public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
for (Variable v : ds.getVariables()) checkIfAxis(v);
int year = ds.readAttributeInteger(null, "YEAR", -1);
int doy = ds.readAttributeInteger(null, "DAY", -1);
double time = ds.readAttributeDouble(null, "TIME", Double.NaN);
if ((year > 0) && (doy > 0) && !Double.isNaN(time)) {
Calendar cal = new GregorianCalendar(TimeZone.getTimeZone("UTC"));
cal.clear();
cal.set(Calendar.YEAR, year);
cal.set(Calendar.DAY_OF_YEAR, doy);
int hour = (int) time;
cal.set(Calendar.HOUR_OF_DAY, hour);
time -= hour;
time *= 60;
int minute = (int) time;
cal.set(Calendar.MINUTE, minute);
time -= minute;
time *= 60;
cal.set(Calendar.SECOND, (int) time);
VariableDS var =
new VariableDS(
ds,
null,
null,
"timeFromAtts",
DataType.LONG,
"",
"seconds since 1970-01-01 00:00",
"time generated from global attributes");
// LOOK : cant handle scalar coordinates yet
// var.addAttribute( new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
ds.addVariable(null, var);
ArrayLong.D0 data = new ArrayLong.D0();
data.set(cal.getTime().getTime() / 1000);
var.setCachedData(data, true);
}
ds.finish();
}
/**
* Add information from the InvDataset to the NetcdfDataset.
*
* @param ds get info from here
* @param ncDataset add to here
*/
public static void annotate(InvDataset ds, NetcdfDataset ncDataset) {
ncDataset.setTitle(ds.getName());
ncDataset.setId(ds.getID());
// add properties as global attributes
for (InvProperty p : ds.getProperties()) {
String name = p.getName();
if (null == ncDataset.findGlobalAttribute(name)) {
ncDataset.addAttribute(null, new Attribute(name, p.getValue()));
}
}
/* ThreddsMetadata.GeospatialCoverage geoCoverage = ds.getGeospatialCoverage();
if (geoCoverage != null) {
if ( null != geoCoverage.getNorthSouthRange()) {
ncDataset.addAttribute(null, new Attribute("geospatial_lat_min", new Double(geoCoverage.getLatSouth())));
ncDataset.addAttribute(null, new Attribute("geospatial_lat_max", new Double(geoCoverage.getLatNorth())));
}
if ( null != geoCoverage.getEastWestRange()) {
ncDataset.addAttribute(null, new Attribute("geospatial_lon_min", new Double(geoCoverage.getLonWest())));
ncDataset.addAttribute(null, new Attribute("geospatial_lon_max", new Double(geoCoverage.getLonEast())));
}
if ( null != geoCoverage.getUpDownRange()) {
ncDataset.addAttribute(null, new Attribute("geospatial_vertical_min", new Double(geoCoverage.getHeightStart())));
ncDataset.addAttribute(null, new Attribute("geospatial_vertical_max", new Double(geoCoverage.getHeightStart() + geoCoverage.getHeightExtent())));
}
}
DateRange timeCoverage = ds.getTimeCoverage();
if (timeCoverage != null) {
ncDataset.addAttribute(null, new Attribute("time_coverage_start", timeCoverage.getStart().toDateTimeStringISO()));
ncDataset.addAttribute(null, new Attribute("time_coverage_end", timeCoverage.getEnd().toDateTimeStringISO()));
} */
ncDataset.finish();
}
public static NetcdfDataset buildTrajectory(List<IObservationGroup> obsGroups) {
// IObservationGroup.DataType tdt = IObservationGroup.DataType.values()[0];
// IObservationGroup.DataType lldt = IObservationGroup.DataType.values()[0];
// IObservationGroup.DataType ddt = IObservationGroup.DataType.values()[0];
// for(IObservationGroup og : obsGroups) {
// tdt = (og.getTimeDataType().compareTo(tdt) > 0) ? og.getTimeDataType() : tdt;
// lldt = (og.getLatLonDataType().compareTo(lldt) > 0) ? og.getLatLonDataType() :
// lldt;
// ddt = (og.getDepthDataType().compareTo(ddt) > 0) ? og.getDepthDataType() : ddt;
// }
NetcdfDataset ncds = null;
File temp = null;
try {
/* Instantiate an empty NetcdfDataset object from the template ncml */
temp = File.createTempFile("ooi", ".ncml");
ncds = getNcdsFromTemplate(temp, "trajectory.ncml");
int nobs = obsGroups.size();
List<Number> allDepths = new ArrayList<Number>();
List<VariableParams> allDn = new ArrayList<VariableParams>();
int nt = nobs;
int nd = 0;
for (IObservationGroup og : obsGroups) {
nd = Math.max(nd, og.getDepths().length);
for (Number d : og.getDepths()) {
if (!allDepths.contains(d)) {
allDepths.add(d);
}
}
for (VariableParams dn : og.getDataNames()) {
if (!allDn.contains(dn)) {
allDn.add(dn);
}
}
}
/* Do the trajectory ID */
/* Do the times */
Number[] times = obsGroups.get(0).getTimes();
IObservationGroup.DataType tdt = obsGroups.get(0).getTimeDataType();
DataType ncdtTime = getNcDataType(tdt);
ncds.findDimension("time").setLength(nt);
Array tarr = Array.factory(ncdtTime, new int[] {nt});
IndexIterator tii = tarr.getIndexIterator();
Variable tvar = ncds.findVariable("time");
tvar.setDataType(getNcDataType(tdt));
tvar.setCachedData(tarr);
/* Do the lats */
IObservationGroup.DataType lldt = obsGroups.get(0).getLatLonDataType();
DataType ncdtLl = getNcDataType(lldt);
Array laarr = Array.factory(ncdtLl, new int[] {nt});
IndexIterator laii = laarr.getIndexIterator();
Variable lavar = ncds.findVariable("lat");
lavar.setDataType(ncdtLl);
lavar.setCachedData(laarr);
/* Do the lons */
Array loarr = Array.factory(ncdtLl, new int[] {nt});
IndexIterator loii = loarr.getIndexIterator();
Variable lovar = ncds.findVariable("lon");
lovar.setDataType(ncdtLl);
lovar.setCachedData(loarr);
/* Iterate over the observation groups and fill the data */
Map<String, String> allAttributes = new HashMap<String, String>();
IObservationGroup og;
HashMap<String, IndexIterator> darrs = new HashMap<String, IndexIterator>();
Number time;
Number depth = allDepths.get(0);
for (int obs = 0; obs < nobs; obs++) {
og = obsGroups.get(obs);
time = og.getTimes()[0];
putArrayData(tii, ncdtTime, time);
putArrayData(loii, ncdtLl, og.getLon());
putArrayData(laii, ncdtLl, og.getLat());
for (VariableParams dn : allDn) {
if (og.getDataNames().contains(dn)) {
DataType ncdtData = getNcDataType(dn.getDataType());
VariableDS dvar = (VariableDS) ncds.findVariable(dn.getShortName());
if (dvar == null) {
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("missing_value",
// missingData));
dvar.addAttribute(new Attribute(CF.STANDARD_NAME, dn.getStandardName()));
Array darr = Array.factory(ncdtData, new int[] {nt});
dvar.setCachedData(darr);
darrs.put(dn.getStandardName(), darr.getIndexIterator());
ncds.addVariable(null, dvar);
}
putArrayData(darrs.get(dn.getStandardName()), ncdtData, og.getData(dn, time, depth));
} else {
/*
* station doesn't have this variable - don't believe
* this can even happen...
*
* NOTE: This would indicate a problem with the above processing where the data-name list
* has been modified prior to contains-checking
*/
}
}
}
/* 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;
}
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;
}
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();
}