// 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());
}
void CheckS(Variable v) throws IOException {
// string
// assert(null != (v = dodsfile.findVariable("types.strings.s")));
// assert v.getName().equals("types.strings.s");
assert v.getRank() == 0;
assert v.getDataType() == DataType.STRING : v.getDataType();
CheckSValue(v.read());
}
void CheckUint16(Variable v) throws IOException {
// uint16
// assert(null != (v = dodsfile.findVariable("types.integers.ui16")));
// assert v.getName().equals("types.integers.ui16");
assert v.getRank() == 0;
assert v.getSize() == 1;
assert v.getDataType() == DataType.SHORT : v.getDataType();
CheckUInt16Value(v.read());
}
void CheckUrl(Variable v) throws IOException {
// url
// assert(null != (v = dodsfile.findVariable("types.strings.u")));
// assert v.getName().equals("types.strings.u");
assert v.getRank() == 0;
assert v.getDataType() == DataType.STRING : v.getDataType();
String str = v.readScalarString();
assert str.equals("http://www.opendap.org") || str.equals("http://www.dods.org") : str;
}
void CheckD(Variable v) throws IOException {
// double
// assert(null != (v = dodsfile.findVariable("types.floats.f64")));
// assert v.getName().equals("types.floats.f64");
assert v.getRank() == 0;
assert v.getSize() == 1;
assert v.getDataType() == DataType.DOUBLE : v.getDataType();
CheckDValue(v.read());
}
void CheckF(Variable v) throws IOException {
// float
// assert(null != (v = dodsfile.findVariable("types.floats.f32")));
// assert v.getName().equals("types.floats.f32");
assert v.getRank() == 0;
assert v.getSize() == 1;
assert v.getDataType() == DataType.FLOAT : v.getDataType();
CheckFValue(v.read());
}
void CheckLong32(Variable v) throws IOException {
// uint32
// assert(null != (v = dodsfile.findVariable("types.integers.ui32")));
// assert v.getName().equals("types.integers.ui32");
assert v.getRank() == 0;
assert v.getSize() == 1;
assert v.getDataType() == DataType.LONG : v.getDataType();
CheckLongValue(v.read());
}
/* 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");
}
/*
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");
}
/**
* Set extra information used by station obs datasets. Use stnIdVName or stnIndexVName.
*
* @param stnIdVName the obs variable that is used to find the station in the stnHash; may be type
* int or a String (char).
* @param stnDescVName optional station var containing station description
*/
public void setStationInfo(
String stnIdVName, String stnDescVName, String stnIndexVName, StationHelper stationHelper) {
this.stnIdVName = stnIdVName;
this.stnDescVName = stnDescVName;
this.stnIndexVName = stnIndexVName;
this.stationHelper = stationHelper;
if (stnIdVName != null) {
Variable stationVar = ncfile.findVariable(stnIdVName);
stationIdType = stationVar.getDataType();
}
}
private void doWrite2(NetcdfFileWriteable ncfile, String varName) throws Exception {
Variable v = ncfile.findVariable(varName);
int[] w = getWeights(v);
int[] shape = v.getShape();
Array aa = Array.factory(v.getDataType().getPrimitiveClassType(), shape);
Index ima = aa.getIndex();
for (int i = 0; i < shape[0]; i++) {
for (int j = 0; j < shape[1]; j++) {
aa.setDouble(ima.set(i, j), (double) (i * w[0] + j * w[1]));
}
}
ncfile.write(varName, aa);
}
@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");
}
/* 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");
}
@Test
public void testArraySubset() throws IOException {
DODSNetcdfFile dodsfile = TestDODSRead.open("test.02?i32[1:10],f64[2:2:10]");
Variable v = null;
Array a = null;
// int32
assert (null != (v = dodsfile.findVariable("i32")));
assert v.getFullName().equals("i32");
assert v.getRank() == 1;
assert v.getSize() == 10;
assert v.getDataType() == DataType.INT;
a = v.read();
assert a.getRank() == 1;
assert a.getSize() == 25;
assert a.getElementType() == int.class;
assert a instanceof ArrayInt.D1;
ArrayInt.D1 ai = (ArrayInt.D1) a;
for (int i = 0; i < 10; i++) {
int val = ai.get(i);
assert (val == i * 2048) : val + " != " + (i * 2048);
}
// uint16
assert null == (v = dodsfile.findVariable("ui16"));
assert null == (v = dodsfile.findVariable("ui32"));
// double
assert (null != (v = dodsfile.findVariable("f64")));
assert v.getFullName().equals("f64");
assert v.getRank() == 1;
assert v.getSize() == 5;
assert v.getDataType() == DataType.DOUBLE : v.getDataType();
a = v.read();
assert a.getRank() == 1;
assert a.getSize() == 25;
assert a.getElementType() == double.class;
assert a instanceof ArrayDouble.D1;
ArrayDouble.D1 ad = (ArrayDouble.D1) a;
double[] tFloat64 =
new double[] {
1.0,
0.9999500004166653,
0.9998000066665778,
0.9995500337489875,
0.9992001066609779,
0.9987502603949663,
0.9982005399352042,
0.9975510002532796,
0.9968017063026194,
0.9959527330119943,
0.9950041652780257,
0.9939560979566968,
0.9928086358538663,
0.9915618937147881,
0.9902159962126371,
0.9887710779360422,
0.9872272833756269,
0.9855847669095608,
0.9838436927881214,
0.9820042351172703,
0.9800665778412416,
0.9780309147241483,
0.9758974493306055,
0.9736663950053749,
0.9713379748520297
};
for (int i = 0; i < 5; i++) {
double val = ad.get(i);
assert Misc.closeEnough(val, tFloat64[i], 1.0e-9);
}
dodsfile.close();
}
// create from a dataset
public ObsBean(Structure obs, StructureData sdata) {
// first choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-5-1") && Double.isNaN(lat)) {
lat = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-6-1") && Double.isNaN(lon)) {
lon = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-30") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-4-1") && (year < 0)) {
year = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-2") && (month < 0)) {
month = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-3") && (day < 0)) {
day = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-4") && (hour < 0)) {
hour = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-5") && (minute < 0)) {
minute = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-4-6") && (sec < 0)) {
sec = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-1-1") && (wmo_block < 0)) {
wmo_block = sdata.convertScalarInt(v.getShortName());
} else if (val.equals("0-1-2") && (wmo_id < 0)) {
wmo_id = sdata.convertScalarInt(v.getShortName());
} else if ((stn == null)
&& (val.equals("0-1-7")
|| val.equals("0-1-194")
|| val.equals("0-1-11")
|| val.equals("0-1-18"))) {
if (v.getDataType().isString()) stn = sdata.getScalarString(v.getShortName());
else stn = Integer.toString(sdata.convertScalarInt(v.getShortName()));
}
}
// second choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-5-2") && Double.isNaN(lat)) {
lat = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-6-2") && Double.isNaN(lon)) {
lon = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-1") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if ((val.equals("0-4-7")) && (sec < 0)) {
sec = sdata.convertScalarInt(v.getShortName());
}
}
// third choice
for (Variable v : obs.getVariables()) {
Attribute att = v.findAttribute("BUFR:TableB_descriptor");
if (att == null) continue;
String val = att.getStringValue();
if (val.equals("0-7-10") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
} else if (val.equals("0-7-2") && Double.isNaN(alt)) {
alt = sdata.convertScalarDouble(v.getShortName());
}
}
}
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);
}
void CheckByte(Variable v) throws IOException {
assert v.getRank() == 0;
assert v.getSize() == 1;
assert v.getDataType() == DataType.BYTE;
CheckByteValue(v.read());
}