public boolean compareVariables(NetcdfFile org, NetcdfFile copy) {
f.format("Original = %s%n", org.getLocation());
f.format("CompareTo= %s%n", copy.getLocation());
boolean ok = true;
for (Variable orgV : org.getVariables()) {
if (orgV.isCoordinateVariable()) continue;
Variable copyVar = copy.findVariable(orgV.getShortName());
if (copyVar == null) {
f.format(" MISSING '%s' in 2nd file%n", orgV.getFullName());
ok = false;
} else {
List<Dimension> dims1 = orgV.getDimensions();
List<Dimension> dims2 = copyVar.getDimensions();
if (!compare(dims1, dims2)) {
f.format(" %s != %s%n", orgV.getNameAndDimensions(), copyVar.getNameAndDimensions());
} else {
// f.format(" ok %s%n", orgV.getName());
}
}
}
f.format("%n");
for (Variable orgV : copy.getVariables()) {
if (orgV.isCoordinateVariable()) continue;
Variable copyVar = org.findVariable(orgV.getShortName());
if (copyVar == null) {
f.format(" MISSING '%s' in 1st file%n", orgV.getFullName());
ok = false;
}
}
return ok;
}
private void copySome(NetcdfFileWriteable ncfile, Variable oldVar, int nelems)
throws IOException {
String newName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());
int[] shape = oldVar.getShape();
int[] origin = new int[oldVar.getRank()];
int size = shape[0];
for (int i = 0; i < size; i += nelems) {
origin[0] = i;
int left = size - i;
shape[0] = Math.min(nelems, left);
Array data;
try {
data = oldVar.read(origin, shape);
if (oldVar.getDataType() == DataType.STRING) {
data = convertToChar(ncfile.findVariable(newName), data);
}
if (data.getSize() > 0) { // zero when record dimension = 0
ncfile.write(newName, origin, data);
if (debug) System.out.println("write " + data.getSize() + " bytes");
}
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IOException(e.getMessage());
}
}
}
public void testAggCoordVar2(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert (data instanceof ArrayInt);
IndexIterator dataI = data.getIndexIterator();
assert dataI.getIntNext() == 0 : dataI.getIntCurrent();
assert dataI.getIntNext() == 1 : dataI.getIntCurrent();
assert dataI.getIntNext() == 2 : dataI.getIntCurrent();
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
public void testAggCoordVar(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert (data instanceof ArrayInt.D1) : data.getClass().getName();
ArrayInt.D1 dataI = (ArrayInt.D1) data;
assert dataI.get(0) == 0;
assert dataI.get(1) == 10;
assert dataI.get(2) == 99;
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
private boolean compareGroups(Group org, Group copy) {
if (showCompare) f.format("compare Group %s to %s %n", org.getName(), copy.getName());
boolean ok = true;
if (!org.getName().equals(copy.getName())) {
f.format(" ** names are different %s != %s %n", org.getName(), copy.getName());
ok = false;
}
// dimensions
ok &= checkAll(org.getDimensions(), copy.getDimensions(), null);
// attributes
ok &= checkAll(org.getAttributes(), copy.getAttributes(), null);
// variables
// cant use object equality, just match on short name
for (Variable orgV : org.getVariables()) {
Variable copyVar = copy.findVariable(orgV.getShortName());
if (copyVar == null) {
f.format(" ** cant find variable %s in 2nd file%n", orgV.getFullName());
ok = false;
} else {
ok &= compareVariables(orgV, copyVar, compareData, true);
}
}
for (Variable copyV : copy.getVariables()) {
Variable orgV = org.findVariable(copyV.getShortName());
if (orgV == null) {
f.format(" ** cant find variable %s in 1st file%n", copyV.getFullName());
ok = false;
}
}
// nested groups
List groups = new ArrayList();
ok &= checkAll(org.getGroups(), copy.getGroups(), groups);
for (int i = 0; i < groups.size(); i += 2) {
Group orgGroup = (Group) groups.get(i);
Group ncmlGroup = (Group) groups.get(i + 1);
ok &= compareGroups(orgGroup, ncmlGroup);
}
return ok;
}
private void copyAll(NetcdfFileWriteable ncfile, Variable oldVar) throws IOException {
String newName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());
Array data = oldVar.read();
try {
if (oldVar.getDataType() == DataType.STRING) {
data = convertToChar(ncfile.findVariable(newName), data);
}
if (data.getSize() > 0) // zero when record dimension = 0
ncfile.write(newName, data);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IOException(e.getMessage() + " for Variable " + oldVar.getFullName());
}
}
public void testAggCoordVarScan(NetcdfFile ncfile) throws IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
int count = 0;
Array data = time.read();
assert (data instanceof ArrayInt);
while (data.hasNext()) {
int val = data.nextInt();
assert val == count * 10 : val + "!=" + count * 10;
count++;
}
}
public void testAggCoordVar3(NetcdfFile ncfile) throws IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.DOUBLE : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
Array data = time.read();
assert (data instanceof ArrayDouble);
IndexIterator dataI = data.getIndexIterator();
double val = dataI.getDoubleNext();
assert Misc.closeEnough(val, 0.0) : val;
assert Misc.closeEnough(dataI.getDoubleNext(), 10.0) : dataI.getDoubleCurrent();
assert Misc.closeEnough(dataI.getDoubleNext(), 99.0) : dataI.getDoubleCurrent();
}
public void testAggCoordVarNoCoordsDir(NetcdfFile ncfile) throws IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.STRING : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
Array data = time.read();
assert (data instanceof ArrayObject);
IndexIterator dataI = data.getIndexIterator();
String coordName = (String) dataI.getObjectNext();
assert coordName.equals("time0Dir.nc") : coordName;
coordName = (String) dataI.getObjectNext();
assert coordName.equals("time1Dir.nc") : coordName;
coordName = (String) dataI.getObjectNext();
assert coordName.equals("time2Dir.nc") : coordName;
}
public void testReadData(NetcdfFile ncfile, String name) throws IOException {
Variable v = ncfile.findVariable(name);
assert null != v;
assert v.getShortName().equals(name);
assert v.getRank() == 3;
assert v.getSize() == 36 : v.getSize();
assert v.getShape()[0] == 3;
assert v.getShape()[1] == 3;
assert v.getShape()[2] == 4;
assert v.getDataType() == DataType.DOUBLE;
assert !v.isCoordinateVariable();
assert v.getDimension(0) == ncfile.findDimension("time");
assert v.getDimension(1) == ncfile.findDimension("lat");
assert v.getDimension(2) == ncfile.findDimension("lon");
Array data = v.read();
assert data.getRank() == 3;
assert data.getSize() == 36;
assert data.getShape()[0] == 3;
assert data.getShape()[1] == 3;
assert data.getShape()[2] == 4;
assert data.getElementType() == double.class;
int[] shape = data.getShape();
Index tIndex = data.getIndex();
for (int i = 0; i < shape[0]; i++)
for (int j = 0; j < shape[1]; j++)
for (int k = 0; k < shape[2]; k++) {
double val = data.getDouble(tIndex.set(i, j, k));
// System.out.println(" "+val);
assert TestUtils.close(val, 100 * i + 10 * j + k) : val;
}
}
public void testCoordVar(NetcdfFile ncfile) {
Variable lat = ncfile.findVariable("lat");
assert null != lat;
assert lat.getShortName().equals("lat");
assert lat.getRank() == 1;
assert lat.getSize() == 3;
assert lat.getShape()[0] == 3;
assert lat.getDataType() == DataType.FLOAT;
assert !lat.isUnlimited();
assert lat.getDimension(0).equals(ncfile.findDimension("lat"));
Attribute att = lat.findAttribute("units");
assert null != att;
assert !att.isArray();
assert att.isString();
assert att.getDataType() == DataType.STRING;
assert att.getStringValue().equals("degrees_north");
assert att.getNumericValue() == null;
assert att.getNumericValue(3) == null;
try {
Array data = lat.read();
assert data.getRank() == 1;
assert data.getSize() == 3;
assert data.getShape()[0] == 3;
assert data.getElementType() == float.class;
IndexIterator dataI = data.getIndexIterator();
assert TestUtils.close(dataI.getDoubleNext(), 41.0);
assert TestUtils.close(dataI.getDoubleNext(), 40.0);
assert TestUtils.close(dataI.getDoubleNext(), 39.0);
} catch (IOException io) {
}
}
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);
}
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();
}
/**
* Constructor
*
* @param v : the netcdf Variable
*/
NcSDUInt16(Variable v) {
super(NcDDS.escapeName(v.getShortName()));
this.ncVar = v;
}
/**
* Constructor
*
* @param ncVar : the netcdf Variable
*/
NcSDByte(Variable ncVar) {
super((ncVar.getShortName()));
this.ncVar = ncVar;
}