Examples of wycs.core.Code$Variable

ucar.nc2.Variable
Represents a "bytecode" in the language of the Wycs theorem prover. Bytecodes are recursively defined trees, where each node is an instance of Code with the following attributes:
- Type. Provides information about the type of operands used in the bytecode.
- Opcode Determines the exact operation described by the bytecode.
- Operands Identifies zero or more operands for this bytecode.
In addition, there are various subclasses of Code which encode additional information (e.g. constant values, variable indices, etc). @author David J. Pearce @param < T>

      if ( !addAxisType( ds, "latitude", AxisType.Lat)) { // directly named


        String vname = ds.findAttValueIgnoreCase(null, "latitude_coordinate", null);
        if (!addAxisType( ds, vname, AxisType.Lat)) { // attribute named


          Variable v = hasUnits(ds, "degrees_north,degrees_N,degreesN,degree_north,degree_N,degreeN");
          if (v != null)
            addAxisType( v, AxisType.Lat); // CF-1
        }
      }
    }


    // longitude
    if (!hasAxisType( ds, AxisType.Lon)) { // already has _CoordinateAxisType


      if ( !addAxisType( ds, "longitude", AxisType.Lon)) { // directly named


        String vname = ds.findAttValueIgnoreCase(null, "longitude_coordinate", null);
        if (!addAxisType( ds, vname, AxisType.Lon)) { // attribute named


          Variable v = hasUnits(ds, "degrees_east,degrees_E,degreesE,degree_east,degree_E,degreeE");
          if (v != null)
            addAxisType( v, AxisType.Lon); // CF-1
        }
      }
    }

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  }




  private boolean addAxisType(NetcdfDataset ds, String vname, AxisType a) {
    if (vname == null) return false;
    Variable v = ds.findVariable(vname);
    if (v == null) return false;
    addAxisType( v, a);
    return true;
  }

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   } Compound String(10);
   */
  public void testStructureArray() throws IOException {
    NetcdfFile ncfile = TestH5.openH5("support/cstr.h5");


    Variable v = ncfile.findVariable("Compound String");
    assert( null != v);
    assert( v.getDataType() == DataType.STRUCTURE);
    assert( v instanceof Structure);
    assert( v.getRank() == 1);
    assert( v.getShape()[0] == 10);


      Array data = v.read();
      assert(data.getElementType() == StructureData.class);
      assert (data instanceof ArrayStructure);
      assert (data.getSize() == 10);
      assert (data.getRank() == 1);

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   type = Layout(8);  type= 2 (chunked) storageSize = (3,16) dataSize=0 dataAddress=1576
   */
  public void testStructureArrayChunked() throws IOException {
    NetcdfFile ncfile = TestH5.openH5("support/cuslab.h5");


    Variable v = ncfile.findVariable("ArrayOfStructures");
    assert( null != v);
    assert( v.getDataType() == DataType.STRUCTURE);
    assert( v instanceof Structure);
    assert( v.getRank() == 1);
    assert( v.getShape()[0] == 30);


    Array data = null;
    try {
      data = v.read();
    } catch (IOException e) { assert false; } // */


    assert(data.getElementType() == StructureData.class);
    assert (data instanceof ArrayStructure);
    assert (data.getSize() == 30);

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    type = Layout(8);  type= 1 (contiguous) storageSize = (10,16) dataSize=0 dataAddress=2048
   */
   public void testStructureWithArrayMember() throws IOException {
    NetcdfFile ncfile = TestH5.openH5("support/DSwith_array_member.h5");


    Variable v = ncfile.findVariable("ArrayOfStructures");
    v.setCaching(false);
    assert( null != v);
    assert( v.getDataType() == DataType.STRUCTURE);
    assert( v instanceof Structure);
    assert( v.getRank() == 1);
    assert( v.getShape()[0] == 10);


    try {
      Array data = v.read(new int[] {4}, new int[] {3});
      assert(data.getElementType() == StructureData.class);
      assert (data instanceof ArrayStructure);
      assert (data.getSize() == 3) : data.getSize();
      assert (data.getRank() == 1);


      int count = 0;
      IndexIterator iter = data.getIndexIterator();
      while (iter.hasNext()) {
        Object o = iter.next();
        assert (o instanceof StructureData);
        StructureData d = (StructureData) o;


        Array arr = d.getArray("a_name");
        assert (arr != null);
        assert (arr.getElementType() == int.class);
        assert (arr instanceof ArrayInt);
        assert (arr.getInt( arr.getIndex()) == 4 + count);
        NCdump.printArray( arr, "a_name", out, null);


        arr = d.getArray("b_name");
        assert (arr != null);
        assert (arr.getElementType() == float.class);
        assert (arr instanceof ArrayFloat);
        assert (arr.getSize() == 3);
        assert (arr.getFloat( arr.getIndex()) == (float) 4.0 + count);
        NCdump.printArray( arr, "b_name", out, null);


        count++;
      }


    }
    catch (InvalidRangeException e) { assert false; }
    catch (IOException e) { assert false; }


    try {
      Array data = v.read();
      assert(data.getElementType() == StructureData.class);
      assert (data instanceof ArrayStructure);
      assert (data.getSize() == 10);
      assert (data.getRank() == 1);

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        Dimension dimT = new Dimension("time", 1, true, false, false);


        ncfile.addDimension(null, dimT);


        String   timeCoordName = "time";
        Variable taxis         = new Variable(ncfile, null, null, timeCoordName);


        taxis.setDataType(DataType.DOUBLE);
        taxis.setDimensions("time");
        taxis.addAttribute(new Attribute("long_name", "time since base date"));
        taxis.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));


        double[] tdata = new double[1];


        tdata[0] = dd.getTime();


        Array dataT = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { 1 }, tdata);


        taxis.setCachedData(dataT, false);


        DateFormatter formatter = new DateFormatter();


        taxis.addAttribute(new Attribute("units", "msecs since " + formatter.toDateTimeStringISO(new Date(0))));
        ncfile.addVariable(null, taxis);
        dims.add(dimT);


        Dimension jDim = new Dimension("y", numY, true, false, false);
        Dimension iDim = new Dimension("x", numX, true, false, false);


        dims.add(jDim);
        dims.add(iDim);
        ncfile.addDimension(null, iDim);
        ncfile.addDimension(null, jDim);
        ncfile.addAttribute(null, new Attribute("cdm_data_type", FeatureType.GRID.toString()));


        String   coordinates = "time y x";
        Variable v           = new Variable(ncfile, null, null, cname);


        v.setDataType(DataType.BYTE);
        v.setDimensions(dims);
        ncfile.addVariable(null, v);
        v.addAttribute(new Attribute("long_name", ctitle));
        v.addAttribute(new Attribute("units", cunit));
        v.setSPobject(new Vinfo(numX, numY, hoff, false));
        v.addAttribute(new Attribute(_Coordinate.Axes, coordinates));


        // create coordinate variables
        Variable xaxis = new Variable(ncfile, null, null, "x");


        xaxis.setDataType(DataType.DOUBLE);
        xaxis.setDimensions("x");
        xaxis.addAttribute(new Attribute("standard_name", "projection x coordinate"));
        xaxis.addAttribute(new Attribute("units", "km"));
        xaxis.addAttribute(new Attribute(_Coordinate.AxisType, "GeoX"));


        double[]       data1      = new double[numX];
        ProjectionImpl projection = new LambertConformal(clat, clon, lat1, lat2);
        double ullat = 51.8294;
        double ullon = -135.8736;
        double lrlat = 17.2454;
        double lrlon = -70.1154;


        ProjectionPointImpl ptul = (ProjectionPointImpl) projection.latLonToProj(new LatLonPointImpl(ullat, ullon));
        ProjectionPointImpl ptlr = (ProjectionPointImpl) projection.latLonToProj(new LatLonPointImpl(lrlat, lrlon));
        ProjectionPointImpl ptc = (ProjectionPointImpl) projection.latLonToProj(new LatLonPointImpl(clat, clon));
        double startX = ptul.getX();
        double startY = ptlr.getY();
        double dx = (ptlr.getX() - ptul.getX())/(numX-1);
        for (int i = 0; i < numX; i++) {
            data1[i] = startX + i*dx;
        }


        Array dataA = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { numX }, data1);


        xaxis.setCachedData(dataA, false);
        ncfile.addVariable(null, xaxis);


        Variable yaxis = new Variable(ncfile, null, null, "y");


        yaxis.setDataType(DataType.DOUBLE);
        yaxis.setDimensions("y");
        yaxis.addAttribute(new Attribute("standard_name", "projection y coordinate"));
        yaxis.addAttribute(new Attribute("units", "km"));
        yaxis.addAttribute(new Attribute(_Coordinate.AxisType, "GeoY"));
        data1 = new double[numY];
        double dy = (ptul.getY() - ptlr.getY())/(numY-1);


        for (int i = 0; i < numY; i++) {
            data1[i] = startY + i*dy;
        }


        dataA = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { numY }, data1);
        yaxis.setCachedData(dataA, false);
        ncfile.addVariable(null, yaxis);


        // projection
        // lower left and upper right corner lat/lons
        // modified cylind. equidistant or  CED with lat/lon ration != 1
        Variable ct = new Variable(ncfile, null, null, projection.getClassName());


        ct.setDataType(DataType.CHAR);
        ct.setDimensions("");


        List params = projection.getProjectionParameters();


        for (int i = 0; i < params.size(); i++) {
            Parameter p = (Parameter) params.get(i);


            ct.addAttribute(new Attribute(p));
        }


        ct.addAttribute(new Attribute(_Coordinate.TransformType, "Projection"));
        //ct.addAttribute(new Attribute(_Coordinate.Axes, "lat lon"));
        ct.addAttribute( new Attribute(_Coordinate.Axes, "x y "));
        // fake data
        dataA = Array.factory(DataType.CHAR.getPrimitiveClassType(), new int[] {});
        dataA.setChar(dataA.getIndex(), ' ');
        ct.setCachedData(dataA, false);
        ncfile.addVariable(null, ct);


        return projection;
    }

View Full Code Here

        Dimension dimT = new Dimension("time", 1, true, false, false);


        ncfile.addDimension(null, dimT);


        String   timeCoordName = "time";
        Variable taxis         = new Variable(ncfile, null, null, timeCoordName);


        taxis.setDataType(DataType.DOUBLE);
        taxis.setDimensions("time");
        taxis.addAttribute(new Attribute("long_name", "time since base date"));
        taxis.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));


        double[] tdata = new double[1];


        tdata[0] = dd.getTime();


        Array dataT = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { 1 }, tdata);


        taxis.setCachedData(dataT, false);


        DateFormatter formatter = new DateFormatter();


        taxis.addAttribute(new Attribute("units", "msecs since " + formatter.toDateTimeStringISO(new Date(0))));
        ncfile.addVariable(null, taxis);
        dims.add(dimT);


        Dimension jDim = new Dimension("lat", numY, true, false, false);
        Dimension iDim = new Dimension("lon", numX, true, false, false);


        dims.add(jDim);
        dims.add(iDim);
        ncfile.addDimension(null, iDim);
        ncfile.addDimension(null, jDim);
        ncfile.addAttribute(null, new Attribute("cdm_data_type", FeatureType.GRID.toString()));


        String   coordinates = "time lat lon";
        Variable v           = new Variable(ncfile, null, null, cname);


        v.setDataType(DataType.BYTE);
        v.setDimensions(dims);
        ncfile.addVariable(null, v);
        v.addAttribute(new Attribute("long_name", ctitle));
        v.addAttribute(new Attribute("units", cunit));
        v.setSPobject(new Vinfo(numX, numY, hoff, false));
        v.addAttribute(new Attribute(_Coordinate.Axes, coordinates));


        // create coordinate variables
        Variable xaxis = new Variable(ncfile, null, null, "lon");
        xaxis.setDataType(DataType.DOUBLE);
        xaxis.setDimensions("lon");
        xaxis.addAttribute(new Attribute("long_name", "longitude"));
        xaxis.addAttribute(new Attribute("units", "degree"));
        xaxis.addAttribute(new Attribute(_Coordinate.AxisType, "Lon"));


        double[] data1 = new double[numX];


        for (int i = 0; i < numX; i++) {
            data1[i] = (double) (rlon1 + i * dlon);
        }


        Array dataA = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { numX }, data1);


        xaxis.setCachedData(dataA, false);
        ncfile.addVariable(null, xaxis);


        Variable yaxis = new Variable(ncfile, null, null, "lat");
        yaxis.setDataType(DataType.DOUBLE);
        yaxis.setDimensions("lat");
        yaxis.addAttribute(new Attribute("long_name", "latitude"));
        yaxis.addAttribute(new Attribute("units", "degree"));
        yaxis.addAttribute(new Attribute(_Coordinate.AxisType, "Lat"));
        data1 = new double[numY];


        for (int i = 0; i < numY; i++) {
            data1[i] = rlat1 + i * dlat;
        }


        dataA = Array.factory(DataType.DOUBLE.getPrimitiveClassType(), new int[] { numY }, data1);
        yaxis.setCachedData(dataA, false);
        ncfile.addVariable(null, yaxis);


        // projection
        // lower left and upper right corner lat/lons
        // modified cylind. equidistant or  CED with lat/lon ration != 1

View Full Code Here

        Array varArray;


        // make the variables


        // time
        Variable timeVar = new Variable(ncfile, null, null, "time");
        timeVar.setDataType(DataType.INT);
        timeVar.setDimensions("time");
        timeVar.addAttribute(new Attribute("units",
                                           "seconds since "
                                           + df.toDateTimeString(nomTime)));
        timeVar.addAttribute(new Attribute("long_name", "time"));
        varArray = new ArrayInt.D1(1);
        ((ArrayInt.D1) varArray).set(0, 0);
        timeVar.setCachedData(varArray, false);
        ncfile.addVariable(null, timeVar);




        // lines and elements
        Variable lineVar = new Variable(ncfile, null, null, "lines");
        lineVar.setDataType(DataType.INT);
        lineVar.setDimensions("lines");
        //lineVar.addAttribute(new Attribute("units", "km"));
        lineVar.addAttribute(new Attribute("standard_name",
                                           "projection_y_coordinate"));
        varArray = new ArrayInt.D1(numLines);
        for (int i = 0; i < numLines; i++) {
            int pos = nav.isFlippedLineCoordinates()
                      ? i
                      : numLines - i - 1;
            ((ArrayInt.D1) varArray).set(i, pos);
        }
        lineVar.setCachedData(varArray, false);
        ncfile.addVariable(null, lineVar);


        Variable elementVar = new Variable(ncfile, null, null, "elements");
        elementVar.setDataType(DataType.INT);
        elementVar.setDimensions("elements");
        //elementVar.addAttribute(new Attribute("units", "km"));
        elementVar.addAttribute(new Attribute("standard_name",
                "projection_x_coordinate"));
        varArray = new ArrayInt.D1(numElements);
        for (int i = 0; i < numElements; i++) {
            ((ArrayInt.D1) varArray).set(i, i);
        }
        elementVar.setCachedData(varArray, false);
        ncfile.addVariable(null, elementVar);




        // TODO: handle bands and calibrations
        Variable bandVar = new Variable(ncfile, null, null, "bands");
        bandVar.setDataType(DataType.INT);
        bandVar.setDimensions("bands");
        bandVar.addAttribute(new Attribute("long_name",
                                           "spectral band number"));
        bandVar.addAttribute(new Attribute("axis", "Z"));
        Array bandArray = new ArrayInt.D1(numBands);
        for (int i = 0; i < numBands; i++) {
            ((ArrayInt.D1) bandArray).set(i, bandMap[i]);
        }
        bandVar.setCachedData(bandArray, false);
        ncfile.addVariable(null, bandVar);


        // the image
        Variable imageVar = new Variable(ncfile, null, null, "image");
        imageVar.setDataType(DataType.INT);
        imageVar.setDimensions(image);
        setCalTypeAttributes(imageVar, getCalType(calName));
        imageVar.addAttribute(new Attribute(getADDescription(af.AD_CALTYPE),
                                            calName));
        imageVar.addAttribute(new Attribute("bands", bandArray));
        imageVar.addAttribute(new Attribute("grid_mapping", "AREAnav"));
        ncfile.addVariable(null, imageVar);




        Variable dirVar = new Variable(ncfile, null, null, "areaDirectory");
        dirVar.setDataType(DataType.INT);
        dirVar.setDimensions("dirSize");
        setAreaDirectoryAttributes(dirVar);
        ArrayInt.D1 dirArray = new ArrayInt.D1(AreaFile.AD_DIRSIZE);
        for (int i = 0; i < AreaFile.AD_DIRSIZE; i++) {
            dirArray.set(i, dirBlock[i]);
        }
        dirVar.setCachedData(dirArray, false);
        ncfile.addVariable(null, dirVar);


        Variable navVar = new Variable(ncfile, null, null, "navBlock");
        navVar.setDataType(DataType.INT);
        navVar.setDimensions("navSize");
        setNavBlockAttributes(navVar);
        ArrayInt.D1 navArray = new ArrayInt.D1(navBlock.length);
        for (int i = 0; i < navBlock.length; i++) {
            navArray.set(i, navBlock[i]);
        }
        navVar.setCachedData(navArray, false);
        ncfile.addVariable(null, navVar);




        // projection variable
        ProjectionImpl projection = new McIDASAreaProjection(af);
        Variable       proj = new Variable(ncfile, null, null, "AREAnav");
        proj.setDataType(DataType.CHAR);
        proj.setDimensions("");


        List params = projection.getProjectionParameters();
        for (int i = 0; i < params.size(); i++) {
            Parameter p = (Parameter) params.get(i);
            proj.addAttribute(new Attribute(p));
        }


        // For now, we have to overwrite the parameter versions of thes
        proj.addAttribute(
            new Attribute(
                "grid_mapping_name", McIDASAreaProjection.GRID_MAPPING_NAME));
        /*
        proj.addAttribute(new Attribute(McIDASAreaProjection.ATTR_AREADIR,
                                        dirArray));
        proj.addAttribute(new Attribute(McIDASAreaProjection.ATTR_NAVBLOCK,
                                        navArray));
        */
        varArray = new ArrayChar.D0();
        ((ArrayChar.D0) varArray).set(' ');
        proj.setCachedData(varArray, false);


        ncfile.addVariable(null, proj);


        // add the attributes
        ncfile.addAttribute(null, new Attribute("Conventions", "CF-1.0"));

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    String location = TestAll.cdmUnitTestDir + "ncml/nc/namExtract/test_agg.ncml";
    System.out.println(" TestOffAggExistingTimeUnitsChange.open "+ location);


    NetcdfFile ncfile = NetcdfDataset.openFile(location, null);


    Variable v = ncfile.findVariable("time");
    assert v != null;
    assert v.getDataType() == DataType.DOUBLE;


    String units = v.getUnitsString();
    assert units != null;
    assert units.equals("hours since 2006-09-25T06:00:00Z");


    int count = 0;
    Array data = v.read();
    NCdumpW.printArray(data, "time", new PrintWriter(System.out), null);
    while (data.hasNext()) {
      assert TestAll.closeEnough(data.nextInt(), (count + 1) * 3);
      count++;
    }

View Full Code Here


    String location = "file:"+ TestAll.cdmUnitTestDir + "ncml/nc/narr/";
    System.out.println(" TestOffAggExistingTimeUnitsChange.testNarrGrib=\n"+ ncml);
    NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml), location, null);


    Variable v = ncfile.findVariable("time");
    assert v != null;
    assert v.getDataType() == DataType.DOUBLE;


    String units = v.getUnitsString();
    assert units != null;
    assert units.equals("hours since 2007-04-11T00:00:00Z") : units;


    int count = 0;
    Array data = v.read();
    NCdumpW.printArray(data, "time", new PrintWriter(System.out), null);
    while (data.hasNext()) {
      assert data.nextInt() == count * 3;
      count++;
    }

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