public boolean compareVariables(NetcdfFile org, NetcdfFile copy) {
f.format("Original = %s%n", org.getLocation());
f.format("CompareTo= %s%n", copy.getLocation());
boolean ok = true;
for (Variable orgV : org.getVariables()) {
if (orgV.isCoordinateVariable()) continue;
Variable copyVar = copy.findVariable(orgV.getShortName());
if (copyVar == null) {
f.format(" MISSING '%s' in 2nd file%n", orgV.getFullName());
ok = false;
} else {
List<Dimension> dims1 = orgV.getDimensions();
List<Dimension> dims2 = copyVar.getDimensions();
if (!compare(dims1, dims2)) {
f.format(" %s != %s%n", orgV.getNameAndDimensions(), copyVar.getNameAndDimensions());
} else {
// f.format(" ok %s%n", orgV.getName());
}
}
}
f.format("%n");
for (Variable orgV : copy.getVariables()) {
if (orgV.isCoordinateVariable()) continue;
Variable copyVar = org.findVariable(orgV.getShortName());
if (copyVar == null) {
f.format(" MISSING '%s' in 1st file%n", orgV.getFullName());
ok = false;
}
}
return ok;
}
private boolean compareGroups(Group org, Group copy) {
if (showCompare) f.format("compare Group %s to %s %n", org.getName(), copy.getName());
boolean ok = true;
if (!org.getName().equals(copy.getName())) {
f.format(" ** names are different %s != %s %n", org.getName(), copy.getName());
ok = false;
}
// dimensions
ok &= checkAll(org.getDimensions(), copy.getDimensions(), null);
// attributes
ok &= checkAll(org.getAttributes(), copy.getAttributes(), null);
// variables
// cant use object equality, just match on short name
for (Variable orgV : org.getVariables()) {
Variable copyVar = copy.findVariable(orgV.getShortName());
if (copyVar == null) {
f.format(" ** cant find variable %s in 2nd file%n", orgV.getFullName());
ok = false;
} else {
ok &= compareVariables(orgV, copyVar, compareData, true);
}
}
for (Variable copyV : copy.getVariables()) {
Variable orgV = org.findVariable(copyV.getShortName());
if (orgV == null) {
f.format(" ** cant find variable %s in 1st file%n", copyV.getFullName());
ok = false;
}
}
// nested groups
List groups = new ArrayList();
ok &= checkAll(org.getGroups(), copy.getGroups(), groups);
for (int i = 0; i < groups.size(); i += 2) {
Group orgGroup = (Group) groups.get(i);
Group ncmlGroup = (Group) groups.get(i + 1);
ok &= compareGroups(orgGroup, ncmlGroup);
}
return ok;
}
private String showMissing(Variable v) {
if (!(v instanceof VariableDS)) return "";
VariableDS ve = (VariableDS) v;
Formatter buff = new Formatter();
buff.format("%s:", v.getFullName());
EnumSet<NetcdfDataset.Enhance> enhanceMode = ve.getEnhanceMode();
buff.format("enhanceMode= %s%n", enhanceMode);
ve.showScaleMissingProxy(buff);
return buff.toString();
}
/** Converts a 3D variable to a {@link Metadata} representation */
private static void convert3DVariable(GridDatatype g, Date date, Map<String, Metadata> metaMap)
throws IOException {
Variable v = g.getVariable();
System.out.println("Reading: " + v.getFullName());
Array values = v.read();
int h = v.getShape(1);
int w = v.getShape(2);
for (int i = 0; i < h; ++i) {
for (int j = 0; j < w; ++j) {
LatLonPoint pt = g.getCoordinateSystem().getLatLon(j, i);
String hash =
GeoHash.encode((float) pt.getLatitude(), (float) pt.getLongitude(), 10).toLowerCase();
Metadata meta = metaMap.get(hash);
if (meta == null) {
/* We need to create Metadata for this location */
meta = new Metadata();
UUID metaUUID = UUID.nameUUIDFromBytes(hash.getBytes());
meta.setName(metaUUID.toString());
SpatialProperties location =
new SpatialProperties((float) pt.getLatitude(), (float) pt.getLongitude());
meta.setSpatialProperties(location);
TemporalProperties time = new TemporalProperties(date.getTime());
meta.setTemporalProperties(time);
metaMap.put(hash, meta);
}
String featureName = v.getFullName().toLowerCase();
float featureValue = values.getFloat(i * w + j);
Feature feature = new Feature(featureName, featureValue);
meta.putAttribute(feature);
}
}
}
private void compareVariableData(
Variable var1, Variable var2, boolean showCompare, boolean justOne) throws IOException {
Array data1 = var1.read();
Array data2 = var2.read();
if (showCompare)
f.format(
" compareArrays %s unlimited=%s size=%d%n",
var1.getNameAndDimensions(), var1.isUnlimited(), data1.getSize());
compareData(var1.getFullName(), data1, data2, justOne);
if (showCompare) f.format(" ok%n");
}
public boolean compareVariables(
Variable org, Variable copy, boolean compareData, boolean justOne) {
boolean ok = true;
if (showCompare)
f.format("compare Variable %s to %s %n", org.getFullName(), copy.getFullName());
if (!org.getFullName().equals(copy.getFullName())) {
f.format(" ** names are different %s != %s %n", org.getFullName(), copy.getFullName());
ok = false;
}
// dimensions
ok &= checkAll(org.getDimensions(), copy.getDimensions(), null);
// attributes
ok &= checkAll(org.getAttributes(), copy.getAttributes(), null);
// coord sys
if ((org instanceof VariableEnhanced) && (copy instanceof VariableEnhanced)) {
VariableEnhanced orge = (VariableEnhanced) org;
VariableEnhanced copye = (VariableEnhanced) copy;
ok &= checkAll(orge.getCoordinateSystems(), copye.getCoordinateSystems(), null);
}
// data !!
if (compareData) {
try {
compareVariableData(org, copy, showCompare, justOne);
} catch (IOException e) {
ByteArrayOutputStream bos = new ByteArrayOutputStream(10000);
e.printStackTrace(new PrintStream(bos));
f.format("%s", bos.toString());
}
}
// nested variables
if (org instanceof Structure) {
if (!(copy instanceof Structure)) {
f.format(" ** %s not Structure%n", org);
ok = false;
} else {
Structure orgS = (Structure) org;
Structure ncmlS = (Structure) copy;
List vars = new ArrayList();
ok &= checkAll(orgS.getVariables(), ncmlS.getVariables(), vars);
for (int i = 0; i < vars.size(); i += 2) {
Variable orgV = (Variable) vars.get(i);
Variable ncmlV = (Variable) vars.get(i + 1);
ok &= compareVariables(orgV, ncmlV, false, true);
}
}
}
return ok;
}
private void copyAll(NetcdfFileWriteable ncfile, Variable oldVar) throws IOException {
String newName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());
Array data = oldVar.read();
try {
if (oldVar.getDataType() == DataType.STRING) {
data = convertToChar(ncfile.findVariable(newName), data);
}
if (data.getSize() > 0) // zero when record dimension = 0
ncfile.write(newName, data);
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IOException(e.getMessage() + " for Variable " + oldVar.getFullName());
}
}
/**
* Make the station variables from a representative station
*
* @param stations list of stations
* @param dim station dimension
* @return the list of variables
*/
protected List<Variable> makeStationVars(List<GempakStation> stations, Dimension dim) {
int numStations = stations.size();
boolean useSTID = true;
for (GempakStation station : stations) {
if (station.getSTID().equals("")) {
useSTID = false;
break;
}
}
List<Variable> vars = new ArrayList<Variable>();
List<String> stnKeyNames = gemreader.getStationKeyNames();
for (String varName : stnKeyNames) {
Variable v = makeStationVariable(varName, dim);
// use STNM or STID as the name or description
Attribute stIDAttr = new Attribute("standard_name", "station_id");
if (varName.equals(GempakStation.STID) && useSTID) {
v.addAttribute(stIDAttr);
}
if (varName.equals(GempakStation.STNM) && !useSTID) {
v.addAttribute(stIDAttr);
}
vars.add(v);
}
// see if we fill these in completely now
if ((dim != null) && (numStations > 0)) {
for (Variable v : vars) {
Array varArray;
if (v.getDataType().equals(DataType.CHAR)) {
int[] shape = v.getShape();
varArray = new ArrayChar.D2(shape[0], shape[1]);
} else {
varArray = get1DArray(v.getDataType(), numStations);
}
int index = 0;
String varname = v.getFullName();
for (GempakStation stn : stations) {
String test = "";
if (varname.equals(GempakStation.STID)) {
test = stn.getName();
} else if (varname.equals(GempakStation.STNM)) {
((ArrayInt.D1) varArray)
.set(
index,
// (int) (stn.getSTNM() / 10));
(int) (stn.getSTNM()));
} else if (varname.equals(GempakStation.SLAT)) {
((ArrayFloat.D1) varArray).set(index, (float) stn.getLatitude());
} else if (varname.equals(GempakStation.SLON)) {
((ArrayFloat.D1) varArray).set(index, (float) stn.getLongitude());
} else if (varname.equals(GempakStation.SELV)) {
((ArrayFloat.D1) varArray).set(index, (float) stn.getAltitude());
} else if (varname.equals(GempakStation.STAT)) {
test = stn.getSTAT();
} else if (varname.equals(GempakStation.COUN)) {
test = stn.getCOUN();
} else if (varname.equals(GempakStation.STD2)) {
test = stn.getSTD2();
} else if (varname.equals(GempakStation.SPRI)) {
((ArrayInt.D1) varArray).set(index, stn.getSPRI());
} else if (varname.equals(GempakStation.SWFO)) {
test = stn.getSWFO();
} else if (varname.equals(GempakStation.WFO2)) {
test = stn.getWFO2();
}
if (!test.equals("")) {
((ArrayChar.D2) varArray).setString(index, test);
}
index++;
}
v.setCachedData(varArray, false);
}
}
return vars;
}
@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();
}