public boolean compareVariables(
Variable org, Variable copy, boolean compareData, boolean justOne) {
boolean ok = true;
if (showCompare)
f.format("compare Variable %s to %s %n", org.getFullName(), copy.getFullName());
if (!org.getFullName().equals(copy.getFullName())) {
f.format(" ** names are different %s != %s %n", org.getFullName(), copy.getFullName());
ok = false;
}
// dimensions
ok &= checkAll(org.getDimensions(), copy.getDimensions(), null);
// attributes
ok &= checkAll(org.getAttributes(), copy.getAttributes(), null);
// coord sys
if ((org instanceof VariableEnhanced) && (copy instanceof VariableEnhanced)) {
VariableEnhanced orge = (VariableEnhanced) org;
VariableEnhanced copye = (VariableEnhanced) copy;
ok &= checkAll(orge.getCoordinateSystems(), copye.getCoordinateSystems(), null);
}
// data !!
if (compareData) {
try {
compareVariableData(org, copy, showCompare, justOne);
} catch (IOException e) {
ByteArrayOutputStream bos = new ByteArrayOutputStream(10000);
e.printStackTrace(new PrintStream(bos));
f.format("%s", bos.toString());
}
}
// nested variables
if (org instanceof Structure) {
if (!(copy instanceof Structure)) {
f.format(" ** %s not Structure%n", org);
ok = false;
} else {
Structure orgS = (Structure) org;
Structure ncmlS = (Structure) copy;
List vars = new ArrayList();
ok &= checkAll(orgS.getVariables(), ncmlS.getVariables(), vars);
for (int i = 0; i < vars.size(); i += 2) {
Variable orgV = (Variable) vars.get(i);
Variable ncmlV = (Variable) vars.get(i + 1);
ok &= compareVariables(orgV, ncmlV, false, true);
}
}
}
return ok;
}
private void doVariable(Variable v, opendap.dap.AttributeTable parentTable) {
List dims = v.getDimensions();
for (int i = 0; i < dims.size(); i++) {
Dimension dim = (Dimension) dims.get(i);
if (dim.isShared()) usedDims.put(dim.getName(), dim);
}
// if (v.getAttributes().size() == 0) return; // LOOK DAP 2 say must have empty
String name = NcDDS.escapeName(v.getShortName());
opendap.dap.AttributeTable table;
if (parentTable == null) {
table = new opendap.dap.AttributeTable(name);
try {
addAttributeTable(name, table);
} catch (AttributeExistsException e) {
log.error("Cant add " + name, e);
}
} else {
table = parentTable.appendContainer(name);
}
addAttributes(table, v, v.getAttributes().iterator());
if (v instanceof Structure) {
Structure s = (Structure) v;
List nested = s.getVariables();
for (int i = 0; i < nested.size(); i++) {
Variable nv = (Variable) nested.get(i);
doVariable(nv, table);
}
}
}
public List<VariableBean> getStructureVariables(Structure s) {
List<VariableBean> vlist = new ArrayList<VariableBean>();
for (Variable v : s.getVariables()) {
vlist.add(new VariableBean(v));
}
return vlist;
}
void makeChildren() {
children = new ArrayList<>();
if (var instanceof Structure) {
Structure s = (Structure) var;
List vars = s.getVariables();
for (int i = 0; i < vars.size(); i++)
children.add(new VariableNode(this, (VariableIF) vars.get(i)));
}
if (debugTree) System.out.println("children=" + var.getShortName() + " ");
}
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);
}
// create from a dataset
public ObsBean(Structure obs, StructureData sdata) {
// first choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-5-1") && Double.isNaN(lat)) {
lat = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-6-1") && Double.isNaN(lon)) {
lon = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-30") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-4-1") && (year < 0)) {
year = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-2") && (month < 0)) {
month = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-3") && (day < 0)) {
day = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-4") && (hour < 0)) {
hour = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-5") && (minute < 0)) {
minute = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-6") && (sec < 0)) {
sec = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-1-1") && (wmo_block < 0)) {
wmo_block = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-1-2") && (wmo_id < 0)) {
wmo_id = sdata.convertScalarInt(v.getShortName());
} else if ((stn == null)
&& (val.equals("0-1-7")
|| val.equals("0-1-194")
|| val.equals("0-1-11")
|| val.equals("0-1-18"))) {
if (v.getDataType().isString()) stn = sdata.getScalarString(v.getShortName());
else stn = Integer.toString(sdata.convertScalarInt(v.getShortName()));
}
}
// second choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-5-2") && Double.isNaN(lat)) {
lat = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-6-2") && Double.isNaN(lon)) {
lon = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-1") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if ((val.equals("0-4-7")) && (sec < 0)) {
sec = sdata.convertScalarInt(v.getShortName());
}
}
// third choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-7-10") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-2") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
}
}
}
Write2ncRect(NetcdfFile bufr, String fileOutName, boolean fill)
throws IOException, InvalidRangeException {
NetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(fileOutName, fill);
if (debug) {
System.out.println("FileWriter write " + bufr.getLocation() + " to " + fileOutName);
}
// global attributes
List<Attribute> glist = bufr.getGlobalAttributes();
for (Attribute att : glist) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
Attribute useAtt;
if (att.isArray()) useAtt = ncfile.addGlobalAttribute(useName, att.getValues());
else if (att.isString()) useAtt = ncfile.addGlobalAttribute(useName, att.getStringValue());
else useAtt = ncfile.addGlobalAttribute(useName, att.getNumericValue());
if (debug) System.out.println("add gatt= " + useAtt);
}
// global dimensions
Dimension recordDim = null;
Map<String, Dimension> dimHash = new HashMap<String, Dimension>();
for (Dimension oldD : bufr.getDimensions()) {
String useName = N3iosp.makeValidNetcdfObjectName(oldD.getName());
boolean isRecord = useName.equals("record");
Dimension newD = ncfile.addDimension(useName, oldD.getLength(), true, false, false);
dimHash.put(newD.getName(), newD);
if (isRecord) recordDim = newD;
if (debug) System.out.println("add dim= " + newD);
}
// Variables
Structure recordStruct = (Structure) bufr.findVariable(BufrIosp.obsRecord);
for (Variable oldVar : recordStruct.getVariables()) {
if (oldVar.getDataType() == DataType.STRUCTURE) continue;
String varName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());
DataType newType = oldVar.getDataType();
List<Dimension> newDims = new ArrayList<Dimension>();
newDims.add(recordDim);
for (Dimension dim : oldVar.getDimensions()) {
newDims.add(ncfile.addDimension(oldVar.getShortName() + "_strlen", dim.getLength()));
}
Variable newVar = ncfile.addVariable(varName, newType, newDims);
if (debug) System.out.println("add var= " + newVar);
// attributes
List<Attribute> attList = oldVar.getAttributes();
for (Attribute att : attList) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
else if (att.isString())
ncfile.addVariableAttribute(varName, useName, att.getStringValue());
else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
}
}
// int max_seq = countSeq(recordStruct);
// Dimension seqD = ncfile.addDimension("level", max_seq);
for (Variable v : recordStruct.getVariables()) {
if (v.getDataType() != DataType.STRUCTURE) continue;
String structName = N3iosp.makeValidNetcdfObjectName(v.getShortName());
int shape[] = v.getShape();
Dimension structDim = ncfile.addDimension(structName, shape[0]);
Structure struct = (Structure) v;
for (Variable seqVar : struct.getVariables()) {
String varName = N3iosp.makeValidNetcdfObjectName(seqVar.getShortName() + "-" + structName);
DataType newType = seqVar.getDataType();
List<Dimension> newDims = new ArrayList<Dimension>();
newDims.add(recordDim);
newDims.add(structDim);
for (Dimension dim : seqVar.getDimensions()) {
newDims.add(ncfile.addDimension(seqVar.getShortName() + "_strlen", dim.getLength()));
}
Variable newVar = ncfile.addVariable(varName, newType, newDims);
if (debug) System.out.println("add var= " + newVar);
// attributes
List<Attribute> attList = seqVar.getAttributes();
for (Attribute att : attList) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
else if (att.isString())
ncfile.addVariableAttribute(varName, useName, att.getStringValue());
else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
}
}
}
// create the file
ncfile.create();
if (debug) System.out.println("File Out= " + ncfile.toString());
// boolean ok = (Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
double total = copyVarData(ncfile, recordStruct);
ncfile.flush();
System.out.println("FileWriter done total bytes = " + total);
ncfile.close();
}