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

/** Test nc2 dods in the JUnit framework. */
public class TestOutstandingIssues extends TestCase {


  public void testByteAttribute() throws IOException {
    String filename = "dods://localhost:8080/thredds/dodsC/CdataScan/profiler/PROFILER_wind_06min_20070514_2354.nc";
    NetcdfDataset ncd = NetcdfDataset.openDataset(filename, true, null);
    assert ncd != null;
    VariableDS v = (VariableDS) ncd.findVariable("uvQualityCode");
    assert v != null;
    assert v.hasMissing();


    int count = 0;
    Array data = v.read();

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        System.out.println(" skip " + m.getHeader());
        continue;
      }
      System.out.println(" read " + m.getHeader());


      NetcdfDataset ncd = null;
      try {
        byte[] mbytes = scan.getMessageBytes(m);
        NetcdfFile ncfile = NetcdfFile.openInMemory("test", mbytes);
        ncd = new NetcdfDataset(ncfile);
        Structure s = (Structure) ncd.findVariable(BufrIosp.obsRecord);
        assert s != null;
        readAll(s);


      } finally {
        if (ncd != null) ncd.close();
      }


      count++;
    }
  }

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      "  <aggregation dimName='time' type='joinExisting'>\n" +
      "    <netcdf location='file:C:\\data\\work\\margolis\\f_0000000.nc'/>\n" +
      "    <netcdf location='file:C:\\data\\work\\margolis\\f_0032400.nc'/>\n" +
      "  </aggregation>\n" +
      "</netcdf>";
    NetcdfDataset aggregatedDataset = NcMLReader.readNcML( new ByteArrayInputStream(ncml.getBytes()), null );
    GridDataset emptyDataset = new GridDataset( aggregatedDataset );
    System.out.printf("empty= %s%n", emptyDataset.getGrids().size());


    assert emptyDataset.getGrids().size() == fullDataset.getGrids().size();
  }

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    dataset.close();
  }


  public void utestSubsetCoordEdges() throws Exception {
    NetcdfDataset fooDataset = NetcdfDataset.openDataset(TestAll.cdmLocalTestDataDir + "dataset/subsetCoordEdges.ncml");


    try {
      GridDataset fooGridDataset = new GridDataset(fooDataset);
      GridDatatype fooGrid = fooGridDataset.findGridDatatype("foo");


      CoordinateAxis1D fooTimeAxis = fooGrid.getCoordinateSystem().getTimeAxis1D();
      CoordinateAxis1D fooLatAxis = (CoordinateAxis1D) fooGrid.getCoordinateSystem().getYHorizAxis();
      CoordinateAxis1D fooLonAxis = (CoordinateAxis1D) fooGrid.getCoordinateSystem().getXHorizAxis();


      // Expected: [0.0, 31.0, 59.0, 90.0, 120.0]
      // Actual:   [0.0, 31.0, 59.0, 90.0, 120.0]
      System.out.println("mid time= " + Arrays.toString(fooTimeAxis.getCoordValues()));
      System.out.println("edge time= " + Arrays.toString(fooTimeAxis.getCoordEdges()));
      System.out.println();


      // Expected: [-90.0, -18.0, 36.0, 72.0, 90.0]
      // Actual:   [-90.0, -18.0, 36.0, 72.0, 90.0]
      System.out.println("mid lat= " + Arrays.toString(fooLatAxis.getCoordValues()));
      System.out.println("edge lat= " + Arrays.toString(fooLatAxis.getCoordEdges()));
      System.out.println();


      // Expected: [0.0, 36.0, 108.0, 216.0, 360.0]
      // Actual:   [0.0, 36.0, 108.0, 216.0, 360.0]
      System.out.println("mid lon= " + Arrays.toString(fooLonAxis.getCoordValues()));
      System.out.println("edge lon= " + Arrays.toString(fooLonAxis.getCoordEdges()));
      System.out.println();




      Range middleRange = new Range(1, 2);
      GridDatatype fooSubGrid = fooGrid.makeSubset(null, null, middleRange, null, middleRange, middleRange);


      CoordinateAxis1D fooSubTimeAxis = fooSubGrid.getCoordinateSystem().getTimeAxis1D();
      CoordinateAxis1D fooSubLatAxis = (CoordinateAxis1D) fooSubGrid.getCoordinateSystem().getYHorizAxis();
      CoordinateAxis1D fooSubLonAxis = (CoordinateAxis1D) fooSubGrid.getCoordinateSystem().getXHorizAxis();


      // Expected: [31.0, 59.0, 90.0]
      // Actual:   [30.25, 59.75, 89.25]
      System.out.println("mid time= " + Arrays.toString(fooSubTimeAxis.getCoordValues()));
      System.out.println("edge time= " + Arrays.toString(fooSubTimeAxis.getCoordEdges()));
      compare(fooSubTimeAxis.getCoordEdges(), new double[] {31.0, 59.0, 90.0} );
      System.out.println();


      // Expected: [-18.0, 36.0, 72.0]
      // Actual:   [-13.5, 31.5, 76.5]
      System.out.println("mid lat= " + Arrays.toString(fooSubLatAxis.getCoordValues()));
      System.out.println("edge lat= " + Arrays.toString(fooSubLatAxis.getCoordEdges()));
      compare(fooSubLatAxis.getCoordEdges(), new double[] {-18.0, 36.0, 72.0} );
      System.out.println();


      // Expected: [36.0, 108.0, 216.0]
      // Actual:   [27.0, 117.0, 207.0]
      System.out.println("mid lon= " + Arrays.toString(fooSubLonAxis.getCoordValues()));
      System.out.println("edge lon= " + Arrays.toString(fooSubLonAxis.getCoordEdges()));
      compare(fooSubLonAxis.getCoordEdges(), new double[] {36.0, 108.0, 216.0} );
      System.out.println();


    } finally {
      fooDataset.close();
    }
  }

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      checkIfChanged();
      return;
    }


    Element ncml = getNcmlElement();
    NetcdfDataset ncd = NcMLReader.readNcML(path, ncml, null);
    ncd.setFileCache( fileCache); // LOOK: this dataset never gets closed


    fmrc = new FmrcImpl( ncd);
    madeFmrc = true;
  }

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              .append( name ).toString();
      return NetcdfDataset.acquireDataset( null, filename, null, -1, null, null); // no enhancement
    }


    makeFmrc();
    NetcdfDataset result = null;
    String location = path;


    if (path.endsWith(FMRC))
      result = fmrc.getFmrcDataset();


    else if (path.endsWith(BEST))
      result = fmrc.getBestTimeSeries();


    else {
      location = name;


      if (type.equals(OFFSET)) {
        int pos1 = name.indexOf(OFFSET_NAME);
        int pos2 = name.indexOf("hr");
        if ((pos1<0) || (pos2<0)) return null;
        String id = name.substring(pos1+OFFSET_NAME.length(), pos2);
        double hour = Double.parseDouble(id);
        result = fmrc.getForecastOffsetDataset( hour);


      } else if (type.equals(RUNS)) {
        int pos1 = name.indexOf(RUN_NAME);
        if (pos1<0) return null;
        String id = name.substring(pos1+RUN_NAME.length());


        DateFormatter formatter = new DateFormatter();
        Date date = formatter.getISODate(id);
        result = fmrc.getRunTimeDataset(date);


      } else if (type.equals(FORECAST)) {
        int pos1 = name.indexOf(FORECAST_NAME);
        if (pos1<0) return null;
        String id = name.substring(pos1+FORECAST_NAME.length());


        DateFormatter formatter = new DateFormatter();
        Date date = formatter.getISODate(id);
        result = fmrc.getForecastTimeDataset(date);
      }
    }


    if (null != result) result.setLocation( location);
    return result;
  }

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  public void testTimeAxisEval() throws IOException {
    /**
     * The following tests BugFixes.evalTimeAxes, called by ucar.nc2.dt.grid.GridCoordSys.isGridCoordSys
     */
    String testFileFullPath = "E:/work/margolis/bugfix/echoTops_runtime.nc";
    GridDataset runtimeDataset = new GridDataset(new NetcdfDataset(NetcdfFile.open(testFileFullPath)));
    if (runtimeDataset.getGrids().isEmpty()) {
      throw new RuntimeException("Runtime data file did not generate a dataset with grids");
    }
    if (runtimeDataset.getGrids().get(0).getCoordinateSystem().getRunTimeAxis() == null) {
      throw new RuntimeException("Runtime data file did not generate a dataset with a RunTime axis");

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     * @throws IOException Should never happen.
     */
    @Test
    public void testUCAR() throws IOException {
        final Metadata metadata;
        final Decoder input = new DecoderWrapper(TestCase.LISTENERS, new NetcdfDataset(open(NCEP)));
        try {
            metadata = new MetadataReader(input).read();
        } finally {
            input.close();
        }

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    @Override
    public GridGeometry[] getGridGeometries() throws IOException {
        if (geometries == null) {
            List<CoordinateSystem> systems = null;
            if (file instanceof NetcdfDataset) {
                final NetcdfDataset ds = (NetcdfDataset) file;
                final EnumSet<NetcdfDataset.Enhance> mode = EnumSet.copyOf(ds.getEnhanceMode());
                if (mode.add(NetcdfDataset.Enhance.CoordSystems)) {
                    ds.enhance(mode);
                }
                systems = ds.getCoordinateSystems();
            }
            geometries = new GridGeometry[(systems != null) ? systems.size() : 0];
            for (int i=0; i<geometries.length; i++) {
                geometries[i] = new GridGeometryWrapper(systems.get(i));
            }

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      //--- Add dataset subset catalog information to metadata
      dsMetadata.addContent(getDatasetSubset(ds));
      
      //--- For atomic dataset's add ncml for dataset to metadata
      if (!ds.hasNestedDatasets()) {
        NetcdfDataset ncD = NetcdfDataset.openDataset("thredds:"+ds.getCatalogUrl());
        NcMLWriter ncmlWriter = new NcMLWriter();
        Element ncml = Xml.loadString(ncmlWriter.writeXML(ncD),false);
        dsMetadata.addContent(ncml);
      }

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