import pickle import os import glob import json import multiprocessing import time import traceback from loguru import logger from tqdm import tqdm from clean_cache import clear_cache_folder from table2tree.feature_tree import * from embedding import * import logging # Ignore warnings from the transformers package logging.getLogger("transformers").setLevel(logging.ERROR) import warnings # Ignore all warnings warnings.filterwarnings("ignore") def excel2tree( file, pkl_dir=None, convert_pkl=True, json_dir : bool = None, convert_json=True, str_dir=None, convert_str=True, embedding_dir=None, convert_embedding=True, structured=False, log=False, vlm_cache=False, ): """ Convert the input excel file into the HO-Tree (FeatureTree) object. Args: file (_type_): the input Excel file path pkl_dir (_type_, optional): _description_. Output path for saving pkl files convert_pkl (bool, optional): _description_. Whether to output the pkl file for the FeatureTree object json_dir (_type_, optional): _description_. Output path for saving JSON files convert_json (bool, optional): _description_. Defaults to True. Whether to output the serialized JSON file for the FeatureTree object str_dir (_type_, optional): _description_. Output path for saving string files convert_str (bool, optional): _description_. Defaults to True. Whether to output the serialized string file for the FeatureTree object embedding_dir (_type_, optional): _description_. Output path for saving embedding files convert_embedding (bool, optional): _description_. Defaults to True. Whether to save embeddings for each table cell for later question answering structured (bool, optional): _description_. Defaults to True. Semi-structured tables by default log (bool, optional): _description_. Defaults to True. Whether to output logs vlm_cache (bool, optional): _description_. Defaults to True. Whether to use caching during VLM conversion Returns: FeatureTree: The convert HO-Tree of the input excel file. """ if not os.path.exists(pkl_dir): os.mkdir(pkl_dir) if not os.path.exists(json_dir): os.mkdir(json_dir) if not os.path.exists(str_dir): os.mkdir(str_dir) if not os.path.exists(embedding_dir): os.mkdir(embedding_dir) name = os.path.basename(file)[:-5] flag = [False, False, False, False] if ( convert_pkl and os.path.exists(os.path.join(pkl_dir, f"{name}.pkl")) ) or not convert_pkl: flag[0] = True if ( convert_json and os.path.exists(os.path.join(json_dir, f"{name}.json")) ) or not convert_json: flag[1] = True if ( convert_str and os.path.exists(os.path.join(str_dir, f"{name}.txt")) ) or not convert_str: flag[2] = True if ( convert_embedding and os.path.exists(os.path.join(embedding_dir, f"{name}.embedding.json")) ) or not convert_embedding: flag[3] = True if flag == [True, True, True, True]: return try: f_tree = get_excel_feature_tree(file, structured=structured, log=log, vlm_cache=vlm_cache) tree_json = f_tree.__json__() tree_str = f_tree.__str__() except Exception as e: logger.error(f"File: {name}.xlsx Error: {e}") with open("./error.txt", "a") as f: f.write(f"process_one_table() error: {name}.xlsx\n") traceback.print_exc() return if convert_pkl: with open(os.path.join(pkl_dir, f"{name}.pkl"), "wb") as f: pickle.dump(f_tree, f) if convert_json: with open(os.path.join(json_dir, f"{name}.json"), "w") as f: json.dump(tree_json, f, indent=4, ensure_ascii=False) if convert_str: with open(os.path.join(str_dir, f"{name}.txt"), "w") as f: f.write(tree_str) if convert_embedding: embedding_dict = EmbeddingModel().get_embedding_dict( f_tree.all_value_list() ) EmbeddingModel().save_embedding_dict( embedding_dict, os.path.join(embedding_dir, f"{name}.embedding.json") ) return f_tree def preprocess_one_pkl( file, json_dir=None, convert_json=True, str_dir=None, convert_str=True, embedding_dir=None, convert_embedding=True, ): """_summary_ Args: file (_type_): _description_ json_dir (_type_, optional): _description_. Defaults to None. convert_json (bool, optional): _description_. Defaults to True. str_dir (_type_, optional): _description_. Defaults to None. convert_str (bool, optional): _description_. Defaults to True. embedding_dir (_type_, optional): _description_. Defaults to None. convert_embedding (bool, optional): _description_. Defaults to True. Returns: _type_: _description_ """ name = os.path.basename(file)[:-4] with open(os.path.join(file), "rb") as f: f_tree: FeatureTree = pickle.load(f) flag = [False, False, False] if ( convert_json and os.path.exists(os.path.join(json_dir, f"{name}.json")) ) or not convert_json: flag[0] = True if ( convert_str and os.path.exists(os.path.join(str_dir, f"{name}.txt")) ) or not convert_str: flag[1] = True if ( convert_embedding and os.path.exists(os.path.join(embedding_dir, f"{name}.embedding.json")) ) or not convert_embedding: flag[2] = True if flag == [True, True, True]: return try: tree_json = f_tree.__json__() tree_str = f_tree.__str__() except Exception as e: logger.error(f"File: {name}.xlsx Error: {e}") with open("./error.txt", "a") as f: f.write(f"process_one_pkl() error: {name}.xlsx\n") traceback.print_exc() return if convert_json: with open(os.path.join(json_dir, f"{name}.txt"), "w") as f: f.write(tree_str) if convert_str: with open(os.path.join(json_dir, f"{name}.json"), "w") as f: json.dump(tree_json, f, indent=4, ensure_ascii=False) if convert_embedding: embedding_dict = EmbeddingModel().get_embedding_dict( f_tree.all_value_list() ) EmbeddingModel().save_embedding_dict( embedding_dict, os.path.join(embedding_dir, f"{name}.embedding.json") ) return f_tree def process_excel_files( files, pkl_dir=None, convert_pkl=True, json_dir : bool = None, convert_json=True, str_dir=None, convert_str=True, embedding_dir=None, convert_embedding=True, structured=False, log=False, vlm_cache=False, ): """ Convert the input excel file list into the HO-Tree (FeatureTree) object. Args: file (_type_): the input Excel file path pkl_dir (_type_, optional): _description_. Output path for saving pkl files convert_pkl (bool, optional): _description_. Whether to output the pkl file for the FeatureTree object json_dir (_type_, optional): _description_. Output path for saving JSON files convert_json (bool, optional): _description_. Defaults to True. Whether to output the serialized JSON file for the FeatureTree object str_dir (_type_, optional): _description_. Output path for saving string files convert_str (bool, optional): _description_. Defaults to True. Whether to output the serialized string file for the FeatureTree object embedding_dir (_type_, optional): _description_. Output path for saving embedding files convert_embedding (bool, optional): _description_. Defaults to True. Whether to save embeddings for each table cell for later question answering structured (bool, optional): _description_. Defaults to True. Semi-structured tables by default log (bool, optional): _description_. Defaults to True. Whether to output logs vlm_cache (bool, optional): _description_. Defaults to True. Whether to use caching during VLM conversion """ if convert_pkl: os.makedirs(pkl_dir, exist_ok=True) if convert_json: os.makedirs(json_dir, exist_ok=True) if convert_str: os.makedirs(str_dir, exist_ok=True) if convert_embedding: os.makedirs(embedding_dir, exist_ok=True) for file in tqdm(files, desc="Processing..."): excel2tree( file, pkl_dir=pkl_dir, convert_pkl=convert_pkl, json_dir=json_dir, convert_json=convert_json, str_dir=str_dir, convert_str=convert_str, embedding_dir=embedding_dir, convert_embedding=convert_embedding, structured=structured, log=log, vlm_cache=vlm_cache, ) def process_pkl_files( files, json_dir=None, convert_json=True, # Whether to output the serialized JSON file for the FeatureTree object str_dir=None, convert_str=True, # Whether to output the serialized string file for the FeatureTree object embedding_dir=None, convert_embedding=True, # Whether to save embeddings for each table cell for later question answering log=False, # Whether to output logs vlm_cache=False, # Whether to use caching during VLM conversion ): if convert_json: os.makedirs(json_dir, exist_ok=True) if convert_str: os.makedirs(str_dir, exist_ok=True) if convert_embedding: os.makedirs(embedding_dir, exist_ok=True) for file in tqdm(files, desc="Processing..."): preprocess_one_pkl( file, json_dir=json_dir, convert_json=convert_json, str_dir=str_dir, convert_str=convert_str, embedding_dir=embedding_dir, convert_embedding=convert_embedding, ) def multi_process_process_excels( files, pkl_dir=None, convert_pkl=True, # Whether to output the pkl file for the FeatureTree object json_dir=None, convert_json=True, # Whether to output the serialized JSON file for the FeatureTree object str_dir=None, convert_str=True, # Whether to output the serialized string file for the FeatureTree object embedding_dir=None, convert_embedding=True, # Whether to save embeddings for each table cell for later question answering structured=False, # Semi-structured tables by default log=False, # Whether to output logs vlm_cache=False, # Whether to use caching during VLM conversion n=6, ): param_list = [ ( file, pkl_dir, convert_pkl, json_dir, convert_json, str_dir, convert_str, embedding_dir, convert_embedding, log, vlm_cache, ) for file in files ] with multiprocessing.Pool(processes=n) as pool: pool.starmap(excel2tree, param_list) print("All jobs completed!") def multi_process_process_pkls( files, json_dir=None, convert_json=True, # Whether to output the serialized JSON file for the FeatureTree object str_dir=None, convert_str=True, # Whether to output the serialized string file for the FeatureTree object embedding_dir=None, convert_embedding=True, # Whether to save embeddings for each table cell for later question answering n=6, ): param_list = [ ( file, json_dir, convert_json, str_dir, convert_str, embedding_dir, convert_embedding, ) for file in files ] with multiprocessing.Pool(processes=n) as pool: pool.starmap(preprocess_one_pkl, param_list) print("All jobs completed!") def main(): clear_cache_folder(CACHE_DIR) # dataset_dir = '/home/zirui/SemiTableQA/data/temptabqa-st/' dataset_dir = '/home/zirui/SemiTableQA/data/wikitq-st-demo/' table_dir = os.path.join(dataset_dir, 'table') pkl_dir = os.path.join(dataset_dir, 'pkl') json_dir = os.path.join(dataset_dir, 'json') str_dir = os.path.join(dataset_dir, 'str') embedding_dir = os.path.join(dataset_dir, 'embedding') files = glob.glob(table_dir + '/*.xlsx') for file in tqdm(files): excel2tree( file, pkl_dir=pkl_dir, convert_pkl=True, json_dir=json_dir, convert_json=True, str_dir=str_dir, convert_str=True, embedding_dir=embedding_dir, convert_embedding=True, structured=False, log=True, vlm_cache=False, ) if __name__ == '__main__': main()