def multiple_samples_collate(batch, fold=False):
"""
Collate function for repeated augmentation. Each instance in the batch has
more than one sample.
Args:
batch (tuple or list): data batch to collate.
Returns:
(tuple): collated data batch.
"""
inputs, labels, video_idx, time, extra_data = zip(*batch)
inputs = [item for sublist in inputs for item in sublist]
labels = [item for sublist in labels for item in sublist]
video_idx = [item for sublist in video_idx for item in sublist]
time = [item for sublist in time for item in sublist]
inputs, labels, video_idx, time, extra_data = (
default_collate(inputs),
default_collate(labels),
default_collate(video_idx),
default_collate(time),
default_collate(extra_data),
)
if fold:
return [inputs], labels, video_idx, time, extra_data
else:
return inputs, labels, video_idx, time, extra_data
def collate(batch):
return {
IMAGE: default_collate([d[IMAGE] for d in batch]).float(),
KEYPOINT_MAP:
default_collate([d[KEYPOINT_MAP] for d in batch]).float(),
MASK: default_collate([d[MASK] for d in batch]).float().unsqueeze(0)
}
def collate_fn(batch):
batch_clips, batch_targets, batch_keys = zip(*batch)
# batch_keys = [key for key in batch_keys]
return default_collate(batch_clips), default_collate(
batch_targets), batch_keys
def maskv3_collate_fn(data):
imgs, masks, targets = zip(*data)
imgs = default_collate(imgs)
targets = default_collate(targets)
return imgs, masks, targets
def collate(batch):
if len(batch) == 0:
return batch
elem = batch[0]
if elem is None:
return None
elif isinstance(elem, container_abcs.Sequence):
if len(
elem
) == 4: # We assume those are the maps, map points, headings and patch_size
scene_map, scene_pts, heading_angle, patch_size = zip(*batch)
if heading_angle[0] is None:
heading_angle = None
else:
heading_angle = torch.Tensor(heading_angle)
map = scene_map[0].get_cropped_maps_from_scene_map_batch(
scene_map,
scene_pts=torch.Tensor(scene_pts),
patch_size=patch_size[0],
rotation=heading_angle)
return map
if isinstance(elem, (str, int)):
return default_collate(batch)
transposed = zip(*batch)
return [collate(samples) for samples in transposed]
elif isinstance(elem, container_abcs.Mapping):
# We have to dill the neighbors structures. Otherwise each tensor is put into
# shared memory separately -> slow, file pointer overhead
# we only do this in multiprocessing
neighbor_dict = {key: [d[key] for d in batch] for key in elem}
return dill.dumps(neighbor_dict) if torch.utils.data.get_worker_info(
) else neighbor_dict
return default_collate(batch)
def detection_collate(batch):
"""
Collate function for detection task. Concatanate bboxes, labels and
metadata from different samples in the first dimension instead of
stacking them to have a batch-size dimension.
Args:
batch (tuple or list): data batch to collate.
Returns:
(tuple): collated detection data batch.
"""
inputs, labels, video_idx, extra_data = zip(*batch)
inputs, video_idx = default_collate(inputs), default_collate(video_idx)
labels = torch.tensor(np.concatenate(labels, axis=0)).float()
collated_extra_data = {}
for key in extra_data[0].keys():
data = [d[key] for d in extra_data]
if key == "boxes" or key == "ori_boxes":
# Append idx info to the bboxes before concatenating them.
bboxes = [
np.concatenate(
[np.full((data[i].shape[0], 1), float(i)), data[i]],
axis=1) for i in range(len(data))
]
bboxes = np.concatenate(bboxes, axis=0)
collated_extra_data[key] = torch.tensor(bboxes).float()
elif key == "metadata":
collated_extra_data[key] = torch.tensor(
list(itertools.chain(*data))).view(-1, 2)
else:
collated_extra_data[key] = default_collate(data)
return inputs, labels, video_idx, collated_extra_data
def collate_fn(batch):
feats, n_feats, logits = zip(*batch)
# the feats have all different lengths
feats = torch.cat(feats, dim=0)
n_feats = default_collate(n_feats)
logits = default_collate(logits)
return feats, n_feats, logits
def collate(batch, *, root=True):
"Puts each data field into a tensor with outer dimension batch size"
if len(batch) == 0:
return batch
error_msg = "batch must contain tensors, numbers, dicts or lists; found {}"
elem_type = type(batch[0])
if torch.is_tensor(batch[0]):
return default_collate(batch)
elif elem_type.__module__ == 'numpy' and elem_type.__name__ != 'str_' \
and elem_type.__name__ != 'string_':
return default_collate(batch)
elif isinstance(batch[0], int_classes):
return batch
elif isinstance(batch[0], float):
return batch
elif isinstance(batch[0], string_classes):
return batch
elif isinstance(batch[0], CameraIntrinsics):
return batch
elif isinstance(batch[0], Mapping):
if root:
return {
key: collate([d[key] for d in batch], root=False)
for key in batch[0]
}
else:
return batch
elif isinstance(batch[0], Sequence):
return [collate(e, root=False) for e in batch]
raise TypeError((error_msg.format(type(batch[0]))))
def bbox_collate(batch):
'''
Padding the bounding box in the collate function
'''
if torch.is_tensor(batch[0][0]):
return default_collate(batch)
if isinstance(batch[0][0], dict) and 'xs' not in batch[0][0] \
and 'masks' not in batch[0][0]:
return default_collate(batch)
if 'masks' not in batch[0][0] and batch[0][0]['xs'].ndim == 0:
return default_collate(batch)
samples = [item[0] for item in batch]
if 'masks' not in batch[0][0]: # do the bbox
# pad the bboxes into xs, ys, ws, hs
data = {
'xs':
pad_sequence([sample['xs'] for sample in samples],
batch_first=True,
padding_value=-1.),
'ys':
pad_sequence([sample['ys'] for sample in samples],
batch_first=True,
padding_value=-1.),
'ws':
pad_sequence([sample['ws'] for sample in samples],
batch_first=True,
padding_value=-1.),
'hs':
pad_sequence([sample['hs'] for sample in samples],
batch_first=True,
padding_value=-1.),
}
else: # only do the masks instead
data = {}
masks = [s['masks'] for s in samples]
if masks == [None] * len(masks):
# Hack: since we can't pass None in pl, we pass a tensor that
# makes the __base__.py has no bbox
data['masks'] = torch.zeros(len(masks), 1, 1, 1)
else:
masks = [
torch.zeros(1, *samples[0]['imgs'].shape[1:])
if m is None else m for m in masks
]
data['masks'] = torch.stack(masks, dim=0)
data['imgs'] = default_collate([item['imgs'] for item in samples])
if 'imgs_cf' in samples[0]:
imgs_cf = [s['imgs_cf'] for s in samples]
if imgs_cf != [None] * len(imgs_cf):
imgs_cf = [
torch.zeros_like(samples[0]['imgs']) if m is None else m
for m in imgs_cf
]
data['imgs_cf'] = torch.stack(imgs_cf, dim=0)
targets = default_collate([item[1] for item in batch])
return [data, targets]
def collate_docs(docs):
dense, doc_ids, tag_ids, tag_offsets = zip(*docs)
return (
default_collate(dense),
default_collate(doc_ids),
torch.cat(tag_ids),
cum_offsets(tag_offsets),
)
def batch_collator(batch):
transposed_batch = list(zip(*batch))
transposed_batch[0] = default_collate(transposed_batch[0])
transposed_batch[1] = default_collate(transposed_batch[1])
if len(transposed_batch) > 4:
transposed_batch[2] = default_collate(transposed_batch[2])
transposed_batch[3] = default_collate(transposed_batch[3])
return transposed_batch
def collate(batch):
if len(batch) == 0:
return batch
elem = batch[0]
if elem is None:
return None
elif isinstance(elem, container_abcs.Sequence):
if len(
elem
) == 4: # We assume those are the maps, map points, headings and patch_size
scene_map, scene_pts, heading_angle, patch_size = zip(*batch)
if heading_angle[0] is None:
heading_angle = None
else:
heading_angle = torch.Tensor(heading_angle)
map = scene_map[0].get_cropped_maps_from_scene_map_batch(
scene_map,
scene_pts=torch.Tensor(scene_pts),
patch_size=patch_size[0],
rotation=heading_angle)
return map
transposed = zip(*batch)
return [collate(samples) for samples in transposed]
elif isinstance(elem, container_abcs.Mapping):
return {key: collate([d[key] for d in batch]) for key in elem}
elif isinstance(elem, torch.Tensor):
batch_shapes = set([el.shape for el in batch])
if len(batch_shapes) != 1:
new_batch = list(batch)
# This is the case when we have different agent_count or largest_state_dim.
max_agent_count = max(batch_shapes,
key=lambda batch_shape: batch_shape[0])[0]
max_largest_state_dim = max(
batch_shapes, key=lambda batch_shape: batch_shape[-1])[-1]
for idx in range(len(batch)):
# num_nodes, time_length, largest_state_dim
curr_shape = batch[idx].shape
if len(curr_shape) == 3:
pad = (0, max_largest_state_dim - curr_shape[-1], 0, 0, 0,
max_agent_count - curr_shape[0])
const = np.nan
elif len(curr_shape) == 2:
pad = (0, max_largest_state_dim - curr_shape[-1], 0, 0)
const = np.nan
else:
pad = (0, max_largest_state_dim - curr_shape[-1])
const = -1
new_batch[idx] = F.pad(batch[idx], pad, "constant", const)
return default_collate(new_batch)
return default_collate(batch)
def caption_collate(batch):
if len(batch[0]) == 3: # is_train=True
return default_collate(batch)
elif len(batch[0]) == 4: # is_train=False
collated = list()
for item_i, item_list in enumerate(zip(*batch)):
if item_i < 3:
collated.append(default_collate(item_list))
else:
collated.append(item_list)
return collated
else:
raise NotImplementedError
def feature_extract_bbox(batch):
inputs, bboxes, segment_indices, indices = zip(*batch)
bboxes = [
np.concatenate([np.full((bboxes[i].shape[0], 1), float(i)), bboxes[i]],
axis=1) for i in range(len(bboxes))
if len(bboxes[i]) > 0
]
if len(bboxes) > 0:
bboxes = torch.tensor(np.concatenate(bboxes, axis=0)).float()
inputs = default_collate(inputs)
segment_indices = default_collate(segment_indices)
indices = default_collate(indices)
return inputs, bboxes, segment_indices, indices
def multi_supervision_collate_fn(batch: Sequence[Dict]) -> Dict:
"""
Custom collate_fn for K2SpeechRecognitionDataset.
It merges the items provided by K2SpeechRecognitionDataset into the following structure:
.. code-block::
{
'features': float tensor of shape (B, T, F)
'supervisions': [
{
'sequence_idx': Tensor[int] of shape (S,)
'text': List[str] of len S
'start_frame': Tensor[int] of shape (S,)
'num_frames': Tensor[int] of shape (S,)
}
]
}
Dimension symbols legend:
* ``B`` - batch size (number of Cuts),
* ``S`` - number of supervision segments (greater or equal to B, as each Cut may have multiple supervisions),
* ``T`` - number of frames of the longest Cut
* ``F`` - number of features
"""
from torch.utils.data._utils.collate import default_collate
dataset_idx_to_batch_idx = {
example['supervisions'][0]['sequence_idx']: batch_idx
for batch_idx, example in enumerate(batch)
}
def update(d: Dict, **kwargs) -> Dict:
for key, value in kwargs.items():
d[key] = value
return d
supervisions = default_collate([
update(sup, sequence_idx=dataset_idx_to_batch_idx[sup['sequence_idx']])
for example in batch
for sup in example['supervisions']
])
feats = default_collate([example['features'] for example in batch])
return {
'features': feats,
'supervisions': supervisions
}
def collate_fn_dailydialog(batch, include_lens=False):
result = default_collate(batch)
if include_lens:
return (result[0],
result[1]), result[2], result[3], result[4], batch[-1][-1]
else:
return result[0], result[2], result[3], result[4], batch[-1][-1]
def mixup_collate(data, alpha=0.1):
"""Implements a batch collate function with MixUp strategy from
`"mixup: Beyond Empirical Risk Minimization" <https://arxiv.org/pdf/1710.09412.pdf>`_
Args:
data (list): list of elements
alpha (float, optional): mixup factor
Example::
>>> import torch
>>> from holocron import utils
>>> loader = torch.utils.data.DataLoader(dataset, batch_size, collate_fn=utils.data.mixup_collate)
"""
inputs, targets = default_collate(data)
# Sample lambda
if alpha > 0:
lam = np.random.beta(alpha, alpha)
else:
lam = 1
# Mix batch indices
batch_size = inputs.size()[0]
index = torch.randperm(batch_size)
# Create the new input and targets
inputs = lam * inputs + (1 - lam) * inputs[index, :]
targets_a, targets_b = targets, targets[index]
return inputs, targets_a, targets_b, lam
def run(dataset_type,
output_dir,
use_intensity,
use_squared_falloff,
dc_count,
_config): # The entire config dict for this experiment
print("dataset_type: {}".format(dataset_type))
dataset = load_data(dataset_type)
all_spad_counts = []
all_intensities = []
for i in range(len(dataset)):
print("Simulating SPAD for entry {}".format(i))
data = default_collate([dataset[i]])
intensity = rgb2gray(data["rgb_cropped"].numpy()/255.)
spad_counts = simulate_spad(depth_truth=data["depth_cropped"].numpy(),
intensity=intensity,
mask=np.ones_like(intensity))
all_spad_counts.append(spad_counts)
all_intensities.append(intensity)
output = {
"config": _config,
"spad": np.array(all_spad_counts),
"intensity": np.concatenate(all_intensities),
}
print("saving {}_int_{}_fall_{}_dc_{}_spad.npy to {}".format(dataset_type,
use_intensity, use_squared_falloff, dc_count,
output_dir))
np.save(os.path.join(output_dir, "{}_int_{}_fall_{}_dc_{}_spad.npy".format(dataset_type,
use_intensity,
use_squared_falloff,
dc_count)), output)
def graph_collate(batch):
a, b, liked = zip(*batch)
return (
collate_docs(a),
collate_docs(b),
default_collate(liked),
)
def collate(batch):
cmap_offset = (ColoredMNIST.cmap -
1) * ColoredMNIST.mean / ColoredMNIST.std
cs = np.random.choice(len(ColoredMNIST.cmap), 2, replace=False)
c1 = ColoredMNIST.cmap[cs[0]]
c2 = ColoredMNIST.cmap[cs[1]]
o1 = cmap_offset[cs[0]]
o2 = cmap_offset[cs[1]]
pair_list = []
for batch_idx in range(len(batch)):
data = batch[batch_idx][0]
target = batch[batch_idx][1]
data1 = data[0]
data2 = data[1]
target1 = target[0]
target2 = target[1]
data1 = torch.cat([
data1 * c1[0] + o1[0], data1 * c1[1] + o1[1],
data1 * c1[2] + o1[2]
],
dim=0)
data2 = torch.cat([
data2 * c2[0] + o2[0], data2 * c2[1] + o2[1],
data2 * c2[2] + o2[2]
],
dim=0)
target1 = (torch.tensor(cs[0]), target1)
target2 = (torch.tensor(cs[1]), target2)
pair = ((data1, data2), (target1, target2))
pair_list.append(pair)
batch = default_collate(pair_list)
return batch
def collate_fn(self, batch: List[Feature]):
word_seq_len = [len(feature.orig_to_tok_index) for feature in batch]
max_seq_len = max(word_seq_len)
max_wordpiece_length = max(
[len(feature.input_ids) for feature in batch])
for i, feature in enumerate(batch):
padding_length = max_wordpiece_length - len(feature.input_ids)
input_ids = feature.input_ids + [self.tokenizer.pad_token_id
] * padding_length
mask = feature.attention_mask + [0] * padding_length
type_ids = feature.token_type_ids + [
self.tokenizer.pad_token_type_id
] * padding_length
padding_word_len = max_seq_len - len(feature.orig_to_tok_index)
orig_to_tok_index = feature.orig_to_tok_index + [
0
] * padding_word_len
label_ids = feature.label_ids + [0] * padding_word_len
batch[i] = Feature(input_ids=np.asarray(input_ids),
attention_mask=np.asarray(mask),
token_type_ids=np.asarray(type_ids),
orig_to_tok_index=np.asarray(orig_to_tok_index),
word_seq_len=feature.word_seq_len,
label_ids=np.asarray(label_ids))
results = Feature(*(default_collate(samples)
for samples in zip(*batch)))
return results
def collate_flatten(batch, x_dim_flatten=5, y_dim_flatten=2):
x, y = default_collate(batch)
if len(x.shape) > x_dim_flatten:
x = x.flatten(start_dim=0, end_dim=len(x.shape) - x_dim_flatten)
if len(y.shape) > y_dim_flatten:
y = y.flatten(start_dim=0, end_dim=len(y.shape) - y_dim_flatten)
return [x, y]
def my_collate(batch):
modified_batch = []
for item in batch:
image, label = item
if label==1 or label==2:
modified_batch.append(item)
return default_collate(modified_batch)
def collate(cls, samples):
"""Collates a sequence of samples containing graphs into a batch
The samples in the sequence can contain multiple types of inputs, such as:
>>> [
>>> (input_graph, tensor, other_tensor, output_graph),
>>> (input_graph, tensor, other_tensor, output_graph),
>>> ...
>>> ]
"""
if isinstance(samples[0], Graph):
return cls.from_graphs(samples)
elif isinstance(samples[0], (str, bytes)):
return samples
elif isinstance(samples[0], collections.abc.Mapping):
return {
key: cls.collate([d[key] for d in samples])
for key in samples[0]
}
elif isinstance(samples[0], collections.abc.Sequence):
transposed = zip(*samples)
return [cls.collate(samples) for samples in transposed]
else:
return default_collate(samples)
def collate(self, samples: Any) -> Any:
if not isinstance(samples, Tensor):
elem = samples[0]
if isinstance(elem, container_abcs.Sequence):
return tuple(zip(*samples))
return default_collate(samples)
return samples.unsqueeze(dim=0)
def list_data_collate(batch: Sequence):
"""
Enhancement for PyTorch DataLoader default collate.
If dataset already returns a list of batch data that generated in transforms, need to merge all data to 1 list.
Then it's same as the default collate behavior.
Note:
Need to use this collate if apply some transforms that can generate batch data.
"""
elem = batch[0]
data = [i for k in batch for i in k] if isinstance(elem, list) else batch
try:
return default_collate(data)
except RuntimeError as re:
re_str = str(re)
if "equal size" in re_str:
re_str += (
"\n\nMONAI hint: if your transforms intentionally create images of different shapes, creating your "
+
"`DataLoader` with `collate_fn=pad_list_data_collate` might solve this problem (check its "
+ "documentation).")
raise RuntimeError(re_str)
except TypeError as re:
re_str = str(re)
if "numpy" in re_str and "Tensor" in re_str:
re_str += (
"\n\nMONAI hint: if your transforms intentionally create mixtures of torch Tensor and numpy ndarray, "
+
"creating your `DataLoader` with `collate_fn=pad_list_data_collate` might solve this problem "
+ "(check its documentation).")
raise TypeError(re_str)
def collate_fn(self, batch: List[Feature]):
word_seq_lens = [len(feature.words) for feature in batch]
max_seq_len = max(word_seq_lens)
max_char_seq_len = -1
for feature in batch:
curr_max_char_seq_len = max(feature.char_seq_lens)
max_char_seq_len = max(curr_max_char_seq_len, max_char_seq_len)
for i, feature in enumerate(batch):
padding_length = max_seq_len - len(feature.words)
words = feature.words + [0] * padding_length
chars = []
char_seq_lens = feature.char_seq_lens + [1] * padding_length
for word_idx in range(feature.word_seq_len):
pad_char_length = max_char_seq_len - feature.char_seq_lens[
word_idx]
word_chars = feature.chars[word_idx] + [0] * pad_char_length
chars.append(word_chars)
for _ in range(max_seq_len - feature.word_seq_len):
chars.append([0] * max_char_seq_len)
labels = feature.labels + [
0
] * padding_length if feature.labels is not None else None
batch[i] = Feature(
words=np.asarray(words),
chars=np.asarray(chars),
char_seq_lens=np.asarray(char_seq_lens),
context_emb=feature.context_emb,
word_seq_len=feature.word_seq_len,
labels=np.asarray(labels) if labels is not None else None)
results = Feature(*(default_collate(samples)
if not check_all_obj_is_None(samples) else None
for samples in zip(*batch)))
return results
def impute(self, x, ids, dropout_threshold=None):
assert len(x) == len(ids)
assert len(x) == self.n_channels
union = sorted(set(reduce(add, ids)))
if len(union) is not 0:
x_hat = []
for s in union:
# print(s, union.index(s))
# available_channels_for_s = [i if s in _ and i in self.enc_channels else None for i, _ in enumerate(ids)]
available_channels_for_s = [
i if s in _ else None for i, _ in enumerate(ids)
]
xs = [
x[ch][ids[ch].index(s)].unsqueeze(0)
if ch is not None else None
for ch in available_channels_for_s
]
qs = [
self.vae[ch].encode(_) if _ is not None else None
for ch, _ in enumerate(xs)
]
zs_ = [_.loc if _ is not None else None for _ in qs]
if dropout_threshold is not None:
zs = [
self.apply_threshold(_, dropout_threshold)
if _ is not None else None for _ in zs_
]
else:
zs = zs_
xs_hat = []
for i in range(self.n_channels):
if i in self.dec_channels:
ps_hat_i = [
self.vae[i].decode(z) for z in zs if z is not None
]
ev_hat_i = [
self.vae[i].p_to_expected_value(_)
for _ in ps_hat_i
]
xs_hat_i = torch.stack(ev_hat_i, 0).mean(0)
if isinstance(ps_hat_i[0],
torch.distributions.Categorical):
xs_hat_i = xs_hat_i.argmax(1, keepdim=True)
xs_hat.append(xs_hat_i)
del ps_hat_i, ev_hat_i, xs_hat_i
else:
xs_hat.append([])
x_hat.append(xs_hat)
del xs_hat
ret = [
_.squeeze() if not isinstance(_, list) else []
for _ in default_collate(x_hat)
]
else:
ret = [[] for _ in x]
return ret
def collate_none_when_even(self, batch):
if self.counter % 2 == 0:
result = None
else:
result = default_collate(batch)
self.counter += 1
return result
def test_collate(batch):
imgs = torch.stack([torch.Tensor(item[0]) for item in batch], 0)
masks_cropped = torch.stack([torch.Tensor(item[1]) for item in batch], 0)
masks_org = [torch.Tensor(item[2]) for item in batch]
meta = default_collate([item[3] for item in batch])
return imgs, masks_cropped, masks_org, meta