private void handleMetadataGroup(Group group, MetadataElement metadataElement)
throws ProductIOException {
List<Variable> variables = group.getVariables();
for (Variable variable : variables) {
final String name = variable.getShortName();
final int dataType = getProductDataType(variable);
Array array;
try {
array = variable.read();
} catch (IOException e) {
throw new ProductIOException(e.getMessage());
}
final ProductData data = ProductData.createInstance(dataType, array.getStorage());
final MetadataAttribute attribute = new MetadataAttribute("data", data, true);
final MetadataElement sdsElement = new MetadataElement(name);
sdsElement.addAttribute(attribute);
metadataElement.addElement(sdsElement);
final List<Attribute> list = variable.getAttributes();
for (Attribute hdfAttribute : list) {
final String attribName = hdfAttribute.getShortName();
if ("units".equals(attribName)) {
attribute.setUnit(hdfAttribute.getStringValue());
} else if ("long_name".equals(attribName)) {
attribute.setDescription(hdfAttribute.getStringValue());
} else {
addAttributeToElement(sdsElement, hdfAttribute);
}
}
}
}
private ProductData.UTC getUTCAttribute(String key, List<Attribute> globalAttributes) {
Attribute attribute = findAttribute(key, globalAttributes);
Boolean isModis = false;
try {
isModis = findAttribute("MODIS_Resolution", globalAttributes).isString();
} catch (Exception ignored) {
}
if (attribute != null) {
String timeString = attribute.getStringValue().trim();
final DateFormat dateFormat = ProductData.UTC.createDateFormat("yyyyDDDHHmmssSSS");
final DateFormat dateFormatModis =
ProductData.UTC.createDateFormat("yyyy-MM-dd HH:mm:ss.SSSSSS");
final DateFormat dateFormatOcts =
ProductData.UTC.createDateFormat("yyyyMMdd HH:mm:ss.SSSSSS");
try {
if (isModis) {
final Date date = dateFormatModis.parse(timeString);
String milliSeconds = timeString.substring(timeString.length() - 3);
return ProductData.UTC.create(date, Long.parseLong(milliSeconds) * 1000);
} else if (productReader.getProductType() == SeadasProductReader.ProductType.Level1A_OCTS) {
final Date date = dateFormatOcts.parse(timeString);
String milliSeconds = timeString.substring(timeString.length() - 3);
return ProductData.UTC.create(date, Long.parseLong(milliSeconds) * 1000);
} else {
final Date date = dateFormat.parse(timeString);
String milliSeconds = timeString.substring(timeString.length() - 3);
return ProductData.UTC.create(date, Long.parseLong(milliSeconds) * 1000);
}
} catch (ParseException ignored) {
}
}
return null;
}
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");
}
/**
* 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 static String getRasterName(Variable variable) {
Attribute attribute = variable.findAttribute(Constants.ORIG_NAME_ATT_NAME);
if (attribute != null) {
return attribute.getStringValue();
} else {
return variable.getName();
}
}
public float getFloatAttribute(String key, List<Attribute> globalAttributes)
throws ProductIOException {
Attribute attribute = findAttribute(key, globalAttributes);
if (attribute == null) {
throw new ProductIOException("Global attribute '" + key + "' is missing.");
} else {
return attribute.getNumericValue(0).floatValue();
}
}
/* (non-Javadoc)
* @see loci.formats.NetCDFService#getAttributeValue(java.lang.String)
*/
public String getAttributeValue(String path) {
String groupName = getDirectory(path);
String attributeName = getName(path);
Group group = getGroup(groupName);
Attribute attribute = group.findAttribute(attributeName);
if (attribute == null) return null;
return arrayToString(attribute.getValues());
}
public String getStringAttribute(String key, List<Attribute> attributeList)
throws ProductIOException {
Attribute attribute = findAttribute(key, attributeList);
if (attribute == null || attribute.getLength() != 1) {
throw new ProductIOException("Global attribute '" + key + "' is missing.");
} else {
return attribute.getStringValue().trim();
}
}
protected void addAttributesToElement(
List<Attribute> globalAttributes, final MetadataElement element) {
for (Attribute attribute : globalAttributes) {
// if (attribute.getName().contains("EV")) {
if (attribute.getShortName().matches(".*(EV|Value|Bad|Nois|Electronics|Dead|Detector).*")) {
} else {
addAttributeToElement(element, attribute);
}
}
}
/* (non-Javadoc)
* @see loci.formats.NetCDFService#getVariableAttributes(java.lang.String)
*/
public Hashtable<String, Object> getVariableAttributes(String name) {
String groupName = getDirectory(name);
String variableName = getName(name);
Group group = getGroup(groupName);
Variable variable = group.findVariable(variableName);
List<Attribute> attributes = variable.getAttributes();
Hashtable<String, Object> toReturn = new Hashtable<String, Object>();
for (Attribute attribute : attributes) {
toReturn.put(attribute.getName(), arrayToString(attribute.getValues()));
}
return toReturn;
}
/**
* Is this the right format for this adapter
*
* @param ncd NetcdfDataset to check
* @return true if the right format
*/
public static boolean isValidFile(NetcdfDataset ncd) {
// return (buildConfig(ncd) != null);
// Check for "center" attribute w/ value of "UCAR/CDAAC".
Attribute attrib = ncd.findGlobalAttributeIgnoreCase("center");
if (attrib == null) {
return false;
}
if (!attrib.isString()) {
return false;
}
if (!attrib.getStringValue().equals("UCAR/CDAAC")) {
return false;
}
return true;
}
public static ThreddsMetadata.Variables extractVariables(
InvDatasetImpl threddsDataset, GridDataset gridDataset) {
thredds.catalog.DataFormatType fileFormat = threddsDataset.getDataFormatType();
if ((fileFormat != null)
&& (fileFormat.equals(DataFormatType.GRIB1) || fileFormat.equals(DataFormatType.GRIB2))) {
boolean isGrib1 = fileFormat.equals(DataFormatType.GRIB1);
ThreddsMetadata.Variables vars = new ThreddsMetadata.Variables(fileFormat.toString());
for (GridDatatype grid : gridDataset.getGrids()) {
ThreddsMetadata.Variable v = new ThreddsMetadata.Variable();
v.setName(grid.getName());
v.setDescription(grid.getDescription());
v.setUnits(grid.getUnitsString());
// ucar.nc2.Attribute att = grid.findAttributeIgnoreCase("GRIB_param_number");
// String paramNumber = (att != null) ? att.getNumericValue().toString() : null;
if (isGrib1) {
v.setVocabularyName(grid.findAttValueIgnoreCase("GRIB_param_name", "ERROR"));
v.setVocabularyId(grid.findAttributeIgnoreCase("GRIB_param_id"));
} else {
String paramDisc = grid.findAttValueIgnoreCase("GRIB_param_discipline", "");
String paramCategory = grid.findAttValueIgnoreCase("GRIB_param_category", "");
String paramName = grid.findAttValueIgnoreCase("GRIB_param_name", "");
v.setVocabularyName(paramDisc + " / " + paramCategory + " / " + paramName);
v.setVocabularyId(grid.findAttributeIgnoreCase("GRIB_param_id"));
}
vars.addVariable(v);
}
vars.sort();
return vars;
} else { // GRID but not GRIB
ThreddsMetadata.Variables vars = new ThreddsMetadata.Variables("CF-1.0");
for (GridDatatype grid : gridDataset.getGrids()) {
ThreddsMetadata.Variable v = new ThreddsMetadata.Variable();
vars.addVariable(v);
v.setName(grid.getName());
v.setDescription(grid.getDescription());
v.setUnits(grid.getUnitsString());
ucar.nc2.Attribute att = grid.findAttributeIgnoreCase("standard_name");
v.setVocabularyName((att != null) ? att.getStringValue() : "N/A");
}
vars.sort();
return vars;
}
}
public String getValue() {
Array value = att.getValues();
try {
return NCdumpW.printArray(value, null, null);
} catch (IOException e) {
return e.getMessage();
}
}
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");
}
/**
* Extract a list of data variables (and their canonical names if possible) from the dataset.
*
* @param threddsDataset open this dataset
* @return ThreddsMetadata.Variables, or null if unable.
* @throws IOException on read error
*/
public static ThreddsMetadata.Variables extractVariables(InvDatasetImpl threddsDataset)
throws IOException {
ThreddsDataFactory.Result result = null;
try {
result = new ThreddsDataFactory().openFeatureDataset(threddsDataset, null);
if (result.fatalError) {
System.out.println(" openDatatype errs=" + result.errLog);
return null;
}
if (result.featureType == FeatureType.GRID) {
// System.out.println(" extractVariables GRID=" + result.location);
GridDataset gridDataset = (GridDataset) result.featureDataset;
return extractVariables(threddsDataset, gridDataset);
} else if ((result.featureType == FeatureType.STATION)
|| (result.featureType == FeatureType.POINT)) {
PointObsDataset pobsDataset = (PointObsDataset) result.featureDataset;
ThreddsMetadata.Variables vars = new ThreddsMetadata.Variables("CF-1.0");
for (VariableSimpleIF vs : pobsDataset.getDataVariables()) {
ThreddsMetadata.Variable v = new ThreddsMetadata.Variable();
vars.addVariable(v);
v.setName(vs.getName());
v.setDescription(vs.getDescription());
v.setUnits(vs.getUnitsString());
ucar.nc2.Attribute att = vs.findAttributeIgnoreCase("standard_name");
v.setVocabularyName((att != null) ? att.getStringValue() : "N/A");
}
vars.sort();
return vars;
}
} finally {
try {
if ((result != null) && (result.featureDataset != null)) result.featureDataset.close();
} catch (IOException ioe) {
logger.error("Closing dataset " + result.featureDataset, ioe);
}
}
return null;
}
/**
* Recursively parses attribute and variable paths, filling <code>attributeList</code> and <code>
* variableList</code>.
*
* @param groups List of groups to recursively parse.
*/
private void parseAttributesAndVariables(List<Group> groups) {
for (Group group : groups) {
String groupName = group.getName();
List<Attribute> attributes = group.getAttributes();
for (Attribute attribute : attributes) {
String attributeName = attribute.getName();
if (!groupName.endsWith("/")) attributeName = "/" + attributeName;
attributeList.add(groupName + attributeName);
}
List<Variable> variables = group.getVariables();
for (Variable variable : variables) {
String variableName = variable.getName();
if (!groupName.endsWith("/")) variableName = "/" + variableName;
variableList.add(variableName);
}
groups = group.getGroups();
parseAttributesAndVariables(groups);
}
}
public static ThreddsMetadata.Variables extractVariables(FeatureDatasetPoint fd) {
ThreddsMetadata.Variables vars = new ThreddsMetadata.Variables("CF-1.5");
List<VariableSimpleIF> dataVars = fd.getDataVariables();
if (dataVars == null) return vars;
for (VariableSimpleIF v : dataVars) {
ThreddsMetadata.Variable tv = new ThreddsMetadata.Variable();
vars.addVariable(tv);
tv.setName(v.getName());
tv.setDescription(v.getDescription());
tv.setUnits(v.getUnitsString());
ucar.nc2.Attribute att = v.findAttributeIgnoreCase("standard_name");
tv.setVocabularyName((att != null) ? att.getStringValue() : "N/A");
}
vars.sort();
return vars;
}
private static IndexCoding readIndexCoding(Variable variable, String indexCodingName)
throws ProductIOException {
final IndexCoding indexCoding = CfIndexCodingPart.readIndexCoding(variable, indexCodingName);
if (indexCoding != null) {
final Attribute descriptionsAtt = variable.findAttributeIgnoreCase(INDEX_DESCRIPTIONS);
if (descriptionsAtt != null) {
final String[] descriptions = descriptionsAtt.getStringValue().split(DESCRIPTION_SEPARATOR);
if (indexCoding.getNumAttributes() == descriptions.length) {
for (int i = 0; i < descriptions.length; i++) {
indexCoding.getAttributeAt(i).setDescription(descriptions[i]);
}
}
}
final Attribute nameAtt = variable.findAttributeIgnoreCase(INDEX_CODING_NAME);
if (nameAtt != null) {
indexCoding.setName(nameAtt.getStringValue());
}
}
return indexCoding;
}
/** Instances which have same content are equal. */
@Override
public boolean equals(Object o) {
if (this == o) return true;
if ((o == null) || !(o instanceof Attribute)) return false;
final Attribute att = (Attribute) o;
if (!name.equals(att.name)) return false;
if (nelems != att.nelems) return false;
if (!dataType.equals(att.dataType)) return false;
if (svalue != null) return svalue.equals(att.getStringValue());
if (values != null) {
for (int i = 0; i < getLength(); i++) {
int r1 = isString() ? getStringValue(i).hashCode() : getNumericValue(i).hashCode();
int r2 =
att.isString() ? att.getStringValue(i).hashCode() : att.getNumericValue(i).hashCode();
if (r1 != r2) return false;
}
}
return true;
}
MetadataAttribute attributeToMetadata(Attribute attribute) {
final int productDataType = getProductDataType(attribute.getDataType(), false, false);
if (productDataType != -1) {
ProductData productData;
if (attribute.isString()) {
productData = ProductData.createInstance(attribute.getStringValue());
} else if (attribute.isArray()) {
productData = ProductData.createInstance(productDataType, attribute.getLength());
productData.setElems(attribute.getValues().getStorage());
} else {
productData = ProductData.createInstance(productDataType, 1);
productData.setElems(attribute.getValues().getStorage());
}
return new MetadataAttribute(attribute.getShortName(), productData, true);
}
return null;
}
private void fixAttributes(Group g) {
for (Variable v : g.getVariables()) {
for (Attribute a : v.getAttributes()) {
if (a.getShortName().equalsIgnoreCase("UNIT") || a.getShortName().equalsIgnoreCase("UNITS"))
a.setShortName(CDM.UNITS);
if (a.getShortName().equalsIgnoreCase("SCALE_FACTOR")) a.setShortName(CDM.SCALE_FACTOR);
if (a.getShortName().equalsIgnoreCase("OFFSET")) a.setShortName(CDM.ADD_OFFSET);
}
}
for (Group ng : g.getGroups()) {
fixAttributes(ng);
}
}
private double[] getValueAsDouble(Attribute att) {
int n = att.getLength();
double[] value = new double[n];
if (debugMissing) System.out.printf("missing_data: ");
for (int i = 0; i < n; i++) {
if (isUnsigned && att.getDataType() == DataType.BYTE)
value[i] = convertScaleOffsetMissing(att.getNumericValue(i).byteValue());
else if (isUnsigned && att.getDataType() == DataType.SHORT)
value[i] = convertScaleOffsetMissing(att.getNumericValue(i).shortValue());
else if (isUnsigned && att.getDataType() == DataType.INT)
value[i] = convertScaleOffsetMissing(att.getNumericValue(i).intValue());
else value[i] = scale * att.getNumericValue(i).doubleValue() + offset;
if (debugMissing) System.out.print(" " + value[i]);
}
if (debugMissing) System.out.println();
return value;
}
/**
* Returns the phenomenon that the given variable represents.
*
* <p>This name will be, in order of preference:
*
* <p>The standard name
*
* <p>The long name
*
* <p>The variable name
*/
private static String getVariableName(Variable var) {
Attribute stdNameAtt = var.findAttributeIgnoreCase("standard_name");
if (stdNameAtt == null || stdNameAtt.getStringValue().trim().equals("")) {
Attribute longNameAtt = var.findAttributeIgnoreCase("long_name");
if (longNameAtt == null || longNameAtt.getStringValue().trim().equals("")) {
return var.getFullName();
} else {
return longNameAtt.getStringValue();
}
} else {
return stdNameAtt.getStringValue();
}
}
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");
}
protected Band addNewBand(Product product, Variable variable) {
final int sceneRasterWidth = product.getSceneRasterWidth();
final int sceneRasterHeight = product.getSceneRasterHeight();
Band band = null;
int variableRank = variable.getRank();
if (variableRank == 2) {
final int[] dimensions = variable.getShape();
final int height = dimensions[0] - leadLineSkip - tailLineSkip;
final int width = dimensions[1];
if (height == sceneRasterHeight && width == sceneRasterWidth) {
final String name = variable.getShortName();
final int dataType = getProductDataType(variable);
band = new Band(name, dataType, width, height);
final String validExpression = bandInfoMap.get(name);
if (validExpression != null && !validExpression.equals("")) {
band.setValidPixelExpression(validExpression);
}
product.addBand(band);
try {
band.setNoDataValue(
(double) variable.findAttribute("bad_value_scaled").getNumericValue().floatValue());
band.setNoDataValueUsed(true);
} catch (Exception ignored) {
}
final List<Attribute> list = variable.getAttributes();
for (Attribute hdfAttribute : list) {
final String attribName = hdfAttribute.getShortName();
if ("units".equals(attribName)) {
band.setUnit(hdfAttribute.getStringValue());
} else if ("long_name".equals(attribName)) {
band.setDescription(hdfAttribute.getStringValue());
} else if ("slope".equals(attribName)) {
band.setScalingFactor(hdfAttribute.getNumericValue(0).doubleValue());
} else if ("intercept".equals(attribName)) {
band.setScalingOffset(hdfAttribute.getNumericValue(0).doubleValue());
}
}
}
}
return band;
}
public void testCoordVar(NetcdfFile ncfile) {
Variable lat = ncfile.findVariable("lat");
assert null != lat;
assert lat.getShortName().equals("lat");
assert lat.getRank() == 1;
assert lat.getSize() == 3;
assert lat.getShape()[0] == 3;
assert lat.getDataType() == DataType.FLOAT;
assert !lat.isUnlimited();
assert lat.getDimension(0).equals(ncfile.findDimension("lat"));
Attribute att = lat.findAttribute("units");
assert null != att;
assert !att.isArray();
assert att.isString();
assert att.getDataType() == DataType.STRING;
assert att.getStringValue().equals("degrees_north");
assert att.getNumericValue() == null;
assert att.getNumericValue(3) == null;
try {
Array data = lat.read();
assert data.getRank() == 1;
assert data.getSize() == 3;
assert data.getShape()[0] == 3;
assert data.getElementType() == float.class;
IndexIterator dataI = data.getIndexIterator();
assert TestUtils.close(dataI.getDoubleNext(), 41.0);
assert TestUtils.close(dataI.getDoubleNext(), 40.0);
assert TestUtils.close(dataI.getDoubleNext(), 39.0);
} catch (IOException io) {
}
}
public static boolean isValidFile(NetcdfFile ds) {
Attribute cdmDtAtt = ds.findGlobalAttributeIgnoreCase("cdm_data_type");
if (cdmDtAtt == null) cdmDtAtt = ds.findGlobalAttributeIgnoreCase("cdm_datatype");
if (cdmDtAtt == null) return false;
if (!cdmDtAtt.isString()) return false;
String cdmDtString = cdmDtAtt.getStringValue();
if (cdmDtString == null) return false;
if (!cdmDtString.equalsIgnoreCase(FeatureType.TRAJECTORY.toString())) return false;
Attribute conventionsAtt = ds.findGlobalAttributeIgnoreCase("Conventions");
if (conventionsAtt == null) return (false);
if (!conventionsAtt.isString()) return (false);
String convString = conventionsAtt.getStringValue();
StringTokenizer stoke = new StringTokenizer(convString, ",");
while (stoke.hasMoreTokens()) {
String toke = stoke.nextToken().trim();
if (toke.equalsIgnoreCase("Unidata Observation Dataset v1.0")) return true;
}
return false;
}
public void readByte() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t3")));
assert (v.getDataType() == DataType.BYTE);
assert (null != (v = dsRead.findVariable("t3")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.BYTE);
Attribute att = vs.findAttribute("_FillValue");
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
System.out.println("_FillValue = " + att.getNumericValue().byteValue());
assert (((byte) 255) == att.getNumericValue().byteValue());
assert (DataType.BYTE == att.getDataType());
assert (vs.hasMissing());
assert (vs.hasFillValue());
assert (vs.isMissing((double) ((byte) 255)));
assert (vs.isFillValue((double) ((byte) 255)));
Array A = vs.read();
assert (A.getElementType() == byte.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.getFloat(ima.set(i, j)) == (i * 10 + j));
}
}
System.out.println("**************TestStandardVar ReadByte");
}
/**
* 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;
}
// 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());
}
}
}