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Re: Searching for working example...

Hoeven, Maarten van der wrote:


Hi all,

I'm using the Java2-lib to create Netcdf-files. I got it working to the
extend that I can create the file (dimensions, variables) and write a
lot of data to it. All in one go. This is working perfectly.

However, I want to walk a slightly different road. That is, to create
only once an empty netcdf-file (only variables and dimensions stored in
it, hence the structure), and after that to write data to it every day.
To put in other words, to update the netcdf-file with daily data.

This must be possible, because I saw some Java1-lib working examples.
However, it must be working a bit different in version 2 of the
Java-lib, because I run into problems. The problems are that I am
messing around with the origin array; I cant get this working.

Like:

ncfile.write("tn", origin, ArrayAbstract.factory(tnArr));

where origin is an int[1]-array.

I understand I have to use origin, to make clear at what position in the
file the new data must be written. But I must be overlooking
something...


Does someone has a working Java-source for me (capable to use with
Netcdf for Java Version 2 (!)), in which an existing netcdf-file is
updated with new data? 

Thanks,
Maarten

+-------------------------------
| Maarten van der Hoeven
| KNMI, De Bilt, The Netherlands
| +31-30-2206 402
| address@hidden
+-------------------------------
--------------------------------------------------------------
Zie ook/see also: http://www.knmi.nl/maildisclaimer.html
attached is an example of creating a file and then later writing to it. let me know if this is adequate. 
package ucar.nc2;

import junit.framework.*;

import ucar.ma2.*;
import ucar.nc2.*;
import java.io.IOException;

/**
 * Simple example to create a new netCDF file corresponding to the following
 * CDL:
 * <pre>
 *  netcdf example {
 *  dimensions:
 *      lat = 3 ;
 *      lon = 4 ;
 *      time = UNLIMITED ;
 *  variables:
 *      int rh(time, lat, lon) ;
 *              rh:long_name="relative humidity" ;
 *              rh:units = "percent" ;
 *      double T(time, lat, lon) ;
 *              T:long_name="surface temperature" ;
 *              T:units = "degC" ;
 *      float lat(lat) ;
 *              lat:units = "degrees_north" ;
 *      float lon(lon) ;
 *              lon:units = "degrees_east" ;
 *      int time(time) ;
 *              time:units = "hours" ;
 *  // global attributes:
 *              :title = "Example Data" ;
 *  data:
 *   rh =
 *     1, 2, 3, 4,
 *     5, 6, 7, 8,
 *     9, 10, 11, 12,
 *     21, 22, 23, 24,
 *     25, 26, 27, 28,
 *     29, 30, 31, 32 ;
 *   T =
 *     1, 2, 3, 4,
 *     2, 4, 6, 8,
 *     3, 6, 9, 12,
 *     2.5, 5, 7.5, 10,
 *     5, 10, 15, 20,
 *     7.5, 15, 22.5, 30 ;
 *   lat = 41, 40, 39 ;
 *   lon = -109, -107, -105, -103 ;
 *   time = 6, 18 ;
 *  }
 * </pre>
 *
 * @author: Russ Rew
 * @author: John Caron
 */
public class TestCreate extends TestCase  {

  static String fileName = TestAll.topDir+"example.nc"; // default name of file 
created

  public TestCreate( String name) {
    super(name);
  }

  public void testCreate() {
    NetcdfFileWriteable ncfile = new NetcdfFileWriteable();
    ncfile.setName(fileName);

    // define dimensions
    Dimension latDim = ncfile.addDimension("lat", 3);
    Dimension lonDim = ncfile.addDimension("lon", 4);
    Dimension timeDim = ncfile.addDimension("time", -1);

    // define Variables
    Dimension[] dim3 = new Dimension[3];
    dim3[0] = timeDim;
    dim3[1] = latDim;
    dim3[2] = lonDim;

    // int rh(time, lat, lon) ;
    //    rh:long_name="relative humidity" ;
    //    rh:units = "percent" ;
    ncfile.addVariable("rh", int.class, dim3);
    ncfile.addVariableAttribute("rh", "long_name", "relative humidity");
    ncfile.addVariableAttribute("rh", "units", "percent");

    // double T(time, lat, lon) ;
    //   T:long_name="surface temperature" ;
    //   T:units = "degC" ;
    ncfile.addVariable("T", double.class, dim3);
    ncfile.addVariableAttribute("T", "long_name", "surface temperature");
    ncfile.addVariableAttribute("T", "units", "degC");

    // float lat(lat) ;
    //   lat:units = "degrees_north" ;
    ncfile.addVariable("lat", float.class, new Dimension[] {latDim});
    ncfile.addVariableAttribute("lat", "units", "degrees_north");

    // float lon(lon) ;
    // lon:units = "degrees_east" ;
    ncfile.addVariable("lon", float.class, new Dimension[] {lonDim});
    ncfile.addVariableAttribute("lon", "units", "degrees_east");

    // int time(time) ;
    //   time:units = "hours" ;
    ncfile.addVariable("time", int.class, new Dimension[] {timeDim});
    ncfile.addVariableAttribute("time", "units", "hours");

    //  :title = "Example Data" ;
    ncfile.addGlobalAttribute("title", "Example Data");

    // create the file
    try {
      ncfile.create();
    }  catch (IOException e) {
      System.err.println("ERROR creating file");
      assert(false);
    }
    //System.out.println( "ncfile = "+ ncfile);

    // write the RH data one value at a time to an Array
    int[][][] rhData = {{{ 1,  2,  3,  4}, { 5,  6,  7,  8}, { 9, 10, 11, 12}},
                        {{21, 22, 23, 24}, {25, 26, 27, 28}, {29, 30, 31, 32}}};

    ArrayInt rhA = new ArrayInt.D3(2, latDim.getLength(), lonDim.getLength());
    int i,j,k;
    Index ima = rhA.getIndex();
    // write
    for (i=0; i<2; i++)
      for (j=0; j<latDim.getLength(); j++)
        for (k=0; k<lonDim.getLength(); k++)
          rhA.setInt(ima.set(i,j,k), rhData[i][j][k]);

    // write rhData out to disk
    try {
      ncfile.write("rh", rhA);
    } catch (IOException e) {
      System.err.println("ERROR writing file");
      assert(false);
    }

    /* Here's an ArrayAbstract approach to set the values of T all at once. */
    double[][][] tData = {
        {{  1, 2,   3,  4}, {2,  4,  6,  8}, {  3,  6,  9,   12}},
        {{2.5, 5, 7.5, 10}, {5, 10, 15, 20}, {7.5, 15, 22.5, 30}}
    };
    try {
      ncfile.write("T", ArrayAbstract.factory(tData));
    } catch (IOException e) {
      System.err.println("ERROR writing file");
      assert(false);
    }

    /* Store the rest of variable values */
   try {
     ncfile.write("lat", ArrayAbstract.factory(new float[] {41, 40, 39}));
     ncfile.write("lon", ArrayAbstract.factory(new float[] {-109, -107, -105, 
-103}));
     ncfile.write("time", ArrayAbstract.factory(new int[] {6, 18}));
   } catch (IOException e) {
     System.err.println("ERROR writing file");
     assert(false);
   }

    // all done
    try {
      ncfile.close();
    } catch (IOException e) {
      System.err.println("ERROR writing file");
      assert(false);
    }

    System.out.println( "*****************Create Netcdf done");

  }

  public void testWriteExisting() {
    NetcdfFileWriteable ncfile = null;
    try {
      ncfile = new NetcdfFileWriteable(fileName);
    } catch (IOException e) {
      System.err.println("ERROR opening file "+fileName);
      assert(false);
    }

    // find dimensions
    Dimension latDim = ncfile.findDimension("lat");
    Dimension lonDim = ncfile.findDimension("lon");
    Dimension timeDim = ncfile.findDimension("time");

    // find Variables
    Variable rh = ncfile.findVariable("rh");

    // create the data values
    ArrayInt rhA = new ArrayInt.D3(2, latDim.getLength(), lonDim.getLength());
    Index ima = rhA.getIndex();
    for (int i=0; i<2; i++)
      for (int j=0; j<latDim.getLength(); j++)
        for (int k=0; k<lonDim.getLength(); k++)
          rhA.setInt(ima.set(i,j,k), (i+1)*(j+1)*(k+1));

    // write rhData out to disk
    int[] origin = new int[3];
    origin[0] = timeDim.getLength(); // starts at the existing length
    try {
      ncfile.write("rh", origin, rhA);
    } catch (IOException e) {
      System.err.println("ERROR writing file");
      assert(false);
    }

    // all done
    try {
      ncfile.close();
    } catch (IOException e) {
      System.err.println("ERROR writing file");
      assert(false);
    }

    System.out.println( " testWriteExisting Netcdf done");
  }

  public void testReadExisting() {
    NetcdfFile ncfile = null;
    try {
      ncfile = new NetcdfFile(fileName);
    } catch (IOException e) {
      System.err.println("ERROR opening file "+fileName);
      assert(false);
    }

    // find dimensions
    Dimension latDim = ncfile.findDimension("lat");
    Dimension lonDim = ncfile.findDimension("lon");
    Dimension timeDim = ncfile.findDimension("time");
    assert timeDim.getLength() == 4;

    // find Variables
    Variable rh = ncfile.findVariable("rh");
    assert rh.getRank() == 3;
    assert rh.getDataType() == DataType.INT;

    try {
      ArrayInt.D3 rhA = (ArrayInt.D3) rh.read();
      Index ima = rhA.getIndex();
      for (int i = 2; i < 4; i++)
        for (int j = 0; j < latDim.getLength(); j++)
          for (int k = 0; k < lonDim.getLength(); k++)
            assert rhA.getInt(ima.set(i, j, k)) ==  (i - 1) * (j + 1) * (k + 1);

    } catch (IOException e) {
      System.err.println("ERROR writing file");
      assert(false);
    }

    // all done
    try {
      ncfile.close();
    } catch (IOException e) {
      System.err.println("ERROR writing file");
      assert(false);
    }

    System.out.println( " testReadExisting Netcdf done");
  }



}