ucar.nc2.ft.point.writer.WriterCFStationProfileCollection Maven / Gradle / Ivy
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package ucar.nc2.ft.point.writer;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants.CF;
import ucar.nc2.dataset.conv.CF1Convention;
import ucar.nc2.ft.PointFeature;
import ucar.nc2.ft.ProfileFeature;
import ucar.nc2.ft.StationProfileFeature;
import ucar.nc2.ft.point.StationFeature;
import ucar.nc2.time.CalendarDate;
import ucar.nc2.units.DateUnit;
import java.io.IOException;
import java.util.*;
/**
* Write a CF "Discrete Sample" station profile collection file.
* Example H.3.5. Contiguous ragged array representation of profiles, H.5.3
* *
* @author caron
* @since 7/14/2014
*/
public class WriterCFStationProfileCollection extends CFPointWriter {
private List stnList;
protected Structure stationStruct; // used for netcdf4 extended
private HashMap stationIndexMap;
private boolean useDesc = false;
private boolean useAlt = false;
private boolean useWmoId = false;
private int desc_strlen = 1, wmo_strlen = 1;
private Map stationVarMap = new HashMap<>();
///////////////////////////////////////////////////
// private Formatter coordNames = new Formatter();
protected Structure profileStruct; // used for netcdf4 extended
private Map profileVarMap = new HashMap<>();
private boolean headerDone = false;
public WriterCFStationProfileCollection(String fileOut, List globalAtts, List dataVars, List extra,
DateUnit timeUnit, String altUnits, CFPointWriterConfig config) throws IOException {
super(fileOut, globalAtts, dataVars, extra, timeUnit, altUnits, config);
writer.addGroupAttribute(null, new Attribute(CF.FEATURE_TYPE, CF.FeatureType.timeSeriesProfile.name()));
}
public void setStations(List stns) throws IOException {
this.stnList = stns;
// see if there's altitude, wmoId for any stations
for (StationFeature stn : stnList) {
if (!Double.isNaN(stn.getAltitude()))
useAlt = true;
if ((stn.getWmoId() != null) && (stn.getWmoId().trim().length() > 0))
useWmoId = true;
if ((stn.getDescription() != null) && (stn.getDescription().trim().length() > 0))
useDesc = true;
// find string lengths
id_strlen = Math.max(id_strlen, stn.getName().length());
if (stn.getDescription() != null) desc_strlen = Math.max(desc_strlen, stn.getDescription().length());
if (stn.getWmoId() != null) wmo_strlen = Math.max(wmo_strlen, stn.getWmoId().length());
}
llbb = CFPointWriterUtils.getBoundingBox(stnList); // gets written in super.finish();
}
public int writeProfile (StationProfileFeature spf, ProfileFeature profile) throws IOException {
profile.resetIteration();
int count = 0;
while (profile.hasNext()) {
PointFeature pf = profile.next();
if (!headerDone) {
if (id_strlen == 0) id_strlen = profile.getName().length() * 2;
writeHeader(spf, profile, pf);
headerDone = true;
}
writeObsData(pf);
count++;
}
Integer stnIndex = stationIndexMap.get(spf.getName());
if (stnIndex == null) {
System.out.printf("BAD station %s%n", spf.getName());
} else {
writeProfileData(stnIndex, profile, count);
}
return count;
}
private void writeHeader(StationProfileFeature stn, ProfileFeature profile, PointFeature obs) throws IOException {
StructureData stnData = stn.getFeatureData();
StructureData profileData = profile.getFeatureData();
StructureData obsData = obs.getFeatureData();
List obsCoords = new ArrayList<>();
// obsCoords.add(VariableSimpleImpl.makeScalar(timeName, "time of measurement", timeUnit.getUnitsString(), DataType.DOUBLE)); // LOOK ??
Formatter coordNames = new Formatter().format("%s %s %s", profileTimeName, latName, lonName);
//if (useAlt) {
obsCoords.add( VariableSimpleImpl.makeScalar(altitudeCoordinateName, "obs altitude", altUnits, DataType.DOUBLE)
.add(new Attribute(CF.STANDARD_NAME, "altitude"))
.add(new Attribute(CF.POSITIVE, CF1Convention.getZisPositive(altitudeCoordinateName, altUnits))));
coordNames.format(" %s", altitudeCoordinateName);
//}
super.writeHeader2(obsCoords, stnData, profileData, obsData, coordNames.toString());
// write the stations
int count = 0;
stationIndexMap = new HashMap<>(2 * stnList.size());
for (StationFeature sf : stnList) {
writeStationData(sf);
stationIndexMap.put(sf.getName(), count);
count++;
}
/* prefill any needed profile vars
if (!isExtendedModel) {
Variable stnIndexVar = writer.findVariable(stationIndexName);
try {
writer.write(stnIndexVar, Array.factory(DataType.INT, new int[]{nfeatures})); // default 0
} catch (InvalidRangeException e) {
e.printStackTrace();
}
Variable profileIdxVar = writer.findVariable(profileIdName);
try {
Array prefill = Array.factory(DataType.INT, new int[]{nfeatures});
MAMath.setDouble(prefill, idMissingValue);
writer.write(stnIndexVar, prefill);
} catch (InvalidRangeException e) {
e.printStackTrace();
}
} */
}
protected void makeFeatureVariables(StructureData stnData, boolean isExtended) throws IOException {
// add the dimensions : extended model can use an unlimited dimension
//Dimension stationDim = isExtended ? writer.addDimension(null, stationDimName, 0, true, true, false) : writer.addDimension(null, stationDimName, nstns);
Dimension stationDim = writer.addDimension(null, stationDimName, stnList.size());
List stnVars = new ArrayList<>();
stnVars.add(VariableSimpleImpl.makeScalar(latName, "station latitude", CDM.LAT_UNITS, DataType.DOUBLE));
stnVars.add(VariableSimpleImpl.makeScalar(lonName, "station longitude", CDM.LON_UNITS, DataType.DOUBLE));
if (useAlt) {
stnVars.add(VariableSimpleImpl.makeScalar(stationAltName, "station altitude", altUnits, DataType.DOUBLE)
.add(new Attribute(CF.STANDARD_NAME, CF.SURFACE_ALTITUDE))
.add(new Attribute(CF.POSITIVE, CF1Convention.getZisPositive(altName, altUnits))));
}
stnVars.add(VariableSimpleImpl.makeString(stationIdName, "station identifier", null, id_strlen)
.add(new Attribute(CF.CF_ROLE, CF.TIMESERIES_ID))); // station_id:cf_role = "timeseries_id";
if (useDesc) stnVars.add(VariableSimpleImpl.makeString(descName, "station description", null, desc_strlen)
.add(new Attribute(CF.STANDARD_NAME, CF.PLATFORM_NAME)));
if (useWmoId) stnVars.add(VariableSimpleImpl.makeString(wmoName, "station WMO id", null, wmo_strlen)
.add(new Attribute(CF.STANDARD_NAME, CF.PLATFORM_ID)));
for (StructureMembers.Member m : stnData.getMembers()) {
if (getDataVar(m.getName()) != null)
stnVars.add(new VariableSimpleAdapter(m));
}
if (isExtended) {
stationStruct = (Structure) writer.addVariable(null, stationStructName, DataType.STRUCTURE, stationDimName);
addCoordinatesExtended(stationStruct, stnVars);
} else {
addCoordinatesClassic(stationDim, stnVars, stationVarMap);
}
}
private int stnRecno = 0;
private void writeStationData(StationFeature stn) throws IOException {
StructureDataScalar stnCoords = new StructureDataScalar("Coords");
stnCoords.addMember(latName, null, null, DataType.DOUBLE, false, stn.getLatLon().getLatitude());
stnCoords.addMember(lonName, null, null, DataType.DOUBLE, false, stn.getLatLon().getLongitude());
if (useAlt) stnCoords.addMember(stationAltName, null, null, DataType.DOUBLE, false, stn.getAltitude());
stnCoords.addMemberString(stationIdName, null, null, stn.getName().trim(), id_strlen);
if (useDesc) stnCoords.addMemberString(descName, null, null, stn.getDescription().trim(), desc_strlen);
if (useWmoId) stnCoords.addMemberString(wmoName, null, null, stn.getWmoId().trim(), wmo_strlen);
StructureDataComposite sdall = new StructureDataComposite();
sdall.add(stnCoords); // coords first so it takes precedence
sdall.add(stn.getFeatureData());
stnRecno = super.writeStructureData(stnRecno, stationStruct, sdall, stationVarMap);
}
@Override
protected void makeMiddleVariables(StructureData profileData, boolean isExtended) throws IOException {
Dimension profileDim = writer.addDimension(null, profileDimName, nfeatures);
// add the profile Variables using the profile dimension
List profileVars = new ArrayList<>();
profileVars.add(VariableSimpleImpl.makeString(profileIdName, "profile identifier", null, id_strlen)
.add(new Attribute(CF.CF_ROLE, CF.PROFILE_ID)) // profileId:cf_role = "profile_id";
.add(new Attribute(CDM.MISSING_VALUE, String.valueOf(idMissingValue))));
profileVars.add(VariableSimpleImpl.makeScalar(numberOfObsName, "number of obs for this profile", null, DataType.INT)
.add(new Attribute(CF.SAMPLE_DIMENSION, recordDimName))); // rowSize:sample_dimension = "obs"
profileVars.add(VariableSimpleImpl.makeScalar(profileTimeName, "nominal time of profile", timeUnit.getUnitsString(), DataType.DOUBLE));
profileVars.add(VariableSimpleImpl.makeScalar(stationIndexName, "station index for this profile", null, DataType.INT)
.add(new Attribute(CF.INSTANCE_DIMENSION, stationDimName)));
for (StructureMembers.Member m : profileData.getMembers()) {
VariableSimpleIF dv = getDataVar(m.getName());
if (dv != null)
profileVars.add(dv);
}
if (isExtended) {
profileStruct = (Structure) writer.addVariable(null, profileStructName, DataType.STRUCTURE, profileDimName);
addCoordinatesExtended(profileStruct, profileVars);
} else {
addCoordinatesClassic(profileDim, profileVars, profileVarMap);
}
}
private int profileRecno = 0;
public void writeProfileData(int stnIndex, ProfileFeature profile, int nobs) throws IOException {
trackBB(profile.getLatLon(), CalendarDate.of(profile.getTime()));
StructureDataScalar profileCoords = new StructureDataScalar("Coords");
profileCoords.addMember(latName, null, null, DataType.DOUBLE, false, profile.getLatLon().getLatitude());
profileCoords.addMember(lonName, null, null, DataType.DOUBLE, false, profile.getLatLon().getLongitude());
//Date date = (profile.getTime() != null) ? (double) profile.getTime().getTime() : 0.0; // LOOK (profile.getTime() != null) ???
double timeInMyUnits = timeUnit.makeValue(profile.getTime());
profileCoords.addMember(profileTimeName, null, null, DataType.DOUBLE, false, timeInMyUnits); // LOOK time not always part of profile
profileCoords.addMemberString(profileIdName, null, null, profile.getName().trim(), id_strlen);
profileCoords.addMember(numberOfObsName, null, null, DataType.INT, false, nobs);
profileCoords.addMember(stationIndexName, null, null, DataType.INT, false, stnIndex);
StructureDataComposite sdall = new StructureDataComposite();
sdall.add(profileCoords); // coords first so it takes precedence
sdall.add(profile.getFeatureData());
profileRecno = super.writeStructureData(profileRecno, profileStruct, sdall, profileVarMap);
}
private int obsRecno = 0;
public void writeObsData(PointFeature pf) throws IOException {
StructureDataScalar coords = new StructureDataScalar("Coords");
coords.addMember(altitudeCoordinateName, null, null, DataType.DOUBLE, false, pf.getLocation().getAltitude());
StructureDataComposite sdall = new StructureDataComposite();
sdall.add(coords); // coords first so it takes precedence
sdall.add(pf.getFeatureData());
obsRecno = super.writeStructureData(obsRecno, record, sdall, dataMap);
}
}
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