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; }
/** * 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")); } }