// create from a dataset
public VariableBean(Variable vs) {
this.vs = vs;
// vs = (v instanceof VariableEnhanced) ? (VariableEnhanced) v : new VariableStandardized( v);
setName(vs.getShortName());
setDescription(vs.getDescription());
setUnits(vs.getUnitsString());
setDataType(vs.getDataType().toString());
// Attribute csAtt = vs.findAttribute("_coordSystems");
// if (csAtt != null)
// setCoordSys( csAtt.getStringValue());
// collect dimensions
StringBuilder lens = new StringBuilder();
StringBuilder names = new StringBuilder();
java.util.List dims = vs.getDimensions();
for (int j = 0; j < dims.size(); j++) {
ucar.nc2.Dimension dim = (ucar.nc2.Dimension) dims.get(j);
if (j > 0) {
lens.append(",");
names.append(",");
}
String name = dim.isShared() ? dim.getName() : "anon";
names.append(name);
lens.append(dim.getLength());
}
setDimensions(names.toString());
setShape(lens.toString());
}
private Variable hasUnits(NetcdfDataset ds, String unitList) {
List<Variable> varList = ds.getVariables();
StringTokenizer stoker = new StringTokenizer(unitList, ",");
while (stoker.hasMoreTokens()) {
String unit = stoker.nextToken();
for (Variable ve : varList) {
String hasUnit = ve.getUnitsString();
if (hasUnit == null) continue;
if (hasUnit.equalsIgnoreCase(unit)) return ve;
}
}
return null;
}
public static Map<String, Metadata> readFile(String file) throws Exception {
NetcdfFile n = NetcdfFile.open(file);
System.out.println("Opened: " + file);
/* Determine the size of our grid */
int xLen = n.findDimension("x").getLength();
int yLen = n.findDimension("y").getLength();
System.out.println("Grid size: " + xLen + "x" + yLen);
/* What time is this set of readings for? */
Variable timeVar = n.findVariable("time");
String timeStr = timeVar.getUnitsString().toUpperCase();
timeStr = timeStr.replace("HOURS SINCE ", "");
timeStr = timeStr.replace("HOUR SINCE ", "");
/* Find the base date (the day) the reading was taken */
Date baseDate = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssX").parse(timeStr);
/* Get the number of hours since the base date this reading was taken */
int offset = timeVar.read().getInt(0);
/* Generate the actual date for this reading */
Calendar calendar = Calendar.getInstance();
calendar.setTime(baseDate);
calendar.set(Calendar.HOUR, calendar.get(Calendar.HOUR) + offset);
System.out.println("Time of collection: " + calendar.getTime());
/* We'll keep a mapping of geolocations -> Galileo Metadata */
Map<String, Metadata> metaMap = new HashMap<>();
/* Determine the lat, lon coordinates for the grid points, and get each
* reading at each grid point. */
NetcdfDataset dataset = new NetcdfDataset(n);
@SuppressWarnings("resource")
GridDataset gridData = new GridDataset(dataset);
for (GridDatatype g : gridData.getGrids()) {
/* Let's look at 3D variables: these have WxH dimensions, plus a
* single plane. A 4D variable would contain elevation
* and multiple planes as a result */
if (g.getShape().length == 3) {
convert3DVariable(g, calendar.getTime(), metaMap);
}
}
return metaMap;
}
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);
}
/**
* Parses a variable recursively into appropriate ViewVariable implementations
*
* @throws IOException
* @throws
*/
private static AbstractViewVariable parseVariableRecursive(Variable var) throws IOException {
List<Dimension> dimensions = var.getDimensions();
// A single dimension means we can parse a SimpleAxis
if (dimensions.size() == 1) {
SimpleAxis axis =
new SimpleAxis(var.getName(), var.getDataType().name(), var.getUnitsString(), null, null);
Dimension d = dimensions.get(0);
axis.setDimensionBounds(new SimpleBounds(0, d.getLength()));
// Read our first and last values
Array first = null, last = null;
try {
first = var.read(new int[] {0}, new int[] {1});
last = var.read(new int[] {d.getLength() - 1}, new int[] {1});
} catch (InvalidRangeException ex) {
throw new IllegalArgumentException(
String.format("Unable to read variable ranges '%1$s'", var), ex);
}
axis.setValueBounds(new SimpleBounds(first.getDouble(0), last.getDouble(0)));
return axis;
// Otherwise we have a multi dimensional variable that we can parse as a grid
} else if (dimensions.size() > 0) {
SimpleGrid grid =
new SimpleGrid(var.getName(), var.getDataType().name(), var.getUnitsString(), null);
List<AbstractViewVariable> childAxes = new ArrayList<>();
// Recursively parse each dimension (which should map to a variable in the parent group)
for (Dimension d : dimensions) {
Variable mappedVariable = d.getGroup().findVariable(d.getName());
if (mappedVariable == null) {
// If the dimension doesn't map to a variable, we can't pull much information out of it
// So instead we'll have to introduce an axis that only includes dimension bounds
log.warn(
String.format(
"Dimension '%1$s' has no matching variable in parent group '%2$s'",
d, d.getGroup()));
SimpleAxis axis = new SimpleAxis(d.getName(), DataType.FLOAT.name(), "????", null, null);
axis.setDimensionBounds(new SimpleBounds(0, d.getLength() - 1));
childAxes.add(axis);
} else {
AbstractViewVariable parsedVar = parseVariableRecursive(mappedVariable);
if (parsedVar != null) childAxes.add(parsedVar);
}
}
if (childAxes.size() > 0) {
grid.setAxes(childAxes.toArray(new AbstractViewVariable[childAxes.size()]));
return grid;
} else {
return null;
}
} else {
// Currently unsupported...
log.warn(
String.format("Variables with 0 dimensions are currently unsupported. var='%1$s'", var));
return null;
}
}
