ucar.nc2.ft.point.writer.WriterCFStationCollection Maven / Gradle / Ivy
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/*
* Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
* See LICENSE for license information.
*/
package ucar.nc2.ft.point.writer;
import com.google.common.collect.ImmutableList;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants.CF;
import ucar.nc2.dataset.CoordinateAxis;
import ucar.nc2.ft.*;
import ucar.nc2.ft.point.StationFeature;
import ucar.nc2.ft.point.StationPointFeature;
import ucar.nc2.time.CalendarDate;
import ucar.nc2.time.CalendarDateUnit;
import ucar.unidata.geoloc.Station;
import javax.annotation.Nullable;
import java.io.IOException;
import java.util.*;
import java.util.stream.Collectors;
/**
* Write a CF "Discrete Sample" station file.
* Example H.7. Timeseries of station data in the indexed ragged array representation.
*
*
*
*
* writeHeader()
* iterate { writeRecord() }
* finish()
*
*
* @see "http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8340320"
* @author caron
* @since Aug 19, 2009
*/
public class WriterCFStationCollection extends CFPointWriter {
//////////////////////////////////////////////////////////
private List stnList;
protected Structure stationStruct; // used for netcdf4 extended
private HashMap stationIndexMap;
private boolean useDesc;
private boolean useAlt;
private boolean useWmoId;
private int desc_strlen = 1, wmo_strlen = 1;
private Map featureVarMap = new HashMap<>();
public WriterCFStationCollection(String fileOut, List globalAtts, List dataVars,
CalendarDateUnit timeUnit, String altUnits, CFPointWriterConfig config) throws IOException {
super(fileOut, globalAtts, dataVars, timeUnit, altUnits, config);
writer.addGroupAttribute(null, new Attribute(CF.FEATURE_TYPE, CF.FeatureType.timeSeries.name()));
writer.addGroupAttribute(null, new Attribute(CF.DSG_REPRESENTATION,
"Timeseries of station data in the indexed ragged array representation, H.2.5"));
}
public WriterCFStationCollection(String fileOut, List globalAtts, List dataVars,
List coordVars, CFPointWriterConfig config) throws IOException {
super(fileOut, globalAtts, dataVars, config, coordVars);
writer.addGroupAttribute(null, new Attribute(CF.FEATURE_TYPE, CF.FeatureType.timeSeries.name()));
writer.addGroupAttribute(null, new Attribute(CF.DSG_REPRESENTATION,
"Timeseries of station data in the indexed ragged array representation, H.2.5"));
}
public void writeHeader(StationTimeSeriesFeatureCollection stations) throws IOException {
writeHeader(stations.getStationFeatures(), null);
}
public void writeHeader(List stns, @Nullable StationPointFeature spf) throws IOException {
this.stnList = stns.stream().distinct().collect(Collectors.toList());
List coords = new ArrayList<>();
List flattenStations = new ArrayList<>();
List stationData = new ArrayList<>();
// see if there's altitude, wmoId for any stations
for (StationFeature stn : stns) {
flattenStations.add((PointFeatureCollection) stn);
stationData.add(stn.getFeatureData());
useAlt = !Double.isNaN(stn.getAltitude());
if ((stn.getWmoId() != null) && (!stn.getWmoId().trim().isEmpty()))
useWmoId = true;
if ((stn.getDescription() != null) && (!stn.getDescription().trim().isEmpty()))
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());
DsgFeatureCollection dsgStation = (DsgFeatureCollection) stn;
if (coords.stream().noneMatch(x -> x.getShortName().equals(dsgStation.getTimeName()))) {
coords
.add(VariableSimpleBuilder
.makeScalar(dsgStation.getTimeName(), "time of measurement", dsgStation.getTimeUnit().getUdUnit(),
DataType.DOUBLE)
.addAttribute(CF.CALENDAR, dsgStation.getTimeUnit().getCalendar().toString()).build());
}
}
llbb = CFPointWriterUtils.getBoundingBox(stnList); // gets written in super.finish();
altitudeCoordinateName = stationAltName;
coords.add(VariableSimpleBuilder
.makeScalar(stationIndexName, "station index for this observation record", null, DataType.INT)
.addAttribute(CF.INSTANCE_DIMENSION, stationDimName).build());
super.writeHeader(coords, flattenStations, stationData, null);
int count = 0;
stationIndexMap = new HashMap<>(stnList.size(), 1.0f);
for (StationFeature stn : stnList) {
writeStationData(stn);
stationIndexMap.put(stn.getName(), count);
count++;
}
}
protected void makeFeatureVariables(List featureDataStructs, boolean isExtended) {
// add the dimensions : extendded 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(VariableSimpleBuilder.makeScalar(latName, "station latitude", CDM.LAT_UNITS, DataType.DOUBLE).build());
stnVars.add(VariableSimpleBuilder.makeScalar(lonName, "station longitude", CDM.LON_UNITS, DataType.DOUBLE).build());
if (useAlt) {
stnVars.add(VariableSimpleBuilder.makeScalar(stationAltName, "station altitude", altUnits, DataType.DOUBLE)
.addAttribute(CF.STANDARD_NAME, CF.STATION_ALTITUDE).build());
}
stnVars.add(VariableSimpleBuilder.makeString(stationIdName, "station identifier", null, id_strlen)
.addAttribute(CF.CF_ROLE, CF.TIMESERIES_ID).build()); // station_id:cf_role = "timeseries_id";
if (useDesc)
stnVars.add(VariableSimpleBuilder.makeString(descName, "station description", null, desc_strlen)
.addAttribute(CF.STANDARD_NAME, CF.PLATFORM_NAME).build());
if (useWmoId)
stnVars.add(VariableSimpleBuilder.makeString(wmoName, "station WMO id", null, wmo_strlen)
.addAttribute(CF.STANDARD_NAME, CF.PLATFORM_ID).build());
for (StructureData featureData : featureDataStructs) {
for (StructureMembers.Member m : featureData.getMembers()) {
if (getDataVar(m.getName()) != null
&& stnVars.stream().noneMatch(x -> x.getShortName().equals(m.getFullName())))
stnVars.add(VariableSimpleBuilder.fromMember(m).build());
}
}
if (isExtended) {
stationStruct = (Structure) writer.addVariable(null, stationStructName, DataType.STRUCTURE, stationDimName);
addCoordinatesExtended(stationStruct, stnVars);
} else {
addCoordinatesClassic(stationDim, stnVars, featureVarMap);
}
}
private int stnRecno;
private void writeStationData(StationFeature stn) throws IOException {
StructureMembers.Builder smb = StructureMembers.builder().setName("Coords");
smb.addMemberScalar(latName, null, null, DataType.DOUBLE, stn.getLatLon().getLatitude());
smb.addMemberScalar(lonName, null, null, DataType.DOUBLE, stn.getLatLon().getLongitude());
smb.addMemberScalar(stationAltName, null, null, DataType.DOUBLE, stn.getAltitude());
smb.addMemberString(stationIdName, null, null, stn.getName().trim(), id_strlen);
if (useDesc)
smb.addMemberString(descName, null, null, stn.getDescription().trim(), desc_strlen);
if (useWmoId)
smb.addMemberString(wmoName, null, null, stn.getWmoId().trim(), wmo_strlen);
StructureData stnCoords = new StructureDataFromMember(smb.build());
StructureDataComposite sdall = StructureDataComposite.create(ImmutableList.of(stnCoords, stn.getFeatureData()));
stnRecno = super.writeStructureData(stnRecno, stationStruct, sdall, featureVarMap);
}
public void writeRecord(Station s, PointFeature sobs, StructureData sdata) throws IOException {
if (s instanceof DsgFeatureCollection) {
DsgFeatureCollection dsgStation = (DsgFeatureCollection) s;
writeRecord(dsgStation.getName(), dsgStation.getTimeName(), sobs.getObservationTime(),
sobs.getObservationTimeAsCalendarDate(), altitudeCoordinateName, sobs.getLocation().getAltitude(), sdata);
} else {
writeRecord(s.getName(), sobs.getFeatureCollection().getTimeName(), sobs.getObservationTime(),
sobs.getObservationTimeAsCalendarDate(), altitudeCoordinateName, sobs.getLocation().getAltitude(), sdata);
}
}
protected int obsRecno;
public void writeRecord(String stnName, double timeCoordValue, CalendarDate obsDate, StructureData sdata)
throws IOException {
writeRecord(stnName, timeName, timeCoordValue, obsDate, altitudeCoordinateName, 0, sdata);
}
public void writeRecord(String stnName, String timeCoordName, double timeCoordValue, CalendarDate obsDate,
String altName, double altValue, StructureData sdata) throws IOException {
trackBB(null, obsDate);
Integer parentIndex = stationIndexMap.get(stnName);
if (parentIndex == null)
throw new RuntimeException("Cant find station " + stnName);
StructureMembers.Builder smb = StructureMembers.builder().setName("Coords");
smb.addMemberScalar(timeCoordName, null, null, DataType.DOUBLE, timeCoordValue);
if (useAlt)
smb.addMemberScalar(altName, null, null, DataType.DOUBLE, altValue);
smb.addMemberScalar(stationIndexName, null, null, DataType.INT, parentIndex);
StructureData coords = new StructureDataFromMember(smb.build());
// coords first so it takes precedence
StructureDataComposite sdall = StructureDataComposite.create(ImmutableList.of(coords, sdata));
obsRecno = super.writeStructureData(obsRecno, record, sdall, dataMap);
}
}
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