/**
* Open a ucar.nc2.ft.PointFeatureCollection, write out in CF point format.
*
* @param fileIn open through TypedDatasetFactory.open(FeatureType.POINT, ..)
* @param fileOut write to this netcdf-3 file
* @param inMemory if true, read file into memory for efficiency
* @return true on success
* @throws IOException on read/write error
*/
public static boolean rewritePointFeatureDataset(String fileIn, String fileOut, boolean inMemory)
throws IOException {
System.out.println(
"Rewrite2 .nc files from " + fileIn + " to " + fileOut + " inMemory= " + inMemory);
long start = System.currentTimeMillis();
// do it in memory for speed
NetcdfFile ncfile = inMemory ? NetcdfFile.openInMemory(fileIn) : NetcdfFile.open(fileIn);
NetcdfDataset ncd = new NetcdfDataset(ncfile);
Formatter errlog = new Formatter();
FeatureDataset fd = FeatureDatasetFactoryManager.wrap(FeatureType.ANY_POINT, ncd, null, errlog);
if (fd == null) return false;
if (fd instanceof FeatureDatasetPoint) {
writePointFeatureCollection((FeatureDatasetPoint) fd, fileOut);
fd.close();
long took = System.currentTimeMillis() - start;
System.out.println(" that took " + (took - start) + " msecs");
return true;
}
return false;
}
private NetcdfDataset getBufrMessageAsDataset(Message m) throws IOException {
byte[] mbytes = scan.getMessageBytes(m);
NetcdfFile ncfile = null;
try {
ncfile = NetcdfFile.openInMemory("test", mbytes, "ucar.nc2.iosp.bufr.BufrIosp");
} catch (Exception e) {
throw new IOException(e);
}
return new NetcdfDataset(ncfile);
}
@Test
public void testReadnetCDFinSequnceFileFormat() throws Exception {
String path = this.getClass().getResource("/ncar.nc").getPath();
Util.writeToSequenceFile("file://" + path, hadoopMaster + "/tmp/ncar.seq", new DefaultCodec());
Map<Text, byte[]> netcdfsequnce = Util.readSequenceFile(hadoopMaster + "/tmp/ncar.seq");
for (Map.Entry<Text, byte[]> entry : netcdfsequnce.entrySet()) {
NetcdfFile ncFile = NetcdfFile.openInMemory(entry.getKey().toString(), entry.getValue());
assertEquals(ncFile.getDimensions().size(), 5);
}
}
@Test
/**
* TODO: python API:
* http://stackoverflow.com/questions/16654251/can-h5py-load-a-file-from-a-byte-array-in-memory
*
* @throws Exception
*/
public void testNASAModisHDFAccess() throws Exception {
File file =
new File(
this.getClass()
.getResource("/MYD13Q1.A2014121.h23v04.005.2014138045119.hdf")
.getPath());
byte[] netcdfinbyte = FileUtils.readFileToByteArray(file);
NetcdfFile netCDFfile = NetcdfFile.openInMemory("inmemory.hdf", netcdfinbyte);
// TODO Processing hdf files
}
@Test
/**
* TODO: python API:
* http://stackoverflow.com/questions/16654251/can-h5py-load-a-file-from-a-byte-array-in-memory
*
* @throws Exception
*/
public void testNetCDFInterfaceToACcessH5() throws Exception {
H5File h5 =
hdf5_getters.hdf5_open_readonly(
this.getClass().getResource("/TRAXLZU12903D05F94.h5").getPath());
double h5_temp = hdf5_getters.get_tempo(h5);
File file = new File(this.getClass().getResource("/TRAXLZU12903D05F94.h5").getPath());
byte[] netcdfinbyte = FileUtils.readFileToByteArray(file);
NetcdfFile netCDFfile = NetcdfFile.openInMemory("inmemory.h5", netcdfinbyte);
Variable var = (Variable) netCDFfile.findVariable("/analysis/songs.tempo");
Array content = var.read(); // 1D array
double netcdf_tempo = content.getDouble(0); // 1 column only
assertEquals(h5_temp, netcdf_tempo, 0.001);
}
/**
* Open a ucar.nc2.dt.PointObsDataset, write out in CF point format.
*
* @param fileIn open through TypedDatasetFactory.open(FeatureType.POINT, ..)
* @param fileOut write to this netcdf-3 file
* @param inMemory if true, read file into memory for efficiency
* @return true on success
* @throws IOException on read/write error
*/
public static boolean rewritePointObsDataset(String fileIn, String fileOut, boolean inMemory)
throws IOException {
System.out.println(
"Rewrite2 .nc files from " + fileIn + " to " + fileOut + " inMemory= " + inMemory);
long start = System.currentTimeMillis();
// do it in memory for speed
NetcdfFile ncfile = inMemory ? NetcdfFile.openInMemory(fileIn) : NetcdfFile.open(fileIn);
NetcdfDataset ncd = new NetcdfDataset(ncfile);
StringBuilder errlog = new StringBuilder();
PointObsDataset pobsDataset =
(PointObsDataset) TypedDatasetFactory.open(FeatureType.POINT, ncd, null, errlog);
if (pobsDataset == null) return false;
writePointObsDataset(pobsDataset, fileOut);
pobsDataset.close();
long took = System.currentTimeMillis() - start;
System.out.println(" that took " + (took - start) + " msecs");
return true;
}
@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));
}