public void testAggCoordVar2(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);
IndexIterator dataI = data.getIndexIterator();
assert dataI.getIntNext() == 0 : dataI.getIntCurrent();
assert dataI.getIntNext() == 1 : dataI.getIntCurrent();
assert dataI.getIntNext() == 2 : dataI.getIntCurrent();
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
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 testDimensions(NetcdfFile ncfile) {
System.out.println("ncfile = \n" + ncfile);
Dimension latDim = ncfile.findDimension("lat");
assert null != latDim;
assert latDim.getShortName().equals("lat");
assert latDim.getLength() == 3;
assert !latDim.isUnlimited();
Dimension lonDim = ncfile.findDimension("lon");
assert null != lonDim;
assert lonDim.getShortName().equals("lon");
assert lonDim.getLength() == 4;
assert !lonDim.isUnlimited();
Dimension timeDim = ncfile.findDimension("time");
assert null != timeDim;
assert timeDim.getShortName().equals("time");
assert timeDim.getLength() == 3 : timeDim.getLength();
}
public void testReadData(NetcdfFile ncfile, String name) throws IOException {
Variable v = ncfile.findVariable(name);
assert null != v;
assert v.getShortName().equals(name);
assert v.getRank() == 3;
assert v.getSize() == 36 : v.getSize();
assert v.getShape()[0] == 3;
assert v.getShape()[1] == 3;
assert v.getShape()[2] == 4;
assert v.getDataType() == DataType.DOUBLE;
assert !v.isCoordinateVariable();
assert v.getDimension(0) == ncfile.findDimension("time");
assert v.getDimension(1) == ncfile.findDimension("lat");
assert v.getDimension(2) == ncfile.findDimension("lon");
Array data = v.read();
assert data.getRank() == 3;
assert data.getSize() == 36;
assert data.getShape()[0] == 3;
assert data.getShape()[1] == 3;
assert data.getShape()[2] == 4;
assert data.getElementType() == double.class;
int[] shape = data.getShape();
Index tIndex = data.getIndex();
for (int i = 0; i < shape[0]; i++)
for (int j = 0; j < shape[1]; j++)
for (int k = 0; k < shape[2]; k++) {
double val = data.getDouble(tIndex.set(i, j, k));
// System.out.println(" "+val);
assert TestUtils.close(val, 100 * i + 10 * j + k) : val;
}
}
public static Map<String, Metadata> readFile(String file) throws Exception {
NetcdfFile n = NetcdfFile.open(file);
System.out.println("Opened: " + file);
/* Determine the size of our grid */
int xLen = n.findDimension("x").getLength();
int yLen = n.findDimension("y").getLength();
System.out.println("Grid size: " + xLen + "x" + yLen);
/* What time is this set of readings for? */
Variable timeVar = n.findVariable("time");
String timeStr = timeVar.getUnitsString().toUpperCase();
timeStr = timeStr.replace("HOURS SINCE ", "");
timeStr = timeStr.replace("HOUR SINCE ", "");
/* Find the base date (the day) the reading was taken */
Date baseDate = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssX").parse(timeStr);
/* Get the number of hours since the base date this reading was taken */
int offset = timeVar.read().getInt(0);
/* Generate the actual date for this reading */
Calendar calendar = Calendar.getInstance();
calendar.setTime(baseDate);
calendar.set(Calendar.HOUR, calendar.get(Calendar.HOUR) + offset);
System.out.println("Time of collection: " + calendar.getTime());
/* We'll keep a mapping of geolocations -> Galileo Metadata */
Map<String, Metadata> metaMap = new HashMap<>();
/* Determine the lat, lon coordinates for the grid points, and get each
* reading at each grid point. */
NetcdfDataset dataset = new NetcdfDataset(n);
@SuppressWarnings("resource")
GridDataset gridData = new GridDataset(dataset);
for (GridDatatype g : gridData.getGrids()) {
/* Let's look at 3D variables: these have WxH dimensions, plus a
* single plane. A 4D variable would contain elevation
* and multiple planes as a result */
if (g.getShape().length == 3) {
convert3DVariable(g, calendar.getTime(), metaMap);
}
}
return metaMap;
}
public void testAggCoordVarScan(NetcdfFile ncfile) throws IOException {
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 : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
int count = 0;
Array data = time.read();
assert (data instanceof ArrayInt);
while (data.hasNext()) {
int val = data.nextInt();
assert val == count * 10 : val + "!=" + count * 10;
count++;
}
}
public void testAggCoordVar3(NetcdfFile ncfile) throws IOException {
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.DOUBLE : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
Array data = time.read();
assert (data instanceof ArrayDouble);
IndexIterator dataI = data.getIndexIterator();
double val = dataI.getDoubleNext();
assert Misc.closeEnough(val, 0.0) : val;
assert Misc.closeEnough(dataI.getDoubleNext(), 10.0) : dataI.getDoubleCurrent();
assert Misc.closeEnough(dataI.getDoubleNext(), 99.0) : dataI.getDoubleCurrent();
}
public void testAggCoordVarNoCoordsDir(NetcdfFile ncfile) throws IOException {
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.STRING : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
Array data = time.read();
assert (data instanceof ArrayObject);
IndexIterator dataI = data.getIndexIterator();
String coordName = (String) dataI.getObjectNext();
assert coordName.equals("time0Dir.nc") : coordName;
coordName = (String) dataI.getObjectNext();
assert coordName.equals("time1Dir.nc") : coordName;
coordName = (String) dataI.getObjectNext();
assert coordName.equals("time2Dir.nc") : coordName;
}
public void testCoordVar(NetcdfFile ncfile) {
Variable lat = ncfile.findVariable("lat");
assert null != lat;
assert lat.getShortName().equals("lat");
assert lat.getRank() == 1;
assert lat.getSize() == 3;
assert lat.getShape()[0] == 3;
assert lat.getDataType() == DataType.FLOAT;
assert !lat.isUnlimited();
assert lat.getDimension(0).equals(ncfile.findDimension("lat"));
Attribute att = lat.findAttribute("units");
assert null != att;
assert !att.isArray();
assert att.isString();
assert att.getDataType() == DataType.STRING;
assert att.getStringValue().equals("degrees_north");
assert att.getNumericValue() == null;
assert att.getNumericValue(3) == null;
try {
Array data = lat.read();
assert data.getRank() == 1;
assert data.getSize() == 3;
assert data.getShape()[0] == 3;
assert data.getElementType() == float.class;
IndexIterator dataI = data.getIndexIterator();
assert TestUtils.close(dataI.getDoubleNext(), 41.0);
assert TestUtils.close(dataI.getDoubleNext(), 40.0);
assert TestUtils.close(dataI.getDoubleNext(), 39.0);
} catch (IOException io) {
}
}
public void testNC3Read() throws IOException {
NetcdfFile ncfile = TestDir.openFileLocal("testWrite.nc");
assert (null != ncfile.findDimension("lat"));
assert (null != ncfile.findDimension("lon"));
Variable temp = null;
assert (null != (temp = ncfile.findVariable("temperature")));
// read entire array
Array A;
try {
A = temp.read();
} catch (IOException e) {
System.err.println("ERROR reading file");
assert (false);
return;
}
assert (A.getRank() == 2);
int i, j;
Index ima = A.getIndex();
int[] shape = A.getShape();
assert shape[0] == 64;
assert shape[1] == 128;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
double dval = A.getDouble(ima.set(i, j));
assert (dval == (double) (i * 1000000 + j * 1000)) : dval;
}
}
// read part of array
int[] origin2 = new int[2];
int[] shape2 = new int[2];
shape2[0] = 1;
shape2[1] = temp.getShape()[1];
try {
A = temp.read(origin2, shape2);
} catch (InvalidRangeException e) {
System.err.println("ERROR reading file " + e);
assert (false);
return;
} catch (IOException e) {
System.err.println("ERROR reading file");
assert (false);
return;
}
assert (A.getRank() == 2);
for (j = 0; j < shape2[1]; j++) {
assert (A.getDouble(ima.set(0, j)) == (double) (j * 1000));
}
// rank reduction
Array Areduce = A.reduce();
Index ima2 = Areduce.getIndex();
assert (Areduce.getRank() == 1);
for (j = 0; j < shape2[1]; j++) {
assert (Areduce.getDouble(ima2.set(j)) == (double) (j * 1000));
}
// read char variable
Variable c = null;
assert (null != (c = ncfile.findVariable("svar")));
try {
A = c.read();
} catch (IOException e) {
assert (false);
}
assert (A instanceof ArrayChar);
ArrayChar ac = (ArrayChar) A;
String val = ac.getString(ac.getIndex());
assert val.equals("Testing 1-2-3") : val;
// System.out.println( "val = "+ val);
// read char variable 2
Variable c2 = null;
assert (null != (c2 = ncfile.findVariable("svar2")));
try {
A = c2.read();
} catch (IOException e) {
assert (false);
}
assert (A instanceof ArrayChar);
ArrayChar ac2 = (ArrayChar) A;
assert (ac2.getString().equals("Two pairs of ladies stockings!"));
// read String Array
Variable c3 = null;
assert (null != (c3 = ncfile.findVariable("names")));
try {
A = c3.read();
} catch (IOException e) {
assert (false);
}
assert (A instanceof ArrayChar);
ArrayChar ac3 = (ArrayChar) A;
ima = ac3.getIndex();
assert (ac3.getString(ima.set(0)).equals("No pairs of ladies stockings!"));
assert (ac3.getString(ima.set(1)).equals("One pair of ladies stockings!"));
assert (ac3.getString(ima.set(2)).equals("Two pairs of ladies stockings!"));
// read String Array - 2
Variable c4 = null;
assert (null != (c4 = ncfile.findVariable("names2")));
try {
A = c4.read();
} catch (IOException e) {
assert (false);
}
assert (A instanceof ArrayChar);
ArrayChar ac4 = (ArrayChar) A;
ima = ac4.getIndex();
assert (ac4.getString(0).equals("0 pairs of ladies stockings!"));
assert (ac4.getString(1).equals("1 pair of ladies stockings!"));
assert (ac4.getString(2).equals("2 pairs of ladies stockings!"));
// System.out.println( "ncfile = "+ ncfile);
ncfile.close();
System.out.println("**************TestRead done");
}
