public void testAggCoordVar(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert (data instanceof ArrayInt.D1) : data.getClass().getName();
ArrayInt.D1 dataI = (ArrayInt.D1) data;
assert dataI.get(0) == 0;
assert dataI.get(1) == 10;
assert dataI.get(2) == 99;
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
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++;
}
/**
* Fill all of the variables/attributes in the ncfile
*
* @param ncfile NetcdfFile object which will be filled.
* @param bst number of seconds since midnight for start of sweep
* @param yr year of start of each sweep
* @param m month of start of each sweep
* @param dda day of start of each sweep
* @param varList ArrayList of Variables of ncfile
* @param recHdr java.util.Map with values for Attributes
*/
public void doNetcdfFileCoordinate(
ucar.nc2.NetcdfFile ncfile,
int[] bst,
short[] yr,
short[] m,
short[] dda,
ArrayList<Variable> varList,
java.util.Map<String, Number> recHdr) {
// prepare attribute values
String[] unit = {" ", "dbZ", "dbZ", "m/sec", "m/sec", "dB"};
String def_datafile = "SIGMET-IRIS";
Short header_length = 80;
Short ray_header_length = 6;
int ngates = 0;
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("HERE!! num_rays="+num_rays);
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();
int nparams = (recHdr.get("nparams").intValue()); // System.out.println("nparams="+nparams);
// define date/time
// int last_t=(int)(ray[nparams*number_sweeps-1][num_rays-1].getTime());
int last_t = volScan.lastRay.getTime();
String sss1 = Short.toString(m[0]);
if (sss1.length() < 2) sss1 = "0" + sss1;
String sss2 = Short.toString(dda[0]);
if (sss2.length() < 2) sss2 = "0" + sss2;
String base_date0 = String.valueOf(yr[0]) + "-" + sss1 + "-" + sss2;
String sss11 = Short.toString(m[number_sweeps - 1]);
if (sss11.length() < 2) sss11 = "0" + sss11;
String sss22 = Short.toString(dda[number_sweeps - 1]);
if (sss22.length() < 2) sss22 = "0" + sss22;
String base_date1 = String.valueOf(yr[number_sweeps - 1]) + "-" + sss11 + "-" + sss22;
String start_time = base_date0 + "T" + calcTime(bst[0], 0) + "Z";
String end_time = base_date1 + "T" + calcTime(bst[number_sweeps - 1], last_t) + "Z";
ncfile.addAttribute(null, new Attribute("time_coverage_start", start_time));
ncfile.addAttribute(null, new Attribute("time_coverage_end", end_time));
// set all of Variables
try {
int sz = varList.size();
ArrayFloat.D2[] dataArr = new ArrayFloat.D2[nparams * number_sweeps];
Index[] dataIndex = new Index[nparams * number_sweeps];
Ray[] rtemp = new Ray[(int) num_rays];
// NCdump.printArray(dataArr[0], "Total_Power", System.out, null);
Variable[] distanceR = new Variable[number_sweeps];
ArrayFloat.D1[] distArr = new ArrayFloat.D1[number_sweeps];
Index[] distIndex = new Index[number_sweeps];
String distName = "distanceR";
for (int i = 0; i < number_sweeps; i++) {
if (number_sweeps > 1) {
distName = "distanceR_sweep_" + (i + 1);
}
for (Variable aVarList : varList) {
if ((aVarList.getShortName()).equals(distName.trim())) {
distanceR[i] = aVarList;
break;
}
}
distArr[i] = (ArrayFloat.D1) Array.factory(DataType.FLOAT, distanceR[i].getShape());
distIndex[i] = distArr[i].getIndex();
// for (int jj=0; jj<num_rays; jj++) { rtemp[jj]=ray[i][jj]; }
ngates = sweep_bins[i];
float stp = calcStep(range_first, range_last, (short) ngates);
for (int ii = 0; ii < ngates; ii++) {
distArr[i].setFloat(distIndex[i].set(ii), (range_first + ii * stp));
}
}
// NCdump.printArray(distArr[0], "distanceR", System.out, null);
List rgp = volScan.getTotalPowerGroups();
if (rgp.size() == 0) rgp = volScan.getReflectivityGroups();
List[] sgp = new ArrayList[number_sweeps];
for (int i = 0; i < number_sweeps; i++) {
sgp[i] = (List) rgp.get((short) i);
}
Variable[] time = new Variable[number_sweeps];
ArrayInt.D1[] timeArr = new ArrayInt.D1[number_sweeps];
Index[] timeIndex = new Index[number_sweeps];
String t_n = "time";
for (int i = 0; i < number_sweeps; i++) {
if (number_sweeps > 1) {
t_n = "time_sweep_" + (i + 1);
}
for (Variable aVarList : varList) {
if ((aVarList.getShortName()).equals(t_n.trim())) {
time[i] = aVarList;
break;
}
}
// if (time[i].getShape().length == 0) {
// continue;
// }
timeArr[i] = (ArrayInt.D1) Array.factory(DataType.INT, time[i].getShape());
timeIndex[i] = timeArr[i].getIndex();
List rlist = sgp[i];
for (int jj = 0; jj < num_rays; jj++) {
rtemp[jj] = (Ray) rlist.get(jj);
} // ray[i][jj]; }
for (int jj = 0; jj < num_rays; jj++) {
timeArr[i].setInt(timeIndex[i].set(jj), rtemp[jj].getTime());
}
}
// NCdump.printArray(timeArr[0], "time", System.out, null);
Variable[] azimuthR = new Variable[number_sweeps];
ArrayFloat.D1[] azimArr = new ArrayFloat.D1[number_sweeps];
Index[] azimIndex = new Index[number_sweeps];
String azimName = "azimuthR";
for (int i = 0; i < number_sweeps; i++) {
if (number_sweeps > 1) {
azimName = "azimuthR_sweep_" + (i + 1);
}
for (Variable aVarList : varList) {
if ((aVarList.getShortName()).equals(azimName.trim())) {
azimuthR[i] = aVarList;
break;
}
}
azimArr[i] = (ArrayFloat.D1) Array.factory(DataType.FLOAT, azimuthR[i].getShape());
azimIndex[i] = azimArr[i].getIndex();
List rlist = sgp[i];
for (int jj = 0; jj < num_rays; jj++) {
rtemp[jj] = (Ray) rlist.get(jj);
} // ray[i][jj]; }
for (int jj = 0; jj < num_rays; jj++) {
azimArr[i].setFloat(azimIndex[i].set(jj), rtemp[jj].getAz());
}
}
// NCdump.printArray(azimArr[0], "azimuthR", System.out, null);
Variable[] elevationR = new Variable[number_sweeps];
ArrayFloat.D1[] elevArr = new ArrayFloat.D1[number_sweeps];
Index[] elevIndex = new Index[number_sweeps];
String elevName = "elevationR";
for (int i = 0; i < number_sweeps; i++) {
if (number_sweeps > 1) {
elevName = "elevationR_sweep_" + (i + 1);
}
for (Variable aVarList : varList) {
if ((aVarList.getShortName()).equals(elevName.trim())) {
elevationR[i] = aVarList;
break;
}
}
elevArr[i] = (ArrayFloat.D1) Array.factory(DataType.FLOAT, elevationR[i].getShape());
elevIndex[i] = elevArr[i].getIndex();
List rlist = sgp[i];
for (int jj = 0; jj < num_rays; jj++) {
rtemp[jj] = (Ray) rlist.get(jj);
} // ray[i][jj]; }
for (int jj = 0; jj < num_rays; jj++) {
elevArr[i].setFloat(elevIndex[i].set(jj), rtemp[jj].getElev());
}
}
// NCdump.printArray(elevArr[0], "elevationR", System.out, null);
Variable numGates = null;
for (int i = 0; i < number_sweeps; i++) {
for (Variable aVarList : varList) {
if ((aVarList.getShortName()).equals("numGates")) {
numGates = aVarList;
break;
}
}
}
ArrayInt.D1 gatesArr = (ArrayInt.D1) Array.factory(DataType.INT, numGates.getShape());
Index gatesIndex = gatesArr.getIndex();
for (int i = 0; i < number_sweeps; i++) {
List rlist = sgp[i];
for (int jj = 0; jj < num_rays; jj++) {
rtemp[jj] = (Ray) rlist.get(jj);
} // ray[i][jj]; }
ngates = rtemp[0].getBins();
gatesArr.setInt(gatesIndex.set(i), ngates);
}
for (int i = 0; i < number_sweeps; i++) {
distanceR[i].setCachedData(distArr[i], false);
time[i].setCachedData(timeArr[i], false);
azimuthR[i].setCachedData(azimArr[i], false);
elevationR[i].setCachedData(elevArr[i], false);
}
numGates.setCachedData(gatesArr, false);
// startSweep.setCachedData(sweepArr, false);
// -------------------------------------------------
// int b=(int)ray[0][0].getBins();
// -- Test of readData() and readToByteChannel() -----------------
/*
Range r1=new Range(356, 359);
Range r2=new Range(0, 15);
java.util.List arlist=new ArrayList();
arlist.add(r1);
arlist.add(r2);
Array testArr=readData(v[0], new Section(arlist));
NCdump.printArray(testArr, "Total_Power_sweep_1", System.out, null);
WritableByteChannel channel=new FileOutputStream(new File("C:\\netcdf\\tt.dat")).getChannel();
long ikk=readToByteChannel(v[0], new Section(arlist), channel);
System.out.println("IKK="+ikk);
channel.close();
*/
// ---------------------------------------------------
} catch (Exception e) {
System.out.println(e.toString());
e.printStackTrace();
}
} // ----------- end of doNetcdf ----------------------------------
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)));
}
/**
* Make the station variables from a representative station
*
* @param stations list of stations
* @param dim station dimension
* @return the list of variables
*/
protected List<Variable> makeStationVars(List<GempakStation> stations, Dimension dim) {
int numStations = stations.size();
boolean useSTID = true;
for (GempakStation station : stations) {
if (station.getSTID().equals("")) {
useSTID = false;
break;
}
}
List<Variable> vars = new ArrayList<Variable>();
List<String> stnKeyNames = gemreader.getStationKeyNames();
for (String varName : stnKeyNames) {
Variable v = makeStationVariable(varName, dim);
// use STNM or STID as the name or description
Attribute stIDAttr = new Attribute("standard_name", "station_id");
if (varName.equals(GempakStation.STID) && useSTID) {
v.addAttribute(stIDAttr);
}
if (varName.equals(GempakStation.STNM) && !useSTID) {
v.addAttribute(stIDAttr);
}
vars.add(v);
}
// see if we fill these in completely now
if ((dim != null) && (numStations > 0)) {
for (Variable v : vars) {
Array varArray;
if (v.getDataType().equals(DataType.CHAR)) {
int[] shape = v.getShape();
varArray = new ArrayChar.D2(shape[0], shape[1]);
} else {
varArray = get1DArray(v.getDataType(), numStations);
}
int index = 0;
String varname = v.getFullName();
for (GempakStation stn : stations) {
String test = "";
if (varname.equals(GempakStation.STID)) {
test = stn.getName();
} else if (varname.equals(GempakStation.STNM)) {
((ArrayInt.D1) varArray)
.set(
index,
// (int) (stn.getSTNM() / 10));
(int) (stn.getSTNM()));
} else if (varname.equals(GempakStation.SLAT)) {
((ArrayFloat.D1) varArray).set(index, (float) stn.getLatitude());
} else if (varname.equals(GempakStation.SLON)) {
((ArrayFloat.D1) varArray).set(index, (float) stn.getLongitude());
} else if (varname.equals(GempakStation.SELV)) {
((ArrayFloat.D1) varArray).set(index, (float) stn.getAltitude());
} else if (varname.equals(GempakStation.STAT)) {
test = stn.getSTAT();
} else if (varname.equals(GempakStation.COUN)) {
test = stn.getCOUN();
} else if (varname.equals(GempakStation.STD2)) {
test = stn.getSTD2();
} else if (varname.equals(GempakStation.SPRI)) {
((ArrayInt.D1) varArray).set(index, stn.getSPRI());
} else if (varname.equals(GempakStation.SWFO)) {
test = stn.getSWFO();
} else if (varname.equals(GempakStation.WFO2)) {
test = stn.getWFO2();
}
if (!test.equals("")) {
((ArrayChar.D2) varArray).setString(index, test);
}
index++;
}
v.setCachedData(varArray, false);
}
}
return vars;
}
@Test
public void testArraySubset() throws IOException {
DODSNetcdfFile dodsfile = TestDODSRead.open("test.02?i32[1:10],f64[2:2:10]");
Variable v = null;
Array a = null;
// int32
assert (null != (v = dodsfile.findVariable("i32")));
assert v.getFullName().equals("i32");
assert v.getRank() == 1;
assert v.getSize() == 10;
assert v.getDataType() == DataType.INT;
a = v.read();
assert a.getRank() == 1;
assert a.getSize() == 25;
assert a.getElementType() == int.class;
assert a instanceof ArrayInt.D1;
ArrayInt.D1 ai = (ArrayInt.D1) a;
for (int i = 0; i < 10; i++) {
int val = ai.get(i);
assert (val == i * 2048) : val + " != " + (i * 2048);
}
// uint16
assert null == (v = dodsfile.findVariable("ui16"));
assert null == (v = dodsfile.findVariable("ui32"));
// double
assert (null != (v = dodsfile.findVariable("f64")));
assert v.getFullName().equals("f64");
assert v.getRank() == 1;
assert v.getSize() == 5;
assert v.getDataType() == DataType.DOUBLE : v.getDataType();
a = v.read();
assert a.getRank() == 1;
assert a.getSize() == 25;
assert a.getElementType() == double.class;
assert a instanceof ArrayDouble.D1;
ArrayDouble.D1 ad = (ArrayDouble.D1) a;
double[] tFloat64 =
new double[] {
1.0,
0.9999500004166653,
0.9998000066665778,
0.9995500337489875,
0.9992001066609779,
0.9987502603949663,
0.9982005399352042,
0.9975510002532796,
0.9968017063026194,
0.9959527330119943,
0.9950041652780257,
0.9939560979566968,
0.9928086358538663,
0.9915618937147881,
0.9902159962126371,
0.9887710779360422,
0.9872272833756269,
0.9855847669095608,
0.9838436927881214,
0.9820042351172703,
0.9800665778412416,
0.9780309147241483,
0.9758974493306055,
0.9736663950053749,
0.9713379748520297
};
for (int i = 0; i < 5; i++) {
double val = ad.get(i);
assert Misc.closeEnough(val, tFloat64[i], 1.0e-9);
}
dodsfile.close();
}
