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;
}
/** Create a DAS for this netcdf file */
NcDAS(NetcdfFile ncfile) {
// Variable attributes
Iterator iter = ncfile.getVariables().iterator();
while (iter.hasNext()) {
Variable v = (Variable) iter.next();
doVariable(v, null);
}
// Global attributes
opendap.dap.AttributeTable gtable = new opendap.dap.AttributeTable("NC_GLOBAL");
int count = addAttributes(gtable, null, ncfile.getGlobalAttributes().iterator());
if (count > 0)
try {
addAttributeTable("NC_GLOBAL", gtable);
} catch (AttributeExistsException e) {
log.error("Cant add NC_GLOBAL", e);
}
// unlimited dimension
iter = ncfile.getDimensions().iterator();
while (iter.hasNext()) {
Dimension d = (Dimension) iter.next();
if (d.isUnlimited()) {
opendap.dap.AttributeTable table = new opendap.dap.AttributeTable("DODS_EXTRA");
try {
table.appendAttribute("Unlimited_Dimension", opendap.dap.Attribute.STRING, d.getName());
addAttributeTable("DODS_EXTRA", table);
} catch (Exception e) {
log.error("Error adding Unlimited_Dimension =" + e);
}
break;
}
}
// unused dimensions
opendap.dap.AttributeTable dimTable = null;
iter = ncfile.getDimensions().iterator();
while (iter.hasNext()) {
Dimension d = (Dimension) iter.next();
if (null == usedDims.get(d.getName())) {
if (dimTable == null) dimTable = new opendap.dap.AttributeTable("EXTRA_DIMENSION");
try {
dimTable.appendAttribute(
d.getName(), opendap.dap.Attribute.INT32, Integer.toString(d.getLength()));
} catch (Exception e) {
log.error("Error adding Unlimited_Dimension =" + e);
}
}
}
if (dimTable != null)
try {
addAttributeTable("EXTRA_DIMENSION", dimTable);
} catch (AttributeExistsException e) {
log.error("Cant add EXTRA_DIMENSION", e);
}
}
private void createDataVariables(List<VariableSimpleIF> dataVars) throws IOException {
/* height variable
Variable heightVar = ncfile.addStringVariable(altName, recordDims, 20);
ncfile.addVariableAttribute(heightVar, new Attribute("long_name", "height of observation"));
ncfile.addVariableAttribute(heightVar, new Attribute("units", altUnits)); */
Variable v = ncfile.addVariable(parentProfileIndex, DataType.INT, recordDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent profile"));
v = ncfile.addVariable(nextObsName, DataType.INT, recordDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "record number of next obs in linked list for this profile"));
// find all dimensions needed by the data variables
for (VariableSimpleIF var : dataVars) {
List<Dimension> dims = var.getDimensions();
dimSet.addAll(dims);
}
// add them
for (Dimension d : dimSet) {
if (!d.isUnlimited())
ncfile.addDimension(d.getName(), d.getLength(), d.isShared(), false, d.isVariableLength());
}
// add the data variables all using the record dimension
for (VariableSimpleIF oldVar : dataVars) {
List<Dimension> dims = oldVar.getDimensions();
StringBuffer dimNames = new StringBuffer(recordDimName);
for (Dimension d : dims) {
if (!d.isUnlimited()) dimNames.append(" ").append(d.getName());
}
Variable newVar =
ncfile.addVariable(oldVar.getName(), oldVar.getDataType(), dimNames.toString());
List<Attribute> atts = oldVar.getAttributes();
for (Attribute att : atts) {
ncfile.addVariableAttribute(newVar, att);
}
}
}
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();
}
/** Instances which have same contents are equal. Careful!! this is not object identity !! */
@Override
public boolean equals(Object oo) {
if (this == oo) return true;
if (!(oo instanceof Dimension)) return false;
Dimension other = (Dimension) oo;
if ((g != null) && !g.equals(other.getGroup())) return false;
if ((getName() == null) && (other.getName() != null)) return false;
if ((getName() != null) && !getName().equals(other.getName())) return false;
return (getLength() == other.getLength())
&& (isUnlimited() == other.isUnlimited())
&& (isVariableLength() == other.isVariableLength())
&& (isShared() == other.isShared());
}
