// create from a dataset
public VariableBean(Variable vs) {
this.vs = vs;
// vs = (v instanceof VariableEnhanced) ? (VariableEnhanced) v : new VariableStandardized( v);
setName(vs.getShortName());
setDescription(vs.getDescription());
setUnits(vs.getUnitsString());
setDataType(vs.getDataType().toString());
// Attribute csAtt = vs.findAttribute("_coordSystems");
// if (csAtt != null)
// setCoordSys( csAtt.getStringValue());
// collect dimensions
StringBuilder lens = new StringBuilder();
StringBuilder names = new StringBuilder();
java.util.List dims = vs.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.getName() : "anon";
names.append(name);
lens.append(dim.getLength());
}
setDimensions(names.toString());
setShape(lens.toString());
}
private void makeMultidimInner(
NetcdfDataset ds, TableConfig parentTable, TableConfig childTable) {
Dimension parentDim = ds.findDimension(parentTable.dimName);
Dimension childDim = ds.findDimension(childTable.innerName);
// divide up the variables between the parent and the child
List<String> obsVars;
List<Variable> vars = ds.getVariables();
List<String> parentVars = new ArrayList<>(vars.size());
obsVars = new ArrayList<>(vars.size());
for (Variable orgV : vars) {
if (orgV instanceof Structure) continue;
Dimension dim0 = orgV.getDimension(0);
if ((dim0 != null) && dim0.equals(parentDim)) {
if ((orgV.getRank() == 1)
|| ((orgV.getRank() == 2) && orgV.getDataType() == DataType.CHAR)) {
parentVars.add(orgV.getShortName());
} else {
Dimension dim1 = orgV.getDimension(1);
if ((dim1 != null) && dim1.equals(childDim)) obsVars.add(orgV.getShortName());
}
}
}
parentTable.vars = parentVars;
childTable.vars = obsVars;
}
/*
Structure {
int a_name;
byte b_name(3);
byte c_name(3);
short d_name(3);
int e_name(3);
long f_name(3);
int g_name(3);
short h_name(3);
int i_name(3);
long j_name(3);
float k_name(3);
double l_name(3);
} CompoundNative(15);
type = Layout(8); type= 1 (contiguous) storageSize = (15,144) dataSize=0 dataAddress=2048
*/
@Test
public void testReadH5StructureArrayMembers() throws java.io.IOException {
try (NetcdfFile ncfile = TestH5.openH5("complex/compound_native.h5")) {
Variable dset = ncfile.findVariable("CompoundNative");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 15);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 15);
Structure s = (Structure) dset;
// read all with the iterator
StructureDataIterator iter = s.getStructureIterator();
while (iter.hasNext()) {
StructureData sd = iter.next();
for (StructureMembers.Member m : sd.getMembers()) {
Array data = sd.getArray(m);
NCdumpW.printArray(data, m.getName(), out, null);
}
}
}
System.out.println("*** testReadH5StructureArrayMembers ok");
}
private void doVariable(Variable v, opendap.dap.AttributeTable parentTable) {
List dims = v.getDimensions();
for (int i = 0; i < dims.size(); i++) {
Dimension dim = (Dimension) dims.get(i);
if (dim.isShared()) usedDims.put(dim.getName(), dim);
}
// if (v.getAttributes().size() == 0) return; // LOOK DAP 2 say must have empty
String name = NcDDS.escapeName(v.getShortName());
opendap.dap.AttributeTable table;
if (parentTable == null) {
table = new opendap.dap.AttributeTable(name);
try {
addAttributeTable(name, table);
} catch (AttributeExistsException e) {
log.error("Cant add " + name, e);
}
} else {
table = parentTable.appendContainer(name);
}
addAttributes(table, v, v.getAttributes().iterator());
if (v instanceof Structure) {
Structure s = (Structure) v;
List nested = s.getVariables();
for (int i = 0; i < nested.size(); i++) {
Variable nv = (Variable) nested.get(i);
doVariable(nv, table);
}
}
}
/* Structure {
int LAT[0];
...
int LAT[149];
} IMAGE_LAT_ARRAY(3600);
type = Layout(8); type= 2 (chunked) storageSize = (1,600) dataSize=0 dataAddress=2548046
*/
@Test
public void testReadOneAtATime() throws java.io.IOException, InvalidRangeException {
try (NetcdfFile ncfile = TestH5.openH5("IASI/IASI.h5")) {
Variable dset = ncfile.findVariable("U-MARF/EPS/IASI_xxx_1C/DATA/IMAGE_LAT_ARRAY");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 3600);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 3600);
Structure s = (Structure) dset;
// read last one - chunked
StructureData sd = s.readStructure(3599);
assert sd.getScalarInt("LAT[0]") == 70862722;
assert sd.getScalarInt("LAT[149]") == 85302263;
// read one at a time
for (int i = 3590; i < d.getLength(); i++) {
s.readStructure(i);
System.out.println(" read structure " + i);
}
}
System.out.println("*** testReadIASI ok");
}
public GridDatatype makeSubset(
Range rt_range, Range e_range, Range t_range, Range z_range, Range y_range, Range x_range)
throws InvalidRangeException {
// get the ranges list
int rank = getRank();
Range[] ranges = new Range[rank];
if (null != getXDimension()) ranges[xDimOrgIndex] = x_range;
if (null != getYDimension()) ranges[yDimOrgIndex] = y_range;
if (null != getZDimension()) ranges[zDimOrgIndex] = z_range;
if (null != getTimeDimension()) ranges[tDimOrgIndex] = t_range;
if (null != getRunTimeDimension()) ranges[rtDimOrgIndex] = rt_range;
if (null != getEnsembleDimension()) ranges[eDimOrgIndex] = e_range;
List<Range> rangesList = Arrays.asList(ranges);
// subset the variable
VariableDS v_section = (VariableDS) vs.section(new Section(rangesList));
List<Dimension> dims = v_section.getDimensions();
for (Dimension dim : dims) {
dim.setShared(true); // make them shared (section will make them unshared)
}
// subset the axes in the GridCoordSys
GridCoordSys gcs_section =
new GridCoordSys(gcs, rt_range, e_range, t_range, z_range, y_range, x_range);
// now we can make the geogrid
return new GeoGrid(dataset, v_section, gcs_section);
}
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;
}
/** get the shape */
public int[] getShape() {
int[] shape = new int[mydims.size()];
for (int i = 0; i < mydims.size(); i++) {
Dimension d = mydims.get(i);
shape[i] = d.getLength();
}
return shape;
}
private int findDimension(Dimension want) {
java.util.List dims = vs.getDimensions();
for (int i = 0; i < dims.size(); i++) {
Dimension d = (Dimension) dims.get(i);
if (d.equals(want)) return i;
}
return -1;
}
private boolean compare(List<Dimension> dims1, List<Dimension> dims2) {
if (dims1.size() != dims2.size()) return false;
for (int i = 0; i < dims1.size(); i++) {
Dimension dim1 = dims1.get(i);
Dimension dim2 = dims2.get(i);
// if (!dim1.getName().equals(dim2.getName())) return false;
if (dim1.getLength() != dim2.getLength()) return false;
}
return true;
}
private int addAttributes(opendap.dap.AttributeTable table, Variable v, Iterator iter) {
int count = 0;
// add attribute table for this variable
while (iter.hasNext()) {
Attribute att = (Attribute) iter.next();
int dods_type = DODSNetcdfFile.convertToDODSType(att.getDataType(), false);
try {
String attName = NcDDS.escapeName(att.getName());
if (att.isString()) {
/* FIX String value = escapeAttributeStringValues(att.getStringValue());
table.appendAttribute(attName, dods_type, "\""+value+"\"");
*/
table.appendAttribute(attName, dods_type, att.getStringValue());
} else {
// cant send signed bytes
if (att.getDataType() == DataType.BYTE) {
boolean signed = false;
for (int i = 0; i < att.getLength(); i++) {
if (att.getNumericValue(i).byteValue() < 0) signed = true;
}
if (signed) // promote to signed short
dods_type = opendap.dap.Attribute.INT16;
}
for (int i = 0; i < att.getLength(); i++)
table.appendAttribute(attName, dods_type, att.getNumericValue(i).toString());
}
count++;
} catch (Exception e) {
log.error(
"Error appending attribute " + att.getName() + " = " + att.getStringValue() + "\n" + e);
}
} // loop over variable attributes
// kludgy thing to map char arrays to DODS Strings
if ((v != null) && (v.getDataType().getPrimitiveClassType() == char.class)) {
int rank = v.getRank();
int strlen = (rank == 0) ? 0 : v.getShape(rank - 1);
Dimension dim = (rank == 0) ? null : v.getDimension(rank - 1);
try {
opendap.dap.AttributeTable dodsTable = table.appendContainer("DODS");
dodsTable.appendAttribute("strlen", opendap.dap.Attribute.INT32, Integer.toString(strlen));
if ((dim != null) && dim.isShared())
dodsTable.appendAttribute("dimName", opendap.dap.Attribute.STRING, dim.getName());
count++;
} catch (Exception e) {
log.error("Error appending attribute strlen\n" + e);
}
}
return count;
}
private int[] getWeights(Variable v) {
int rank = v.getRank();
int[] w = new int[rank];
for (int n = 0; n < rank; n++) {
Dimension dim = v.getDimension(n);
String dimName = dim.getName();
if (dimName.equals("time")) w[n] = 1000;
if (dimName.equals("z")) w[n] = 100;
if (dimName.equals("y")) w[n] = 10;
if (dimName.equals("x")) w[n] = 1;
}
return w;
}
@Test
public void testH5StructureDS() throws java.io.IOException {
int a_name = 0;
String[] b_name =
new String[] {
"A fight is a contract that takes two people to honor.",
"A combative stance means that you've accepted the contract.",
"In which case, you deserve what you get.",
" -- Professor Cheng Man-ch'ing"
};
String c_name = "Hello!";
// H5header.setDebugFlags(new ucar.nc2.util.DebugFlagsImpl("H5header/header"));
try (NetcdfDataset ncfile =
NetcdfDataset.openDataset(TestH5.testDir + "complex/compound_complex.h5")) {
Variable dset = ncfile.findVariable("CompoundComplex");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 6);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 6);
Structure s = (Structure) dset;
// read all with the iterator
StructureDataIterator iter = s.getStructureIterator();
while (iter.hasNext()) {
StructureData sd = iter.next();
assert sd.getScalarInt("a_name") == a_name;
a_name++;
assert sd.getScalarString("c_name").equals(c_name);
String[] results = sd.getJavaArrayString(sd.findMember("b_name"));
assert results.length == b_name.length;
int count = 0;
for (String r : results) assert r.equals(b_name[count++]);
for (StructureMembers.Member m : sd.getMembers()) {
Array data = sd.getArray(m);
NCdumpW.printArray(data, m.getName(), out, null);
}
}
}
System.out.println("*** testH5StructureDS ok");
}
// convert to shared dimensions
private void setSharedDimensions(
Variable v, List<Element> values, List<Dimension> unknownDims, String location) {
if (values.size() == 0) return;
// remove the "scalar" dumbension
Iterator<Element> iter = values.iterator();
while (iter.hasNext()) {
Element value = iter.next();
String dimName = value.getText().trim();
if (dimName.equalsIgnoreCase("scalar")) iter.remove();
}
// gotta have same number of dimensions
List<Dimension> oldDims = v.getDimensions();
if (oldDims.size() != values.size()) {
log.error("Different number of dimensions for {} {}", v, location);
return;
}
List<Dimension> newDims = new ArrayList<>();
Group group = v.getParentGroup();
for (int i = 0; i < values.size(); i++) {
Element value = values.get(i);
String dimName = value.getText().trim();
dimName = NetcdfFile.makeValidCdmObjectName(dimName);
Dimension dim = group.findDimension(dimName);
Dimension oldDim = oldDims.get(i);
if (dim == null) dim = checkUnknownDims(dimName, unknownDims, oldDim, location);
if (dim == null) {
log.error(
"Unknown Dimension= {} for variable = {} {} ", dimName, v.getFullName(), location);
return;
}
if (dim.getLength() != oldDim.getLength()) {
log.error(
"Shared dimension ("
+ dim.getShortName()
+ ") has different length than data dimension ("
+ oldDim.getShortName()
+ ") shared="
+ dim.getLength()
+ " org="
+ oldDim.getLength()
+ " for "
+ v
+ " "
+ location);
return;
}
newDims.add(dim);
}
v.setDimensions(newDims);
if (showWork) System.out.printf(" set shared dimensions for %s %n", v.getNameAndDimensions());
}
/** Create a DAS for this netcdf file */
NcDAS(NetcdfFile ncfile) {
// Variable attributes
Iterator iter = ncfile.getVariables().iterator();
while (iter.hasNext()) {
Variable v = (Variable) iter.next();
doVariable(v, null);
}
// Global attributes
opendap.dap.AttributeTable gtable = new opendap.dap.AttributeTable("NC_GLOBAL");
int count = addAttributes(gtable, null, ncfile.getGlobalAttributes().iterator());
if (count > 0)
try {
addAttributeTable("NC_GLOBAL", gtable);
} catch (AttributeExistsException e) {
log.error("Cant add NC_GLOBAL", e);
}
// unlimited dimension
iter = ncfile.getDimensions().iterator();
while (iter.hasNext()) {
Dimension d = (Dimension) iter.next();
if (d.isUnlimited()) {
opendap.dap.AttributeTable table = new opendap.dap.AttributeTable("DODS_EXTRA");
try {
table.appendAttribute("Unlimited_Dimension", opendap.dap.Attribute.STRING, d.getName());
addAttributeTable("DODS_EXTRA", table);
} catch (Exception e) {
log.error("Error adding Unlimited_Dimension =" + e);
}
break;
}
}
// unused dimensions
opendap.dap.AttributeTable dimTable = null;
iter = ncfile.getDimensions().iterator();
while (iter.hasNext()) {
Dimension d = (Dimension) iter.next();
if (null == usedDims.get(d.getName())) {
if (dimTable == null) dimTable = new opendap.dap.AttributeTable("EXTRA_DIMENSION");
try {
dimTable.appendAttribute(
d.getName(), opendap.dap.Attribute.INT32, Integer.toString(d.getLength()));
} catch (Exception e) {
log.error("Error adding Unlimited_Dimension =" + e);
}
}
}
if (dimTable != null)
try {
addAttributeTable("EXTRA_DIMENSION", dimTable);
} catch (AttributeExistsException e) {
log.error("Cant add EXTRA_DIMENSION", e);
}
}
/** Instances which have same contents are equal. Careful!! this is not object identity !! */
@Override
public boolean equals(Object oo) {
if (this == oo) return true;
if (!(oo instanceof Dimension)) return false;
Dimension other = (Dimension) oo;
if ((g != null) && !g.equals(other.getGroup())) return false;
if ((getName() == null) && (other.getName() != null)) return false;
if ((getName() != null) && !getName().equals(other.getName())) return false;
return (getLength() == other.getLength())
&& (isUnlimited() == other.isUnlimited())
&& (isVariableLength() == other.isVariableLength())
&& (isShared() == other.isShared());
}
public VariableBean(VariableEnhanced v) {
this.ve = v;
setName(v.getFullName());
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());
StringBuilder buff = new StringBuilder();
List<CoordinateSystem> csList = v.getCoordinateSystems();
for (CoordinateSystem cs : csList) {
if (firstCoordSys == null) firstCoordSys = cs;
else buff.append("; ");
buff.append(cs.getName());
Formatter gridBuff = new Formatter();
if (GridCoordSys.isGridCoordSys(gridBuff, cs, v)) {
addDataType("grid");
} /* else if (PointDatasetDefaultHandler.isPointFeatureDataset(ds)) {
addDataType("point");
} */
}
setCoordSys(buff.toString());
}
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 createDataVariables(List<VariableSimpleIF> dataVars) throws IOException {
/* height variable
Variable heightVar = ncfile.addStringVariable(altName, recordDims, 20);
ncfile.addVariableAttribute(heightVar, new Attribute("long_name", "height of observation"));
ncfile.addVariableAttribute(heightVar, new Attribute("units", altUnits)); */
Variable v = ncfile.addVariable(parentProfileIndex, DataType.INT, recordDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent profile"));
v = ncfile.addVariable(nextObsName, DataType.INT, recordDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "record number of next obs in linked list for this profile"));
// find all dimensions needed by the data variables
for (VariableSimpleIF var : dataVars) {
List<Dimension> dims = var.getDimensions();
dimSet.addAll(dims);
}
// add them
for (Dimension d : dimSet) {
if (!d.isUnlimited())
ncfile.addDimension(d.getName(), d.getLength(), d.isShared(), false, d.isVariableLength());
}
// add the data variables all using the record dimension
for (VariableSimpleIF oldVar : dataVars) {
List<Dimension> dims = oldVar.getDimensions();
StringBuffer dimNames = new StringBuffer(recordDimName);
for (Dimension d : dims) {
if (!d.isUnlimited()) dimNames.append(" ").append(d.getName());
}
Variable newVar =
ncfile.addVariable(oldVar.getName(), oldVar.getDataType(), dimNames.toString());
List<Attribute> atts = oldVar.getAttributes();
for (Attribute att : atts) {
ncfile.addVariableAttribute(newVar, att);
}
}
}
/* Structure {
char EntryName(64);
char Definition(1024);
char Unit(1024);
char Scale Factor(1024);
} TIME_DESCR(60);
type = Layout(8); type= 2 (chunked) storageSize = (1,3136) dataSize=0 dataAddress=684294
*/
@Test
public void testReadManyAtATime() throws java.io.IOException, InvalidRangeException {
try (NetcdfFile ncfile = TestH5.openH5("IASI/IASI.h5")) {
Variable dset = ncfile.findVariable("U-MARF/EPS/IASI_xxx_1C/DATA/TIME_DESCR");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 60);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 60);
ArrayStructure data = (ArrayStructure) dset.read();
StructureMembers.Member m = data.getStructureMembers().findMember("EntryName");
assert m != null;
for (int i = 0; i < dset.getSize(); i++) {
String r = data.getScalarString(i, m);
if (i % 2 == 0) assert r.equals("TIME[" + i / 2 + "]-days") : r + " at " + i;
else assert r.equals("TIME[" + i / 2 + "]-milliseconds") : r + " at " + i;
}
}
System.out.println("*** testReadManyAtATime ok");
}
// look if the wanted dimension is in the unknownDims list.
private Dimension checkUnknownDims(
String wantDim, List<Dimension> unknownDims, Dimension oldDim, String location) {
for (Dimension dim : unknownDims) {
if (dim.getShortName().equals(wantDim)) {
int len = oldDim.getLength();
if (len == 0) dim.setUnlimited(true); // allow zero length dimension !!
dim.setLength(len); // use existing (anon) dimension
Group parent = dim.getGroup();
parent.addDimensionIfNotExists(dim); // add to the parent
unknownDims.remove(dim); // remove from list LOOK is this ok?
log.warn("unknownDim {} length set to {}{}", wantDim, oldDim.getLength(), location);
return dim;
}
}
return null;
}
/**
* Create a new GeoGrid that is a logical subset of this GeoGrid.
*
* @param t_range subset the time dimension, or null if you want all of it
* @param z_range subset the vertical dimension, or null if you want all of it
* @param bbox a lat/lon bounding box, or null if you want all x,y
* @param z_stride use only if z_range is null, then take all z with this stride (1 means all)
* @param y_stride use this stride on the y coordinate (1 means all)
* @param x_stride use this stride on the x coordinate (1 means all)
* @return subsetted GeoGrid
* @throws InvalidRangeException if bbox does not intersect GeoGrid
*/
public GeoGrid subset(
Range t_range, Range z_range, LatLonRect bbox, int z_stride, int y_stride, int x_stride)
throws InvalidRangeException {
if ((z_range == null) && (z_stride > 1)) {
Dimension zdim = getZDimension();
if (zdim != null) z_range = new Range(0, zdim.getLength() - 1, z_stride);
}
Range y_range = null, x_range = null;
if (bbox != null) {
List yx_ranges = gcs.getRangesFromLatLonRect(bbox);
y_range = (Range) yx_ranges.get(0);
x_range = (Range) yx_ranges.get(1);
}
if (y_stride > 1) {
if (y_range == null) {
Dimension ydim = getYDimension();
y_range = new Range(0, ydim.getLength() - 1, y_stride);
} else {
y_range = new Range(y_range.first(), y_range.last(), y_stride);
}
}
if (x_stride > 1) {
if (x_range == null) {
Dimension xdim = getXDimension();
x_range = new Range(0, xdim.getLength() - 1, x_stride);
} else {
x_range = new Range(x_range.first(), x_range.last(), x_stride);
}
}
return subset(t_range, z_range, y_range, x_range);
}
public void testWriteStandardVar() throws Exception {
NetcdfFileWriteable ncfile = new NetcdfFileWriteable(filename, false);
// define dimensions
Dimension latDim = ncfile.addDimension("lat", 2);
Dimension lonDim = ncfile.addDimension("lon", 3);
ArrayList dims = new ArrayList();
dims.add(latDim);
dims.add(lonDim);
// case 1
ncfile.addVariable("t1", DataType.DOUBLE, dims);
ncfile.addVariableAttribute("t1", CDM.SCALE_FACTOR, new Double(2.0));
ncfile.addVariableAttribute("t1", "add_offset", new Double(77.0));
// case 2
ncfile.addVariable("t2", DataType.BYTE, dims);
ncfile.addVariableAttribute("t2", CDM.SCALE_FACTOR, new Short((short) 2));
ncfile.addVariableAttribute("t2", "add_offset", new Short((short) 77));
// case 3
ncfile.addVariable("t3", DataType.BYTE, dims);
ncfile.addVariableAttribute("t3", "_FillValue", new Byte((byte) 255));
// case 4
ncfile.addVariable("t4", DataType.SHORT, dims);
ncfile.addVariableAttribute("t4", CDM.MISSING_VALUE, new Short((short) -9999));
// case 5
ncfile.addVariable("t5", DataType.SHORT, dims);
ncfile.addVariableAttribute("t5", CDM.MISSING_VALUE, new Short((short) -9999));
ncfile.addVariableAttribute("t5", CDM.SCALE_FACTOR, new Short((short) 2));
ncfile.addVariableAttribute("t5", "add_offset", new Short((short) 77));
// case 1
ncfile.addVariable("m1", DataType.DOUBLE, dims);
ncfile.addVariableAttribute("m1", CDM.MISSING_VALUE, -999.99);
// create the file
ncfile.create();
// write t1
ArrayDouble A = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
int i, j;
Index ima = A.getIndex();
// write
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) A.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
int[] origin = new int[2];
ncfile.write("t1", origin, A);
// write t2
ArrayByte Ab = new ArrayByte.D2(latDim.getLength(), lonDim.getLength());
ima = Ab.getIndex();
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) Ab.setByte(ima.set(i, j), (byte) (i * 10 + j));
ncfile.write("t2", origin, Ab);
// write t3
ncfile.write("t3", origin, Ab);
// write t4
Array As = new ArrayShort.D2(latDim.getLength(), lonDim.getLength());
ima = As.getIndex();
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) As.setShort(ima.set(i, j), (short) (i * 10 + j));
ncfile.write("t4", origin, As);
As.setShort(ima.set(0, 0), (short) -9999);
ncfile.write("t5", origin, As);
// write m1
ArrayDouble.D2 Ad = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) Ad.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
Ad.set(1, 1, -999.99);
ncfile.write("m1", new int[2], Ad);
// all done
ncfile.close();
System.out.println("**************TestStandardVar Write done");
}
/**
* Build the configuration from the dataset
*
* @param ncd NetcdfDataset
* @return the trajectory configuration
*/
private static Config buildConfig(NetcdfDataset ncd) {
// already did this in isValid, but we'll keep here for later refactor
Attribute attrib = ncd.findGlobalAttributeIgnoreCase("center");
if (attrib == null) {
return null;
}
if (!attrib.isString()) {
return null;
}
if (!attrib.getStringValue().equals("UCAR/CDAAC")) {
return null;
}
// Check for start_time, stop_time
attrib = ncd.findGlobalAttributeIgnoreCase("start_time");
if (attrib == null) {
return null;
}
if (attrib.isString()) {
return null;
}
double startTime = attrib.getNumericValue().doubleValue();
attrib = ncd.findGlobalAttributeIgnoreCase("stop_time");
if (attrib == null) {
return null;
}
if (attrib.isString()) {
return null;
}
double endTime = attrib.getNumericValue().doubleValue();
// Check that only one dimension and that it is the alt dimension.
List list = ncd.getRootGroup().getDimensions();
if (list.size() != 1) {
return null;
}
Dimension d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
Config trajConfig = new Config();
trajConfig.setTimeDim(d);
// Check for latitude variable with time dimension and units convertable to "degrees_north".
Variable var = ncd.getRootGroup().findVariable(latVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
String units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "degrees_north")) {
return null;
}
trajConfig.setLatVar(var);
// Make the time Variable
int numTimes = d.getLength();
double[] times = new double[numTimes];
// Variable timeVar = new Variable(var);
// timeVar.setName(timeVarName);
VariableDS timeVar =
new VariableDS(
ncd,
ncd.getRootGroup(),
null,
timeVarName,
DataType.DOUBLE,
timeDimName,
"seconds since 1980-01-06 00:00:00",
"Time coordinate");
// Variable timeVar = new Variable(ncd, ncd.getRootGroup(), null,
// timeVarName);
// timeVar.setDataType(DataType.DOUBLE);
// timeVar.setDimensions(list);
// Attribute newUnits =
// new Attribute("units", "seconds since 1980-01-06 00:00:00");
// timeVar.addAttribute(newUnits);
timeVar.setCachedData(
Array.makeArray(DataType.DOUBLE, numTimes, endTime, ((startTime - endTime) / numTimes)),
true);
ncd.addVariable(ncd.getRootGroup(), timeVar);
trajConfig.setTimeVar(timeVar);
// Check for longitude variable with time dimension and units convertable to "degrees_east".
var = ncd.getRootGroup().findVariable(lonVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "degrees_east")) {
return null;
}
trajConfig.setLonVar(var);
// Check for altitude variable with time dimension and units convertable to "m".
var = ncd.getRootGroup().findVariable(elevVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "meters")) {
return null;
}
trajConfig.setElevVar(var);
trajConfig.setTrajectoryId(trajId);
return trajConfig;
}
public static void main(String args[]) throws Exception {
long start = System.currentTimeMillis();
Map<String, ucar.unidata.geoloc.Station> staHash =
new HashMap<String, ucar.unidata.geoloc.Station>();
String location = "R:/testdata/sounding/netcdf/Upperair_20070401_0000.nc";
NetcdfDataset ncfile = NetcdfDataset.openDataset(location);
ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
// look through record varibles, for those that have "manLevel" dimension
// make a StructureData object for those
StructureMembers sm = new StructureMembers("manLevel");
Dimension manDim = ncfile.findDimension("manLevel");
Structure record = (Structure) ncfile.findVariable("record");
List<Variable> allList = record.getVariables();
List<VariableSimpleIF> varList = new ArrayList<VariableSimpleIF>();
for (Variable v : allList) {
if ((v.getRank() == 1) && v.getDimension(0).equals(manDim)) {
// public VariableDS(NetcdfDataset ds, Group group, Structure parentStructure, String
// shortName, DataType dataType,
// String dims, String units, String desc) {
varList.add(
new VariableDS(
ncfile,
null,
null,
v.getShortName(),
v.getDataType(),
"",
v.getUnitsString(),
v.getDescription()));
// (String name, String desc, String units, DataType dtype, int []shape)
sm.addMember(
v.getShortName(),
v.getDescription(),
v.getUnitsString(),
v.getDataType(),
new int[0]); // scalar
}
}
ArrayStructureMA manAS = new ArrayStructureMA(sm, new int[] {manDim.getLength()});
// need the date units
Variable time = ncfile.findVariable("synTime");
String timeUnits = ncfile.findAttValueIgnoreCase(time, "units", null);
timeUnits = StringUtil.remove(timeUnits, '('); // crappy fsl'ism
timeUnits = StringUtil.remove(timeUnits, ')');
DateUnit timeUnit = new DateUnit(timeUnits);
// extract stations
int nrecs = 0;
StructureDataIterator iter = record.getStructureIterator();
while (iter.hasNext()) {
StructureData sdata = iter.next();
String name = sdata.getScalarString("staName");
ucar.unidata.geoloc.Station s = staHash.get(name);
if (s == null) {
float lat = sdata.convertScalarFloat("staLat");
float lon = sdata.convertScalarFloat("staLon");
float elev = sdata.convertScalarFloat("staElev");
s = new StationImpl(name, "", lat, lon, elev);
staHash.put(name, s);
}
nrecs++;
}
List<ucar.unidata.geoloc.Station> stnList =
Arrays.asList(staHash.values().toArray(new ucar.unidata.geoloc.Station[staHash.size()]));
Collections.sort(stnList);
// create the writer
WriterProfileObsDataset writer =
new WriterProfileObsDataset(location + ".out", "rewrite " + location);
writer.writeHeader(stnList, varList, nrecs, "prMan");
// extract records
iter = record.getStructureIterator();
while (iter.hasNext()) {
StructureData sdata = iter.next();
String name = sdata.getScalarString("staName");
double timeValue = sdata.convertScalarDouble("synTime");
Date date = timeUnit.makeDate(timeValue);
// transfer to the ArrayStructure
List<String> names = sm.getMemberNames();
for (String mname : names) {
manAS.setMemberArray(mname, sdata.getArray(mname));
}
// each level is weritten as a seperate structure
int numMand = sdata.getScalarInt("numMand");
if (numMand >= manDim.getLength()) continue;
for (int i = 0; i < numMand; i++) {
StructureData useData = manAS.getStructureData(i);
writer.writeRecord(name, date, useData);
}
}
writer.finish();
long took = System.currentTimeMillis() - start;
System.out.println("That took = " + took);
}
/**
* Opens the NetCDF dataset at the given location, using the dataset cache if {@code location}
* represents an NcML aggregation. We cannot use the cache for OPeNDAP or single NetCDF files
* because the underlying data may have changed and the NetcdfDataset cache may cache a dataset
* forever. In the case of NcML we rely on the fact that server administrators ought to have set a
* "recheckEvery" parameter for NcML aggregations that may change with time. It is desirable to
* use the dataset cache for NcML aggregations because they can be time-consuming to assemble and
* we don't want to do this every time a map is drawn.
*
* @param location The location of the data: a local NetCDF file, an NcML aggregation file or an
* OPeNDAP location, {@literal i.e.} anything that can be passed to
* NetcdfDataset.openDataset(location).
* @return a {@link NetcdfDataset} object for accessing the data at the given location.
* @throws IOException if there was an error reading from the data source.
*/
private NetcdfDataset openAndAggregateDataset(String location) throws IOException, EdalException {
NetcdfDataset nc;
if (location.startsWith("dods://") || location.startsWith("http://")) {
/*
* We have a remote dataset
*/
nc = CdmUtils.openDataset(location);
} else {
/*
* We have a local dataset
*/
List<File> files = null;
try {
files = CdmUtils.expandGlobExpression(location);
} catch (NullPointerException e) {
System.out.println("NPE processing location: " + location);
throw e;
}
if (files.size() == 0) {
throw new EdalException(
"The location " + location + " doesn't refer to any existing files.");
}
if (files.size() == 1) {
location = files.get(0).getAbsolutePath();
nc = CdmUtils.openDataset(location);
} else {
/*
* We have multiple files in a glob expression. We write some
* NcML and use the NetCDF aggregation libs to parse this into
* an aggregated dataset.
*
* If we have already generated the ncML on a previous call,
* just use that.
*/
if (ncmlString == null) {
/*
* Find the name of the time dimension
*/
NetcdfDataset first = openAndAggregateDataset(files.get(0).getAbsolutePath());
String timeDimName = null;
for (Variable var : first.getVariables()) {
if (var.isCoordinateVariable()) {
for (Attribute attr : var.getAttributes()) {
if (attr.getFullName().equalsIgnoreCase("units")
&& attr.getStringValue().contains(" since ")) {
/*
* This is the time dimension. Since this is
* a co-ordinate variable, there is only 1
* dimension
*/
Dimension timeDimension = var.getDimension(0);
timeDimName = timeDimension.getFullName();
}
}
}
}
first.close();
if (timeDimName == null) {
throw new EdalException("Cannot join multiple files without time dimensions");
}
/*
* We can't assume that the glob expression will have
* returned the files in time order.
*
* We could assume that alphabetical == time ordered (and
* for properly named files it will - but let's not rely on
* our users having sensible naming conventions...
*
* Sort the list using a comparator which opens the file and
* gets the first value of the time dimension
*/
final String aggDimName = timeDimName;
Collections.sort(
files,
new Comparator<File>() {
@Override
public int compare(File ncFile1, File ncFile2) {
NetcdfFile nc1 = null;
NetcdfFile nc2 = null;
try {
nc1 = NetcdfFile.open(ncFile1.getAbsolutePath());
nc2 = NetcdfFile.open(ncFile2.getAbsolutePath());
Variable timeVar1 = nc1.findVariable(aggDimName);
Variable timeVar2 = nc2.findVariable(aggDimName);
long time1 = timeVar1.read().getLong(0);
long time2 = timeVar2.read().getLong(0);
return Long.compare(time1, time2);
} catch (Exception e) {
/*
* There was a problem reading the data. Sort
* alphanumerically by filename and hope for the
* best...
*
* This catches all exceptions because however
* it fails this is still our best option.
*
* If the error is a genuine problem, it'll show
* up as soon as we try and aggregate.
*/
return ncFile1.getAbsolutePath().compareTo(ncFile2.getAbsolutePath());
} finally {
if (nc1 != null) {
try {
nc1.close();
} catch (IOException e) {
log.error("Problem closing netcdf file", e);
}
}
if (nc2 != null) {
try {
nc2.close();
} catch (IOException e) {
log.error("Problem closing netcdf file", e);
}
}
}
}
});
/*
* Now create the NcML string and use it to create an
* aggregated dataset
*/
StringBuffer ncmlStringBuffer = new StringBuffer();
ncmlStringBuffer.append(
"<netcdf xmlns=\"http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2\">");
ncmlStringBuffer.append(
"<aggregation dimName=\"" + timeDimName + "\" type=\"joinExisting\">");
for (File file : files) {
ncmlStringBuffer.append("<netcdf location=\"" + file.getAbsolutePath() + "\"/>");
}
ncmlStringBuffer.append("</aggregation>");
ncmlStringBuffer.append("</netcdf>");
ncmlString = ncmlStringBuffer.toString();
}
nc = NcMLReader.readNcML(new StringReader(ncmlString), null);
}
}
return nc;
}
private FeatureType amendGrid(
Element gridElem, NetcdfFile ncfile, Group parent, String location) {
List<Dimension> unknownDims = new ArrayList<>();
// always has x and y dimension
String xdimSizeS = gridElem.getChild("XDim").getText().trim();
String ydimSizeS = gridElem.getChild("YDim").getText().trim();
int xdimSize = Integer.parseInt(xdimSizeS);
int ydimSize = Integer.parseInt(ydimSizeS);
parent.addDimensionIfNotExists(new Dimension("XDim", xdimSize));
parent.addDimensionIfNotExists(new Dimension("YDim", ydimSize));
/* see HdfEosModisConvention
UpperLeftPointMtrs=(-20015109.354000,1111950.519667)
LowerRightMtrs=(-18903158.834333,-0.000000)
Projection=GCTP_SNSOID
ProjParams=(6371007.181000,0,0,0,0,0,0,0,0,0,0,0,0)
SphereCode=-1
*/
Element proj = gridElem.getChild("Projection");
if (proj != null) {
Variable crs = new Variable(ncfile, parent, null, HDFEOS_CRS);
crs.setDataType(DataType.SHORT);
crs.setDimensions(""); // scalar
crs.setCachedData(Array.makeArray(DataType.SHORT, 1, 0, 0)); // fake data
parent.addVariable(crs);
addAttributeIfExists(gridElem, HDFEOS_CRS_Projection, crs, false);
addAttributeIfExists(gridElem, HDFEOS_CRS_UpperLeft, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_LowerRight, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_ProjParams, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_SphereCode, crs, false);
}
// global Dimensions
Element d = gridElem.getChild("Dimension");
List<Element> dims = d.getChildren();
for (Element elem : dims) {
String name = elem.getChild("DimensionName").getText().trim();
name = NetcdfFile.makeValidCdmObjectName(name);
if (name.equalsIgnoreCase("scalar")) continue;
String sizeS = elem.getChild("Size").getText().trim();
int length = Integer.parseInt(sizeS);
Dimension old = parent.findDimension(name);
if ((old == null) || (old.getLength() != length)) {
if (length > 0) {
Dimension dim = new Dimension(name, length);
if (parent.addDimensionIfNotExists(dim) && showWork)
System.out.printf(" Add dimension %s %n", dim);
} else {
log.warn("Dimension {} has size {} {} ", sizeS, name, location);
Dimension udim = new Dimension(name, 1);
udim.setGroup(parent);
unknownDims.add(udim);
if (showWork) System.out.printf(" Add dimension %s %n", udim);
}
}
}
// Geolocation Variables
Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
if (geoFieldsG != null) {
Element floc = gridElem.getChild("GeoField");
List<Element> varsLoc = floc.getChildren();
for (Element elem : varsLoc) {
String varname = elem.getChild("GeoFieldName").getText().trim();
Variable v = geoFieldsG.findVariable(varname);
// if (v == null)
// v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, location);
}
}
// Data Variables
Group dataG = parent.findGroup(DATA_FIELDS);
if (dataG == null)
dataG =
parent.findGroup(
DATA_FIELDS2); // eg C:\data\formats\hdf4\eos\mopitt\MOP03M-200501-L3V81.0.1.hdf
if (dataG != null) {
Element f = gridElem.getChild("DataField");
List<Element> vars = f.getChildren();
for (Element elem : vars) {
String varname = elem.getChild("DataFieldName").getText().trim();
varname = NetcdfFile.makeValidCdmObjectName(varname);
Variable v = dataG.findVariable(varname);
// if (v == null)
// v = dataG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, location);
}
// get projection
String projS = null;
Element projElem = gridElem.getChild("Projection");
if (projElem != null) projS = projElem.getText().trim();
boolean isLatLon = "GCTP_GEO".equals(projS);
// look for XDim, YDim coordinate variables
if (isLatLon) {
for (Variable v : dataG.getVariables()) {
if (v.isCoordinateVariable()) {
if (v.getShortName().equals("YDim")) {
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
v.addAttribute(new Attribute(CDM.UNITS, CDM.LAT_UNITS));
}
if (v.getShortName().equals("XDim"))
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
}
}
}
}
return FeatureType.GRID;
}
private FeatureType amendSwath(NetcdfFile ncfile, Element swathElem, Group parent) {
FeatureType featureType = FeatureType.SWATH;
List<Dimension> unknownDims = new ArrayList<>();
// Dimensions
Element d = swathElem.getChild("Dimension");
List<Element> dims = d.getChildren();
for (Element elem : dims) {
String name = elem.getChild("DimensionName").getText().trim();
name = NetcdfFile.makeValidCdmObjectName(name);
if (name.equalsIgnoreCase("scalar")) continue;
String sizeS = elem.getChild("Size").getText().trim();
int length = Integer.parseInt(sizeS);
if (length > 0) {
Dimension dim = parent.findDimensionLocal(name);
if (dim != null) { // already added - may be dimension scale ?
if (dim.getLength() != length) { // ok as long as it matches
log.error("Conflicting Dimensions = {} {}", dim, ncfile.getLocation());
throw new IllegalStateException("Conflicting Dimensions = " + name);
}
} else {
dim = new Dimension(name, length);
if (parent.addDimensionIfNotExists(dim) && showWork)
System.out.printf(" Add dimension %s %n", dim);
}
} else {
log.warn("Dimension " + name + " has size " + sizeS, ncfile.getLocation());
Dimension udim = new Dimension(name, 1);
udim.setGroup(parent);
unknownDims.add(udim);
if (showWork) System.out.printf(" Add dimension %s %n", udim);
}
}
// Dimension Maps
Element dmap = swathElem.getChild("DimensionMap");
List<Element> dimMaps = dmap.getChildren();
for (Element elem : dimMaps) {
String geoDimName = elem.getChild("GeoDimension").getText().trim();
geoDimName = NetcdfFile.makeValidCdmObjectName(geoDimName);
String dataDimName = elem.getChild("DataDimension").getText().trim();
dataDimName = NetcdfFile.makeValidCdmObjectName(dataDimName);
String offsetS = elem.getChild("Offset").getText().trim();
String incrS = elem.getChild("Increment").getText().trim();
int offset = Integer.parseInt(offsetS);
int incr = Integer.parseInt(incrS);
// make new variable for this dimension map
Variable v = new Variable(ncfile, parent, null, dataDimName);
v.setDimensions(geoDimName);
v.setDataType(DataType.INT);
int npts = (int) v.getSize();
Array data = Array.makeArray(v.getDataType(), npts, offset, incr);
v.setCachedData(data, true);
v.addAttribute(new Attribute("_DimensionMap", ""));
parent.addVariable(v);
if (showWork) System.out.printf(" Add dimensionMap %s %n", v);
}
// Geolocation Variables
Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
if (geoFieldsG != null) {
Variable latAxis = null, lonAxis = null;
Element floc = swathElem.getChild("GeoField");
List<Element> varsLoc = floc.getChildren();
for (Element elem : varsLoc) {
String varname = elem.getChild("GeoFieldName").getText().trim();
Variable v = geoFieldsG.findVariable(varname);
// if (v == null)
// v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
AxisType axis = addAxisType(ncfile, v);
if (axis == AxisType.Lat) latAxis = v;
if (axis == AxisType.Lon) lonAxis = v;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
if (showWork) System.out.printf(" set coordinate %s %n", v);
}
if ((latAxis != null) && (lonAxis != null)) {
List<Dimension> xyDomain = CoordinateSystem.makeDomain(new Variable[] {latAxis, lonAxis});
if (xyDomain.size() < 2) featureType = FeatureType.PROFILE; // ??
}
}
// Data Variables
Group dataG = parent.findGroup(DATA_FIELDS);
if (dataG == null) dataG = parent.findGroup(DATA_FIELDS2);
if (dataG != null) {
Element f = swathElem.getChild("DataField");
List<Element> vars = f.getChildren();
for (Element elem : vars) {
Element dataFieldNameElem = elem.getChild("DataFieldName");
if (dataFieldNameElem == null) continue;
String varname = NetcdfFile.makeValidCdmObjectName(dataFieldNameElem.getText().trim());
Variable v = dataG.findVariable(varname);
// if (v == null)
// v = dataG.findVariable( H4header.createValidObjectName(varname));
if (v == null) {
log.error("Cant find variable {} {}", varname, ncfile.getLocation());
continue;
}
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
}
}
return featureType;
}
@Override
public Product createProduct() throws ProductIOException {
int[] dims;
int sceneHeight = 0;
int sceneWidth = 0;
Group geodata = ncFile.findGroup("geophysical_data");
if (productReader.getProductType() == SeadasProductReader.ProductType.OISST) {
dims = ncFile.getVariables().get(4).getShape();
sceneHeight = dims[2];
sceneWidth = dims[3];
mustFlipY = true;
} else if (productReader.getProductType() == SeadasProductReader.ProductType.ANCCLIM) {
List<Variable> vars = ncFile.getVariables();
for (Variable v : vars) {
if (v.getRank() == 2) {
dims = v.getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
}
}
} else {
if (geodata != null) {
dims = geodata.getVariables().get(0).getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
} else {
ucar.nc2.Dimension latdim = ncFile.findDimension("lat");
ucar.nc2.Dimension londim = ncFile.findDimension("lon");
if (latdim != null) {
sceneHeight = latdim.getLength();
sceneWidth = londim.getLength();
} else {
dims = ncFile.getVariables().get(0).getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
}
}
}
String productName = productReader.getInputFile().getName();
try {
productName = getStringAttribute("Product_Name");
} catch (Exception ignored) {
}
SeadasProductReader.ProductType productType = productReader.getProductType();
Product product = new Product(productName, productType.toString(), sceneWidth, sceneHeight);
product.setDescription(productName);
product.setFileLocation(productReader.getInputFile());
product.setProductReader(productReader);
addGlobalMetadata(product);
addSmiMetadata(product);
// variableMap = addBands(product, ncFile.getVariables());
variableMap = addSmiBands(product, ncFile.getVariables());
try {
addGeocoding(product);
} catch (Exception ignored) {
}
addFlagsAndMasks(product);
if (productReader.getProductType() == SeadasProductReader.ProductType.Bathy) {
mustFlipY = true;
Dimension tileSize = new Dimension(640, 320);
product.setPreferredTileSize(tileSize);
}
return product;
}
public void testWritePermute() throws Exception {
NetcdfFileWriteable ncfile = new NetcdfFileWriteable();
ncfile.setName(TestLocal.cdmTestDataDir + "permuteTest.nc");
// define dimensions
Dimension xDim = ncfile.addDimension("x", 3);
Dimension yDim = ncfile.addDimension("y", 5);
Dimension zDim = ncfile.addDimension("z", 4);
Dimension tDim = ncfile.addDimension("time", 2);
// define Variables
ncfile.addVariable("time", double.class, new Dimension[] {tDim});
ncfile.addVariableAttribute("time", "units", "secs since 1-1-1 00:00");
ncfile.addVariable("z", double.class, new Dimension[] {zDim});
ncfile.addVariableAttribute("z", "units", "meters");
ncfile.addVariableAttribute("z", "positive", "up");
ncfile.addVariable("y", double.class, new Dimension[] {yDim});
ncfile.addVariableAttribute("y", "units", "degrees_north");
ncfile.addVariable("x", double.class, new Dimension[] {xDim});
ncfile.addVariableAttribute("x", "units", "degrees_east");
ncfile.addVariable("tzyx", double.class, new Dimension[] {tDim, zDim, yDim, xDim});
ncfile.addVariableAttribute("tzyx", "units", "K");
ncfile.addVariable("tzxy", double.class, new Dimension[] {tDim, zDim, xDim, yDim});
ncfile.addVariableAttribute("tzxy", "units", "K");
ncfile.addVariable("tyxz", double.class, new Dimension[] {tDim, yDim, xDim, zDim});
ncfile.addVariableAttribute("tyxz", "units", "K");
ncfile.addVariable("txyz", double.class, new Dimension[] {tDim, xDim, yDim, zDim});
ncfile.addVariableAttribute("txyz", "units", "K");
ncfile.addVariable("zyxt", double.class, new Dimension[] {zDim, yDim, xDim, tDim});
ncfile.addVariableAttribute("zyxt", "units", "K");
ncfile.addVariable("zxyt", double.class, new Dimension[] {zDim, xDim, yDim, tDim});
ncfile.addVariableAttribute("zxyt", "units", "K");
ncfile.addVariable("yxzt", double.class, new Dimension[] {yDim, xDim, zDim, tDim});
ncfile.addVariableAttribute("yxzt", "units", "K");
ncfile.addVariable("xyzt", double.class, new Dimension[] {xDim, yDim, zDim, tDim});
ncfile.addVariableAttribute("xyzt", "units", "K");
// missing one dimension
ncfile.addVariable("zyx", double.class, new Dimension[] {zDim, yDim, xDim});
ncfile.addVariable("txy", double.class, new Dimension[] {tDim, xDim, yDim});
ncfile.addVariable("yxz", double.class, new Dimension[] {yDim, xDim, zDim});
ncfile.addVariable("xzy", double.class, new Dimension[] {xDim, zDim, yDim});
ncfile.addVariable("yxt", double.class, new Dimension[] {yDim, xDim, tDim});
ncfile.addVariable("xyt", double.class, new Dimension[] {xDim, yDim, tDim});
ncfile.addVariable("xyz", double.class, new Dimension[] {xDim, yDim, zDim});
// missing two dimension
ncfile.addVariable("yx", double.class, new Dimension[] {yDim, xDim});
ncfile.addVariable("xy", double.class, new Dimension[] {xDim, yDim});
ncfile.addVariable("yz", double.class, new Dimension[] {yDim, zDim});
ncfile.addVariable("xz", double.class, new Dimension[] {xDim, zDim});
ncfile.addVariable("yt", double.class, new Dimension[] {yDim, tDim});
ncfile.addVariable("xt", double.class, new Dimension[] {xDim, tDim});
ncfile.addVariable("ty", double.class, new Dimension[] {tDim, yDim});
ncfile.addVariable("tx", double.class, new Dimension[] {tDim, xDim});
// add global attributes
ncfile.addGlobalAttribute("Convention", "COARDS");
// create the file
try {
ncfile.create();
} catch (IOException e) {
System.err.println("ERROR creating file");
assert (false);
}
// write time data
int len = tDim.getLength();
ArrayDouble A = new ArrayDouble.D1(len);
Index ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3600));
int[] origin = new int[1];
try {
ncfile.write("time", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing time");
assert (false);
}
// write z data
len = zDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 10));
try {
ncfile.write("z", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing z");
assert (false);
}
// write y data
len = yDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3));
try {
ncfile.write("y", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing y");
assert (false);
}
// write x data
len = xDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 5));
try {
ncfile.write("x", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing x");
assert (false);
}
// write tzyx data
doWrite4(ncfile, "tzyx");
doWrite4(ncfile, "tzxy");
doWrite4(ncfile, "txyz");
doWrite4(ncfile, "tyxz");
doWrite4(ncfile, "zyxt");
doWrite4(ncfile, "zxyt");
doWrite4(ncfile, "xyzt");
doWrite4(ncfile, "yxzt");
doWrite3(ncfile, "zyx");
doWrite3(ncfile, "txy");
doWrite3(ncfile, "yxz");
doWrite3(ncfile, "xzy");
doWrite3(ncfile, "yxt");
doWrite3(ncfile, "xyt");
doWrite3(ncfile, "yxt");
doWrite3(ncfile, "xyz");
doWrite2(ncfile, "yx");
doWrite2(ncfile, "xy");
doWrite2(ncfile, "yz");
doWrite2(ncfile, "xz");
doWrite2(ncfile, "yt");
doWrite2(ncfile, "xt");
doWrite2(ncfile, "ty");
doWrite2(ncfile, "tx");
if (show) System.out.println("ncfile = " + ncfile);
// all done
try {
ncfile.close();
} catch (IOException e) {
System.err.println("ERROR writing file");
assert (false);
}
System.out.println("*****************Test Write done");
}
