Example #1
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;
  }
Example #2
0
  /**
   * Amend the given NetcdfFile with metadata from HDF-EOS structMetadata
   *
   * @param ncfile Amend this file
   * @param structMetadata structMetadata as String
   * @throws IOException on read error
   */
  private void amendFromODL(NetcdfFile ncfile, String structMetadata) throws IOException {
    Group rootg = ncfile.getRootGroup();

    ODLparser parser = new ODLparser();
    Element root = parser.parseFromString(structMetadata); // now we have the ODL in JDOM elements
    FeatureType featureType = null;

    // SWATH
    Element swathStructure = root.getChild("SwathStructure");
    if (swathStructure != null) {
      List<Element> swaths = swathStructure.getChildren();
      for (Element elemSwath : swaths) {
        Element swathNameElem = elemSwath.getChild("SwathName");
        if (swathNameElem == null) {
          log.warn("No SwathName element in {} {} ", elemSwath.getName(), ncfile.getLocation());
          continue;
        }
        String swathName = NetcdfFile.makeValidCdmObjectName(swathNameElem.getText().trim());
        Group swathGroup = findGroupNested(rootg, swathName);
        // if (swathGroup == null)
        //  swathGroup = findGroupNested(rootg, H4header.createValidObjectName(swathName));

        if (swathGroup != null) {
          featureType = amendSwath(ncfile, elemSwath, swathGroup);
        } else {
          log.warn("Cant find swath group {} {}", swathName, ncfile.getLocation());
        }
      }
    }

    // GRID
    Element gridStructure = root.getChild("GridStructure");
    if (gridStructure != null) {
      List<Element> grids = gridStructure.getChildren();
      for (Element elemGrid : grids) {
        Element gridNameElem = elemGrid.getChild("GridName");
        if (gridNameElem == null) {
          log.warn("No GridName element in {} {} ", elemGrid.getName(), ncfile.getLocation());
          continue;
        }
        String gridName = NetcdfFile.makeValidCdmObjectName(gridNameElem.getText().trim());
        Group gridGroup = findGroupNested(rootg, gridName);
        // if (gridGroup == null)
        //  gridGroup = findGroupNested(rootg, H4header.createValidObjectName(gridName));
        if (gridGroup != null) {
          featureType = amendGrid(elemGrid, ncfile, gridGroup, ncfile.getLocation());
        } else {
          log.warn("Cant find Grid group {} {}", gridName, ncfile.getLocation());
        }
      }
    }

    // POINT - NOT DONE YET
    Element pointStructure = root.getChild("PointStructure");
    if (pointStructure != null) {
      List<Element> pts = pointStructure.getChildren();
      for (Element elem : pts) {
        Element nameElem = elem.getChild("PointName");
        if (nameElem == null) {
          log.warn("No PointName element in {} {}", elem.getName(), ncfile.getLocation());
          continue;
        }
        String name = nameElem.getText().trim();
        Group ptGroup = findGroupNested(rootg, name);
        // if (ptGroup == null)
        //  ptGroup = findGroupNested(rootg, H4header.createValidObjectName(name));
        if (ptGroup != null) {
          featureType = FeatureType.POINT;
        } else {
          log.warn("Cant find Point group {} {}", name, ncfile.getLocation());
        }
      }
    }

    if (featureType != null) {
      if (showWork) System.out.println("***EOS featureType= " + featureType.toString());
      rootg.addAttribute(new Attribute(CF.FEATURE_TYPE, featureType.toString()));
      // rootg.addAttribute(new Attribute(CDM.CONVENTIONS, "HDFEOS"));
    }
  }