public GridDatatype makeSubset(
Range rt_range, Range e_range, Range t_range, Range z_range, Range y_range, Range x_range)
throws InvalidRangeException {
// get the ranges list
int rank = getRank();
Range[] ranges = new Range[rank];
if (null != getXDimension()) ranges[xDimOrgIndex] = x_range;
if (null != getYDimension()) ranges[yDimOrgIndex] = y_range;
if (null != getZDimension()) ranges[zDimOrgIndex] = z_range;
if (null != getTimeDimension()) ranges[tDimOrgIndex] = t_range;
if (null != getRunTimeDimension()) ranges[rtDimOrgIndex] = rt_range;
if (null != getEnsembleDimension()) ranges[eDimOrgIndex] = e_range;
List<Range> rangesList = Arrays.asList(ranges);
// subset the variable
VariableDS v_section = (VariableDS) vs.section(new Section(rangesList));
List<Dimension> dims = v_section.getDimensions();
for (Dimension dim : dims) {
dim.setShared(true); // make them shared (section will make them unshared)
}
// subset the axes in the GridCoordSys
GridCoordSys gcs_section =
new GridCoordSys(gcs, rt_range, e_range, t_range, z_range, y_range, x_range);
// now we can make the geogrid
return new GeoGrid(dataset, v_section, gcs_section);
}
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");
}
/**
* DO NOT USE DIRECTLY. public by accident. Calculate scale/offset/missing value info. This may
* change the DataType.
*/
public void enhance(Set<NetcdfDataset.Enhance> mode) {
this.enhanceMode = EnumSet.copyOf(mode);
boolean alreadyScaleOffsetMissing = false;
boolean alreadyEnumConversion = false;
// see if underlying variable has enhancements already applied
if (orgVar != null && orgVar instanceof VariableDS) {
VariableDS orgVarDS = (VariableDS) orgVar;
EnumSet<NetcdfDataset.Enhance> orgEnhanceMode = orgVarDS.getEnhanceMode();
if (orgEnhanceMode != null) {
if (orgEnhanceMode.contains(NetcdfDataset.Enhance.ScaleMissing)) {
alreadyScaleOffsetMissing = true;
this.enhanceMode.add(
NetcdfDataset.Enhance
.ScaleMissing); // Note: promote the enhancement to the wrapped variable
}
if (orgEnhanceMode.contains(NetcdfDataset.Enhance.ConvertEnums)) {
alreadyEnumConversion = true;
this.enhanceMode.add(
NetcdfDataset.Enhance
.ConvertEnums); // Note: promote the enhancement to the wrapped variable
}
}
}
// do we need to calculate the ScaleMissing ?
if (!alreadyScaleOffsetMissing
&& (dataType.isNumeric() || dataType == DataType.CHAR)
&& mode.contains(NetcdfDataset.Enhance.ScaleMissing)
|| mode.contains(NetcdfDataset.Enhance.ScaleMissingDefer)) {
this.scaleMissingProxy = new EnhanceScaleMissingImpl(this);
// promote the data type if ScaleMissing is set
if (mode.contains(NetcdfDataset.Enhance.ScaleMissing)
&& scaleMissingProxy.hasScaleOffset()
&& (scaleMissingProxy.getConvertedDataType() != getDataType())) {
setDataType(scaleMissingProxy.getConvertedDataType());
removeAttributeIgnoreCase("_Unsigned");
}
// do we need to actually convert data ?
needScaleOffsetMissing =
mode.contains(NetcdfDataset.Enhance.ScaleMissing)
&& (scaleMissingProxy.hasScaleOffset() || scaleMissingProxy.getUseNaNs());
}
// do we need to do enum conversion ?
if (!alreadyEnumConversion
&& mode.contains(NetcdfDataset.Enhance.ConvertEnums)
&& dataType.isEnum()) {
this.needEnumConversion = true;
// LOOK promote data type to STRING ????
setDataType(DataType.STRING);
removeAttributeIgnoreCase("_Unsigned");
}
}
/**
* Convert (in place) all values in the given array that are considered as "missing" to Float.NaN,
* according to isMissingData(val).
*
* @param values input array
* @return input array, with missing values converted to NaNs.
*/
public float[] setMissingToNaN(float[] values) {
if (!vs.hasMissing()) return values;
final int length = values.length;
for (int i = 0; i < length; i++) {
double value = values[i];
if (vs.isMissing(value)) values[i] = Float.NaN;
}
return values;
}
private String showMissing(Variable v) {
if (!(v instanceof VariableDS)) return "";
VariableDS ve = (VariableDS) v;
Formatter buff = new Formatter();
buff.format("%s:", v.getFullName());
EnumSet<NetcdfDataset.Enhance> enhanceMode = ve.getEnhanceMode();
buff.format("enhanceMode= %s%n", enhanceMode);
ve.showScaleMissingProxy(buff);
return buff.toString();
}
// 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;
}
private int findDimension(Dimension want) {
java.util.List dims = vs.getDimensions();
for (int i = 0; i < dims.size(); i++) {
Dimension d = (Dimension) dims.get(i);
if (d.equals(want)) return i;
}
return -1;
}
public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
for (Variable v : ds.getVariables()) checkIfAxis(v);
int year = ds.readAttributeInteger(null, "YEAR", -1);
int doy = ds.readAttributeInteger(null, "DAY", -1);
double time = ds.readAttributeDouble(null, "TIME", Double.NaN);
if ((year > 0) && (doy > 0) && !Double.isNaN(time)) {
Calendar cal = new GregorianCalendar(TimeZone.getTimeZone("UTC"));
cal.clear();
cal.set(Calendar.YEAR, year);
cal.set(Calendar.DAY_OF_YEAR, doy);
int hour = (int) time;
cal.set(Calendar.HOUR_OF_DAY, hour);
time -= hour;
time *= 60;
int minute = (int) time;
cal.set(Calendar.MINUTE, minute);
time -= minute;
time *= 60;
cal.set(Calendar.SECOND, (int) time);
VariableDS var =
new VariableDS(
ds,
null,
null,
"timeFromAtts",
DataType.LONG,
"",
"seconds since 1970-01-01 00:00",
"time generated from global attributes");
// LOOK : cant handle scalar coordinates yet
// var.addAttribute( new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
ds.addVariable(null, var);
ArrayLong.D0 data = new ArrayLong.D0();
data.set(cal.getTime().getTime() / 1000);
var.setCachedData(data, true);
}
ds.finish();
}
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();
}
/**
* Constructor.
*
* @param dataset belongs to this dataset
* @param dsvar wraps this Variable
* @param gcs has this grid coordinate system
*/
public GeoGrid(GridDataset dataset, VariableDS dsvar, GridCoordSys gcs) {
this.dataset = dataset;
this.vs = dsvar;
this.gcs = gcs;
CoordinateAxis xaxis = gcs.getXHorizAxis();
if (xaxis instanceof CoordinateAxis1D) {
xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0));
yDimOrgIndex = findDimension(gcs.getYHorizAxis().getDimension(0));
} else { // 2D case
yDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(0));
xDimOrgIndex = findDimension(gcs.getXHorizAxis().getDimension(1));
}
if (gcs.getVerticalAxis() != null)
zDimOrgIndex = findDimension(gcs.getVerticalAxis().getDimension(0));
if (gcs.getTimeAxis() != null) {
if (gcs.getTimeAxis1D() != null)
tDimOrgIndex = findDimension(gcs.getTimeAxis1D().getDimension(0));
else tDimOrgIndex = findDimension(gcs.getTimeAxis().getDimension(1));
}
if (gcs.getEnsembleAxis() != null)
eDimOrgIndex = findDimension(gcs.getEnsembleAxis().getDimension(0));
if (gcs.getRunTimeAxis() != null)
rtDimOrgIndex = findDimension(gcs.getRunTimeAxis().getDimension(0));
// construct canonical dimension list
int count = 0;
this.mydims = new ArrayList<Dimension>();
if ((rtDimOrgIndex >= 0) && (rtDimOrgIndex != tDimOrgIndex)) {
mydims.add(dsvar.getDimension(rtDimOrgIndex));
rtDimNewIndex = count++;
}
if (eDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(eDimOrgIndex));
eDimNewIndex = count++;
}
if (tDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(tDimOrgIndex));
tDimNewIndex = count++;
}
if (zDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(zDimOrgIndex));
zDimNewIndex = count++;
}
if (yDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(yDimOrgIndex));
yDimNewIndex = count++;
}
if (xDimOrgIndex >= 0) {
mydims.add(dsvar.getDimension(xDimOrgIndex));
xDimNewIndex = count;
}
}
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 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");
}
/**
* Constructor. If scale/offset attributes are found, remove them from the decorated variable.
*
* @param forVar the Variable to decorate.
* @param useNaNs pre-fill isMissing() data with NaNs
* @param fillValueIsMissing use _FillValue for isMissing()
* @param invalidDataIsMissing use valid_range for isMissing()
* @param missingDataIsMissing use missing_value for isMissing()
*/
EnhanceScaleMissingImpl(
VariableDS forVar,
boolean useNaNs,
boolean fillValueIsMissing,
boolean invalidDataIsMissing,
boolean missingDataIsMissing) {
this.fillValueIsMissing = fillValueIsMissing;
this.invalidDataIsMissing = invalidDataIsMissing;
this.missingDataIsMissing = missingDataIsMissing;
// see if underlying variable has scale/offset already applied
Variable orgVar = forVar.getOriginalVariable();
if (orgVar instanceof VariableDS) {
VariableDS orgVarDS = (VariableDS) orgVar;
EnumSet<NetcdfDataset.Enhance> orgEnhanceMode = orgVarDS.getEnhanceMode();
if ((orgEnhanceMode != null) && orgEnhanceMode.contains(NetcdfDataset.Enhance.ScaleMissing))
return;
}
// the other possibility is that you want to apply scale and offset to a signed value, then
// declare the result unsigned
// this.isUnsigned = (orgVar != null) ? orgVar.isUnsigned() : forVar.isUnsigned();
this.isUnsigned = forVar.isUnsigned();
this.convertedDataType = forVar.getDataType();
DataType scaleType = null, missType = null, validType = null, fillType = null;
if (debug) System.out.println("EnhancementsImpl for Variable = " + forVar.getFullName());
Attribute att;
// scale and offset
if (null != (att = forVar.findAttribute(CDM.SCALE_FACTOR))) {
if (!att.isString()) {
scale = att.getNumericValue().doubleValue();
hasScaleOffset = true;
scaleType = att.getDataType();
forVar.remove(att);
if (debug) System.out.println("scale = " + scale + " type " + scaleType);
}
}
if (null != (att = forVar.findAttribute(CDM.ADD_OFFSET))) {
if (!att.isString()) {
offset = att.getNumericValue().doubleValue();
hasScaleOffset = true;
DataType offType = att.getDataType();
if (rank(offType) > rank(scaleType)) scaleType = offType;
forVar.remove(att);
if (debug) System.out.println("offset = " + offset);
}
}
////// missing data : valid_range. assume here its in units of unpacked data. correct this below
Attribute validRangeAtt;
if (null != (validRangeAtt = forVar.findAttribute(CDM.VALID_RANGE))) {
if (!validRangeAtt.isString() && validRangeAtt.getLength() > 1) {
valid_min = validRangeAtt.getNumericValue(0).doubleValue();
valid_max = validRangeAtt.getNumericValue(1).doubleValue();
hasValidRange = true;
validType = validRangeAtt.getDataType();
if (hasScaleOffset) forVar.remove(validRangeAtt);
if (debug) System.out.println("valid_range = " + valid_min + " " + valid_max);
}
}
Attribute validMinAtt = null, validMaxAtt = null;
if (!hasValidRange) {
if (null != (validMinAtt = forVar.findAttribute("valid_min"))) {
if (!validMinAtt.isString()) {
valid_min = validMinAtt.getNumericValue().doubleValue();
hasValidMin = true;
validType = validMinAtt.getDataType();
if (hasScaleOffset) forVar.remove(validMinAtt);
if (debug) System.out.println("valid_min = " + valid_min);
}
}
if (null != (validMaxAtt = forVar.findAttribute("valid_max"))) {
if (!validMaxAtt.isString()) {
valid_max = validMaxAtt.getNumericValue().doubleValue();
hasValidMax = true;
DataType t = validMaxAtt.getDataType();
if (rank(t) > rank(validType)) validType = t;
if (hasScaleOffset) forVar.remove(validMaxAtt);
if (debug) System.out.println("valid_min = " + valid_max);
}
}
}
boolean hasValidData = hasValidMin || hasValidMax || hasValidRange;
if (hasValidMin && hasValidMax) hasValidRange = true;
/// _FillValue
if ((null != (att = forVar.findAttribute(CDM.FILL_VALUE))) && !att.isString()) {
double[] values = getValueAsDouble(att); // LOOK double WTF ??
if (values.length > 0) {
fillValue = values[0];
hasFillValue = true;
fillType = att.getDataType();
if (hasScaleOffset) forVar.remove(att);
if (debug) System.out.println("missing_datum from _FillValue = " + fillValue);
}
}
/// missing_value
if (null != (att = forVar.findAttribute(CDM.MISSING_VALUE))) {
if (att.isString()) {
String svalue = att.getStringValue();
if (forVar.getDataType() == DataType.CHAR) {
missingValue = new double[1];
if (svalue.length() == 0) missingValue[0] = 0;
else missingValue[0] = svalue.charAt(0);
missType = DataType.CHAR;
hasMissingValue = true;
} else { // not a CHAR - try to fix problem where they use a numeric value as a String
// attribute
try {
missingValue = new double[1];
missingValue[0] = Double.parseDouble(svalue);
missType = att.getDataType();
hasMissingValue = true;
} catch (NumberFormatException ex) {
if (debug)
System.out.println(
"String missing_value not parsable as double= " + att.getStringValue());
}
}
} else { // not a string
missingValue = getValueAsDouble(att);
missType = att.getDataType();
for (double mv : missingValue)
if (!Double.isNaN(mv))
hasMissingValue = true; // dont need to do anything if its already a NaN
}
if (hasScaleOffset) forVar.remove(att);
}
// missing
boolean hasMissing =
(invalidDataIsMissing && hasValidData)
|| (fillValueIsMissing && hasFillValue)
|| (missingDataIsMissing && hasMissingValue);
/// assign convertedDataType if needed
if (hasScaleOffset) {
convertedDataType = forVar.getDataType();
if (hasMissing) {
// has missing data : must be float or double
if (rank(scaleType) > rank(convertedDataType)) convertedDataType = scaleType;
if (missingDataIsMissing && rank(missType) > rank(convertedDataType))
convertedDataType = missType;
if (fillValueIsMissing && rank(fillType) > rank(convertedDataType))
convertedDataType = fillType;
if (invalidDataIsMissing && rank(validType) > rank(convertedDataType))
convertedDataType = validType;
if (rank(convertedDataType) < rank(DataType.DOUBLE)) convertedDataType = DataType.FLOAT;
} else {
// no missing data; can use wider of data and scale
if (rank(scaleType) > rank(convertedDataType)) convertedDataType = scaleType;
}
if (debug) System.out.println("assign dataType = " + convertedDataType);
// validData may be external or internal
if (hasValidData) {
DataType orgType = forVar.getDataType();
// If valid_range is the same type as scale_factor (actually the wider of
// scale_factor and add_offset) and this is wider than the external data, then it
// will be interpreted as being in the units of the internal (unpacked) data.
// Otherwise it is in the units of the external (unpacked) data.
// we assumed unpacked data above, redo if its really packed data
if (!((rank(validType) == rank(scaleType)) && (rank(scaleType) >= rank(orgType)))) {
if (validRangeAtt != null) {
double[] values = getValueAsDouble(validRangeAtt);
valid_min = values[0];
valid_max = values[1];
} else {
if (validMinAtt != null) {
double[] values = getValueAsDouble(validMinAtt);
valid_min = values[0];
}
if (validMaxAtt != null) {
double[] values = getValueAsDouble(validMaxAtt);
valid_max = values[0];
}
}
}
}
}
if (hasMissing
&& ((convertedDataType == DataType.DOUBLE) || (convertedDataType == DataType.FLOAT)))
this.useNaNs = useNaNs;
if (debug) System.out.println("this.useNaNs = " + this.useNaNs);
}
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");
}
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");
}
/**
* Convenience function; lookup Attribute by name.
*
* @param name the name of the attribute
* @return the attribute, or null if not found
*/
public Attribute findAttributeIgnoreCase(String name) {
return vs.findAttributeIgnoreCase(name);
}
public String getShortName() {
return vs.getShortName();
}
/** get the standardized description */
public String getDescription() {
return vs.getDescription();
}
/** get the unit as a string */
public String getUnitsString() {
String units = vs.getUnitsString();
return (units == null) ? "" : units;
}
/** get the data type */
public DataType getDataType() {
return vs.getDataType();
}
/** true if there may be missing data, see VariableDS.hasMissing() */
public boolean hasMissingData() {
return vs.hasMissing();
}
public List<Attribute> getAttributes() {
return vs.getAttributes();
}
/** if val is missing data, see VariableDS.isMissingData() */
public boolean isMissingData(double val) {
return vs.isMissing(val);
}
/**
* This reads an arbitrary data slice, returning the data in canonical order (rt-e-t-z-y-x). If
* any dimension does not exist, ignore it.
*
* @param rt if < 0, get all of runtime dim; if valid index, fix slice to that value.
* @param e if < 0, get all of ensemble dim; if valid index, fix slice to that value.
* @param t if < 0, get all of time dim; if valid index, fix slice to that value.
* @param z if < 0, get all of z dim; if valid index, fix slice to that value.
* @param y if < 0, get all of y dim; if valid index, fix slice to that value.
* @param x if < 0, get all of x dim; if valid index, fix slice to that value.
* @return data[rt,e,t,z,y,x], eliminating missing or fixed dimension.
*/
public Array readDataSlice(int rt, int e, int t, int z, int y, int x) throws java.io.IOException {
int rank = vs.getRank();
int[] start = new int[rank];
int[] shape = new int[rank];
for (int i = 0; i < rank; i++) {
start[i] = 0;
shape[i] = 1;
}
Dimension xdim = getXDimension();
Dimension ydim = getYDimension();
Dimension zdim = getZDimension();
Dimension tdim = getTimeDimension();
Dimension edim = getEnsembleDimension();
Dimension rtdim = getRunTimeDimension();
// construct the shape of the data volume to be read
if (rtdim != null) {
if ((rt >= 0) && (rt < rtdim.getLength())) start[rtDimOrgIndex] = rt; // fix rt
else {
shape[rtDimOrgIndex] = rtdim.getLength(); // all of rt
}
}
if (edim != null) {
if ((e >= 0) && (e < edim.getLength())) start[eDimOrgIndex] = e; // fix e
else {
shape[eDimOrgIndex] = edim.getLength(); // all of e
}
}
if (tdim != null) {
if ((t >= 0) && (t < tdim.getLength())) start[tDimOrgIndex] = t; // fix t
else {
shape[tDimOrgIndex] = tdim.getLength(); // all of t
}
}
if (zdim != null) {
if ((z >= 0) && (z < zdim.getLength())) start[zDimOrgIndex] = z; // fix z
else {
shape[zDimOrgIndex] = zdim.getLength(); // all of z
}
}
if (ydim != null) {
if ((y >= 0) && (y < ydim.getLength())) start[yDimOrgIndex] = y; // fix y
else {
shape[yDimOrgIndex] = ydim.getLength(); // all of y
}
}
if (xdim != null) {
if ((x >= 0) && (x < xdim.getLength())) // all of x
start[xDimOrgIndex] = x; // fix x
else {
shape[xDimOrgIndex] = xdim.getLength(); // all of x
}
}
if (debugArrayShape) {
System.out.println("read shape from org variable = ");
for (int i = 0; i < rank; i++)
System.out.println(
" start = "
+ start[i]
+ " shape = "
+ shape[i]
+ " name = "
+ vs.getDimension(i).getName());
}
// read it
Array dataVolume;
try {
dataVolume = vs.read(start, shape);
} catch (Exception ex) {
log.error(
"GeoGrid.getdataSlice() on dataset " + getFullName() + " " + dataset.getLocation(), ex);
throw new java.io.IOException(ex.getMessage());
}
// LOOK: the real problem is the lack of named dimensions in the Array object
// figure out correct permutation for canonical ordering for permute
List<Dimension> oldDims = new ArrayList<Dimension>(vs.getDimensions());
int[] permuteIndex = new int[dataVolume.getRank()];
int count = 0;
if (oldDims.contains(rtdim)) permuteIndex[count++] = oldDims.indexOf(rtdim);
if (oldDims.contains(edim)) permuteIndex[count++] = oldDims.indexOf(edim);
if (oldDims.contains(tdim)) permuteIndex[count++] = oldDims.indexOf(tdim);
if (oldDims.contains(zdim)) permuteIndex[count++] = oldDims.indexOf(zdim);
if (oldDims.contains(ydim)) permuteIndex[count++] = oldDims.indexOf(ydim);
if (oldDims.contains(xdim)) permuteIndex[count] = oldDims.indexOf(xdim);
if (debugArrayShape) {
System.out.println("oldDims = ");
for (Dimension oldDim : oldDims) System.out.println(" oldDim = " + oldDim.getName());
System.out.println("permute dims = ");
for (int aPermuteIndex : permuteIndex)
System.out.println(" oldDim index = " + aPermuteIndex);
}
// check to see if we need to permute
boolean needPermute = false;
for (int i = 0; i < permuteIndex.length; i++) {
if (i != permuteIndex[i]) needPermute = true;
}
// permute to the order rt,e,t,z,y,x
if (needPermute) dataVolume = dataVolume.permute(permuteIndex);
// eliminate fixed dimensions, but not all dimensions of length 1.
count = 0;
if (rtdim != null) {
if (rt >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (edim != null) {
if (e >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (tdim != null) {
if (t >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (zdim != null) {
if (z >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (ydim != null) {
if (y >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (xdim != null) {
if (x >= 0) dataVolume = dataVolume.reduce(count);
}
return dataVolume;
}
public String getName() {
return vs.getFullName();
}
