ucar.nc2.dt.point.WriterStationObsDataset Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of cdm Show documentation
Show all versions of cdm Show documentation
The NetCDF-Java Library is a Java interface to NetCDF files,
as well as to many other types of scientific data formats.
The newest version!
/*
* Copyright 1998-2009 University Corporation for Atmospheric Research/Unidata
*
* Portions of this software were developed by the Unidata Program at the
* University Corporation for Atmospheric Research.
*
* Access and use of this software shall impose the following obligations
* and understandings on the user. The user is granted the right, without
* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
* documentation for any purpose whatsoever, provided that this entire
* notice appears in all copies of the software, derivative works and
* supporting documentation. Further, UCAR requests that the user credit
* UCAR/Unidata in any publications that result from the use of this
* software or in any product that includes this software. The names UCAR
* and/or Unidata, however, may not be used in any advertising or publicity
* to endorse or promote any products or commercial entity unless specific
* written permission is obtained from UCAR/Unidata. The user also
* understands that UCAR/Unidata is not obligated to provide the user with
* any support, consulting, training or assistance of any kind with regard
* to the use, operation and performance of this software nor to provide
* the user with any updates, revisions, new versions or "bug fixes."
*
* THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
* INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
* FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
* NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
* WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
*/
package ucar.nc2.dt.point;
import ucar.nc2.dt.*;
import ucar.nc2.*;
import ucar.nc2.constants.FeatureType;
import ucar.nc2.dataset.NetcdfDataset;
import ucar.nc2.units.DateFormatter;
import ucar.ma2.*;
import ucar.ma2.DataType;
import ucar.unidata.geoloc.LatLonRect;
import ucar.unidata.geoloc.LatLonPointImpl;
import java.util.*;
import java.io.*;
/**
* Write StationObsDataset in Unidata Station Obs Convention.
*
* @deprecated use ucar.nc2.ft.point
* @author caron
*/
public class WriterStationObsDataset {
private static final String recordDimName = "record";
private static final String stationDimName = "station";
private static final String latName = "latitude";
private static final String lonName = "longitude";
private static final String altName = "altitude";
private static final String timeName = "time";
private static final String idName = "station_id";
private static final String descName = "station_description";
private static final String wmoName = "wmo_id";
private static final String firstChildName = "firstChild";
private static final String lastChildName = "lastChild";
private static final String numChildName = "numChildren";
private static final String nextChildName = "nextChild";
private static final String prevChildName = "prevChild";
private static final String parentName = "parent_index";
// private static final String timeStrLenDim = "time_strlen";
private DateFormatter dateFormatter = new DateFormatter();
private int name_strlen, desc_strlen, wmo_strlen;
private NetcdfFileWriteable ncfile;
private String title;
private Set dimSet = new HashSet();
private List recordDims = new ArrayList();
private List stationDims = new ArrayList();
private List stnList;
private Date minDate = null;
private Date maxDate = null;
private boolean useAlt = false;
private boolean useWmoId = false;
private boolean debug = false;
public WriterStationObsDataset(String fileOut, String title) throws IOException {
ncfile = NetcdfFileWriteable.createNew(fileOut, false);
ncfile.setFill( false);
this.title = title;
}
public void writeHeader(List stns, List vars) throws IOException {
createGlobalAttributes();
createStations(stns);
createDataVariables(vars);
ncfile.create(); // done with define mode
writeStationData(stns); // write out the station info
// now write the observations
if (! (Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE))
throw new IllegalStateException("can't add record variable");
}
private void createGlobalAttributes() {
ncfile.addGlobalAttribute("Conventions", "Unidata Observation Dataset v1.0");
ncfile.addGlobalAttribute("cdm_datatype", "Station");
ncfile.addGlobalAttribute("title", title);
ncfile.addGlobalAttribute("desc", "Extracted by THREDDS/Netcdf Subset Service");
/* ncfile.addGlobalAttribute("observationDimension", recordDimName);
ncfile.addGlobalAttribute("stationDimension", stationDimName);
ncfile.addGlobalAttribute("latitude_coordinate", latName);
ncfile.addGlobalAttribute("longitude_coordinate", lonName);
ncfile.addGlobalAttribute("time_coordinate", timeName); */
}
private void createStations(List stnList) throws IOException {
int nstns = stnList.size();
// see if there's altitude, wmoId for any stations
for (int i = 0; i < nstns; i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
if (!Double.isNaN(stn.getAltitude()))
useAlt = true;
if ((stn.getWmoId() != null) && (stn.getWmoId().trim().length() > 0))
useWmoId = true;
}
/* if (useAlt)
ncfile.addGlobalAttribute("altitude_coordinate", altName); */
// find string lengths
for (int i = 0; i < nstns; i++) {
ucar.unidata.geoloc.Station station = stnList.get(i);
name_strlen = Math.max(name_strlen, station.getName().length());
desc_strlen = Math.max(desc_strlen, station.getDescription().length());
if (useWmoId) wmo_strlen = Math.max(wmo_strlen, station.getName().length());
}
LatLonRect llbb = getBoundingBox(stnList);
ncfile.addGlobalAttribute("geospatial_lat_min", Double.toString(llbb.getLowerLeftPoint().getLatitude()));
ncfile.addGlobalAttribute("geospatial_lat_max", Double.toString(llbb.getUpperRightPoint().getLatitude()));
ncfile.addGlobalAttribute("geospatial_lon_min", Double.toString(llbb.getLowerLeftPoint().getLongitude()));
ncfile.addGlobalAttribute("geospatial_lon_max", Double.toString(llbb.getUpperRightPoint().getLongitude()));
// add the dimensions
Dimension recordDim = ncfile.addUnlimitedDimension(recordDimName);
recordDims.add(recordDim);
Dimension stationDim = ncfile.addDimension(stationDimName, nstns);
stationDims.add(stationDim);
// add the station Variables using the station dimension
Variable v = ncfile.addVariable(latName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "degrees_north"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station latitude"));
v = ncfile.addVariable(lonName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "degrees_east"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station longitude"));
if (useAlt) {
v = ncfile.addVariable(altName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "meters"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station altitude"));
}
v = ncfile.addStringVariable(idName, stationDims, name_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station identifier"));
v = ncfile.addStringVariable(descName, stationDims, desc_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station description"));
if (useWmoId) {
v = ncfile.addStringVariable(wmoName, stationDims, wmo_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station WMO id"));
}
v = ncfile.addVariable(numChildName, DataType.INT, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "number of children in linked list for this station"));
v = ncfile.addVariable(lastChildName, DataType.INT, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "record number of last child in linked list for this station"));
v = ncfile.addVariable(firstChildName, DataType.INT, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "record number of first child in linked list for this station"));
// time variable
Variable timeVar = ncfile.addStringVariable(timeName, recordDims, 20);
ncfile.addVariableAttribute(timeVar, new Attribute("long_name", "ISO-8601 Date"));
v = ncfile.addVariable(prevChildName, DataType.INT, recordDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "record number of previous child in linked list"));
v = ncfile.addVariable(parentName, DataType.INT, recordDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent station"));
v = ncfile.addVariable(nextChildName, DataType.INT, recordDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "record number of next child in linked list"));
}
private void createDataVariables(List dataVars) throws IOException {
// find all dimensions needed by the data variables
for (VariableSimpleIF var : dataVars) {
List dims = var.getDimensions();
dimSet.addAll(dims);
}
// add them
for (Dimension d : dimSet) {
if (!d.isUnlimited())
ncfile.addDimension(d.getShortName(), d.getLength(), d.isShared(), false, d.isVariableLength());
}
// add the data variables all using the record dimension
for (VariableSimpleIF oldVar : dataVars) {
List dims = oldVar.getDimensions();
StringBuilder dimNames = new StringBuilder(recordDimName);
for (Dimension d : dims) {
if (!d.isUnlimited())
dimNames.append(" ").append(d.getShortName());
}
Variable newVar = ncfile.addVariable(oldVar.getShortName(), oldVar.getDataType(), dimNames.toString());
List atts = oldVar.getAttributes();
for (Attribute att : atts) {
ncfile.addVariableAttribute(newVar, att);
}
}
}
private HashMap stationMap;
private class StationTracker {
int numChildren = 0;
int lastChild = -1;
int parent_index;
List link = new ArrayList(); // recnums
StationTracker(int parent_index) {
this.parent_index = parent_index;
}
}
private void writeStationData(List stnList) throws IOException {
this.stnList = stnList;
int nstns = stnList.size();
stationMap = new HashMap(2 * nstns);
if (debug) System.out.println("stationMap created");
// now write the station data
ArrayDouble.D1 latArray = new ArrayDouble.D1(nstns);
ArrayDouble.D1 lonArray = new ArrayDouble.D1(nstns);
ArrayDouble.D1 altArray = new ArrayDouble.D1(nstns);
ArrayObject.D1 idArray = new ArrayObject.D1(String.class, nstns);
ArrayObject.D1 descArray = new ArrayObject.D1(String.class, nstns);
ArrayObject.D1 wmoArray = new ArrayObject.D1(String.class, nstns);
for (int i = 0; i < stnList.size(); i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
stationMap.put(stn.getName(), new StationTracker(i));
latArray.set(i, stn.getLatitude());
lonArray.set(i, stn.getLongitude());
if (useAlt) altArray.set(i, stn.getAltitude());
idArray.set(i, stn.getName());
descArray.set(i, stn.getDescription());
if (useWmoId) wmoArray.set(i, stn.getWmoId());
}
try {
ncfile.write(latName, latArray);
ncfile.write(lonName, lonArray);
if (useAlt) ncfile.write(altName, altArray);
ncfile.writeStringData(idName, idArray);
ncfile.writeStringData(descName, descArray);
if (useWmoId) ncfile.writeStringData(wmoName, wmoArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
}
private void writeDataFinish() throws IOException {
ArrayInt.D1 nextChildArray = new ArrayInt.D1(recno);
int nstns = stnList.size();
ArrayInt.D1 firstArray = new ArrayInt.D1(nstns);
ArrayInt.D1 lastArray = new ArrayInt.D1(nstns);
ArrayInt.D1 numArray = new ArrayInt.D1(nstns);
for (int i = 0; i < stnList.size(); i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
StationTracker tracker = stationMap.get(stn.getName());
lastArray.set(i, tracker.lastChild);
numArray.set(i, tracker.numChildren);
int first = (tracker.link.size() > 0) ? tracker.link.get(0) : -1;
firstArray.set(i, first);
if (tracker.link.size() > 0) {
// construct forward link
List nextList = tracker.link;
for (int j = 0; j < nextList.size() - 1; j++) {
Integer curr = nextList.get(j);
Integer next = nextList.get(j + 1);
nextChildArray.set(curr, next);
}
Integer curr = nextList.get(nextList.size() - 1);
nextChildArray.set(curr, -1);
}
}
try {
ncfile.write(firstChildName, firstArray);
ncfile.write(lastChildName, lastArray);
ncfile.write(numChildName, numArray);
ncfile.write(nextChildName, nextChildArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
// if there is no data
if (minDate == null) minDate = new Date();
if (maxDate == null) maxDate = new Date();
ncfile.updateAttribute(null, new Attribute("time_coverage_start", dateFormatter.toDateTimeStringISO(minDate)));
ncfile.updateAttribute(null, new Attribute("time_coverage_end", dateFormatter.toDateTimeStringISO(maxDate)));
}
private int recno = 0;
private ArrayObject.D1 timeArray = new ArrayObject.D1(String.class, 1);
private ArrayInt.D1 prevArray = new ArrayInt.D1(1);
private ArrayInt.D1 parentArray = new ArrayInt.D1(1);
private int[] origin = new int[1];
private int[] originTime = new int[2];
public void writeRecord(StationObsDatatype sobs, StructureData sdata) throws IOException {
if (debug) System.out.println("sobs= " + sobs + "; station = " + sobs.getStation());
writeRecord(sobs.getStation().getName(), sobs.getObservationTimeAsDate(), sdata);
}
public void writeRecord(String stnName, Date obsDate, StructureData sdata) throws IOException {
StationTracker tracker = stationMap.get(stnName);
// needs to be wrapped as an ArrayStructure, even though we are only writing one at a time.
ArrayStructureW sArray = new ArrayStructureW(sdata.getStructureMembers(), new int[]{1});
sArray.setStructureData(sdata, 0);
// date is handled specially
if ((minDate == null) || minDate.after(obsDate)) minDate = obsDate;
if ((maxDate == null) || maxDate.before(obsDate)) maxDate = obsDate;
timeArray.set(0, dateFormatter.toDateTimeStringISO(obsDate));
prevArray.set(0, tracker.lastChild);
parentArray.set(0, tracker.parent_index);
tracker.link.add(recno);
tracker.lastChild = recno;
tracker.numChildren++;
// write the recno record
origin[0] = recno;
originTime[0] = recno;
try {
ncfile.write("record", origin, sArray);
ncfile.writeStringData(timeName, originTime, timeArray);
ncfile.write(prevChildName, originTime, prevArray);
ncfile.write(parentName, originTime, parentArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
recno++;
}
public void finish() throws IOException {
writeDataFinish();
ncfile.close();
}
private LatLonRect getBoundingBox(List stnList) {
ucar.unidata.geoloc.Station s = (ucar.unidata.geoloc.Station) stnList.get(0);
LatLonPointImpl llpt = new LatLonPointImpl();
llpt.set(s.getLatitude(), s.getLongitude());
LatLonRect rect = new LatLonRect(llpt, .001, .001);
for (int i = 1; i < stnList.size(); i++) {
s = (ucar.unidata.geoloc.Station) stnList.get(i);
llpt.set(s.getLatitude(), s.getLongitude());
rect.extend(llpt);
}
return rect;
}
// not tested
private void write(StationObsDataset sobsDataset) throws IOException {
createGlobalAttributes();
createStations(sobsDataset.getStations());
ncfile.addGlobalAttribute("time_coverage_start", dateFormatter.toDateTimeStringISO(sobsDataset.getStartDate()));
ncfile.addGlobalAttribute("time_coverage_end", dateFormatter.toDateTimeStringISO(sobsDataset.getEndDate()));
createDataVariables(sobsDataset.getDataVariables());
// global attributes
List gatts = sobsDataset.getGlobalAttributes();
for (int i = 0; i < gatts.size(); i++) {
Attribute att = (Attribute) gatts.get(i);
ncfile.addGlobalAttribute(att);
}
// done with define mode
ncfile.create();
// write out the station info
writeStationData(sobsDataset.getStations());
// now write the observations
if (! (Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE))
throw new IllegalStateException("can't add record variable");
int[] origin = new int[1];
int[] originTime = new int[2];
int recno = 0;
ArrayStructureW sArray = null;
ArrayObject.D1 timeArray = new ArrayObject.D1(String.class, 1);
DataIterator diter = sobsDataset.getDataIterator(1000 * 1000);
while (diter.hasNext()) {
StationObsDatatype sobs = (StationObsDatatype) diter.nextData();
StructureData recordData = sobs.getData();
// needs to be wrapped as an ArrayStructure, even though we are only writing one at a time.
if (sArray == null)
sArray = new ArrayStructureW(recordData.getStructureMembers(), new int[]{1});
sArray.setStructureData(recordData, 0);
// date is handled specially
timeArray.set(0, dateFormatter.toDateTimeStringISO(sobs.getObservationTimeAsDate()));
// write the recno record
origin[0] = recno;
originTime[0] = recno;
try {
ncfile.write("record", origin, sArray);
ncfile.writeStringData(timeName, originTime, timeArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
recno++;
}
ncfile.close();
}
public static void main(String args[]) throws IOException {
long start = System.currentTimeMillis();
String location = "C:/data/metars/Surface_METAR_20070513_0000.nc";
StringBuilder errlog = new StringBuilder();
StationObsDataset sobs = (StationObsDataset) TypedDatasetFactory.open(FeatureType.STATION, location, null, errlog);
String fileOut = "C:/temp/Surface_METAR_20070513_0000.rewrite.nc";
WriterStationObsDataset writer = new WriterStationObsDataset(fileOut, "test");
List stns = sobs.getStations();
List stnList = new ArrayList();
ucar.unidata.geoloc.Station s = (ucar.unidata.geoloc.Station) stns.get(0);
stnList.add(s);
List varList = new ArrayList();
varList.add(sobs.getDataVariable("wind_speed"));
writer.writeHeader(stnList, varList);
DataIterator iter = sobs.getDataIterator(s);
while (iter.hasNext()) {
StationObsDatatype sobsData = (StationObsDatatype) iter.nextData();
StructureData data = sobsData.getData();
writer.writeRecord(sobsData, data);
}
writer.finish();
long took = System.currentTimeMillis() - start;
System.out.println("That took = " + took);
}
}
© 2015 - 2024 Weber Informatics LLC | Privacy Policy