@Test
/**
* Find min/max/average precipitation for a randomly-positioned but fixed-size region from a nc
* file output: filename,origin,size key: value:min, max, average
*
* @throws Exception
*/
public void testProcessingNASANexDataInNetCDF() throws Exception {
final int SIZE = 100;
File file = new File(this.getClass().getResource("/ncar.nc").getPath());
byte[] netcdfinbyte = FileUtils.readFileToByteArray(file);
// use any dummy filename for file in memory
NetcdfFile netCDFfile = NetcdfFile.openInMemory("inmemory.nc", netcdfinbyte);
Variable time = netCDFfile.findVariable("time");
ArrayDouble.D1 days = (ArrayDouble.D1) time.read();
Variable lat = netCDFfile.findVariable("lat");
if (lat == null) {
logger.error("Cannot find Variable latitude(lat)");
return;
}
ArrayFloat.D1 absolutelat = (ArrayFloat.D1) lat.read();
Variable lon = netCDFfile.findVariable("lon");
if (lon == null) {
logger.error("Cannot find Variable longitude(lon)");
return;
}
ArrayFloat.D1 absolutelon = (ArrayFloat.D1) lon.read();
Variable pres = netCDFfile.findVariable("pr");
if (pres == null) {
logger.error("Cannot find Variable precipitation(pr)");
return;
}
Random rand = new Random();
int orig_lat = rand.nextInt((int) lat.getSize());
orig_lat = Math.min(orig_lat, (int) (lat.getSize() - SIZE));
int orig_lon = rand.nextInt((int) lon.getSize());
orig_lon = Math.min(orig_lon, (int) (lon.getSize() - SIZE));
int[] origin = new int[] {0, orig_lat, orig_lon};
int[] size = new int[] {1, SIZE, SIZE};
ArrayFloat.D3 data3D = (ArrayFloat.D3) pres.read(origin, size);
double max = Double.NEGATIVE_INFINITY;
double min = Double.POSITIVE_INFINITY;
double sum = 0;
for (int j = 0; j < SIZE; j++) {
for (int k = 0; k < SIZE; k++) {
double current = data3D.get(0, j, k);
max = (current > max ? current : max);
min = (current < min ? current : min);
sum += current;
}
}
logger.info(
days
+ ","
+ absolutelat.get(orig_lat)
+ ","
+ absolutelon.get(orig_lon)
+ ","
+ SIZE
+ ":"
+ min
+ ","
+ max
+ ","
+ sum / (SIZE * SIZE));
}
/**
* 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;
}
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);
}