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());
}
// @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();
}
/**
* 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 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);
}
}
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());
}
}
// 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;
}
// 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;
}
/**
* 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);
}
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());
}
/**
* 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;
}
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 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;
}
