void initTransientFire(boolean useseverity, String dir) {
String filename = dir + "fire.nc";
NetcdfFile ncfile = null;
File spfile = new File(filename);
if (spfile.exists()) {
try {
ncfile = NetcdfFile.open(filename);
Variable fyearV = ncfile.findVariable("FIRE");
trfireyearA = fyearV.read();
Variable fseasonV = ncfile.findVariable("SEASON");
trfireseasonA = fseasonV.read();
if (useseverity) {
Variable fsevV = ncfile.findVariable("SEVERITY");
trseverityA = fsevV.read();
}
} catch (IOException ioe) {
System.out.println(ioe.getMessage());
} finally {
if (ncfile != null) {
try {
ncfile.close();
} catch (IOException ioee) {
System.out.println(ioee.getMessage());
}
}
}
} else { // file not exist
System.out.println("Input file: " + filename + " NOT existed");
System.exit(-1);
}
};
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 void check(NetcdfFile ncfile, int n) throws IOException, InvalidRangeException {
Variable v = ncfile.findVariable("time");
assert v != null;
System.out.printf(" time= %s%n", v.getNameAndDimensions());
assert v.getSize() == n : v.getSize();
v = ncfile.findVariable("eta");
assert v != null;
assert v.getRank() == 3 : v.getRank();
}
/* 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");
}
/**
* Clones the attributes of one NetCDF file into another.
*
* @param infile - The source NetCDF file
* @param inVarName - The variable name to be copied
* @param outfile - The destination NetCDF file
* @param outVarName - The output variable name
*/
private void cloneAttributes(
NetcdfFile infile, String inVarName, NetcdfFileWriteable outfile, String outVarName) {
// Find the variable
Variable vi = infile.findVariable(inVarName);
// Grab all of its attributes - unchecked, but should be OK.
List<Attribute> l = vi.getAttributes();
for (Attribute a : l) {
if (a.getName().equalsIgnoreCase("units") && inVarName.equalsIgnoreCase("time")) {
Attribute aa = new Attribute("units", "days since 1900-12-31 00:00:00");
outfile.addVariableAttribute(outVarName, aa);
} else if (a.getName().equalsIgnoreCase("time_origin")
&& inVarName.equalsIgnoreCase("time")) {
Attribute aa = new Attribute("time_origin", "1900-12-31 00:00:00");
outfile.addVariableAttribute(outVarName, aa);
} else if (a.getName().equalsIgnoreCase("calendar")) {
Attribute aa = new Attribute("calendar", "standard");
outfile.addVariableAttribute(outVarName, aa);
} else {
outfile.addVariableAttribute(outVarName, a);
}
}
}
public void testAggCoordVar2(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert (data instanceof ArrayInt);
IndexIterator dataI = data.getIndexIterator();
assert dataI.getIntNext() == 0 : dataI.getIntCurrent();
assert dataI.getIntNext() == 1 : dataI.getIntCurrent();
assert dataI.getIntNext() == 2 : dataI.getIntCurrent();
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
public void readByte2Short() throws Exception {
Variable t2 = null;
assert (null != (t2 = ncfileRead.findVariable("t2")));
assert (t2.getDataType() == DataType.BYTE);
Attribute att = t2.findAttribute(CDM.SCALE_FACTOR);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
assert (2 == att.getNumericValue().doubleValue());
assert (DataType.SHORT == att.getDataType());
assert (null != (t2 = dsRead.findVariable("t2")));
assert t2 instanceof VariableEnhanced;
VariableDS vs = (VariableDS) t2;
assert (vs.getDataType() == DataType.SHORT) : vs.getDataType();
assert (!vs.hasMissing());
Array A = vs.read();
assert (A.getElementType() == short.class) : A.getElementType();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getShort(ima.set(i, j)) == (2 * (i * 10 + j) + 77));
}
}
System.out.println("**************TestStandardVar readByte2Short");
}
public void addInputParamMetadata(Product product) throws ProductIOException {
Variable inputParams = ncFile.findVariable("Input_Parameters");
if (inputParams != null) {
final MetadataElement inputParamsMeta = new MetadataElement("Input_Parameters");
Array array;
try {
array = inputParams.read();
} catch (IOException e) {
throw new ProductIOException(e.getMessage());
}
String[] lines = array.toString().split("\n");
for (String line : lines) {
String[] parts = line.split("=");
if (parts.length == 2) {
final String name = parts[0].trim();
final String value = parts[1].trim();
final ProductData data = ProductData.createInstance(ProductData.TYPE_ASCII, value);
final MetadataAttribute attribute = new MetadataAttribute(name, data, true);
inputParamsMeta.addAttribute(attribute);
}
}
final MetadataElement metadataRoot = product.getMetadataRoot();
metadataRoot.addElement(inputParamsMeta);
}
}
public void testAggCoordVar(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1;
assert time.getSize() == 3;
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.DOUBLE;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert data.getRank() == 1;
assert data.getSize() == 3;
assert data.getShape()[0] == 3;
assert data.getElementType() == double.class;
int count = 0;
IndexIterator dataI = data.getIndexIterator();
while (dataI.hasNext()) {
assert Misc.closeEnough(dataI.getDoubleNext(), result[count]);
count++;
}
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
/**
* Sets the v-velocity file to be used by this class
*
* @param _velocityFile - the v-velocity NetCDF object
* @param vName - the name of the v variable
* @throws IOException
*/
public void setVFile(String _velocityFile, String vName) throws IOException {
this.vName = vName;
vFile = NetcdfFile.open(_velocityFile);
if (vFile != null) {
vVar = vFile.findVariable(vName);
}
}
/*
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 void testAggCoordVar(NetcdfFile ncfile) {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT;
assert time.getDimension(0) == ncfile.findDimension("time");
try {
Array data = time.read();
assert (data instanceof ArrayInt.D1) : data.getClass().getName();
ArrayInt.D1 dataI = (ArrayInt.D1) data;
assert dataI.get(0) == 0;
assert dataI.get(1) == 10;
assert dataI.get(2) == 99;
} catch (IOException io) {
io.printStackTrace();
assert false;
}
}
/**
* Create a new vertical transform for Ocean_S_coordinate_g2
*
* @param ds dataset
* @param timeDim time dimension
* @param params list of transformation Parameters
*/
public OceanSG2(NetcdfFile ds, Dimension timeDim, List<Parameter> params) {
super(timeDim);
String etaName = getParameterStringValue(params, ETA);
String sName = getParameterStringValue(params, S);
String depthName = getParameterStringValue(params, DEPTH);
String depthCName = getParameterStringValue(params, DEPTH_C);
String cName = getParameterStringValue(params, C);
etaVar = ds.findVariable(etaName);
sVar = ds.findVariable(sName);
depthVar = ds.findVariable(depthName);
depthCVar = ds.findVariable(depthCName);
cVar = ds.findVariable(cName);
units = ds.findAttValueIgnoreCase(depthVar, CDM.UNITS, "none");
}
@Ignore("files not available")
@Test
public void testCacheTiming() throws IOException, InvalidRangeException {
String filename = "file:testCacheTiming.xml";
System.out.printf("%s%n", filename);
String cacheDirName = TestDir.temporaryLocalDataDir + "testAggExistingCache/";
System.out.printf("cacheDir=%s%n", cacheDirName);
File cacheDir = new File(cacheDirName);
FileUtils.deleteDirectory(cacheDir); // from commons-io
assert !cacheDir.exists();
DiskCache2 cache = new DiskCache2(cacheDirName, false, 0, 0);
cache.setAlwaysUseCache(true);
Assert.assertEquals(cache.getRootDirectory(), cacheDirName);
assert new File(cache.getRootDirectory()).exists();
Aggregation.setPersistenceCache(cache);
AggregationExisting.countCacheUse = 0;
long start = System.currentTimeMillis();
try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml2), filename, null)) {
System.out.printf("%nTestNcmlAggExisting.open %s%n", filename);
Variable time = ncfile.findVariable("time");
System.out.printf(" Variable %s%n", time.getNameAndDimensions());
time.read();
}
System.out.printf(" countCacheUse = %d%n", AggregationExisting.countCacheUse);
long took = System.currentTimeMillis() - start;
System.out.printf(" first took %d msecs%n", took);
AggregationExisting.countCacheUse = 0;
start = System.currentTimeMillis();
try (NetcdfFile ncfile = NcMLReader.readNcML(new StringReader(ncml2), filename, null)) {
System.out.printf("%nTestNcmlAggExisting.open %s%n", filename);
Variable time = ncfile.findVariable("time");
System.out.printf(" Variable %s%n", time.getNameAndDimensions());
time.read();
}
System.out.printf(" countCacheUse = %d%n", AggregationExisting.countCacheUse);
took = System.currentTimeMillis() - start;
System.out.printf(" second took %d msecs%n", took);
}
private boolean checkTime(long time) {
/*
* Right now, the lookups are based solely on the dimensions (lats,
* lons, depth, time) of the u velocity files, assuming that u, v and w
* share common Dimensions. Otherwise we'd need to set up independent
* XYZ and T lookups for UV and W increasing computational overhead,
* when this really shouldn't be necessary. BUT, it might be a good idea
* to ensure that the velocity files are consistent.
*/
int uidx = Collections.binarySearch(uKeys, time);
// int vidx = Collections.binarySearch(vKeys, time);
// int widx = Collections.binarySearch(wKeys, time);
if (uidx == -1 || uidx > uKeys.size()) {
return false;
}
if (uidx < 0) {
uidx = -(uidx + 2);
}
// if (vidx < 0) {
// vidx = -(vidx + 2);
// }
// if (widx < 0) {
// widx = -(widx + 2);
// }
if (pidx != uidx) {
uFile = uFiles.get(uKeys.get(uidx));
vFile = vFiles.get(vKeys.get(uidx));
wFile = wFiles.get(wKeys.get(uidx));
uVar = uFile.findVariable(uName);
vVar = vFile.findVariable(vName);
wVar = wFile.findVariable(wName);
setTLookup(tName);
pidx = uidx;
}
return true;
}
/**
* Sets the name of the lookup variable for the Time position
*
* @param name
*/
public void setTLookup(String name) {
tVar = uFile.findVariable(tName);
if (tVar == null) {
System.out.println(
"Incorrect variable match:\n\nVariables in local config file: " + tName + ".");
System.out.println("Velocity file variables: " + uFile.getVariables().toString() + "\n");
}
tloc = new IndexLookup_Nearest(tVar);
}
public void testStride() throws IOException, InvalidRangeException {
System.out.println("ncfile opened = " + location + "\n" + ncfile);
Variable time = ncfile.findVariable("time");
ArrayInt all = (ArrayInt) time.read();
for (int i = 0; i < all.getSize(); i++) assert (all.getInt(i) == i + 1);
testStride("0:13:3");
for (int i = 1; i < 12; i++) testStride("0:13:" + i);
}
/**
* Sets the name of the lookup variable for the North-South position
*
* @param name
*/
public void setYLookup(String name) {
latVar = uFile.findVariable(latName);
if (latVar == null) {
System.out.println(
"Incorrect variable match:\n\nVariables in local config file: " + latName + ".");
System.out.println("Velocity file variables: " + uFile.getVariables().toString() + "\n");
}
yloc = new IndexLookup_Nearest(latVar, 0); // dimension 0 because slices
// have 2D lat/lon
bounds[2][0] = yloc.getMinVal();
bounds[2][1] = yloc.getMaxVal();
}
public void readShortMissing() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t4")));
assert (v.getDataType() == DataType.SHORT);
// default use of missing_value
assert (null != (v = dsRead.findVariable("t4")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.SHORT);
Attribute att = vs.findAttribute(CDM.MISSING_VALUE);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
System.out.println("missing_value = " + att.getNumericValue().shortValue());
assert (((short) -9999) == att.getNumericValue().shortValue());
assert (DataType.SHORT == att.getDataType());
assert (vs.hasMissing());
assert (vs.hasMissingValue());
assert (vs.isMissing((double) ((short) -9999)));
assert (vs.isMissingValue((double) ((short) -9999)));
Array A = vs.read();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getFloat(ima.set(i, j)) == (i * 10 + j));
}
}
// turn off missing data
vs.setMissingDataIsMissing(false);
assert (vs.getDataType() == DataType.SHORT);
assert (!vs.hasMissing());
assert (vs.hasMissingValue());
assert (!vs.isMissing((double) ((short) -9999)));
assert (vs.isMissingValue((double) ((short) -9999)));
vs.setMissingDataIsMissing(true);
assert (vs.hasMissing());
assert (vs.isMissing((double) ((short) -9999)));
System.out.println("**************TestStandardVar Read readShortMissing");
}
/*
Structure {
int a_name;
String b_name(4);
char c_name(6);
short d_name(5, 4);
float e_name;
double f_name(10);
byte g_name;
} CompoundComplex(6);
type = Layout(8); type= 1 (contiguous) storageSize = (6,224) dataSize=0 dataAddress=2048
*/
@Test
public void testReadH5Structure() 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 (NetcdfFile ncfile = TestH5.openH5("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("*** testReadH5Structure ok");
}
public static void main(String args[])
throws Exception, IOException, InstantiationException, IllegalAccessException {
String fileIn = "z:/nowrad/BREF_951207_2230";
// String fileIn = "c:/data/image/Nids/n0r_20041013_1852";
ucar.nc2.NetcdfFile.registerIOProvider(ucar.nc2.iosp.nowrad.NOWRadiosp.class);
ucar.nc2.NetcdfFile ncf = ucar.nc2.NetcdfFile.open(fileIn);
// List alist = ncf.getGlobalAttributes();
ucar.nc2.Variable v = ncf.findVariable("BaseReflectivity");
int[] origin = {0, 0};
int[] shape = {300, 36};
ArrayByte data = (ArrayByte) v.read(origin, shape);
ncf.close();
}
public static Map<String, Metadata> readFile(String file) throws Exception {
NetcdfFile n = NetcdfFile.open(file);
System.out.println("Opened: " + file);
/* Determine the size of our grid */
int xLen = n.findDimension("x").getLength();
int yLen = n.findDimension("y").getLength();
System.out.println("Grid size: " + xLen + "x" + yLen);
/* What time is this set of readings for? */
Variable timeVar = n.findVariable("time");
String timeStr = timeVar.getUnitsString().toUpperCase();
timeStr = timeStr.replace("HOURS SINCE ", "");
timeStr = timeStr.replace("HOUR SINCE ", "");
/* Find the base date (the day) the reading was taken */
Date baseDate = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssX").parse(timeStr);
/* Get the number of hours since the base date this reading was taken */
int offset = timeVar.read().getInt(0);
/* Generate the actual date for this reading */
Calendar calendar = Calendar.getInstance();
calendar.setTime(baseDate);
calendar.set(Calendar.HOUR, calendar.get(Calendar.HOUR) + offset);
System.out.println("Time of collection: " + calendar.getTime());
/* We'll keep a mapping of geolocations -> Galileo Metadata */
Map<String, Metadata> metaMap = new HashMap<>();
/* Determine the lat, lon coordinates for the grid points, and get each
* reading at each grid point. */
NetcdfDataset dataset = new NetcdfDataset(n);
@SuppressWarnings("resource")
GridDataset gridData = new GridDataset(dataset);
for (GridDatatype g : gridData.getGrids()) {
/* Let's look at 3D variables: these have WxH dimensions, plus a
* single plane. A 4D variable would contain elevation
* and multiple planes as a result */
if (g.getShape().length == 3) {
convert3DVariable(g, calendar.getTime(), metaMap);
}
}
return metaMap;
}
public void readDouble() throws Exception {
Variable t1 = null;
assert (null != (t1 = ncfileRead.findVariable("t1")));
assert (t1.getDataType() == DataType.DOUBLE);
Attribute att = t1.findAttribute(CDM.SCALE_FACTOR);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
assert (2.0 == att.getNumericValue().doubleValue());
assert (DataType.DOUBLE == att.getDataType());
// read
Array A = t1.read();
int i, j;
Index ima = A.getIndex();
int[] shape = A.getShape();
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getDouble(ima.set(i, j)) == (double) (i * 10.0 + j));
}
}
assert (null != (t1 = dsRead.findVariable("t1")));
assert t1 instanceof VariableEnhanced;
VariableEnhanced dsVar = (VariableEnhanced) t1;
assert (dsVar.getDataType() == DataType.DOUBLE);
A = dsVar.read();
ima = A.getIndex();
shape = A.getShape();
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getDouble(ima.set(i, j)) == (2.0 * (i * 10.0 + j) + 77.0));
}
}
assert (null == t1.findAttribute(CDM.SCALE_FACTOR));
assert (null == t1.findAttribute("add_offset"));
System.out.println("**************TestStandardVar ReadDouble");
}
public void test1() throws IOException, InvalidRangeException {
String filename = "file:./" + TestNcML.topDir + "aggSynthetic.xml";
NetcdfFile ncfile = NcMLReader.readNcML(filename, null);
Variable v = ncfile.findVariable("time");
assert v != null;
String testAtt = ncfile.findAttValueIgnoreCase(v, "units", null);
assert testAtt != null;
assert testAtt.equals("months since 2000-6-16 6:00");
testDimensions(ncfile);
testCoordVar(ncfile);
testAggCoordVar(ncfile);
testReadData(ncfile, "T");
testReadSlice(ncfile, "T");
ncfile.close();
}
public void testAggCoordVar3(NetcdfFile ncfile) throws IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.DOUBLE : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
Array data = time.read();
assert (data instanceof ArrayDouble);
IndexIterator dataI = data.getIndexIterator();
double val = dataI.getDoubleNext();
assert Misc.closeEnough(val, 0.0) : val;
assert Misc.closeEnough(dataI.getDoubleNext(), 10.0) : dataI.getDoubleCurrent();
assert Misc.closeEnough(dataI.getDoubleNext(), 99.0) : dataI.getDoubleCurrent();
}
public void testAggCoordVarScan(NetcdfFile ncfile) throws IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1 : time.getRank();
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.INT : time.getDataType();
assert time.getDimension(0) == ncfile.findDimension("time");
int count = 0;
Array data = time.read();
assert (data instanceof ArrayInt);
while (data.hasNext()) {
int val = data.nextInt();
assert val == count * 10 : val + "!=" + count * 10;
count++;
}
}
/** Sets the name of the lookup variable for vertical position */
public void setZLookup(String name) {
zVar = uFile.findVariable(zName);
if (zVar == null) {
throw new IllegalArgumentException(
"Incorrect variable match:\n\nVariables in local config file: "
+ zName
+ ".\nVelocity file variables: "
+ uFile.getVariables().toString()
+ "\n");
}
zloc = new IndexLookup_Nearest(zVar);
if (positiveDown) {
zloc.setNegate(true);
}
bounds[1][0] = zloc.getMinVal();
bounds[1][1] = zloc.getMaxVal();
}
public void testStride(String stride) throws IOException, InvalidRangeException {
Variable time = ncfile.findVariable("time");
ArrayInt all = (ArrayInt) time.read();
ArrayInt correct = (ArrayInt) all.section(new Section(stride).getRanges());
System.out.printf("correct(%s) %s", stride, NCdumpW.toString(correct));
ArrayInt data = (ArrayInt) time.read(stride);
System.out.printf("data(%s) %s%n", stride, NCdumpW.toString(data));
Index ci = correct.getIndex();
Index di = data.getIndex();
for (int i = 0; i < data.getSize(); i++)
assert (data.getInt(di.set(i)) == correct.getInt(ci.set(i)))
: stride
+ " index "
+ i
+ " = "
+ data.getInt(di.set(i))
+ " != "
+ correct.getInt(ci.set(i));
}
/**
* Sets the name of the lookup variable for the East-West position
*
* @param name
*/
public void setXLookup(String name) {
lonVar = uFile.findVariable(lonName);
if (lonVar == null) {
System.out.println(
"Incorrect variable match:\n\nVariables in local config file: " + lonName + ".");
System.out.println("Velocity file variables: " + uFile.getVariables().toString() + "\n");
}
int dim = 0;
if (lonVar.getRank() > 1) {
dim = 1;
}
xloc = new IndexLookup_Nearest(lonVar, dim); // dimension 1 because
// slices
// have 2D lat/lon
bounds[3][0] = xloc.getMinVal();
bounds[3][1] = xloc.getMaxVal();
}
public void testAggCoordVarSubsetDefeatLocalCache(NetcdfFile ncfile)
throws InvalidRangeException, IOException {
Variable time = ncfile.findVariable("time");
assert null != time;
assert time.getShortName().equals("time");
assert time.getRank() == 1;
assert time.getSize() == 3;
assert time.getShape()[0] == 3;
assert time.getDataType() == DataType.DOUBLE;
assert time.getDimension(0) == ncfile.findDimension("time");
time.setCachedData(null, false);
Array data = time.read("1:2");
assert data.getRank() == 1;
assert data.getSize() == 2;
assert data.getShape()[0] == 2;
assert data.getElementType() == double.class;
int count = 0;
IndexIterator dataI = data.getIndexIterator();
while (dataI.hasNext()) {
assert Misc.closeEnough(dataI.getDoubleNext(), result[count + 1]);
count++;
}
time.setCachedData(null, false);
data = time.read("0:2:2");
assert data.getRank() == 1;
assert data.getSize() == 2;
assert data.getShape()[0] == 2;
assert data.getElementType() == double.class;
count = 0;
dataI = data.getIndexIterator();
while (dataI.hasNext()) {
assert Misc.closeEnough(dataI.getDoubleNext(), result[count * 2]);
count++;
}
}