/**
* Retrieves a group based on its fully qualified path.
*
* @param path Fully qualified path to the group.
* @return Group or <code>root</code> if the group cannot be found.
*/
private Group getGroup(String path) {
if (path.indexOf("/") == -1) {
return root;
}
StringTokenizer tokens = new StringTokenizer(path, "/");
Group parent = root;
while (tokens.hasMoreTokens()) {
parent = parent.findGroup(tokens.nextToken());
}
return parent == null ? root : parent;
}
@Test
public void testForStructMetadata() throws IOException {
System.out.printf("TestH4eosReadAll %s%n", filename);
try (NetcdfFile ncfile = NetcdfFile.open(filename)) {
Group root = ncfile.getRootGroup();
Group g = root.findGroup("HDFEOS INFORMATION");
if (g == null) g = ncfile.getRootGroup();
Variable dset = g.findVariable("StructMetadata.0");
assert (dset != null);
}
}
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;
}
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;
}
public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
ds.addAttribute(null, new Attribute("FeatureType", FeatureType.IMAGE.toString())); // LOOK
Group vhrr = ds.findGroup("VHRR");
Group loc = vhrr.findGroup("Geo-Location");
Variable lat = loc.findVariable("Latitude");
lat.addAttribute(new Attribute(CDM.UNITS, "degrees_north"));
lat.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
Variable lon = loc.findVariable("Longitude");
lon.addAttribute(new Attribute(CDM.UNITS, "degrees_east"));
lon.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
int[] shape = lat.getShape();
assert shape.length == 2;
Dimension scan = new Dimension("scan", shape[0]);
Dimension xscan = new Dimension("xscan", shape[1]);
vhrr.addDimension(scan);
vhrr.addDimension(xscan);
lat.setDimensions("scan xscan");
lon.setDimensions("scan xscan");
Group data = vhrr.findGroup("Image Data");
for (Variable v : data.getVariables()) {
int[] vs = v.getShape();
if ((vs.length == 2) && (vs[0] == shape[0]) && (vs[1] == shape[1])) {
v.setDimensions("scan xscan");
v.addAttribute(new Attribute(_Coordinate.Axes, "lat lon time"));
}
}
/* Group PRODUCT_METADATA {
Group PRODUCT_DETAILS {
PRODUCT_DETAILS:UNIQUE_ID = "3AVHR_22NOV2007_0902";
PRODUCT_DETAILS:PRODUCT_TYPE = "STANDARD(FULL DISK) ";
PRODUCT_DETAILS:PROCESSING_SOFTWARE = "InPGS_XXXXXXXXXXXXXX";
PRODUCT_DETAILS:SPACECRAFT_ID = "INSAT-3A ";
PRODUCT_DETAILS:SENSOR_ID = "VHR";
PRODUCT_DETAILS:ACQUISITION_TYPE = "FULL FRAME ";
PRODUCT_DETAILS:ACQUISITION_DATE = "22NOV2007";
PRODUCT_DETAILS:ACQUISITION_TIME_IN_GMT = "0902";
PRODUCT_DETAILS:PRODUCT_NAME = " FULL DISK";
PRODUCT_DETAILS:PROCESSING_LEVEL = "L1B";
PRODUCT_DETAILS:BAND_COMBINATION = "Visible(VIS),Thermal Infrared(TIR),Water Vapour(WV)";
PRODUCT_DETAILS:PRODUCT_CODE = "ST00001HD";
} */
Group info = ds.findGroup("PRODUCT_METADATA/PRODUCT_DETAILS");
String dateS = info.findAttribute("ACQUISITION_DATE").getStringValue();
String timeS = info.findAttribute("ACQUISITION_TIME_IN_GMT").getStringValue();
SimpleDateFormat format = new SimpleDateFormat("ddMMMyyyyHHmm");
format.setTimeZone(java.util.TimeZone.getTimeZone("GMT"));
try {
Date d = format.parse(dateS + timeS);
VariableDS time =
new VariableDS(
ds,
vhrr,
null,
"time",
DataType.LONG,
"",
"seconds since 1970-01-01 00:00",
"time generated from PRODUCT_METADATA/PRODUCT_DETAILS");
time.addAttribute(
new Attribute(
_Coordinate.AxisType,
AxisType.Time.toString())); // // LOOK : cant handle scalar coordinates yet ??
time.addAttribute(new Attribute("IsoDate", new DateFormatter().toDateTimeStringISO(d)));
CoordinateAxis1D timeAxis = new CoordinateAxis1D(ds, time);
ds.addVariable(vhrr, timeAxis);
ArrayLong.D0 timeData = new ArrayLong.D0();
timeData.set(d.getTime() / 1000);
time.setCachedData(timeData, true);
} catch (ParseException e) {
e.printStackTrace();
throw new IOException(e.getMessage());
}
ds.finish();
}