeException("Cant read start_date="+start_date);
    }


    Variable v = ds.findVariable("time_offset");
    v.addAttribute(new Attribute( "units", "seconds since "+dfo.toDateTimeString(start)));


    Group root = ds.getRootGroup();
    root.addAttribute(new Attribute( "Convention", "Suomi-Station-CDM"));    
    ds.finish();
  }

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    super.findCoordinateAxes(ds);
  }


  protected AxisType getAxisType( NetcdfDataset ncd, VariableEnhanced v) {


    AxisType atype = super.getAxisType(ncd, v);
    if (atype != null) return atype;


    String unit = v.getUnitsString();
    if (unit == null)
      return null;

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  private static void mergeOverwriteDataType( ThreddsMetadataBuilder first,
                                              ThreddsMetadataBuilder second,
                                              ThreddsMetadataBuilder mergedThreddsMetadata )
  {
    FeatureType dataType = second.getDataType() != null ? second.getDataType() : first.getDataType();
    if ( dataType != null )
      mergedThreddsMetadata.setDataType( dataType );
  }

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      ThreddsDataFactory.Result result = new ThreddsDataFactory().openDatatype( location, task);
      errlog.append( result.errLog);
      return (result.fatalError) ? null : result.tds;
    } */


    NetcdfDataset ncd = NetcdfDataset.acquireDataset( location, task);
    return open( datatype, ncd, task, errlog);
  }

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