/**
* 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);
}
}
}
private int addAttributes(opendap.dap.AttributeTable table, Variable v, Iterator iter) {
int count = 0;
// add attribute table for this variable
while (iter.hasNext()) {
Attribute att = (Attribute) iter.next();
int dods_type = DODSNetcdfFile.convertToDODSType(att.getDataType(), false);
try {
String attName = NcDDS.escapeName(att.getName());
if (att.isString()) {
/* FIX String value = escapeAttributeStringValues(att.getStringValue());
table.appendAttribute(attName, dods_type, "\""+value+"\"");
*/
table.appendAttribute(attName, dods_type, att.getStringValue());
} else {
// cant send signed bytes
if (att.getDataType() == DataType.BYTE) {
boolean signed = false;
for (int i = 0; i < att.getLength(); i++) {
if (att.getNumericValue(i).byteValue() < 0) signed = true;
}
if (signed) // promote to signed short
dods_type = opendap.dap.Attribute.INT16;
}
for (int i = 0; i < att.getLength(); i++)
table.appendAttribute(attName, dods_type, att.getNumericValue(i).toString());
}
count++;
} catch (Exception e) {
log.error(
"Error appending attribute " + att.getName() + " = " + att.getStringValue() + "\n" + e);
}
} // loop over variable attributes
// kludgy thing to map char arrays to DODS Strings
if ((v != null) && (v.getDataType().getPrimitiveClassType() == char.class)) {
int rank = v.getRank();
int strlen = (rank == 0) ? 0 : v.getShape(rank - 1);
Dimension dim = (rank == 0) ? null : v.getDimension(rank - 1);
try {
opendap.dap.AttributeTable dodsTable = table.appendContainer("DODS");
dodsTable.appendAttribute("strlen", opendap.dap.Attribute.INT32, Integer.toString(strlen));
if ((dim != null) && dim.isShared())
dodsTable.appendAttribute("dimName", opendap.dap.Attribute.STRING, dim.getName());
count++;
} catch (Exception e) {
log.error("Error appending attribute strlen\n" + e);
}
}
return count;
}
/* (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;
}
/**
* 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 void read5kmlatlong() {
NetcdfFile ncfile = null;
try {
ncfile = NetcdfFile.open("/home/kerryn/Desktop/Temp/treecover_30pts_lat.nc");
String xrange = "Band1";
Variable xrangeVar = ncfile.findVariable(xrange);
Array xrangeData = xrangeVar.read();
NCdump.printArray(xrangeData, xrange, System.out, null);
String yrange = "GDAL_Geographics";
Variable yrangeVar = ncfile.findVariable(yrange);
Array yrangeData = yrangeVar.read();
NCdump.printArray(yrangeData, yrange, System.out, null);
List<ucar.nc2.Attribute> yattr = yrangeVar.getAttributes();
for (ucar.nc2.Attribute attr : yattr) {
String attrName = attr.getName();
Array attrValue = attr.getValues();
attrValue.getElementType();
double value = attrValue.getDouble(0);
System.out.println(attrName + "=" + value);
}
// [Northernmost_Northing = -37.51903101958847, Southernmost_Northing = -38.49309598467985,
// Easternmost_Easting = 145.56979076552813, Westernmost_Easting = 144.4949604592204,
// spatial_ref = "GEOGCS[\"WGS 84\",DATUM[\"WGS_1984\",SPHEROID[\"WGS
// 84\",6378137,298.257223563,AUTHORITY[\"EPSG\",\"7030\"]],AUTHORITY[\"EPSG\",\"6326\"]],PRIMEM[\"Greenwich\",0],UNIT[\"degree\",0.0174532925199433],AUTHORITY[\"EPSG\",\"4326\"]]", GeoTransform = "144.495 0.0335884 0 -37.519 0 -0.0335884 ", grid_mapping_name = "Geographics Coordinate System", long_name = "Grid_latitude"]
// String zrange = "z_range";
// Variable zrangeVar = ncfile.findVariable(zrange);
// Array zrangeData = zrangeVar.read();
// NCdump.printArray(zrangeData, zrange, System.out, null);
//
// String spacing = "spacing";
// Variable spacingVar = ncfile.findVariable(spacing);
// Array spacingData = spacingVar.read();
// NCdump.printArray(spacingData, spacing, System.out, null);
//
// String dimension = "dimension";
// Variable dimensionVar = ncfile.findVariable(dimension);
// Array dimensionData = dimensionVar.read();
// NCdump.printArray(dimensionData, dimension, System.out, null);
//
// String z = "z";
// Variable zVar = ncfile.findVariable(z);
// Array zData = zVar.read();
// NCdump.printArray(zData, z, System.out, null);
// int count = 0;
// //for (int x=0;x<94;x++)
// for (int x=0;x<30;x++) // 106.92 km
// {
// //for (int y=0;y<108;y++)
// for (int y=0;y<30;y++) // 93.06 km
// {
// double item = zData.getDouble(count);
// long percent = Math.round(item * 100);
// if (percent < 0)
// {
// percent = 0;
// }
// String percentStr = new Integer((int)percent).toString();
// if (percentStr.length() == 1)
// {
// percentStr = "0" + percentStr;
// }
// if (percentStr.equals("00"))
// {
// percentStr = " ";
// }
//
// //System.out.println(x + " " + y + " " + item);
// System.out.print( " " + percentStr);
// count ++;
// }
// System.out.println();
// }
} catch (IOException ioe) {
ioe.printStackTrace();
}
}
Write2ncRect(NetcdfFile bufr, String fileOutName, boolean fill)
throws IOException, InvalidRangeException {
NetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(fileOutName, fill);
if (debug) {
System.out.println("FileWriter write " + bufr.getLocation() + " to " + fileOutName);
}
// global attributes
List<Attribute> glist = bufr.getGlobalAttributes();
for (Attribute att : glist) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
Attribute useAtt;
if (att.isArray()) useAtt = ncfile.addGlobalAttribute(useName, att.getValues());
else if (att.isString()) useAtt = ncfile.addGlobalAttribute(useName, att.getStringValue());
else useAtt = ncfile.addGlobalAttribute(useName, att.getNumericValue());
if (debug) System.out.println("add gatt= " + useAtt);
}
// global dimensions
Dimension recordDim = null;
Map<String, Dimension> dimHash = new HashMap<String, Dimension>();
for (Dimension oldD : bufr.getDimensions()) {
String useName = N3iosp.makeValidNetcdfObjectName(oldD.getName());
boolean isRecord = useName.equals("record");
Dimension newD = ncfile.addDimension(useName, oldD.getLength(), true, false, false);
dimHash.put(newD.getName(), newD);
if (isRecord) recordDim = newD;
if (debug) System.out.println("add dim= " + newD);
}
// Variables
Structure recordStruct = (Structure) bufr.findVariable(BufrIosp.obsRecord);
for (Variable oldVar : recordStruct.getVariables()) {
if (oldVar.getDataType() == DataType.STRUCTURE) continue;
String varName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());
DataType newType = oldVar.getDataType();
List<Dimension> newDims = new ArrayList<Dimension>();
newDims.add(recordDim);
for (Dimension dim : oldVar.getDimensions()) {
newDims.add(ncfile.addDimension(oldVar.getShortName() + "_strlen", dim.getLength()));
}
Variable newVar = ncfile.addVariable(varName, newType, newDims);
if (debug) System.out.println("add var= " + newVar);
// attributes
List<Attribute> attList = oldVar.getAttributes();
for (Attribute att : attList) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
else if (att.isString())
ncfile.addVariableAttribute(varName, useName, att.getStringValue());
else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
}
}
// int max_seq = countSeq(recordStruct);
// Dimension seqD = ncfile.addDimension("level", max_seq);
for (Variable v : recordStruct.getVariables()) {
if (v.getDataType() != DataType.STRUCTURE) continue;
String structName = N3iosp.makeValidNetcdfObjectName(v.getShortName());
int shape[] = v.getShape();
Dimension structDim = ncfile.addDimension(structName, shape[0]);
Structure struct = (Structure) v;
for (Variable seqVar : struct.getVariables()) {
String varName = N3iosp.makeValidNetcdfObjectName(seqVar.getShortName() + "-" + structName);
DataType newType = seqVar.getDataType();
List<Dimension> newDims = new ArrayList<Dimension>();
newDims.add(recordDim);
newDims.add(structDim);
for (Dimension dim : seqVar.getDimensions()) {
newDims.add(ncfile.addDimension(seqVar.getShortName() + "_strlen", dim.getLength()));
}
Variable newVar = ncfile.addVariable(varName, newType, newDims);
if (debug) System.out.println("add var= " + newVar);
// attributes
List<Attribute> attList = seqVar.getAttributes();
for (Attribute att : attList) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
else if (att.isString())
ncfile.addVariableAttribute(varName, useName, att.getStringValue());
else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
}
}
}
// create the file
ncfile.create();
if (debug) System.out.println("File Out= " + ncfile.toString());
// boolean ok = (Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
double total = copyVarData(ncfile, recordStruct);
ncfile.flush();
System.out.println("FileWriter done total bytes = " + total);
ncfile.close();
}
public String getName() {
return att.getName();
}
public Attribute findAttributeIgnoreCase(String name) {
for (Attribute att : getAttributes()) if (att.getName().equalsIgnoreCase(name)) return att;
return null;
}