/**
* 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;
}
}
/**
* 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;
}