/**
* Helper class for using the netcdf-3 record dimension.
*
* @author caron
* @since Feb 29, 2008
*/
public class RecordDatasetHelper {
private static org.slf4j.Logger log =
org.slf4j.LoggerFactory.getLogger(RecordDatasetHelper.class);
protected NetcdfDataset ncfile;
protected String obsTimeVName, nomTimeVName;
protected String latVName, lonVName, zcoordVName, zcoordUnits;
protected String stnIdVName, stnIndexVName, stnDescVName;
protected StationHelper stationHelper;
protected DataType stationIdType;
protected StructureDS recordVar;
protected Dimension obsDim;
protected LatLonRect boundingBox;
protected double minDate, maxDate;
protected DateUnit timeUnit;
protected double altScaleFactor = 1.0;
protected Formatter errs = null;
protected boolean showErrors = true;
/**
* Constructor.
*
* @param ncfile the netccdf file
* @param typedDataVariables list of data variables; all record variables will be added to this
* list, except . You can remove extra
* @param obsTimeVName observation time variable name (required)
* @param nomTimeVName nominal time variable name (may be null)
* @throws IllegalArgumentException if ncfile has no unlimited dimension and recDimName is null.
*/
public RecordDatasetHelper(
NetcdfDataset ncfile,
String obsTimeVName,
String nomTimeVName,
List<VariableSimpleIF> typedDataVariables,
String recDimName,
Formatter errBuffer) {
this.ncfile = ncfile;
this.obsTimeVName = obsTimeVName;
this.nomTimeVName = nomTimeVName;
this.errs = errBuffer;
// check if we already have a structure vs if we have to add it.
if (this.ncfile.hasUnlimitedDimension()) {
this.ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
this.recordVar = (StructureDS) this.ncfile.getRootGroup().findVariable("record");
this.obsDim = ncfile.getUnlimitedDimension();
} else {
if (recDimName == null)
throw new IllegalArgumentException(
"File <"
+ this.ncfile.getLocation()
+ "> has no unlimited dimension, specify psuedo record dimension with observationDimension global attribute.");
this.obsDim = this.ncfile.getRootGroup().findDimension(recDimName);
this.recordVar = new StructurePseudoDS(this.ncfile, null, "record", null, obsDim);
}
// create member variables
List<Variable> recordMembers = ncfile.getVariables();
for (Variable v : recordMembers) {
if (v == recordVar) continue;
if (v.isScalar()) continue;
if (v.getDimension(0) == this.obsDim) typedDataVariables.add(v);
}
// need the time units
Variable timeVar = ncfile.findVariable(obsTimeVName);
String timeUnitString =
ncfile.findAttValueIgnoreCase(timeVar, CDM.UNITS, "seconds since 1970-01-01");
try {
timeUnit = new DateUnit(timeUnitString);
} catch (Exception e) {
if (null != errs) errs.format("Error on string = %s == %s%n", timeUnitString, e.getMessage());
try {
timeUnit = new DateUnit("seconds since 1970-01-01");
} catch (Exception e1) {
// cant happen
}
}
}
/**
* Set extra information used by station obs datasets. Use stnIdVName or stnIndexVName.
*
* @param stnIdVName the obs variable that is used to find the station in the stnHash; may be type
* int or a String (char).
* @param stnDescVName optional station var containing station description
*/
public void setStationInfo(
String stnIdVName, String stnDescVName, String stnIndexVName, StationHelper stationHelper) {
this.stnIdVName = stnIdVName;
this.stnDescVName = stnDescVName;
this.stnIndexVName = stnIndexVName;
this.stationHelper = stationHelper;
if (stnIdVName != null) {
Variable stationVar = ncfile.findVariable(stnIdVName);
stationIdType = stationVar.getDataType();
}
}
public void setLocationInfo(String latVName, String lonVName, String zcoordVName) {
this.latVName = latVName;
this.lonVName = lonVName;
this.zcoordVName = zcoordVName;
// check for meter conversion
if (zcoordVName != null) {
Variable v = ncfile.findVariable(zcoordVName);
zcoordUnits = ncfile.findAttValueIgnoreCase(v, CDM.UNITS, null);
if (zcoordUnits != null)
try {
altScaleFactor = getMetersConversionFactor(zcoordUnits);
} catch (Exception e) {
if (errs != null) errs.format("%s", e.getMessage());
}
}
}
// make structure variable names to shortNames so StructureData sdata can
// access it members
public void setShortNames(
String latVName, String lonVName, String altVName, String obsTimeVName, String nomTimeVName) {
this.latVName = latVName;
this.lonVName = lonVName;
this.zcoordVName = altVName;
this.obsTimeVName = obsTimeVName;
this.nomTimeVName = nomTimeVName;
}
protected static double getMetersConversionFactor(String unitsString) throws Exception {
SimpleUnit unit = SimpleUnit.factoryWithExceptions(unitsString);
return unit.convertTo(1.0, SimpleUnit.meterUnit);
}
public Structure getRecordVar() {
return (this.recordVar);
}
public int getRecordCount() {
Dimension unlimitedDim = ncfile.getUnlimitedDimension();
return unlimitedDim.getLength();
}
public void setTimeUnit(DateUnit timeUnit) {
this.timeUnit = timeUnit;
}
public DateUnit getTimeUnit() {
return this.timeUnit;
}
public LatLonPoint getLocation(StructureData sdata) {
StructureMembers members = sdata.getStructureMembers();
double lat = sdata.convertScalarDouble(members.findMember(latVName));
double lon = sdata.convertScalarDouble(members.findMember(lonVName));
return new LatLonPointImpl(lat, lon);
}
public double getLatitude(StructureData sdata) {
StructureMembers members = sdata.getStructureMembers();
return sdata.convertScalarDouble(members.findMember(latVName));
}
public double getLongitude(StructureData sdata) {
StructureMembers members = sdata.getStructureMembers();
return sdata.convertScalarDouble(members.findMember(lonVName));
}
public double getZcoordinate(StructureData sdata) {
StructureMembers members = sdata.getStructureMembers();
return (zcoordVName == null)
? Double.NaN
: sdata.convertScalarDouble(members.findMember(zcoordVName));
}
public String getZcoordUnits() {
return zcoordUnits;
}
public Date getObservationTimeAsDate(StructureData sdata) {
return timeUnit.makeDate(getObservationTime(sdata));
}
public double getObservationTime(StructureData sdata) {
return getTime(sdata.findMember(obsTimeVName), sdata);
}
private double getTime(StructureMembers.Member timeVar, StructureData sdata) {
if (timeVar == null) return 0.0;
if ((timeVar.getDataType() == DataType.CHAR) || (timeVar.getDataType() == DataType.STRING)) {
String time = sdata.getScalarString(timeVar);
CalendarDate date = CalendarDateFormatter.isoStringToCalendarDate(null, time);
if (date == null) {
log.error("Cant parse date - not ISO formatted, = " + time);
return 0.0;
}
return date.getMillis() / 1000.0;
} else {
return sdata.convertScalarDouble(timeVar);
}
}
/*
* This reads through all the records in the dataset, and constructs a list of
* RecordPointObs or RecordStationObs. It does not cache the data.
* <p>If stnIdVName is not null, its a StationDataset, then construct a Station HashMap of StationImpl
* objects. Add the RecordStationObs into the list of obs for that station.
*
* @param cancel allow user to cancel
* @return List of RecordPointObs or RecordStationObs
* @throws IOException on read error
*
public List<RecordPointObs> readAllCreateObs(CancelTask cancel) throws IOException {
// see if its a station or point dataset
boolean hasStations = stnIdVName != null;
if (hasStations)
stnHash = new HashMap<Object, Station>();
// get min and max date and lat,lon
double minDate = Double.MAX_VALUE;
double maxDate = -Double.MAX_VALUE;
double minLat = Double.MAX_VALUE;
double maxLat = -Double.MAX_VALUE;
double minLon = Double.MAX_VALUE;
double maxLon = -Double.MAX_VALUE;
// read all the data, create a RecordObs
StructureMembers members = null;
List<RecordPointObs> records = new ArrayList<RecordPointObs>();
int recno = 0;
Structure.Iterator ii = recordVar.getStructureIterator();
while (ii.hasNext()) {
StructureData sdata = ii.next();
if (members == null)
members = sdata.getStructureMembers();
Object stationId = null;
if (hasStations) {
if (stationIdType == DataType.INT) {
stationId = sdata.getScalarInt(stnIdVName);
} else
stationId = sdata.getScalarString(stnIdVName).trim();
}
String desc = (stnDescVName == null) ? null : sdata.getScalarString(stnDescVName);
double lat = sdata.getScalarDouble(latVName);
double lon = sdata.getScalarDouble(lonVName);
double alt = (altVName == null) ? 0.0 : altScaleFactor * sdata.getScalarDouble(altVName);
double obsTime = sdata.convertScalarDouble(members.findMember(obsTimeVName));
double nomTime = (nomTimeVName == null) ? obsTime : sdata.convertScalarDouble(members.findMember(nomTimeVName));
//double obsTime = sdata.convertScalarDouble( members.findMember( obsTimeVName) );
//double nomTime = (nomTimeVName == null) ? obsTime : sdata.convertScalarDouble( members.findMember( nomTimeVName));
if (hasStations) {
Station stn = stnHash.get(stationId);
if (stn == null) {
stn = new Station(stationId.toString(), desc, lat, lon, alt);
stnHash.put(stationId, stn);
}
RecordStationObs stnObs = new RecordStationObs(stn, obsTime, nomTime, timeUnit, recno);
records.add(stnObs);
//stn.addObs( stnObs);
} else {
records.add(new RecordPointObs(new EarthLocation(lat, lon, alt), obsTime, nomTime, timeUnit, recno));
}
// track date range and bounding box
minDate = Math.min(minDate, obsTime);
maxDate = Math.max(maxDate, obsTime);
minLat = Math.min(minLat, lat);
maxLat = Math.max(maxLat, lat);
minLon = Math.min(minLon, lon);
maxLon = Math.max(maxLon, lon);
recno++;
if ((cancel != null) && cancel.isCancel()) return null;
}
boundingBox = new LatLonRect(new LatLonPointImpl(minLat, minLon), new LatLonPointImpl(maxLat, maxLon));
return records;
}
/* private boolean debugBB = false;
public List getData(ArrayList records, LatLonRect boundingBox, CancelTask cancel) throws IOException {
if (debugBB) System.out.println("Want bb= "+boundingBox);
ArrayList result = new ArrayList();
for (int i = 0; i < records.size(); i++) {
RecordDatasetHelper.RecordPointObs r = (RecordDatasetHelper.RecordPointObs) records.get(i);
if (boundingBox.contains(r.getLatLon())) {
if (debugBB) System.out.println(" ok latlon= "+r.getLatLon());
result.add( r);
}
if ((cancel != null) && cancel.isCancel()) return null;
}
return result;
}
// return List<PointObsDatatype>
public List getData(ArrayList records, LatLonRect boundingBox, double startTime, double endTime, CancelTask cancel) throws IOException {
if (debugBB) System.out.println("Want bb= "+boundingBox);
ArrayList result = new ArrayList();
for (int i = 0; i < records.size(); i++) {
RecordDatasetHelper.RecordPointObs r = (RecordDatasetHelper.RecordPointObs) records.get(i);
if (boundingBox.contains(r.getLatLon())) {
if (debugBB) System.out.println(" ok latlon= "+r.getLatLon());
double timeValue = r.getObservationTime();
if ((timeValue >= startTime) && (timeValue <= endTime))
result.add( r);
}
if ((cancel != null) && cancel.isCancel()) return null;
}
return result;
} */
//////////////////////////////////////////////////////////////////////////////////////
public PointFeature factory(StationImpl s, StructureData sdata, int recno) {
if (s == null) return new RecordPointObs(sdata, recno);
else return new RecordStationObs(s, sdata, recno);
}
class RecordPointObs extends PointFeatureImpl {
protected int recno;
protected StructureData sdata;
RecordPointObs(int recno) {
super(RecordDatasetHelper.this.timeUnit);
this.recno = recno;
}
// Constructor for the case where you keep track of the location, time of each record, but not
// the data.
protected RecordPointObs(
EarthLocation location, double obsTime, double nomTime, DateUnit timeUnit, int recno) {
super(location, obsTime, nomTime, timeUnit);
this.recno = recno;
}
// Constructor for when you already have the StructureData and want to wrap it in a
// StationObsDatatype
protected RecordPointObs(StructureData sdata, int recno) {
super(RecordDatasetHelper.this.timeUnit);
this.sdata = sdata;
this.recno = recno;
StructureMembers members = sdata.getStructureMembers();
obsTime = getTime(members.findMember(obsTimeVName), sdata);
nomTime = (nomTimeVName == null) ? obsTime : getTime(members.findMember(nomTimeVName), sdata);
// this assumes the lat/lon/alt is stored in the obs record
double lat = sdata.convertScalarDouble(members.findMember(latVName));
double lon = sdata.convertScalarDouble(members.findMember(lonVName));
double alt =
(zcoordVName == null)
? 0.0
: altScaleFactor * sdata.convertScalarDouble(members.findMember(zcoordVName));
location = new EarthLocationImpl(lat, lon, alt);
}
public String getId() {
return Integer.toString(recno);
}
public LatLonPoint getLatLon() {
return new LatLonPointImpl(location.getLatitude(), location.getLongitude());
}
public StructureData getFeatureData() throws IOException {
if (null == sdata) {
try {
// deal with files that are updating // LOOK kludge?
if (recno > getRecordCount()) {
int n = getRecordCount();
ncfile.syncExtend();
log.info(
"RecordPointObs.getData recno="
+ recno
+ " > "
+ n
+ "; after sync= "
+ getRecordCount());
}
sdata = recordVar.readStructure(recno);
} catch (ucar.ma2.InvalidRangeException e) {
e.printStackTrace();
throw new IOException(e.getMessage());
}
}
return sdata;
}
public ucar.ma2.StructureData getDataAll() throws java.io.IOException {
return getFeatureData();
}
}
//////////////////////////////////////////////////////////////////////////////////////
// a PointObs with the location info stored as a Station
class RecordStationObs extends RecordPointObs {
private Station station;
/**
* Constructor for the case where you keep track of the station, time of each record, but the
* data reading is deferred.
*
* @param station data is for this Station
* @param obsTime observation time
* @param nomTime nominal time (may be NaN)
* @param recno data is at this record number
*/
protected RecordStationObs(
Station station, double obsTime, double nomTime, DateUnit timeUnit, int recno) {
super(station, obsTime, nomTime, timeUnit, recno);
this.station = station;
}
// Constructor for when you have everything
protected RecordStationObs(
Station station, double obsTime, double nomTime, StructureData sdata, int recno) {
super(recno);
this.station = station;
this.location = station;
this.obsTime = obsTime;
this.nomTime = nomTime;
this.sdata = sdata;
}
// Constructor for when you already have the StructureData and Station, and calculate times
protected RecordStationObs(Station station, StructureData sdata, int recno) {
super(recno);
this.station = station;
this.location = station;
this.sdata = sdata;
StructureMembers members = sdata.getStructureMembers();
obsTime = getTime(members.findMember(obsTimeVName), sdata);
nomTime = (nomTimeVName == null) ? obsTime : getTime(members.findMember(nomTimeVName), sdata);
}
// Constructor for when you already have the StructureData, and need to find Station and times
protected RecordStationObs(StructureData sdata, int recno, boolean useId) {
super(recno);
this.recno = recno;
this.sdata = sdata;
this.timeUnit = RecordDatasetHelper.this.timeUnit;
StructureMembers members = sdata.getStructureMembers();
obsTime = getTime(members.findMember(obsTimeVName), sdata);
nomTime = (nomTimeVName == null) ? obsTime : getTime(members.findMember(nomTimeVName), sdata);
if (useId) {
// this assumes the station id/name is stored in the obs record
String stationId;
if (stationIdType == DataType.INT) {
stationId = Integer.toString(sdata.getScalarInt(stnIdVName));
} else stationId = sdata.getScalarString(stnIdVName).trim();
station = stationHelper.getStation(stationId);
if (null != errs)
errs.format(" cant find station id = <%s> when reading record %d%n", stationId, recno);
log.error(" cant find station id = <" + stationId + "> when reading record " + recno);
} else {
// use a station index
List<Station> stations = stationHelper.getStations();
int stationIndex = sdata.getScalarInt(stnIndexVName);
if (stationIndex < 0 || stationIndex >= stations.size()) {
if (null != errs)
errs.format(
" cant find station at index =%d when reading record %d%n", stationIndex, recno);
log.error(
"cant find station at index = " + stationIndex + " when reading record " + recno);
} else station = stations.get(stationIndex);
}
location = station;
}
}
}
/**
* _more_
*
* @author edavis
* @since 4.0
*/
public class WcsCoverage {
private static org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(WcsCoverage.class);
private GridDataset.Gridset coverage;
private WcsDataset dataset;
private String name;
private String label;
private String description;
private GridCoordSystem coordSys;
private String nativeCRS;
private String defaultRequestCrs;
private List<WcsRequest.Format> supportedCoverageFormatList;
private HashMap<String, WcsRangeField> range;
public WcsCoverage(GridDataset.Gridset coverage, WcsDataset dataset) {
this.dataset = dataset;
if (this.dataset == null) {
log.error("WcsCoverage(): non-null dataset required.");
throw new IllegalArgumentException("Non-null dataset required.");
}
this.coverage = coverage;
if (this.coverage == null) {
log.error("WcsCoverage(): non-null coverage required.");
throw new IllegalArgumentException("Non-null coverage required.");
}
this.coordSys = coverage.getGeoCoordSystem();
if (this.coordSys == null) {
log.error("WcsCoverage(): Coverage must have non-null coordinate system.");
throw new IllegalArgumentException("Non-null coordinate system required.");
}
this.name = this.coordSys.getName();
this.label = this.coordSys.getName();
this.range = new HashMap<String, WcsRangeField>();
StringBuilder descripSB =
new StringBuilder("All parameters on the \"")
.append(this.name)
.append("\" coordinate system: ");
for (GridDatatype curField : this.coverage.getGrids()) {
String stdName = curField.findAttValueIgnoreCase("standard_name", "");
descripSB.append(stdName.length() == 0 ? curField.getFullName() : stdName).append(",");
WcsRangeField field = new WcsRangeField(curField);
range.put(field.getName(), field);
}
descripSB.setCharAt(descripSB.length() - 1, '.');
this.description = descripSB.toString();
this.nativeCRS = EPSG_OGC_CF_Helper.getWcs1_0CrsId(this.coordSys.getProjection());
this.defaultRequestCrs = "OGC:CRS84";
this.supportedCoverageFormatList = new ArrayList<WcsRequest.Format>();
// this.supportedCoverageFormatList = "application/x-netcdf";
this.supportedCoverageFormatList.add(WcsRequest.Format.GeoTIFF);
this.supportedCoverageFormatList.add(WcsRequest.Format.GeoTIFF_Float);
this.supportedCoverageFormatList.add(WcsRequest.Format.NetCDF3);
}
GridDataset.Gridset getGridset() {
return coverage;
}
public String getName() {
return this.name;
}
public String getLabel() {
return this.label;
}
public String getDescription() {
return this.description;
}
public GridCoordSystem getCoordinateSystem() {
return coordSys;
}
public String getDefaultRequestCrs() {
return defaultRequestCrs;
}
public String getNativeCrs() {
return nativeCRS;
}
public List<WcsRequest.Format> getSupportedCoverageFormatList() {
return Collections.unmodifiableList(supportedCoverageFormatList);
}
public boolean isSupportedCoverageFormat(WcsRequest.Format covFormat) {
return this.supportedCoverageFormatList.contains(covFormat);
}
public boolean isRangeFieldName(String fieldName) {
return range.containsKey(fieldName);
}
public Set<String> getRangeFieldNames() {
return range.keySet();
}
public Collection<WcsRangeField> getRange() {
return range.values();
}
private static DiskCache2 diskCache = null;
public static void setDiskCache(DiskCache2 _diskCache) {
diskCache = _diskCache;
}
private static DiskCache2 getDiskCache() {
if (diskCache == null) {
log.error("getDiskCache(): Disk cache has not been set.");
throw new IllegalStateException(
"Disk cache must be set before calling GetCoverage.getDiskCache().");
}
return diskCache;
}
public File writeCoverageDataToFile(
WcsRequest.Format format,
LatLonRect bboxLatLonRect,
AxisSubset vertSubset,
List<String> rangeSubset,
CalendarDateRange timeRange)
throws WcsException {
boolean zRangeDone = false;
boolean tRangeDone = false;
try {
// Get the height range.
Range zRange = vertSubset != null ? vertSubset.getRange() : null;
zRangeDone = true;
// Get the time range.
Range tRange = null;
if (timeRange != null) {
CoordinateAxis1DTime timeAxis = this.coordSys.getTimeAxis1D();
int startIndex = timeAxis.findTimeIndexFromCalendarDate(timeRange.getStart());
int endIndex = timeAxis.findTimeIndexFromCalendarDate(timeRange.getEnd());
tRange = new Range(startIndex, endIndex);
tRangeDone = true;
}
if (format == WcsRequest.Format.GeoTIFF || format == WcsRequest.Format.GeoTIFF_Float) {
if (rangeSubset.size() != 1) {
String msg =
"GeoTIFF response encoding only available for single range field selection ["
+ rangeSubset
+ "].";
log.error("writeCoverageDataToFile(): " + msg);
throw new WcsException(WcsException.Code.InvalidParameterValue, "RangeSubset", msg);
}
String reqRangeFieldName = rangeSubset.get(0);
File dir = new File(getDiskCache().getRootDirectory());
File tifFile = File.createTempFile("WCS", ".tif", dir);
if (log.isDebugEnabled())
log.debug("writeCoverageDataToFile(): tifFile=" + tifFile.getPath());
WcsRangeField rangeField = this.range.get(reqRangeFieldName);
GridDatatype subset =
rangeField.getGridDatatype().makeSubset(tRange, zRange, bboxLatLonRect, 1, 1, 1);
Array data = subset.readDataSlice(0, 0, -1, -1);
GeotiffWriter writer = new GeotiffWriter(tifFile.getPath());
writer.writeGrid(
this.dataset.getDataset(), subset, data, format == WcsRequest.Format.GeoTIFF);
writer.close();
return tifFile;
} else if (format == WcsRequest.Format.NetCDF3) {
File dir = new File(getDiskCache().getRootDirectory());
File outFile = File.createTempFile("WCS", ".nc", dir);
if (log.isDebugEnabled())
log.debug("writeCoverageDataToFile(): ncFile=" + outFile.getPath());
// WTF ?? this.coordSys.getVerticalAxis().isNumeric();
NetcdfFileWriter writer =
NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFile.getAbsolutePath());
CFGridWriter2.writeFile(
this.dataset.getDataset(),
rangeSubset,
bboxLatLonRect,
null,
1,
zRange,
timeRange,
1,
true,
writer);
return outFile;
} else {
log.error(
"writeCoverageDataToFile(): Unsupported response encoding format [" + format + "].");
throw new WcsException(
WcsException.Code.InvalidFormat,
"Format",
"Unsupported response encoding format [" + format + "].");
}
} catch (InvalidRangeException e) {
String msg = "Failed to subset coverage [" + this.getName();
if (!zRangeDone) msg += "] along vertical axis [" + vertSubset + "]. ";
else if (!tRangeDone) msg += "] along time axis [" + timeRange + "]. ";
else msg += "] in horizontal plane [" + bboxLatLonRect + "]. ";
log.error("writeCoverageDataToFile(): " + msg + e.getMessage());
throw new WcsException(WcsException.Code.CoverageNotDefined, "", msg);
} catch (IOException e) {
log.error(
"writeCoverageDataToFile(): Failed to write file for requested coverage <"
+ this.getName()
+ ">: "
+ e.getMessage());
throw new WcsException(
WcsException.Code.UNKNOWN, "", "Problem creating coverage [" + this.getName() + "].");
}
}
}
/**
* A georeferencing "gridded" VariableEnhanced, that has a GridCoordSys. In VisAD data model, it is
* a sampled Field. The dimension are put into canonical order: (rt, e, t, z, y, x).
*
* <p>
*
* <p>Implementation note: If the Horizontal axes are 2D, the x and y dimensions are arbitrarily
* chosen to be gcs.getXHorizAxis().getDimension(1), gcs.getXHorizAxis().getDimension(0)
* respectively.
*
* <p>
*
* @author caron
*/
public class GeoGrid implements NamedObject, ucar.nc2.dt.GridDatatype {
private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(GeoGrid.class);
private static final boolean debugArrayShape = false;
private final GridDataset dataset;
private final GridCoordSys gcs;
private final VariableDS vs;
private int xDimOrgIndex = -1,
yDimOrgIndex = -1,
zDimOrgIndex = -1,
tDimOrgIndex = -1,
eDimOrgIndex = -1,
rtDimOrgIndex = -1;
private int xDimNewIndex = -1,
yDimNewIndex = -1,
zDimNewIndex = -1,
tDimNewIndex = -1,
eDimNewIndex = -1,
rtDimNewIndex = -1;
private final List<Dimension> mydims;
/**
* Constructor.
*
* @param dataset belongs to this dataset
* @param dsvar wraps this Variable
* @param gcs has this grid coordinate system
*/
public GeoGrid(GridDataset dataset, VariableDS dsvar, GridCoordSys gcs) {
this.dataset = dataset;
this.vs = dsvar;
this.gcs = gcs;
CoordinateAxis xaxis = gcs.getXHorizAxis();
if (xaxis instanceof CoordinateAxis1D) {
xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0));
yDimOrgIndex = findDimension(gcs.getYHorizAxis().getDimension(0));
} else { // 2D case
yDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0));
xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(1));
}
if (gcs.getVerticalAxis() != null)
zDimOrgIndex = findDimension(gcs.getVerticalAxis().getDimension(0));
if (gcs.getTimeAxis() != null) {
if (gcs.getTimeAxis1D() != null)
tDimOrgIndex = findDimension(gcs.getTimeAxis1D().getDimension(0));
else tDimOrgIndex = findDimension(gcs.getTimeAxis().getDimension(1));
}
if (gcs.getEnsembleAxis() != null)
eDimOrgIndex = findDimension(gcs.getEnsembleAxis().getDimension(0));
if (gcs.getRunTimeAxis() != null)
rtDimOrgIndex = findDimension(gcs.getRunTimeAxis().getDimension(0));
// construct canonical dimension list
int count = 0;
this.mydims = new ArrayList<Dimension>();
if ((rtDimOrgIndex >= 0) && (rtDimOrgIndex != tDimOrgIndex)) {
mydims.add(dsvar.getDimension(rtDimOrgIndex));
rtDimNewIndex = count++;
}
if (eDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(eDimOrgIndex));
eDimNewIndex = count++;
}
if (tDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(tDimOrgIndex));
tDimNewIndex = count++;
}
if (zDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(zDimOrgIndex));
zDimNewIndex = count++;
}
if (yDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(yDimOrgIndex));
yDimNewIndex = count++;
}
if (xDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(xDimOrgIndex));
xDimNewIndex = count;
}
}
private int findDimension(Dimension want) {
java.util.List dims = vs.getDimensions();
for (int i = 0; i < dims.size(); i++) {
Dimension d = (Dimension) dims.get(i);
if (d.equals(want)) return i;
}
return -1;
}
/**
* Returns an ArrayList containing the dimensions used by this geoGrid. The dimension are put into
* canonical order: (rt, e, t, z, y, x). Note that the z and t dimensions are optional. If the
* Horizontal axes are 2D, the x and y dimensions are arbitrarily chosen to be
* gcs.getXHorizAxis().getDimension(1), gcs.getXHorizAxis().getDimension(0), respectively.
*
* @return List with objects of type Dimension, in canonical order.
*/
public java.util.List<Dimension> getDimensions() {
return new ArrayList<Dimension>(mydims);
}
/**
* get the ith dimension
*
* @param i : which dimension
* @return ith Dimension
*/
public Dimension getDimension(int i) {
if ((i < 0) || (i >= mydims.size())) return null;
return mydims.get(i);
}
/** get the time Dimension, if it exists */
public Dimension getTimeDimension() {
return tDimNewIndex < 0 ? null : getDimension(tDimNewIndex);
}
/** get the z Dimension, if it exists */
public Dimension getZDimension() {
return zDimNewIndex < 0 ? null : getDimension(zDimNewIndex);
}
/** get the y Dimension, if it exists */
public Dimension getYDimension() {
return yDimNewIndex < 0 ? null : getDimension(yDimNewIndex);
}
/** get the x Dimension, if it exists */
public Dimension getXDimension() {
return xDimNewIndex < 0 ? null : getDimension(xDimNewIndex);
}
/** get the ensemble Dimension, if it exists */
public Dimension getEnsembleDimension() {
return eDimNewIndex < 0 ? null : getDimension(eDimNewIndex);
}
/** get the run time Dimension, if it exists */
public Dimension getRunTimeDimension() {
return rtDimNewIndex < 0 ? null : getDimension(rtDimNewIndex);
}
/** get the time Dimension index in the geogrid (canonical order), or -1 if none */
public int getTimeDimensionIndex() {
return tDimNewIndex;
}
/** get the z Dimension index in the geogrid (canonical order), or -1 if none */
public int getZDimensionIndex() {
return zDimNewIndex;
}
/** get the y Dimension index in the geogrid (canonical order) */
public int getYDimensionIndex() {
return yDimNewIndex;
}
/** get the x Dimension index in the geogrid (canonical order) */
public int getXDimensionIndex() {
return xDimNewIndex;
}
/** get the ensemble Dimension index in the geogrid (canonical order) */
public int getEnsembleDimensionIndex() {
return eDimNewIndex;
}
/** get the runtime Dimension index in the geogrid (canonical order) */
public int getRunTimeDimensionIndex() {
return rtDimNewIndex;
}
/**
* Convenience function; lookup Attribute by name.
*
* @param name the name of the attribute
* @return the attribute, or null if not found
*/
public Attribute findAttributeIgnoreCase(String name) {
return vs.findAttributeIgnoreCase(name);
}
/**
* Convenience function; lookup Attribute value by name. Must be String valued
*
* @param attName name of the attribute
* @param defaultValue if not found, use this as the default
* @return Attribute string value, or default if not found.
*/
public String findAttValueIgnoreCase(String attName, String defaultValue) {
return dataset.getNetcdfDataset().findAttValueIgnoreCase((Variable) vs, attName, defaultValue);
}
// implementation of GridDatatype interface
/** get the rank */
public int getRank() {
return mydims.size();
}
/** get the shape */
public int[] getShape() {
int[] shape = new int[mydims.size()];
for (int i = 0; i < mydims.size(); i++) {
Dimension d = mydims.get(i);
shape[i] = d.getLength();
}
return shape;
}
/** get the data type */
public DataType getDataType() {
return vs.getDataType();
}
public List<Attribute> getAttributes() {
return vs.getAttributes();
}
public VariableDS getVariable() {
return vs;
}
public String getFullName() {
return vs.getFullName();
}
public String getName() {
return vs.getFullName();
}
public String getShortName() {
return vs.getShortName();
}
/** get the GridCoordSys for this GeoGrid. */
public GridCoordSystem getCoordinateSystem() {
return gcs;
}
/** get the Projection. */
public ProjectionImpl getProjection() {
return gcs.getProjection();
}
/** @return ArrayList of thredds.util.NamedObject, from the GridCoordSys. */
public List<NamedObject> getLevels() {
return gcs.getLevels();
}
/** @return ArrayList of thredds.util.NamedObject, from the GridCoordSys. */
public List<NamedObject> getTimes() {
return gcs.getTimes();
}
/** get the standardized description */
public String getDescription() {
return vs.getDescription();
}
/** get the unit as a string */
public String getUnitsString() {
String units = vs.getUnitsString();
return (units == null) ? "" : units;
}
/**
* @return getUnitsString()
* @deprecated use getUnitsString()
*/
public java.lang.String getUnitString() {
return getUnitsString();
}
// public ucar.unidata.geoloc.ProjectionImpl getProjection() { return gcs.getProjection(); }
/** true if there may be missing data, see VariableDS.hasMissing() */
public boolean hasMissingData() {
return vs.hasMissing();
}
/** if val is missing data, see VariableDS.isMissingData() */
public boolean isMissingData(double val) {
return vs.isMissing(val);
}
/**
* Convert (in place) all values in the given array that are considered as "missing" to Float.NaN,
* according to isMissingData(val).
*
* @param values input array
* @return input array, with missing values converted to NaNs.
*/
public float[] setMissingToNaN(float[] values) {
if (!vs.hasMissing()) return values;
final int length = values.length;
for (int i = 0; i < length; i++) {
double value = values[i];
if (vs.isMissing(value)) values[i] = Float.NaN;
}
return values;
}
/**
* Get the minimum and the maximum data value of the previously read Array, skipping missing
* values as defined by isMissingData(double val).
*
* @param a Array to get min/max values
* @return both min and max value.
*/
public MAMath.MinMax getMinMaxSkipMissingData(Array a) {
if (!hasMissingData()) return MAMath.getMinMax(a);
IndexIterator iter = a.getIndexIterator();
double max = -Double.MAX_VALUE;
double min = Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if (isMissingData(val)) continue;
if (val > max) max = val;
if (val < min) min = val;
}
return new MAMath.MinMax(min, max);
}
/**
* Reads in the data "volume" at the given time index. If its a product set, put into canonical
* order (z-y-x). If not a product set, reorder to (z,i,j), where i, j are from the original
*
* @param t time index; ignored if no time axis.
* @return data[z,y,x] or data[y,x] if no z axis.
*/
public Array readVolumeData(int t) throws java.io.IOException {
// if (gcs.isProductSet())
return readDataSlice(t, -1, -1, -1);
/* else { // 2D XY
int rank = vs.getRank();
int[] shape = vs.getShape();
int [] start = new int[rank];
CoordinateAxis taxis = gcs.getTimeAxis();
if (taxis != null) {
if ((t >= 0) && (t < taxis.getSize()))
shape[ tDim] = 1; // fix t
start[ tDim] = t;
}
if (debugArrayShape) {
System.out.println("getDataVolume shape = ");
for (int i=0; i<rank; i++)
System.out.println(" start = "+start[i]+" shape = "+ shape[i]);
}
Array dataVolume;
try {
dataVolume = vs.read( start, shape);
} catch (Exception e) {
System.out.println("Exception: GeoGridImpl.getdataSlice() on dataset "+getName());
e.printStackTrace();
throw new java.io.IOException(e.getMessage());
}
// no reordering FIX
return dataVolume.reduce();
} */
}
/**
* Reads a Y-X "horizontal slice" at the given time and vertical index. If its a product set, put
* into canonical order (y-x).
*
* @param t time index; ignored if no time axis.
* @param z vertical index; ignored if no z axis.
* @return data[y,x]
* @throws java.io.IOException on read error
*/
public Array readYXData(int t, int z) throws java.io.IOException {
return readDataSlice(t, z, -1, -1);
}
/**
* Reads a Z-Y "vertical slice" at the given time and x index. If its a product set, put into
* canonical order (z-y).
*
* @param t time index; ignored if no time axis.
* @param x x index; ignored if no x axis.
* @return data[z,y]
* @throws java.io.IOException on read error
*/
public Array readZYData(int t, int x) throws java.io.IOException {
return readDataSlice(t, -1, -1, x);
}
/**
* @throws java.io.IOException on read error
* @deprecated use readDataSlice
*/
public Array getDataSlice(int t, int z, int y, int x) throws java.io.IOException {
return readDataSlice(t, z, y, x);
}
/**
* This reads an arbitrary data slice, returning the data in canonical order (t-z-y-x). If any
* dimension does not exist, ignore it.
*
* @param t if < 0, get all of time dim; if valid index, fix slice to that value.
* @param z if < 0, get all of z dim; if valid index, fix slice to that value.
* @param y if < 0, get all of y dim; if valid index, fix slice to that value.
* @param x if < 0, get all of x dim; if valid index, fix slice to that value.
* @return data[t,z,y,x], eliminating missing or fixed dimension.
*/
public Array readDataSlice(int t, int z, int y, int x) throws java.io.IOException {
return readDataSlice(0, 0, t, z, y, x);
}
/**
* This reads an arbitrary data slice, returning the data in canonical order (rt-e-t-z-y-x). If
* any dimension does not exist, ignore it.
*
* @param rt if < 0, get all of runtime dim; if valid index, fix slice to that value.
* @param e if < 0, get all of ensemble dim; if valid index, fix slice to that value.
* @param t if < 0, get all of time dim; if valid index, fix slice to that value.
* @param z if < 0, get all of z dim; if valid index, fix slice to that value.
* @param y if < 0, get all of y dim; if valid index, fix slice to that value.
* @param x if < 0, get all of x dim; if valid index, fix slice to that value.
* @return data[rt,e,t,z,y,x], eliminating missing or fixed dimension.
*/
public Array readDataSlice(int rt, int e, int t, int z, int y, int x) throws java.io.IOException {
int rank = vs.getRank();
int[] start = new int[rank];
int[] shape = new int[rank];
for (int i = 0; i < rank; i++) {
start[i] = 0;
shape[i] = 1;
}
Dimension xdim = getXDimension();
Dimension ydim = getYDimension();
Dimension zdim = getZDimension();
Dimension tdim = getTimeDimension();
Dimension edim = getEnsembleDimension();
Dimension rtdim = getRunTimeDimension();
// construct the shape of the data volume to be read
if (rtdim != null) {
if ((rt >= 0) && (rt < rtdim.getLength())) start[rtDimOrgIndex] = rt; // fix rt
else {
shape[rtDimOrgIndex] = rtdim.getLength(); // all of rt
}
}
if (edim != null) {
if ((e >= 0) && (e < edim.getLength())) start[eDimOrgIndex] = e; // fix e
else {
shape[eDimOrgIndex] = edim.getLength(); // all of e
}
}
if (tdim != null) {
if ((t >= 0) && (t < tdim.getLength())) start[tDimOrgIndex] = t; // fix t
else {
shape[tDimOrgIndex] = tdim.getLength(); // all of t
}
}
if (zdim != null) {
if ((z >= 0) && (z < zdim.getLength())) start[zDimOrgIndex] = z; // fix z
else {
shape[zDimOrgIndex] = zdim.getLength(); // all of z
}
}
if (ydim != null) {
if ((y >= 0) && (y < ydim.getLength())) start[yDimOrgIndex] = y; // fix y
else {
shape[yDimOrgIndex] = ydim.getLength(); // all of y
}
}
if (xdim != null) {
if ((x >= 0) && (x < xdim.getLength())) // all of x
start[xDimOrgIndex] = x; // fix x
else {
shape[xDimOrgIndex] = xdim.getLength(); // all of x
}
}
if (debugArrayShape) {
System.out.println("read shape from org variable = ");
for (int i = 0; i < rank; i++)
System.out.println(
" start = "
+ start[i]
+ " shape = "
+ shape[i]
+ " name = "
+ vs.getDimension(i).getName());
}
// read it
Array dataVolume;
try {
dataVolume = vs.read(start, shape);
} catch (Exception ex) {
log.error(
"GeoGrid.getdataSlice() on dataset " + getFullName() + " " + dataset.getLocation(), ex);
throw new java.io.IOException(ex.getMessage());
}
// LOOK: the real problem is the lack of named dimensions in the Array object
// figure out correct permutation for canonical ordering for permute
List<Dimension> oldDims = new ArrayList<Dimension>(vs.getDimensions());
int[] permuteIndex = new int[dataVolume.getRank()];
int count = 0;
if (oldDims.contains(rtdim)) permuteIndex[count++] = oldDims.indexOf(rtdim);
if (oldDims.contains(edim)) permuteIndex[count++] = oldDims.indexOf(edim);
if (oldDims.contains(tdim)) permuteIndex[count++] = oldDims.indexOf(tdim);
if (oldDims.contains(zdim)) permuteIndex[count++] = oldDims.indexOf(zdim);
if (oldDims.contains(ydim)) permuteIndex[count++] = oldDims.indexOf(ydim);
if (oldDims.contains(xdim)) permuteIndex[count] = oldDims.indexOf(xdim);
if (debugArrayShape) {
System.out.println("oldDims = ");
for (Dimension oldDim : oldDims) System.out.println(" oldDim = " + oldDim.getName());
System.out.println("permute dims = ");
for (int aPermuteIndex : permuteIndex)
System.out.println(" oldDim index = " + aPermuteIndex);
}
// check to see if we need to permute
boolean needPermute = false;
for (int i = 0; i < permuteIndex.length; i++) {
if (i != permuteIndex[i]) needPermute = true;
}
// permute to the order rt,e,t,z,y,x
if (needPermute) dataVolume = dataVolume.permute(permuteIndex);
// eliminate fixed dimensions, but not all dimensions of length 1.
count = 0;
if (rtdim != null) {
if (rt >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (edim != null) {
if (e >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (tdim != null) {
if (t >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (zdim != null) {
if (z >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (ydim != null) {
if (y >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (xdim != null) {
if (x >= 0) dataVolume = dataVolume.reduce(count);
}
return dataVolume;
}
//////////////////////////////////
/**
* Create a new GeoGrid that is a logical subset of this GeoGrid.
*
* @param t_range subset the time dimension, or null if you want all of it
* @param z_range subset the vertical dimension, or null if you want all of it
* @param bbox a lat/lon bounding box, or null if you want all x,y
* @param z_stride use only if z_range is null, then take all z with this stride (1 means all)
* @param y_stride use this stride on the y coordinate (1 means all)
* @param x_stride use this stride on the x coordinate (1 means all)
* @return subsetted GeoGrid
* @throws InvalidRangeException if bbox does not intersect GeoGrid
*/
public GeoGrid subset(
Range t_range, Range z_range, LatLonRect bbox, int z_stride, int y_stride, int x_stride)
throws InvalidRangeException {
if ((z_range == null) && (z_stride > 1)) {
Dimension zdim = getZDimension();
if (zdim != null) z_range = new Range(0, zdim.getLength() - 1, z_stride);
}
Range y_range = null, x_range = null;
if (bbox != null) {
List yx_ranges = gcs.getRangesFromLatLonRect(bbox);
y_range = (Range) yx_ranges.get(0);
x_range = (Range) yx_ranges.get(1);
}
if (y_stride > 1) {
if (y_range == null) {
Dimension ydim = getYDimension();
y_range = new Range(0, ydim.getLength() - 1, y_stride);
} else {
y_range = new Range(y_range.first(), y_range.last(), y_stride);
}
}
if (x_stride > 1) {
if (x_range == null) {
Dimension xdim = getXDimension();
x_range = new Range(0, xdim.getLength() - 1, x_stride);
} else {
x_range = new Range(x_range.first(), x_range.last(), x_stride);
}
}
return subset(t_range, z_range, y_range, x_range);
}
public GridDatatype makeSubset(
Range t_range, Range z_range, LatLonRect bbox, int z_stride, int y_stride, int x_stride)
throws InvalidRangeException {
return subset(t_range, z_range, bbox, z_stride, y_stride, x_stride);
}
/**
* Create a new GeoGrid that is a logical subset of this GeoGrid.
*
* @param t_range subset the time dimension, or null if you want all of it
* @param z_range subset the vertical dimension, or null if you want all of it
* @param y_range subset the y dimension, or null if you want all of it
* @param x_range subset the x dimension, or null if you want all of it
* @return subsetted GeoGrid
* @throws InvalidRangeException if any of the ranges are invalid
*/
public GeoGrid subset(Range t_range, Range z_range, Range y_range, Range x_range)
throws InvalidRangeException {
return (GeoGrid) makeSubset(null, null, t_range, z_range, y_range, x_range);
}
public GridDatatype makeSubset(
Range rt_range, Range e_range, Range t_range, Range z_range, Range y_range, Range x_range)
throws InvalidRangeException {
// get the ranges list
int rank = getRank();
Range[] ranges = new Range[rank];
if (null != getXDimension()) ranges[xDimOrgIndex] = x_range;
if (null != getYDimension()) ranges[yDimOrgIndex] = y_range;
if (null != getZDimension()) ranges[zDimOrgIndex] = z_range;
if (null != getTimeDimension()) ranges[tDimOrgIndex] = t_range;
if (null != getRunTimeDimension()) ranges[rtDimOrgIndex] = rt_range;
if (null != getEnsembleDimension()) ranges[eDimOrgIndex] = e_range;
List<Range> rangesList = Arrays.asList(ranges);
// subset the variable
VariableDS v_section = (VariableDS) vs.section(new Section(rangesList));
List<Dimension> dims = v_section.getDimensions();
for (Dimension dim : dims) {
dim.setShared(true); // make them shared (section will make them unshared)
}
// subset the axes in the GridCoordSys
GridCoordSys gcs_section =
new GridCoordSys(gcs, rt_range, e_range, t_range, z_range, y_range, x_range);
// now we can make the geogrid
return new GeoGrid(dataset, v_section, gcs_section);
}
/////////////////////////////////////////////////////////////////////////////////
/** Instances which have same name and coordinate system are equal. */
public boolean equals(Object oo) {
if (this == oo) return true;
if (!(oo instanceof GeoGrid)) return false;
GeoGrid d = (GeoGrid) oo;
if (!getFullName().equals(d.getFullName())) return false;
if (!getCoordinateSystem().equals(d.getCoordinateSystem())) return false;
return true;
}
/** Override Object.hashCode() to be consistent with equals. */
public int hashCode() {
if (hashCode == 0) {
int result = 17;
// result = 37*result + dataset.getName().hashCode();
result = 37 * result + getFullName().hashCode();
result = 37 * result + getCoordinateSystem().hashCode();
hashCode = result;
}
return hashCode;
}
private int hashCode = 0; // Bloch, item 8
/** string representation */
public String toString() {
return getFullName();
}
/** nicely formatted information */
public String getInfo() {
StringBuilder buf = new StringBuilder(200);
buf.setLength(0);
buf.append(getFullName());
Format.tab(buf, 30, true);
buf.append(getUnitsString());
Format.tab(buf, 60, true);
buf.append(hasMissingData());
Format.tab(buf, 66, true);
buf.append(getDescription());
return buf.toString();
}
public int compareTo(GridDatatype g) {
return getFullName().compareTo(g.getFullName());
}
}
