Example #1
0
  // convert to shared dimensions
  private void setSharedDimensions(
      Variable v, List<Element> values, List<Dimension> unknownDims, String location) {
    if (values.size() == 0) return;

    // remove the "scalar" dumbension
    Iterator<Element> iter = values.iterator();
    while (iter.hasNext()) {
      Element value = iter.next();
      String dimName = value.getText().trim();
      if (dimName.equalsIgnoreCase("scalar")) iter.remove();
    }

    // gotta have same number of dimensions
    List<Dimension> oldDims = v.getDimensions();
    if (oldDims.size() != values.size()) {
      log.error("Different number of dimensions for {} {}", v, location);
      return;
    }

    List<Dimension> newDims = new ArrayList<>();
    Group group = v.getParentGroup();

    for (int i = 0; i < values.size(); i++) {
      Element value = values.get(i);
      String dimName = value.getText().trim();
      dimName = NetcdfFile.makeValidCdmObjectName(dimName);

      Dimension dim = group.findDimension(dimName);
      Dimension oldDim = oldDims.get(i);
      if (dim == null) dim = checkUnknownDims(dimName, unknownDims, oldDim, location);

      if (dim == null) {
        log.error(
            "Unknown Dimension= {} for variable = {} {} ", dimName, v.getFullName(), location);
        return;
      }
      if (dim.getLength() != oldDim.getLength()) {
        log.error(
            "Shared dimension ("
                + dim.getShortName()
                + ") has different length than data dimension ("
                + oldDim.getShortName()
                + ") shared="
                + dim.getLength()
                + " org="
                + oldDim.getLength()
                + " for "
                + v
                + " "
                + location);
        return;
      }
      newDims.add(dim);
    }
    v.setDimensions(newDims);
    if (showWork) System.out.printf(" set shared dimensions for %s %n", v.getNameAndDimensions());
  }
Example #2
0
  private static String getStructMetadata(Group eosGroup) throws IOException {
    StringBuilder sbuff = null;
    String structMetadata = null;

    int n = 0;
    while (true) {
      Variable structMetadataVar = eosGroup.findVariable("StructMetadata." + n);
      if (structMetadataVar == null) break;
      if ((structMetadata != null) && (sbuff == null)) { // more than 1 StructMetadata
        sbuff = new StringBuilder(64000);
        sbuff.append(structMetadata);
      }

      // read and parse the ODL
      Array A = structMetadataVar.read();
      if (A instanceof ArrayChar.D1) {
        ArrayChar ca = (ArrayChar) A;
        structMetadata = ca.getString(); // common case only StructMetadata.0, avoid extra copy
      } else if (A instanceof ArrayObject.D0) {
        ArrayObject ao = (ArrayObject) A;
        structMetadata = (String) ao.getObject(0);
      } else {
        log.error("Unsupported array type {} for StructMetadata", A.getElementType());
      }

      if (sbuff != null) sbuff.append(structMetadata);
      n++;
    }
    return (sbuff != null) ? sbuff.toString() : structMetadata;
  }
Example #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;
  }