public TableConfig getConfig(FeatureType wantFeatureType, NetcdfDataset ds, Formatter errlog)
throws IOException {
TableConfig topTable = new TableConfig(Table.Type.Top, "singleTrajectory");
CoordinateAxis coordAxis = CoordSysEvaluator.findCoordByType(ds, AxisType.Time);
if (coordAxis == null) {
errlog.format("Cant find a time coordinate");
return null;
}
final Dimension innerDim = coordAxis.getDimension(0);
boolean obsIsStruct = Evaluator.hasNetcdf3RecordStructure(ds) && innerDim.isUnlimited();
TableConfig obsTable = new TableConfig(Table.Type.Structure, innerDim.getShortName());
obsTable.dimName = innerDim.getShortName();
obsTable.time = coordAxis.getFullName();
obsTable.structName = obsIsStruct ? "record" : innerDim.getShortName();
obsTable.structureType =
obsIsStruct
? TableConfig.StructureType.Structure
: TableConfig.StructureType.PsuedoStructure;
CoordSysEvaluator.findCoords(
obsTable,
ds,
new CoordSysEvaluator.Predicate() {
public boolean match(CoordinateAxis axis) {
return innerDim.equals(axis.getDimension(0));
}
});
topTable.addChild(obsTable);
return topTable;
}
public static DateRange extractDateRange(GridDataset gridDataset) {
DateRange maxDateRange = null;
for (GridDataset.Gridset gridset : gridDataset.getGridsets()) {
GridCoordSystem gsys = gridset.getGeoCoordSystem();
DateRange dateRange;
CoordinateAxis1DTime time1D = gsys.getTimeAxis1D();
if (time1D != null) {
dateRange = time1D.getDateRange();
} else {
CoordinateAxis time = gsys.getTimeAxis();
if (time == null) continue;
try {
DateUnit du = new DateUnit(time.getUnitsString());
Date minDate = du.makeDate(time.getMinValue());
Date maxDate = du.makeDate(time.getMaxValue());
dateRange = new DateRange(minDate, maxDate);
} catch (Exception e) {
logger.warn("Illegal Date Unit " + time.getUnitsString());
continue;
}
}
if (maxDateRange == null) maxDateRange = dateRange;
else maxDateRange.extend(dateRange);
}
return maxDateRange;
}
static void doOne(
String dir, String filename, int ngrids, int ncoordSys, int ncoordAxes, int nVertCooordAxes)
throws Exception {
System.out.println("test read GridDataset = " + dir + filename);
ucar.nc2.dt.grid.GridDataset gridDs = GridDataset.open(dir + filename);
int countGrids = gridDs.getGrids().size();
int countCoordAxes = gridDs.getNetcdfDataset().getCoordinateAxes().size();
int countCoordSys = gridDs.getNetcdfDataset().getCoordinateSystems().size();
// count vertical axes
int countVertCooordAxes = 0;
List axes = gridDs.getNetcdfDataset().getCoordinateAxes();
for (int i = 0; i < axes.size(); i++) {
CoordinateAxis axis = (CoordinateAxis) axes.get(i);
AxisType t = axis.getAxisType();
if ((t == AxisType.GeoZ) || (t == AxisType.Height) || (t == AxisType.Pressure))
countVertCooordAxes++;
}
Iterator iter = gridDs.getGridsets().iterator();
while (iter.hasNext()) {
GridDataset.Gridset gridset = (GridDataset.Gridset) iter.next();
GridCoordSys gcs = gridset.getGeoCoordSys();
// if (gcs.hasTimeAxis())
// System.out.println(" "+gcs.isDate()+" "+gcs.getName());
}
if (showCount) {
System.out.println(" grids=" + countGrids + ((ngrids < 0) ? " *" : ""));
System.out.println(" coordSys=" + countCoordSys + ((ncoordSys < 0) ? " *" : ""));
System.out.println(" coordAxes=" + countCoordAxes + ((ncoordAxes < 0) ? " *" : ""));
System.out.println(" vertAxes=" + countVertCooordAxes + ((nVertCooordAxes < 0) ? " *" : ""));
}
if (ngrids >= 0) assert ngrids == countGrids : "Grids " + ngrids + " != " + countGrids;
// if (ncoordSys >= 0)
// assert ncoordSys == countCoordSys : "CoordSys " + ncoordSys + " != " + countCoordSys;
// if (ncoordAxes >= 0)
// assert ncoordAxes == countCoordAxes : "CoordAxes " + ncoordAxes + " != " + countCoordAxes;
if (nVertCooordAxes >= 0)
assert nVertCooordAxes == countVertCooordAxes
: "VertAxes " + nVertCooordAxes + " != " + countVertCooordAxes;
gridDs.close();
}
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());
}
}
private void showValues(CoordinateAxis axis) {
try {
if (axis instanceof CoordinateAxis1D && axis.isNumeric()) {
CoordinateAxis1D axis1D = (CoordinateAxis1D) axis;
printArray("midpoints=", axis1D.getCoordValues());
if (!axis1D.isInterval()) {
printArray("edges=", axis1D.getCoordEdges());
} else {
printArray("bound1=", axis1D.getBound1());
printArray("bound2=", axis1D.getBound2());
Formatter f = new Formatter();
double[] mid = axis1D.getCoordValues();
double[] b1 = axis1D.getBound1();
double[] b2 = axis1D.getBound2();
for (int i = 0; i < b1.length; i++) {
f.format("%f (%f,%f) = %f%n", mid[i], b1[i], b2[i], b2[i] - b1[i]);
}
infoTA.appendLine(f.toString());
}
} else if (axis instanceof CoordinateAxis2D && axis.isNumeric()) {
infoTA.appendLine(NCdumpW.printVariableData(axis, null));
showValues2D((CoordinateAxis2D) axis);
} else {
infoTA.appendLine(NCdumpW.printVariableData(axis, null));
}
} catch (IOException e1) {
e1.printStackTrace();
infoTA.appendLine(e1.getMessage());
}
}
public AxisBean(CoordinateAxis v) {
this.axis = v;
setName(v.getFullName());
setCoordVar(v.isCoordinateVariable());
setDescription(v.getDescription());
setUnits(v.getUnitsString());
// collect dimensions
StringBuilder lens = new StringBuilder();
StringBuilder names = new StringBuilder();
java.util.List dims = v.getDimensions();
for (int j = 0; j < dims.size(); j++) {
ucar.nc2.Dimension dim = (ucar.nc2.Dimension) dims.get(j);
if (j > 0) {
lens.append(",");
names.append(",");
}
String name = dim.isShared() ? dim.getShortName() : "anon";
names.append(name);
lens.append(dim.getLength());
}
setDims(names.toString());
setShape(lens.toString());
AxisType at = v.getAxisType();
if (at != null) setAxisType(at.toString());
String p = v.getPositive();
if (p != null) setPositive(p);
if (v instanceof CoordinateAxis1D) {
CoordinateAxis1D v1 = (CoordinateAxis1D) v;
if (v1.isRegular()) setRegular(Double.toString(v1.getIncrement()));
}
isLayer = (null != axis.findAttribute(_Coordinate.ZisLayer));
isInterval = axis.isInterval();
}
private void showValueDiffs(CoordinateAxis axis) {
if (!axis.isNumeric()) return;
try {
if (axis instanceof CoordinateAxis1D) {
CoordinateAxis1D axis1D = (CoordinateAxis1D) axis;
double[] mids = axis1D.getCoordValues();
double[] diffs = new double[mids.length];
for (int i = 0; i < mids.length - 1; i++) diffs[i] = mids[i + 1] - mids[i];
printArrays("midpoint differences", mids, diffs);
} else if (axis instanceof CoordinateAxis2D) {
CoordinateAxis2D axis2D = (CoordinateAxis2D) axis;
ArrayDouble.D2 mids = axis2D.getCoordValuesArray();
int[] shape = mids.getShape();
ArrayDouble.D2 diffx =
(ArrayDouble.D2) Array.factory(DataType.DOUBLE, new int[] {shape[0], shape[1] - 1});
for (int j = 0; j < shape[0]; j++) {
for (int i = 0; i < shape[1] - 1; i++) {
double diff = mids.get(j, i + 1) - mids.get(j, i);
diffx.set(j, i, diff);
}
}
infoTA.appendLine(NCdumpW.toString(diffx, "diff in x", null));
ArrayDouble.D2 diffy =
(ArrayDouble.D2) Array.factory(DataType.DOUBLE, new int[] {shape[0] - 1, shape[1]});
for (int j = 0; j < shape[0] - 1; j++) {
for (int i = 0; i < shape[1]; i++) {
double diff = mids.get(j + 1, i) - mids.get(j, i);
diffy.set(j, i, diff);
}
}
infoTA.appendLine("\n\n\n");
infoTA.appendLine(NCdumpW.toString(diffy, "diff in y", null));
}
} catch (Exception e1) {
e1.printStackTrace();
infoTA.appendLine(e1.getMessage());
}
}
public boolean isContig() {
return axis.isContiguous();
}