public void readByte2Short() throws Exception {
Variable t2 = null;
assert (null != (t2 = ncfileRead.findVariable("t2")));
assert (t2.getDataType() == DataType.BYTE);
Attribute att = t2.findAttribute(CDM.SCALE_FACTOR);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
assert (2 == att.getNumericValue().doubleValue());
assert (DataType.SHORT == att.getDataType());
assert (null != (t2 = dsRead.findVariable("t2")));
assert t2 instanceof VariableEnhanced;
VariableDS vs = (VariableDS) t2;
assert (vs.getDataType() == DataType.SHORT) : vs.getDataType();
assert (!vs.hasMissing());
Array A = vs.read();
assert (A.getElementType() == short.class) : A.getElementType();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getShort(ima.set(i, j)) == (2 * (i * 10 + j) + 77));
}
}
System.out.println("**************TestStandardVar readByte2Short");
}
public void getTransientSeverity(int trfiresev[], int cid) {
Index fireind = trseverityA.getIndex();
for (int i = 0; i < ConstTime.MAX_TR_FIR_OCR_NUM; i++) {
trfiresev[i] = trseverityA.getInt(fireind.set(cid, i));
}
};
public void getTransientFireSeason(int trfireseason[], int cid) {
Index fireind = trfireseasonA.getIndex();
for (int i = 0; i < ConstTime.MAX_TR_FIR_OCR_NUM; i++) {
trfireseason[i] = trfireseasonA.getInt(fireind.set(cid, i));
}
};
public void getSpinupSeverity(int spfiresev[], int cid) {
Index severity = spseverityA.getIndex();
for (int i = 0; i < ConstTime.MAX_SP_FIR_OCR_NUM; i++) {
spfiresev[i] = spseverityA.getInt(severity.set(cid, i));
}
};
public void getSpinupFireSeason(int spfireseason[], int cid) {
Index fireyri = spfireseasonA.getIndex();
for (int i = 0; i < ConstTime.MAX_SP_FIR_OCR_NUM; i++) {
spfireseason[i] = spfireseasonA.getInt(fireyri.set(cid, i));
}
};
/**
* Create a scalar numeric-valued Attribute.
*
* @param name name of Attribute
* @param val value of Attribute
*/
public Attribute(String name, Number val) {
this.name = name;
int[] shape = new int[1];
shape[0] = 1;
DataType dt = DataType.getType(val.getClass());
Array vala = Array.factory(dt.getPrimitiveClassType(), shape);
Index ima = vala.getIndex();
vala.setDouble(ima.set0(0), val.doubleValue());
setValues(vala);
}
private static Array createTargetArray(int sizeY, int sizeX) {
final Array fillArray = Array.factory(DataType.BYTE, new int[] {1, sizeY, sizeX});
final Index index = fillArray.getIndex();
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
index.set(0, y, x);
fillArray.setByte(index, Watermask.INVALID_WATER_FRACTION);
}
}
return fillArray;
}
private Array convertToChar(Variable newVar, Array oldData) {
ArrayChar newData = (ArrayChar) Array.factory(DataType.CHAR, newVar.getShape());
Index ima = newData.getIndex();
IndexIterator ii = oldData.getIndexIterator();
while (ii.hasNext()) {
String s = (String) ii.getObjectNext();
int[] c = ii.getCurrentCounter();
for (int i = 0; i < c.length; i++) ima.setDim(i, c[i]);
newData.setString(ima, s);
}
return newData;
}
public void readShortMissing() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t4")));
assert (v.getDataType() == DataType.SHORT);
// default use of missing_value
assert (null != (v = dsRead.findVariable("t4")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.SHORT);
Attribute att = vs.findAttribute(CDM.MISSING_VALUE);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
System.out.println("missing_value = " + att.getNumericValue().shortValue());
assert (((short) -9999) == att.getNumericValue().shortValue());
assert (DataType.SHORT == att.getDataType());
assert (vs.hasMissing());
assert (vs.hasMissingValue());
assert (vs.isMissing((double) ((short) -9999)));
assert (vs.isMissingValue((double) ((short) -9999)));
Array A = vs.read();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getFloat(ima.set(i, j)) == (i * 10 + j));
}
}
// turn off missing data
vs.setMissingDataIsMissing(false);
assert (vs.getDataType() == DataType.SHORT);
assert (!vs.hasMissing());
assert (vs.hasMissingValue());
assert (!vs.isMissing((double) ((short) -9999)));
assert (vs.isMissingValue((double) ((short) -9999)));
vs.setMissingDataIsMissing(true);
assert (vs.hasMissing());
assert (vs.isMissing((double) ((short) -9999)));
System.out.println("**************TestStandardVar Read readShortMissing");
}
private ArrayDouble.D1 makeHeight1D(
Array eta, Array s, Array depth, Array c, double depth_c, int x_index, int y_index) {
int nz = (int) s.getSize();
Index sIndex = s.getIndex();
Index cIndex = c.getIndex();
Index etaIndex = eta.getIndex();
Index depthIndex = depth.getIndex();
ArrayDouble.D1 height = new ArrayDouble.D1(nz);
for (int z = 0; z < nz; z++) {
double sz = s.getDouble(sIndex.set(z));
double cz = c.getDouble(cIndex.set(z));
double term1 = depth_c * sz;
double fac1 = depth.getDouble(depthIndex.set(y_index, x_index));
double term2 = fac1 * cz;
double Sterm = (term1 + term2) / (depth_c + fac1);
double term3 = eta.getDouble(etaIndex.set(y_index, x_index));
double term4 = (term3 + fac1) * Sterm;
double hterm = term3 + term4;
height.set(z, hterm);
}
return height;
}
private void doWrite2(NetcdfFileWriteable ncfile, String varName) throws Exception {
Variable v = ncfile.findVariable(varName);
int[] w = getWeights(v);
int[] shape = v.getShape();
Array aa = Array.factory(v.getDataType().getPrimitiveClassType(), shape);
Index ima = aa.getIndex();
for (int i = 0; i < shape[0]; i++) {
for (int j = 0; j < shape[1]; j++) {
aa.setDouble(ima.set(i, j), (double) (i * w[0] + j * w[1]));
}
}
ncfile.write(varName, aa);
}
@Override
public final Array apply(Array sourceArray, Item sourceColumn) throws RuleException {
final int[] shape = getContext().getTargetVariable().getShape();
final int sizeY = shape[1];
final int sizeX = shape[2];
final Array targetArray = createTargetArray(sizeY, sizeX);
final Reader observationReader = getContext().getObservationReader();
if (observationReader == null) {
return targetArray;
}
final int recordNo = getContext().getObservation().getRecordNo();
final GeoCoding geoCoding;
try {
geoCoding = observationReader.getGeoCoding(recordNo);
} catch (IOException ignored) {
return targetArray;
}
final Point point =
getContext().getMatchup().getRefObs().getPoint().getGeometry().getFirstPoint();
final double lon = point.getX();
final double lat = point.getY();
final PixelLocator pixelLocator = new GeoCodingWrapper(geoCoding);
final Point2D p = new Point2D.Double();
final boolean found = pixelLocator.getPixelLocation(lon, lat, p);
if (found) {
final Watermask watermask = Container.WATERMASK;
final Index index = targetArray.getIndex();
final int minX = (int) Math.max(p.getX() - sizeX / 2, 0.0);
final int maxX =
(int) Math.min(p.getX() + sizeX / 2, observationReader.getElementCount() - 1);
final int minY = (int) Math.max(p.getY() - sizeY / 2, 0.0);
final int maxY =
(int) Math.min(p.getY() + sizeY / 2, observationReader.getScanLineCount() - 1);
for (int y = minY, yi = 0; y <= maxY; y++, yi++) {
for (int x = minX, xi = 0; x <= maxX; x++, xi++) {
final byte waterFraction =
watermask.getWaterFraction(x, y, pixelLocator, stepCountX, stepCountY);
targetArray.setByte(index.set(0, yi, xi), waterFraction);
}
}
}
return targetArray;
}
public void readDouble() throws Exception {
Variable t1 = null;
assert (null != (t1 = ncfileRead.findVariable("t1")));
assert (t1.getDataType() == DataType.DOUBLE);
Attribute att = t1.findAttribute(CDM.SCALE_FACTOR);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
assert (2.0 == att.getNumericValue().doubleValue());
assert (DataType.DOUBLE == att.getDataType());
// read
Array A = t1.read();
int i, j;
Index ima = A.getIndex();
int[] shape = A.getShape();
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getDouble(ima.set(i, j)) == (double) (i * 10.0 + j));
}
}
assert (null != (t1 = dsRead.findVariable("t1")));
assert t1 instanceof VariableEnhanced;
VariableEnhanced dsVar = (VariableEnhanced) t1;
assert (dsVar.getDataType() == DataType.DOUBLE);
A = dsVar.read();
ima = A.getIndex();
shape = A.getShape();
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getDouble(ima.set(i, j)) == (2.0 * (i * 10.0 + j) + 77.0));
}
}
assert (null == t1.findAttribute(CDM.SCALE_FACTOR));
assert (null == t1.findAttribute("add_offset"));
System.out.println("**************TestStandardVar ReadDouble");
}
public void readSlice(NetcdfFile ncfile, int[] origin, int[] shape, String name)
throws IOException, InvalidRangeException {
Variable v = ncfile.findVariable(name);
Array data = v.read(origin, shape);
assert data.getRank() == 3;
assert data.getSize() == shape[0] * shape[1] * shape[2];
assert data.getShape()[0] == shape[0] : data.getShape()[0] + " " + shape[0];
assert data.getShape()[1] == shape[1];
assert data.getShape()[2] == shape[2];
assert data.getElementType() == double.class;
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 + origin[0]) + 10 * j + k) : val;
}
}
public void readDoubleMissing() throws Exception {
VariableDS v = null;
assert (null != (v = (VariableDS) dsRead.findVariable("m1")));
assert (v.getDataType() == DataType.DOUBLE);
Array A = v.read();
Index ima = A.getIndex();
double val = A.getFloat(ima.set(1, 1));
assert Double.isNaN(val);
assert v.isMissing(val);
// reread with useNans off
v.setUseNaNs(false);
v.createNewCache();
A = v.read();
ima = A.getIndex();
val = A.getFloat(ima.set(1, 1));
assert TestAll.closeEnough(val, -999.99) : val;
assert v.isMissing(val);
}
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 void readByte() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t3")));
assert (v.getDataType() == DataType.BYTE);
assert (null != (v = dsRead.findVariable("t3")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.BYTE);
Attribute att = vs.findAttribute("_FillValue");
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
System.out.println("_FillValue = " + att.getNumericValue().byteValue());
assert (((byte) 255) == att.getNumericValue().byteValue());
assert (DataType.BYTE == att.getDataType());
assert (vs.hasMissing());
assert (vs.hasFillValue());
assert (vs.isMissing((double) ((byte) 255)));
assert (vs.isFillValue((double) ((byte) 255)));
Array A = vs.read();
assert (A.getElementType() == byte.class) : A.getElementType();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getFloat(ima.set(i, j)) == (i * 10 + j));
}
}
System.out.println("**************TestStandardVar ReadByte");
}
@Before
public void setUp() {
int nlayers = 11;
zeros_3D = Array.factory(Double.class, new int[] {1, nlayers, 3, 3});
ones_3D = Array.factory(Double.class, new int[] {1, nlayers, 3, 3});
u3D1 = Array.factory(Double.class, new int[] {1, nlayers, 3, 3});
v3D1 = Array.factory(Double.class, new int[] {1, nlayers, 3, 3});
u3D2 = Array.factory(Double.class, new int[] {1, nlayers, 3, 3});
v3D2 = Array.factory(Double.class, new int[] {1, nlayers, 3, 3});
Index idx = zeros_3D.getIndex();
for (int k = 0; k < nlayers; k++) {
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
zeros_3D.setDouble(idx.set(0, k, i, j), 0);
ones_3D.setDouble(idx, 1);
u3D1.setDouble(idx, j);
v3D1.setDouble(idx, i);
u3D2.setDouble(idx, 2 - j);
v3D2.setDouble(idx, 2 - i);
}
}
}
}
/**
* Projects the arrays of longitudes and latitudes to a Cylindrical Equidistant Projection to
* bring x,y and z into a uniform coordinate system (meters).
*
* @param lons
* @param lats
* @return
*/
private Array[] prj2meters(Array lons, Array lats) {
Array[] out = new Array[2];
assert Arrays.equals(lats.getShape(), lons.getShape());
Index ltidx = Index.factory(lats.getShape());
Index lnidx = Index.factory(lons.getShape());
Array lats_prj = Array.factory(java.lang.Double.class, lats.getShape());
Array lons_prj = Array.factory(java.lang.Double.class, lons.getShape());
for (int i = 0; i < lats.getSize(); i++) {
for (int j = 0; j < lons.getSize(); j++) {
float lon_dd = lons.getFloat(lnidx.set(j));
float lat_dd = lats.getFloat(ltidx.set(i));
double[] prj = MatrixUtilities.lonlat2ceqd(new double[] {lon_dd, lat_dd});
lons_prj.setDouble(lnidx.set(j), prj[0]);
lats_prj.setDouble(ltidx.set(i), prj[1]);
}
}
out[0] = lons_prj;
out[1] = lats_prj;
return out;
}
/**
* Make height from the given data. <br>
* height(x,y,z) = eta(x,y) + ( eta(x,y) + depth([n],x,y) ) * S(x,y,z)
*
* <p>where, S(x,y,z) = (depth_c*s(z) + (depth([n],x,y) * C(z)) / (depth_c + depth([n],x,y)) /
*
* @param eta eta Array
* @param s s Array
* @param depth depth Array
* @param c c Array
* @param depth_c value of depth_c
* @return height data
*/
private ArrayDouble.D3 makeHeight(Array eta, Array s, Array depth, Array c, double depth_c) {
int nz = (int) s.getSize();
Index sIndex = s.getIndex();
Index cIndex = c.getIndex();
int[] shape2D = eta.getShape();
int ny = shape2D[0];
int nx = shape2D[1];
Index etaIndex = eta.getIndex();
Index depthIndex = depth.getIndex();
ArrayDouble.D3 height = new ArrayDouble.D3(nz, ny, nx);
for (int z = 0; z < nz; z++) {
double sz = s.getDouble(sIndex.set(z));
double cz = c.getDouble(cIndex.set(z));
double term1 = depth_c * sz;
for (int y = 0; y < ny; y++) {
for (int x = 0; x < nx; x++) {
double fac1 = depth.getDouble(depthIndex.set(y, x));
double term2 = fac1 * cz;
double Sterm = (term1 + term2) / (depth_c + fac1);
double term3 = eta.getDouble(etaIndex.set(y, x));
double term4 = (term3 + fac1) * Sterm;
double hterm = term3 + term4;
height.set(z, y, x, hterm);
}
}
}
return height;
}
/**
* Calculates change in the y direction
*
* @param arr - a 3x3 array of numbers
* @return
*/
private float dy(Array arr) {
Index idx = Index.factory(arr.getShape());
float e = arr.getFloat(idx.set(1, 1));
if (Float.isNaN(e)) {
return Float.NaN;
}
float a = arr.getFloat(idx.set(0, 0));
float b = arr.getFloat(idx.set(0, 1));
float c = arr.getFloat(idx.set(0, 2));
float g = arr.getFloat(idx.set(2, 0));
float h = arr.getFloat(idx.set(2, 1));
float i = arr.getFloat(idx.set(2, 2));
a = Float.isNaN(a) ? 0 : a;
b = Float.isNaN(b) ? 0 : b;
c = Float.isNaN(c) ? 0 : c;
g = Float.isNaN(g) ? 0 : g;
h = Float.isNaN(h) ? 0 : h;
i = Float.isNaN(i) ? 0 : i;
return ((g + 2 * h + i) - (a + 2 * b + c)) / 8;
}
public void testStride(String stride) throws IOException, InvalidRangeException {
Variable time = ncfile.findVariable("time");
ArrayInt all = (ArrayInt) time.read();
ArrayInt correct = (ArrayInt) all.section(new Section(stride).getRanges());
System.out.printf("correct(%s) %s", stride, NCdumpW.toString(correct));
ArrayInt data = (ArrayInt) time.read(stride);
System.out.printf("data(%s) %s%n", stride, NCdumpW.toString(data));
Index ci = correct.getIndex();
Index di = data.getIndex();
for (int i = 0; i < data.getSize(); i++)
assert (data.getInt(di.set(i)) == correct.getInt(ci.set(i)))
: stride
+ " index "
+ i
+ " = "
+ data.getInt(di.set(i))
+ " != "
+ correct.getInt(ci.set(i));
}
/**
* Calculates change in the x direction
*
* @param arr - a 3x3 array of numbers
* @return
*/
private float dx(Array arr) {
Index idx = Index.factory(arr.getShape());
float e = arr.getFloat(idx.set(1, 1));
if (Float.isNaN(e)) {
return Float.NaN;
}
float a = arr.getFloat(idx.set(0, 0));
float c = arr.getFloat(idx.set(0, 2));
float d = arr.getFloat(idx.set(1, 0));
float f = arr.getFloat(idx.set(1, 2));
float g = arr.getFloat(idx.set(2, 0));
float i = arr.getFloat(idx.set(2, 2));
a = Float.isNaN(a) ? 0 : a;
c = Float.isNaN(c) ? 0 : c;
d = Float.isNaN(d) ? 0 : d;
f = Float.isNaN(f) ? 0 : f;
g = Float.isNaN(g) ? 0 : g;
i = Float.isNaN(i) ? 0 : i;
return ((c + 2 * f + i) - (a + 2 * d + g)) / 8;
}
/**
* @param index
* @return
*/
@Override
public double getRT(int index) {
Array a = this.c.getScanAcquisitionTime();
Index idx = a.getIndex();
return a.getDouble(idx.set(index));
}
/**
* 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 ----------------------------------
public void testWritePermute() throws Exception {
NetcdfFileWriteable ncfile = new NetcdfFileWriteable();
ncfile.setName(TestLocal.cdmTestDataDir + "permuteTest.nc");
// define dimensions
Dimension xDim = ncfile.addDimension("x", 3);
Dimension yDim = ncfile.addDimension("y", 5);
Dimension zDim = ncfile.addDimension("z", 4);
Dimension tDim = ncfile.addDimension("time", 2);
// define Variables
ncfile.addVariable("time", double.class, new Dimension[] {tDim});
ncfile.addVariableAttribute("time", "units", "secs since 1-1-1 00:00");
ncfile.addVariable("z", double.class, new Dimension[] {zDim});
ncfile.addVariableAttribute("z", "units", "meters");
ncfile.addVariableAttribute("z", "positive", "up");
ncfile.addVariable("y", double.class, new Dimension[] {yDim});
ncfile.addVariableAttribute("y", "units", "degrees_north");
ncfile.addVariable("x", double.class, new Dimension[] {xDim});
ncfile.addVariableAttribute("x", "units", "degrees_east");
ncfile.addVariable("tzyx", double.class, new Dimension[] {tDim, zDim, yDim, xDim});
ncfile.addVariableAttribute("tzyx", "units", "K");
ncfile.addVariable("tzxy", double.class, new Dimension[] {tDim, zDim, xDim, yDim});
ncfile.addVariableAttribute("tzxy", "units", "K");
ncfile.addVariable("tyxz", double.class, new Dimension[] {tDim, yDim, xDim, zDim});
ncfile.addVariableAttribute("tyxz", "units", "K");
ncfile.addVariable("txyz", double.class, new Dimension[] {tDim, xDim, yDim, zDim});
ncfile.addVariableAttribute("txyz", "units", "K");
ncfile.addVariable("zyxt", double.class, new Dimension[] {zDim, yDim, xDim, tDim});
ncfile.addVariableAttribute("zyxt", "units", "K");
ncfile.addVariable("zxyt", double.class, new Dimension[] {zDim, xDim, yDim, tDim});
ncfile.addVariableAttribute("zxyt", "units", "K");
ncfile.addVariable("yxzt", double.class, new Dimension[] {yDim, xDim, zDim, tDim});
ncfile.addVariableAttribute("yxzt", "units", "K");
ncfile.addVariable("xyzt", double.class, new Dimension[] {xDim, yDim, zDim, tDim});
ncfile.addVariableAttribute("xyzt", "units", "K");
// missing one dimension
ncfile.addVariable("zyx", double.class, new Dimension[] {zDim, yDim, xDim});
ncfile.addVariable("txy", double.class, new Dimension[] {tDim, xDim, yDim});
ncfile.addVariable("yxz", double.class, new Dimension[] {yDim, xDim, zDim});
ncfile.addVariable("xzy", double.class, new Dimension[] {xDim, zDim, yDim});
ncfile.addVariable("yxt", double.class, new Dimension[] {yDim, xDim, tDim});
ncfile.addVariable("xyt", double.class, new Dimension[] {xDim, yDim, tDim});
ncfile.addVariable("xyz", double.class, new Dimension[] {xDim, yDim, zDim});
// missing two dimension
ncfile.addVariable("yx", double.class, new Dimension[] {yDim, xDim});
ncfile.addVariable("xy", double.class, new Dimension[] {xDim, yDim});
ncfile.addVariable("yz", double.class, new Dimension[] {yDim, zDim});
ncfile.addVariable("xz", double.class, new Dimension[] {xDim, zDim});
ncfile.addVariable("yt", double.class, new Dimension[] {yDim, tDim});
ncfile.addVariable("xt", double.class, new Dimension[] {xDim, tDim});
ncfile.addVariable("ty", double.class, new Dimension[] {tDim, yDim});
ncfile.addVariable("tx", double.class, new Dimension[] {tDim, xDim});
// add global attributes
ncfile.addGlobalAttribute("Convention", "COARDS");
// create the file
try {
ncfile.create();
} catch (IOException e) {
System.err.println("ERROR creating file");
assert (false);
}
// write time data
int len = tDim.getLength();
ArrayDouble A = new ArrayDouble.D1(len);
Index ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3600));
int[] origin = new int[1];
try {
ncfile.write("time", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing time");
assert (false);
}
// write z data
len = zDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 10));
try {
ncfile.write("z", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing z");
assert (false);
}
// write y data
len = yDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3));
try {
ncfile.write("y", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing y");
assert (false);
}
// write x data
len = xDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 5));
try {
ncfile.write("x", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing x");
assert (false);
}
// write tzyx data
doWrite4(ncfile, "tzyx");
doWrite4(ncfile, "tzxy");
doWrite4(ncfile, "txyz");
doWrite4(ncfile, "tyxz");
doWrite4(ncfile, "zyxt");
doWrite4(ncfile, "zxyt");
doWrite4(ncfile, "xyzt");
doWrite4(ncfile, "yxzt");
doWrite3(ncfile, "zyx");
doWrite3(ncfile, "txy");
doWrite3(ncfile, "yxz");
doWrite3(ncfile, "xzy");
doWrite3(ncfile, "yxt");
doWrite3(ncfile, "xyt");
doWrite3(ncfile, "yxt");
doWrite3(ncfile, "xyz");
doWrite2(ncfile, "yx");
doWrite2(ncfile, "xy");
doWrite2(ncfile, "yz");
doWrite2(ncfile, "xz");
doWrite2(ncfile, "yt");
doWrite2(ncfile, "xt");
doWrite2(ncfile, "ty");
doWrite2(ncfile, "tx");
if (show) System.out.println("ncfile = " + ncfile);
// all done
try {
ncfile.close();
} catch (IOException e) {
System.err.println("ERROR writing file");
assert (false);
}
System.out.println("*****************Test Write done");
}
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");
}
public void testWriteStandardVar() throws Exception {
NetcdfFileWriteable ncfile = new NetcdfFileWriteable(filename, false);
// define dimensions
Dimension latDim = ncfile.addDimension("lat", 2);
Dimension lonDim = ncfile.addDimension("lon", 3);
ArrayList dims = new ArrayList();
dims.add(latDim);
dims.add(lonDim);
// case 1
ncfile.addVariable("t1", DataType.DOUBLE, dims);
ncfile.addVariableAttribute("t1", CDM.SCALE_FACTOR, new Double(2.0));
ncfile.addVariableAttribute("t1", "add_offset", new Double(77.0));
// case 2
ncfile.addVariable("t2", DataType.BYTE, dims);
ncfile.addVariableAttribute("t2", CDM.SCALE_FACTOR, new Short((short) 2));
ncfile.addVariableAttribute("t2", "add_offset", new Short((short) 77));
// case 3
ncfile.addVariable("t3", DataType.BYTE, dims);
ncfile.addVariableAttribute("t3", "_FillValue", new Byte((byte) 255));
// case 4
ncfile.addVariable("t4", DataType.SHORT, dims);
ncfile.addVariableAttribute("t4", CDM.MISSING_VALUE, new Short((short) -9999));
// case 5
ncfile.addVariable("t5", DataType.SHORT, dims);
ncfile.addVariableAttribute("t5", CDM.MISSING_VALUE, new Short((short) -9999));
ncfile.addVariableAttribute("t5", CDM.SCALE_FACTOR, new Short((short) 2));
ncfile.addVariableAttribute("t5", "add_offset", new Short((short) 77));
// case 1
ncfile.addVariable("m1", DataType.DOUBLE, dims);
ncfile.addVariableAttribute("m1", CDM.MISSING_VALUE, -999.99);
// create the file
ncfile.create();
// write t1
ArrayDouble A = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
int i, j;
Index ima = A.getIndex();
// write
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) A.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
int[] origin = new int[2];
ncfile.write("t1", origin, A);
// write t2
ArrayByte Ab = new ArrayByte.D2(latDim.getLength(), lonDim.getLength());
ima = Ab.getIndex();
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) Ab.setByte(ima.set(i, j), (byte) (i * 10 + j));
ncfile.write("t2", origin, Ab);
// write t3
ncfile.write("t3", origin, Ab);
// write t4
Array As = new ArrayShort.D2(latDim.getLength(), lonDim.getLength());
ima = As.getIndex();
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) As.setShort(ima.set(i, j), (short) (i * 10 + j));
ncfile.write("t4", origin, As);
As.setShort(ima.set(0, 0), (short) -9999);
ncfile.write("t5", origin, As);
// write m1
ArrayDouble.D2 Ad = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) Ad.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
Ad.set(1, 1, -999.99);
ncfile.write("m1", new int[2], Ad);
// all done
ncfile.close();
System.out.println("**************TestStandardVar Write done");
}
/**
* 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 void readShort2FloatMissing() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t5")));
assert (v.getDataType() == DataType.SHORT);
// standard convert with missing data
assert (null != (v = dsRead.findVariable("t5")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.FLOAT);
assert (vs.hasMissing());
assert (vs.hasMissingValue());
double mv = 2 * (-9999) + 77;
assert (vs.isMissing((double) mv));
assert (vs.isMissingValue((double) mv));
Array A = vs.read();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
assert (vs.isMissing(A.getFloat(ima.set(0, 0))));
for (i = 0; i < shape[0]; i++) {
for (j = 1; j < shape[1]; j++) {
float val = A.getFloat(ima.set(i, j));
float want = 2 * (i * 10 + j) + 77;
if (val != want) System.out.println(i + " " + j + " " + val + " " + want);
assert (val == want);
}
}
// useNaNs
vs.setUseNaNs(true);
assert (vs.getDataType() == DataType.FLOAT);
assert (vs.hasMissing());
assert (vs.hasMissingValue());
double mv2 = 2 * (-9999) + 77;
assert (vs.isMissing((double) mv2));
assert (vs.isMissingValue((double) mv2));
Array A2 = vs.read();
Index ima2 = A2.getIndex();
int[] shape2 = A2.getShape();
double mval = A2.getFloat(ima2.set(0, 0));
assert vs.isMissing(mval);
assert Double.isNaN(mval);
for (i = 0; i < shape2[0]; i++) {
for (j = 1; j < shape2[1]; j++) {
float val = A2.getFloat(ima2.set(i, j));
float want = 2 * (i * 10 + j) + 77;
if (val != want) System.out.println(i + " " + j + " " + val + " " + want);
assert (val == want) : val + " != " + want;
}
}
assert (null == vs.findAttribute(CDM.SCALE_FACTOR));
assert (null == vs.findAttribute("add_offset"));
assert (null == vs.findAttribute(CDM.MISSING_VALUE));
System.out.println("**************TestStandardVar Read readShort2FloatMissing");
}