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");
}
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");
}
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");
}
/**
* 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);
}