private VertCoord readVertCoord(GribCollectionProto.Coord pc) throws IOException {
boolean isLayer = (pc.getBoundCount() > 0);
List<VertCoord.Level> coords = new ArrayList<VertCoord.Level>(pc.getValuesCount());
for (int i = 0; i < pc.getValuesCount(); i++)
coords.add(new VertCoord.Level(pc.getValues(i), isLayer ? pc.getBound(i) : 0));
return new VertCoord(pc.getCode(), coords, isLayer);
}
private boolean createPartitionedIndex(Formatter f) throws IOException {
long start = System.currentTimeMillis();
// create partitions based on TimePartitionCollections object
for (CollectionManager dcm : tpc.makePartitions()) {
tp.addPartition(dcm);
}
List<TimePartition.Partition> bad = new ArrayList<TimePartition.Partition>();
for (TimePartition.Partition dc : tp.getPartitions()) {
try {
dc.makeGribCollection(f); // ensure collection has been read successfully
if (trace) f.format(" Open partition %s%n", dc.getDcm().getCollectionName());
} catch (Throwable t) {
logger.error(" Failed to open partition " + dc.getName(), t);
f.format(" FAIL on partition %s (remove) %n", dc.getDcm().getCollectionName());
bad.add(dc); // LOOK may be a file leak ?
}
}
// remove ones that failed
for (TimePartition.Partition p : bad) tp.removePartition(p);
// choose the "canonical" partition, aka prototype
int n = tp.getPartitions().size();
if (n == 0) {
logger.error(" Nothing in this partition = " + tp.getName());
f.format(" FAIL Partition empty collection = %s%n", tp.getName());
return false;
}
int idx = tpc.getProtoIndex(n);
TimePartition.Partition canon = tp.getPartitions().get(idx);
f.format(" Using canonical partition %s%n", canon.getDcm().getCollectionName());
// check consistency across vert and ens coords
if (!checkPartitions(canon, f)) {
logger.error(
" Partition check failed, index not written on {} message = {}",
tp.getName(),
f.toString());
f.format(" FAIL Partition check collection = %s%n", tp.getName());
return false;
}
// make the time coordinates, place results into canon
createPartitionedTimeCoordinates(canon, f);
// ready to write the index file
writeIndex(canon, f);
// close open gc's
tp.cleanup();
long took = System.currentTimeMillis() - start;
f.format(" CreatePartitionedIndex took %d msecs%n", took);
return true;
}
@Override
protected void readTimePartitions(
GribCollection.GroupHcs group, GribCollectionProto.Group proto) {
List<TimeCoord> list = new ArrayList<TimeCoord>(proto.getTimeCoordUnionsCount());
for (int i = 0; i < proto.getTimeCoordUnionsCount(); i++) {
GribCollectionProto.TimeCoordUnion tpu = proto.getTimeCoordUnions(i);
list.add(readTimePartition(tpu, i));
}
group.timeCoords = list;
}
private GribCollectionProto.Group writeGroupProto(Group g) throws IOException {
GribCollectionProto.Group.Builder b = GribCollectionProto.Group.newBuilder();
b.setGds(ByteString.copyFrom(g.gdss.getRawBytes()));
b.setGdsHash(g.gdsHash);
for (Grib2Rectilyser.VariableBag vb : g.rect.getGribvars())
b.addVariables(writeVariableProto(g.rect, vb));
List<TimeCoord> timeCoords = g.rect.getTimeCoords();
for (int i = 0; i < timeCoords.size(); i++)
b.addTimeCoords(writeCoordProto(timeCoords.get(i), i));
List<VertCoord> vertCoords = g.rect.getVertCoords();
for (int i = 0; i < vertCoords.size(); i++)
b.addVertCoords(writeCoordProto(vertCoords.get(i), i));
List<EnsCoord> ensCoords = g.rect.getEnsCoords();
for (int i = 0; i < ensCoords.size(); i++) b.addEnsCoords(writeCoordProto(ensCoords.get(i), i));
for (Integer aFileSet : g.fileSet) b.addFileno(aFileSet);
if (g.nameOverride != null) b.setName(g.nameOverride);
return b.build();
}
private TimeCoord readTimeCoord(GribCollectionProto.Coord pc) throws IOException {
if (pc.getBoundCount() > 0) { // its an interval
List<TimeCoord.Tinv> coords = new ArrayList<TimeCoord.Tinv>(pc.getValuesCount());
for (int i = 0; i < pc.getValuesCount(); i++)
coords.add(new TimeCoord.Tinv((int) pc.getValues(i), (int) pc.getBound(i)));
return new TimeCoord(pc.getCode(), pc.getUnit(), coords);
} else {
List<Integer> coords = new ArrayList<Integer>(pc.getValuesCount());
for (float value : pc.getValuesList()) coords.add((int) value);
return new TimeCoord(pc.getCode(), pc.getUnit(), coords);
}
}
protected TimeCoord readTimePartition(GribCollectionProto.TimeCoordUnion pc, int timeIndex) {
int[] partition = new int[pc.getPartitionCount()];
int[] index = new int[pc.getPartitionCount()]; // better be the same
for (int i = 0; i < pc.getPartitionCount(); i++) {
partition[i] = pc.getPartition(i);
index[i] = pc.getIndex(i);
}
if (pc.getBoundCount() > 0) { // its an interval
List<TimeCoord.Tinv> coords = new ArrayList<TimeCoord.Tinv>(pc.getValuesCount());
for (int i = 0; i < pc.getValuesCount(); i++)
coords.add(new TimeCoord.Tinv((int) pc.getValues(i), (int) pc.getBound(i)));
TimeCoordUnion tc = new TimeCoordUnion(pc.getCode(), pc.getUnit(), coords, partition, index);
return tc.setIndex(timeIndex);
} else {
List<Integer> coords = new ArrayList<Integer>(pc.getValuesCount());
for (float value : pc.getValuesList()) coords.add((int) value);
TimeCoordUnion tc = new TimeCoordUnion(pc.getCode(), pc.getUnit(), coords, partition, index);
return tc.setIndex(timeIndex);
}
}
private GribCollectionProto.Group writeGroupProto(GribCollection.GroupHcs g) throws IOException {
GribCollectionProto.Group.Builder b = GribCollectionProto.Group.newBuilder();
b.setGds(ByteString.copyFrom(g.rawGds));
b.setGdsHash(g.gdsHash);
for (GribCollection.VariableIndex vb : g.varIndex)
b.addVariables(writeVariableProto((TimePartition.VariableIndexPartitioned) vb));
for (int i = 0; i < g.timeCoordPartitions.size(); i++)
b.addTimeCoordUnions(writeTimeCoordUnionProto(g.timeCoordPartitions.get(i), i));
List<VertCoord> vertCoords = g.vertCoords;
for (int i = 0; i < vertCoords.size(); i++)
b.addVertCoords(writeCoordProto(vertCoords.get(i), i));
List<EnsCoord> ensCoords = g.ensCoords;
for (int i = 0; i < ensCoords.size(); i++) b.addEnsCoords(writeCoordProto(ensCoords.get(i), i));
return b.build();
}
private boolean createPartitionedTimeCoordinates(TimePartition.Partition canon, Formatter f)
throws IOException {
List<TimePartition.Partition> partitions = tp.getPartitions();
boolean ok = true;
// for each group in canonical Partition
for (GribCollection.GroupHcs firstGroup : canon.makeGribCollection(f).getGroups()) {
String gname = firstGroup.getId();
if (trace) f.format(" Check Group %s%n", gname);
// get list of corresponding groups from all the time partition, so we dont have to keep
// looking it up
List<PartGroup> pgList = new ArrayList<PartGroup>(partitions.size());
for (TimePartition.Partition dc : partitions) {
GribCollection.GroupHcs gg = dc.makeGribCollection(f).findGroupById(gname);
if (gg == null) logger.error(" Cant find group {} in partition {}", gname, dc.getName());
else pgList.add(new PartGroup(gg, dc));
}
// unique time coordinate unions
List<TimeCoordUnion> unionList = new ArrayList<TimeCoordUnion>();
// for each variable in canonical Partition
for (GribCollection.VariableIndex viCanon : firstGroup.varIndex) {
if (trace) f.format(" Check variable %s%n", viCanon);
TimeCoord tcCanon = viCanon.getTimeCoord();
List<TimeCoord> tcPartitions = new ArrayList<TimeCoord>(pgList.size());
// for each partition, get the time index
for (PartGroup pg : pgList) {
// get corresponding variable
GribCollection.VariableIndex vi2 = pg.group.findVariableByHash(viCanon.cdmHash);
if (vi2 == null) { // apparently not in the file
f.format(
" WARN Cant find variable %s in partition %s / %s%n",
viCanon, pg.tpp.getName(), pg.group.getId());
tcPartitions.add(null);
} else {
if (vi2.timeIdx < 0 || vi2.timeIdx >= pg.group.timeCoords.size()) {
logger.error(" timeIdx out of range var= {} on partition {}", vi2, pg.tpp.getName());
tcPartitions.add(null);
} else {
TimeCoord tc2 = vi2.getTimeCoord();
if (tc2.isInterval() != tcCanon.isInterval()) {
logger.error(
" timeIdx wrong interval type var= {} on partition {}", vi2, pg.tpp.getName());
tcPartitions.add(null);
} else {
tcPartitions.add(tc2);
}
}
}
}
// union of time coordinates
TimeCoordUnion union = new TimeCoordUnion(tcCanon.getCode(), tcPartitions, tcCanon);
// store result in the first group
viCanon.partTimeCoordIdx =
TimeCoordUnion.findUnique(unionList, union); // this merges identical TimeCoordUnion
}
/* turn TimeIndex into TimeCoord
for (int tidx = 0; tidx <unionList.size(); tidx++) {
TimeCoordUnion union = unionList.get(tidx);
f.format(" %s %d: timeIndexList=", firstGroup.hcs.getName(), tidx);
for (int idx : union.) f.format("%d,",idx);
f.format("%n");
} */
// store results in first group
firstGroup.timeCoordPartitions = unionList;
}
return ok;
}
// consistency check on variables : compare each variable to corresponding one in proto
// also set the groupno and partno for each partition
private boolean checkPartitions(TimePartition.Partition canon, Formatter f) throws IOException {
List<TimePartition.Partition> partitions = tp.getPartitions();
int npart = partitions.size();
boolean ok = true;
// for each group in canonical Partition
GribCollection canonGc = canon.makeGribCollection(f);
for (GribCollection.GroupHcs firstGroup : canonGc.getGroups()) {
String gname = firstGroup.getId();
if (trace) f.format(" Check Group %s%n", gname);
// hash proto variables for quick lookup
Map<Integer, GribCollection.VariableIndex> check =
new HashMap<Integer, GribCollection.VariableIndex>(firstGroup.varIndex.size());
List<GribCollection.VariableIndex> varIndexP =
new ArrayList<GribCollection.VariableIndex>(firstGroup.varIndex.size());
for (GribCollection.VariableIndex vi : firstGroup.varIndex) {
TimePartition.VariableIndexPartitioned vip = tp.makeVariableIndexPartitioned(vi, npart);
varIndexP.add(vip);
check.put(vi.cdmHash, vip); // replace with its evil twin
}
firstGroup.varIndex = varIndexP; // replace with its evil twin
// for each partition
for (int partno = 0; partno < npart; partno++) {
TimePartition.Partition tpp = partitions.get(partno);
if (trace) f.format(" Check Partition %s%n", tpp.getName());
// get corresponding group
GribCollection gc = tpp.makeGribCollection(f);
int groupIdx = gc.findGroupIdxById(firstGroup.getId());
if (groupIdx < 0) {
f.format(" Cant find group %s in partition %s%n", gname, tpp.getName());
ok = false;
continue;
}
GribCollection.GroupHcs group = gc.getGroup(groupIdx);
// for each variable in partition group
for (int varIdx = 0; varIdx < group.varIndex.size(); varIdx++) {
GribCollection.VariableIndex vi2 = group.varIndex.get(varIdx);
if (trace) f.format(" Check variable %s%n", vi2);
int flag = 0;
GribCollection.VariableIndex vi1 = check.get(vi2.cdmHash); // compare with proto variable
if (vi1 == null) {
f.format(
" WARN Cant find variable %s from %s in proto - ignoring that variable%n",
vi2, tpp.getName());
continue; // we can tolerate this
}
// compare vert coordinates
VertCoord vc1 = vi1.getVertCoord();
VertCoord vc2 = vi2.getVertCoord();
if ((vc1 == null) != (vc2 == null)) {
f.format(
" ERR Vert coordinates existence on variable %s in %s doesnt match%n",
vi2, tpp.getName());
ok = false;
} else if ((vc1 != null) && !vc1.equalsData(vc2)) {
f.format(
" WARN Vert coordinates values on variable %s in %s dont match%n",
vi2, tpp.getName());
f.format(" canon vc = %s%n", vc1);
f.format(" this vc = %s%n", vc2);
flag |= TimePartition.VERT_COORDS_DIFFER;
}
// compare ens coordinates
EnsCoord ec1 = vi1.getEnsCoord();
EnsCoord ec2 = vi2.getEnsCoord();
if ((ec1 == null) != (ec2 == null)) {
f.format(
" ERR Ensemble coordinates existence on variable %s in %s doesnt match%n",
vi2, tpp.getName());
ok = false;
} else if ((ec1 != null) && !ec1.equalsData(ec2)) {
f.format(
" WARN Ensemble coordinates values on variable %s in %s dont match%n",
vi2, tpp.getName());
f.format(" canon ec = %s%n", ec1);
f.format(" this ec = %s%n", ec2);
flag |= TimePartition.ENS_COORDS_DIFFER;
}
((TimePartition.VariableIndexPartitioned) vi1)
.setPartitionIndex(partno, groupIdx, varIdx, flag);
} // loop over variable
} // loop over partition
} // loop over group
if (ok) f.format(" Partition check: vert, ens coords OK%n");
return ok;
}
private EnsCoord readEnsCoord(GribCollectionProto.Coord pc) throws IOException {
List<EnsCoord.Coord> coords = new ArrayList<EnsCoord.Coord>(pc.getValuesCount());
for (int i = 0; i < pc.getValuesCount(); i += 2)
coords.add(new EnsCoord.Coord((int) pc.getValues(i), (int) pc.getValues(i + 1)));
return new EnsCoord(coords);
}
// read all records in all files,
// divide into groups based on GDS hash
// each group has an arraylist of all records that belong to it.
// for each group, run rectlizer to derive the coordinates and variables
public List<Group> makeAggregatedGroups(
List<String> filenames, CollectionManager.Force force, Formatter f) throws IOException {
Map<Integer, Group> gdsMap = new HashMap<Integer, Group>();
boolean intvMerge = mergeIntvDefault;
f.format("GribCollection %s: makeAggregatedGroups%n", gc.getName());
int total = 0;
int fileno = 0;
for (CollectionManager dcm : collections) {
f.format(" dcm= %s%n", dcm);
FeatureCollectionConfig.GribConfig config =
(FeatureCollectionConfig.GribConfig)
dcm.getAuxInfo(FeatureCollectionConfig.AUX_GRIB_CONFIG);
Map<Integer, Integer> gdsConvert = (config != null) ? config.gdsHash : null;
FeatureCollectionConfig.GribIntvFilter intvMap = (config != null) ? config.intvFilter : null;
intvMerge =
(config == null) || (config.intvMerge == null) ? mergeIntvDefault : config.intvMerge;
for (MFile mfile : dcm.getFiles()) {
// f.format("%3d: %s%n", fileno, mfile.getPath());
filenames.add(mfile.getPath());
Grib2Index index = null;
try {
index =
(Grib2Index)
GribIndex.readOrCreateIndexFromSingleFile(
false, !isSingleFile, mfile, config, force, f);
} catch (IOException ioe) {
logger.warn(
"GribCollectionBuilder {}: reading/Creating gbx9 index failed err={}",
gc.getName(),
ioe.getMessage());
f.format(
"GribCollectionBuilder: reading/Creating gbx9 index failed err=%s%n skipping %s%n",
ioe.getMessage(), mfile.getPath() + GribIndex.IDX_EXT);
continue;
}
for (Grib2Record gr : index.getRecords()) {
if (this.tables == null) {
Grib2SectionIdentification ids =
gr.getId(); // so all records must use the same table (!)
this.tables =
Grib2Customizer.factory(
ids.getCenter_id(),
ids.getSubcenter_id(),
ids.getMaster_table_version(),
ids.getLocal_table_version());
if (config != null)
tables.setTimeUnitConverter(
config
.getTimeUnitConverter()); // LOOK doesnt really work with multiple collections
}
if (intvMap != null && filterTinv(gr, intvMap, f)) continue; // skip
gr.setFile(fileno); // each record tracks which file it belongs to
int gdsHash =
gr.getGDSsection().getGDS().hashCode(); // use GDS hash code to group records
if (gdsConvert != null
&& gdsConvert.get(gdsHash)
!= null) // allow external config to muck with gdsHash. Why? because of error in
// encoding
gdsHash = (Integer) gdsConvert.get(gdsHash); // and we need exact hash matching
Group g = gdsMap.get(gdsHash);
if (g == null) {
g = new Group(gr.getGDSsection(), gdsHash);
gdsMap.put(gdsHash, g);
}
g.records.add(gr);
total++;
}
fileno++;
}
}
f.format(" total grib records= %d%n", total);
Grib2Rectilyser.Counter c = new Grib2Rectilyser.Counter(); // debugging
List<Group> result = new ArrayList<Group>(gdsMap.values());
for (Group g : result) {
g.rect = new Grib2Rectilyser(tables, g.records, g.gdsHash, intvMerge);
f.format(" GDS hash %d == ", g.gdsHash);
g.rect.make(f, c, filenames);
}
f.format(
" Rectilyser: nvars=%d records unique=%d total=%d dups=%d (%f) %n",
c.vars, c.recordsUnique, c.records, c.dups, ((float) c.dups) / c.records);
return result;
}