def make_binary_alignment_dataset(input_prefix, output_prefix,
num_workers):
nseq = [0]
def merge_result(worker_result):
nseq[0] += worker_result["nseq"]
input_file = input_prefix
offsets = find_offsets(input_file, num_workers)
(first_chunk, *more_chunks) = zip(offsets, offsets[1:])
pool = None
if num_workers > 1:
pool = Pool(processes=num_workers - 1)
for worker_id, (start_offset, end_offset) in enumerate(more_chunks,
start=1):
prefix = "{}{}".format(output_prefix, worker_id)
pool.apply_async(
binarize_alignments,
(
args,
input_file,
utils.parse_alignment,
prefix,
start_offset,
end_offset,
),
callback=merge_result,
)
pool.close()
ds = indexed_dataset.make_builder(dataset_dest_file(
args, output_prefix, None, "bin"),
impl=args.dataset_impl)
merge_result(
Binarizer.binarize_alignments(
input_file,
utils.parse_alignment,
lambda t: ds.add_item(t),
offset=first_chunk[0],
end=first_chunk[1],
))
if num_workers > 1:
pool.join()
for worker_id in range(1, num_workers):
prefix = "{}{}".format(output_prefix, worker_id)
temp_file_path = dataset_dest_prefix(args, prefix, None)
ds.merge_file_(temp_file_path)
os.remove(indexed_dataset.data_file_path(temp_file_path))
os.remove(indexed_dataset.index_file_path(temp_file_path))
ds.finalize(dataset_dest_file(args, output_prefix, None, "idx"))
logger.info("[alignments] {}: parsed {} alignments".format(
input_file, nseq[0]))
def binarize_alignments(args, filename, parse_alignment, output_prefix, offset, end):
ds = indexed_dataset.make_builder(dataset_dest_file(args, output_prefix, None, "bin"),
impl=args.dataset_impl, vocab_size=None)
def consumer(tensor):
ds.add_item(tensor)
res = Binarizer.binarize_alignments(filename, parse_alignment, consumer, offset=offset,
end=end)
ds.finalize(dataset_dest_file(args, output_prefix, None, "idx"))
return res
def make_binary_alignment_dataset(input_prefix, output_prefix,
num_workers):
nseq = [0]
def merge_result(worker_result):
nseq[0] += worker_result["nseq"]
input_file = input_prefix
offsets = Binarizer.find_offsets(input_file, num_workers)
pool = None
if num_workers > 1:
pool = Pool(processes=num_workers - 1)
for worker_id in range(1, num_workers):
prefix = "{}{}".format(output_prefix, worker_id)
pool.apply_async(
binarize_alignments,
(
args,
input_file,
utils.parse_alignment,
prefix,
offsets[worker_id],
offsets[worker_id + 1],
),
callback=merge_result,
)
pool.close()
ds = indexed_dataset.make_builder(dataset_dest_file(
args, output_prefix, None, "bin"),
impl=args.dataset_impl)
merge_result(
Binarizer.binarize_alignments(
input_file,
utils.parse_alignment,
lambda t: ds.add_item(t),
offset=0,
end=offsets[1],
))
if num_workers > 1:
pool.join()
for worker_id in range(1, num_workers):
prefix = "{}{}".format(output_prefix, worker_id)
temp_file_path = dataset_dest_prefix(args, prefix, None)
ds.merge_file_(temp_file_path)
os.remove(indexed_dataset.data_file_path(temp_file_path))
os.remove(indexed_dataset.index_file_path(temp_file_path))
ds.finalize(dataset_dest_file(args, output_prefix, None, "idx"))
print("| [alignments] {}: parsed {} alignments".format(
input_file, nseq[0]))
