// @todo Make sure units are degrees_east
public double getLongitude(int point) throws IOException // required, units degrees_east
{
Array array = null;
try {
array = getLongitude(this.getPointRange(point));
} catch (InvalidRangeException e) {
IllegalArgumentException iae =
new IllegalArgumentException(
"Point <"
+ point
+ "> not in valid range <0, "
+ (this.getNumberPoints() - 1)
+ ">: "
+ e.getMessage());
iae.initCause(e);
throw iae;
}
if (array instanceof ArrayDouble) {
return (array.getDouble(array.getIndex()));
} else if (array instanceof ArrayFloat) {
return (array.getFloat(array.getIndex()));
} else {
throw new IOException(
"Longitude variable not float or double <" + array.getElementType().toString() + ">.");
}
}
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());
}
}
}
// @todo Make sure units are meters
public double getElevation(int point)
throws IOException // optional; units meters; missing = NaN.
{
Array array = null;
try {
array = getElevation(this.getPointRange(point));
} catch (InvalidRangeException e) {
IllegalArgumentException iae =
new IllegalArgumentException(
"Point <"
+ point
+ "> not in valid range <0, "
+ (this.getNumberPoints() - 1)
+ ">: "
+ e.getMessage());
iae.initCause(e);
throw iae;
}
if (array instanceof ArrayDouble) {
return array.getDouble(array.getIndex());
} else if (array instanceof ArrayFloat) {
return array.getFloat(array.getIndex());
} else {
throw new IOException(
"Elevation variable not float or double <" + array.getElementType().toString() + ">.");
}
}
public double getTimeValue(int point) throws IOException {
Array array = null;
try {
array = getTime(this.getPointRange(point));
} catch (InvalidRangeException e) {
IllegalArgumentException iae =
new IllegalArgumentException(
"Point <"
+ point
+ "> not in valid range <0, "
+ (this.getNumberPoints() - 1)
+ ">: "
+ e.getMessage());
iae.initCause(e);
throw iae;
}
if (array instanceof ArrayDouble) {
return (array.getDouble(array.getIndex()));
} else if (array instanceof ArrayFloat) {
return (array.getFloat(array.getIndex()));
} else if (array instanceof ArrayInt) {
return (array.getInt(array.getIndex()));
} else {
throw new IOException(
"Time variable not float, double, or integer <"
+ array.getElementType().toString()
+ ">.");
}
}
public StructureData getData() throws IOException {
if (sdata != null) return sdata;
try {
return (SingleTrajectory.this.getData(point));
} catch (InvalidRangeException e) {
throw new IllegalStateException(e.getMessage());
}
}
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++;
}
Array readFully() throws IOException {
if (origin == null) {
return binVariable.read();
} else {
try {
return binVariable.read(origin, shape).reduce();
} catch (InvalidRangeException e) {
throw new IOException(e.getMessage());
}
}
}
Array read(int firstIndex, int length) throws IOException {
try {
if (origin == null) {
return binVariable.read(new int[] {firstIndex}, new int[] {length});
} else {
int[] originFull = origin.clone();
int[] shapeFull = shape.clone();
originFull[binDimIndex] = firstIndex;
shapeFull[binDimIndex] = length;
return binVariable.read(originFull, shapeFull).reduce();
}
} catch (InvalidRangeException e) {
throw new IOException(e.getMessage());
}
}
public Range getFullRange() {
Range range = null;
try {
range = new Range(0, this.getNumberPoints() - 1);
} catch (InvalidRangeException e) {
IllegalStateException ise =
new IllegalStateException(
"Full trajectory range invalid <0, "
+ (this.getNumberPoints() - 1)
+ ">: "
+ e.getMessage());
ise.initCause(e);
throw (ise);
}
return range;
}
public Array getData(int point, String parameterName) throws IOException {
try {
return (getData(this.getPointRange(point), parameterName));
} catch (InvalidRangeException e) {
IllegalArgumentException iae =
new IllegalArgumentException(
"Point <"
+ point
+ "> not in valid range <0, "
+ (this.getNumberPoints() - 1)
+ ">: "
+ e.getMessage());
iae.initCause(e);
throw iae;
}
}
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 static void doVar(NetcdfDataset netcdfdataset, String varS, String limits) {
System.out.println("\r---------\r\r");
ucar.nc2.Variable var = netcdfdataset.findVariable(varS);
System.out.println(var.getName() + " " + var.getSize());
Array arr;
try {
arr = var.read(limits);
NCdump.printArray(arr, "array", System.out, null);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (InvalidRangeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
/** Main-type execution */
public void go() {
System.out.println("Writing to " + outputWFile + "...");
try {
uFile = NetcdfDataset.openDataset(inputUFile);
vFile = NetcdfDataset.openDataset(inputVFile);
bathy = new NetCDF_FloatGrid_3D(inputBathyFile, inLatName, inLonName);
generate(uFile, vFile);
} catch (IOException e) {
e.printStackTrace();
} catch (InvalidRangeException e) {
e.printStackTrace();
}
System.out.println("Complete.");
}
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);
}
}
protected synchronized void invalidateLines(SkipBadNav skipBadNav, Variable latitude)
throws IOException {
final int[] shape = latitude.getShape();
try {
int lineCount = shape[0];
final int[] start = new int[] {0, 0};
// just grab the first and last pixel for each scan line
final int[] stride = new int[] {1, shape[1] - 1};
final int[] count = new int[] {shape[0], shape[1]};
Section section = new Section(start, count, stride);
Array array;
synchronized (ncFile) {
array = latitude.read(section);
}
for (int i = 0; i < lineCount; i++) {
int ix = i * 2;
float valstart = array.getFloat(ix);
float valend = array.getFloat(ix + 1);
if (skipBadNav.isBadNav(valstart) || skipBadNav.isBadNav(valend)) {
leadLineSkip++;
} else {
break;
}
}
for (int i = lineCount; i-- > 0; ) {
int ix = i * 2;
float valstart = array.getFloat(ix);
float valend = array.getFloat(ix + 1);
if (skipBadNav.isBadNav(valstart) || skipBadNav.isBadNav(valend)) {
tailLineSkip++;
} else {
break;
}
}
} catch (InvalidRangeException e) {
throw new IOException(e.getMessage());
}
}
/**
* Copies the contents of single NetCDF files into a block file
*
* @param map
* @param ncf_out
*/
private void copyContent(TreeMap<Long, NetcdfFile> map, NetcdfFileWriteable ncf_out) {
try {
// Write the static information for 1D axes.
ncf_out.write(outTimeName, timeArr);
ncf_out.write(outDepthName, depthArr);
ncf_out.write(outLatName, latArr);
ncf_out.write(outLonName, lonArr);
Iterator<Long> it = map.keySet().iterator();
int ct = 0;
while (it.hasNext()) {
long time = it.next();
System.out.print("\t" + ct + "\tWorking on " + new Date(time));
NetcdfFile copyfile = map.get(time);
int timesteps = copyfile.findDimension(inTimeName).getLength();
Variable invar = copyfile.findVariable(inVarName);
int[] shape = invar.getShape();
shape[0] = 1;
for (int i = 0; i < timesteps; i++) {
int[] origin_in = new int[] {i, 0, 0, 0};
int[] origin_out = new int[] {ct, 0, 0, 0};
ncf_out.write(outVarName, origin_out, invar.read(origin_in, shape));
ct++;
}
System.out.println("\tDone.");
}
} catch (IOException e) {
e.printStackTrace();
} catch (InvalidRangeException e) {
e.printStackTrace();
}
}
public StructureData getFeatureData() throws IOException {
if (null == sdata) {
try {
// deal with files that are updating // LOOK kludge?
if (recno > getRecordCount()) {
int n = getRecordCount();
ncfile.syncExtend();
log.info(
"RecordPointObs.getData recno="
+ recno
+ " > "
+ n
+ "; after sync= "
+ getRecordCount());
}
sdata = recordVar.readStructure(recno);
} catch (ucar.ma2.InvalidRangeException e) {
e.printStackTrace();
throw new IOException(e.getMessage());
}
}
return sdata;
}
public void initialize(String dir) throws IOException {
// Set Time Zone to UTC
formatUTC.setTimeZone(TimeZone.getTimeZone("UTC"));
this.dir = dir;
File f = new File(dir);
// Ensure the path is a directory
if (!f.isDirectory()) {
throw new IllegalArgumentException(f.getName() + " is not a directory.");
}
// Filter the list of files
File[] fa = f.listFiles(new FilenamePatternFilter(".*_[uvw].*\\.nc"));
if (fa == null) {
throw new IOException("File list is empty.");
}
for (File fil : fa) {
String name = fil.getName();
NetcdfFile ncf = NetcdfFile.open(fil.getPath());
tVar = ncf.findVariable(tName);
if (tVar == null) {
System.out.println(
"WARNING: Time variable "
+ tVar
+ " was not found in "
+ fil.getPath()
+ " when initializing the VelocityReader. This file will be skipped.");
continue;
}
Array arr = tVar.read();
// Convert into a java array
double[] ja = (double[]) arr.copyTo1DJavaArray();
// Determine the minimum and maximum times
long[] minmax = new long[2];
minmax[0] = TimeConvert.HYCOMToMillis((long) ja[0]);
minmax[1] = TimeConvert.HYCOMToMillis((long) ja[ja.length - 1]);
// Put into an index linking start time with the associated file
if (name.lastIndexOf("_u") > 0) {
if (uFiles.containsKey(minmax[0])) {
System.out.print(
"WARNING: Velocity files have duplicate time keys. "
+ name
+ "/"
+ uFiles.get(minmax[0])
+ " at "
+ new Date(minmax[0]));
System.out.println(" Skipping latter file.");
} else {
uFiles.put(minmax[0], ncf);
}
}
if (name.lastIndexOf("_v") > 0) {
if (vFiles.containsKey(minmax[0])) {
System.out.print(
"WARNING: Velocity files have duplicate time keys. "
+ name
+ "/"
+ vFiles.get(minmax[0])
+ " at "
+ new Date(minmax[0]));
System.out.println(" Skipping latter file.");
} else {
vFiles.put(minmax[0], ncf);
}
}
if (name.lastIndexOf("_w") > 0) {
if (wFiles.containsKey(minmax[0])) {
System.out.print(
"WARNING: Velocity files have duplicate time keys. "
+ name
+ "/"
+ wFiles.get(minmax[0])
+ " at "
+ new Date(minmax[0]));
System.out.println(" Skipping latter file.");
} else {
wFiles.put(minmax[0], ncf);
}
}
}
// If there are no files in one of the index collections, then exit.
if (uFiles.size() == 0 || vFiles.size() == 0 || wFiles.size() == 0) {
System.out.println(
"Velocity directory is empty, or files/variables are not named properly."
+ "Files must be named as *_u*, *_v*, and *_w*.");
System.exit(0);
}
uKeys = new ArrayList<Long>(uFiles.keySet());
vKeys = new ArrayList<Long>(vFiles.keySet());
wKeys = new ArrayList<Long>(wFiles.keySet());
// Populate uFile, vFile and wFile with the first entry so that they
// are not null
uFile = uFiles.get(uKeys.get(0));
vFile = vFiles.get(vKeys.get(0));
wFile = wFiles.get(wKeys.get(0));
uVar = uFile.findVariable(uName);
vVar = vFile.findVariable(vName);
wVar = wFile.findVariable(wName);
// Latitude and depth are read here because they should not change
// and therefore can be input once only.
latVar = uFile.findVariable(latName);
lonVar = uFile.findVariable(lonName);
zVar = uFile.findVariable(zName);
setXLookup(lonName);
setYLookup(latName);
setZLookup(zName);
if (positiveDown) {
zloc.setNegate(true);
}
bounds[0][0] = uKeys.get(0);
NetcdfFile lastfile = uFiles.get(uKeys.get(uKeys.size() - 1));
Variable t = lastfile.findVariable(tName);
double last;
try {
last = t.read(new int[] {t.getShape(0) - 1}, new int[] {1}).getDouble(0);
bounds[0][1] = TimeConvert.HYCOMToMillis((long) last);
} catch (InvalidRangeException e) {
e.printStackTrace();
}
}
public File writeCoverageDataToFile(
WcsRequest.Format format,
LatLonRect bboxLatLonRect,
AxisSubset vertSubset,
List<String> rangeSubset,
CalendarDateRange timeRange)
throws WcsException {
boolean zRangeDone = false;
boolean tRangeDone = false;
try {
// Get the height range.
Range zRange = vertSubset != null ? vertSubset.getRange() : null;
zRangeDone = true;
// Get the time range.
Range tRange = null;
if (timeRange != null) {
CoordinateAxis1DTime timeAxis = this.coordSys.getTimeAxis1D();
int startIndex = timeAxis.findTimeIndexFromCalendarDate(timeRange.getStart());
int endIndex = timeAxis.findTimeIndexFromCalendarDate(timeRange.getEnd());
tRange = new Range(startIndex, endIndex);
tRangeDone = true;
}
if (format == WcsRequest.Format.GeoTIFF || format == WcsRequest.Format.GeoTIFF_Float) {
if (rangeSubset.size() != 1) {
String msg =
"GeoTIFF response encoding only available for single range field selection ["
+ rangeSubset
+ "].";
log.error("writeCoverageDataToFile(): " + msg);
throw new WcsException(WcsException.Code.InvalidParameterValue, "RangeSubset", msg);
}
String reqRangeFieldName = rangeSubset.get(0);
File dir = new File(getDiskCache().getRootDirectory());
File tifFile = File.createTempFile("WCS", ".tif", dir);
if (log.isDebugEnabled())
log.debug("writeCoverageDataToFile(): tifFile=" + tifFile.getPath());
WcsRangeField rangeField = this.range.get(reqRangeFieldName);
GridDatatype subset =
rangeField.getGridDatatype().makeSubset(tRange, zRange, bboxLatLonRect, 1, 1, 1);
Array data = subset.readDataSlice(0, 0, -1, -1);
GeotiffWriter writer = new GeotiffWriter(tifFile.getPath());
writer.writeGrid(
this.dataset.getDataset(), subset, data, format == WcsRequest.Format.GeoTIFF);
writer.close();
return tifFile;
} else if (format == WcsRequest.Format.NetCDF3) {
File dir = new File(getDiskCache().getRootDirectory());
File outFile = File.createTempFile("WCS", ".nc", dir);
if (log.isDebugEnabled())
log.debug("writeCoverageDataToFile(): ncFile=" + outFile.getPath());
// WTF ?? this.coordSys.getVerticalAxis().isNumeric();
NetcdfFileWriter writer =
NetcdfFileWriter.createNew(NetcdfFileWriter.Version.netcdf3, outFile.getAbsolutePath());
CFGridWriter2.writeFile(
this.dataset.getDataset(),
rangeSubset,
bboxLatLonRect,
null,
1,
zRange,
timeRange,
1,
true,
writer);
return outFile;
} else {
log.error(
"writeCoverageDataToFile(): Unsupported response encoding format [" + format + "].");
throw new WcsException(
WcsException.Code.InvalidFormat,
"Format",
"Unsupported response encoding format [" + format + "].");
}
} catch (InvalidRangeException e) {
String msg = "Failed to subset coverage [" + this.getName();
if (!zRangeDone) msg += "] along vertical axis [" + vertSubset + "]. ";
else if (!tRangeDone) msg += "] along time axis [" + timeRange + "]. ";
else msg += "] in horizontal plane [" + bboxLatLonRect + "]. ";
log.error("writeCoverageDataToFile(): " + msg + e.getMessage());
throw new WcsException(WcsException.Code.CoverageNotDefined, "", msg);
} catch (IOException e) {
log.error(
"writeCoverageDataToFile(): Failed to write file for requested coverage <"
+ this.getName()
+ ">: "
+ e.getMessage());
throw new WcsException(
WcsException.Code.UNKNOWN, "", "Problem creating coverage [" + this.getName() + "].");
}
}
public static void generateObs(NetcdfDataset netcdfdataset) {
try {
ucar.nc2.Variable lon = netcdfdataset.findVariable("lon");
ucar.nc2.Variable lat = netcdfdataset.findVariable("lat");
ucar.nc2.Variable time = netcdfdataset.findVariable("time");
ucar.nc2.Variable BAssta = netcdfdataset.findVariable("BAssta");
Array dataLat = lat.read();
int[] shapeLat = lat.getShape();
Index indexLat = dataLat.getIndex();
Array dataLon = lon.read();
int[] shapeLon = lon.getShape();
Index indexLon = dataLon.getIndex();
Array dataTime = time.read();
Index indexTime = dataTime.getIndex();
// mbari
double minLat = 34.955;
double maxLat = 38.260;
double minLon = -124.780;
double maxLon = -121.809;
int minIndexLat = -Integer.MAX_VALUE;
int minIndexLon = Integer.MAX_VALUE;
int maxIndexlat = Integer.MIN_VALUE;
int maxIndexLon = Integer.MIN_VALUE;
// lon is ginve as +
// int[][] indexLatLon = new int[shapeLat[0]][shapeLon[0]];
List lats = new ArrayList<Integer>();
List lons = new ArrayList<Integer>();
// get lats
for (int i = 0; i < shapeLat[0]; i++) {
Double lat_d = dataLat.getDouble(indexLat.set(i));
if (lat_d >= minLat && lat_d <= maxLat) {
minIndexLat = i;
lats.add(i);
}
}
for (int j = 0; j < shapeLon[0]; j++) {
Double lon_d = dataLon.getDouble(indexLon.set(j));
if (lon_d > 180) {
lon_d = -360 + lon_d;
}
if (lon_d >= minLon && lon_d <= maxLon) {
lons.add(j);
}
}
// get values:
ucar.nc2.Variable bassta = netcdfdataset.findVariable("BAssta");
int indMinLat = (Integer) lats.get(0);
int indMaxLat = (Integer) lats.get(lats.size() - 1);
int indMinLon = (Integer) lons.get(0);
int indMaxLon = (Integer) lons.get(lons.size() - 1);
int indMinTime = 0;
int indMaxTime = time.getShape()[0] - 1;
String s = createString(indMinLat, indMaxLat, indMinLon, indMaxLon, indMinTime, indMaxTime);
// doVar(netcdfdataset, "BAssta", s);
// Array dataVar= bassta.read();
// bassta.getShape()
// System.out.println("lats size: " + lats.size()+" "+"lons size:
// "+lons.size());
// for a given lat lon get time series
// 1st lat lon
s = createString(indMinLat, indMinLat, indMinLon, indMinLon, indMinTime, indMaxTime);
Array arr = BAssta.read(s);
int[] shapeArr = arr.getShape();
Index index = arr.getIndex();
System.out.println(shapeArr);
// [74, 1, 1, 1]
for (int i = 0; i < shapeArr[0]; i++) {
Double d = arr.getDouble(index.set(i, 0, 0, 0));
Double t = dataTime.getDouble(indexTime.set(i));
String timeS = TimeUtil.getISOFromMillisec(t * 1000);
System.out.println(t + " " + timeS + " " + d);
}
// lat lon are fixed, only varying time
// basta[time,alt,lat,lon]
// NCdump.printArray(arr, "array", System.out, null);
// doVar(netcdfdataset, "BAssta", s);
// doVar(netcdfdataset, "time", indMinTime + ":" + indMaxTime);
// while (i < lon.getSize()) {
// System.out.println("obs" + i + " " + lat + " " + lon);
// i++;
// }
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (InvalidRangeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
/**
* 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;
}
/**
* Retrieves velocities as a vector [u,v,w] based on given positions
*
* @param time - time coordinate in milliseconds
* @param z - depth coordinate
* @param lon - longitude (decimal degrees)
* @param lat - latitude (decimal degrees)
*/
@Override
public synchronized double[] getVelocities(long time, double z, double lon, double lat) {
if (Double.isNaN(lon) || Double.isNaN(lat)) {
throw new IllegalArgumentException("Latitude or Longitude value is NaN");
}
// Completely outside the time bounds
if (time < bounds[0][0] || time > bounds[0][1]) {
this.notifyAll();
return null;
}
// Completely outside the vertical bounds
if (z < bounds[1][0] || z > bounds[1][1]) {
this.notifyAll();
return null;
}
// Completely outside the north-south bounds - return null as opposed
// to NODATA
if (lat < bounds[2][0] || lat > bounds[2][1]) {
this.notifyAll();
return null;
}
// Completely outside the east-west bounds
if (lon < bounds[3][0] || lon > bounds[3][1]) {
this.notifyAll();
return null;
}
checkTime(time);
try {
int js, is, ks, ts;
// Searching for the cell indices nearest to the given location
is = yloc.lookup(lat);
js = xloc.lookup(lon);
ks = zloc.lookup(z);
ts = tloc.lookup(TimeConvert.millisToHYCOM(time));
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
// ATTENTION!!!! THE ORDER IS VERY IMPORTANT HERE!!!! Latitude (i/y)
// and then Longitude (j/x). That's the way it is set up in the
// NetCDF File. The best way would be to have automatic order
// detection
// somehow....
// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
// Handling data edges
int i_lhs = halfKernel;
int i_rhs = halfKernel;
int j_lhs = halfKernel;
int j_rhs = halfKernel;
int k_lhs = zHalfKernel;
int k_rhs = zHalfKernel;
if (is < halfKernel) {
i_lhs = is;
}
if (is + halfKernel >= yloc.arraySize()) {
i_rhs = yloc.arraySize() - is - 1;
}
if (js < halfKernel) {
j_lhs = js;
}
if (js + halfKernel >= xloc.arraySize()) {
j_rhs = xloc.arraySize() - js - 1;
}
if (ks < zHalfKernel) {
k_lhs = ks;
}
if (ks + zHalfKernel >= zloc.arraySize()) {
k_rhs = zloc.arraySize() - ks - 1;
}
int istart = is - i_lhs;
int jstart = js - j_lhs;
int kstart = ks - k_lhs;
// LHS + RHS + middle
int idim = i_lhs + i_rhs + 1;
int jdim = j_lhs + j_rhs + 1;
int kdim = k_lhs + k_rhs + 1;
// Splines cannot be used with only 2 points. If we are using a
// kernel size of 3 and it is reduced due to edge effects, then
// slide the window.
if (kdim == 2) {
if (kstart != 0) {
kstart -= (k_rhs + 1);
}
kdim = zKernelSize;
}
int blocksize = idim * jdim * kdim;
// int semiblock = (idim * (jdim + 1) * kdim) / 3;
int[] origin = new int[] {ts, kstart, istart, jstart};
int[] shape = new int[] {1, kdim, idim, jdim};
try {
uArr = uVar.read(origin, shape);
uArr = uArr.reduce();
} catch (InvalidRangeException e) {
// Should not occur. Checking done above.
e.printStackTrace();
}
try {
vArr = vVar.read(origin, shape);
vArr = vArr.reduce();
} catch (InvalidRangeException e) {
// Should not occur. Checking done above.
e.printStackTrace();
}
if (zloc.isIn_Bounds() >= 0) {
try {
wArr = wVar.read(origin, shape);
wArr = wArr.reduce();
} catch (InvalidRangeException e) {
// Should not occur. Checking done above.
e.printStackTrace();
}
}
float[][][] autmp = (float[][][]) uArr.copyToNDJavaArray();
float[][][] avtmp = (float[][][]) vArr.copyToNDJavaArray();
float[][][] awtmp = (float[][][]) wArr.copyToNDJavaArray();
// Mitigate NODATA values
int uct = 0;
double usum = 0;
double uavg = 0;
double ussq = 0;
double uvar = 0;
int vct = 0;
double vsum = 0;
double vavg = 0;
double vssq = 0;
double vvar = 0;
int wct = 0;
double wsum = 0;
double wavg = 0;
double wssq = 0;
double wvar = 0;
for (int i = 0; i < idim; i++) {
for (int j = 0; j < jdim; j++) {
for (int k = 0; k < kdim; k++) {
if (autmp[k][i][j] < cutoff && !Double.isNaN(autmp[k][i][j])) {
uct++;
usum += autmp[k][i][j];
uavg = usum / uct;
ussq += autmp[k][i][j] * autmp[k][i][j];
uvar = ussq / uct - uavg * uavg;
// } else {
// if ((k > 0) && Double.isNaN(autmp[k - 1][i][j]))
// {
// autmp[k][i][j] = 0;
// }
}
}
}
}
for (int i = 0; i < idim; i++) {
for (int j = 0; j < jdim; j++) {
for (int k = 0; k < kdim; k++) {
if (avtmp[k][i][j] < cutoff && !Double.isNaN(avtmp[k][i][j])) {
vct++;
vsum += avtmp[k][i][j];
vavg = vsum / vct;
vssq += avtmp[k][i][j] * avtmp[k][i][j];
vvar = vssq / vct - vavg * vavg;
// } else {
// if ((k > 0)
// && Double.isNaN(avtmp[k - 1][i][j])) {
// avtmp[k][i][j] = 0;
// }
}
}
}
}
if (zloc.isIn_Bounds() >= 0) {
for (int i = 0; i < idim; i++) {
for (int j = 0; j < jdim; j++) {
for (int k = 0; k < kdim; k++) {
if (awtmp[k][i][j] < cutoff && !Double.isNaN(awtmp[k][i][j])) {
wct++;
wsum += awtmp[k][i][j];
wavg = wsum / wct;
wssq += awtmp[k][i][j] * awtmp[k][i][j];
wvar = wssq / wct - wavg * wavg;
// } else {
// if ((k > 0)
// && Double.isNaN(awtmp[k - 1][i][j])) {
// awtmp[k][i][j] = 0;
// }
}
}
}
}
}
nearNoData = false;
// If there are null values...
if (uct < blocksize) {
nearNoData = true;
// If there are more than (io-1)^2, return null
/*
* if (uct < semiblock) { velocities = NODATA; averages =
* NODATA; variances = NODATA; return NODATA; }
*/
// Otherwise mitigate by replacing using the average value.
for (int i = 0; i < idim; i++) {
for (int j = 0; j < jdim; j++) {
for (int k = 0; k < kdim; k++) {
if (autmp[k][i][j] > cutoff || Double.isNaN(autmp[k][i][j])) {
if (ks == 0) {
autmp[k][i][j] = 0;
}
autmp[k][i][j] = (float) uavg;
}
}
}
}
}
if (vct < blocksize) {
nearNoData = true;
// If there are more than halfKernel/2, return null
/*
* if (vct < semiblock) { this.notifyAll(); velocities = NODATA;
* averages = NODATA; variances = NODATA; return NODATA; }
*/
// Otherwise mitigate by replacing using the average value.
for (int i = 0; i < idim; i++) {
for (int j = 0; j < jdim; j++) {
for (int k = 0; k < kdim; k++) {
if (avtmp[k][i][j] > cutoff || Double.isNaN(avtmp[k][i][j])) {
avtmp[k][i][j] = (float) vavg;
}
}
}
}
}
if (zloc.isIn_Bounds() >= 0) {
if (wct < blocksize) {
nearNoData = true;
// If there are more than (halfKernel-1)^2, return null
/*
* if (wct < semiblock) { this.notifyAll(); velocities =
* NODATA; averages = NODATA; variances = NODATA; return
* NODATA; }
*/
// Otherwise mitigate by replacing using the average value.
for (int i = 0; i < idim; i++) {
for (int j = 0; j < jdim; j++) {
for (int k = 0; k < kdim; k++) {
if (awtmp[k][i][j] > cutoff || Double.isNaN(awtmp[k][i][j])) {
awtmp[k][i][j] = (float) wavg;
}
}
}
}
}
}
/*
* Convert the Arrays into Java arrays - because latitude and z
* should be consistent among files, we subset from a constant
* array.
*/
double[] latja = Arrays.copyOfRange(yloc.getJavaArray(), istart, istart + idim);
double[] lonja = Arrays.copyOfRange(xloc.getJavaArray(), jstart, jstart + jdim);
double[] zja = Arrays.copyOfRange(zloc.getJavaArray(), kstart, kstart + kdim);
// Obtain the interpolated values
TricubicSplineInterpolator tci = new TricubicSplineInterpolator();
TricubicSplineInterpolatingFunction tsf = tci.interpolate(zja, latja, lonja, autmp);
// u = tcs.interpolate(z, lat, lon);
u = tsf.value(z, lat, lon);
// tcs.setValues(avtmp);
// v = tcs.interpolate(z, lat, lon);
tsf = tci.interpolate(zja, latja, lonja, avtmp);
v = tsf.value(z, lat, lon);
if (zloc.isIn_Bounds() >= 0) {
// tcs.setValues(awtmp);
// w = tcs.interpolate(z, lat, lon);
tsf = tci.interpolate(zja, latja, lonja, awtmp);
w = tsf.value(z, lat, lon);
} else {
w = 0;
}
// If there is something strange with the values, return NODATA.
if (Math.abs(u) > cutoff) {
u = 0.0f;
v = 0.0f;
w = 0.0f;
this.notifyAll();
velocities = NODATA;
averages = NODATA;
variances = NODATA;
return NODATA;
} else if (Math.abs(v) > cutoff) {
u = 0.0f;
v = 0.0f;
w = 0.0f;
this.notifyAll();
velocities = NODATA;
averages = NODATA;
variances = NODATA;
return NODATA;
} else if (Math.abs(w) > cutoff) {
u = 0.0f;
v = 0.0f;
w = 0.0f;
this.notifyAll();
velocities = NODATA;
averages = NODATA;
variances = NODATA;
return NODATA;
}
if (Double.isNaN(u) || Double.isNaN(v) || Double.isNaN(w)) {
u = 0.0f;
v = 0.0f;
w = 0.0f;
this.notifyAll();
velocities = NODATA;
averages = NODATA;
variances = NODATA;
return NODATA;
}
// Otherwise return the interpolated values.
this.notifyAll();
velocities = new double[] {u, v, w};
averages = new double[] {uavg, vavg, wavg};
// Correct running population variance to be sample variance.
double ucorr = (double) uct / (double) (uct - 1);
double vcorr = (double) vct / (double) (vct - 1);
double wcorr = (double) wct / (double) (wct - 1);
variances = new double[] {uvar * ucorr, vvar * vcorr, wvar * wcorr};
return velocities;
// If for some reason there was an error reading from the file,
// return null.
} catch (IOException e) {
System.out.println("WARNING: Error reading from velocity files.\n\n");
e.printStackTrace();
}
this.notifyAll();
return null;
}
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)));
}
// 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;
}
protected Map<Band, Variable> addSmiBands(Product product, List<Variable> variables) {
final int sceneRasterWidth = product.getSceneRasterWidth();
final int sceneRasterHeight = product.getSceneRasterHeight();
Map<Band, Variable> bandToVariableMap = new HashMap<Band, Variable>();
for (Variable variable : variables) {
int variableRank = variable.getRank();
if (variableRank == 2) {
final int[] dimensions = variable.getShape();
final int height = dimensions[0];
final int width = dimensions[1];
if (height == sceneRasterHeight && width == sceneRasterWidth) {
String name = variable.getShortName();
if (name.equals("l3m_data")) {
try {
name = getStringAttribute("Parameter") + " " + getStringAttribute("Measure");
} catch (Exception e) {
e.printStackTrace();
}
}
final int dataType = getProductDataType(variable);
final Band band = new Band(name, dataType, width, height);
// band = new Band(name, dataType, width, height);
product.addBand(band);
try {
Attribute fillvalue = variable.findAttribute("_FillValue");
if (fillvalue == null) {
fillvalue = variable.findAttribute("Fill");
}
if (fillvalue != null) {
band.setNoDataValue((double) fillvalue.getNumericValue().floatValue());
band.setNoDataValueUsed(true);
}
} catch (Exception ignored) {
}
bandToVariableMap.put(band, variable);
// Set units, if defined
try {
band.setUnit(getStringAttribute("Units"));
} catch (Exception ignored) {
}
final List<Attribute> list = variable.getAttributes();
double[] validMinMax = {0.0, 0.0};
for (Attribute hdfAttribute : list) {
final String attribName = hdfAttribute.getShortName();
if ("units".equals(attribName)) {
band.setUnit(hdfAttribute.getStringValue());
} else if ("long_name".equalsIgnoreCase(attribName)) {
band.setDescription(hdfAttribute.getStringValue());
} else if ("slope".equalsIgnoreCase(attribName)) {
band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("intercept".equalsIgnoreCase(attribName)) {
band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("scale_factor".equals(attribName)) {
band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("add_offset".equals(attribName)) {
band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
} else if (attribName.startsWith("valid_")) {
if ("valid_min".equals(attribName)) {
validMinMax[0] = hdfAttribute.getNumericValue(0).doubleValue();
} else if ("valid_max".equals(attribName)) {
validMinMax[1] = hdfAttribute.getNumericValue(0).doubleValue();
} else if ("valid_range".equals(attribName)) {
validMinMax[0] = hdfAttribute.getNumericValue(0).doubleValue();
validMinMax[1] = hdfAttribute.getNumericValue(1).doubleValue();
}
}
}
if (validMinMax[0] != validMinMax[1]) {
double[] minmax = {0.0, 0.0};
minmax[0] = validMinMax[0];
minmax[1] = validMinMax[1];
if (band.getScalingFactor() != 1.0) {
minmax[0] *= band.getScalingFactor();
minmax[1] *= band.getScalingFactor();
}
if (band.getScalingOffset() != 0.0) {
minmax[0] += band.getScalingOffset();
minmax[1] += band.getScalingOffset();
}
String validExp = format("%s >= %.2f && %s <= %.2f", name, minmax[0], name, minmax[1]);
band.setValidPixelExpression(
validExp); // .format(name, validMinMax[0], name, validMinMax[1]));
}
}
} else if (variableRank == 4) {
final int[] dimensions = variable.getShape();
final int height = dimensions[2];
final int width = dimensions[3];
if (height == sceneRasterHeight && width == sceneRasterWidth) {
String name = variable.getShortName();
final int dataType = getProductDataType(variable);
final Band band = new Band(name, dataType, width, height);
// band = new Band(name, dataType, width, height);
Variable sliced = null;
try {
sliced = variable.slice(0, 0).slice(0, 0);
} catch (InvalidRangeException e) {
e.printStackTrace(); // Todo change body of catch statement.
}
bandToVariableMap.put(band, sliced);
product.addBand(band);
try {
Attribute fillvalue = variable.findAttribute("_FillValue");
if (fillvalue != null) {
band.setNoDataValue((double) fillvalue.getNumericValue().floatValue());
band.setNoDataValueUsed(true);
}
} catch (Exception ignored) {
}
// Set units, if defined
try {
band.setUnit(getStringAttribute("units"));
} catch (Exception ignored) {
}
final List<Attribute> list = variable.getAttributes();
for (Attribute hdfAttribute : list) {
final String attribName = hdfAttribute.getShortName();
if ("scale_factor".equals(attribName)) {
band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("add_offset".equals(attribName)) {
band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
}
}
}
}
}
return bandToVariableMap;
}
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);
}
