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");
}
private void makeVariableNoCoords(
NetcdfFile ncfile, int datatype, String shortName, String longName, Variable from) {
Variable v = new Variable(ncfile, null, null, shortName);
v.setDataType(DataType.BYTE);
v.setDimensions(from.getDimensions());
ncfile.addVariable(null, v);
v.addAttribute(new Attribute(CDM.UNITS, Cinrad2Record.getDatatypeUnits(datatype)));
v.addAttribute(new Attribute(CDM.LONG_NAME, longName));
byte[] b = new byte[2];
b[0] = Cinrad2Record.MISSING_DATA;
b[1] = Cinrad2Record.BELOW_THRESHOLD;
Array missingArray = Array.factory(DataType.BYTE.getPrimitiveClassType(), new int[] {2}, b);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, missingArray));
v.addAttribute(
new Attribute("signal_below_threshold", new Byte(Cinrad2Record.BELOW_THRESHOLD)));
v.addAttribute(
new Attribute(CDM.SCALE_FACTOR, new Float(Cinrad2Record.getDatatypeScaleFactor(datatype))));
v.addAttribute(
new Attribute(CDM.ADD_OFFSET, new Float(Cinrad2Record.getDatatypeAddOffset(datatype))));
v.addAttribute(new Attribute(CDM.UNSIGNED, "true"));
Attribute fromAtt = from.findAttribute(_Coordinate.Axes);
v.addAttribute(new Attribute(_Coordinate.Axes, fromAtt));
Vgroup vgFrom = (Vgroup) from.getSPobject();
Vgroup vg = new Vgroup(datatype, vgFrom.map);
v.setSPobject(vg);
}
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 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) {
}
}
/**
* Setup needed for all SingleTrajectoryObsDatatypes. Can only be called once.
*
* <p>Units of time varible must be udunits time units. Units of latitude variable must be
* convertible to "degrees_north" by udunits. Units of longitude variable must be convertible to
* "degrees_east" by udunits. Units of altitude variable must be convertible to "meters" by
* udunits.
*
* @throws IllegalArgumentException if units of time, latitude, longitude, or altitude variables
* are not as required.
* @throws IllegalStateException if this method has already been called.
*/
public void setTrajectoryInfo(Config trajConfig) throws IOException {
if (timeDim != null)
throw new IllegalStateException("The setTrajectoryInfo() method can only be called once.");
this.trajectoryId = trajConfig.getTrajectoryId();
this.timeDim = trajConfig.getTimeDim();
this.timeVar = trajConfig.getTimeVar();
this.latVar = trajConfig.getLatVar();
this.lonVar = trajConfig.getLonVar();
this.elevVar = trajConfig.getElevVar();
trajectoryNumPoint = this.timeDim.getLength();
timeVarUnitsString = this.timeVar.findAttribute("units").getStringValue();
// Check that time, lat, lon, elev units are acceptable.
if (DateUnit.getStandardDate(timeVarUnitsString) == null) {
throw new IllegalArgumentException(
"Units of time variable <" + timeVarUnitsString + "> not a date unit.");
}
String latVarUnitsString = this.latVar.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(latVarUnitsString, "degrees_north")) {
throw new IllegalArgumentException(
"Units of lat var <" + latVarUnitsString + "> not compatible with \"degrees_north\".");
}
String lonVarUnitsString = this.lonVar.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(lonVarUnitsString, "degrees_east")) {
throw new IllegalArgumentException(
"Units of lon var <" + lonVarUnitsString + "> not compatible with \"degrees_east\".");
}
String elevVarUnitsString = this.elevVar.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(elevVarUnitsString, "meters")) {
throw new IllegalArgumentException(
"Units of elev var <" + elevVarUnitsString + "> not compatible with \"meters\".");
}
try {
elevVarUnitsConversionFactor = getMetersConversionFactor(elevVarUnitsString);
} catch (Exception e) {
throw new IllegalArgumentException(
"Exception on getMetersConversionFactor() for the units of elev var <"
+ elevVarUnitsString
+ ">.");
}
if (this.ncfile.hasUnlimitedDimension()
&& this.ncfile.getUnlimitedDimension().equals(timeDim)) {
Object result = this.ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
if ((result != null) && (Boolean) result)
this.recordVar = (Structure) this.ncfile.getRootGroup().findVariable("record");
else this.recordVar = new StructurePseudo(this.ncfile, null, "record", timeDim);
} else {
this.recordVar = new StructurePseudo(this.ncfile, null, "record", timeDim);
}
// @todo HACK, HACK, HACK - remove once addRecordStructure() deals with ncd attribute changes.
Variable elevVarInRecVar = this.recordVar.findVariable(this.elevVar.getFullNameEscaped());
if (!elevVarUnitsString.equals(elevVarInRecVar.findAttribute("units").getStringValue())) {
elevVarInRecVar.addAttribute(new Attribute("units", elevVarUnitsString));
}
trajectoryVarsMap = new HashMap();
// for ( Iterator it = this.recordVar.getVariables().iterator(); it.hasNext(); )
for (Iterator it = this.ncfile.getRootGroup().getVariables().iterator(); it.hasNext(); ) {
Variable curVar = (Variable) it.next();
if (curVar.getRank() > 0
&& !curVar.equals(this.timeVar)
&& !curVar.equals(this.latVar)
&& !curVar.equals(this.lonVar)
&& !curVar.equals(this.elevVar)
&& (this.recordVar == null ? true : !curVar.equals(this.recordVar))) {
MyTypedDataVariable typedVar = new MyTypedDataVariable(new VariableDS(null, curVar, true));
dataVariables.add(typedVar);
trajectoryVarsMap.put(typedVar.getShortName(), typedVar);
}
}
trajectory =
new SingleTrajectory(
this.trajectoryId,
trajectoryNumPoint,
this.timeVar,
timeVarUnitsString,
this.latVar,
this.lonVar,
this.elevVar,
dataVariables,
trajectoryVarsMap);
startDate = trajectory.getTime(0);
endDate = trajectory.getTime(trajectoryNumPoint - 1);
((SingleTrajectory) trajectory).setStartDate(startDate);
((SingleTrajectory) trajectory).setEndDate(endDate);
}
