public TableConfig getConfig(FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog)
throws IOException {
TableConfig topTable = new TableConfig(Table.Type.Top, "singleTrajectory");
CoordinateAxis coordAxis = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
if (coordAxis == null) {
errlog.format("Cant find a time coordinate");
return null;
}
final Dimension innerDim = coordAxis.getDimension(0);
boolean obsIsStruct = Evaluator.hasNetcdf3RecordStructure(ds) && innerDim.isUnlimited();
TableConfig obsTable = new TableConfig(Table.Type.Structure, innerDim.getShortName());
obsTable.dimName = innerDim.getShortName();
obsTable.time = coordAxis.getFullName();
obsTable.structName = obsIsStruct ? "record" : innerDim.getShortName();
obsTable.structureType =
obsIsStruct
? TableConfig.StructureType.Structure
: TableConfig.StructureType.PsuedoStructure;
CoordSysEvaluator.findCoords(
obsTable,
ds,
new CoordSysEvaluator.Predicate() {
public boolean match(CoordinateAxis axis) {
return innerDim.equals(axis.getDimension(0));
}
});
topTable.addChild(obsTable);
return topTable;
}
// convert to shared dimensions
private void setSharedDimensions(
Variable v, List<Element> values, List<Dimension> unknownDims, String location) {
if (values.size() == 0) return;
// remove the "scalar" dumbension
Iterator<Element> iter = values.iterator();
while (iter.hasNext()) {
Element value = iter.next();
String dimName = value.getText().trim();
if (dimName.equalsIgnoreCase("scalar")) iter.remove();
}
// gotta have same number of dimensions
List<Dimension> oldDims = v.getDimensions();
if (oldDims.size() != values.size()) {
log.error("Different number of dimensions for {} {}", v, location);
return;
}
List<Dimension> newDims = new ArrayList<>();
Group group = v.getParentGroup();
for (int i = 0; i < values.size(); i++) {
Element value = values.get(i);
String dimName = value.getText().trim();
dimName = NetcdfFile.makeValidCdmObjectName(dimName);
Dimension dim = group.findDimension(dimName);
Dimension oldDim = oldDims.get(i);
if (dim == null) dim = checkUnknownDims(dimName, unknownDims, oldDim, location);
if (dim == null) {
log.error(
"Unknown Dimension= {} for variable = {} {} ", dimName, v.getFullName(), location);
return;
}
if (dim.getLength() != oldDim.getLength()) {
log.error(
"Shared dimension ("
+ dim.getShortName()
+ ") has different length than data dimension ("
+ oldDim.getShortName()
+ ") shared="
+ dim.getLength()
+ " org="
+ oldDim.getLength()
+ " for "
+ v
+ " "
+ location);
return;
}
newDims.add(dim);
}
v.setDimensions(newDims);
if (showWork) System.out.printf(" set shared dimensions for %s %n", v.getNameAndDimensions());
}
public void testDimensions(NetcdfFile ncfile) {
System.out.println("ncfile = \n" + ncfile);
Dimension latDim = ncfile.findDimension("lat");
assert null != latDim;
assert latDim.getShortName().equals("lat");
assert latDim.getLength() == 3;
assert !latDim.isUnlimited();
Dimension lonDim = ncfile.findDimension("lon");
assert null != lonDim;
assert lonDim.getShortName().equals("lon");
assert lonDim.getLength() == 4;
assert !lonDim.isUnlimited();
Dimension timeDim = ncfile.findDimension("time");
assert null != timeDim;
assert timeDim.getShortName().equals("time");
assert timeDim.getLength() == 3 : timeDim.getLength();
}
// look if the wanted dimension is in the unknownDims list.
private Dimension checkUnknownDims(
String wantDim, List<Dimension> unknownDims, Dimension oldDim, String location) {
for (Dimension dim : unknownDims) {
if (dim.getShortName().equals(wantDim)) {
int len = oldDim.getLength();
if (len == 0) dim.setUnlimited(true); // allow zero length dimension !!
dim.setLength(len); // use existing (anon) dimension
Group parent = dim.getGroup();
parent.addDimensionIfNotExists(dim); // add to the parent
unknownDims.remove(dim); // remove from list LOOK is this ok?
log.warn("unknownDim {} length set to {}{}", wantDim, oldDim.getLength(), location);
return dim;
}
}
return null;
}
public VariableBean(VariableEnhanced v) {
this.ve = v;
setName(v.getFullName());
setDescription(v.getDescription());
setUnits(v.getUnitsString());
// collect dimensions
StringBuilder lens = new StringBuilder();
StringBuilder names = new StringBuilder();
java.util.List dims = v.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.getShortName() : "anon";
names.append(name);
lens.append(dim.getLength());
}
setDims(names.toString());
setShape(lens.toString());
StringBuilder buff = new StringBuilder();
List<CoordinateSystem> csList = v.getCoordinateSystems();
for (CoordinateSystem cs : csList) {
if (firstCoordSys == null) firstCoordSys = cs;
else buff.append("; ");
buff.append(cs.getName());
Formatter gridBuff = new Formatter();
if (GridCoordSys.isGridCoordSys(gridBuff, cs, v)) {
addDataType("grid");
} /* else if (PointDatasetDefaultHandler.isPointFeatureDataset(ds)) {
addDataType("point");
} */
}
setCoordSys(buff.toString());
}
public AxisBean(CoordinateAxis v) {
this.axis = v;
setName(v.getFullName());
setCoordVar(v.isCoordinateVariable());
setDescription(v.getDescription());
setUnits(v.getUnitsString());
// collect dimensions
StringBuilder lens = new StringBuilder();
StringBuilder names = new StringBuilder();
java.util.List dims = v.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.getShortName() : "anon";
names.append(name);
lens.append(dim.getLength());
}
setDims(names.toString());
setShape(lens.toString());
AxisType at = v.getAxisType();
if (at != null) setAxisType(at.toString());
String p = v.getPositive();
if (p != null) setPositive(p);
if (v instanceof CoordinateAxis1D) {
CoordinateAxis1D v1 = (CoordinateAxis1D) v;
if (v1.isRegular()) setRegular(Double.toString(v1.getIncrement()));
}
isLayer = (null != axis.findAttribute(_Coordinate.ZisLayer));
isInterval = axis.isInterval();
}
public String toString() {
return d.getShortName();
}
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);
}