public Float10TrajectoryObsDataset(NetcdfDataset ncd) throws IOException {
super(ncd);
// Get the names of the two coordinate variables and dimensions
// and grab the variables and dimensions themselves.
trajDimName = trajDimNameDefault;
trajVarName = trajVarNameDefault;
timeDimName = timeDimNameDefault;
timeVarName = timeVarNameDefault;
latVarName = latVarNameDefault;
lonVarName = lonVarNameDefault;
elevVarName = elevVarNameDefault;
Variable latVar = ncd.getRootGroup().findVariable(latVarName);
latVar.addAttribute(new Attribute("units", "degrees_north"));
Variable lonVar = ncd.getRootGroup().findVariable(lonVarName);
lonVar.addAttribute(new Attribute("units", "degrees_east"));
this.setTrajectoryInfo(
netcdfDataset.getRootGroup().findDimension(trajDimName),
netcdfDataset.getRootGroup().findVariable(trajVarName),
netcdfDataset.getRootGroup().findDimension(timeDimName),
netcdfDataset.getRootGroup().findVariable(timeVarName),
netcdfDataset.getRootGroup().findVariable(latVarName),
netcdfDataset.getRootGroup().findVariable(lonVarName),
netcdfDataset.getRootGroup().findVariable(elevVarName));
}
public Array getData(Range range, String parameterName)
throws IOException, InvalidRangeException {
Variable variable = ncfile.getRootGroup().findVariable(parameterName);
int varRank = variable.getRank();
int[] varShape = variable.getShape();
List section = new ArrayList(varRank);
section.add(range);
for (int i = 1; i < varRank; i++) {
section.add(new Range(0, varShape[i] - 1));
}
Array array = variable.read(section);
if (array.getShape()[0] == 1) {
return (array.reduce(0));
} else {
return (array);
}
// return( array.getShape()[0] == 1 ? array.reduce( 0 ) : array);
}
// @todo Make sure units are meters
public Array getElevation(Range range) throws IOException, InvalidRangeException {
List section = new ArrayList(1);
section.add(range);
Array a = elevVar.read(section);
if (elevVarUnitsConversionFactor == 1.0) return (a);
for (IndexIterator it = a.getIndexIterator(); it.hasNext(); ) {
if (elevVar.getDataType() == DataType.DOUBLE) {
double val = it.getDoubleNext();
it.setDoubleCurrent(val * elevVarUnitsConversionFactor);
} else if (elevVar.getDataType() == DataType.FLOAT) {
float val = it.getFloatNext();
it.setFloatCurrent((float) (val * elevVarUnitsConversionFactor));
} else if (elevVar.getDataType() == DataType.INT) {
int val = it.getIntNext();
it.setIntCurrent((int) (val * elevVarUnitsConversionFactor));
} else if (elevVar.getDataType() == DataType.LONG) {
long val = it.getLongNext();
it.setLongCurrent((long) (val * elevVarUnitsConversionFactor));
} else {
throw new IllegalStateException(
"Elevation variable type <"
+ elevVar.getDataType().toString()
+ "> not double, float, int, or long.");
}
}
return (a);
}
public static void main(String args[]) throws Exception {
long start = System.currentTimeMillis();
Map<String, ucar.unidata.geoloc.Station> staHash =
new HashMap<String, ucar.unidata.geoloc.Station>();
String location = "R:/testdata/sounding/netcdf/Upperair_20070401_0000.nc";
NetcdfDataset ncfile = NetcdfDataset.openDataset(location);
ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
// look through record varibles, for those that have "manLevel" dimension
// make a StructureData object for those
StructureMembers sm = new StructureMembers("manLevel");
Dimension manDim = ncfile.findDimension("manLevel");
Structure record = (Structure) ncfile.findVariable("record");
List<Variable> allList = record.getVariables();
List<VariableSimpleIF> varList = new ArrayList<VariableSimpleIF>();
for (Variable v : allList) {
if ((v.getRank() == 1) && v.getDimension(0).equals(manDim)) {
// public VariableDS(NetcdfDataset ds, Group group, Structure parentStructure, String
// shortName, DataType dataType,
// String dims, String units, String desc) {
varList.add(
new VariableDS(
ncfile,
null,
null,
v.getShortName(),
v.getDataType(),
"",
v.getUnitsString(),
v.getDescription()));
// (String name, String desc, String units, DataType dtype, int []shape)
sm.addMember(
v.getShortName(),
v.getDescription(),
v.getUnitsString(),
v.getDataType(),
new int[0]); // scalar
}
}
ArrayStructureMA manAS = new ArrayStructureMA(sm, new int[] {manDim.getLength()});
// need the date units
Variable time = ncfile.findVariable("synTime");
String timeUnits = ncfile.findAttValueIgnoreCase(time, "units", null);
timeUnits = StringUtil.remove(timeUnits, '('); // crappy fsl'ism
timeUnits = StringUtil.remove(timeUnits, ')');
DateUnit timeUnit = new DateUnit(timeUnits);
// extract stations
int nrecs = 0;
StructureDataIterator iter = record.getStructureIterator();
while (iter.hasNext()) {
StructureData sdata = iter.next();
String name = sdata.getScalarString("staName");
ucar.unidata.geoloc.Station s = staHash.get(name);
if (s == null) {
float lat = sdata.convertScalarFloat("staLat");
float lon = sdata.convertScalarFloat("staLon");
float elev = sdata.convertScalarFloat("staElev");
s = new StationImpl(name, "", lat, lon, elev);
staHash.put(name, s);
}
nrecs++;
}
List<ucar.unidata.geoloc.Station> stnList =
Arrays.asList(staHash.values().toArray(new ucar.unidata.geoloc.Station[staHash.size()]));
Collections.sort(stnList);
// create the writer
WriterProfileObsDataset writer =
new WriterProfileObsDataset(location + ".out", "rewrite " + location);
writer.writeHeader(stnList, varList, nrecs, "prMan");
// extract records
iter = record.getStructureIterator();
while (iter.hasNext()) {
StructureData sdata = iter.next();
String name = sdata.getScalarString("staName");
double timeValue = sdata.convertScalarDouble("synTime");
Date date = timeUnit.makeDate(timeValue);
// transfer to the ArrayStructure
List<String> names = sm.getMemberNames();
for (String mname : names) {
manAS.setMemberArray(mname, sdata.getArray(mname));
}
// each level is weritten as a seperate structure
int numMand = sdata.getScalarInt("numMand");
if (numMand >= manDim.getLength()) continue;
for (int i = 0; i < numMand; i++) {
StructureData useData = manAS.getStructureData(i);
writer.writeRecord(name, date, useData);
}
}
writer.finish();
long took = System.currentTimeMillis() - start;
System.out.println("That took = " + took);
}
// @todo Make sure units are degrees_east
public Array getLongitude(Range range) throws IOException, InvalidRangeException {
List section = new ArrayList(1);
section.add(range);
return (lonVar.read(section));
}
/**
* Setup needed for all SingleTrajectoryObsDatatypes. Can only be called once.
*
* <p>Units of time varible must be udunits time units. Units of latitude variable must be
* convertible to "degrees_north" by udunits. Units of longitude variable must be convertible to
* "degrees_east" by udunits. Units of altitude variable must be convertible to "meters" by
* udunits.
*
* @throws IllegalArgumentException if units of time, latitude, longitude, or altitude variables
* are not as required.
* @throws IllegalStateException if this method has already been called.
*/
public void setTrajectoryInfo(Config trajConfig) throws IOException {
if (timeDim != null)
throw new IllegalStateException("The setTrajectoryInfo() method can only be called once.");
this.trajectoryId = trajConfig.getTrajectoryId();
this.timeDim = trajConfig.getTimeDim();
this.timeVar = trajConfig.getTimeVar();
this.latVar = trajConfig.getLatVar();
this.lonVar = trajConfig.getLonVar();
this.elevVar = trajConfig.getElevVar();
trajectoryNumPoint = this.timeDim.getLength();
timeVarUnitsString = this.timeVar.findAttribute("units").getStringValue();
// Check that time, lat, lon, elev units are acceptable.
if (DateUnit.getStandardDate(timeVarUnitsString) == null) {
throw new IllegalArgumentException(
"Units of time variable <" + timeVarUnitsString + "> not a date unit.");
}
String latVarUnitsString = this.latVar.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(latVarUnitsString, "degrees_north")) {
throw new IllegalArgumentException(
"Units of lat var <" + latVarUnitsString + "> not compatible with \"degrees_north\".");
}
String lonVarUnitsString = this.lonVar.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(lonVarUnitsString, "degrees_east")) {
throw new IllegalArgumentException(
"Units of lon var <" + lonVarUnitsString + "> not compatible with \"degrees_east\".");
}
String elevVarUnitsString = this.elevVar.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(elevVarUnitsString, "meters")) {
throw new IllegalArgumentException(
"Units of elev var <" + elevVarUnitsString + "> not compatible with \"meters\".");
}
try {
elevVarUnitsConversionFactor = getMetersConversionFactor(elevVarUnitsString);
} catch (Exception e) {
throw new IllegalArgumentException(
"Exception on getMetersConversionFactor() for the units of elev var <"
+ elevVarUnitsString
+ ">.");
}
if (this.ncfile.hasUnlimitedDimension()
&& this.ncfile.getUnlimitedDimension().equals(timeDim)) {
Object result = this.ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
if ((result != null) && (Boolean) result)
this.recordVar = (Structure) this.ncfile.getRootGroup().findVariable("record");
else this.recordVar = new StructurePseudo(this.ncfile, null, "record", timeDim);
} else {
this.recordVar = new StructurePseudo(this.ncfile, null, "record", timeDim);
}
// @todo HACK, HACK, HACK - remove once addRecordStructure() deals with ncd attribute changes.
Variable elevVarInRecVar = this.recordVar.findVariable(this.elevVar.getFullNameEscaped());
if (!elevVarUnitsString.equals(elevVarInRecVar.findAttribute("units").getStringValue())) {
elevVarInRecVar.addAttribute(new Attribute("units", elevVarUnitsString));
}
trajectoryVarsMap = new HashMap();
// for ( Iterator it = this.recordVar.getVariables().iterator(); it.hasNext(); )
for (Iterator it = this.ncfile.getRootGroup().getVariables().iterator(); it.hasNext(); ) {
Variable curVar = (Variable) it.next();
if (curVar.getRank() > 0
&& !curVar.equals(this.timeVar)
&& !curVar.equals(this.latVar)
&& !curVar.equals(this.lonVar)
&& !curVar.equals(this.elevVar)
&& (this.recordVar == null ? true : !curVar.equals(this.recordVar))) {
MyTypedDataVariable typedVar = new MyTypedDataVariable(new VariableDS(null, curVar, true));
dataVariables.add(typedVar);
trajectoryVarsMap.put(typedVar.getShortName(), typedVar);
}
}
trajectory =
new SingleTrajectory(
this.trajectoryId,
trajectoryNumPoint,
this.timeVar,
timeVarUnitsString,
this.latVar,
this.lonVar,
this.elevVar,
dataVariables,
trajectoryVarsMap);
startDate = trajectory.getTime(0);
endDate = trajectory.getTime(trajectoryNumPoint - 1);
((SingleTrajectory) trajectory).setStartDate(startDate);
((SingleTrajectory) trajectory).setEndDate(endDate);
}
public static boolean isValidFile(NetcdfDataset ds) {
// Check that has a time dimension and a trajectory dimension.
List list = ds.getRootGroup().getDimensions();
if (list.size() != 2) return (false);
Dimension d;
for (int i = 0; i < 2; i++) {
d = (Dimension) list.get(i);
if (!d.getShortName().equals(timeDimNameDefault)
&& !d.getShortName().equals(trajDimNameDefault)) return (false);
}
// Check that has a trajectory coordinate variable.
Variable var = ds.getRootGroup().findVariable(trajVarNameDefault);
if (var == null) return (false);
list = var.getDimensions();
if (list.size() != 1) return (false);
d = (Dimension) list.get(0);
if (!d.getShortName().equals(trajDimNameDefault)) return (false);
// Check that has a time coordinate variable with units that are udunits time
var = ds.getRootGroup().findVariable(timeVarNameDefault);
if (var == null) return (false);
list = var.getDimensions();
if (list.size() != 1) return (false);
d = (Dimension) list.get(0);
if (!d.getShortName().equals(timeDimNameDefault)) return (false);
String units = var.findAttribute("units").getStringValue();
Date date = DateUnit.getStandardDate("0 " + units);
if (date == null) return (false);
// Check for variable latitude(time) with units of "deg".
var = ds.getRootGroup().findVariable(latVarNameDefault);
if (var == null) return (false);
list = var.getDimensions();
if (list.size() != 2) return (false);
for (int i = 0; i < 2; i++) {
d = (Dimension) list.get(i);
if (!d.getShortName().equals(timeDimNameDefault)
&& !d.getShortName().equals(trajDimNameDefault)) return (false);
}
// units = var.findAttribute( "units").getStringValue();
// if ( ! SimpleUnit.isCompatible( units, "degrees_north")) return( false);
// Check for variable longitude(time) with units of "deg".
var = ds.getRootGroup().findVariable(lonVarNameDefault);
if (var == null) return (false);
list = var.getDimensions();
if (list.size() != 2) return (false);
for (int i = 0; i < 2; i++) {
d = (Dimension) list.get(i);
if (!d.getShortName().equals(timeDimNameDefault)
&& !d.getShortName().equals(trajDimNameDefault)) return (false);
}
// units = var.findAttribute( "units").getStringValue();
// if ( ! SimpleUnit.isCompatible( units, "degrees_east")) return( false);
// Check for variable altitude(time) with units of "m".
var = ds.getRootGroup().findVariable(elevVarNameDefault);
if (var == null) return (false);
list = var.getDimensions();
if (list.size() != 2) return (false);
for (int i = 0; i < 2; i++) {
d = (Dimension) list.get(i);
if (!d.getShortName().equals(timeDimNameDefault)
&& !d.getShortName().equals(trajDimNameDefault)) return (false);
}
units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "m")) return (false);
return (true);
}
