/**
* Extract a list of data variables (and their canonical names if possible) from the dataset.
*
* @param threddsDataset open this dataset
* @return ThreddsMetadata.Variables, or null if unable.
* @throws IOException on read error
*/
public static ThreddsMetadata.Variables extractVariables(InvDatasetImpl threddsDataset)
throws IOException {
ThreddsDataFactory.Result result = null;
try {
result = new ThreddsDataFactory().openFeatureDataset(threddsDataset, null);
if (result.fatalError) {
System.out.println(" openDatatype errs=" + result.errLog);
return null;
}
if (result.featureType == FeatureType.GRID) {
// System.out.println(" extractVariables GRID=" + result.location);
GridDataset gridDataset = (GridDataset) result.featureDataset;
return extractVariables(threddsDataset, gridDataset);
} else if ((result.featureType == FeatureType.STATION)
|| (result.featureType == FeatureType.POINT)) {
PointObsDataset pobsDataset = (PointObsDataset) result.featureDataset;
ThreddsMetadata.Variables vars = new ThreddsMetadata.Variables("CF-1.0");
for (VariableSimpleIF vs : pobsDataset.getDataVariables()) {
ThreddsMetadata.Variable v = new ThreddsMetadata.Variable();
vars.addVariable(v);
v.setName(vs.getName());
v.setDescription(vs.getDescription());
v.setUnits(vs.getUnitsString());
ucar.nc2.Attribute att = vs.findAttributeIgnoreCase("standard_name");
v.setVocabularyName((att != null) ? att.getStringValue() : "N/A");
}
vars.sort();
return vars;
}
} finally {
try {
if ((result != null) && (result.featureDataset != null)) result.featureDataset.close();
} catch (IOException ioe) {
logger.error("Closing dataset " + result.featureDataset, ioe);
}
}
return null;
}
/**
* Extract the lat/lon/alt bounding boxes from the dataset.
*
* @param threddsDataset open this dataset
* @return ThreddsMetadata.GeospatialCoverage, or null if unable.
* @throws IOException on read error
*/
public static ThreddsMetadata.GeospatialCoverage extractGeospatial(InvDatasetImpl threddsDataset)
throws IOException {
ThreddsDataFactory.Result result = null;
try {
result = new ThreddsDataFactory().openFeatureDataset(threddsDataset, null);
if (result.fatalError) {
System.out.println(" openDatatype errs=" + result.errLog);
return null;
}
if (result.featureType == FeatureType.GRID) {
System.out.println(" GRID=" + result.location);
GridDataset gridDataset = (GridDataset) result.featureDataset;
return extractGeospatial(gridDataset);
} else if (result.featureType == FeatureType.POINT) {
PointObsDataset pobsDataset = (PointObsDataset) result.featureDataset;
LatLonRect llbb = pobsDataset.getBoundingBox();
if (null != llbb) {
ThreddsMetadata.GeospatialCoverage gc = new ThreddsMetadata.GeospatialCoverage();
gc.setBoundingBox(llbb);
return gc;
}
} else if (result.featureType == FeatureType.STATION) {
StationObsDataset sobsDataset = (StationObsDataset) result.featureDataset;
LatLonRect llbb = sobsDataset.getBoundingBox();
if (null != llbb) {
ThreddsMetadata.GeospatialCoverage gc = new ThreddsMetadata.GeospatialCoverage();
gc.setBoundingBox(llbb);
return gc;
}
}
} finally {
try {
if ((result != null) && (result.featureDataset != null)) result.featureDataset.close();
} catch (IOException ioe) {
logger.error("Closing dataset " + result.featureDataset, ioe);
}
}
return null;
}
/**
* Open a ucar.nc2.dt.PointObsDataset, write out in CF point format.
*
* @param fileIn open through TypedDatasetFactory.open(FeatureType.POINT, ..)
* @param fileOut write to this netcdf-3 file
* @param inMemory if true, read file into memory for efficiency
* @return true on success
* @throws IOException on read/write error
*/
public static boolean rewritePointObsDataset(String fileIn, String fileOut, boolean inMemory)
throws IOException {
System.out.println(
"Rewrite2 .nc files from " + fileIn + " to " + fileOut + " inMemory= " + inMemory);
long start = System.currentTimeMillis();
// do it in memory for speed
NetcdfFile ncfile = inMemory ? NetcdfFile.openInMemory(fileIn) : NetcdfFile.open(fileIn);
NetcdfDataset ncd = new NetcdfDataset(ncfile);
StringBuilder errlog = new StringBuilder();
PointObsDataset pobsDataset =
(PointObsDataset) TypedDatasetFactory.open(FeatureType.POINT, ncd, null, errlog);
if (pobsDataset == null) return false;
writePointObsDataset(pobsDataset, fileOut);
pobsDataset.close();
long took = System.currentTimeMillis() - start;
System.out.println(" that took " + (took - start) + " msecs");
return true;
}
/**
* write data from a ucar.nc2.dt.PointObsDataset into CF point format.
*
* @param pobsDataset rewrite data from here
* @param fileOut write to tehis netcdf-3 file
* @throws IOException on read/write error
*/
public static void writePointObsDataset(PointObsDataset pobsDataset, String fileOut)
throws IOException {
// see if we have an altitude
String altUnits = null;
DataIterator iterOne = pobsDataset.getDataIterator(-1);
while (iterOne.hasNext()) {
PointObsDatatype pobsData = (PointObsDatatype) iterOne.nextData();
ucar.unidata.geoloc.EarthLocation loc = pobsData.getLocation();
altUnits = Double.isNaN(loc.getAltitude()) ? null : "meters";
break;
}
List<VariableSimpleIF> vars = pobsDataset.getDataVariables();
List<PointObVar> nvars = new ArrayList<PointObVar>(vars.size());
// put vars in order
for (VariableSimpleIF v : vars) {
if (v.getDataType().isNumeric()) nvars.add(new PointObVar(v));
}
int ndoubles = vars.size();
double[] dvals = new double[ndoubles];
for (VariableSimpleIF v : vars) {
if (v.getDataType().isString()) nvars.add(new PointObVar(v));
}
String[] svals = new String[vars.size() - ndoubles];
FileOutputStream fos = new FileOutputStream(fileOut);
DataOutputStream out = new DataOutputStream(fos);
CFPointObWriter writer =
new CFPointObWriter(out, pobsDataset.getGlobalAttributes(), altUnits, nvars, -1);
DataIterator iter = pobsDataset.getDataIterator(1000 * 1000);
while (iter.hasNext()) {
PointObsDatatype pobsData = (PointObsDatatype) iter.nextData();
StructureData sdata = pobsData.getData();
int dcount = 0;
int scount = 0;
for (PointObVar v : nvars) {
if (v.getDataType().isNumeric()) {
Array data = sdata.getArray(v.getName());
data.resetLocalIterator();
if (data.hasNext()) dvals[dcount++] = data.nextDouble();
} else if (v.getDataType().isString()) {
ArrayChar data = (ArrayChar) sdata.getArray(v.getName());
svals[scount++] = data.getString();
}
}
ucar.unidata.geoloc.EarthLocation loc = pobsData.getLocation();
writer.addPoint(
loc.getLatitude(),
loc.getLongitude(),
loc.getAltitude(),
pobsData.getObservationTimeAsDate(),
dvals,
svals);
}
writer.finish();
}