/**
* Set the sounding in the table
*
* @param sounding the sounding
* @throws RemoteException Java RMI problem
* @throws VisADException problem dissecting data
*/
private void setSounding(Field sounding) throws VisADException, RemoteException {
domainData = null;
// domain values
Set domain = sounding.getDomainSet();
CoordinateSystem cs = domain.getCoordinateSystem();
float[][] domSamples = domain.getSamples(false);
if ((cs != null)) {
float[][] domFloats = Set.copyFloats(domSamples);
// Must convert from the default coordinate domain system to
// the domain coordinate system of the sounding.
String fromUnit = sounding.getDomainUnits()[0].toString();
String toUnit = cs.getCoordinateSystemUnits()[0].toString();
if (!fromUnit.equals(toUnit) && SimpleUnit.isCompatible(fromUnit, toUnit)) {
float conversionFactor = (float) SimpleUnit.getConversionFactor(fromUnit, toUnit);
for (int i = 0; i < domFloats.length; i++) {
for (int j = 0; j < domFloats[i].length; j++) {
domFloats[i][j] = domFloats[i][j] * conversionFactor;
}
}
}
float[][] refData = cs.toReference(domFloats);
domainData = new float[][] {domSamples[0], refData[0]};
}
// range values
RealType[] rangeComps = ((FunctionType) sounding.getType()).getRealComponents();
rangeData = sounding.getFloats(false);
// wind
if (rangeComps.length > 2) {
transformWinds = (showUAndV && !haveUV) || (!showUAndV && haveUV);
if (!transformWinds) {
for (int i = 2; i < 4; i++) {
columnNames[numDomainCols + i] =
makeColumnName(rangeComps[i], rangeComps[i].getDefaultUnit());
}
} else {
RealTupleType refType = windTransform.getReference();
Unit[] refUnits = windTransform.getReferenceUnits();
for (int i = 0; i < 2; i++) {
columnNames[numDomainCols + i + 2] =
makeColumnName((RealType) refType.getComponent(i), refUnits[i]);
}
float[][] newVals =
windTransform.toReference(Set.copyFloats(new float[][] {rangeData[2], rangeData[3]}));
rangeData[2] = newVals[0];
rangeData[3] = newVals[1];
}
}
sorter.setTableModel(model);
}
/**
* Build the configuration from the dataset
*
* @param ncd NetcdfDataset
* @return the trajectory configuration
*/
private static Config buildConfig(NetcdfDataset ncd) {
// already did this in isValid, but we'll keep here for later refactor
Attribute attrib = ncd.findGlobalAttributeIgnoreCase("center");
if (attrib == null) {
return null;
}
if (!attrib.isString()) {
return null;
}
if (!attrib.getStringValue().equals("UCAR/CDAAC")) {
return null;
}
// Check for start_time, stop_time
attrib = ncd.findGlobalAttributeIgnoreCase("start_time");
if (attrib == null) {
return null;
}
if (attrib.isString()) {
return null;
}
double startTime = attrib.getNumericValue().doubleValue();
attrib = ncd.findGlobalAttributeIgnoreCase("stop_time");
if (attrib == null) {
return null;
}
if (attrib.isString()) {
return null;
}
double endTime = attrib.getNumericValue().doubleValue();
// Check that only one dimension and that it is the alt dimension.
List list = ncd.getRootGroup().getDimensions();
if (list.size() != 1) {
return null;
}
Dimension d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
Config trajConfig = new Config();
trajConfig.setTimeDim(d);
// Check for latitude variable with time dimension and units convertable to "degrees_north".
Variable var = ncd.getRootGroup().findVariable(latVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
String units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "degrees_north")) {
return null;
}
trajConfig.setLatVar(var);
// Make the time Variable
int numTimes = d.getLength();
double[] times = new double[numTimes];
// Variable timeVar = new Variable(var);
// timeVar.setName(timeVarName);
VariableDS timeVar =
new VariableDS(
ncd,
ncd.getRootGroup(),
null,
timeVarName,
DataType.DOUBLE,
timeDimName,
"seconds since 1980-01-06 00:00:00",
"Time coordinate");
// Variable timeVar = new Variable(ncd, ncd.getRootGroup(), null,
// timeVarName);
// timeVar.setDataType(DataType.DOUBLE);
// timeVar.setDimensions(list);
// Attribute newUnits =
// new Attribute("units", "seconds since 1980-01-06 00:00:00");
// timeVar.addAttribute(newUnits);
timeVar.setCachedData(
Array.makeArray(DataType.DOUBLE, numTimes, endTime, ((startTime - endTime) / numTimes)),
true);
ncd.addVariable(ncd.getRootGroup(), timeVar);
trajConfig.setTimeVar(timeVar);
// Check for longitude variable with time dimension and units convertable to "degrees_east".
var = ncd.getRootGroup().findVariable(lonVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "degrees_east")) {
return null;
}
trajConfig.setLonVar(var);
// Check for altitude variable with time dimension and units convertable to "m".
var = ncd.getRootGroup().findVariable(elevVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "meters")) {
return null;
}
trajConfig.setElevVar(var);
trajConfig.setTrajectoryId(trajId);
return trajConfig;
}
protected static double getMetersConversionFactor(String unitsString) throws Exception {
SimpleUnit unit = SimpleUnit.factoryWithExceptions(unitsString);
return unit.convertTo(1.0, SimpleUnit.meterUnit);
}
/**
* 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);
}
/** create a NetcdfDataset out of this NetcdfFile, adding coordinates etc. */
public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
// latitude
if (!hasAxisType(ds, AxisType.Lat)) { // already has _CoordinateAxisType
if (!addAxisType(ds, "latitude", AxisType.Lat)) { // directly named
String vname = ds.findAttValueIgnoreCase(null, "latitude_coordinate", null);
if (!addAxisType(ds, vname, AxisType.Lat)) { // attribute named
Variable v =
hasUnits(ds, "degrees_north,degrees_N,degreesN,degree_north,degree_N,degreeN");
if (v != null) addAxisType(v, AxisType.Lat); // CF-1
}
}
}
// longitude
if (!hasAxisType(ds, AxisType.Lon)) { // already has _CoordinateAxisType
if (!addAxisType(ds, "longitude", AxisType.Lon)) { // directly named
String vname = ds.findAttValueIgnoreCase(null, "longitude_coordinate", null);
if (!addAxisType(ds, vname, AxisType.Lon)) { // attribute named
Variable v = hasUnits(ds, "degrees_east,degrees_E,degreesE,degree_east,degree_E,degreeE");
if (v != null) addAxisType(v, AxisType.Lon); // CF-1
}
}
}
// altitude
if (!hasAxisType(ds, AxisType.Height)) { // already has _CoordinateAxisType
if (!addAxisType(ds, "altitude", AxisType.Height)) { // directly named
if (!addAxisType(ds, "depth", AxisType.Height)) { // directly named
String vname = ds.findAttValueIgnoreCase(null, "altitude_coordinate", null);
if (!addAxisType(ds, vname, AxisType.Height)) { // attribute named
for (int i = 0; i < ds.getVariables().size(); i++) {
VariableEnhanced ve = (VariableEnhanced) ds.getVariables().get(i);
String positive = ds.findAttValueIgnoreCase((Variable) ve, "positive", null);
if (positive != null) {
addAxisType((Variable) ve, AxisType.Height); // CF-1
break;
}
}
}
}
}
}
// time
if (!hasAxisType(ds, AxisType.Time)) { // already has _CoordinateAxisType
if (!addAxisType(ds, "time", AxisType.Time)) { // directly named
String vname = ds.findAttValueIgnoreCase(null, "time_coordinate", null);
if (!addAxisType(ds, vname, AxisType.Time)) { // attribute named
for (int i = 0; i < ds.getVariables().size(); i++) {
VariableEnhanced ve = (VariableEnhanced) ds.getVariables().get(i);
String unit = ve.getUnitsString();
if (unit == null) continue;
if (SimpleUnit.isDateUnit(unit)) {
addAxisType((Variable) ve, AxisType.Time); // CF-1
break;
}
}
}
}
}
}
/**
* Add this coord as a variable in the netCDF file
*
* @param ncfile netCDF file to add to
* @param g group in file
*/
void addToNetcdfFile(NetcdfFile ncfile, Group g) {
if (dontUseVertical) {
typicalRecord = null;
return;
}
if (g == null) {
g = ncfile.getRootGroup();
}
// coordinate axis
Variable v = new Variable(ncfile, g, null, getVariableName());
v.setDataType(DataType.DOUBLE);
String desc = lookup.getLevelDescription(typicalRecord);
if (lookup instanceof Grib2GridTableLookup && usesBounds) {
desc = "Layer between " + desc;
}
v.addAttribute(new Attribute("long_name", desc));
v.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));
// positive attribute needed for CF-1 Height and Pressure
if (positive != null) {
v.addAttribute(new Attribute("positive", positive));
}
if (units != null) {
AxisType axisType;
if (SimpleUnit.isCompatible("millibar", units)) {
axisType = AxisType.Pressure;
} else if (SimpleUnit.isCompatible("m", units)) {
axisType = AxisType.Height;
} else {
axisType = AxisType.GeoZ;
}
if (lookup instanceof Grib2GridTableLookup || lookup instanceof Grib1GridTableLookup) {
v.addAttribute(
new Attribute("GRIB_level_type", Integer.toString(typicalRecord.getLevelType1())));
} else {
v.addAttribute(
new Attribute("level_type", Integer.toString(typicalRecord.getLevelType1())));
}
v.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));
}
if (coordValues == null) {
coordValues = new double[levels.size()];
for (int i = 0; i < levels.size(); i++) {
LevelCoord lc = (LevelCoord) levels.get(i);
coordValues[i] = lc.mid;
}
}
Array dataArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length}, coordValues);
v.setDimensions(getVariableName());
v.setCachedData(dataArray, true);
ncfile.addVariable(g, v);
if (usesBounds) {
String boundsDimName = "bounds_dim";
if (g.findDimension(boundsDimName) == null) {
ncfile.addDimension(g, new Dimension(boundsDimName, 2, true));
}
String bname = getVariableName() + "_bounds";
v.addAttribute(new Attribute("bounds", bname));
v.addAttribute(new Attribute(_Coordinate.ZisLayer, "true"));
Variable b = new Variable(ncfile, g, null, bname);
b.setDataType(DataType.DOUBLE);
b.setDimensions(getVariableName() + " " + boundsDimName);
b.addAttribute(new Attribute("long_name", "bounds for " + v.getName()));
b.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));
Array boundsArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length, 2});
ucar.ma2.Index ima = boundsArray.getIndex();
for (int i = 0; i < coordValues.length; i++) {
LevelCoord lc = (LevelCoord) levels.get(i);
boundsArray.setDouble(ima.set(i, 0), lc.value1);
boundsArray.setDouble(ima.set(i, 1), lc.value2);
}
b.setCachedData(boundsArray, true);
ncfile.addVariable(g, b);
}
if (factors != null) {
// check if already created
if (g == null) {
g = ncfile.getRootGroup();
}
if (g.findVariable("hybrida") != null) return;
v.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate"));
v.addAttribute(new Attribute("formula_terms", "ap: hybrida b: hybridb ps: Pressure"));
// create hybrid factor variables
// add hybrida variable
Variable ha = new Variable(ncfile, g, null, "hybrida");
ha.setDataType(DataType.DOUBLE);
ha.addAttribute(new Attribute("long_name", "level_a_factor"));
ha.addAttribute(new Attribute("units", ""));
ha.setDimensions(getVariableName());
// add data
int middle = factors.length / 2;
double[] adata;
double[] bdata;
if (levels.size() < middle) { // only partial data wanted
adata = new double[levels.size()];
bdata = new double[levels.size()];
} else {
adata = new double[middle];
bdata = new double[middle];
}
for (int i = 0; i < middle && i < levels.size(); i++) adata[i] = factors[i];
Array haArray = Array.factory(DataType.DOUBLE, new int[] {adata.length}, adata);
ha.setCachedData(haArray, true);
ncfile.addVariable(g, ha);
// add hybridb variable
Variable hb = new Variable(ncfile, g, null, "hybridb");
hb.setDataType(DataType.DOUBLE);
hb.addAttribute(new Attribute("long_name", "level_b_factor"));
hb.addAttribute(new Attribute("units", ""));
hb.setDimensions(getVariableName());
// add data
for (int i = 0; i < middle && i < levels.size(); i++) bdata[i] = factors[i + middle];
Array hbArray = Array.factory(DataType.DOUBLE, new int[] {bdata.length}, bdata);
hb.setCachedData(hbArray, true);
ncfile.addVariable(g, hb);
/* // TODO: delete next time modifying code
double[] adata = new double[ middle ];
for( int i = 0; i < middle; i++ )
adata[ i ] = factors[ i ];
Array haArray = Array.factory(DataType.DOUBLE, new int[]{adata.length}, adata);
ha.setCachedData(haArray, true);
ncfile.addVariable(g, ha);
// add hybridb variable
Variable hb = new Variable(ncfile, g, null, "hybridb");
hb.setDataType(DataType.DOUBLE);
hb.addAttribute(new Attribute("long_name", "level_b_factor" ));
//hb.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate" ));
hb.addAttribute(new Attribute("units", ""));
hb.setDimensions(getVariableName());
// add data
double[] bdata = new double[ middle ];
for( int i = 0; i < middle; i++ )
bdata[ i ] = factors[ i + middle ];
Array hbArray = Array.factory(DataType.DOUBLE, new int[]{bdata.length}, bdata);
hb.setCachedData(hbArray, true);
ncfile.addVariable(g, hb);
*/
}
}
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);
}