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