ProteinGPT-Llama3 / minigpt4 /datasets /builders /pdb_base_dataset_builder.py
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"""
This file is from
Copyright (c) 2022, salesforce.com, inc.
All rights reserved.
SPDX-License-Identifier: BSD-3-Clause
For full license text, see the LICENSE_Lavis file in the repo root or https://opensource.org/licenses/BSD-3-Clause
"""
import logging
import os
import shutil
import warnings
from omegaconf import OmegaConf
import torch.distributed as dist
from torchvision.datasets.utils import download_url
import minigpt4.common.utils as utils
from minigpt4.common.dist_utils import is_dist_avail_and_initialized, is_main_process
from minigpt4.common.registry import registry
from minigpt4.processors.base_processor import BaseProcessor
class PDB_BaseDatasetBuilder:
train_dataset_cls, eval_dataset_cls = None, None
def __init__(self, cfg=None):
super().__init__()
if cfg is None:
# help to create datasets from default config.
self.config = load_dataset_config(self.default_config_path())
elif isinstance(cfg, str):
self.config = load_dataset_config(cfg)
else:
# when called from task.build_dataset()
self.config = cfg
self.data_type = self.config.data_type
self.text_processors = {"train": BaseProcessor(), "eval": BaseProcessor()}
def build_datasets(self):
# download, split, etc...
# only called on 1 GPU/TPU in distributed
if is_main_process():
self._download_data()
if is_dist_avail_and_initialized():
dist.barrier()
# at this point, all the annotations and image/videos should be all downloaded to the specified locations.
logging.info("Building datasets...")
datasets = self.build() # dataset['train'/'val'/'test']
return datasets
def build_processors(self):
txt_proc_cfg = self.config.get("text_processor")
if txt_proc_cfg is not None:
txt_train_cfg = txt_proc_cfg.get("train")
txt_eval_cfg = txt_proc_cfg.get("eval")
self.text_processors["train"] = self._build_proc_from_cfg(txt_train_cfg)
self.text_processors["eval"] = self._build_proc_from_cfg(txt_eval_cfg)
@staticmethod
def _build_proc_from_cfg(cfg):
return (
registry.get_processor_class(cfg.name).from_config(cfg)
if cfg is not None
else None
)
@classmethod
def default_config_path(cls, type="default"):
return utils.get_abs_path(cls.DATASET_CONFIG_DICT[type])
def _download_data(self):
self._download_ann()
self._download_vis()
def _download_ann(self):
"""
Download annotation files if necessary.
All the vision-language datasets should have annotations of unified format.
storage_path can be:
(1) relative/absolute: will be prefixed with env.cache_root to make full path if relative.
(2) basename/dirname: will be suffixed with base name of URL if dirname is provided.
Local annotation paths should be relative.
"""
anns = self.config.build_info.annotations
splits = anns.keys()
cache_root = registry.get_path("cache_root")
for split in splits:
info = anns[split]
urls, storage_paths = info.get("url", None), info.storage
if isinstance(urls, str):
urls = [urls]
if isinstance(storage_paths, str):
storage_paths = [storage_paths]
assert len(urls) == len(storage_paths)
for url_or_filename, storage_path in zip(urls, storage_paths):
# if storage_path is relative, make it full by prefixing with cache_root.
if not os.path.isabs(storage_path):
storage_path = os.path.join(cache_root, storage_path)
dirname = os.path.dirname(storage_path)
if not os.path.exists(dirname):
os.makedirs(dirname)
if os.path.isfile(url_or_filename):
src, dst = url_or_filename, storage_path
if not os.path.exists(dst):
shutil.copyfile(src=src, dst=dst)
else:
logging.info("Using existing file {}.".format(dst))
else:
if os.path.isdir(storage_path):
# if only dirname is provided, suffix with basename of URL.
raise ValueError(
"Expecting storage_path to be a file path, got directory {}".format(
storage_path
)
)
else:
filename = os.path.basename(storage_path)
download_url(url=url_or_filename, root=dirname, filename=filename)
def _download_vis(self):
storage_path = self.config.build_info.get(self.data_type).storage
storage_path = utils.get_cache_path(storage_path)
if not os.path.exists(storage_path):
warnings.warn(
f"""
The specified path {storage_path} for visual inputs does not exist.
Please provide a correct path to the visual inputs or
refer to datasets/download_scripts/README.md for downloading instructions.
"""
)
def build(self):
"""
Create by split datasets inheriting torch.utils.data.Datasets.
# build() can be dataset-specific. Overwrite to customize.
"""
self.build_processors()
build_info = self.config.build_info
ann_info = build_info.annotations
vis_info = build_info.get(self.data_type)
datasets = dict()
for split in ann_info.keys():
if split not in ["train", "val", "test"]:
continue
is_train = split == "train"
# processors
text_processor = (
self.text_processors["train"]
if is_train
else self.text_processors["eval"]
)
# annotation path
ann_paths = ann_info.get(split).storage
if isinstance(ann_paths, str):
ann_paths = [ann_paths]
abs_ann_paths = []
for ann_path in ann_paths:
if not os.path.isabs(ann_path):
ann_path = utils.get_cache_path(ann_path)
abs_ann_paths.append(ann_path)
ann_paths = abs_ann_paths
# visual data storage path
vis_path = os.path.join(vis_info.storage, split)
if not os.path.isabs(vis_path):
# vis_path = os.path.join(utils.get_cache_path(), vis_path)
vis_path = utils.get_cache_path(vis_path)
if not os.path.exists(vis_path):
warnings.warn("storage path {} does not exist.".format(vis_path))
# create datasets
dataset_cls = self.train_dataset_cls if is_train else self.eval_dataset_cls
datasets[split] = dataset_cls(
text_processor=text_processor,
ann_paths=ann_paths,
vis_root=vis_path,
)
return datasets
def load_dataset_config(cfg_path):
cfg = OmegaConf.load(cfg_path).datasets
cfg = cfg[list(cfg.keys())[0]]
return cfg