private static Array getNcScalar(Number inNum, IObservationGroup.DataType dataType) {
Array ret = null;
switch (dataType) {
case INT:
ret = new ArrayInt.D0();
((ArrayInt.D0) ret).set(inNum.intValue());
break;
case LONG:
ret = new ArrayLong.D0();
((ArrayLong.D0) ret).set(inNum.longValue());
break;
case FLOAT:
ret = new ArrayFloat.D0();
((ArrayFloat.D0) ret).set(inNum.floatValue());
break;
case DOUBLE:
ret = new ArrayDouble.D0();
((ArrayDouble.D0) ret).set(inNum.doubleValue());
break;
}
return ret;
}
private void writeDataFinish() throws IOException {
// finish global variables
ArrayInt.D0 totalArray = new ArrayInt.D0();
totalArray.set(profileIndex);
try {
ncfile.write(numProfilesTotalName, totalArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
// finish the station data
int nstns = stnList.size();
ArrayInt.D1 firstProfileArray = new ArrayInt.D1(nstns);
ArrayInt.D1 numProfileArray = new ArrayInt.D1(nstns);
ArrayInt.D1 nextProfileArray = new ArrayInt.D1(nprofiles);
for (int i = 0; i < stnList.size(); i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
StationTracker tracker = stationMap.get(stn.getName());
numProfileArray.set(i, tracker.numChildren);
int first = (tracker.link.size() > 0) ? tracker.link.get(0) : -1;
firstProfileArray.set(i, first);
if (tracker.link.size() > 0) {
// construct forward link
List<Integer> nextList = tracker.link;
for (int j = 0; j < nextList.size() - 1; j++) {
Integer curr = nextList.get(j);
Integer next = nextList.get(j + 1);
nextProfileArray.set(curr, next);
}
Integer curr = nextList.get(nextList.size() - 1);
nextProfileArray.set(curr, -1);
}
}
try {
ncfile.write(firstProfileName, firstProfileArray);
ncfile.write(numProfilesName, numProfileArray);
ncfile.write(nextProfileName, nextProfileArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
// finish the profile data
ArrayInt.D1 nextObsArray = new ArrayInt.D1(recno);
ArrayInt.D1 firstObsArray = new ArrayInt.D1(nprofiles);
ArrayInt.D1 numObsArray = new ArrayInt.D1(nprofiles);
for (int i = 0; i < stnList.size(); i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
StationTracker stnTracker = stationMap.get(stn.getName());
Set<Date> dates = stnTracker.profileMap.keySet();
for (Date date : dates) {
ProfileTracker proTracker = stnTracker.profileMap.get(date);
int trackerIndex = proTracker.parent_index;
numObsArray.set(trackerIndex, proTracker.numChildren);
int first = (proTracker.link.size() > 0) ? proTracker.link.get(0) : -1;
firstObsArray.set(trackerIndex, first);
if (proTracker.link.size() > 0) {
// construct forward link
List<Integer> nextList = proTracker.link;
for (int j = 0; j < nextList.size() - 1; j++) {
Integer curr = nextList.get(j);
Integer next = nextList.get(j + 1);
nextObsArray.set(curr, next);
}
Integer curr = nextList.get(nextList.size() - 1);
nextObsArray.set(curr, -1);
}
}
}
try {
ncfile.write(firstObsName, firstObsArray);
ncfile.write(numObsName, numObsArray);
ncfile.write(nextObsName, nextObsArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
// finish the obs data
ncfile.updateAttribute(
null, new Attribute("time_coverage_start", dateFormatter.toDateTimeStringISO(minDate)));
ncfile.updateAttribute(
null, new Attribute("time_coverage_end", dateFormatter.toDateTimeStringISO(maxDate)));
}
public static NetcdfDataset buildStation(IObservationGroup obsGroup) {
if (obsGroup.getDepths().length > 1) {
return buildStationProfile(obsGroup);
}
NetcdfDataset ncds = null;
File temp = null;
try {
/* Instantiate an empty NetcdfDataset object from the template ncml */
temp = File.createTempFile("ooi", ".ncml");
ncds = getNcdsFromTemplate(temp, "station.ncml");
Map<String, String> allAttributes = new HashMap<String, String>();
allAttributes.putAll(obsGroup.getAttributes());
/* Do the station Id */
ArrayInt.D0 aid = new ArrayInt.D0();
aid.set(obsGroup.getId());
ncds.findVariable("stnId").setCachedData(aid);
/* Do the times */
Number[] times = obsGroup.getTimes();
IObservationGroup.DataType tdt = obsGroup.getTimeDataType();
ncds.findDimension("time").setLength(times.length);
Variable tvar = ncds.findVariable("time");
tvar.setDataType(getNcDataType(tdt));
tvar.setCachedData(getNcArray(times, tdt));
/* Do the lat & lon */
IObservationGroup.DataType lldt = obsGroup.getLatLonDataType();
DataType ncdtLl = getNcDataType(lldt);
Variable laVar = ncds.findVariable("lat");
laVar.setDataType(ncdtLl);
laVar.setCachedData(getNcScalar(obsGroup.getLat(), lldt));
Variable loVar = ncds.findVariable("lon");
loVar.setDataType(ncdtLl);
loVar.setCachedData(getNcScalar(obsGroup.getLon(), lldt));
/* Do the depth */
IObservationGroup.DataType ddt = obsGroup.getDepthDataType();
VariableDS zVar =
new VariableDS(
ncds, null, null, "stnDepth", getNcDataType(ddt), "", "m", "station depth");
zVar.addAttribute(new Attribute("positive", "down"));
ncds.addVariable(null, zVar);
Number depth = obsGroup.getDepths()[0];
zVar.setCachedData(getNcScalar(obsGroup.getDepths()[0], ddt));
/* Do the data variables */
for (VariableParams dn : obsGroup.getDataNames()) {
DataType ncdtData = getNcDataType(dn.getDataType());
VariableDS dvar =
new VariableDS(
ncds,
null,
null,
dn.getShortName(),
ncdtData,
"time",
dn.getUnits(),
dn.getDescription());
dvar.addAttribute(new Attribute(CF.COORDINATES, "time lon lat"));
dvar.addAttribute(new Attribute(CF.STANDARD_NAME, dn.getStandardName()));
Array adata = Array.factory(ncdtData, new int[] {times.length});
IndexIterator aii = adata.getIndexIterator();
dvar.setCachedData(adata);
ncds.addVariable(null, dvar);
for (int ti = 0; ti < times.length; ti++) {
putArrayData(aii, ncdtData, obsGroup.getData(dn, times[ti], depth));
}
}
/* Add global attributes */
for (String key : allAttributes.keySet()) {
ncds.addAttribute(null, new Attribute(key, allAttributes.get(key)));
}
} catch (FileNotFoundException ex) {
Logger.getLogger(NcdsFactory.class.getName()).log(Level.SEVERE, null, ex);
} catch (IOException ex) {
Logger.getLogger(NcdsFactory.class.getName()).log(Level.SEVERE, null, ex);
} finally {
if (temp != null) {
if (!temp.delete()) {
temp.deleteOnExit();
}
}
if (ncds != null) {
ncds.finish();
}
}
return ncds;
}
