Examples of ucar.nc2.NetcdfFileWriteable

ucar.nc2.Variable
Create/Write netCDF-3 formatted files.
When a file is first created, it is in is "define mode", where the header objects (Dimensions, Attributes and Variables) may be added, deleted and modified, but no data may be written. Once create() is called, you can no longer modify the header, but you can now write data. An existing file is opened in write mode.
If setRedefine(true) is called, the file goes into define mode, and header objects can be changed. When setRedefine(false) is called, the new header is written, and the old file data is copied to the new file. This can be quite costly. @author caron @see NetcdfFile

       final int NY = 12;




       // Create the file.
       String filename = "simple_xy.nc";
       NetcdfFileWriteable dataFile = null;


       try {
           dataFile = NetcdfFileWriteable.createNew(filename, false);


           // Create netCDF dimensions,
            Dimension xDim = dataFile.addDimension("x", NX );
            Dimension yDim = dataFile.addDimension("y", NY );


            ArrayList dims =  new ArrayList();


            // define dimensions
            dims.add( xDim);
            dims.add( yDim);




           // Define a netCDF variable. The type of the variable in this case
           // is ncInt (32-bit integer).
           dataFile.addVariable("data", DataType.INT, dims);
                 
           // create the file
           dataFile.create();


            // This is the data array we will write. It will just be filled
            // with a progression of numbers for this example.
           ArrayInt.D2 dataOut = new ArrayInt.D2( xDim.getLength(), yDim.getLength());


           // Create some pretend data. If this wasn't an example program, we
           // would have some real data to write, for example, model output.
           int i,j;


           for (i=0; i<xDim.getLength(); i++) {
                for (j=0; j<yDim.getLength(); j++) {
                    dataOut.set(i,j, i * NY + j);
                }
           }


           // Write the pretend data to the file. Although netCDF supports
           // reading and writing subsets of data, in this case we write all
           // the data in one operation.
          dataFile.write("data", dataOut);




       } catch (IOException e) {
              e.printStackTrace();
       } catch (InvalidRangeException e) {
              e.printStackTrace();
       } finally {
            if (null != dataFile)
            try {
                dataFile.close();
            } catch (IOException ioe) {
                ioe.printStackTrace();
            }
       }

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      }
    }
  }


  public void alterExistingFile(String url) throws IOException {
    NetcdfFileWriteable file = null;
    try {
      file = NetcdfFileWriteable.openExisting(url, false);
      file.setRedefineMode(true);
      //Group rootGroup = file.getRootGroup();
      //Group headerDataGroup = new Group(file, rootGroup, "header_data");
      //file.addGroup(rootGroup, headerDataGroup);
      file.addVariable(null, newVarName, DataType.FLOAT, "z y x");
    } finally {
      if (file != null) {
        file.setRedefineMode(false);
        file.flush();
        file.close();
      }
    }
  }

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  // section reading for member data
  static public ucar.ma2.Array readSection(ParsedSectionSpec cer) throws IOException, InvalidRangeException {
    Variable inner = null;
    List<Range> totalRanges = new ArrayList<Range>();
    ParsedSectionSpec current = cer;
    while (current != null) {
      totalRanges.addAll( current.section.getRanges());
      inner = current.v;
      current = current.child;
    }

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    Section total = new Section( totalRanges);
    Array result = Array.factory(inner.getDataType(), total.getShape());


    // must be a Structure
    Structure outer = (Structure) cer.v;
    Structure outerSubset = outer.select( cer.child.v.getShortName()); // allows IOSPs to optimize for  this case
    ArrayStructure outerData = (ArrayStructure) outerSubset.read(cer.section);
    extractSection( cer.child, outerData, result.getIndexIterator());


    result.setUnsigned(cer.v.isUnsigned());
    return result;
  }

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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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    return 0;
  }


  // section reading for member data
  static public ucar.ma2.Array readSection(ParsedSectionSpec cer) throws IOException, InvalidRangeException {
    Variable inner = null;
    List<Range> totalRanges = new ArrayList<Range>();
    ParsedSectionSpec current = cer;
    while (current != null) {
      totalRanges.addAll( current.section.getRanges());
      inner = current.v;
      current = current.child;
    }


    Section total = new Section( totalRanges);
    Array result = Array.factory(inner.getDataType(), total.getShape());


    // must be a Structure
    Structure outer = (Structure) cer.v;
    Structure outerSubset = outer.select( cer.child.v.getShortName()); // allows IOSPs to optimize for  this case
    ArrayStructure outerData = (ArrayStructure) outerSubset.read(cer.section);

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    String timeVars = ds.findAttValueIgnoreCase(null, "timeVariables", "");
    StringTokenizer stoker = new StringTokenizer( timeVars, ", ");
    while (stoker.hasMoreTokens()) {
      String vname = stoker.nextToken();
      Variable v = ds.findVariable(vname);
      if (v != null) {
        v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
      } else {
        parseInfo.format(" cant find time variable %s\n", vname);
      }
    }


    String locVars = ds.findAttValueIgnoreCase(null, "stationLocationVariables", "");
    stoker = new StringTokenizer( locVars, ", ");
    int count = 0;
    while (stoker.hasMoreTokens()) {
      String vname = stoker.nextToken();
      Variable v = ds.findVariable(vname);
      if (v != null) {
        AxisType atype = count == 0 ? AxisType.Lat : count == 1 ? AxisType.Lon : AxisType.Height;
        v.addAttribute(new Attribute(_Coordinate.AxisType, atype.toString()));
      } else {
        parseInfo.format(" cant find time variable %s\n",vname);
      }
      count++;
    }

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   */
  public AtmosLnPressure(NetcdfFile ds, Dimension timeDim, List<Parameter> params) {
    super(timeDim);


    String p0name = getParameterStringValue(params, P0);
    Variable p0var = ds.findVariable(p0name);
    double p0;
    try {
      p0 = p0var.readScalarDouble();
    } catch (IOException e) {
      throw new IllegalArgumentException("AtmosLnPressure failed to read "
          + p0name + " err= " + e.getMessage());
    }


    String levName = getParameterStringValue(params, LEV);
    Variable levVar = ds.findVariable(levName);


    try {
      Array lev = levVar.read();
      assert lev.getRank() == 1;
      pressure = new ArrayDouble.D1( (int) lev.getSize());
      IndexIterator ii = pressure.getIndexIterator();
      while (lev.hasNext()) {
        double result = p0 * Math.exp(-lev.nextDouble());

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