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dataUtils.py
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import os
import sys
sys.path.append(os.path.dirname(os.path.abspath(__file__)))
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
from tqdm import tqdm
from pathlib import Path
import time
import pdb
from joblib import Parallel, delayed
import numpy as np
from nltk.corpus import stopwords
from skeleton import *
from audio import *
from text import *
from common import *
from argsUtils import *
import bisect
import torch
from torch.utils.data import Dataset, DataLoader, ConcatDataset, Sampler
from torch.utils.data._utils.collate import default_collate
from transformers import BertTokenizer
import logging
logging.getLogger('transformers').setLevel(logging.CRITICAL)
from functools import partial
class DummyData(Dataset):
def __init__(self, variable_list=['pose', 'audio'], length=1000, random=False, pause=False):
super(DummyData, self).__init__()
self.variable_list = variable_list
self.len = length
self.pause = pause
if random:
self.data = {variable:torch.rand(self.len, 30, 50) + 1 for variable in self.variable_list}
else:
self.data = {variable:torch.arange(self.len) + 1 for variable in self.variable_list}
def __getitem__(self, idx):
if self.pause:
time.sleep(self.pause)
return {variable:self.data[variable][idx].to(torch.double) for variable in self.variable_list}
def __len__(self):
return self.len
class Data(Modality):
r'''
Wrapper for DataLoaders
Arguments:
path2data (str): path to dataset.
speaker (str): speaker name.
modalities (list of str): list of modalities to wrap in the dataloader. These modalities are basically keys of the hdf5 files which were preprocessed earlier (default: ``['pose/data', 'audio/log_mel']``)
fs_new (list, optional): new frequency of modalities, to which the data is up/downsampled to. (default: ``[15, 15]``).
time (float, optional): time snippet length in seconds. (default: ``4.3``).
split (tuple or None, optional): split fraction of train and dev sets. Must add up to less than 1. If ``None``, use ``dataset`` columns in the master dataframe (loaded in self.df) to decide train, dev and test split. (default: ``None``).
batch_size (int, optional): batch size of the dataloader. (default: ``100``).
shuffle (boolean, optional): set to ``True`` to have the data reshuffled at every epoch (default: ``False``).
num_workers (int, optional): set to values >0 to have more workers to load the data. argument for torch.utils.data.DataLoader. (default: ``15``).
Example::
from data.dataUtils import Data
data = Data('../dataset/groot/data/', 'oliver', ['pose/data'], [15])
for batch in data.train:
break
print(batch).
'''
def __init__(self, path2data, speaker,
modalities = ['pose/data', 'audio/log_mel_512'],
fs_new=[15, 15], time=4.3,
split=None,
batch_size=100, shuffle=True, num_workers=0,
window_hop=0,
load_data=True,
style_iters=0,
num_training_sample=None,
sample_all_styles=0,
repeat_text=1,
quantile_sample=None,
quantile_num_training_sample=None,
weighted=0,
filler=0,
num_training_iters=None):
super().__init__(path2data=path2data)
self.path2data = path2data
self.speaker = speaker
self.modalities = modalities
self.fs_new = fs_new
self.time = time
self.split = split
self.batch_size = batch_size
self.shuffle = shuffle
self.num_workers = num_workers
self.window_hop = window_hop
self.load_data = load_data
self.style_iters = style_iters ## used to call a train sampler
self.num_training_sample = num_training_sample
self.sample_all_styles = sample_all_styles
self.repeat_text = repeat_text
self.quantile_sample = quantile_sample
self.quantile_num_training_sample = quantile_num_training_sample
self.weighted = weighted
self.filler = filler
if self.filler:
self.stopwords = stopwords.words('english')
self.tokenizer = BertTokenizer.from_pretrained('bert-base-uncased')
else:
self.stopwords, self.tokenizer = None, None
self.num_training_iters = num_training_iters
self.text_in_modalities = False
for modality in self.modalities:
if 'text' in modality:
self.text_in_modalities = True
self.missing = MissingData(self.path2data)
if isinstance(self.speaker, str):
self.speaker = [self.speaker]
## Load all modalities
self.modality_classes = self._load_modality_classes()
## Load the master table
self.df = pd.read_csv((Path(self.path2data)/'cmu_intervals_df.csv').as_posix())
self.df = self.df.append(pd.read_csv((Path(self.path2data)/'cmu_intervals_df_transforms.csv').as_posix())) ## file with evil twins
self.df.loc[:, 'interval_id'] = self.df['interval_id'].apply(str)
## Check for missing_data
#self.missing_data
if speaker[0] == 'all':
# self.df = self.get_df_subset('speaker', self.speakers)
self.speaker = self.speakers
else:
pass
# self.df = self.get_df_subset('speaker', speaker)
self.df = self.get_df_subset('speaker', self.speaker)
## Create Style Dictionary
self.style_dict = {sp:i for i, sp in enumerate(self.speaker)}
assert len(self.df.values), 'speaker `{}` not found'.format(speaker)
#if self.load_data:
## get train-dev-test split
self.datasets = self.tdt_split()
self.dataLoader_kwargs = {'batch_size':batch_size,
'shuffle':shuffle,
'num_workers':num_workers,
'pin_memory':False}
## if not repeat_text, do not repeat the word vectors to match the fs
#if True: #not self.repeat_text:
if self.text_in_modalities:
## always keep text/token_duration at the end to comply with the collate_fn_pad
pad_keys = ['text/w2v', 'text/bert', 'text/filler', 'text/tokens', 'text/token_duration']
self.dataLoader_kwargs.update({'collate_fn':partial(collate_fn_pad, pad_key=pad_keys, dim=0)})
self.update_dataloaders(time, window_hop)
def _load_modality_classes(self):
modality_map = {}
for modality in self.modalities:
mod = modality.split('/')[0]
modality_map[modality] = self.mod_map(mod)
return modality_map
def mod_map(self, mod):
mod_map_dict = {
'pose': Skeleton2D,
'audio': Audio,
'text': Text
}
return mod_map_dict[mod](path2data=self.path2data, speaker=self.speaker)
# def get_df_subset(self, column, value):
# if isinstance(value, list):
# return self.df[self.df[column].isin(value)]
# else:
# return self.df[self.df[column] == value]
def getSpeaker(self, x):
return self.get_df_subset('interval_id', x)['speaker'].values[0]
def getPath2file(self, x):
return (Path(self.path2data)/'processed'/self.getSpeaker(x)/str(x)).as_posix() + '.h5'
def getStyle(self, interval_id):
df_subset = self.get_df_subset('interval_id', interval_id)
speaker = df_subset.speaker.iloc[0]
try:
style = self.style_dict[speaker]
except:
raise 'speaker style for {} not found'.format(speaker)
return style
def get_transforms_missing_intervals(self, missing_intervals):
transforms = []
for speaker in self.speaker:
if '|' in speaker:
transforms.append(speaker.split('|')[-1])
transforms = sorted(list(set(transforms)))
new_missing_intervals = set()
for transform in transforms:
for interval in missing_intervals:
new_missing_intervals.update({'{}|{}'.format(interval, transform)})
missing_intervals.update(new_missing_intervals)
return missing_intervals
def order_intervals(self, intervals):
interval_dict = {i:[] for i in self.style_dict}
for interval in intervals:
interval_dict[self.getSpeaker(interval)].append(interval)
intervals_dict = [(k, interval_dict[k]) for k in interval_dict]
ordered_intervals = []
for tup in intervals_dict:
ordered_intervals += tup[1]
return intervals_dict, ordered_intervals
@property
def minidataKwargs(self):
minidataKwargs = {'modalities':self.modalities,
'fs_new':self.fs_new,
'time':self.time,
'modality_classes':self.modality_classes,
'window_hop':self.window_hop,
'repeat_text':self.repeat_text,
'text_in_modalities':self.text_in_modalities,
'filler':self.filler,
'stopwords':self.stopwords,
'tokenizer':self.tokenizer}
return minidataKwargs
def get_minidata_list(self, intervals):
return [MiniData(self.getPath2file(interval_id), style=self.getStyle(interval_id), **self.minidataKwargs)
for interval_id in tqdm(intervals)]
def tdt_split(self):
if not self.split:
df_train = self.get_df_subset('dataset', 'train')
df_dev = self.get_df_subset('dataset', 'dev')
df_test = self.get_df_subset('dataset', 'test')
else:
length = self.df.shape[0]
end_train = int(length*self.split[0])
start_dev = end_train
end_dev = int(start_dev + length*self.split[1])
start_test = end_dev
df_train = self.df[:end_train]
df_dev = self.df[start_dev:end_dev]
df_test = self.df[start_test:]
## get missing intervals
missing_intervals = self.missing.load_intervals()
missing_intervals = self.get_transforms_missing_intervals(missing_intervals)
## get new train/dev/test intervals
get_intervals = lambda x: sorted(list(set(x['interval_id'].unique()) - missing_intervals))
train_intervals = get_intervals(df_train)
dev_intervals = get_intervals(df_dev)
test_intervals = get_intervals(df_test)
self.train_intervals_all = train_intervals
self.dev_intervals_all = dev_intervals
self.test_intervals_all = test_intervals
if not self.load_data: ## load a sample of the data just to get the shape
train_intervals = train_intervals[:10]
dev_intervals = dev_intervals[:10]
test_intervals = test_intervals[:10]
## update_train_intervals
train_intervals, dev_intervals, test_intervals, train_intervals_dict = self.update_intervals(train_intervals, dev_intervals, test_intervals)
self.train_intervals = train_intervals
self.dev_intervals = dev_intervals
self.test_intervals = test_intervals
dataset_train = ConcatDatasetIndex(self.get_minidata_list(train_intervals))
dataset_dev = ConcatDatasetIndex(self.get_minidata_list(dev_intervals))
dataset_test = ConcatDatasetIndex(self.get_minidata_list(test_intervals))
self.dataset_train = dataset_train
self.train_intervals_dict = train_intervals_dict
self.train_sampler = self.get_train_sampler(dataset_train, train_intervals_dict)
return {'train': dataset_train,
'dev': dataset_dev,
'test': dataset_test}
def update_dataloaders(self, time, window_hop):
## update idx_list for all minidata
for key in self.datasets:
for d_ in self.datasets[key].datasets:
d_.update_idx_list(time, window_hop)
train_dataLoader_kwargs = self.dataLoader_kwargs.copy()
if self.train_sampler:
train_dataLoader_kwargs['shuffle'] = False
self.train = DataLoader(ConcatDatasetIndex(self.datasets['train'].datasets), sampler=self.train_sampler, **train_dataLoader_kwargs)
self.dev = DataLoader(ConcatDatasetIndex(self.datasets['dev'].datasets), **self.dataLoader_kwargs)
self.test = DataLoader(ConcatDatasetIndex(self.datasets['test'].datasets), **self.dataLoader_kwargs)
def get_alternate_class_sampler(self, dataset, intervals_dict, num_samples):
class_count = []
interval_offset = 0
for tup in intervals_dict:
count = 0
for i in range(len(tup[1])):
count+=len(dataset.datasets[i+interval_offset])
class_count.append(count)
interval_offset += len(tup[1])
return AlternateClassSampler(class_count, num_samples*self.batch_size)
def update_intervals(self, train_intervals, dev_intervals, test_intervals):
def subsample_intervals(x):
temp = []
for x_ in x:
if self.sample_all_styles > 0:
temp.extend(x_[1][:self.sample_all_styles])
elif self.sample_all_styles == -1:
temp.extend(x_[1])
return temp
if self.sample_all_styles != 0:
train_intervals_dict, train_intervals = self.order_intervals(train_intervals)
dev_intervals_dict, dev_intervals = self.order_intervals(dev_intervals)
test_intervals_dict, test_intervals = self.order_intervals(test_intervals)
train_intervals = subsample_intervals(train_intervals_dict)
dev_intervals = subsample_intervals(dev_intervals_dict)
test_intervals = subsample_intervals(test_intervals_dict)
elif self.style_iters > 0: ## using AlternateClassSampler
train_intervals_dict, train_intervals = self.order_intervals(train_intervals)
else:
train_intervals_dict = None
return train_intervals, dev_intervals, test_intervals, train_intervals_dict
def get_quantile_sample(self, data, q):
pose_modality = None
for key in self.modalities:
if 'pose' in key:
pose_modality = key
break
assert pose_modality is not None, "can't find pose modality"
if isinstance(q, float) or isinstance(q, int):
if q<1:
kind = 'above'
elif q>1:
kind = 'rebalance'
q = int(q)
else:
raise 'q can\'t be 1 or negative'
elif isinstance(q, list):
assert np.array([q_<=1 and q_>=0 for q_ in q]).all(), 'quantile_sample is in [0,1]'
assert len(q) == 2
kind = 'tail'
## get distribution of velocities
diff = lambda x, idx: x[1:, idx] - x[:-1, idx]
vel = lambda x, idx: (((diff(x, idx))**2).sum(-1)**0.5).mean()
samples = []
for batch in tqdm(data, desc='quantile_sample_calc'):
pose = batch[pose_modality]
pose = pose.reshape(pose.shape[0], 2, -1).transpose(0, 2, 1)
samples.append(vel(pose, list(range(1, pose.shape[1]))))
min_sample, max_sample = min(samples), max(samples)
if kind == 'above':
v0 = np.quantile(np.array(samples, dtype=np.float), q)
print('above {} percentile'.format(v0))
elif kind == 'tail':
v0 = [np.quantile(np.array(samples, dtype=np.float), q[0]), np.quantile(np.array(samples, dtype=np.float), q[1])]
print('below {} and above {} percentile'.format(*v0))
elif kind == 'rebalance':
v0 = torch.arange(min_sample, max_sample+1e-5, (max_sample - min_sample)/q)
print('rebalaced data'+(' {}'*len(v0)).format(*v0))
def in_subset(v, v0):
if kind == 'above':
return v > v0
elif kind == 'tail':
return (v > v0[1]) or (v < v0[0])
elif kind == 'rebalance':
starts, ends = v0[:-1], v0[1:]
interval = ((starts <= v) * (v <= ends))
if interval.any():
return interval.int().argmax().item()
else:
raise 'incorrect interval'
if kind in ['tail', 'above']:
subset_idx = []
elif kind == 'rebalance':
subset_idx = [[] for _ in range(len(v0) - 1)]
for i, batch in tqdm(enumerate(data), desc='quantile subset'):
pose = batch[pose_modality]
pose = pose.reshape(pose.shape[0], 2, -1).transpose(0, 2, 1)
v = vel(pose, list(range(1, pose.shape[1])))
if kind in ['tail', 'above']:
if in_subset(v, v0):
subset_idx.append(i)
elif kind == 'rebalance':
subset_idx[in_subset(v, v0)].append(i)
return subset_idx, kind
def get_train_sampler(self, dataset_train, train_intervals_dict):
## Style iterations with AlternateClassSampler
if self.style_iters > 0 and self.sample_all_styles == 0:
train_sampler = self.get_alternate_class_sampler(dataset_train, train_intervals_dict, self.style_iters)
## Sampler with lesser number of samples for few-shot learning.
elif self.num_training_sample is not None:
subset_idx = torch.randperm(len(dataset_train))
train_sampler = torch.utils.data.SubsetRandomSampler(subset_idx[:self.num_training_sample])
elif self.quantile_sample is not None:
subset_idx, kind = self.get_quantile_sample(dataset_train, self.quantile_sample)
if kind in ['above', 'tail']:
train_sampler = torch.utils.data.SubsetRandomSampler(subset_idx)
elif kind in ['rebalance'] and self.quantile_num_training_sample is not None:
subset_idx = [torch.LongTensor(li) for li in subset_idx]
train_sampler = BalanceClassSampler(subset_idx, int(self.quantile_num_training_sample)*self.batch_size)
elif self.weighted:
train_sampler = torch.utils.data.WeightedRandomSampler([1]*len(dataset_train), self.weighted*self.batch_size)
elif self.num_training_iters is not None:
train_sampler = torch.utils.data.RandomSampler(dataset_train, num_samples=self.num_training_iters*self.batch_size, replacement=True)
else:
train_sampler = torch.utils.data.RandomSampler(dataset_train)
#train_sampler = None
return train_sampler
def close_hdf5_files(self, files):
for h5 in files:
h5.close()
@property
def shape(self):
for minidata in self.train.dataset.datasets:
if len(minidata) > 0:
break
shape = {}
for modality, feats_shape in zip(self.modalities, minidata.shapes):
start = minidata.idx_start_list_dict[modality][0]
end = minidata.idx_end_list_dict[modality][0]
interval = minidata.idx_interval_dict[modality]
length = len(range(start, end, interval))
shape.update({modality:[length, feats_shape[-1]]})
return shape
class MiniData(Dataset, HDF5):
def __init__(self, path2h5, modalities, fs_new, time, modality_classes, window_hop, style=0, repeat_text=1, text_in_modalities=False, filler=0, **kwargs):
super(MiniData, self).__init__()
self.path2h5 = path2h5
self.modalities = modalities
self.fs_new = fs_new
self.time = time
self.modality_classes = modality_classes
self.window_hop = window_hop
self.style = style
self.repeat_text = repeat_text
self.text_in_modalities = text_in_modalities
self.filler = filler
## load modality shapes and maybe data
self.shapes = []
self.data = []
for modality in self.modalities:
try:
data, h5 = self.load(self.path2h5, modality)
except:
print(self.path2h5, modality)
sys.exit(1)
self.shapes.append(data.shape)
self.data.append(data[()])
h5.close()
if self.text_in_modalities:
try:
self.text_df = pd.read_hdf(self.path2h5, key='text/meta')
except:
self.text_df = None
if self.filler:
self.stopwords = kwargs['stopwords']
self.tokenizer = kwargs['tokenizer']
## create idx lists
self.idx_start_list_dict = {}
self.idx_end_list_dict = {}
self.idx_interval_dict = {}
self.update_idx_list(self.time, self.window_hop)
def update_idx_list(self, time, window_hop=0):
for modality, fs_new, shape in zip(self.modalities, self.fs_new, self.shapes):
fs = self.modality_classes[modality].fs(modality)
window = int(time*fs)
assert window_hop < window, 'hop size {} must be less than window size {}'.format(window_hop, int(time*fs))
fs_ratio = round(fs/fs_new)
self.idx_interval_dict[modality] = fs_ratio
if not window_hop:
time_splits = np.r_[range(0, shape[0]-window, int(window))]
else:
time_splits = np.r_[range(0, shape[0]-window, int(window_hop*fs_ratio))]
self.idx_start_list_dict[modality] = time_splits[:]
self.idx_end_list_dict[modality] = time_splits + window
#len_starts = [len(self.idx_start_list_dict[modality]) for modality in self.idx_start_list_dict]
#raise len_starts[0] == len_starts[1], 'number of idxes are not consistent in file {}'.format(self.path2h5)
def __len__(self):
return min([len(self.idx_start_list_dict[modality]) for modality in self.modalities])
#return len(self.idx_start_list_dict[self.modalities[0]])
def __getitem__(self, idx):
item = {}
## args.modalities = ['pose/normalize', 'text/w2v']
for i, modality in enumerate(self.modalities):
## read from loaded data
data = self.data[i]
## open h5 file
#data, h5 = self.load(self.path2h5, modality)
start = self.idx_start_list_dict[modality][idx]
end = self.idx_end_list_dict[modality][idx]
interval = self.idx_interval_dict[modality]
item[modality] = data[start:end:interval].astype(np.float64)
start_time = data[0:start:interval].shape[0] / self.fs_new[-1]
if 'text' in modality:
vec = item[modality]
indices = [0] ## starts in 64 frames
if self.text_df is None or modality == 'text/tokens': ## to be used with self.repeat_text = 0
for t in range(1, vec.shape[0]):
if (vec[t] - vec[indices[-1]]).sum() != 0:
indices.append(t)
else:
text_df_ = self.text_df[(start <= self.text_df['end_frame']) & (end > self.text_df['start_frame'])]
starts_ = text_df_['start_frame'].values - start
starts_[0] = 0
indices = list(starts_.astype(np.int))
if not self.repeat_text:
item.update({modality:vec[indices]}) ## if self.repeat_text == 0, update the text modality
## add filler masks
if self.filler:
filler = np.zeros((len(indices),))
if self.text_df is None:
pass ## if text_df is not available, assume no word is filler
else:
words = self.text_df[(start <= self.text_df['end_frame']) & (end > self.text_df['start_frame'])].Word.values
words = [word.lower() for word in words]
if 'bert' in modality or 'tokens' in modality:
words = self.tokenizer.tokenize(' '.join(words))
for i, word in enumerate(words[:len(indices)]):
if word in self.stopwords:
filler[i] = 1
if self.repeat_text:
filler_ = np.zeros((vec.shape[0], ))
end_indices = indices[1:] + [vec.shape[0]]
for i, (st, en) in enumerate(zip(indices, end_indices)):
filler_[st:en] = filler[i]
filler = filler_
item.update({'text/filler':filler})
## duration of each word
indices_arr = np.array(indices).astype(np.int)
length_word = np.zeros_like(indices_arr)
length_word[:-1] = indices_arr[1:] - indices_arr[:-1]
duration = (end-start)/interval
length_word[-1] = duration - indices_arr[-1]
item.update({'text/token_duration':length_word.astype(np.int)})
## close h5 file
#h5.close()
## start and end times of audio in the interval
#start_time = self.fs_new[-1] * data[0:start:interval].shape[0]
duration = item[self.modalities[0]].shape[0]/self.fs_new[-1]
#duration = ((end-start)/interval)/self.fs_new[-1]
end_time = start_time + duration
item.update({'meta':{'interval_id':Path(self.path2h5).stem,
'start':start_time,
'end':end_time,
'idx':idx}})
item['style'] = np.zeros(item[self.modalities[0]].shape[0]) + self.style
return item
def close_h5_files(self, files):
for h5 in files:
h5.close()
class AlternateClassSampler(Sampler):
def __init__(self, class_count, num_samples, replacement=True):
self.num_samples_per_class = num_samples//len(class_count)
self.num_samples = self.num_samples_per_class*len(class_count)
self.class_count = class_count
self.starts = [0]
self.ends = []
for counts in self.class_count:
self.starts.append(self.starts[-1]+counts)
self.ends.append(self.starts[-1])
self.starts = self.starts[:-1]
def __iter__(self):
return iter(torch.stack([torch.randint(start, end, size=(self.num_samples_per_class, )) for start, end in zip(self.starts, self.ends)], dim=1).view(-1).tolist())
def __len__(self):
return self.num_samples
class BalanceClassSampler(Sampler):
def __init__(self, classes, num_samples, replacement=True):
self.classes = classes
self.update_classes()
self.num_samples_per_class = num_samples//len(self.classes)
self.num_samples = self.num_samples_per_class*len(self.classes)
def update_classes(self):
cl_list = []
for cl in self.classes:
if cl.shape[0] > 0:
cl_list.append(cl)
self.classes = cl_list
def __iter__(self):
return iter(torch.stack([class_idx[torch.randint(0, len(class_idx), size=(self.num_samples_per_class,))] for class_idx in self.classes], dim=1).view(-1).tolist())
def __len__(self):
return self.num_samples
class ConcatDatasetIndex(ConcatDataset):
def __init__(self, datasets):
super().__init__(datasets)
def __getitem__(self, idx):
if idx < 0:
if -idx > len(self):
raise ValueError("absolute value of index should not exceed dataset length")
idx = len(self) + idx
dataset_idx = bisect.bisect_right(self.cumulative_sizes, idx)
if dataset_idx == 0:
sample_idx = idx
else:
sample_idx = idx - self.cumulative_sizes[dataset_idx - 1]
batch = self.datasets[dataset_idx][sample_idx]
if isinstance(batch, dict):
batch.update({'idx':idx})
return batch
def unittest(args, exp_num):
path2data = args.path2data
speaker = args.speaker
modalities = args.modalities
fs_new = args.fs_new
time = args.time
split = args.split
batch_size = args.batch_size
shuffle = args.shuffle
data = Data(path2data=path2data,
speaker=speaker,
modalities=modalities,
fs_new=fs_new,
time=time,
split=split,
batch_size=batch_size,
shuffle=shuffle)
print('Speaker: {}'.format(speaker))
for batch in tqdm(data.train):
continue
sizes = {modality:batch[modality].shape for modality in modalities}
print('train')
print(sizes)
for batch in tqdm(data.dev):
continue
sizes = {modality:batch[modality].shape for modality in modalities}
print('dev')
print(sizes)
for batch in tqdm(data.test):
continue
sizes = {modality:batch[modality].shape for modality in modalities}
print('test')
print(sizes)
if __name__ == '__main__':
argparseNloop(unittest)