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 writeHeader(
List<ucar.unidata.geoloc.Station> stns,
List<VariableSimpleIF> vars,
int nprofiles,
String altVarName)
throws IOException {
createGlobalAttributes();
createStations(stns);
createProfiles(nprofiles);
// dummys, update in finish()
ncfile.addGlobalAttribute("zaxis_coordinate", altVarName);
ncfile.addGlobalAttribute("time_coverage_start", dateFormatter.toDateTimeStringISO(new Date()));
ncfile.addGlobalAttribute("time_coverage_end", dateFormatter.toDateTimeStringISO(new Date()));
createDataVariables(vars);
ncfile.create(); // done with define mode
writeStationData(stns); // write out the station info
// now write the observations
if (!(Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE))
throw new IllegalStateException("can't add record variable");
}
private void createGlobalAttributes() {
ncfile.addGlobalAttribute("Conventions", "Unidata Observation Dataset v1.0");
ncfile.addGlobalAttribute("cdm_datatype", "Profile");
ncfile.addGlobalAttribute("title", title);
ncfile.addGlobalAttribute("desc", "Extracted by THREDDS/Netcdf Subset Service");
/* ncfile.addGlobalAttribute("observationDimension", recordDimName);
ncfile.addGlobalAttribute("stationDimension", stationDimName);
ncfile.addGlobalAttribute("latitude_coordinate", latName);
ncfile.addGlobalAttribute("longitude_coordinate", lonName);
ncfile.addGlobalAttribute("time_coordinate", timeName); */
}
public void writeRecord(String stnName, Date obsDate, StructureData sdata) throws IOException {
StationTracker stnTracker = stationMap.get(stnName);
ProfileTracker proTracker = stnTracker.profileMap.get(obsDate);
if (proTracker == null) {
proTracker = new ProfileTracker(profileIndex);
stnTracker.profileMap.put(obsDate, proTracker);
stnTracker.link.add(profileIndex);
stnTracker.lastChild = profileIndex;
stnTracker.numChildren++;
try {
originTime[0] = profileIndex; // 2d index
timeArray.set(0, dateFormatter.toDateTimeStringISO(obsDate));
parentArray.set(0, stnTracker.parent_index);
ncfile.writeStringData(timeName, originTime, timeArray);
ncfile.write(parentStationIndex, originTime, parentArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
profileIndex++;
}
// needs to be wrapped as an ArrayStructure, even though we are only writing one at a time.
ArrayStructureW sArray = new ArrayStructureW(sdata.getStructureMembers(), new int[] {1});
sArray.setStructureData(sdata, 0);
// track the min and max date
if ((minDate == null) || minDate.after(obsDate)) minDate = obsDate;
if ((maxDate == null) || maxDate.before(obsDate)) maxDate = obsDate;
timeArray.set(0, dateFormatter.toDateTimeStringISO(obsDate));
parentArray.set(0, proTracker.parent_index);
proTracker.link.add(recno);
proTracker.lastChild = recno; // not currently used
proTracker.numChildren++;
// write the recno record
origin[0] = recno; // 1d index
originTime[0] = recno; // 2d index
try {
ncfile.write("record", origin, sArray);
ncfile.write(parentProfileIndex, originTime, parentArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
recno++;
}
private void doWrite2(NetcdfFileWriteable ncfile, String varName) throws Exception {
Variable v = ncfile.findVariable(varName);
int[] w = getWeights(v);
int[] shape = v.getShape();
Array aa = Array.factory(v.getDataType().getPrimitiveClassType(), shape);
Index ima = aa.getIndex();
for (int i = 0; i < shape[0]; i++) {
for (int j = 0; j < shape[1]; j++) {
aa.setDouble(ima.set(i, j), (double) (i * w[0] + j * w[1]));
}
}
ncfile.write(varName, aa);
}
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());
}
}
private void writeStationData(List<ucar.unidata.geoloc.Station> stnList) throws IOException {
this.stnList = stnList;
int nstns = stnList.size();
stationMap = new HashMap<String, StationTracker>(2 * nstns);
if (debug) System.out.println("stationMap created");
// now write the station data
ArrayDouble.D1 latArray = new ArrayDouble.D1(nstns);
ArrayDouble.D1 lonArray = new ArrayDouble.D1(nstns);
ArrayDouble.D1 altArray = new ArrayDouble.D1(nstns);
ArrayObject.D1 idArray = new ArrayObject.D1(String.class, nstns);
ArrayObject.D1 descArray = new ArrayObject.D1(String.class, nstns);
ArrayObject.D1 wmoArray = new ArrayObject.D1(String.class, nstns);
for (int i = 0; i < stnList.size(); i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
stationMap.put(stn.getName(), new StationTracker(i));
latArray.set(i, stn.getLatitude());
lonArray.set(i, stn.getLongitude());
if (useAlt) altArray.set(i, stn.getAltitude());
idArray.set(i, stn.getName());
descArray.set(i, stn.getDescription());
if (useWmoId) wmoArray.set(i, stn.getWmoId());
}
try {
ncfile.write(latName, latArray);
ncfile.write(lonName, lonArray);
if (useAlt) ncfile.write(altName, altArray);
ncfile.writeStringData(idName, idArray);
ncfile.writeStringData(descName, descArray);
if (useWmoId) ncfile.writeStringData(wmoName, wmoArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(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);
}
}
}
private void writeDataFinish() throws IOException {
// finish global variables
ArrayInt.D0 totalArray = new ArrayInt.D0();
totalArray.set(profileIndex);
try {
ncfile.write(numProfilesTotalName, totalArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
// finish the station data
int nstns = stnList.size();
ArrayInt.D1 firstProfileArray = new ArrayInt.D1(nstns);
ArrayInt.D1 numProfileArray = new ArrayInt.D1(nstns);
ArrayInt.D1 nextProfileArray = new ArrayInt.D1(nprofiles);
for (int i = 0; i < stnList.size(); i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
StationTracker tracker = stationMap.get(stn.getName());
numProfileArray.set(i, tracker.numChildren);
int first = (tracker.link.size() > 0) ? tracker.link.get(0) : -1;
firstProfileArray.set(i, first);
if (tracker.link.size() > 0) {
// construct forward link
List<Integer> nextList = tracker.link;
for (int j = 0; j < nextList.size() - 1; j++) {
Integer curr = nextList.get(j);
Integer next = nextList.get(j + 1);
nextProfileArray.set(curr, next);
}
Integer curr = nextList.get(nextList.size() - 1);
nextProfileArray.set(curr, -1);
}
}
try {
ncfile.write(firstProfileName, firstProfileArray);
ncfile.write(numProfilesName, numProfileArray);
ncfile.write(nextProfileName, nextProfileArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
// finish the profile data
ArrayInt.D1 nextObsArray = new ArrayInt.D1(recno);
ArrayInt.D1 firstObsArray = new ArrayInt.D1(nprofiles);
ArrayInt.D1 numObsArray = new ArrayInt.D1(nprofiles);
for (int i = 0; i < stnList.size(); i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
StationTracker stnTracker = stationMap.get(stn.getName());
Set<Date> dates = stnTracker.profileMap.keySet();
for (Date date : dates) {
ProfileTracker proTracker = stnTracker.profileMap.get(date);
int trackerIndex = proTracker.parent_index;
numObsArray.set(trackerIndex, proTracker.numChildren);
int first = (proTracker.link.size() > 0) ? proTracker.link.get(0) : -1;
firstObsArray.set(trackerIndex, first);
if (proTracker.link.size() > 0) {
// construct forward link
List<Integer> nextList = proTracker.link;
for (int j = 0; j < nextList.size() - 1; j++) {
Integer curr = nextList.get(j);
Integer next = nextList.get(j + 1);
nextObsArray.set(curr, next);
}
Integer curr = nextList.get(nextList.size() - 1);
nextObsArray.set(curr, -1);
}
}
}
try {
ncfile.write(firstObsName, firstObsArray);
ncfile.write(numObsName, numObsArray);
ncfile.write(nextObsName, nextObsArray);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IllegalStateException(e);
}
// finish the obs data
ncfile.updateAttribute(
null, new Attribute("time_coverage_start", dateFormatter.toDateTimeStringISO(minDate)));
ncfile.updateAttribute(
null, new Attribute("time_coverage_end", dateFormatter.toDateTimeStringISO(maxDate)));
}
private void createProfiles(int nprofiles) throws IOException {
this.nprofiles = nprofiles;
// add the dimensions
Dimension profileDim = ncfile.addDimension(profileDimName, nprofiles);
profileDims.add(profileDim);
Variable v = ncfile.addVariable(numObsName, DataType.INT, profileDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "number of children in linked list for this profile"));
v = ncfile.addVariable(numProfilesTotalName, DataType.INT, "");
ncfile.addVariableAttribute(v, new Attribute("long_name", "number of valid profiles"));
v = ncfile.addVariable(firstObsName, DataType.INT, profileDimName);
ncfile.addVariableAttribute(
v,
new Attribute("long_name", "record number of first obs in linked list for this profile"));
// time variable
Variable timeVar = ncfile.addStringVariable(timeName, profileDims, 20);
ncfile.addVariableAttribute(
timeVar, new Attribute("long_name", "ISO-8601 Date - time of observation"));
v = ncfile.addVariable(parentStationIndex, DataType.INT, profileDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent station"));
v = ncfile.addVariable(nextProfileName, DataType.INT, profileDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "index of next profile in linked list for this station"));
}
private void createStations(List<ucar.unidata.geoloc.Station> stnList) throws IOException {
int nstns = stnList.size();
// see if there's altitude, wmoId for any stations
for (int i = 0; i < nstns; i++) {
ucar.unidata.geoloc.Station stn = stnList.get(i);
// if (!Double.isNaN(stn.getAltitude()))
// useAlt = true;
if ((stn.getWmoId() != null) && (stn.getWmoId().trim().length() > 0)) useWmoId = true;
}
/* if (useAlt)
ncfile.addGlobalAttribute("altitude_coordinate", altName); */
// find string lengths
for (int i = 0; i < nstns; i++) {
ucar.unidata.geoloc.Station station = stnList.get(i);
name_strlen = Math.max(name_strlen, station.getName().length());
desc_strlen = Math.max(desc_strlen, station.getDescription().length());
if (useWmoId) wmo_strlen = Math.max(wmo_strlen, station.getName().length());
}
LatLonRect llbb = getBoundingBox(stnList);
ncfile.addGlobalAttribute(
"geospatial_lat_min", Double.toString(llbb.getLowerLeftPoint().getLatitude()));
ncfile.addGlobalAttribute(
"geospatial_lat_max", Double.toString(llbb.getUpperRightPoint().getLatitude()));
ncfile.addGlobalAttribute(
"geospatial_lon_min", Double.toString(llbb.getLowerLeftPoint().getLongitude()));
ncfile.addGlobalAttribute(
"geospatial_lon_max", Double.toString(llbb.getUpperRightPoint().getLongitude()));
// add the dimensions
Dimension recordDim = ncfile.addUnlimitedDimension(recordDimName);
recordDims.add(recordDim);
Dimension stationDim = ncfile.addDimension(stationDimName, nstns);
stationDims.add(stationDim);
// add the station Variables using the station dimension
Variable v = ncfile.addVariable(latName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "degrees_north"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station latitude"));
v = ncfile.addVariable(lonName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "degrees_east"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station longitude"));
if (useAlt) {
v = ncfile.addVariable(altName, DataType.DOUBLE, stationDimName);
ncfile.addVariableAttribute(v, new Attribute("units", "meters"));
ncfile.addVariableAttribute(v, new Attribute("long_name", "station altitude"));
}
v = ncfile.addStringVariable(idName, stationDims, name_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station identifier"));
v = ncfile.addStringVariable(descName, stationDims, desc_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station description"));
if (useWmoId) {
v = ncfile.addStringVariable(wmoName, stationDims, wmo_strlen);
ncfile.addVariableAttribute(v, new Attribute("long_name", "station WMO id"));
}
v = ncfile.addVariable(numProfilesName, DataType.INT, stationDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "number of profiles in linked list for this station"));
v = ncfile.addVariable(firstProfileName, DataType.INT, stationDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "index of first profile in linked list for this station"));
}
public void setLength(long size) {
ncfile.setLength(size);
}
public WriterProfileObsDataset(String fileOut, String title) throws IOException {
ncfile = NetcdfFileWriteable.createNew(fileOut, false);
ncfile.setFill(false);
this.title = title;
}
public void testWritePermute() throws Exception {
NetcdfFileWriteable ncfile = new NetcdfFileWriteable();
ncfile.setName(TestLocal.cdmTestDataDir + "permuteTest.nc");
// define dimensions
Dimension xDim = ncfile.addDimension("x", 3);
Dimension yDim = ncfile.addDimension("y", 5);
Dimension zDim = ncfile.addDimension("z", 4);
Dimension tDim = ncfile.addDimension("time", 2);
// define Variables
ncfile.addVariable("time", double.class, new Dimension[] {tDim});
ncfile.addVariableAttribute("time", "units", "secs since 1-1-1 00:00");
ncfile.addVariable("z", double.class, new Dimension[] {zDim});
ncfile.addVariableAttribute("z", "units", "meters");
ncfile.addVariableAttribute("z", "positive", "up");
ncfile.addVariable("y", double.class, new Dimension[] {yDim});
ncfile.addVariableAttribute("y", "units", "degrees_north");
ncfile.addVariable("x", double.class, new Dimension[] {xDim});
ncfile.addVariableAttribute("x", "units", "degrees_east");
ncfile.addVariable("tzyx", double.class, new Dimension[] {tDim, zDim, yDim, xDim});
ncfile.addVariableAttribute("tzyx", "units", "K");
ncfile.addVariable("tzxy", double.class, new Dimension[] {tDim, zDim, xDim, yDim});
ncfile.addVariableAttribute("tzxy", "units", "K");
ncfile.addVariable("tyxz", double.class, new Dimension[] {tDim, yDim, xDim, zDim});
ncfile.addVariableAttribute("tyxz", "units", "K");
ncfile.addVariable("txyz", double.class, new Dimension[] {tDim, xDim, yDim, zDim});
ncfile.addVariableAttribute("txyz", "units", "K");
ncfile.addVariable("zyxt", double.class, new Dimension[] {zDim, yDim, xDim, tDim});
ncfile.addVariableAttribute("zyxt", "units", "K");
ncfile.addVariable("zxyt", double.class, new Dimension[] {zDim, xDim, yDim, tDim});
ncfile.addVariableAttribute("zxyt", "units", "K");
ncfile.addVariable("yxzt", double.class, new Dimension[] {yDim, xDim, zDim, tDim});
ncfile.addVariableAttribute("yxzt", "units", "K");
ncfile.addVariable("xyzt", double.class, new Dimension[] {xDim, yDim, zDim, tDim});
ncfile.addVariableAttribute("xyzt", "units", "K");
// missing one dimension
ncfile.addVariable("zyx", double.class, new Dimension[] {zDim, yDim, xDim});
ncfile.addVariable("txy", double.class, new Dimension[] {tDim, xDim, yDim});
ncfile.addVariable("yxz", double.class, new Dimension[] {yDim, xDim, zDim});
ncfile.addVariable("xzy", double.class, new Dimension[] {xDim, zDim, yDim});
ncfile.addVariable("yxt", double.class, new Dimension[] {yDim, xDim, tDim});
ncfile.addVariable("xyt", double.class, new Dimension[] {xDim, yDim, tDim});
ncfile.addVariable("xyz", double.class, new Dimension[] {xDim, yDim, zDim});
// missing two dimension
ncfile.addVariable("yx", double.class, new Dimension[] {yDim, xDim});
ncfile.addVariable("xy", double.class, new Dimension[] {xDim, yDim});
ncfile.addVariable("yz", double.class, new Dimension[] {yDim, zDim});
ncfile.addVariable("xz", double.class, new Dimension[] {xDim, zDim});
ncfile.addVariable("yt", double.class, new Dimension[] {yDim, tDim});
ncfile.addVariable("xt", double.class, new Dimension[] {xDim, tDim});
ncfile.addVariable("ty", double.class, new Dimension[] {tDim, yDim});
ncfile.addVariable("tx", double.class, new Dimension[] {tDim, xDim});
// add global attributes
ncfile.addGlobalAttribute("Convention", "COARDS");
// create the file
try {
ncfile.create();
} catch (IOException e) {
System.err.println("ERROR creating file");
assert (false);
}
// write time data
int len = tDim.getLength();
ArrayDouble A = new ArrayDouble.D1(len);
Index ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3600));
int[] origin = new int[1];
try {
ncfile.write("time", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing time");
assert (false);
}
// write z data
len = zDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 10));
try {
ncfile.write("z", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing z");
assert (false);
}
// write y data
len = yDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3));
try {
ncfile.write("y", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing y");
assert (false);
}
// write x data
len = xDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 5));
try {
ncfile.write("x", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing x");
assert (false);
}
// write tzyx data
doWrite4(ncfile, "tzyx");
doWrite4(ncfile, "tzxy");
doWrite4(ncfile, "txyz");
doWrite4(ncfile, "tyxz");
doWrite4(ncfile, "zyxt");
doWrite4(ncfile, "zxyt");
doWrite4(ncfile, "xyzt");
doWrite4(ncfile, "yxzt");
doWrite3(ncfile, "zyx");
doWrite3(ncfile, "txy");
doWrite3(ncfile, "yxz");
doWrite3(ncfile, "xzy");
doWrite3(ncfile, "yxt");
doWrite3(ncfile, "xyt");
doWrite3(ncfile, "yxt");
doWrite3(ncfile, "xyz");
doWrite2(ncfile, "yx");
doWrite2(ncfile, "xy");
doWrite2(ncfile, "yz");
doWrite2(ncfile, "xz");
doWrite2(ncfile, "yt");
doWrite2(ncfile, "xt");
doWrite2(ncfile, "ty");
doWrite2(ncfile, "tx");
if (show) System.out.println("ncfile = " + ncfile);
// all done
try {
ncfile.close();
} catch (IOException e) {
System.err.println("ERROR writing file");
assert (false);
}
System.out.println("*****************Test Write done");
}
public void testWriteStandardVar() throws Exception {
NetcdfFileWriteable ncfile = new NetcdfFileWriteable(filename, false);
// define dimensions
Dimension latDim = ncfile.addDimension("lat", 2);
Dimension lonDim = ncfile.addDimension("lon", 3);
ArrayList dims = new ArrayList();
dims.add(latDim);
dims.add(lonDim);
// case 1
ncfile.addVariable("t1", DataType.DOUBLE, dims);
ncfile.addVariableAttribute("t1", CDM.SCALE_FACTOR, new Double(2.0));
ncfile.addVariableAttribute("t1", "add_offset", new Double(77.0));
// case 2
ncfile.addVariable("t2", DataType.BYTE, dims);
ncfile.addVariableAttribute("t2", CDM.SCALE_FACTOR, new Short((short) 2));
ncfile.addVariableAttribute("t2", "add_offset", new Short((short) 77));
// case 3
ncfile.addVariable("t3", DataType.BYTE, dims);
ncfile.addVariableAttribute("t3", "_FillValue", new Byte((byte) 255));
// case 4
ncfile.addVariable("t4", DataType.SHORT, dims);
ncfile.addVariableAttribute("t4", CDM.MISSING_VALUE, new Short((short) -9999));
// case 5
ncfile.addVariable("t5", DataType.SHORT, dims);
ncfile.addVariableAttribute("t5", CDM.MISSING_VALUE, new Short((short) -9999));
ncfile.addVariableAttribute("t5", CDM.SCALE_FACTOR, new Short((short) 2));
ncfile.addVariableAttribute("t5", "add_offset", new Short((short) 77));
// case 1
ncfile.addVariable("m1", DataType.DOUBLE, dims);
ncfile.addVariableAttribute("m1", CDM.MISSING_VALUE, -999.99);
// create the file
ncfile.create();
// write t1
ArrayDouble A = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
int i, j;
Index ima = A.getIndex();
// write
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) A.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
int[] origin = new int[2];
ncfile.write("t1", origin, A);
// write t2
ArrayByte Ab = new ArrayByte.D2(latDim.getLength(), lonDim.getLength());
ima = Ab.getIndex();
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) Ab.setByte(ima.set(i, j), (byte) (i * 10 + j));
ncfile.write("t2", origin, Ab);
// write t3
ncfile.write("t3", origin, Ab);
// write t4
Array As = new ArrayShort.D2(latDim.getLength(), lonDim.getLength());
ima = As.getIndex();
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) As.setShort(ima.set(i, j), (short) (i * 10 + j));
ncfile.write("t4", origin, As);
As.setShort(ima.set(0, 0), (short) -9999);
ncfile.write("t5", origin, As);
// write m1
ArrayDouble.D2 Ad = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) Ad.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
Ad.set(1, 1, -999.99);
ncfile.write("m1", new int[2], Ad);
// all done
ncfile.close();
System.out.println("**************TestStandardVar Write done");
}
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();
}
public void finish() throws IOException {
writeDataFinish();
ncfile.close();
}
private double copyVarData(NetcdfFileWriteable ncfile, Structure recordStruct)
throws IOException, InvalidRangeException {
int nrecs = (int) recordStruct.getSize();
int sdataSize = recordStruct.getElementSize();
double total = 0;
double totalRecordBytes = 0;
for (int count = 0; count < nrecs; count++) {
StructureData recordData = recordStruct.readStructure(count);
for (StructureMembers.Member m : recordData.getMembers()) {
if (m.getDataType() == DataType.STRUCTURE) {
int countLevel = 0;
ArrayStructure seq1 = recordData.getArrayStructure(m);
StructureDataIterator iter = seq1.getStructureDataIterator();
try {
while (iter.hasNext()) {
StructureData seqData = iter.next();
for (StructureMembers.Member seqm : seqData.getMembers()) {
Array data = seqData.getArray(seqm);
int[] shape = data.getShape();
int[] newShape = new int[data.getRank() + 2];
newShape[0] = 1;
newShape[1] = 1;
for (int i = 0; i < data.getRank(); i++) newShape[i + 1] = shape[i];
int[] origin = new int[data.getRank() + 2];
origin[0] = count;
origin[1] = countLevel;
String mname = seqm.getName() + "-" + m.getName();
if (debug && (count == 0) && (countLevel == 0))
System.out.println("write to = " + mname);
ncfile.write(mname, origin, data.reshape(newShape));
}
countLevel++;
}
} finally {
iter.finish();
}
} else {
Array data = recordData.getArray(m);
int[] shape = data.getShape();
int[] newShape = new int[data.getRank() + 1];
newShape[0] = 1;
for (int i = 0; i < data.getRank(); i++) newShape[i + 1] = shape[i];
int[] origin = new int[data.getRank() + 1];
origin[0] = count;
if (debug && (count == 0)) System.out.println("write to = " + m.getName());
ncfile.write(m.getName(), origin, data.reshape(newShape));
}
}
totalRecordBytes += sdataSize;
}
total += totalRecordBytes;
totalRecordBytes /= 1000 * 1000;
if (debug)
System.out.println(
"write record var; total = " + totalRecordBytes + " Mbytes # recs=" + nrecs);
return total;
}
