public void testAggCoordVar(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1;
assert time.getSize() == 3;
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.DOUBLE;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert data.getRank() == 1;
assert data.getSize() == 3;
assert data.getShape()[0] == 3;
assert data.getElementType() == double.class;
int count = 0;
IndexIterator dataI = data.getIndexIterator();
while (dataI.hasNext()) {
assert Misc.closeEnough(dataI.getDoubleNext(), result[count]);
count++;
}
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
// @todo Make sure units are meters
public Array getElevation(Range range) throws IOException, InvalidRangeException {
List section = new ArrayList(1);
section.add(range);
Array a = elevVar.read(section);
if (elevVarUnitsConversionFactor == 1.0) return (a);
for (IndexIterator it = a.getIndexIterator(); it.hasNext(); ) {
if (elevVar.getDataType() == DataType.DOUBLE) {
double val = it.getDoubleNext();
it.setDoubleCurrent(val * elevVarUnitsConversionFactor);
} else if (elevVar.getDataType() == DataType.FLOAT) {
float val = it.getFloatNext();
it.setFloatCurrent((float) (val * elevVarUnitsConversionFactor));
} else if (elevVar.getDataType() == DataType.INT) {
int val = it.getIntNext();
it.setIntCurrent((int) (val * elevVarUnitsConversionFactor));
} else if (elevVar.getDataType() == DataType.LONG) {
long val = it.getLongNext();
it.setLongCurrent((long) (val * elevVarUnitsConversionFactor));
} else {
throw new IllegalStateException(
"Elevation variable type <"
+ elevVar.getDataType().toString()
+ "> not double, float, int, or long.");
}
}
return (a);
}
public void testEnhanceDefer() throws IOException {
NetcdfDataset ncd =
NetcdfDataset.openDataset(
filename, EnumSet.of(NetcdfDataset.Enhance.ScaleMissing), -1, null, null);
VariableDS enhancedVar = (VariableDS) ncd.findVariable("t1");
NetcdfDataset ncdefer =
NetcdfDataset.openDataset(
filename, EnumSet.of(NetcdfDataset.Enhance.ScaleMissingDefer), -1, null, null);
VariableDS deferVar = (VariableDS) ncdefer.findVariable("t1");
Array data = enhancedVar.read();
Array dataDefer = deferVar.read();
System.out.printf("Enhanced=");
NCdumpW.printArray(data);
System.out.printf("%nDeferred=");
NCdumpW.printArray(dataDefer);
System.out.printf("%nProcessed=");
CompareNetcdf2 nc = new CompareNetcdf2(new Formatter(System.out), false, false, true);
assert !nc.compareData(enhancedVar.getShortName(), data, dataDefer, false);
IndexIterator ii = dataDefer.getIndexIterator();
while (ii.hasNext()) {
double val = deferVar.convertScaleOffsetMissing(ii.getDoubleNext());
ii.setDoubleCurrent(val);
}
NCdumpW.printArray(dataDefer);
assert nc.compareData(enhancedVar.getShortName(), data, dataDefer, false);
ncd.close();
ncdefer.close();
}
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;
}
}
/**
* Read data from a top level Variable and send data to a WritableByteChannel.
*
* @param v2 Variable
* @param section wanted section of data of Variable. The section list is a list of ucar.ma2.Range
* which define the requested data subset.
* @param channel WritableByteChannel object - channel that can write bytes.
* @return the number of bytes written, possibly zero.
*/
public long readToByteChannel11(
ucar.nc2.Variable v2, Section section, WritableByteChannel channel)
throws java.io.IOException, ucar.ma2.InvalidRangeException {
Array data = readData(v2, section);
float[] ftdata = new float[(int) data.getSize()];
byte[] bytedata = new byte[(int) data.getSize() * 4];
IndexIterator iter = data.getIndexIterator();
int i = 0;
ByteBuffer buffer = ByteBuffer.allocateDirect(bytedata.length);
while (iter.hasNext()) {
ftdata[i] = iter.getFloatNext();
bytedata[i] = new Float(ftdata[i]).byteValue();
buffer.put(bytedata[i]);
i++;
}
buffer = ByteBuffer.wrap(bytedata);
// write the bytes to the channel
int count = channel.write(buffer);
System.out.println("COUNT=" + count);
// check if all bytes where written
if (buffer.hasRemaining()) {
// if not all bytes were written, move the unwritten bytes to the beginning and
// set position just after the last unwritten byte
buffer.compact();
} else {
buffer.clear();
}
return (long) count;
}
private float testReadScalar(Variable v) throws IOException {
if (show) System.out.printf(" read %s%n", v.getNameAndDimensions());
assert (null != v);
Array a = v.read();
assert (null != a);
IndexIterator ii = a.getIndexIterator();
return ii.getFloatNext();
}
private void convertScaleOffsetUnsignedInt(IndexIterator iterIn, IndexIterator iterOut) {
boolean checkMissing = useNaNs && hasMissing();
while (iterIn.hasNext()) {
int valb = iterIn.getIntNext();
double val = scale * DataType.unsignedIntToLong(valb) + offset;
iterOut.setDoubleNext(checkMissing && isMissing_(val) ? Double.NaN : val);
}
}
// get a list of station obs for this station
public List getData(Station s, CancelTask cancel) throws IOException {
ArrayStructure stationData = readData("ID " + s.getName(), cancel);
ArrayList stationObs = new ArrayList();
IndexIterator ii = stationData.getIndexIterator();
while (ii.hasNext()) {
stationObs.add(new StationObs((Station) s, (StructureData) ii.getObjectNext()));
}
return stationObs;
}
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;
}
protected Array convertEnums(Array values) {
DataType dt = DataType.getType(values.getElementType());
if (!dt.isNumeric()) System.out.println("HEY");
Array result = Array.factory(DataType.STRING, values.getShape());
IndexIterator ii = result.getIndexIterator();
values.resetLocalIterator();
while (values.hasNext()) {
String sval = lookupEnumString(values.nextInt());
ii.setObjectNext(sval);
}
return result;
}
/**
* Get the minimum and the maximum data value of the previously read Array, skipping missing
* values as defined by isMissingData(double val).
*
* @param a Array to get min/max values
* @return both min and max value.
*/
public MAMath.MinMax getMinMaxSkipMissingData(Array a) {
if (!hasMissingData()) return MAMath.getMinMax(a);
IndexIterator iter = a.getIndexIterator();
double max = -Double.MAX_VALUE;
double min = Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if (isMissingData(val)) continue;
if (val > max) max = val;
if (val < min) min = val;
}
return new MAMath.MinMax(min, max);
}
// for jon blower
private Array getEnhancedArray(VariableDS vds) throws IOException {
Array data = vds.read();
EnumSet<NetcdfDataset.Enhance> mode = vds.getEnhanceMode();
if (mode.contains(NetcdfDataset.Enhance.ScaleMissing)) return data;
if (!mode.contains(NetcdfDataset.Enhance.ScaleMissingDefer))
throw new IllegalStateException("Must include " + NetcdfDataset.Enhance.ScaleMissingDefer);
IndexIterator ii = data.getIndexIterator();
while (ii.hasNext()) {
double val = vds.convertScaleOffsetMissing(ii.getDoubleNext());
ii.setDoubleCurrent(val);
}
return data;
}
// test offset only gets applied once
public void testWrapOnce() throws IOException {
String filename = TestAll.cdmUnitTestDir + "ncml/coords/testCoordScaling.ncml";
System.out.printf("%s%n", filename);
NetcdfDataset ncd = ucar.nc2.dataset.NetcdfDataset.openDataset(filename);
Variable v = ncd.findCoordinateAxis("Longitude");
assert v != null;
assert v instanceof CoordinateAxis1D;
// if offset is applied twice, the result is not in +-180 range
Array data = v.read();
NCdumpW.printArray(data);
IndexIterator ii = data.getIndexIterator();
while (ii.hasNext()) {
assert Math.abs(ii.getDoubleNext()) < 180 : ii.getDoubleCurrent();
}
}
private static void putArrayData(IndexIterator ii, DataType dataType, Number data) {
switch (dataType) {
case INT:
ii.setIntNext(data.intValue());
break;
case LONG:
ii.setLongNext(data.longValue());
break;
case FLOAT:
ii.setFloatNext(data.floatValue());
break;
case DOUBLE:
ii.setDoubleNext(data.doubleValue());
break;
}
}
private void readOneRadial(Ray r, Range gateRange, IndexIterator ii) throws IOException {
if (r == null) {
for (int i = gateRange.first(); i <= gateRange.last(); i += gateRange.stride())
ii.setFloatNext(Float.NaN);
return;
}
r.readData(volScan.raf, gateRange, ii);
}
private void readOneRadial(Cinrad2Record r, int datatype, Range gateRange, IndexIterator ii)
throws IOException {
if (r == null) {
for (int i = gateRange.first(); i <= gateRange.last(); i += gateRange.stride())
ii.setByteNext(Cinrad2Record.MISSING_DATA);
return;
}
r.readData(volScan.raf, datatype, gateRange, ii);
}
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 testAggCoordVarSubsetDefeatLocalCache(NetcdfFile ncfile)
throws InvalidRangeException, IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1;
assert time.getSize() == 3;
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.DOUBLE;
assert time.getDimension(0) == ncfile.findDimension("time");
time.setCachedData(null, false);
Array data = time.read("1:2");
assert data.getRank() == 1;
assert data.getSize() == 2;
assert data.getShape()[0] == 2;
assert data.getElementType() == double.class;
int count = 0;
IndexIterator dataI = data.getIndexIterator();
while (dataI.hasNext()) {
assert Misc.closeEnough(dataI.getDoubleNext(), result[count + 1]);
count++;
}
time.setCachedData(null, false);
data = time.read("0:2:2");
assert data.getRank() == 1;
assert data.getSize() == 2;
assert data.getShape()[0] == 2;
assert data.getElementType() == double.class;
count = 0;
dataI = data.getIndexIterator();
while (dataI.hasNext()) {
assert Misc.closeEnough(dataI.getDoubleNext(), result[count * 2]);
count++;
}
}
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;
}
/**
* Convert Data with scale and offset. Also translate missing data to NaNs if useNaNs = true.
*
* @param in data to convert
* @return converted data.
*/
private Array convertScaleOffset(Array in) {
if (!hasScaleOffset) return in;
if (debugRead) System.out.println("convertScaleOffset ");
Array out = Array.factory(convertedDataType.getPrimitiveClassType(), in.getShape());
IndexIterator iterIn = in.getIndexIterator();
IndexIterator iterOut = out.getIndexIterator();
if (isUnsigned && in.getElementType() == byte.class)
convertScaleOffsetUnsignedByte(iterIn, iterOut);
else if (isUnsigned && in.getElementType() == short.class)
convertScaleOffsetUnsignedShort(iterIn, iterOut);
else if (isUnsigned && in.getElementType() == int.class)
convertScaleOffsetUnsignedInt(iterIn, iterOut);
else {
boolean checkMissing = useNaNs && hasMissing();
while (iterIn.hasNext()) {
double val = scale * iterIn.getDoubleNext() + offset;
iterOut.setDoubleNext(checkMissing && isMissing_(val) ? Double.NaN : val);
}
}
return out;
}
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) {
}
}
/**
* Translate missing data to NaNs. Data must be DOUBLE or FLOAT
*
* @param in convert this array
* @return same array, with missing values replaced by NaNs
*/
private Array convertMissing(Array in) {
if (debugRead) System.out.println("convertMissing ");
IndexIterator iterIn = in.getIndexIterator();
if (in.getElementType() == double.class) {
while (iterIn.hasNext()) {
double val = iterIn.getDoubleNext();
if (isMissing_(val)) iterIn.setDoubleCurrent(Double.NaN);
}
} else if (in.getElementType() == float.class) {
while (iterIn.hasNext()) {
float val = iterIn.getFloatNext();
if (isMissing_(val)) iterIn.setFloatCurrent(Float.NaN);
}
}
return in;
}
private void showValuesAsDates(CoordinateAxis axis) {
String units = axis.getUnitsString();
String cal = getCalendarAttribute(axis);
CalendarDateUnit cdu = CalendarDateUnit.of(cal, units);
try {
infoTA.appendLine(units);
infoTA.appendLine(NCdumpW.printVariableData(axis, null));
if (axis.getDataType().isNumeric()) {
if (axis instanceof CoordinateAxis2D) {
showDates2D((CoordinateAxis2D) axis, cdu);
} else if (axis instanceof CoordinateAxis1D) { // 1D
showDates1D((CoordinateAxis1D) axis, cdu);
} else { // > 2D
Array data = axis.read();
IndexIterator ii = data.getIndexIterator();
while (ii.hasNext()) {
double val = ii.getDoubleNext();
infoTA.appendLine(makeCalendarDateStringOrMissing(cdu, val));
}
}
} else { // must be iso dates
Array data = axis.read();
Formatter f = new Formatter();
if (data instanceof ArrayChar) {
ArrayChar dataS = (ArrayChar) data;
ArrayChar.StringIterator iter = dataS.getStringIterator();
while (iter.hasNext()) f.format(" %s%n", iter.next());
infoTA.appendLine(f.toString());
} else if (data instanceof ArrayObject) {
IndexIterator iter = data.getIndexIterator();
while (iter.hasNext()) f.format(" %s%n", iter.next());
infoTA.appendLine(f.toString());
}
}
} catch (Exception ex) {
ex.printStackTrace();
infoTA.appendLine(ex.getMessage());
}
}
private boolean compareData(String name, Array data1, Array data2, double tol, boolean justOne) {
boolean ok = true;
if (data1.getSize() != data2.getSize()) {
f.format(" DIFF %s: size %d !== %d%n", name, data1.getSize(), data2.getSize());
ok = false;
}
if (data1.getElementType() != data2.getElementType()) {
f.format(
" DIFF %s: element type %s !== %s%n",
name, data1.getElementType(), data2.getElementType());
ok = false;
}
if (!ok) return false;
DataType dt = DataType.getType(data1.getElementType());
IndexIterator iter1 = data1.getIndexIterator();
IndexIterator iter2 = data2.getIndexIterator();
if (dt == DataType.DOUBLE) {
while (iter1.hasNext() && iter2.hasNext()) {
double v1 = iter1.getDoubleNext();
double v2 = iter2.getDoubleNext();
if (!Double.isNaN(v1) || !Double.isNaN(v2))
if (!closeEnough(v1, v2, tol)) {
f.format(
" DIFF %s: %f != %f count=%s diff = %f pdiff = %f %n",
name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
ok = false;
if (justOne) break;
}
}
} else if (dt == DataType.FLOAT) {
while (iter1.hasNext() && iter2.hasNext()) {
float v1 = iter1.getFloatNext();
float v2 = iter2.getFloatNext();
if (!Float.isNaN(v1) || !Float.isNaN(v2))
if (!closeEnough(v1, v2, (float) tol)) {
f.format(
" DIFF %s: %f != %f count=%s diff = %f pdiff = %f %n",
name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
ok = false;
if (justOne) break;
}
}
} else if (dt == DataType.INT) {
while (iter1.hasNext() && iter2.hasNext()) {
int v1 = iter1.getIntNext();
int v2 = iter2.getIntNext();
if (v1 != v2) {
f.format(
" DIFF %s: %d != %d count=%s diff = %f pdiff = %f %n",
name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
ok = false;
if (justOne) break;
}
}
} else if (dt == DataType.SHORT) {
while (iter1.hasNext() && iter2.hasNext()) {
short v1 = iter1.getShortNext();
short v2 = iter2.getShortNext();
if (v1 != v2) {
f.format(
" DIFF %s: %d != %d count=%s diff = %f pdiff = %f %n",
name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
ok = false;
if (justOne) break;
}
}
} else if (dt == DataType.BYTE) {
while (iter1.hasNext() && iter2.hasNext()) {
byte v1 = iter1.getByteNext();
byte v2 = iter2.getByteNext();
if (v1 != v2) {
f.format(
" DIFF %s: %d != %d count=%s diff = %f pdiff = %f %n",
name, v1, v2, iter1, diff(v1, v2), pdiff(v1, v2));
ok = false;
if (justOne) break;
}
}
} else if (dt == DataType.STRUCTURE) {
while (iter1.hasNext() && iter2.hasNext()) {
compareStructureData(
(StructureData) iter1.next(), (StructureData) iter2.next(), tol, justOne);
}
}
return ok;
}
private void makeCoordinateDataWithMissing(
int datatype,
Variable time,
Variable elev,
Variable azi,
Variable nradialsVar,
Variable ngatesVar,
List groups) {
Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
Index timeIndex = timeData.getIndex();
Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
Index elevIndex = elevData.getIndex();
Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
Index aziIndex = aziData.getIndex();
Array nradialsData =
Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
IndexIterator nradialsIter = nradialsData.getIndexIterator();
Array ngatesData =
Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
IndexIterator ngatesIter = ngatesData.getIndexIterator();
// first fill with missing data
IndexIterator ii = timeData.getIndexIterator();
while (ii.hasNext()) ii.setIntNext(MISSING_INT);
ii = elevData.getIndexIterator();
while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);
ii = aziData.getIndexIterator();
while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);
// now set the coordinate variables from the Cinrad2Record radial
int last_msecs = Integer.MIN_VALUE;
int nscans = groups.size();
try {
for (int scan = 0; scan < nscans; scan++) {
List scanGroup = (List) groups.get(scan);
int nradials = scanGroup.size();
Cinrad2Record first = null;
for (int j = 0; j < nradials; j++) {
Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
if (first == null) first = r;
int radial = r.radial_num - 1;
timeData.setInt(timeIndex.set(scan, radial), r.data_msecs);
elevData.setFloat(elevIndex.set(scan, radial), r.getElevation());
aziData.setFloat(aziIndex.set(scan, radial), r.getAzimuth());
if (r.data_msecs < last_msecs)
logger.warn("makeCoordinateData time out of order " + r.data_msecs);
last_msecs = r.data_msecs;
}
nradialsIter.setIntNext(nradials);
ngatesIter.setIntNext(first.getGateCount(datatype));
}
} catch (java.lang.ArrayIndexOutOfBoundsException ae) {
logger.debug("Cinrad2IOSP.uncompress ", ae);
}
time.setCachedData(timeData, false);
elev.setCachedData(elevData, false);
azi.setCachedData(aziData, false);
nradialsVar.setCachedData(nradialsData, false);
ngatesVar.setCachedData(ngatesData, false);
}
private void showDates2D(CoordinateAxis2D axis2D, CalendarDateUnit cdu) {
Formatter f = new Formatter();
if (axis2D.isInterval()) {
ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
ArrayDouble.D3 bounds = axis2D.getCoordBoundsArray();
if (bounds == null) {
infoTA.appendLine("No bounds for interval " + axis2D.getFullName());
return;
}
IndexIterator coordIter = coords.getIndexIterator();
IndexIterator boundsIter = bounds.getIndexIterator();
while (coordIter.hasNext()) {
double coordValue = coordIter.getDoubleNext();
if (!boundsIter.hasNext()) break;
double bounds1 = boundsIter.getDoubleNext();
if (!boundsIter.hasNext()) break;
double bounds2 = boundsIter.getDoubleNext();
f.format(
"%s (%s,%s)%n",
makeCalendarDateStringOrMissing(cdu, coordValue),
makeCalendarDateStringOrMissing(cdu, bounds1),
makeCalendarDateStringOrMissing(cdu, bounds2));
}
} else {
ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
IndexIterator coordIter = coords.getIndexIterator();
while (coordIter.hasNext()) {
double coordValue = coordIter.getDoubleNext();
f.format("%s%n", makeCalendarDateStringOrMissing(cdu, coordValue));
}
}
infoTA.appendLine(f.toString());
}
private void showValues2D(CoordinateAxis2D axis2D) {
Formatter f = new Formatter();
if (axis2D.isInterval()) {
ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
ArrayDouble.D3 bounds = axis2D.getCoordBoundsArray();
if (bounds == null) {
infoTA.appendLine("No bounds for interval " + axis2D.getFullName());
return;
}
IndexIterator coordIter = coords.getIndexIterator();
IndexIterator boundsIter = bounds.getIndexIterator();
while (coordIter.hasNext()) {
double coordValue = coordIter.getDoubleNext();
if (!boundsIter.hasNext()) break;
double bounds1 = boundsIter.getDoubleNext();
if (!boundsIter.hasNext()) break;
double bounds2 = boundsIter.getDoubleNext();
f.format("%f (%f,%f) = %f%n", coordValue, bounds1, bounds2, bounds2 - bounds1);
}
} else {
ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
IndexIterator coordIter = coords.getIndexIterator();
while (coordIter.hasNext()) {
double coordValue = coordIter.getDoubleNext();
f.format("%f%n", coordValue);
}
}
infoTA.appendLine(f.toString());
}
private void writeCoordinateVariable(VariableEntry variable, NetcdfFileWriteable ncFile)
throws IOException, InvalidRangeException {
int[] dimensions = {variable.getSize()};
Array array;
// so far, everything is a float or an int
// way too much code duplication but I'm done fightin java for now
if (variable.getType() == DataType.INT) {
array = new ArrayInt(dimensions);
int tempInt = 0;
IndexIterator iter = array.getIndexIterator();
while (iter.hasNext()) {
iter.getIntNext();
iter.setIntCurrent(tempInt);
tempInt++;
}
ncFile.write(variable.getVariableName(), array);
} else if (variable.getType() == DataType.FLOAT) {
array = new ArrayFloat(dimensions);
float tempFloat = 0;
IndexIterator iter = array.getIndexIterator();
while (iter.hasNext()) {
iter.getFloatNext();
iter.setFloatCurrent(tempFloat);
tempFloat++;
}
ncFile.write(variable.getVariableName(), array);
} else if (variable.getType() == DataType.LONG) {
array = new ArrayLong(dimensions);
long tempLong = 0;
IndexIterator iter = array.getIndexIterator();
while (iter.hasNext()) {
iter.getLongNext();
iter.setLongCurrent(tempLong);
tempLong++;
}
ncFile.write(variable.getVariableName(), array);
}
// ncFile.write(variable.getVariableName(),array);
}
private int populateFile2(
NetcdfFileWriteable ncFile,
String varName,
DataType dataType,
int[] dimensions,
int valueCounter,
Random generator)
throws IOException, InvalidRangeException {
long singleWriteSize = maxMemory / dataType.getSize();
int highestNonWriteDim = determineHighestNonWriteDimension(dimensions, singleWriteSize);
int[] singleStep = createWriteStep(dimensions, singleWriteSize, highestNonWriteDim);
int numStepWrites = determineNumberOfStepWrites(singleStep, singleWriteSize);
System.out.println(
"SingleWriteSize: "
+ singleWriteSize
+ " datatype size: "
+ dataType.getSize()
+ " singleStep: "
+ arrayToString(singleStep)
+ " numberStepsPerWrite: "
+ numStepWrites);
int[] allOnes = new int[dimensions.length];
int[] allZeros = new int[dimensions.length];
for (int i = 0; i < allOnes.length; i++) {
allOnes[i] = 1;
allZeros[i] = 0;
}
Index origin = new Index(dimensions, allOnes);
long totalSize = origin.getSize();
long writtenSoFar = 0;
boolean done = false;
while (!done) {
for (int i = 0; i < numStepWrites; i++) {
// this is a crack at an optimization
if ((highestNonWriteDim >= 0)
&& ((origin.getCurrentCounter()[highestNonWriteDim] + numStepWrites)
<= dimensions[highestNonWriteDim])) {
singleStep[highestNonWriteDim] = numStepWrites;
System.out.println("JUST OPTIMIZED. New write step: " + arrayToString(singleStep));
// keep 'i' right
i += numStepWrites - 1;
} else {
singleStep[highestNonWriteDim] = 1;
}
Array array = new ArrayInt(singleStep);
IndexIterator iter = array.getIndexIterator();
while (iter.hasNext()) {
iter.getIntNext();
// uncomment the following line for a random distribution
// iter.setIntCurrent((int) (Math.abs(generator.nextGaussian()) * 40) );
// uncomment this line for an incrementing value
iter.setIntCurrent(valueCounter);
valueCounter++;
// book keeping
writtenSoFar++;
// origin.incr();
}
System.out.println(
"Writing to file: "
+ ncFile.getLocation()
+ ". var_name: "
+ varName
+ " origin: "
+ arrayToString(origin.getCurrentCounter())
+ " writeSize: "
+ array.getSize()
+ " write shape: "
+ arrayToString(singleStep));
// write to the actual file
ncFile.write(varName, origin.getCurrentCounter(), array);
// update origin accordingly
for (int j = 0; j < Index.computeSize(singleStep); j++) {
// writtenSoFar++;
origin.incr();
}
System.out.println(
"\tcurrentIndex: "
+ arrayToString(origin.getCurrentCounter())
+ " currentElement: "
+ origin.currentElement()
+ " totalsize: "
+ (totalSize)
+ " writtenSoFar: "
+ writtenSoFar);
if (writtenSoFar >= totalSize) {
done = true;
break;
}
}
}
return valueCounter;
}
private void makeCoordinateData(
int datatype,
Variable time,
Variable elev,
Variable azi,
Variable nradialsVar,
Variable ngatesVar,
List groups) {
Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
IndexIterator timeDataIter = timeData.getIndexIterator();
Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
IndexIterator elevDataIter = elevData.getIndexIterator();
Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
IndexIterator aziDataIter = aziData.getIndexIterator();
Array nradialsData =
Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
IndexIterator nradialsIter = nradialsData.getIndexIterator();
Array ngatesData =
Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
IndexIterator ngatesIter = ngatesData.getIndexIterator();
int last_msecs = Integer.MIN_VALUE;
int nscans = groups.size();
int maxRadials = volScan.getMaxRadials();
for (int i = 0; i < nscans; i++) {
List scanGroup = (List) groups.get(i);
int nradials = scanGroup.size();
Cinrad2Record first = null;
for (int j = 0; j < nradials; j++) {
Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
if (first == null) first = r;
timeDataIter.setIntNext(r.data_msecs);
elevDataIter.setFloatNext(r.getElevation());
aziDataIter.setFloatNext(r.getAzimuth());
if (r.data_msecs < last_msecs)
logger.warn("makeCoordinateData time out of order " + r.data_msecs);
last_msecs = r.data_msecs;
}
for (int j = nradials; j < maxRadials; j++) {
timeDataIter.setIntNext(MISSING_INT);
elevDataIter.setFloatNext(MISSING_FLOAT);
aziDataIter.setFloatNext(MISSING_FLOAT);
}
nradialsIter.setIntNext(nradials);
ngatesIter.setIntNext(first.getGateCount(datatype));
}
time.setCachedData(timeData, false);
elev.setCachedData(elevData, false);
azi.setCachedData(aziData, false);
nradialsVar.setCachedData(nradialsData, false);
ngatesVar.setCachedData(ngatesData, false);
}