|
|
|
|
|
|
|
|
|
|
|
import shutil |
|
import struct |
|
from functools import lru_cache |
|
|
|
import numpy as np |
|
import torch |
|
from fairseq.dataclass.constants import DATASET_IMPL_CHOICES |
|
from fairseq.data.fasta_dataset import FastaDataset |
|
from fairseq.file_io import PathManager |
|
from fairseq.data.huffman import HuffmanMMapIndexedDataset, HuffmanMMapIndex |
|
|
|
from . import FairseqDataset |
|
|
|
from typing import Union |
|
|
|
|
|
def best_fitting_int_dtype( |
|
max_int_to_represent, |
|
) -> Union[np.uint16, np.uint32, np.int64]: |
|
|
|
if max_int_to_represent is None: |
|
return np.uint32 |
|
elif max_int_to_represent < 65500: |
|
return np.uint16 |
|
elif max_int_to_represent < 4294967295: |
|
return np.uint32 |
|
else: |
|
return np.int64 |
|
|
|
|
|
|
|
|
|
def get_available_dataset_impl(): |
|
return list(map(str, DATASET_IMPL_CHOICES)) |
|
|
|
|
|
def infer_dataset_impl(path): |
|
if IndexedRawTextDataset.exists(path): |
|
return "raw" |
|
elif IndexedDataset.exists(path): |
|
with open(index_file_path(path), "rb") as f: |
|
magic = f.read(8) |
|
if magic == IndexedDataset._HDR_MAGIC: |
|
return "cached" |
|
elif magic == MMapIndexedDataset.Index._HDR_MAGIC[:8]: |
|
return "mmap" |
|
elif magic == HuffmanMMapIndex._HDR_MAGIC[:8]: |
|
return "huffman" |
|
else: |
|
return None |
|
elif FastaDataset.exists(path): |
|
return "fasta" |
|
else: |
|
return None |
|
|
|
|
|
def make_builder(out_file, impl, vocab_size=None): |
|
if impl == "mmap": |
|
return MMapIndexedDatasetBuilder( |
|
out_file, dtype=best_fitting_int_dtype(vocab_size) |
|
) |
|
elif impl == "fasta": |
|
raise NotImplementedError |
|
elif impl == "huffman": |
|
raise ValueError( |
|
"Use HuffmanCodeBuilder directly as it has a different interface." |
|
) |
|
else: |
|
return IndexedDatasetBuilder(out_file) |
|
|
|
|
|
def make_dataset(path, impl, fix_lua_indexing=False, dictionary=None): |
|
if impl == "raw" and IndexedRawTextDataset.exists(path): |
|
assert dictionary is not None |
|
return IndexedRawTextDataset(path, dictionary) |
|
elif impl == "lazy" and IndexedDataset.exists(path): |
|
return IndexedDataset(path, fix_lua_indexing=fix_lua_indexing) |
|
elif impl == "cached" and IndexedDataset.exists(path): |
|
return IndexedCachedDataset(path, fix_lua_indexing=fix_lua_indexing) |
|
elif impl == "mmap" and MMapIndexedDataset.exists(path): |
|
return MMapIndexedDataset(path) |
|
elif impl == "fasta" and FastaDataset.exists(path): |
|
from fairseq.data.fasta_dataset import EncodedFastaDataset |
|
|
|
return EncodedFastaDataset(path, dictionary) |
|
elif impl == "huffman" and HuffmanMMapIndexedDataset.exists(path): |
|
return HuffmanMMapIndexedDataset(path) |
|
return None |
|
|
|
|
|
def dataset_exists(path, impl): |
|
if impl == "raw": |
|
return IndexedRawTextDataset.exists(path) |
|
elif impl == "mmap": |
|
return MMapIndexedDataset.exists(path) |
|
elif impl == "huffman": |
|
return HuffmanMMapIndexedDataset.exists(path) |
|
else: |
|
return IndexedDataset.exists(path) |
|
|
|
|
|
def read_longs(f, n): |
|
a = np.empty(n, dtype=np.int64) |
|
f.readinto(a) |
|
return a |
|
|
|
|
|
def write_longs(f, a): |
|
f.write(np.array(a, dtype=np.int64)) |
|
|
|
|
|
_code_to_dtype = { |
|
1: np.uint8, |
|
2: np.int8, |
|
3: np.int16, |
|
4: np.int32, |
|
5: np.int64, |
|
6: np.float64, |
|
7: np.double, |
|
8: np.uint16, |
|
9: np.uint32, |
|
10: np.uint64, |
|
} |
|
|
|
|
|
def _dtype_header_code(dtype) -> int: |
|
for k in _code_to_dtype.keys(): |
|
if _code_to_dtype[k] == dtype: |
|
return k |
|
raise ValueError(dtype) |
|
|
|
|
|
def index_file_path(prefix_path): |
|
return prefix_path + ".idx" |
|
|
|
|
|
def data_file_path(prefix_path): |
|
return prefix_path + ".bin" |
|
|
|
|
|
class IndexedDataset(FairseqDataset): |
|
"""Loader for TorchNet IndexedDataset""" |
|
|
|
_HDR_MAGIC = b"TNTIDX\x00\x00" |
|
|
|
def __init__(self, path, fix_lua_indexing=False): |
|
super().__init__() |
|
self.path = path |
|
self.fix_lua_indexing = fix_lua_indexing |
|
self.data_file = None |
|
self.read_index(path) |
|
|
|
def read_index(self, path): |
|
with open(index_file_path(path), "rb") as f: |
|
magic = f.read(8) |
|
assert magic == self._HDR_MAGIC, ( |
|
"Index file doesn't match expected format. " |
|
"Make sure that --dataset-impl is configured properly." |
|
) |
|
version = f.read(8) |
|
assert struct.unpack("<Q", version) == (1,) |
|
code, self.element_size = struct.unpack("<QQ", f.read(16)) |
|
self.dtype = _code_to_dtype[code] |
|
self._len, self.s = struct.unpack("<QQ", f.read(16)) |
|
self.dim_offsets = read_longs(f, self._len + 1) |
|
self.data_offsets = read_longs(f, self._len + 1) |
|
self.sizes = read_longs(f, self.s) |
|
|
|
def read_data(self, path): |
|
self.data_file = open(data_file_path(path), "rb", buffering=0) |
|
|
|
def check_index(self, i): |
|
if i < 0 or i >= self._len: |
|
raise IndexError("index out of range") |
|
|
|
def __del__(self): |
|
if self.data_file: |
|
self.data_file.close() |
|
|
|
@lru_cache(maxsize=8) |
|
def __getitem__(self, i) -> torch.Tensor: |
|
if not self.data_file: |
|
self.read_data(self.path) |
|
self.check_index(i) |
|
tensor_size = self.sizes[self.dim_offsets[i] : self.dim_offsets[i + 1]] |
|
a = np.empty(tensor_size, dtype=self.dtype) |
|
self.data_file.seek(self.data_offsets[i] * self.element_size) |
|
self.data_file.readinto(a) |
|
item = torch.from_numpy(a).long() |
|
if self.fix_lua_indexing: |
|
item -= 1 |
|
return item |
|
|
|
def __len__(self): |
|
return self._len |
|
|
|
def num_tokens(self, index): |
|
return self.sizes[index] |
|
|
|
def size(self, index): |
|
return self.sizes[index] |
|
|
|
@staticmethod |
|
def exists(path): |
|
return PathManager.exists(index_file_path(path)) and PathManager.exists( |
|
data_file_path(path) |
|
) |
|
|
|
@property |
|
def supports_prefetch(self): |
|
return False |
|
|
|
|
|
class IndexedCachedDataset(IndexedDataset): |
|
def __init__(self, path, fix_lua_indexing=False): |
|
super().__init__(path, fix_lua_indexing=fix_lua_indexing) |
|
self.cache = None |
|
self.cache_index = {} |
|
|
|
@property |
|
def supports_prefetch(self): |
|
return True |
|
|
|
def prefetch(self, indices): |
|
if all(i in self.cache_index for i in indices): |
|
return |
|
if not self.data_file: |
|
self.read_data(self.path) |
|
indices = sorted(set(indices)) |
|
total_size = 0 |
|
for i in indices: |
|
total_size += self.data_offsets[i + 1] - self.data_offsets[i] |
|
self.cache = np.empty(total_size, dtype=self.dtype) |
|
ptx = 0 |
|
self.cache_index.clear() |
|
for i in indices: |
|
self.cache_index[i] = ptx |
|
size = self.data_offsets[i + 1] - self.data_offsets[i] |
|
a = self.cache[ptx : ptx + size] |
|
self.data_file.seek(self.data_offsets[i] * self.element_size) |
|
self.data_file.readinto(a) |
|
ptx += size |
|
if self.data_file: |
|
|
|
self.data_file.close() |
|
self.data_file = None |
|
|
|
@lru_cache(maxsize=8) |
|
def __getitem__(self, i): |
|
self.check_index(i) |
|
tensor_size = self.sizes[self.dim_offsets[i] : self.dim_offsets[i + 1]] |
|
a = np.empty(tensor_size, dtype=self.dtype) |
|
ptx = self.cache_index[i] |
|
np.copyto(a, self.cache[ptx : ptx + a.size]) |
|
item = torch.from_numpy(a).long() |
|
if self.fix_lua_indexing: |
|
item -= 1 |
|
return item |
|
|
|
|
|
class IndexedRawTextDataset(FairseqDataset): |
|
"""Takes a text file as input and binarizes it in memory at instantiation. |
|
Original lines are also kept in memory""" |
|
|
|
def __init__(self, path, dictionary, append_eos=True, reverse_order=False): |
|
self.tokens_list = [] |
|
self.lines = [] |
|
self.sizes = [] |
|
self.append_eos = append_eos |
|
self.reverse_order = reverse_order |
|
self.read_data(path, dictionary) |
|
self.size = len(self.tokens_list) |
|
|
|
def read_data(self, path, dictionary): |
|
with open(path, "r", encoding="utf-8") as f: |
|
for line in f: |
|
self.lines.append(line.strip("\n")) |
|
tokens = dictionary.encode_line( |
|
line, |
|
add_if_not_exist=False, |
|
append_eos=self.append_eos, |
|
reverse_order=self.reverse_order, |
|
).long() |
|
self.tokens_list.append(tokens) |
|
self.sizes.append(len(tokens)) |
|
self.sizes = np.array(self.sizes) |
|
|
|
def check_index(self, i): |
|
if i < 0 or i >= self.size: |
|
raise IndexError("index out of range") |
|
|
|
@lru_cache(maxsize=8) |
|
def __getitem__(self, i): |
|
self.check_index(i) |
|
return self.tokens_list[i] |
|
|
|
def get_original_text(self, i): |
|
self.check_index(i) |
|
return self.lines[i] |
|
|
|
def __del__(self): |
|
pass |
|
|
|
def __len__(self): |
|
return self.size |
|
|
|
def num_tokens(self, index): |
|
return self.sizes[index] |
|
|
|
def size(self, index): |
|
return self.sizes[index] |
|
|
|
@staticmethod |
|
def exists(path): |
|
return PathManager.exists(path) |
|
|
|
|
|
class IndexedDatasetBuilder: |
|
element_sizes = { |
|
np.uint8: 1, |
|
np.int8: 1, |
|
np.int16: 2, |
|
np.int32: 4, |
|
np.int64: 8, |
|
np.float64: 4, |
|
np.double: 8, |
|
} |
|
|
|
def __init__(self, out_file, dtype=np.int32): |
|
self.out_file = open(out_file, "wb") |
|
self.dtype = dtype |
|
self.data_offsets = [0] |
|
self.dim_offsets = [0] |
|
self.sizes = [] |
|
self.element_size = self.element_sizes[self.dtype] |
|
|
|
def add_item(self, tensor): |
|
|
|
bytes = self.out_file.write(np.array(tensor.numpy() + 1, dtype=self.dtype)) |
|
self.data_offsets.append(self.data_offsets[-1] + bytes / self.element_size) |
|
for s in tensor.size(): |
|
self.sizes.append(s) |
|
self.dim_offsets.append(self.dim_offsets[-1] + len(tensor.size())) |
|
|
|
def merge_file_(self, another_file): |
|
index = IndexedDataset(another_file) |
|
assert index.dtype == self.dtype |
|
|
|
begin = self.data_offsets[-1] |
|
for offset in index.data_offsets[1:]: |
|
self.data_offsets.append(begin + offset) |
|
self.sizes.extend(index.sizes) |
|
begin = self.dim_offsets[-1] |
|
for dim_offset in index.dim_offsets[1:]: |
|
self.dim_offsets.append(begin + dim_offset) |
|
|
|
with open(data_file_path(another_file), "rb") as f: |
|
while True: |
|
data = f.read(1024) |
|
if data: |
|
self.out_file.write(data) |
|
else: |
|
break |
|
|
|
def finalize(self, index_file): |
|
self.out_file.close() |
|
index = open(index_file, "wb") |
|
index.write(b"TNTIDX\x00\x00") |
|
index.write(struct.pack("<Q", 1)) |
|
index.write( |
|
struct.pack("<QQ", _dtype_header_code(self.dtype), self.element_size) |
|
) |
|
index.write(struct.pack("<QQ", len(self.data_offsets) - 1, len(self.sizes))) |
|
write_longs(index, self.dim_offsets) |
|
write_longs(index, self.data_offsets) |
|
write_longs(index, self.sizes) |
|
index.close() |
|
|
|
|
|
def _warmup_mmap_file(path): |
|
with open(path, "rb") as stream: |
|
while stream.read(100 * 1024 * 1024): |
|
pass |
|
|
|
|
|
class MMapIndexedDataset(torch.utils.data.Dataset): |
|
class Index: |
|
_HDR_MAGIC = b"MMIDIDX\x00\x00" |
|
|
|
@classmethod |
|
def writer(cls, path, dtype): |
|
class _Writer: |
|
def __enter__(self): |
|
self._file = open(path, "wb") |
|
|
|
self._file.write(cls._HDR_MAGIC) |
|
self._file.write(struct.pack("<Q", 1)) |
|
self._file.write(struct.pack("<B", _dtype_header_code(dtype))) |
|
|
|
return self |
|
|
|
@staticmethod |
|
def _get_pointers(sizes): |
|
dtype_size = dtype().itemsize |
|
address = 0 |
|
pointers = [] |
|
|
|
for size in sizes: |
|
pointers.append(address) |
|
address += size * dtype_size |
|
|
|
return pointers |
|
|
|
def write(self, sizes): |
|
pointers = self._get_pointers(sizes) |
|
|
|
self._file.write(struct.pack("<Q", len(sizes))) |
|
|
|
sizes = np.array(sizes, dtype=np.int32) |
|
self._file.write(sizes.tobytes(order="C")) |
|
del sizes |
|
|
|
pointers = np.array(pointers, dtype=np.int64) |
|
self._file.write(pointers.tobytes(order="C")) |
|
del pointers |
|
|
|
def __exit__(self, exc_type, exc_val, exc_tb): |
|
self._file.close() |
|
|
|
return _Writer() |
|
|
|
def __init__(self, path): |
|
with open(path, "rb") as stream: |
|
magic_test = stream.read(9) |
|
assert self._HDR_MAGIC == magic_test, ( |
|
"Index file doesn't match expected format. " |
|
"Make sure that --dataset-impl is configured properly." |
|
) |
|
version = struct.unpack("<Q", stream.read(8)) |
|
assert (1,) == version |
|
|
|
(dtype_code,) = struct.unpack("<B", stream.read(1)) |
|
self._dtype = _code_to_dtype[dtype_code] |
|
self._dtype_size = self._dtype().itemsize |
|
|
|
self._len = struct.unpack("<Q", stream.read(8))[0] |
|
offset = stream.tell() |
|
|
|
_warmup_mmap_file(path) |
|
|
|
self._bin_buffer_mmap = np.memmap(path, mode="r", order="C") |
|
self._bin_buffer = memoryview(self._bin_buffer_mmap) |
|
self._sizes = np.frombuffer( |
|
self._bin_buffer, dtype=np.int32, count=self._len, offset=offset |
|
) |
|
self._pointers = np.frombuffer( |
|
self._bin_buffer, |
|
dtype=np.int64, |
|
count=self._len, |
|
offset=offset + self._sizes.nbytes, |
|
) |
|
|
|
def __del__(self): |
|
self._bin_buffer_mmap._mmap.close() |
|
del self._bin_buffer_mmap |
|
|
|
@property |
|
def dtype(self): |
|
return self._dtype |
|
|
|
@property |
|
def sizes(self): |
|
return self._sizes |
|
|
|
@lru_cache(maxsize=8) |
|
def __getitem__(self, i): |
|
return self._pointers[i], self._sizes[i] |
|
|
|
def __len__(self): |
|
return self._len |
|
|
|
def __init__(self, path): |
|
super().__init__() |
|
|
|
self._path = None |
|
self._index = None |
|
self._bin_buffer = None |
|
|
|
self._do_init(path) |
|
|
|
def __getstate__(self): |
|
return self._path |
|
|
|
def __setstate__(self, state): |
|
self._do_init(state) |
|
|
|
def _do_init(self, path): |
|
self._path = path |
|
self._index = self.Index(index_file_path(self._path)) |
|
|
|
_warmup_mmap_file(data_file_path(self._path)) |
|
self._bin_buffer_mmap = np.memmap( |
|
data_file_path(self._path), mode="r", order="C" |
|
) |
|
self._bin_buffer = memoryview(self._bin_buffer_mmap) |
|
|
|
def __del__(self): |
|
self._bin_buffer_mmap._mmap.close() |
|
del self._bin_buffer_mmap |
|
del self._index |
|
|
|
def __len__(self): |
|
return len(self._index) |
|
|
|
@lru_cache(maxsize=8) |
|
def __getitem__(self, i): |
|
ptr, size = self._index[i] |
|
np_array = np.frombuffer( |
|
self._bin_buffer, dtype=self._index.dtype, count=size, offset=ptr |
|
) |
|
if self._index.dtype != np.int64: |
|
np_array = np_array.astype(np.int64) |
|
|
|
return torch.from_numpy(np_array) |
|
|
|
@property |
|
def sizes(self): |
|
return self._index.sizes |
|
|
|
@property |
|
def supports_prefetch(self): |
|
return False |
|
|
|
@staticmethod |
|
def exists(path): |
|
return PathManager.exists(index_file_path(path)) and PathManager.exists( |
|
data_file_path(path) |
|
) |
|
|
|
|
|
def get_indexed_dataset_to_local(path) -> str: |
|
local_index_path = PathManager.get_local_path(index_file_path(path)) |
|
local_data_path = PathManager.get_local_path(data_file_path(path)) |
|
|
|
assert local_index_path.endswith(".idx") and local_data_path.endswith(".bin"), ( |
|
"PathManager.get_local_path does not return files with expected patterns: " |
|
f"{local_index_path} and {local_data_path}" |
|
) |
|
|
|
local_path = local_data_path[:-4] |
|
assert local_path == local_index_path[:-4] |
|
return local_path |
|
|
|
|
|
class MMapIndexedDatasetBuilder: |
|
def __init__(self, out_file, dtype=np.int64): |
|
self._data_file = open(out_file, "wb") |
|
self._dtype = dtype |
|
self._sizes = [] |
|
|
|
def add_item(self, tensor): |
|
np_array = np.array(tensor.numpy(), dtype=self._dtype) |
|
self._data_file.write(np_array.tobytes(order="C")) |
|
self._sizes.append(np_array.size) |
|
|
|
def merge_file_(self, another_file): |
|
|
|
index = MMapIndexedDataset.Index(index_file_path(another_file)) |
|
assert index.dtype == self._dtype |
|
|
|
for size in index.sizes: |
|
self._sizes.append(size) |
|
|
|
|
|
with open(data_file_path(another_file), "rb") as f: |
|
shutil.copyfileobj(f, self._data_file) |
|
|
|
def finalize(self, index_file): |
|
self._data_file.close() |
|
|
|
with MMapIndexedDataset.Index.writer(index_file, self._dtype) as index: |
|
index.write(self._sizes) |
|
|