@Override
public void run() {
Database database = input.getDatabase();
Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
DistanceQuery<O> distanceQuery = database.getDistanceQuery(relation, distance);
KNNQuery<O> knnQ = database.getKNNQuery(distanceQuery, DatabaseQuery.HINT_HEAVY_USE);
// open file.
try (RandomAccessFile file = new RandomAccessFile(out, "rw");
FileChannel channel = file.getChannel();
// and acquire a file write lock
FileLock lock = channel.lock()) {
// write magic header
file.writeInt(KNN_CACHE_MAGIC);
int bufsize = k * 12 * 2 + 10; // Initial size, enough for 2 kNN.
ByteBuffer buffer = ByteBuffer.allocateDirect(bufsize);
FiniteProgress prog =
LOG.isVerbose() ? new FiniteProgress("Computing kNN", relation.size(), LOG) : null;
for (DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
final KNNList nn = knnQ.getKNNForDBID(it, k);
final int nnsize = nn.size();
// Grow the buffer when needed:
if (nnsize * 12 + 10 > bufsize) {
while (nnsize * 12 + 10 > bufsize) {
bufsize <<= 1;
}
buffer = ByteBuffer.allocateDirect(bufsize);
}
buffer.clear();
ByteArrayUtil.writeUnsignedVarint(buffer, it.internalGetIndex());
ByteArrayUtil.writeUnsignedVarint(buffer, nnsize);
int c = 0;
for (DoubleDBIDListIter ni = nn.iter(); ni.valid(); ni.advance(), c++) {
ByteArrayUtil.writeUnsignedVarint(buffer, ni.internalGetIndex());
buffer.putDouble(ni.doubleValue());
}
if (c != nn.size()) {
throw new AbortException("Sizes did not agree. Cache is invalid.");
}
buffer.flip();
channel.write(buffer);
LOG.incrementProcessed(prog);
}
LOG.ensureCompleted(prog);
lock.release();
} catch (IOException e) {
LOG.exception(e);
}
// FIXME: close!
}
@Override
public void processNewResult(ResultHierarchy hier, Result result) {
List<Clustering<?>> crs = ResultUtil.getClusteringResults(result);
if (crs.size() < 1) {
return;
}
Database db = ResultUtil.findDatabase(hier);
Relation<O> rel = db.getRelation(distance.getInputTypeRestriction());
DistanceQuery<O> dq = db.getDistanceQuery(rel, distance);
for (Clustering<?> c : crs) {
evaluateClustering(db, rel, dq, c);
}
}