Exemple #1
0
 // look if the wanted dimension is in the  unknownDims list.
 private Dimension checkUnknownDims(
     String wantDim, List<Dimension> unknownDims, Dimension oldDim, String location) {
   for (Dimension dim : unknownDims) {
     if (dim.getShortName().equals(wantDim)) {
       int len = oldDim.getLength();
       if (len == 0) dim.setUnlimited(true); // allow zero length dimension !!
       dim.setLength(len); // use existing (anon) dimension
       Group parent = dim.getGroup();
       parent.addDimensionIfNotExists(dim); // add to the parent
       unknownDims.remove(dim); // remove from list LOOK is this ok?
       log.warn("unknownDim {} length set to {}{}", wantDim, oldDim.getLength(), location);
       return dim;
     }
   }
   return null;
 }
Exemple #2
0
  private FeatureType amendGrid(
      Element gridElem, NetcdfFile ncfile, Group parent, String location) {
    List<Dimension> unknownDims = new ArrayList<>();

    // always has x and y dimension
    String xdimSizeS = gridElem.getChild("XDim").getText().trim();
    String ydimSizeS = gridElem.getChild("YDim").getText().trim();
    int xdimSize = Integer.parseInt(xdimSizeS);
    int ydimSize = Integer.parseInt(ydimSizeS);
    parent.addDimensionIfNotExists(new Dimension("XDim", xdimSize));
    parent.addDimensionIfNotExists(new Dimension("YDim", ydimSize));

    /* see HdfEosModisConvention
    UpperLeftPointMtrs=(-20015109.354000,1111950.519667)
    		LowerRightMtrs=(-18903158.834333,-0.000000)
    		Projection=GCTP_SNSOID
    		ProjParams=(6371007.181000,0,0,0,0,0,0,0,0,0,0,0,0)
    		SphereCode=-1
     */
    Element proj = gridElem.getChild("Projection");
    if (proj != null) {
      Variable crs = new Variable(ncfile, parent, null, HDFEOS_CRS);
      crs.setDataType(DataType.SHORT);
      crs.setDimensions(""); // scalar
      crs.setCachedData(Array.makeArray(DataType.SHORT, 1, 0, 0)); // fake data
      parent.addVariable(crs);

      addAttributeIfExists(gridElem, HDFEOS_CRS_Projection, crs, false);
      addAttributeIfExists(gridElem, HDFEOS_CRS_UpperLeft, crs, true);
      addAttributeIfExists(gridElem, HDFEOS_CRS_LowerRight, crs, true);
      addAttributeIfExists(gridElem, HDFEOS_CRS_ProjParams, crs, true);
      addAttributeIfExists(gridElem, HDFEOS_CRS_SphereCode, crs, false);
    }

    // global Dimensions
    Element d = gridElem.getChild("Dimension");
    List<Element> dims = d.getChildren();
    for (Element elem : dims) {
      String name = elem.getChild("DimensionName").getText().trim();
      name = NetcdfFile.makeValidCdmObjectName(name);
      if (name.equalsIgnoreCase("scalar")) continue;

      String sizeS = elem.getChild("Size").getText().trim();
      int length = Integer.parseInt(sizeS);
      Dimension old = parent.findDimension(name);
      if ((old == null) || (old.getLength() != length)) {
        if (length > 0) {
          Dimension dim = new Dimension(name, length);
          if (parent.addDimensionIfNotExists(dim) && showWork)
            System.out.printf(" Add dimension %s %n", dim);
        } else {
          log.warn("Dimension {} has size {} {} ", sizeS, name, location);
          Dimension udim = new Dimension(name, 1);
          udim.setGroup(parent);
          unknownDims.add(udim);
          if (showWork) System.out.printf(" Add dimension %s %n", udim);
        }
      }
    }

    // Geolocation Variables
    Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
    if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);

    if (geoFieldsG != null) {
      Element floc = gridElem.getChild("GeoField");
      List<Element> varsLoc = floc.getChildren();
      for (Element elem : varsLoc) {
        String varname = elem.getChild("GeoFieldName").getText().trim();
        Variable v = geoFieldsG.findVariable(varname);
        // if (v == null)
        //  v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
        assert v != null : varname;

        Element dimList = elem.getChild("DimList");
        List<Element> values = dimList.getChildren("value");
        setSharedDimensions(v, values, unknownDims, location);
      }
    }

    // Data Variables
    Group dataG = parent.findGroup(DATA_FIELDS);
    if (dataG == null)
      dataG =
          parent.findGroup(
              DATA_FIELDS2); // eg C:\data\formats\hdf4\eos\mopitt\MOP03M-200501-L3V81.0.1.hdf

    if (dataG != null) {
      Element f = gridElem.getChild("DataField");
      List<Element> vars = f.getChildren();
      for (Element elem : vars) {
        String varname = elem.getChild("DataFieldName").getText().trim();
        varname = NetcdfFile.makeValidCdmObjectName(varname);
        Variable v = dataG.findVariable(varname);
        // if (v == null)
        //  v = dataG.findVariable( H4header.createValidObjectName(varname));
        assert v != null : varname;

        Element dimList = elem.getChild("DimList");
        List<Element> values = dimList.getChildren("value");
        setSharedDimensions(v, values, unknownDims, location);
      }

      // get projection
      String projS = null;
      Element projElem = gridElem.getChild("Projection");
      if (projElem != null) projS = projElem.getText().trim();
      boolean isLatLon = "GCTP_GEO".equals(projS);

      // look for XDim, YDim coordinate variables
      if (isLatLon) {
        for (Variable v : dataG.getVariables()) {
          if (v.isCoordinateVariable()) {
            if (v.getShortName().equals("YDim")) {
              v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
              v.addAttribute(new Attribute(CDM.UNITS, CDM.LAT_UNITS));
            }
            if (v.getShortName().equals("XDim"))
              v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
          }
        }
      }
    }
    return FeatureType.GRID;
  }
Exemple #3
0
  private FeatureType amendSwath(NetcdfFile ncfile, Element swathElem, Group parent) {
    FeatureType featureType = FeatureType.SWATH;
    List<Dimension> unknownDims = new ArrayList<>();

    // Dimensions
    Element d = swathElem.getChild("Dimension");
    List<Element> dims = d.getChildren();
    for (Element elem : dims) {
      String name = elem.getChild("DimensionName").getText().trim();
      name = NetcdfFile.makeValidCdmObjectName(name);

      if (name.equalsIgnoreCase("scalar")) continue;
      String sizeS = elem.getChild("Size").getText().trim();
      int length = Integer.parseInt(sizeS);
      if (length > 0) {
        Dimension dim = parent.findDimensionLocal(name);
        if (dim != null) { // already added - may be dimension scale ?
          if (dim.getLength() != length) { // ok as long as it matches
            log.error("Conflicting Dimensions = {} {}", dim, ncfile.getLocation());
            throw new IllegalStateException("Conflicting Dimensions = " + name);
          }
        } else {
          dim = new Dimension(name, length);
          if (parent.addDimensionIfNotExists(dim) && showWork)
            System.out.printf(" Add dimension %s %n", dim);
        }
      } else {
        log.warn("Dimension " + name + " has size " + sizeS, ncfile.getLocation());
        Dimension udim = new Dimension(name, 1);
        udim.setGroup(parent);
        unknownDims.add(udim);
        if (showWork) System.out.printf(" Add dimension %s %n", udim);
      }
    }

    // Dimension Maps
    Element dmap = swathElem.getChild("DimensionMap");
    List<Element> dimMaps = dmap.getChildren();
    for (Element elem : dimMaps) {
      String geoDimName = elem.getChild("GeoDimension").getText().trim();
      geoDimName = NetcdfFile.makeValidCdmObjectName(geoDimName);
      String dataDimName = elem.getChild("DataDimension").getText().trim();
      dataDimName = NetcdfFile.makeValidCdmObjectName(dataDimName);

      String offsetS = elem.getChild("Offset").getText().trim();
      String incrS = elem.getChild("Increment").getText().trim();
      int offset = Integer.parseInt(offsetS);
      int incr = Integer.parseInt(incrS);

      // make new variable for this dimension map
      Variable v = new Variable(ncfile, parent, null, dataDimName);
      v.setDimensions(geoDimName);
      v.setDataType(DataType.INT);
      int npts = (int) v.getSize();
      Array data = Array.makeArray(v.getDataType(), npts, offset, incr);
      v.setCachedData(data, true);
      v.addAttribute(new Attribute("_DimensionMap", ""));
      parent.addVariable(v);
      if (showWork) System.out.printf(" Add dimensionMap %s %n", v);
    }

    // Geolocation Variables
    Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
    if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
    if (geoFieldsG != null) {
      Variable latAxis = null, lonAxis = null;
      Element floc = swathElem.getChild("GeoField");
      List<Element> varsLoc = floc.getChildren();
      for (Element elem : varsLoc) {
        String varname = elem.getChild("GeoFieldName").getText().trim();
        Variable v = geoFieldsG.findVariable(varname);
        // if (v == null)
        //  v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
        assert v != null : varname;
        AxisType axis = addAxisType(ncfile, v);
        if (axis == AxisType.Lat) latAxis = v;
        if (axis == AxisType.Lon) lonAxis = v;

        Element dimList = elem.getChild("DimList");
        List<Element> values = dimList.getChildren("value");
        setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
        if (showWork) System.out.printf(" set coordinate %s %n", v);
      }
      if ((latAxis != null) && (lonAxis != null)) {
        List<Dimension> xyDomain = CoordinateSystem.makeDomain(new Variable[] {latAxis, lonAxis});
        if (xyDomain.size() < 2) featureType = FeatureType.PROFILE; // ??
      }
    }

    // Data Variables
    Group dataG = parent.findGroup(DATA_FIELDS);
    if (dataG == null) dataG = parent.findGroup(DATA_FIELDS2);
    if (dataG != null) {
      Element f = swathElem.getChild("DataField");
      List<Element> vars = f.getChildren();
      for (Element elem : vars) {
        Element dataFieldNameElem = elem.getChild("DataFieldName");
        if (dataFieldNameElem == null) continue;
        String varname = NetcdfFile.makeValidCdmObjectName(dataFieldNameElem.getText().trim());
        Variable v = dataG.findVariable(varname);
        // if (v == null)
        //  v = dataG.findVariable( H4header.createValidObjectName(varname));
        if (v == null) {
          log.error("Cant find variable {} {}", varname, ncfile.getLocation());
          continue;
        }

        Element dimList = elem.getChild("DimList");
        List<Element> values = dimList.getChildren("value");
        setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
      }
    }

    return featureType;
  }