/**
* Wrap the given Variable, making it into a VariableDS. Delegate data reading to the original
* variable. Take all metadata from original variable. Does not share cache, iosp.
*
* @param g logical container, if null use orgVar's group
* @param orgVar the original Variable to wrap. The original Variable is not modified. Must not be
* a Structure, use StructureDS instead.
* @param enhance if true, use NetcdfDataset.defaultEnhanceMode to define what enhancements are
* made. Note that this can change DataType and data values. You can also call enhance()
* later. If orgVar is VariableDS, then enhance is inherited from there, and this parameter is
* ignored.
*/
public VariableDS(Group g, Variable orgVar, boolean enhance) {
super(orgVar);
if (g != null)
this.group =
g; // otherwise super() sets group; this affects the long name and the dimensions.
setDimensions(getDimensionsString()); // reset the dimensions
if (orgVar instanceof Structure)
throw new IllegalArgumentException(
"VariableDS must not wrap a Structure; name=" + orgVar.getName());
// dont share cache, iosp : all IO is delegated
this.ncfile = null;
this.spiObject = null;
createNewCache();
this.orgVar = orgVar;
this.orgDataType = orgVar.getDataType();
if (orgVar instanceof VariableDS) {
VariableDS ncVarDS = (VariableDS) orgVar;
this.enhanceProxy = ncVarDS.enhanceProxy;
this.scaleMissingProxy = ncVarDS.scaleMissingProxy;
this.enhanceMode = ncVarDS.enhanceMode;
} else {
this.enhanceProxy = new EnhancementsImpl(this);
if (enhance) {
enhance(NetcdfDataset.getDefaultEnhanceMode());
} else {
this.scaleMissingProxy = new EnhanceScaleMissingImpl();
}
}
}
/**
* Make a new VariableDS, delegate data reading to the original variable, but otherwise dont take
* any info from it. This is used by NcML explicit mode.
*
* @param group the containing group; may not be null
* @param parent parent Structure, may be null
* @param shortName variable shortName, must be unique within the Group
* @param orgVar the original Variable to wrap. The original Variable is not modified. Must not be
* a Structure, use StructureDS instead.
*/
public VariableDS(Group group, Structure parent, String shortName, Variable orgVar) {
super(null, group, parent, shortName);
setDimensions(getDimensionsString()); // reset the dimensions
if (orgVar instanceof Structure)
throw new IllegalArgumentException(
"VariableDS must not wrap a Structure; name=" + orgVar.getName());
// dont share cache, iosp : all IO is delegated
this.ncfile = null;
this.spiObject = null;
createNewCache();
this.orgVar = orgVar;
this.orgDataType = orgVar.getDataType();
this.enhanceProxy = new EnhancementsImpl(this);
this.scaleMissingProxy = new EnhanceScaleMissingImpl();
}
/**
* Add this coord as a variable in the netCDF file
*
* @param ncfile netCDF file to add to
* @param g group in file
*/
void addToNetcdfFile(NetcdfFile ncfile, Group g) {
if (dontUseVertical) {
typicalRecord = null;
return;
}
if (g == null) {
g = ncfile.getRootGroup();
}
// coordinate axis
Variable v = new Variable(ncfile, g, null, getVariableName());
v.setDataType(DataType.DOUBLE);
String desc = lookup.getLevelDescription(typicalRecord);
if (lookup instanceof Grib2GridTableLookup && usesBounds) {
desc = "Layer between " + desc;
}
v.addAttribute(new Attribute("long_name", desc));
v.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));
// positive attribute needed for CF-1 Height and Pressure
if (positive != null) {
v.addAttribute(new Attribute("positive", positive));
}
if (units != null) {
AxisType axisType;
if (SimpleUnit.isCompatible("millibar", units)) {
axisType = AxisType.Pressure;
} else if (SimpleUnit.isCompatible("m", units)) {
axisType = AxisType.Height;
} else {
axisType = AxisType.GeoZ;
}
if (lookup instanceof Grib2GridTableLookup || lookup instanceof Grib1GridTableLookup) {
v.addAttribute(
new Attribute("GRIB_level_type", Integer.toString(typicalRecord.getLevelType1())));
} else {
v.addAttribute(
new Attribute("level_type", Integer.toString(typicalRecord.getLevelType1())));
}
v.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));
}
if (coordValues == null) {
coordValues = new double[levels.size()];
for (int i = 0; i < levels.size(); i++) {
LevelCoord lc = (LevelCoord) levels.get(i);
coordValues[i] = lc.mid;
}
}
Array dataArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length}, coordValues);
v.setDimensions(getVariableName());
v.setCachedData(dataArray, true);
ncfile.addVariable(g, v);
if (usesBounds) {
String boundsDimName = "bounds_dim";
if (g.findDimension(boundsDimName) == null) {
ncfile.addDimension(g, new Dimension(boundsDimName, 2, true));
}
String bname = getVariableName() + "_bounds";
v.addAttribute(new Attribute("bounds", bname));
v.addAttribute(new Attribute(_Coordinate.ZisLayer, "true"));
Variable b = new Variable(ncfile, g, null, bname);
b.setDataType(DataType.DOUBLE);
b.setDimensions(getVariableName() + " " + boundsDimName);
b.addAttribute(new Attribute("long_name", "bounds for " + v.getName()));
b.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));
Array boundsArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length, 2});
ucar.ma2.Index ima = boundsArray.getIndex();
for (int i = 0; i < coordValues.length; i++) {
LevelCoord lc = (LevelCoord) levels.get(i);
boundsArray.setDouble(ima.set(i, 0), lc.value1);
boundsArray.setDouble(ima.set(i, 1), lc.value2);
}
b.setCachedData(boundsArray, true);
ncfile.addVariable(g, b);
}
if (factors != null) {
// check if already created
if (g == null) {
g = ncfile.getRootGroup();
}
if (g.findVariable("hybrida") != null) return;
v.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate"));
v.addAttribute(new Attribute("formula_terms", "ap: hybrida b: hybridb ps: Pressure"));
// create hybrid factor variables
// add hybrida variable
Variable ha = new Variable(ncfile, g, null, "hybrida");
ha.setDataType(DataType.DOUBLE);
ha.addAttribute(new Attribute("long_name", "level_a_factor"));
ha.addAttribute(new Attribute("units", ""));
ha.setDimensions(getVariableName());
// add data
int middle = factors.length / 2;
double[] adata;
double[] bdata;
if (levels.size() < middle) { // only partial data wanted
adata = new double[levels.size()];
bdata = new double[levels.size()];
} else {
adata = new double[middle];
bdata = new double[middle];
}
for (int i = 0; i < middle && i < levels.size(); i++) adata[i] = factors[i];
Array haArray = Array.factory(DataType.DOUBLE, new int[] {adata.length}, adata);
ha.setCachedData(haArray, true);
ncfile.addVariable(g, ha);
// add hybridb variable
Variable hb = new Variable(ncfile, g, null, "hybridb");
hb.setDataType(DataType.DOUBLE);
hb.addAttribute(new Attribute("long_name", "level_b_factor"));
hb.addAttribute(new Attribute("units", ""));
hb.setDimensions(getVariableName());
// add data
for (int i = 0; i < middle && i < levels.size(); i++) bdata[i] = factors[i + middle];
Array hbArray = Array.factory(DataType.DOUBLE, new int[] {bdata.length}, bdata);
hb.setCachedData(hbArray, true);
ncfile.addVariable(g, hb);
/* // TODO: delete next time modifying code
double[] adata = new double[ middle ];
for( int i = 0; i < middle; i++ )
adata[ i ] = factors[ i ];
Array haArray = Array.factory(DataType.DOUBLE, new int[]{adata.length}, adata);
ha.setCachedData(haArray, true);
ncfile.addVariable(g, ha);
// add hybridb variable
Variable hb = new Variable(ncfile, g, null, "hybridb");
hb.setDataType(DataType.DOUBLE);
hb.addAttribute(new Attribute("long_name", "level_b_factor" ));
//hb.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate" ));
hb.addAttribute(new Attribute("units", ""));
hb.setDimensions(getVariableName());
// add data
double[] bdata = new double[ middle ];
for( int i = 0; i < middle; i++ )
bdata[ i ] = factors[ i + middle ];
Array hbArray = Array.factory(DataType.DOUBLE, new int[]{bdata.length}, bdata);
hb.setCachedData(hbArray, true);
ncfile.addVariable(g, hb);
*/
}
}
/**
* Constructor
*
* @param ncVar: the netcdf Variable
*/
NcSDFloat64(Variable ncVar) {
super(ncVar.getName());
this.ncVar = ncVar;
}
