public Array readData(Variable v2, Section section) throws IOException, InvalidRangeException {
Vgroup vgroup = (Vgroup) v2.getSPobject();
Range scanRange = section.getRange(0);
Range radialRange = section.getRange(1);
Range gateRange = section.getRange(2);
Array data = Array.factory(v2.getDataType().getPrimitiveClassType(), section.getShape());
IndexIterator ii = data.getIndexIterator();
for (int i = scanRange.first(); i <= scanRange.last(); i += scanRange.stride()) {
Cinrad2Record[] mapScan = vgroup.map[i];
readOneScan(mapScan, radialRange, gateRange, vgroup.datatype, ii);
}
return data;
}
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 void makeCoordinateDataWithMissing(
int datatype,
Variable time,
Variable elev,
Variable azi,
Variable nradialsVar,
Variable ngatesVar,
List groups) {
Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
Index timeIndex = timeData.getIndex();
Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
Index elevIndex = elevData.getIndex();
Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
Index aziIndex = aziData.getIndex();
Array nradialsData =
Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
IndexIterator nradialsIter = nradialsData.getIndexIterator();
Array ngatesData =
Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
IndexIterator ngatesIter = ngatesData.getIndexIterator();
// first fill with missing data
IndexIterator ii = timeData.getIndexIterator();
while (ii.hasNext()) ii.setIntNext(MISSING_INT);
ii = elevData.getIndexIterator();
while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);
ii = aziData.getIndexIterator();
while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);
// now set the coordinate variables from the Cinrad2Record radial
int last_msecs = Integer.MIN_VALUE;
int nscans = groups.size();
try {
for (int scan = 0; scan < nscans; scan++) {
List scanGroup = (List) groups.get(scan);
int nradials = scanGroup.size();
Cinrad2Record first = null;
for (int j = 0; j < nradials; j++) {
Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
if (first == null) first = r;
int radial = r.radial_num - 1;
timeData.setInt(timeIndex.set(scan, radial), r.data_msecs);
elevData.setFloat(elevIndex.set(scan, radial), r.getElevation());
aziData.setFloat(aziIndex.set(scan, radial), r.getAzimuth());
if (r.data_msecs < last_msecs)
logger.warn("makeCoordinateData time out of order " + r.data_msecs);
last_msecs = r.data_msecs;
}
nradialsIter.setIntNext(nradials);
ngatesIter.setIntNext(first.getGateCount(datatype));
}
} catch (java.lang.ArrayIndexOutOfBoundsException ae) {
logger.debug("Cinrad2IOSP.uncompress ", ae);
}
time.setCachedData(timeData, false);
elev.setCachedData(elevData, false);
azi.setCachedData(aziData, false);
nradialsVar.setCachedData(nradialsData, false);
ngatesVar.setCachedData(ngatesData, false);
}
private void makeCoordinateData(
int datatype,
Variable time,
Variable elev,
Variable azi,
Variable nradialsVar,
Variable ngatesVar,
List groups) {
Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
IndexIterator timeDataIter = timeData.getIndexIterator();
Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
IndexIterator elevDataIter = elevData.getIndexIterator();
Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
IndexIterator aziDataIter = aziData.getIndexIterator();
Array nradialsData =
Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
IndexIterator nradialsIter = nradialsData.getIndexIterator();
Array ngatesData =
Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
IndexIterator ngatesIter = ngatesData.getIndexIterator();
int last_msecs = Integer.MIN_VALUE;
int nscans = groups.size();
int maxRadials = volScan.getMaxRadials();
for (int i = 0; i < nscans; i++) {
List scanGroup = (List) groups.get(i);
int nradials = scanGroup.size();
Cinrad2Record first = null;
for (int j = 0; j < nradials; j++) {
Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
if (first == null) first = r;
timeDataIter.setIntNext(r.data_msecs);
elevDataIter.setFloatNext(r.getElevation());
aziDataIter.setFloatNext(r.getAzimuth());
if (r.data_msecs < last_msecs)
logger.warn("makeCoordinateData time out of order " + r.data_msecs);
last_msecs = r.data_msecs;
}
for (int j = nradials; j < maxRadials; j++) {
timeDataIter.setIntNext(MISSING_INT);
elevDataIter.setFloatNext(MISSING_FLOAT);
aziDataIter.setFloatNext(MISSING_FLOAT);
}
nradialsIter.setIntNext(nradials);
ngatesIter.setIntNext(first.getGateCount(datatype));
}
time.setCachedData(timeData, false);
elev.setCachedData(elevData, false);
azi.setCachedData(aziData, false);
nradialsVar.setCachedData(nradialsData, false);
ngatesVar.setCachedData(ngatesData, false);
}