/* 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");
}
public List<VariableBean> getStructureVariables(Structure s) {
List<VariableBean> vlist = new ArrayList<VariableBean>();
for (Variable v : s.getVariables()) {
vlist.add(new VariableBean(v));
}
return vlist;
}
@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");
}
private void setObs(Message m) {
java.util.List<ObsBean> beanList = new ArrayList<ObsBean>();
try {
NetcdfDataset ncd = getBufrMessageAsDataset(m);
Variable v = ncd.findVariable(BufrIosp.obsRecord);
if ((v != null) && (v instanceof Structure)) {
Structure obs = (Structure) v;
StructureDataIterator iter = obs.getStructureIterator();
while (iter.hasNext()) {
beanList.add(new ObsBean(obs, iter.next()));
}
}
} catch (Exception ex) {
JOptionPane.showMessageDialog(BufrMessageViewer.this, ex.getMessage());
ex.printStackTrace();
}
obsTable.setBeans(beanList);
}
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);
}
// 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());
}
}
}