private void makeVariableNoCoords(
NetcdfFile ncfile, int datatype, String shortName, String longName, Variable from) {
Variable v = new Variable(ncfile, null, null, shortName);
v.setDataType(DataType.BYTE);
v.setDimensions(from.getDimensions());
ncfile.addVariable(null, v);
v.addAttribute(new Attribute(CDM.UNITS, Cinrad2Record.getDatatypeUnits(datatype)));
v.addAttribute(new Attribute(CDM.LONG_NAME, longName));
byte[] b = new byte[2];
b[0] = Cinrad2Record.MISSING_DATA;
b[1] = Cinrad2Record.BELOW_THRESHOLD;
Array missingArray = Array.factory(DataType.BYTE.getPrimitiveClassType(), new int[] {2}, b);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, missingArray));
v.addAttribute(
new Attribute("signal_below_threshold", new Byte(Cinrad2Record.BELOW_THRESHOLD)));
v.addAttribute(
new Attribute(CDM.SCALE_FACTOR, new Float(Cinrad2Record.getDatatypeScaleFactor(datatype))));
v.addAttribute(
new Attribute(CDM.ADD_OFFSET, new Float(Cinrad2Record.getDatatypeAddOffset(datatype))));
v.addAttribute(new Attribute(CDM.UNSIGNED, "true"));
Attribute fromAtt = from.findAttribute(_Coordinate.Axes);
v.addAttribute(new Attribute(_Coordinate.Axes, fromAtt));
Vgroup vgFrom = (Vgroup) from.getSPobject();
Vgroup vg = new Vgroup(datatype, vgFrom.map);
v.setSPobject(vg);
}
/**
* Make the missing variable
*
* @return the missing variable
*/
protected Variable makeMissingVariable() {
Variable var = new Variable(ncfile, null, null, MISSING_VAR);
var.setDataType(DataType.BYTE);
var.setDimensions((List<Dimension>) null);
var.addAttribute(new Attribute("description", "missing flag - 1 means all params are missing"));
var.addAttribute(new Attribute("missing_value", new Byte((byte) 1)));
return var;
}
/**
* Make a variable from a GempakParmaeter
*
* @param param GempakParameter
* @param dims Variable dimensions
* @return the Variable
*/
protected Variable makeParamVariable(GempakParameter param, List<Dimension> dims) {
Variable var = new Variable(ncfile, null, null, param.getName());
var.setDataType(DataType.FLOAT);
var.setDimensions(dims);
var.addAttribute(new Attribute("long_name", param.getDescription()));
String units = param.getUnit();
if ((units != null) && !units.equals("")) {
var.addAttribute(new Attribute(CDM.UNITS, units));
}
var.addAttribute(new Attribute("missing_value", RMISS));
return var;
}
/**
* Add this as a variable to the netCDF file
*
* @param ncfile the netCDF file
* @param g the group in the file
*/
void addToNetcdfFile(NetcdfFile ncfile, Group g) {
Variable v = new Variable(ncfile, g, null, getName());
v.setDimensions(v.getShortName());
v.setDataType(DataType.STRING);
v.addAttribute(new Attribute("long_name", "ensemble"));
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Ensemble.toString()));
String[] data = new String[getNEnsembles()];
for (int i = 0; i < getNEnsembles(); i++) {
EnsCoord ec = ensCoords.get(i);
data[i] = Grib2Tables.codeTable4_6(ec.type) + " " + ec.number;
}
Array dataArray = Array.factory(DataType.STRING, new int[] {getNEnsembles()}, data);
v.setCachedData(dataArray, false);
ncfile.addVariable(g, v);
}
/**
* Define Dimensions, Variables, Attributes in ncfile
*
* @param raf ucar.unidata.io.RandomAccessFile corresponds of SIGMET datafile.
* @param ncfile an empty NetcdfFile object which will be filled.
* @param hdrNames java.util.Map with values for "StationName.." Attributes
* @return ArrayList of Variables of ncfile
*/
public ArrayList<Variable> init(
ucar.unidata.io.RandomAccessFile raf,
ucar.nc2.NetcdfFile ncfile,
java.util.Map<String, String> hdrNames)
throws java.io.IOException {
// prepare attribute values
String[] data_name = {
" ", "TotalPower", "Reflectivity", "Velocity", "Width", "Differential_Reflectivity"
};
String[] unit = {" ", "dbZ", "dbZ", "m/sec", "m/sec", "dB"};
int[] type = {1, 2, 3, 4, 5};
String def_datafile = "SIGMET-IRIS";
String tim = "";
int ngates = 0;
recHdr = readRecordsHdr(raf);
hdrNames = readStnNames(raf);
String stnName = hdrNames.get("StationName");
String stnName_util = hdrNames.get("StationName_SetupUtility");
float radar_lat =
recHdr.get("radar_lat").floatValue(); // System.out.println("rad_lat="+radar_lat);
float radar_lon =
recHdr.get("radar_lon").floatValue(); // System.out.println("rad_lon="+radar_lon);
short ground_height =
recHdr.get("ground_height").shortValue(); // System.out.println("ground_H="+ground_height);
short radar_height =
recHdr.get("radar_height").shortValue(); // System.out.println("radar_H="+radar_height);
int radar_alt =
(recHdr.get("radar_alt").intValue()) / 100; // System.out.println("rad_alt="+radar_alt);
short num_rays =
recHdr.get("num_rays").shortValue(); // System.out.println("num_rays="+num_rays);
short bins = recHdr.get("bins").shortValue(); // System.out.println("bins="+bins);
float range_first =
(recHdr.get("range_first").intValue())
* 0.01f; // System.out.println("range_1st="+range_first);
float range_last =
(recHdr.get("range_last").intValue()) * 0.01f; // System.out.println("step="+step);
short number_sweeps = recHdr.get("number_sweeps").shortValue();
// System.out.println("number_sweeps="+number_sweeps);
int nparams = (recHdr.get("nparams").intValue()); // System.out.println("nparams="+nparams);
short year = recHdr.get("year").shortValue(); // System.out.println("year="+year);
short month = recHdr.get("month").shortValue();
short day = recHdr.get("day").shortValue();
int base_time = (recHdr.get("base_time").intValue());
// define number of gates for every sweep
sweep_bins = new int[nparams * number_sweeps];
if (number_sweeps > 1) {
sweep_bins = volScan.getNumberGates();
} else {
for (int kk = 0; kk < nparams; kk++) {
sweep_bins[kk] = bins;
}
}
// add Dimensions
Dimension scanR = new Dimension("scanR", number_sweeps, true);
Dimension radial = new Dimension("radial", num_rays, true);
Dimension[] gateR = new Dimension[number_sweeps];
String dim_name = "gateR";
for (int j = 0; j < number_sweeps; j++) {
if (number_sweeps > 1) {
dim_name = "gateR_sweep_" + (j + 1);
}
gateR[j] = new Dimension(dim_name, sweep_bins[j], true);
}
ncfile.addDimension(null, scanR);
ncfile.addDimension(null, radial);
for (int j = 0; j < number_sweeps; j++) {
ncfile.addDimension(null, gateR[j]);
}
ArrayList<Dimension> dims0 = new ArrayList<Dimension>();
ArrayList<Dimension> dims1 = new ArrayList<Dimension>();
ArrayList<Dimension> dims2 = new ArrayList<Dimension>();
ArrayList<Dimension> dims3 = new ArrayList<Dimension>();
ArrayList<Variable> varList = new ArrayList<Variable>();
Variable[][] v = new Variable[nparams][number_sweeps];
String var_name = "";
for (int j = 0; j < nparams; j++) {
int tp = type[j];
var_name = data_name[tp];
for (int jj = 0; jj < number_sweeps; jj++) {
if (number_sweeps > 1) {
var_name = data_name[tp] + "_sweep_" + (jj + 1);
}
v[j][jj] = new Variable(ncfile, null, null, var_name);
v[j][jj].setDataType(DataType.FLOAT);
dims2.add(radial);
dims2.add(gateR[jj]);
v[j][jj].setDimensions(dims2);
v[j][jj].addAttribute(new Attribute(CDM.LONG_NAME, var_name));
v[j][jj].addAttribute(new Attribute(CDM.UNITS, unit[tp]));
String coordinates = "time elevationR azimuthR distanceR";
v[j][jj].addAttribute(new Attribute(_Coordinate.Axes, coordinates));
v[j][jj].addAttribute(new Attribute(CDM.MISSING_VALUE, -999.99f));
ncfile.addVariable(null, v[j][jj]);
varList.add(v[j][jj]);
dims2.clear();
}
}
tsu_sec = new int[number_sweeps];
String[] tsu = new String[number_sweeps];
String[] time_units = new String[number_sweeps];
tsu_sec = volScan.getStartSweep();
for (int i = 0; i < number_sweeps; i++) {
String st1 = Short.toString(month);
if (st1.length() < 2) st1 = "0" + st1;
String st2 = Short.toString(day);
if (st2.length() < 2) st2 = "0" + st2;
date0 = String.valueOf(year) + "-" + st1 + "-" + st2;
tsu[i] = date0 + "T" + calcTime(tsu_sec[i], 0) + "Z";
}
for (int j = 0; j < number_sweeps; j++) {
time_units[j] = "secs since " + tsu[j];
}
dims0.add(radial);
// add "time" variable
Variable[] time = new Variable[number_sweeps];
String tm = "time";
String tm_name = "";
for (int j = 0; j < number_sweeps; j++) {
tm_name = tm;
if (number_sweeps > 1) {
tm_name = tm + "_sweep_" + (j + 1);
}
time[j] = new Variable(ncfile, null, null, tm_name);
time[j].setDataType(DataType.INT);
time[j].setDimensions(dims0);
time[j].addAttribute(new Attribute(CDM.LONG_NAME, "time from start of sweep"));
time[j].addAttribute(new Attribute(CDM.UNITS, time_units[j]));
time[j].addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
time[j].addAttribute(new Attribute(CDM.MISSING_VALUE, -99));
ncfile.addVariable(null, time[j]);
varList.add(time[j]);
}
// add "elevationR" variable
Variable[] elevationR = new Variable[number_sweeps];
String ele = "elevationR";
String ele_name = "";
for (int j = 0; j < number_sweeps; j++) {
ele_name = ele;
if (number_sweeps > 1) {
ele_name = ele + "_sweep_" + (j + 1);
}
elevationR[j] = new Variable(ncfile, null, null, ele_name);
elevationR[j].setDataType(DataType.FLOAT);
elevationR[j].setDimensions(dims0);
elevationR[j].addAttribute(new Attribute(CDM.LONG_NAME, "elevation angle"));
elevationR[j].addAttribute(new Attribute(CDM.UNITS, "degrees"));
elevationR[j].addAttribute(
new Attribute(_Coordinate.AxisType, AxisType.RadialElevation.toString()));
elevationR[j].addAttribute(new Attribute(CDM.MISSING_VALUE, -999.99f));
ncfile.addVariable(null, elevationR[j]);
varList.add(elevationR[j]);
}
// add "azimuthR" variable
Variable[] azimuthR = new Variable[number_sweeps];
String azim = "azimuthR";
String azim_name = "";
for (int j = 0; j < number_sweeps; j++) {
azim_name = azim;
if (number_sweeps > 1) {
azim_name = azim + "_sweep_" + (j + 1);
}
azimuthR[j] = new Variable(ncfile, null, null, azim_name);
azimuthR[j].setDataType(DataType.FLOAT);
azimuthR[j].setDimensions(dims0);
azimuthR[j].addAttribute(new Attribute(CDM.LONG_NAME, "azimuth angle"));
azimuthR[j].addAttribute(new Attribute(CDM.UNITS, "degrees"));
azimuthR[j].addAttribute(
new Attribute(_Coordinate.AxisType, AxisType.RadialAzimuth.toString()));
azimuthR[j].addAttribute(new Attribute(CDM.MISSING_VALUE, -999.99f));
ncfile.addVariable(null, azimuthR[j]);
varList.add(azimuthR[j]);
}
// add "distanceR" variable
Variable[] distanceR = new Variable[number_sweeps];
String dName = "distanceR";
String dist_name = "";
for (int j = 0; j < number_sweeps; j++) {
dist_name = dName;
if (number_sweeps > 1) {
dist_name = dName + "_sweep_" + (j + 1);
}
distanceR[j] = new Variable(ncfile, null, null, dist_name);
distanceR[j].setDataType(DataType.FLOAT);
dims1.add(gateR[j]);
distanceR[j].setDimensions(dims1);
distanceR[j].addAttribute(new Attribute(CDM.LONG_NAME, "radial distance"));
distanceR[j].addAttribute(new Attribute(CDM.UNITS, "m"));
distanceR[j].addAttribute(
new Attribute(_Coordinate.AxisType, AxisType.RadialDistance.toString()));
ncfile.addVariable(null, distanceR[j]);
varList.add(distanceR[j]);
dims1.clear();
}
// add "numGates" variable
dims3.add(scanR);
Variable numGates = new Variable(ncfile, null, null, "numGates");
numGates.setDataType(DataType.INT);
numGates.setDimensions(dims3);
numGates.addAttribute(new Attribute(CDM.LONG_NAME, "number of gates in the sweep"));
ncfile.addVariable(null, numGates);
varList.add(numGates);
// add global attributes
ncfile.addAttribute(null, new Attribute("definition", "SIGMET-IRIS RAW"));
ncfile.addAttribute(
null, new Attribute("description", "SIGMET-IRIS data are reading by Netcdf IOSP"));
ncfile.addAttribute(null, new Attribute("StationName", stnName));
ncfile.addAttribute(null, new Attribute("StationName_SetupUtility", stnName_util));
ncfile.addAttribute(null, new Attribute("radar_lat", radar_lat));
ncfile.addAttribute(null, new Attribute("radar_lon", radar_lon));
ncfile.addAttribute(null, new Attribute("ground_height", ground_height));
ncfile.addAttribute(null, new Attribute("radar_height", radar_height));
ncfile.addAttribute(null, new Attribute("radar_alt", radar_alt));
ncfile.addAttribute(null, new Attribute("num_data_types", nparams));
ncfile.addAttribute(null, new Attribute("number_sweeps", number_sweeps));
String sn = "start_sweep";
String snn = "";
for (int j = 0; j < number_sweeps; j++) {
snn = sn;
if (number_sweeps > 1) {
snn = sn + "_" + (j + 1);
}
ncfile.addAttribute(null, new Attribute(snn, tsu[j]));
}
ncfile.addAttribute(null, new Attribute("num_rays", num_rays));
ncfile.addAttribute(null, new Attribute("max_number_gates", bins));
ncfile.addAttribute(null, new Attribute("range_first", range_first));
ncfile.addAttribute(null, new Attribute("range_last", range_last));
ncfile.addAttribute(null, new Attribute("DataType", "Radial"));
ncfile.addAttribute(null, new Attribute(CDM.CONVENTIONS, _Coordinate.Convention));
// --------- fill all of values in the ncfile ------
doNetcdfFileCoordinate(
ncfile, volScan.base_time, volScan.year, volScan.month, volScan.day, varList, recHdr);
ncfile.finish();
return varList;
}
private FeatureType amendGrid(
Element gridElem, NetcdfFile ncfile, Group parent, String location) {
List<Dimension> unknownDims = new ArrayList<>();
// always has x and y dimension
String xdimSizeS = gridElem.getChild("XDim").getText().trim();
String ydimSizeS = gridElem.getChild("YDim").getText().trim();
int xdimSize = Integer.parseInt(xdimSizeS);
int ydimSize = Integer.parseInt(ydimSizeS);
parent.addDimensionIfNotExists(new Dimension("XDim", xdimSize));
parent.addDimensionIfNotExists(new Dimension("YDim", ydimSize));
/* see HdfEosModisConvention
UpperLeftPointMtrs=(-20015109.354000,1111950.519667)
LowerRightMtrs=(-18903158.834333,-0.000000)
Projection=GCTP_SNSOID
ProjParams=(6371007.181000,0,0,0,0,0,0,0,0,0,0,0,0)
SphereCode=-1
*/
Element proj = gridElem.getChild("Projection");
if (proj != null) {
Variable crs = new Variable(ncfile, parent, null, HDFEOS_CRS);
crs.setDataType(DataType.SHORT);
crs.setDimensions(""); // scalar
crs.setCachedData(Array.makeArray(DataType.SHORT, 1, 0, 0)); // fake data
parent.addVariable(crs);
addAttributeIfExists(gridElem, HDFEOS_CRS_Projection, crs, false);
addAttributeIfExists(gridElem, HDFEOS_CRS_UpperLeft, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_LowerRight, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_ProjParams, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_SphereCode, crs, false);
}
// global Dimensions
Element d = gridElem.getChild("Dimension");
List<Element> dims = d.getChildren();
for (Element elem : dims) {
String name = elem.getChild("DimensionName").getText().trim();
name = NetcdfFile.makeValidCdmObjectName(name);
if (name.equalsIgnoreCase("scalar")) continue;
String sizeS = elem.getChild("Size").getText().trim();
int length = Integer.parseInt(sizeS);
Dimension old = parent.findDimension(name);
if ((old == null) || (old.getLength() != length)) {
if (length > 0) {
Dimension dim = new Dimension(name, length);
if (parent.addDimensionIfNotExists(dim) && showWork)
System.out.printf(" Add dimension %s %n", dim);
} else {
log.warn("Dimension {} has size {} {} ", sizeS, name, location);
Dimension udim = new Dimension(name, 1);
udim.setGroup(parent);
unknownDims.add(udim);
if (showWork) System.out.printf(" Add dimension %s %n", udim);
}
}
}
// Geolocation Variables
Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
if (geoFieldsG != null) {
Element floc = gridElem.getChild("GeoField");
List<Element> varsLoc = floc.getChildren();
for (Element elem : varsLoc) {
String varname = elem.getChild("GeoFieldName").getText().trim();
Variable v = geoFieldsG.findVariable(varname);
// if (v == null)
// v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, location);
}
}
// Data Variables
Group dataG = parent.findGroup(DATA_FIELDS);
if (dataG == null)
dataG =
parent.findGroup(
DATA_FIELDS2); // eg C:\data\formats\hdf4\eos\mopitt\MOP03M-200501-L3V81.0.1.hdf
if (dataG != null) {
Element f = gridElem.getChild("DataField");
List<Element> vars = f.getChildren();
for (Element elem : vars) {
String varname = elem.getChild("DataFieldName").getText().trim();
varname = NetcdfFile.makeValidCdmObjectName(varname);
Variable v = dataG.findVariable(varname);
// if (v == null)
// v = dataG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, location);
}
// get projection
String projS = null;
Element projElem = gridElem.getChild("Projection");
if (projElem != null) projS = projElem.getText().trim();
boolean isLatLon = "GCTP_GEO".equals(projS);
// look for XDim, YDim coordinate variables
if (isLatLon) {
for (Variable v : dataG.getVariables()) {
if (v.isCoordinateVariable()) {
if (v.getShortName().equals("YDim")) {
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
v.addAttribute(new Attribute(CDM.UNITS, CDM.LAT_UNITS));
}
if (v.getShortName().equals("XDim"))
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
}
}
}
}
return FeatureType.GRID;
}
private FeatureType amendSwath(NetcdfFile ncfile, Element swathElem, Group parent) {
FeatureType featureType = FeatureType.SWATH;
List<Dimension> unknownDims = new ArrayList<>();
// Dimensions
Element d = swathElem.getChild("Dimension");
List<Element> dims = d.getChildren();
for (Element elem : dims) {
String name = elem.getChild("DimensionName").getText().trim();
name = NetcdfFile.makeValidCdmObjectName(name);
if (name.equalsIgnoreCase("scalar")) continue;
String sizeS = elem.getChild("Size").getText().trim();
int length = Integer.parseInt(sizeS);
if (length > 0) {
Dimension dim = parent.findDimensionLocal(name);
if (dim != null) { // already added - may be dimension scale ?
if (dim.getLength() != length) { // ok as long as it matches
log.error("Conflicting Dimensions = {} {}", dim, ncfile.getLocation());
throw new IllegalStateException("Conflicting Dimensions = " + name);
}
} else {
dim = new Dimension(name, length);
if (parent.addDimensionIfNotExists(dim) && showWork)
System.out.printf(" Add dimension %s %n", dim);
}
} else {
log.warn("Dimension " + name + " has size " + sizeS, ncfile.getLocation());
Dimension udim = new Dimension(name, 1);
udim.setGroup(parent);
unknownDims.add(udim);
if (showWork) System.out.printf(" Add dimension %s %n", udim);
}
}
// Dimension Maps
Element dmap = swathElem.getChild("DimensionMap");
List<Element> dimMaps = dmap.getChildren();
for (Element elem : dimMaps) {
String geoDimName = elem.getChild("GeoDimension").getText().trim();
geoDimName = NetcdfFile.makeValidCdmObjectName(geoDimName);
String dataDimName = elem.getChild("DataDimension").getText().trim();
dataDimName = NetcdfFile.makeValidCdmObjectName(dataDimName);
String offsetS = elem.getChild("Offset").getText().trim();
String incrS = elem.getChild("Increment").getText().trim();
int offset = Integer.parseInt(offsetS);
int incr = Integer.parseInt(incrS);
// make new variable for this dimension map
Variable v = new Variable(ncfile, parent, null, dataDimName);
v.setDimensions(geoDimName);
v.setDataType(DataType.INT);
int npts = (int) v.getSize();
Array data = Array.makeArray(v.getDataType(), npts, offset, incr);
v.setCachedData(data, true);
v.addAttribute(new Attribute("_DimensionMap", ""));
parent.addVariable(v);
if (showWork) System.out.printf(" Add dimensionMap %s %n", v);
}
// Geolocation Variables
Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
if (geoFieldsG != null) {
Variable latAxis = null, lonAxis = null;
Element floc = swathElem.getChild("GeoField");
List<Element> varsLoc = floc.getChildren();
for (Element elem : varsLoc) {
String varname = elem.getChild("GeoFieldName").getText().trim();
Variable v = geoFieldsG.findVariable(varname);
// if (v == null)
// v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
AxisType axis = addAxisType(ncfile, v);
if (axis == AxisType.Lat) latAxis = v;
if (axis == AxisType.Lon) lonAxis = v;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
if (showWork) System.out.printf(" set coordinate %s %n", v);
}
if ((latAxis != null) && (lonAxis != null)) {
List<Dimension> xyDomain = CoordinateSystem.makeDomain(new Variable[] {latAxis, lonAxis});
if (xyDomain.size() < 2) featureType = FeatureType.PROFILE; // ??
}
}
// Data Variables
Group dataG = parent.findGroup(DATA_FIELDS);
if (dataG == null) dataG = parent.findGroup(DATA_FIELDS2);
if (dataG != null) {
Element f = swathElem.getChild("DataField");
List<Element> vars = f.getChildren();
for (Element elem : vars) {
Element dataFieldNameElem = elem.getChild("DataFieldName");
if (dataFieldNameElem == null) continue;
String varname = NetcdfFile.makeValidCdmObjectName(dataFieldNameElem.getText().trim());
Variable v = dataG.findVariable(varname);
// if (v == null)
// v = dataG.findVariable( H4header.createValidObjectName(varname));
if (v == null) {
log.error("Cant find variable {} {}", varname, ncfile.getLocation());
continue;
}
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
}
}
return featureType;
}
/**
* Make a station variable
*
* @param varname variable name
* @param firstDim station dimension
* @return corresponding variable
*/
protected Variable makeStationVariable(String varname, Dimension firstDim) {
String longName = varname;
String unit = null;
DataType type = DataType.CHAR;
List<Dimension> dims = new ArrayList<Dimension>();
List<Attribute> attrs = new ArrayList<Attribute>();
if (firstDim != null) {
dims.add(firstDim);
}
if (varname.equals(GempakStation.STID)) {
longName = "Station identifier";
dims.add(DIM_LEN8);
} else if (varname.equals(GempakStation.STNM)) {
longName = "WMO station id";
type = DataType.INT;
} else if (varname.equals(GempakStation.SLAT)) {
longName = "latitude";
unit = "degrees_north";
type = DataType.FLOAT;
attrs.add(new Attribute("standard_name", "latitude"));
} else if (varname.equals(GempakStation.SLON)) {
longName = "longitude";
unit = "degrees_east";
type = DataType.FLOAT;
attrs.add(new Attribute("standard_name", "longitude"));
} else if (varname.equals(GempakStation.SELV)) {
longName = "altitude";
unit = "meter";
type = DataType.FLOAT;
attrs.add(new Attribute(CF.POSITIVE, CF.POSITIVE_UP));
attrs.add(new Attribute("standard_name", "station_altitude"));
} else if (varname.equals(GempakStation.STAT)) {
longName = "state or province";
dims.add(DIM_LEN2);
} else if (varname.equals(GempakStation.COUN)) {
longName = "country code";
dims.add(DIM_LEN2);
} else if (varname.equals(GempakStation.STD2)) {
longName = "Extended station id";
dims.add(DIM_LEN4);
} else if (varname.equals(GempakStation.SPRI)) {
longName = "Station priority";
type = DataType.INT;
} else if (varname.equals(GempakStation.SWFO)) {
longName = "WFO code";
dims.add(DIM_LEN4);
} else if (varname.equals(GempakStation.WFO2)) {
longName = "Second WFO code";
dims.add(DIM_LEN4);
}
Variable v = new Variable(ncfile, null, null, varname);
v.setDataType(type);
v.addAttribute(new Attribute("long_name", longName));
if (unit != null) {
v.addAttribute(new Attribute(CDM.UNITS, unit));
}
if (type.equals(DataType.FLOAT)) {
v.addAttribute(new Attribute("missing_value", RMISS));
} else if (type.equals(DataType.INT)) {
v.addAttribute(new Attribute("missing_value", IMISS));
}
if (!attrs.isEmpty()) {
for (Attribute attr : attrs) {
v.addAttribute(attr);
}
}
if (!dims.isEmpty()) {
v.setDimensions(dims);
} else {
v.setDimensions((String) null);
}
return v;
}
/**
* Add this coord as a variable in the netCDF file
*
* @param ncfile netCDF file to add to
* @param g group in file
*/
void addToNetcdfFile(NetcdfFile ncfile, Group g) {
if (dontUseVertical) {
typicalRecord = null;
return;
}
if (g == null) {
g = ncfile.getRootGroup();
}
// coordinate axis
Variable v = new Variable(ncfile, g, null, getVariableName());
v.setDataType(DataType.DOUBLE);
String desc = lookup.getLevelDescription(typicalRecord);
if (lookup instanceof Grib2GridTableLookup && usesBounds) {
desc = "Layer between " + desc;
}
v.addAttribute(new Attribute("long_name", desc));
v.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));
// positive attribute needed for CF-1 Height and Pressure
if (positive != null) {
v.addAttribute(new Attribute("positive", positive));
}
if (units != null) {
AxisType axisType;
if (SimpleUnit.isCompatible("millibar", units)) {
axisType = AxisType.Pressure;
} else if (SimpleUnit.isCompatible("m", units)) {
axisType = AxisType.Height;
} else {
axisType = AxisType.GeoZ;
}
if (lookup instanceof Grib2GridTableLookup || lookup instanceof Grib1GridTableLookup) {
v.addAttribute(
new Attribute("GRIB_level_type", Integer.toString(typicalRecord.getLevelType1())));
} else {
v.addAttribute(
new Attribute("level_type", Integer.toString(typicalRecord.getLevelType1())));
}
v.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));
}
if (coordValues == null) {
coordValues = new double[levels.size()];
for (int i = 0; i < levels.size(); i++) {
LevelCoord lc = (LevelCoord) levels.get(i);
coordValues[i] = lc.mid;
}
}
Array dataArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length}, coordValues);
v.setDimensions(getVariableName());
v.setCachedData(dataArray, true);
ncfile.addVariable(g, v);
if (usesBounds) {
String boundsDimName = "bounds_dim";
if (g.findDimension(boundsDimName) == null) {
ncfile.addDimension(g, new Dimension(boundsDimName, 2, true));
}
String bname = getVariableName() + "_bounds";
v.addAttribute(new Attribute("bounds", bname));
v.addAttribute(new Attribute(_Coordinate.ZisLayer, "true"));
Variable b = new Variable(ncfile, g, null, bname);
b.setDataType(DataType.DOUBLE);
b.setDimensions(getVariableName() + " " + boundsDimName);
b.addAttribute(new Attribute("long_name", "bounds for " + v.getName()));
b.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));
Array boundsArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length, 2});
ucar.ma2.Index ima = boundsArray.getIndex();
for (int i = 0; i < coordValues.length; i++) {
LevelCoord lc = (LevelCoord) levels.get(i);
boundsArray.setDouble(ima.set(i, 0), lc.value1);
boundsArray.setDouble(ima.set(i, 1), lc.value2);
}
b.setCachedData(boundsArray, true);
ncfile.addVariable(g, b);
}
if (factors != null) {
// check if already created
if (g == null) {
g = ncfile.getRootGroup();
}
if (g.findVariable("hybrida") != null) return;
v.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate"));
v.addAttribute(new Attribute("formula_terms", "ap: hybrida b: hybridb ps: Pressure"));
// create hybrid factor variables
// add hybrida variable
Variable ha = new Variable(ncfile, g, null, "hybrida");
ha.setDataType(DataType.DOUBLE);
ha.addAttribute(new Attribute("long_name", "level_a_factor"));
ha.addAttribute(new Attribute("units", ""));
ha.setDimensions(getVariableName());
// add data
int middle = factors.length / 2;
double[] adata;
double[] bdata;
if (levels.size() < middle) { // only partial data wanted
adata = new double[levels.size()];
bdata = new double[levels.size()];
} else {
adata = new double[middle];
bdata = new double[middle];
}
for (int i = 0; i < middle && i < levels.size(); i++) adata[i] = factors[i];
Array haArray = Array.factory(DataType.DOUBLE, new int[] {adata.length}, adata);
ha.setCachedData(haArray, true);
ncfile.addVariable(g, ha);
// add hybridb variable
Variable hb = new Variable(ncfile, g, null, "hybridb");
hb.setDataType(DataType.DOUBLE);
hb.addAttribute(new Attribute("long_name", "level_b_factor"));
hb.addAttribute(new Attribute("units", ""));
hb.setDimensions(getVariableName());
// add data
for (int i = 0; i < middle && i < levels.size(); i++) bdata[i] = factors[i + middle];
Array hbArray = Array.factory(DataType.DOUBLE, new int[] {bdata.length}, bdata);
hb.setCachedData(hbArray, true);
ncfile.addVariable(g, hb);
/* // TODO: delete next time modifying code
double[] adata = new double[ middle ];
for( int i = 0; i < middle; i++ )
adata[ i ] = factors[ i ];
Array haArray = Array.factory(DataType.DOUBLE, new int[]{adata.length}, adata);
ha.setCachedData(haArray, true);
ncfile.addVariable(g, ha);
// add hybridb variable
Variable hb = new Variable(ncfile, g, null, "hybridb");
hb.setDataType(DataType.DOUBLE);
hb.addAttribute(new Attribute("long_name", "level_b_factor" ));
//hb.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate" ));
hb.addAttribute(new Attribute("units", ""));
hb.setDimensions(getVariableName());
// add data
double[] bdata = new double[ middle ];
for( int i = 0; i < middle; i++ )
bdata[ i ] = factors[ i + middle ];
Array hbArray = Array.factory(DataType.DOUBLE, new int[]{bdata.length}, bdata);
hb.setCachedData(hbArray, true);
ncfile.addVariable(g, hb);
*/
}
}
public Variable makeVariable(
NetcdfFile ncfile,
int datatype,
String shortName,
String longName,
String abbrev,
List groups)
throws IOException {
int nscans = groups.size();
if (nscans == 0) {
throw new IllegalStateException("No data for " + shortName);
}
// get representative record
List firstGroup = (List) groups.get(0);
Cinrad2Record firstRecord = (Cinrad2Record) firstGroup.get(0);
int ngates = firstRecord.getGateCount(datatype);
String scanDimName = "scan" + abbrev;
String gateDimName = "gate" + abbrev;
Dimension scanDim = new Dimension(scanDimName, nscans);
Dimension gateDim = new Dimension(gateDimName, ngates);
ncfile.addDimension(null, scanDim);
ncfile.addDimension(null, gateDim);
ArrayList dims = new ArrayList();
dims.add(scanDim);
dims.add(radialDim);
dims.add(gateDim);
Variable v = new Variable(ncfile, null, null, shortName);
v.setDataType(DataType.BYTE);
v.setDimensions(dims);
ncfile.addVariable(null, v);
v.addAttribute(new Attribute(CDM.UNITS, Cinrad2Record.getDatatypeUnits(datatype)));
v.addAttribute(new Attribute(CDM.LONG_NAME, longName));
byte[] b = new byte[2];
b[0] = Cinrad2Record.MISSING_DATA;
b[1] = Cinrad2Record.BELOW_THRESHOLD;
Array missingArray = Array.factory(DataType.BYTE.getPrimitiveClassType(), new int[] {2}, b);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, missingArray));
v.addAttribute(
new Attribute("signal_below_threshold", new Byte(Cinrad2Record.BELOW_THRESHOLD)));
v.addAttribute(
new Attribute(CDM.SCALE_FACTOR, new Float(Cinrad2Record.getDatatypeScaleFactor(datatype))));
v.addAttribute(
new Attribute(CDM.ADD_OFFSET, new Float(Cinrad2Record.getDatatypeAddOffset(datatype))));
v.addAttribute(new Attribute(CDM.UNSIGNED, "true"));
ArrayList dim2 = new ArrayList();
dim2.add(scanDim);
dim2.add(radialDim);
// add time coordinate variable
String timeCoordName = "time" + abbrev;
Variable timeVar = new Variable(ncfile, null, null, timeCoordName);
timeVar.setDataType(DataType.INT);
timeVar.setDimensions(dim2);
ncfile.addVariable(null, timeVar);
// int julianDays = volScan.getTitleJulianDays();
// Date d = Cinrad2Record.getDate( julianDays, 0);
// Date d = Cinrad2Record.getDate(volScan.getTitleJulianDays(), volScan.getTitleMsecs());
Date d = volScan.getStartDate();
String units = "msecs since " + formatter.toDateTimeStringISO(d);
timeVar.addAttribute(new Attribute(CDM.LONG_NAME, "time since base date"));
timeVar.addAttribute(new Attribute(CDM.UNITS, units));
timeVar.addAttribute(new Attribute(CDM.MISSING_VALUE, new Integer(MISSING_INT)));
timeVar.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
// add elevation coordinate variable
String elevCoordName = "elevation" + abbrev;
Variable elevVar = new Variable(ncfile, null, null, elevCoordName);
elevVar.setDataType(DataType.FLOAT);
elevVar.setDimensions(dim2);
ncfile.addVariable(null, elevVar);
elevVar.addAttribute(new Attribute(CDM.UNITS, "degrees"));
elevVar.addAttribute(
new Attribute(
CDM.LONG_NAME,
"elevation angle in degres: 0 = parallel to pedestal base, 90 = perpendicular"));
elevVar.addAttribute(new Attribute(CDM.MISSING_VALUE, new Float(MISSING_FLOAT)));
elevVar.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.RadialElevation.toString()));
// add azimuth coordinate variable
String aziCoordName = "azimuth" + abbrev;
Variable aziVar = new Variable(ncfile, null, null, aziCoordName);
aziVar.setDataType(DataType.FLOAT);
aziVar.setDimensions(dim2);
ncfile.addVariable(null, aziVar);
aziVar.addAttribute(new Attribute(CDM.UNITS, "degrees"));
aziVar.addAttribute(
new Attribute(CDM.LONG_NAME, "azimuth angle in degrees: 0 = true north, 90 = east"));
aziVar.addAttribute(new Attribute(CDM.MISSING_VALUE, new Float(MISSING_FLOAT)));
aziVar.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.RadialAzimuth.toString()));
// add gate coordinate variable
String gateCoordName = "distance" + abbrev;
Variable gateVar = new Variable(ncfile, null, null, gateCoordName);
gateVar.setDataType(DataType.FLOAT);
gateVar.setDimensions(gateDimName);
Array data =
Array.makeArray(
DataType.FLOAT,
ngates,
(double) firstRecord.getGateStart(datatype),
(double) firstRecord.getGateSize(datatype));
gateVar.setCachedData(data, false);
ncfile.addVariable(null, gateVar);
radarRadius = firstRecord.getGateStart(datatype) + ngates * firstRecord.getGateSize(datatype);
gateVar.addAttribute(new Attribute(CDM.UNITS, "m"));
gateVar.addAttribute(new Attribute(CDM.LONG_NAME, "radial distance to start of gate"));
gateVar.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.RadialDistance.toString()));
// add number of radials variable
String nradialsName = "numRadials" + abbrev;
Variable nradialsVar = new Variable(ncfile, null, null, nradialsName);
nradialsVar.setDataType(DataType.INT);
nradialsVar.setDimensions(scanDim.getName());
nradialsVar.addAttribute(new Attribute(CDM.LONG_NAME, "number of valid radials in this scan"));
ncfile.addVariable(null, nradialsVar);
// add number of gates variable
String ngateName = "numGates" + abbrev;
Variable ngateVar = new Variable(ncfile, null, null, ngateName);
ngateVar.setDataType(DataType.INT);
ngateVar.setDimensions(scanDim.getName());
ngateVar.addAttribute(new Attribute(CDM.LONG_NAME, "number of valid gates in this scan"));
ncfile.addVariable(null, ngateVar);
makeCoordinateDataWithMissing(
datatype, timeVar, elevVar, aziVar, nradialsVar, ngateVar, groups);
// back to the data variable
String coordinates =
timeCoordName + " " + elevCoordName + " " + aziCoordName + " " + gateCoordName;
v.addAttribute(new Attribute(_Coordinate.Axes, coordinates));
// make the record map
int nradials = radialDim.getLength();
Cinrad2Record[][] map = new Cinrad2Record[nscans][nradials];
for (int i = 0; i < groups.size(); i++) {
Cinrad2Record[] mapScan = map[i];
List group = (List) groups.get(i);
for (int j = 0; j < group.size(); j++) {
Cinrad2Record r = (Cinrad2Record) group.get(j);
int radial = r.radial_num - 1;
mapScan[radial] = r;
}
}
Vgroup vg = new Vgroup(datatype, map);
v.setSPobject(vg);
return v;
}
public void open(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask)
throws IOException {
NexradStationDB.init();
volScan = new Cinrad2VolumeScan(raf, cancelTask);
if (volScan.hasDifferentDopplarResolutions())
throw new IllegalStateException("volScan.hasDifferentDopplarResolutions");
radialDim = new Dimension("radial", volScan.getMaxRadials());
ncfile.addDimension(null, radialDim);
makeVariable(
ncfile,
Cinrad2Record.REFLECTIVITY,
"Reflectivity",
"Reflectivity",
"R",
volScan.getReflectivityGroups());
int velocity_type =
(volScan.getDopplarResolution() == Cinrad2Record.DOPPLER_RESOLUTION_HIGH_CODE)
? Cinrad2Record.VELOCITY_HI
: Cinrad2Record.VELOCITY_LOW;
Variable v =
makeVariable(
ncfile,
velocity_type,
"RadialVelocity",
"Radial Velocity",
"V",
volScan.getVelocityGroups());
makeVariableNoCoords(
ncfile, Cinrad2Record.SPECTRUM_WIDTH, "SpectrumWidth", "Spectrum Width", v);
if (volScan.getStationId() != null) {
ncfile.addAttribute(null, new Attribute("Station", volScan.getStationId()));
ncfile.addAttribute(null, new Attribute("StationName", volScan.getStationName()));
ncfile.addAttribute(
null, new Attribute("StationLatitude", new Double(volScan.getStationLatitude())));
ncfile.addAttribute(
null, new Attribute("StationLongitude", new Double(volScan.getStationLongitude())));
ncfile.addAttribute(
null,
new Attribute("StationElevationInMeters", new Double(volScan.getStationElevation())));
double latRadiusDegrees = Math.toDegrees(radarRadius / ucar.unidata.geoloc.Earth.getRadius());
ncfile.addAttribute(
null,
new Attribute(
"geospatial_lat_min", new Double(volScan.getStationLatitude() - latRadiusDegrees)));
ncfile.addAttribute(
null,
new Attribute(
"geospatial_lat_max", new Double(volScan.getStationLatitude() + latRadiusDegrees)));
double cosLat = Math.cos(Math.toRadians(volScan.getStationLatitude()));
double lonRadiusDegrees =
Math.toDegrees(radarRadius / cosLat / ucar.unidata.geoloc.Earth.getRadius());
ncfile.addAttribute(
null,
new Attribute(
"geospatial_lon_min", new Double(volScan.getStationLongitude() - lonRadiusDegrees)));
ncfile.addAttribute(
null,
new Attribute(
"geospatial_lon_max", new Double(volScan.getStationLongitude() + lonRadiusDegrees)));
// add a radial coordinate transform (experimental)
Variable ct = new Variable(ncfile, null, null, "radialCoordinateTransform");
ct.setDataType(DataType.CHAR);
ct.setDimensions(""); // scalar
ct.addAttribute(new Attribute("transform_name", "Radial"));
ct.addAttribute(new Attribute("center_latitude", new Double(volScan.getStationLatitude())));
ct.addAttribute(new Attribute("center_longitude", new Double(volScan.getStationLongitude())));
ct.addAttribute(new Attribute("center_elevation", new Double(volScan.getStationElevation())));
ct.addAttribute(new Attribute(_Coordinate.TransformType, "Radial"));
ct.addAttribute(
new Attribute(_Coordinate.AxisTypes, "RadialElevation RadialAzimuth RadialDistance"));
Array data =
Array.factory(DataType.CHAR.getPrimitiveClassType(), new int[0], new char[] {' '});
ct.setCachedData(data, true);
ncfile.addVariable(null, ct);
}
DateFormatter formatter = new DateFormatter();
ncfile.addAttribute(null, new Attribute(CDM.CONVENTIONS, _Coordinate.Convention));
ncfile.addAttribute(null, new Attribute("format", volScan.getDataFormat()));
ncfile.addAttribute(null, new Attribute(CF.FEATURE_TYPE, FeatureType.RADIAL.toString()));
// Date d = Cinrad2Record.getDate(volScan.getTitleJulianDays(), volScan.getTitleMsecs());
// ncfile.addAttribute(null, new Attribute("base_date", formatter.toDateOnlyString(d)));
ncfile.addAttribute(
null,
new Attribute(
"time_coverage_start", formatter.toDateTimeStringISO(volScan.getStartDate())));
; // .toDateTimeStringISO(d)));
ncfile.addAttribute(
null,
new Attribute("time_coverage_end", formatter.toDateTimeStringISO(volScan.getEndDate())));
ncfile.addAttribute(
null,
new Attribute(CDM.HISTORY, "Direct read of Nexrad Level 2 file into NetCDF-Java 2.2 API"));
ncfile.addAttribute(null, new Attribute("DataType", "Radial"));
ncfile.addAttribute(
null,
new Attribute(
"Title",
"Nexrad Level 2 Station "
+ volScan.getStationId()
+ " from "
+ formatter.toDateTimeStringISO(volScan.getStartDate())
+ " to "
+ formatter.toDateTimeStringISO(volScan.getEndDate())));
ncfile.addAttribute(
null,
new Attribute(
"Summary",
"Weather Surveillance Radar-1988 Doppler (WSR-88D) "
+ "Level II data are the three meteorological base data quantities: reflectivity, mean radial velocity, and "
+ "spectrum width."));
ncfile.addAttribute(
null,
new Attribute(
"keywords",
"WSR-88D; NEXRAD; Radar Level II; reflectivity; mean radial velocity; spectrum width"));
ncfile.addAttribute(
null,
new Attribute(
"VolumeCoveragePatternName",
Cinrad2Record.getVolumeCoveragePatternName(volScan.getVCP())));
ncfile.addAttribute(
null, new Attribute("VolumeCoveragePattern", new Integer(volScan.getVCP())));
ncfile.addAttribute(
null,
new Attribute(
"HorizonatalBeamWidthInDegrees", new Double(Cinrad2Record.HORIZONTAL_BEAM_WIDTH)));
ncfile.finish();
}
public static NetcdfDataset buildStation(IObservationGroup obsGroup) {
if (obsGroup.getDepths().length > 1) {
return buildStationProfile(obsGroup);
}
NetcdfDataset ncds = null;
File temp = null;
try {
/* Instantiate an empty NetcdfDataset object from the template ncml */
temp = File.createTempFile("ooi", ".ncml");
ncds = getNcdsFromTemplate(temp, "station.ncml");
Map<String, String> allAttributes = new HashMap<String, String>();
allAttributes.putAll(obsGroup.getAttributes());
/* Do the station Id */
ArrayInt.D0 aid = new ArrayInt.D0();
aid.set(obsGroup.getId());
ncds.findVariable("stnId").setCachedData(aid);
/* Do the times */
Number[] times = obsGroup.getTimes();
IObservationGroup.DataType tdt = obsGroup.getTimeDataType();
ncds.findDimension("time").setLength(times.length);
Variable tvar = ncds.findVariable("time");
tvar.setDataType(getNcDataType(tdt));
tvar.setCachedData(getNcArray(times, tdt));
/* Do the lat & lon */
IObservationGroup.DataType lldt = obsGroup.getLatLonDataType();
DataType ncdtLl = getNcDataType(lldt);
Variable laVar = ncds.findVariable("lat");
laVar.setDataType(ncdtLl);
laVar.setCachedData(getNcScalar(obsGroup.getLat(), lldt));
Variable loVar = ncds.findVariable("lon");
loVar.setDataType(ncdtLl);
loVar.setCachedData(getNcScalar(obsGroup.getLon(), lldt));
/* Do the depth */
IObservationGroup.DataType ddt = obsGroup.getDepthDataType();
VariableDS zVar =
new VariableDS(
ncds, null, null, "stnDepth", getNcDataType(ddt), "", "m", "station depth");
zVar.addAttribute(new Attribute("positive", "down"));
ncds.addVariable(null, zVar);
Number depth = obsGroup.getDepths()[0];
zVar.setCachedData(getNcScalar(obsGroup.getDepths()[0], ddt));
/* Do the data variables */
for (VariableParams dn : obsGroup.getDataNames()) {
DataType ncdtData = getNcDataType(dn.getDataType());
VariableDS dvar =
new VariableDS(
ncds,
null,
null,
dn.getShortName(),
ncdtData,
"time",
dn.getUnits(),
dn.getDescription());
dvar.addAttribute(new Attribute(CF.COORDINATES, "time lon lat"));
dvar.addAttribute(new Attribute(CF.STANDARD_NAME, dn.getStandardName()));
Array adata = Array.factory(ncdtData, new int[] {times.length});
IndexIterator aii = adata.getIndexIterator();
dvar.setCachedData(adata);
ncds.addVariable(null, dvar);
for (int ti = 0; ti < times.length; ti++) {
putArrayData(aii, ncdtData, obsGroup.getData(dn, times[ti], depth));
}
}
/* Add global attributes */
for (String key : allAttributes.keySet()) {
ncds.addAttribute(null, new Attribute(key, allAttributes.get(key)));
}
} catch (FileNotFoundException ex) {
Logger.getLogger(NcdsFactory.class.getName()).log(Level.SEVERE, null, ex);
} catch (IOException ex) {
Logger.getLogger(NcdsFactory.class.getName()).log(Level.SEVERE, null, ex);
} finally {
if (temp != null) {
if (!temp.delete()) {
temp.deleteOnExit();
}
}
if (ncds != null) {
ncds.finish();
}
}
return ncds;
}
public static NetcdfDataset buildTrajectory(List<IObservationGroup> obsGroups) {
// IObservationGroup.DataType tdt = IObservationGroup.DataType.values()[0];
// IObservationGroup.DataType lldt = IObservationGroup.DataType.values()[0];
// IObservationGroup.DataType ddt = IObservationGroup.DataType.values()[0];
// for(IObservationGroup og : obsGroups) {
// tdt = (og.getTimeDataType().compareTo(tdt) > 0) ? og.getTimeDataType() : tdt;
// lldt = (og.getLatLonDataType().compareTo(lldt) > 0) ? og.getLatLonDataType() :
// lldt;
// ddt = (og.getDepthDataType().compareTo(ddt) > 0) ? og.getDepthDataType() : ddt;
// }
NetcdfDataset ncds = null;
File temp = null;
try {
/* Instantiate an empty NetcdfDataset object from the template ncml */
temp = File.createTempFile("ooi", ".ncml");
ncds = getNcdsFromTemplate(temp, "trajectory.ncml");
int nobs = obsGroups.size();
List<Number> allDepths = new ArrayList<Number>();
List<VariableParams> allDn = new ArrayList<VariableParams>();
int nt = nobs;
int nd = 0;
for (IObservationGroup og : obsGroups) {
nd = Math.max(nd, og.getDepths().length);
for (Number d : og.getDepths()) {
if (!allDepths.contains(d)) {
allDepths.add(d);
}
}
for (VariableParams dn : og.getDataNames()) {
if (!allDn.contains(dn)) {
allDn.add(dn);
}
}
}
/* Do the trajectory ID */
/* Do the times */
Number[] times = obsGroups.get(0).getTimes();
IObservationGroup.DataType tdt = obsGroups.get(0).getTimeDataType();
DataType ncdtTime = getNcDataType(tdt);
ncds.findDimension("time").setLength(nt);
Array tarr = Array.factory(ncdtTime, new int[] {nt});
IndexIterator tii = tarr.getIndexIterator();
Variable tvar = ncds.findVariable("time");
tvar.setDataType(getNcDataType(tdt));
tvar.setCachedData(tarr);
/* Do the lats */
IObservationGroup.DataType lldt = obsGroups.get(0).getLatLonDataType();
DataType ncdtLl = getNcDataType(lldt);
Array laarr = Array.factory(ncdtLl, new int[] {nt});
IndexIterator laii = laarr.getIndexIterator();
Variable lavar = ncds.findVariable("lat");
lavar.setDataType(ncdtLl);
lavar.setCachedData(laarr);
/* Do the lons */
Array loarr = Array.factory(ncdtLl, new int[] {nt});
IndexIterator loii = loarr.getIndexIterator();
Variable lovar = ncds.findVariable("lon");
lovar.setDataType(ncdtLl);
lovar.setCachedData(loarr);
/* Iterate over the observation groups and fill the data */
Map<String, String> allAttributes = new HashMap<String, String>();
IObservationGroup og;
HashMap<String, IndexIterator> darrs = new HashMap<String, IndexIterator>();
Number time;
Number depth = allDepths.get(0);
for (int obs = 0; obs < nobs; obs++) {
og = obsGroups.get(obs);
time = og.getTimes()[0];
putArrayData(tii, ncdtTime, time);
putArrayData(loii, ncdtLl, og.getLon());
putArrayData(laii, ncdtLl, og.getLat());
for (VariableParams dn : allDn) {
if (og.getDataNames().contains(dn)) {
DataType ncdtData = getNcDataType(dn.getDataType());
VariableDS dvar = (VariableDS) ncds.findVariable(dn.getShortName());
if (dvar == null) {
dvar =
new VariableDS(
ncds,
null,
null,
dn.getShortName(),
ncdtData,
"time",
dn.getUnits(),
dn.getDescription());
dvar.addAttribute(new Attribute(CF.COORDINATES, "time lon lat"));
// dvar.addAttribute(new Attribute("missing_value",
// missingData));
dvar.addAttribute(new Attribute(CF.STANDARD_NAME, dn.getStandardName()));
Array darr = Array.factory(ncdtData, new int[] {nt});
dvar.setCachedData(darr);
darrs.put(dn.getStandardName(), darr.getIndexIterator());
ncds.addVariable(null, dvar);
}
putArrayData(darrs.get(dn.getStandardName()), ncdtData, og.getData(dn, time, depth));
} else {
/*
* station doesn't have this variable - don't believe
* this can even happen...
*
* NOTE: This would indicate a problem with the above processing where the data-name list
* has been modified prior to contains-checking
*/
}
}
}
/* Add global attributes */
for (String key : allAttributes.keySet()) {
ncds.addAttribute(null, new Attribute(key, allAttributes.get(key)));
}
} catch (FileNotFoundException ex) {
Logger.getLogger(NcdsFactory.class.getName()).log(Level.SEVERE, null, ex);
} catch (IOException ex) {
Logger.getLogger(NcdsFactory.class.getName()).log(Level.SEVERE, null, ex);
} finally {
if (temp != null) {
if (!temp.delete()) {
temp.deleteOnExit();
}
}
if (ncds != null) {
ncds.finish();
}
}
return ncds;
}