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The NetCDF-Java Library is a Java interface to NetCDF files,
as well as to many other types of scientific data formats.
/*
* Copyright 1998-2009 University Corporation for Atmospheric Research/Unidata
*
* Portions of this software were developed by the Unidata Program at the
* University Corporation for Atmospheric Research.
*
* Access and use of this software shall impose the following obligations
* and understandings on the user. The user is granted the right, without
* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
* documentation for any purpose whatsoever, provided that this entire
* notice appears in all copies of the software, derivative works and
* supporting documentation. Further, UCAR requests that the user credit
* UCAR/Unidata in any publications that result from the use of this
* software or in any product that includes this software. The names UCAR
* and/or Unidata, however, may not be used in any advertising or publicity
* to endorse or promote any products or commercial entity unless specific
* written permission is obtained from UCAR/Unidata. The user also
* understands that UCAR/Unidata is not obligated to provide the user with
* any support, consulting, training or assistance of any kind with regard
* to the use, operation and performance of this software nor to provide
* the user with any updates, revisions, new versions or "bug fixes."
*
* THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
* INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
* FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
* NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
* WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
*/
package ucar.nc2.iosp.bufr;
import java.util.List;
import java.util.ArrayList;
import java.util.Iterator;
/**
* Convert a list of data descriptors to a tree of DataDescriptor objects.
* Expand Table D, process table C operators.
*
* @author caron
* @since Jul 14, 2008
*/
public class DataDescriptorTreeConstructor {
static private org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(DataDescriptorTreeConstructor.class);
//////////////////////////////////////////////////////////////////////////////////
private DataDescriptor root;
public DataDescriptor factory(TableLookup lookup, BufrDataDescriptionSection dds) {
root = new DataDescriptor();
// convert ids to DataDescriptor
List keys = decode(dds.getDataDescriptors(), lookup);
// unwind replications inside compound (!!??)
keys = preflatten(keys);
// make replicated keys into subKeys, constituting a tree
List tree = replicate(keys);
// flatten the compounds
root.subKeys = new ArrayList();
flatten(root.subKeys, tree);
// process the operators
operate( root.subKeys);
// count the size
root.total_nbits = root.countBits();
return root;
}
// convert ids to DataDescriptors, expand table D
private List decode(List keyDesc, TableLookup lookup) {
if (keyDesc == null) return null;
List keys = new ArrayList();
for (short id : keyDesc) {
DataDescriptor dd = new DataDescriptor(id, lookup);
keys.add( dd);
if (dd.f == 3) {
List subDesc = lookup.getDescriptorsTableD(dd.fxy);
if (subDesc == null)
dd.bad = true;
else
dd.subKeys = decode(subDesc, lookup);
}
}
return keys;
}
// look for replication, move replicated items into subtree
private List replicate(List keys) {
List tree = new ArrayList();
Iterator dkIter = keys.iterator();
while (dkIter.hasNext()) {
DataDescriptor dk = dkIter.next();
if (dk.f == 1) {
dk.subKeys = new ArrayList();
dk.replication = dk.y; // replication count
if (dk.replication == 0) { // delayed repliction
root.isVarLength = true; // variable sized data == defered replication == sequence data
// the next one is the replication count size
DataDescriptor replication = dkIter.next();
if (replication.y == 0)
dk.replicationCountSize = 1; // ??
else if (replication.y == 1)
dk.replicationCountSize = 8;
else if (replication.y == 2)
dk.replicationCountSize = 16;
else if (replication.y == 11)
dk.repetitionCountSize = 8;
else if (replication.y == 12)
dk.repetitionCountSize = 16;
else
log.error("Unknown replication type= "+replication);
}
// transfer to the subKey list
for (int j = 0; j < dk.x && dkIter.hasNext(); j++) {
dk.subKeys.add( dkIter.next());
}
// recurse
dk.subKeys = replicate(dk.subKeys);
} else if ((dk.f == 3) && (dk.subKeys != null)) {
dk.subKeys = replicate( dk.subKeys); // do at all levels
}
tree.add(dk);
}
return tree;
}
/* Use case:
3-62-1 : HEADR
0-4-194 : FORECAST TIME
0-1-205 : STATION NUMBER -- 6 DIGITS
0-1-198 : REPORT IDENTIFIER
0-5-2 : Latitude (coarse accuracy)
0-6-2 : Longitude (coarse accuracy)
0-10-194: GRID-POINT ELEVATION
0-2-196 : CLASS OF PROFILE OUTPUT
3-60-2 :
1-01-000: replication
0-31-1 : Delayed descriptor replication factor
3-62-2 : PROFILE
0-10-4 : Pressure
0-12-1 : Temperature/dry-bulb temperature
0-11-3 : u-component
where the 3-62-2 should be replicated.
This is from NCEP bufrtab.ETACLS1. Not sure if others use this idiom.
*/
// preflatten replications inside a top level compound (!)
private List preflatten(List tree) {
List result = new ArrayList(tree.size());
for (DataDescriptor key : tree) {
boolean preflatten = false;
if ((key.f == 3) && (key.subKeys != null)) {
List subkeys = key.subKeys;
for (int i=0; i have) {
preflatten = true;
// ScannerSystem.out.printf("preflatten replication %d > %d%n", need, have);
}
}
}
}
if (preflatten)
result.addAll(key.subKeys);
else
result.add(key);
}
return result;
}
// flatten the compounds (type 3); but dont remove bad ones
private void flatten(List result, List tree) {
for (DataDescriptor key : tree) {
if (key.bad) {
root.isBad = true;
result.add(key); // add it anyway so we can see it in debug
continue;
}
if ((key.f == 3) && (key.subKeys != null)) {
flatten(result, key.subKeys);
} else if (key.f == 1) { // flatten the subtrees
List subTree = new ArrayList();
flatten(subTree, key.subKeys);
key.subKeys = subTree;
result.add(key);
} else {
result.add(key);
}
}
}
private DataDescriptor changeWidth = null; // 02 01 Y
private DataDescriptor changeScale = null; // 02 02 Y
private DataDescriptor changeRefval = null; // 02 03 Y
private DataPresentIndicator dpi = null; // assume theres only one in effect at a time
private void operate(List tree) {
if (tree == null) return;
boolean hasAssFields = false;
// boolean hasDpiFields = false;
DataDescriptor.AssociatedField assField = null; // 02 04 Y
Iterator iter = tree.iterator();
while (iter.hasNext()) {
DataDescriptor dd = iter.next();
if (dd.f == 2) {
if (dd.x == 1) {
changeWidth = (dd.y == 0) ? null : dd;
iter.remove();
} else if (dd.x == 2) {
changeScale = (dd.y == 0) ? null : dd;
iter.remove();
// throw new UnsupportedOperationException("2-2-Y (change scale)");
} else if (dd.x == 3) {
changeRefval = (dd.y == 255) ? null : dd;
iter.remove();
// throw new UnsupportedOperationException("2-3-Y (change reference values)"); // untested - no examples
} else if (dd.x == 4) {
assField = (dd.y == 0) ? null : new DataDescriptor.AssociatedField(dd.y);
iter.remove();
hasAssFields = true;
} else if (dd.x == 5) { // char data - this allows arbitrary string to be inserted
dd.type = 1; // String
dd.bitWidth = dd.y * 8;
dd.name = "Note";
} else if (dd.x == 6) {
// see L3-82 (3.1.6.5)
// "Y bits of data are described by the immediately following descriptor". could they speak English?
iter.remove();
if ((dd.y != 0) && iter.hasNext()) { // fnmoc using 2-6-0 as cancel (apparently)
DataDescriptor next = iter.next();
next.bitWidth = dd.y;
}
} else if (dd.x == 36) {
if (iter.hasNext()) {
DataDescriptor dpi_dd = iter.next(); // this should be a replicated data present field
dpi = new DataPresentIndicator(tree, dpi_dd);
dd.dpi = dpi;
dpi_dd.dpi = dpi;
}
} else if ((dd.x == 37) && (dd.y == 255)) { // cancel dpi
dpi = null;
} else if ((dd.x == 24) && (dd.y == 255)) {
dd.dpi = dpi;
}
} else if (dd.subKeys != null) {
operate(dd.subKeys);
} else if (dd.f == 0) {
if (dd.type != 3) { // numeric or string or enum, not compound
if (changeWidth != null)
dd.bitWidth += changeWidth.y-128;
if (changeScale != null)
dd.scale += changeScale.y-128;
if (changeRefval != null)
dd.refVal += changeRefval.y-128; // LOOK wrong
}
if ((dd.f == 0) && (assField != null)) {
assField.nfields++;
dd.assField = assField;
assField.dataFldName = dd.name;
}
}
}
if (hasAssFields) addAssFields(tree);
// if (hasDpiFields) addDpiFields(tree);
}
private void addAssFields(List tree) {
if (tree == null) return;
int index = 0;
while (index < tree.size()) {
DataDescriptor dd = tree.get(index);
if (dd.assField != null) {
DataDescriptor.AssociatedField assField = dd.assField;
if ((dd.f == 0) && (dd.x == 31) && (dd.y == 21)) { // the meaning field
dd.name = assField.dataFldName+"_associated_field_significance";
dd.assField = null;
} else {
DataDescriptor assDD = dd.makeAssociatedField(assField.nbits);
tree.add(index, assDD);
index++;
}
}
index++;
}
}
/* private void addDpiFields(List tree) {
if (tree == null) return;
Iterator iter = tree.iterator();
while (iter.hasNext()) {
DataDescriptor dd = iter.next();
if (dd.dpi != null) { // make this into a compound type
dd.name = "firstOrderStatistics";
dd.type = 3;
dd.replication = 1;
dd.subKeys = new ArrayList();
while (iter.hasNext()) {
DataDescriptor dd2 = iter.next();
iter.remove();
dd.subKeys.add(dd2);
if (dd2 == dd.dpi.stop) {
dd2.subKeys = new ArrayList();
dd2.subKeys.add(dd.dpi.statField);
dd.dpi.statField.dpi = dd.dpi; // also need it here
//dd.dpi = null;
// DataDescriptor extra = dd.dpi.linear.get(184); // temp kludge
// for (int i=0; i< dd2.replication; i++)
// dd.subKeys.add(extra);
break;
}
}
System.out.printf("addDpiFields for %s %n", dd);
}
}
}
/* private DataPresentIndicator processDataPresentIndicator(List tree, int hellRealmIndex) {
DataPresentIndicator dpi = new DataPresentIndicator();
Iterator iter = tree.iterator();
while (iter.hasNext()) {
DataDescriptor dd = iter.next();
if ((dd.f == 2) && (dd.x == hellRealmIndex) && (dd.y == 0)) {
dpi.start = dd;
while (iter.hasNext()) {
dd = iter.next();
if (dd.f == 1) {
for (DataDescriptor dd2 : dd.getSubKeys()){
if ((dd2.f == 2) && (dd2.x == hellRealmIndex) && (dd2.y == 255)) {
dpi.stop = dd;
dpi.statField = dd2;
} else if ((dd2.f == 0) && (dd2.x == 31) && (dd2.y == 31)) {
dpi.dataPresent = dd;
}
}
}
}
}
}
dpi.linear = new ArrayList();
linearize(tree, dpi);
// LOOK System.out.printf("DPI: data count = %d linear count = %d %n", dpi.dataPresent.replication, dpi.linear.size());
return dpi;
} */
static class DataPresentIndicator {
DataDescriptor dataPresent; // replication of bit present field
List linear = new ArrayList(); // linear list of dds
DataPresentIndicator(List tree, DataDescriptor dpi_dd) {
this.dataPresent = dpi_dd;
linear = new ArrayList();
linearize(tree);
}
int getNfields() { return dataPresent.replication; }
private void linearize(List tree) {
for (DataDescriptor dd : tree) {
if (dd.f == 0) {
linear.add(dd);
} else if (dd.f == 1) {
for (int i = 0; i < dd.replication; i++) // whut about defered replication hahahahahah
linearize(dd.getSubKeys());
}
}
}
}
}