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load_data.py
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load_data.py
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import os
import random
import torch
from scipy.sparse import csr_matrix
import numpy as np
from collections import defaultdict
from data import load_eva_data
import pickle
from tqdm import tqdm
# import lmdb
class DataLoader:
def __init__(self, args):
KGs, non_train, left_ents, right_ents, train_ill, test_ill, eval_ill, test_ill_ = load_eva_data(args)
ent_num = KGs['ent_num']
rel_num = KGs['rel_num']
self.img_ill = KGs['img_ill']
self.use_img_ill = args.use_img_ill
self.images_list = KGs['images_list']
self.rel_features = KGs['rel_features']
self.att_features = KGs['att_features']
self.num_att_left = KGs['num_att_left']
self.num_att_right = KGs['num_att_right']
self.id2name = KGs['id2name']
self.id2rel = KGs['id2rel']
self.left_ents = [i for i in range(len(left_ents))]
self.right_ents = [len(left_ents) + i for i in range(len(right_ents))]
old_ids = np.array(left_ents+right_ents)
# new_ids = torch.arange(len(self.left_ents+self.right_ents))
# old2new = torch.zeros(len(self.left_ents+self.right_ents)).long()
# old2new[old_ids] = new_ids
# self.old2new = old2new
self.old_ids = old_ids
if args.mm:
self.images_list = self.images_list[self.old_ids]
self.old2new_dict = {oldid:newid for newid,oldid in enumerate(left_ents+right_ents)}
triples = KGs['triples']
triples = [(self.old2new_dict[tri[0]],tri[1],self.old2new_dict[tri[2]]) for tri in triples]
train_ill = np.array([(self.old2new_dict[tri[0]],self.old2new_dict[tri[1]]) for tri in train_ill])
test_ill = np.array([(self.old2new_dict[tri[0]],self.old2new_dict[tri[1]]) for tri in test_ill])
if args.mm:
self.img_ill = np.array([(self.old2new_dict[tri[0]],self.old2new_dict[tri[1]]) for tri in self.img_ill])
# self.att_features_text = np.array(KGs['att_features'])
self.att2rel ,self.rels = self.process_rels(self.att_features)
self.att_ids = [self.old2new_dict[i[0]] for i in self.att_features]
self.ids_att = {}
for att_index,ids in enumerate(self.att_ids):
if ids not in self.ids_att:
self.ids_att[ids] = []
self.ids_att[ids].append(att_index)
# self.test_cache_url = os.path.join(args.data_path, args.data_choice, args.data_split, f'test_{args.data_rate}')
# self.test_cache = {}
if args.mm:
if args.topk == 0:
if os.path.exists(os.path.join(args.data_path, args.data_choice, args.data_split, 'att_features.npy')):
self.att_features = np.load(os.path.join(args.data_path, args.data_choice, args.data_split, 'att_features.npy'), allow_pickle=True)
self.att_rel_features = np.load(os.path.join(args.data_path, args.data_choice, args.data_split, 'att_rel_features.npy'), allow_pickle=True)
self.att_val_features = np.load(os.path.join(args.data_path, args.data_choice, args.data_split, 'att_val_features.npy'), allow_pickle=True)
else:
self.att_features, self.att_rel_features,self.att_val_features = self.bert_feature()
np.save(os.path.join(args.data_path, args.data_choice, args.data_split, 'att_features.npy'), self.att_features)
np.save(os.path.join(args.data_path, args.data_choice, args.data_split, 'att_rel_features.npy'), self.att_rel_features)
np.save(os.path.join(args.data_path, args.data_choice, args.data_split, 'att_val_features.npy'), self.att_val_features)
else:
if os.path.exists(os.path.join(args.data_path, args.data_choice, args.data_split, f'att_features{args.topk}.npy')):
self.att_features = np.load(os.path.join(args.data_path, args.data_choice, args.data_split, f'att_features{args.topk}.npy'), allow_pickle=True)
self.att_rel_features = np.load(os.path.join(args.data_path, args.data_choice, args.data_split, f'att_rel_features{args.topk}.npy'), allow_pickle=True)
self.att_val_features = np.load(os.path.join(args.data_path, args.data_choice, args.data_split, f'att_val_features{args.topk}.npy'), allow_pickle=True)
else:
self.att_features, self.att_rel_features,self.att_val_features = self.bert_feature()
np.save(os.path.join(args.data_path, args.data_choice, args.data_split, f'att_features{args.topk}.npy'), self.att_features)
np.save(os.path.join(args.data_path, args.data_choice, args.data_split, f'att_rel_features{args.topk}.npy'), self.att_rel_features)
np.save(os.path.join(args.data_path, args.data_choice, args.data_split, f'att_val_features{args.topk}.npy'), self.att_val_features)
# for i1,i2 in train_ill:
# f1 = self.att_features[np.array(self.att_ids)==i1]
# f2 = self.att_features[np.array(self.att_ids)==i2]
# print('-'*30)
# print('1',self.att_features_text[np.array(self.att_ids)==i1])
# print('2',self.att_features_text[np.array(self.att_ids)==i2])
# for f1i in f1:
# for f2i in f2:
# print(f1i.dot(f2i))
# f1 = self.att_rel_features[self.att2rel[np.array(self.att_ids)==i1]]
# f2 = self.att_rel_features[self.att2rel[np.array(self.att_ids)==i2]]
# print()
# for f1i in f1:
# for f2i in f2:
# print(f1i.dot(f2i))
# f1 = self.att_val_features[np.array(self.att_ids)==i1]
# f2 = self.att_val_features[np.array(self.att_ids)==i2]
# print()
# for f1i in f1:
# for f2i in f2:
# print(f1i.dot(f2i))
self.n_ent = ent_num
self.n_rel = rel_num
self.filters = defaultdict(lambda: set())
self.fact_triple = triples
self.train_triple = self.ill2triples(train_ill)
self.valid_triple = eval_ill # None
self.test_triple = self.ill2triples(test_ill)
# add inverse
self.fact_data = self.double_triple(self.fact_triple)
# self.train_data = np.array(self.double_triple(self.train_triple))
# self.valid_data = self.double_triple(self.valid_triple)
self.test_data = self.double_triple(self.test_triple, ill=True)
self.test_data = np.array(self.test_data)
self.train_data = self.double_triple(self.train_triple, ill=True)
self.train_data = np.array(self.train_data)
if self.use_img_ill:
self.img_ill_triple = self.img_ill2triples(self.img_ill)
self.img_ill_triple = self.double_triple(self.img_ill_triple, ill=True)
self.img_ill_triple = np.array(self.img_ill_triple)
self.img_ill_data = torch.LongTensor(self.img_ill_triple).cuda()
# self.KG,self.M_sub = self.load_graph(self.fact_data) # do it in shuffle_train
self.tKG = self.load_graph(self.fact_data + self.double_triple(self.train_triple, ill=True))
self.tKG = torch.LongTensor(self.tKG).cuda()
# in torch
idd = np.concatenate([np.expand_dims(np.arange(self.n_ent), 1), 2 * self.n_rel * np.ones((self.n_ent, 1)),
np.expand_dims(np.arange(self.n_ent), 1)], 1)
self.fact_data = np.concatenate([np.array(self.fact_data), idd], 0)
self.fact_data = torch.LongTensor(self.fact_data).cuda()
# self.node2index = {}
# for i, triple in enumerate(self.train_triple):
# h, r, t = triple
# assert h not in self.node2index
# assert t not in self.node2index
# self.node2index[h] = i
# self.node2index[t] = i
# self.train_triple = torch.LongTensor(self.train_triple).cuda()
self.n_test = len(self.test_data)
self.n_train = len(self.train_data)
self.shuffle_train()
# if os.path.exists(self.test_cache_url):
# self.test_env = lmdb.open(self.test_cache_url)
# else:
# self.test_env = lmdb.open(self.test_cache_url, map_size=200*1024 * 1024 * 1024, max_dbs=1)
# self.preprocess_test()
def process_rels(self, atts):
rels = []
rels2index = {}
cur = 0
att2rel = []
for i,att in enumerate(atts):
if att[1] not in rels2index:
rels2index[att[1]] = cur
rels.append(att[1])
cur += 1
att2rel.append(rels2index[att[1]])
return np.array(att2rel),rels
def bert_feature(self, ):
from sentence_transformers import SentenceTransformer
from transformers import BertTokenizer, BertModel
tokenizer = BertTokenizer.from_pretrained('bert-base-uncased')
# model = BertModel.from_pretrained("bert-base-uncased").cuda()
# model = SentenceTransformer('sentence-transformers/all-MiniLM-L6-v2').cuda()
model = SentenceTransformer('sentence-transformers/LaBSE').cuda()
outputs = []
texts = [a + ' ' + str(v) for i,a,v in self.att_features]
batch_size = 2048
sent_batch = [texts[i:i + batch_size] for i in range(0, len(texts), batch_size)]
for sent in sent_batch:
# encoded_input = tokenizer(sent, return_tensors='pt', padding=True, truncation=True, max_length=512)
# #cuda
# encoded_input.data['input_ids'] = encoded_input.data['input_ids'].cuda()
# encoded_input.data['attention_mask'] = encoded_input.data['attention_mask'].cuda()
# encoded_input.data['token_type_ids'] = encoded_input.data['token_type_ids'].cuda()
with torch.no_grad():
# output = model(**encoded_input)
output = model.encode(sent)
outputs.append(output)
outputs = np.concatenate(outputs)
# batch_size = 512
sent_batch = [self.rels[i:i + batch_size] for i in range(0, len(self.rels), batch_size)]
rel_outputs = []
for sent in sent_batch:
# encoded_input = tokenizer(sent, return_tensors='pt', padding=True, truncation=True, max_length=512)
# #cuda
# encoded_input.data['input_ids'] = encoded_input.data['input_ids'].cuda()
# encoded_input.data['attention_mask'] = encoded_input.data['attention_mask'].cuda()
# encoded_input.data['token_type_ids'] = encoded_input.data['token_type_ids'].cuda()
with torch.no_grad():
# output = model(**encoded_input)
output = model.encode(sent)
rel_outputs.append(output)
rel_outputs = np.concatenate(rel_outputs)
vals = [str(i[2]) for i in self.att_features]
# batch_size = 512
sent_batch = [vals[i:i + batch_size] for i in range(0, len(vals), batch_size)]
val_outputs = []
for sent in sent_batch:
# encoded_input = tokenizer(sent, return_tensors='pt', padding=True, truncation=True, max_length=512)
# #cuda
# encoded_input.data['input_ids'] = encoded_input.data['input_ids'].cuda()
# encoded_input.data['attention_mask'] = encoded_input.data['attention_mask'].cuda()
# encoded_input.data['token_type_ids'] = encoded_input.data['token_type_ids'].cuda()
with torch.no_grad():
# output = model(**encoded_input)
output = model.encode(sent)
val_outputs.append(output)
val_outputs = np.concatenate(val_outputs)
del model
return outputs, rel_outputs, val_outputs
def ill2triples(self, ill):
return [(i[0], self.n_rel * 2 + 1, i[1]) for i in ill]
def img_ill2triples(self, ill):
return [(i[0], self.n_rel * 2 + 3, i[1]) for i in ill]
# def read_triples(self, filename):
# triples = []
# with open(os.path.join(self.task_dir, filename)) as f:
# for line in f:
# h, r, t = line.strip().split()
# h, r, t = self.entity2id[h], self.relation2id[r], self.entity2id[t]
# triples.append([h, r, t])
# self.filters[(h, r)].add(t)
# self.filters[(t, r + self.n_rel)].add(h)
# return triples
def double_triple(self, triples, ill=False):
new_triples = []
for triple in triples:
h, r, t = triple
new_triples.append([t, r + self.n_rel if not ill else r+1, h])
return triples + new_triples
def load_graph(self, triples):
idd = np.concatenate([np.expand_dims(np.arange(self.n_ent), 1), 2 * self.n_rel * np.ones((self.n_ent, 1)),
np.expand_dims(np.arange(self.n_ent), 1)], 1)
KG = np.concatenate([np.array(triples), idd], 0)
# n_fact = len(KG)
# M_sub = csr_matrix((np.ones((n_fact,)), (np.arange(n_fact), KG[:, 0])),
# shape=(n_fact, self.n_ent))
return KG
def get_subgraphs(self, head_nodes, layer=3,mode='train',sim=None):
all_edges = []
for index,head_node in enumerate(head_nodes):
all_edge = self.get_subgraph(head_node, index, layer, mode,sim=sim)
all_edges.append(all_edge)
all_nodes = []
layer_edges = []
old_nodes_new_idxs = []
old_nodes = []
for i in range(layer):
edges = []
for j in range(len(all_edges)):
edges.append(all_edges[j][i])
edges = torch.cat(edges, dim=0)
edges = edges.long()
head_nodes, head_index = torch.unique(edges[:, [0, 1]], dim=0, sorted=True, return_inverse=True)
tail_nodes, tail_index = torch.unique(edges[:, [0, 3]], dim=0, sorted=True, return_inverse=True)
sampled_edges = torch.cat([edges, head_index.unsqueeze(1), tail_index.unsqueeze(1)], 1)
mask = sampled_edges[:, 2] == (self.n_rel * 2)
old_node, old_idx = head_index[mask].sort()
old_nodes_new_idx = tail_index[mask][old_idx]
all_nodes.append(tail_nodes)
layer_edges.append(sampled_edges)
old_nodes_new_idxs.append(old_nodes_new_idx)
old_nodes.append(old_node)
return all_nodes, layer_edges, old_nodes_new_idxs, old_nodes
#
def get_subgraph(self, head_node, index, layer, mode, max_size=500, sim=None):
if mode == 'train':
# # set false to self.node2index[node]
# mask = torch.ones(len(self.train_triple), dtype=torch.bool).cuda()
# mask[self.node2index[head_node.item()]] = False
# support = self.train_triple[mask]
# reverse_support = support[:, [2, 1, 0]]
# reverse_support[:, 1] += 1
# support = torch.cat((support, reverse_support), dim=0)
# KG = torch.cat((support,self.fact_data),dim=0)
KG=self.KG
else:
KG = self.tKG
if sim is not None:
KG = torch.cat((KG, sim), dim=0)
if self.use_img_ill:
KG = torch.cat((KG, self.img_ill_data), dim=0)
row, col = KG[:, 0], KG[:, 2]
node_mask = row.new_empty(self.n_ent, dtype=torch.bool)
# edge_mask = row.new_empty(row.size(0), dtype=torch.bool)
subsets = [torch.LongTensor([head_node]).cuda()]
raw_layer_edges = []
for i in range(layer):
node_mask.fill_(False)
node_mask[subsets[-1]] = True
edge_mask = torch.index_select(node_mask, 0, row)
subsets.append(torch.unique(col[edge_mask]))
raw_layer_edges.append(edge_mask)
# nodes, edges, old_nodes_new_idx = self.get_neighbors(nodes.data.cpu().numpy())
# delete target not in the other KG
tail_node = self.left_ents if head_node.item() >= len(self.left_ents) else self.right_ents
tail_node = torch.LongTensor(tail_node).cuda()
node_mask_ = row.new_empty(self.n_ent, dtype=torch.bool)
node_mask_.fill_(False)
node_mask_[tail_node] = True
tail_set = subsets[-1]
node_mask.fill_(False)
node_mask[tail_set] = True
node_mask = node_mask & node_mask_
layer_edges = []
for i in reversed(range(layer)):
edge_mask = torch.index_select(node_mask, 0, col)
edge_mask = edge_mask & raw_layer_edges[i]
node_mask_.fill_(False)
node_mask_[row[edge_mask]] = True
node_mask = node_mask | node_mask_
layer_edges.append(KG[edge_mask])
layer_edges = layer_edges[::-1]
batched_edges = []
for i in range(layer):
layer_edges[i] = torch.unique(layer_edges[i], dim=0)
batched_edges.append(torch.cat([torch.ones(len(layer_edges[i])).unsqueeze(1).cuda() * index, layer_edges[i]], 1))
return batched_edges
def get_vis_subgraph(self, head_node, tail_node, layer, max_size=500, sim=None):
KG = self.tKG
if sim is not None:
KG = torch.cat((KG, sim), dim=0)
row, col = KG[:, 0], KG[:, 2]
node_mask = row.new_empty(self.n_ent, dtype=torch.bool)
# edge_mask = row.new_empty(row.size(0), dtype=torch.bool)
subsets = [torch.LongTensor([head_node]).cuda()]
raw_layer_edges = []
for i in range(layer):
node_mask.fill_(False)
node_mask[subsets[-1]] = True
edge_mask = torch.index_select(node_mask, 0, row)
subsets.append(torch.unique(col[edge_mask]))
raw_layer_edges.append(edge_mask)
# nodes, edges, old_nodes_new_idx = self.get_neighbors(nodes.data.cpu().numpy())
# delete target not in the other KG
# tail_node = self.left_ents if head_node.item() >= len(self.left_ents) else self.right_ents
tail_node = torch.LongTensor([tail_node]).cuda()
node_mask_ = row.new_empty(self.n_ent, dtype=torch.bool)
node_mask_.fill_(False)
node_mask_[tail_node] = True
tail_set = subsets[-1]
node_mask.fill_(False)
node_mask[tail_set] = True
node_mask = node_mask & node_mask_
layer_edges = []
for i in reversed(range(layer)):
edge_mask = torch.index_select(node_mask, 0, col)
edge_mask = edge_mask & raw_layer_edges[i]
node_mask_.fill_(False)
node_mask_[row[edge_mask]] = True
node_mask = node_mask | node_mask_
layer_edges.append(KG[edge_mask])
layer_edges = layer_edges[::-1]
batched_edges = []
for i in range(layer):
layer_edges[i] = torch.unique(layer_edges[i], dim=0)
batched_edges.append(layer_edges[i])
return batched_edges
# def get_neighbors(self, nodes, mode='train', n_hop=0):
# if mode == 'train':
# KG = self.KG
# M_sub = self.M_sub
# else:
# KG = self.tKG
# M_sub = self.tM_sub
# # if self.test_cache
#
# # nodes: n_node x 2 with (batch_idx, node_idx)
# node_1hot = csr_matrix((np.ones(len(nodes)), (nodes[:, 1], nodes[:, 0])), shape=(self.n_ent, nodes.shape[0])) # (n_ent, batch_size)
# edge_1hot = M_sub.dot(node_1hot)
# edges = np.nonzero(edge_1hot)
# sampled_edges = np.concatenate([np.expand_dims(edges[1], 1), KG[edges[0]]],
# axis=1) # (batch_idx, head, rela, tail)
# sampled_edges = torch.LongTensor(sampled_edges).cuda()
#
# # index to nodes
# head_nodes, head_index = torch.unique(sampled_edges[:, [0, 1]], dim=0, sorted=True, return_inverse=True)
# tail_nodes, tail_index = torch.unique(sampled_edges[:, [0, 3]], dim=0, sorted=True, return_inverse=True)
#
# sampled_edges = torch.cat([sampled_edges, head_index.unsqueeze(1), tail_index.unsqueeze(1)], 1)
#
# mask = sampled_edges[:, 2] == (self.n_rel * 2)
# _, old_idx = head_index[mask].sort()
# old_nodes_new_idx = tail_index[mask][old_idx]
#
# return tail_nodes, sampled_edges, old_nodes_new_idx
# def get_neighbor(self, node, mode='train', n_hop=0):
# if mode == 'train':
# # set false to self.node2index[node]
# mask = torch.ones(len(self.train_triple), dtype=torch.bool)
# mask[self.node2index[node]] = False
# KG = torch.cat(self.train_triple[mask],self.fact_data)
#
# else:
# KG = self.tKG
# # if self.test_cache
#
# # nodes: n_node x 2 with (batch_idx, node_idx)
# # node_1hot = csr_matrix((np.ones(len(nodes)), (nodes[:, 1], nodes[:, 0])), shape=(self.n_ent, nodes.shape[0])) # (n_ent, batch_size)
# # edge_1hot = M_sub.dot(node_1hot)
# edges = KG[:, 0]==node
# edges = np.nonzero(edges)
# sampled_edges = KG[edges[0]] # (head, rela, tail)
# sampled_edges = torch.LongTensor(sampled_edges).cuda()
#
# # index to nodes
# head_nodes, head_index = torch.unique(sampled_edges[:, 1], dim=0, sorted=True, return_inverse=True)
# tail_nodes, tail_index = torch.unique(sampled_edges[:, 3], dim=0, sorted=True, return_inverse=True)
#
# sampled_edges = torch.cat([sampled_edges, head_index.unsqueeze(1), tail_index.unsqueeze(1)], 1)
#
# # mask = sampled_edges[:, 2] == (self.n_rel * 2)
# # _, old_idx = head_index[mask].sort()
# # old_nodes_new_idx = tail_index[mask][old_idx]
#
# return tail_nodes, sampled_edges
def get_batch(self, batch_idx, steps=2, data='train'):
if data == 'train':
return self.train_data[batch_idx]
if data == 'valid':
return None
if data == 'test':
return self.test_data[batch_idx]
# subs = []
# rels = []
# objs = []
#
# subs = query[batch_idx, 0]
# rels = query[batch_idx, 1]
# objs = np.zeros((len(batch_idx), self.n_ent))
# for i in range(len(batch_idx)):
# objs[i][answer[batch_idx[i]]] = 1
# return subs, rels, objs
def shuffle_train(self, ):
# fact_triple = np.array(self.fact_triple)
# train_triple = np.array(self.train_triple)
# all_triple = np.concatenate([fact_triple, train_triple], axis=0)
# n_all = len(all_triple)
# rand_idx = np.random.permutation(n_all)
# all_triple = all_triple[rand_idx]
# random shuffle train_triples
random.shuffle(self.train_triple)
# support/query split 3/1
support_triple = self.train_triple[:len(self.train_triple) * 3 // 4]
query_triple = self.train_triple[len(self.train_triple) * 3 // 4:]
# add inverse triples
support_triple = self.double_triple(support_triple, ill=True)
query_triple = self.double_triple(query_triple, ill=True)
support = torch.LongTensor(support_triple).cuda()
self.KG = torch.cat((support,self.fact_data),dim=0)
# now the fact triples are fact_triple + support_triple
# self.KG, self.M_sub = self.load_graph(self.fact_data + support_triple)
self.n_train = len(query_triple)
self.train_data = np.array(query_triple)
# # increase the ratio of fact_data, e.g., 3/4->4/5, can increase the performance
# self.fact_data = self.double_triple(all_triple[:n_all * 3 // 4].tolist())
# self.train_data = np.array(self.double_triple(all_triple[n_all * 3 // 4:].tolist()))
# self.n_train = len(self.train_data)
# self.KG,self.M_sub = self.load_graph(self.fact_data)
print('n_train:', self.n_train, 'n_test:', self.n_test)
def preprocess_test(self, ):
batch_size = 4
n_data = self.n_test
n_batch = n_data // batch_size + (n_data % batch_size > 0)
for i in tqdm(range(n_batch)):
start = i * batch_size
end = min(n_data, (i + 1) * batch_size)
batch_idx = np.arange(start, end)
triple = self.get_batch(batch_idx, data='test')
subs, rels, objs = triple[:, 0], triple[:, 1], triple[:, 2]
print(subs, rels, objs)
n = len(subs)
q_sub = torch.LongTensor(subs).cuda()
nodes = torch.cat([torch.arange(n).unsqueeze(1).cuda(), q_sub.unsqueeze(1)], 1)
for h in range(5):
nodes, edges, old_nodes_new_idx = self.get_neighbors(nodes.data.cpu().numpy(), mode='test',
n_hop=h)
# to np
# self.test_cache[(i, h)] = (nodes.cpu().numpy(), edges.cpu().numpy(), old_nodes_new_idx.cpu().numpy())
# use lmdb write
with self.test_env.begin(write=True) as txn:
txn.put(f'{i}_{h}'.encode(), pickle.dumps((nodes.cpu().numpy(), edges.cpu().numpy(), old_nodes_new_idx.cpu().numpy())))
# pickle.dump(self.test_cache, open(self.test_cache_url, 'wb'))
def get_test_cache(self, batch_idx, h):
#use lmdb read
with self.test_env.begin(write=False) as txn:
nodes, edges, old_nodes_new_idx = pickle.loads(txn.get(f'{batch_idx}_{h}'.encode()))
return nodes, edges, old_nodes_new_idx
# return self.test_cache[(batch_idx, h)]
# def save_cache(self):
# with open(self.cache_path, 'wb') as f:
# pickle.dump(self.edge_cache, f)
#
# def load_cache(self):
# with open(self.cache_path, 'rb') as f:
# self.edge_cache = pickle.load(f)
# print("load cache from {}".format(self.cache_path))