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");
}
/**
* Generates an empty template for a block
*
* @param files
* @param outputFile
* @return
*/
private NetcdfFileWriteable makeTemplate(TreeMap<Long, NetcdfFile> files, String outputFile) {
NetcdfFileWriteable ncf_out = null;
if (!(new File(outputDir).exists())) {
throw new IllegalArgumentException("Directory " + outputDir + " does not exist.");
}
try {
ncf_in = files.get((new ArrayList<Long>(files.keySet())).get(0));
Variable time = ncf_in.findVariable(inTimeName);
if (time == null) {
List<Variable> var = ncf_in.getVariables();
System.out.println(
"WARNING: Variable "
+ inTimeName
+ " was not found. File variables are:\n"
+ Arrays.toString(var.toArray()));
}
Variable depth = ncf_in.findVariable(inDepthName);
if (depth == null && ncf_in.getDimensions().size() > 3) {
List<Variable> var = ncf_in.getVariables();
System.out.println(
"WARNING: Depth variable "
+ inDepthName
+ " not found, and the number of dimensions is greater than 3."
+ " File variables are:\n"
+ Arrays.toString(var.toArray()));
}
Variable lat = ncf_in.findVariable(inLatName);
if (lat == null) {
List<Variable> var = ncf_in.getVariables();
System.out.println(
"WARNING: Variable "
+ inLatName
+ " was not found. File variables are:\n"
+ Arrays.toString(var.toArray()));
}
Variable lon = ncf_in.findVariable(inLonName);
if (lon == null) {
List<Variable> var = ncf_in.getVariables();
System.out.println(
"WARNING: Variable "
+ inLonName
+ " was not found. File variables are:\n"
+ Arrays.toString(var.toArray()));
}
int latidx = lat.findDimensionIndex(inVerticalDim);
int lonidx = lon.findDimensionIndex(inHorizontalDim);
int latlen = lat.getDimension(latidx).getLength();
int lonlen = lon.getDimension(lonidx).getLength();
Long[] la = files.keySet().toArray(new Long[files.size()]);
timeArr = Array.factory(DataType.DOUBLE, new int[] {files.size()});
for (int i = 0; i < la.length; i++) {
timeArr.setDouble(i, TimeConvert.millisToHYCOM(la[i]));
}
if (depth != null) {
depthArr = depth.read();
if (reverseDepth) {
for (int i = 0; i < depthArr.getShape()[0]; i++) {
if (i != 0) {
depthArr.setDouble(i, -depthArr.getDouble(i));
} else {
depthArr.setDouble(i, 0);
}
}
}
}
int[] latshape = ones(lat.getRank());
latshape[latidx] = latlen;
latArr = (lat.read(new int[lat.getRank()], latshape)).reduce();
int[] lonshape = ones(lon.getRank());
lonshape[lonidx] = lonlen;
lonArr = (lon.read(new int[lon.getRank()], lonshape)).reduce();
ncf_out = NetcdfFileWriteable.createNew(outputFile, false);
// Add Dimensions
Dimension timeDim = new Dimension(outTimeName, timeArr.getShape()[0]);
Dimension depthDim = null;
if (depthArr != null) {
depthDim = new Dimension(outDepthName, depthArr.getShape()[0]);
}
Dimension latDim = new Dimension(outLatName, latArr.getShape()[0]);
Dimension lonDim = new Dimension(outLonName, lonArr.getShape()[0]);
ncf_out.addDimension(null, timeDim);
if (depthDim != null) {
ncf_out.addDimension(null, depthDim);
}
ncf_out.addDimension(null, latDim);
ncf_out.addDimension(null, lonDim);
// Add Variables
ncf_out.addVariable(outTimeName, DataType.DOUBLE, new Dimension[] {timeDim});
if (depthDim != null) {
ncf_out.addVariable(outDepthName, DataType.DOUBLE, new Dimension[] {depthDim});
}
ncf_out.addVariable(outLatName, DataType.DOUBLE, new Dimension[] {latDim});
ncf_out.addVariable(outLonName, DataType.DOUBLE, new Dimension[] {lonDim});
Dimension[] dims = null;
if (depthDim == null) {
dims = new Dimension[] {timeDim, latDim, lonDim};
} else {
dims = new Dimension[] {timeDim, depthDim, latDim, lonDim};
}
ncf_out.addVariable(outVarName, DataType.FLOAT, dims);
// Add attribute information (cloned from source)
cloneAttributes(ncf_in, inTimeName, ncf_out, outTimeName);
cloneAttributes(ncf_in, inDepthName, ncf_out, outDepthName);
cloneAttributes(ncf_in, inLatName, ncf_out, outLatName);
cloneAttributes(ncf_in, inLonName, ncf_out, outLonName);
cloneAttributes(ncf_in, inVarName, ncf_out, outVarName);
ncf_out.create();
} catch (IOException e) {
e.printStackTrace();
} catch (InvalidRangeException e) {
e.printStackTrace();
}
return ncf_out;
}
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");
}
@Override
public void create() throws IOException {
netcdfFileWriteable.create();
}
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 static void main2(String args[]) throws Exception {
final int NLVL = 2;
final int NLAT = 6;
final int NLON = 12;
final int NumberOfRecords = 2;
final float SAMPLE_PRESSURE = 900.0f;
final float SAMPLE_TEMP = 9.0f;
final float START_LAT = 25.0f;
final float START_LON = -125.0f;
// Create the file.
String filename = "pres_temp_4D.nc";
NetcdfFileWriteable dataFile = null;
try {
// Create new netcdf-3 file with the given filename
dataFile = NetcdfFileWriteable.createNew(filename, false);
// add dimensions where time dimension is unlimit
Dimension lvlDim = dataFile.addDimension("level", NLVL);
Dimension latDim = dataFile.addDimension("latitude", NLAT);
Dimension lonDim = dataFile.addDimension("longitude", NLON);
Dimension timeDim = dataFile.addDimension("time", 1000); // should
// not be
// need
// second
// argument
ArrayList dims = null;
// Define the coordinate variables.
dataFile.addVariable("latitude", DataType.FLOAT, new Dimension[] {latDim});
dataFile.addVariable("longitude", DataType.FLOAT, new Dimension[] {lonDim});
// Define units attributes for data variables.
dataFile.addVariableAttribute("latitude", "units", "degrees_north");
dataFile.addVariableAttribute("longitude", "units", "degrees_east");
// Define the netCDF variables for the pressure and temperature
// data.
dims = new ArrayList();
dims.add(timeDim);
dims.add(lvlDim);
dims.add(latDim);
dims.add(lonDim);
dataFile.addVariable("pressure", DataType.FLOAT, dims);
dataFile.addVariable("temperature", DataType.FLOAT, dims);
// Define units attributes for data variables.
dataFile.addVariableAttribute("pressure", "units", "hPa");
dataFile.addVariableAttribute("temperature", "units", "celsius");
// Create some pretend data. If this wasn't an example program, we
// would have some real data to write for example, model output.
ArrayFloat.D1 lats = new ArrayFloat.D1(latDim.getLength());
ArrayFloat.D1 lons = new ArrayFloat.D1(lonDim.getLength());
int i, j;
for (i = 0; i < latDim.getLength(); i++) {
lats.set(i, START_LAT + 5.f * i);
}
for (j = 0; j < lonDim.getLength(); j++) {
lons.set(j, START_LON + 5.f * j);
}
// Create the pretend data. This will write our surface pressure and
// surface temperature data.
ArrayFloat.D4 dataTemp =
new ArrayFloat.D4(
NumberOfRecords, lvlDim.getLength(), latDim.getLength(), lonDim.getLength());
ArrayFloat.D4 dataPres =
new ArrayFloat.D4(
NumberOfRecords, lvlDim.getLength(), latDim.getLength(), lonDim.getLength());
for (int record = 0; record < NumberOfRecords; record++) {
i = 0;
for (int lvl = 0; lvl < NLVL; lvl++)
for (int lat = 0; lat < NLAT; lat++)
for (int lon = 0; lon < NLON; lon++) {
dataPres.set(record, lvl, lat, lon, SAMPLE_PRESSURE + i);
dataTemp.set(record, lvl, lat, lon, SAMPLE_TEMP + i++);
}
}
// Create the file. At this point the (empty) file will be written
// to disk
dataFile.create();
// A newly created Java integer array to be initialized to zeros.
int[] origin = new int[4];
dataFile.write("latitude", lats);
dataFile.write("longitude", lons);
dataFile.write("pressure", origin, dataPres);
dataFile.write("temperature", origin, dataTemp);
dataFile.close();
} catch (IOException e) {
e.printStackTrace(System.err);
} catch (InvalidRangeException e) {
e.printStackTrace(System.err);
} finally {
// if (dataFile != null) {
// try {
// dataFile.close();
// } catch (IOException ioe) {
// ioe.printStackTrace();
// }
// }
}
System.out.println("*** SUCCESS writing example file " + filename);
}
private void writeCDFChromatogram(
File file, IChromatogramMSD chromatogram, IProgressMonitor monitor) throws IOException {
NetcdfFileWriteable cdfChromatogram = NetcdfFileWriteable.createNew(file.getAbsolutePath());
DimensionSupport dimensionSupport = new DimensionSupport(cdfChromatogram, chromatogram);
AttributeSupport.setAttributes(cdfChromatogram, chromatogram);
Dimension errorNumber = dimensionSupport.getErrorNumber();
Dimension byteString64 = dimensionSupport.getByteString64();
Dimension byteString32 = dimensionSupport.getByteString32();
Dimension numberOfScans = dimensionSupport.getNumberOfScans();
Dimension instrumentNumber = dimensionSupport.getInstrumentNumber();
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_ERROR_LOG, errorNumber, byteString64, "");
dimensionSupport.addVariableDoubleD1(
CDFConstants.VARIABLE_A_D_SAMPLING_RATE, numberOfScans, dimensionSupport.NULL_VALUE_DOUBLE);
dimensionSupport.addVariableShortD1(
CDFConstants.VARIABLE_A_D_COADDITION_FACTOR,
numberOfScans,
dimensionSupport.NULL_VALUE_SHORT);
dimensionSupport.addVariableScanAcquisitionTime();
dimensionSupport.addVariableDoubleD1(
CDFConstants.VARIABLE_SCAN_DURATION, numberOfScans, dimensionSupport.NULL_VALUE_DOUBLE);
dimensionSupport.addVariableDoubleD1(
CDFConstants.VARIABLE_INTER_SCAN_TIME, numberOfScans, dimensionSupport.NULL_VALUE_DOUBLE);
dimensionSupport.addVariableDoubleD1(
CDFConstants.VARIABLE_RESOLUTION, numberOfScans, dimensionSupport.NULL_VALUE_DOUBLE);
dimensionSupport.addVariableActualScanNumber();
dimensionSupport.addVariableTotalIntensity();
dimensionSupport.addVariableDoubleD1(CDFConstants.VARIABLE_MASS_RANGE_MIN, numberOfScans, 0);
// dimensionSupport.addVariableMassRangeMin();
dimensionSupport.addVariableMassRangeMax();
dimensionSupport.addVariableDoubleD1(
CDFConstants.VARIABLE_TIME_RANGE_MIN, numberOfScans, dimensionSupport.NULL_VALUE_DOUBLE);
dimensionSupport.addVariableDoubleD1(
CDFConstants.VARIABLE_TIME_RANGE_MAX, numberOfScans, dimensionSupport.NULL_VALUE_DOUBLE);
dimensionSupport.addVariableScanIndex();
dimensionSupport.addVariablePointCount();
dimensionSupport.addVariableIntD1(CDFConstants.VARIABLE_FLAG_COUNT, numberOfScans, 0);
/*
* mass values, time values, intensity values
*/
dimensionSupport.addVariableScanValues();
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_NAME, instrumentNumber, byteString32, "Gas Chromatograph");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_ID, instrumentNumber, byteString32, "");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_MFR, instrumentNumber, byteString32, "");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_MODEL, instrumentNumber, byteString32, "");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_SERIAL_NO, instrumentNumber, byteString32, "");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_SW_VERSION, instrumentNumber, byteString32, "");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_FW_VERSION, instrumentNumber, byteString32, "");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_OS_VERSION, instrumentNumber, byteString32, "");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_APP_VERSION, instrumentNumber, byteString32, "");
dimensionSupport.addVariableCharD2(
CDFConstants.VARIABLE_INSTRUMENT_COMMENTS, instrumentNumber, byteString32, "");
try {
monitor.subTask(IConstants.EXPORT_DATA_ENTRIES);
cdfChromatogram.create();
ArrayList<IDataEntry> dataEntries = dimensionSupport.getDataEntries();
for (IDataEntry entry : dataEntries) {
monitor.subTask(entry.getVarName());
cdfChromatogram.write(entry.getVarName(), entry.getValues());
}
cdfChromatogram.close();
cdfChromatogram = null;
} catch (IOException e) {
logger.warn(e);
} catch (InvalidRangeException e) {
logger.warn(e);
} finally {
if (cdfChromatogram != null) {
try {
cdfChromatogram.close();
} catch (IOException e) {
logger.warn(e);
}
}
}
}
// return the last value written to the file
private int createFile(String variableName, DataType dataType, int writeSeed) {
// hacky init
this._unlimitedDim = null;
ArrayList<ArrayList<VariableEntry>> variableListList =
new ArrayList<ArrayList<VariableEntry>>();
// seperate method to define the variables for this file
/*
ArrayList<VariableEntry> variableList3 = defineDataForThisFile3();
variableListList.add(variableList3);
ArrayList<VariableEntry> variableList1 = defineDataForThisFile1();
variableListList.add(variableList1);
*/
ArrayList<VariableEntry> variableList2 = defineDataForThisFile2();
variableListList.add(variableList2);
Date now = new Date();
Random generator = new Random(now.getTime());
int valueCounter = writeSeed;
String filename = Long.toString(now.getTime()) + ".nc";
try {
// create the file
NetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(filename, false);
// this loop needs to define all the meta-data prior to any data being written
// set the metadata
System.out.println("\t calling writeNetcdfMetadata for file " + ncfile.getLocation());
ncfile = this.writeNetcdfMetadata(ncfile, variableName, variableListList);
// this is only called once per file
ncfile.create();
int suffixInt = 1;
for (ArrayList<VariableEntry> variableList : variableListList) {
// write out coordinate variables
for (VariableEntry entry : variableList) {
writeCoordinateVariable(entry, ncfile);
}
// pull out the dimensions of the variables from variableList
int[] dimensions = new int[variableList.size()];
for (int i = 0; i < dimensions.length; i++) {
dimensions[i] = variableList.get(i).getSize();
}
// write data to the file
valueCounter =
this.populateFile2(
ncfile,
variableName + Integer.toString(suffixInt),
dataType,
dimensions,
valueCounter,
generator);
suffixInt++;
}
// close the file
ncfile.close();
} catch (IOException ioe) {
System.out.println("IOException: " + ioe.toString());
} catch (InvalidRangeException e) {
System.out.println("InvalidRangeException: " + e.toString());
}
return valueCounter;
}
/**
* Creates the w file
*
* @param uFile - the input east-west velocity file
* @param vFile - the input north-south velocity file
* @throws InvalidRangeException
* @throws IOException
*/
private void generate(NetcdfDataset uFile, NetcdfDataset vFile)
throws InvalidRangeException, IOException {
// Set up empty arrays for ranges and dimensions.
dims = new ArrayList<Dimension>();
// Create the output file
outfile = NetcdfFileWriteable.createNew(outputWFile, false);
// Construct the data set dimensions - Time, Depth, Latitude and
// Longitude (in order)
int uTimeLength = uFile.findDimension(inTimeName).getLength();
int uLayerLength = uFile.findDimension(inLayerName).getLength();
int uXLength = uFile.findDimension(inXName).getLength();
int uYLength = uFile.findDimension(inYName).getLength();
int vTimeLength = vFile.findDimension(inTimeName).getLength();
int vLayerLength = vFile.findDimension(inLayerName).getLength();
int vXLength = vFile.findDimension(inXName).getLength();
int vYLength = vFile.findDimension(inYName).getLength();
Dimension timeDim = outfile.addDimension(outTimeName, Math.min(uTimeLength, vTimeLength));
Dimension layerDim = outfile.addDimension(outLayerName, Math.min(uLayerLength, vLayerLength));
Dimension yDim = outfile.addDimension(outYName, Math.min(uYLength, vYLength));
Dimension xDim = outfile.addDimension(outXName, Math.min(uXLength, vXLength));
// Add to a list - this becomes the coordinate system for the output
// variable. The order is *very* important!
dims.add(timeDim);
dims.add(layerDim);
dims.add(yDim);
dims.add(xDim);
// Create variables in the output file
outfile.addVariable(outTimeName, DataType.DOUBLE, new Dimension[] {timeDim});
outfile.addVariable(outLayerName, DataType.DOUBLE, new Dimension[] {layerDim});
outfile.addVariable(outLatName, DataType.DOUBLE, new Dimension[] {yDim, xDim});
outfile.addVariable(outLonName, DataType.DOUBLE, new Dimension[] {yDim, xDim});
// outfile.setLargeFile(true);
outfile.addVariable(outVarName, DataType.FLOAT, dims);
// Add attribute information (cloned from source)
cloneAttributes(uFile, inTimeName, outfile, outTimeName);
cloneAttributes(uFile, inLayerName, outfile, outLayerName);
cloneAttributes(uFile, inLatName, outfile, outLatName);
cloneAttributes(uFile, inLonName, outfile, outLonName);
// Finalizes the structure of the output file, making the changes real.
outfile.create();
// Write the static information for 1D axes.
outfile.write(outTimeName, uFile.findVariable(inTimeName).read());
outfile.write(outLayerName, uFile.findVariable(inLayerName).read());
outfile.write(outLatName, uFile.findVariable(inLatName).read());
outfile.write(outLonName, uFile.findVariable(inLonName).read());
Variable u = uFile.findVariable(inUName);
Variable v = vFile.findVariable(inVName);
Variable latdim = uFile.findVariable(inLatName);
Variable londim = uFile.findVariable(inLonName);
Variable zdim = uFile.findVariable(inLayerName);
// Read the depth array
Array depth_array = zdim.read(new int[] {0}, new int[] {uLayerLength});
double[] depths;
if (depth_array.getClass().getName().contains("Float")) {
float[] tmp = (float[]) depth_array.copyTo1DJavaArray();
depths = new double[tmp.length];
for (int i = 0; i < tmp.length; i++) {
depths[i] = tmp[i];
}
} else {
depths = (double[]) depth_array.copyTo1DJavaArray();
}
// Determine the size and midpoint of the depth bins
double[] binz = new double[depths.length - 1];
float[] mpz = new float[depths.length - 1];
for (int i = 0; i < depths.length - 1; i++) {
binz[i] = depths[i + 1] - depths[i];
mpz[i] = (float) (depths[i + 1] + depths[i]) / 2;
}
float[] nan = new float[uLayerLength];
for (int n = 0; n < uLayerLength; n++) {
nan[n] = Float.NaN;
}
// Write the collar as NaNs.
Array nana = Array.factory(java.lang.Float.class, new int[] {1, uLayerLength, 1, 1}, nan);
for (int t = 0; t < u.getShape(0); t++) {
for (int j = 0; j < u.getShape(3); j++) {
outfile.write(outVarName, new int[] {t, 0, 0, j}, nana);
outfile.write(outVarName, new int[] {t, 0, u.getShape(2) - 1, j}, nana);
}
for (int i = 1; i < u.getShape(2) - 1; i++) {
outfile.write(outVarName, new int[] {t, 0, i, 0}, nana);
outfile.write(outVarName, new int[] {t, 0, i, u.getShape(3) - 1}, nana);
}
}
// Calculate w values for each time, depth, lat and lon
// using 3x3 (horizontal) vertical pencils
for (int t = 0; t < u.getShape(0); t++) {
for (int i = 1; i < u.getShape(2) - 1; i++) {
Array lta =
latdim
.read(
new int[] {i - 1, 0}, // move for
// speed
new int[] {3, 1})
.reduce();
double currentLat = lta.getDouble(1);
for (int j = 1; j < u.getShape(3) - 1; j++) {
float[] w_arr = new float[uLayerLength];
if (i == 0 || j == 0 || i == u.getShape(2) - 1 || j == u.getShape(3) - 1) {
for (int n = 0; n < w_arr.length; n++) {
w_arr[n] = Float.NaN;
}
continue;
}
Array lna = londim.read(new int[] {0, j - 1}, new int[] {1, 3}).reduce();
double currentLon = lna.getDouble(1);
float maxZ = bathy.value_at_lonlat((float) currentLon, (float) currentLat);
boolean alwaysNaN = true;
for (int k = u.getShape(1) - 1; k >= 0; k--) {
// If the bathymetry says we're on land, then all values
// will be NaN. This type of check is required because
// the value does not equal java.Float.NaN, but
// 1.2676506E30.
if (maxZ > bathy_cutoff) {
w_arr[k] = Float.NaN;
continue;
}
if (k == 0) {
if (!alwaysNaN) {
w_arr[k] = 0;
} else {
w_arr[k] = Float.NaN;
}
continue;
}
if (maxZ < mpz[k - 1]) {
w_arr[k] = Float.NaN;
continue;
}
Array ua = u.read(new int[] {t, k, i - 1, j - 1}, new int[] {1, 1, 3, 3}).reduce();
Array va = v.read(new int[] {t, k, i - 1, j - 1}, new int[] {1, 1, 3, 3}).reduce();
float dz = calcdz(k, mpz, maxZ);
if (Float.isNaN(dz)) {
w_arr[k] = dz;
continue;
}
float dwdz = calcdwdz(lta, lna, ua, va);
if (Float.isNaN(dwdz)) {
continue;
}
if (alwaysNaN) {
w_arr[k] = dwdz;
alwaysNaN = false;
} else {
w_arr[k] = w_arr[k + 1] + dwdz;
}
}
Array warra =
Array.factory(java.lang.Float.class, new int[] {1, uLayerLength, 1, 1}, w_arr);
outfile.write(outVarName, new int[] {t, 0, i, j}, warra);
}
System.out.println("\tRow " + i + " complete.");
}
System.out.printf("Time %d of " + (u.getShape(0)) + " is complete.\n", t + 1);
}
}
