def get_loaders(args, pre_transforms, train=True):
multi_gpu = args.multi_gpu
local_rank = args.local_rank
dataset_json = os.path.join(args.input)
with open(dataset_json) as f:
datalist = json.load(f)
total_d = len(datalist)
datalist = datalist[0:args.limit] if args.limit else datalist
total_l = len(datalist)
if multi_gpu:
datalist = partition_dataset(
data=datalist,
num_partitions=dist.get_world_size(),
even_divisible=True,
shuffle=True,
seed=args.seed,
)[local_rank]
if train:
train_datalist, val_datalist = partition_dataset(
datalist,
ratios=[args.split, (1 - args.split)],
shuffle=True,
seed=args.seed,
)
train_ds = PersistentDataset(train_datalist,
pre_transforms,
cache_dir=args.cache_dir)
train_loader = DataLoader(train_ds,
batch_size=args.batch,
shuffle=True,
num_workers=16)
logging.info(
"{}:: Total Records used for Training is: {}/{}/{}".format(
local_rank, len(train_ds), total_l, total_d))
else:
train_loader = None
val_datalist = datalist
val_ds = PersistentDataset(val_datalist,
pre_transforms,
cache_dir=args.cache_dir)
val_loader = DataLoader(val_ds, batch_size=args.batch, num_workers=8)
logging.info("{}:: Total Records used for Validation is: {}/{}/{}".format(
local_rank, len(val_ds), total_l, total_d))
return train_loader, val_loader
def __init__(
self,
dataset: Dataset,
image_key: Optional[str] = "image",
label_key: Optional[str] = "label",
meta_key_postfix: str = "meta_dict",
num_workers: int = 0,
**kwargs,
):
"""
Args:
dataset: dataset from which to load the data.
image_key: key name of images (default: ``image``).
label_key: key name of labels (default: ``label``).
meta_key_postfix: use `{image_key}_{meta_key_postfix}` to fetch the meta data from dict,
the meta data is a dictionary object (default: ``meta_dict``).
num_workers: how many subprocesses to use for data loading.
``0`` means that the data will be loaded in the main process (default: ``0``).
kwargs: other parameters (except batch_size) for DataLoader (this class forces to use ``batch_size=1``).
"""
self.data_loader = DataLoader(dataset=dataset,
batch_size=1,
num_workers=num_workers,
**kwargs)
self.image_key = image_key
self.label_key = label_key
if image_key:
self.meta_key = f"{image_key}_{meta_key_postfix}"
self.all_meta_data: List = []
def __init__(
self,
dataset: Dataset,
image_key: Optional[str] = "image",
label_key: Optional[str] = "label",
meta_key: Optional[KeysCollection] = None,
meta_key_postfix: str = DEFAULT_POST_FIX,
num_workers: int = 0,
**kwargs,
):
"""
Args:
dataset: dataset from which to load the data.
image_key: key name of images (default: ``image``).
label_key: key name of labels (default: ``label``).
meta_key: explicitly indicate the key of the corresponding meta data dictionary.
for example, for data with key `image`, the metadata by default is in `image_meta_dict`.
the meta data is a dictionary object which contains: filename, affine, original_shape, etc.
if None, will try to construct meta_keys by `{image_key}_{meta_key_postfix}`.
meta_key_postfix: use `{image_key}_{meta_key_postfix}` to fetch the meta data from dict,
the meta data is a dictionary object (default: ``meta_dict``).
num_workers: how many subprocesses to use for data loading.
``0`` means that the data will be loaded in the main process (default: ``0``).
kwargs: other parameters (except `batch_size` and `num_workers`) for DataLoader,
this class forces to use ``batch_size=1``.
"""
self.data_loader = DataLoader(dataset=dataset, batch_size=1, num_workers=num_workers, **kwargs)
self.image_key = image_key
self.label_key = label_key
self.meta_key = meta_key or f"{image_key}_{meta_key_postfix}"
self.all_meta_data: List = []
def __call__(
self,
data: Dict[str, Any],
num_examples: int = 10
) -> Union[Tuple[NdarrayOrTensor, NdarrayOrTensor, NdarrayOrTensor, float],
NdarrayOrTensor]:
"""
Args:
data: dictionary data to be processed.
num_examples: number of realisations to be processed and results combined.
Returns:
- if `return_full_data==False`: mode, mean, std, vvc. The mode, mean and standard deviation are
calculated across `num_examples` outputs at each voxel. The volume variation coefficient (VVC)
is `std/mean` across the whole output, including `num_examples`. See original paper for clarification.
- if `return_full_data==False`: data is returned as-is after applying the `inferrer_fn` and then
concatenating across the first dimension containing `num_examples`. This allows the user to perform
their own analysis if desired.
"""
d = dict(data)
# check num examples is multiple of batch size
if num_examples % self.batch_size != 0:
raise ValueError("num_examples should be multiple of batch size.")
# generate batch of data of size == batch_size, dataset and dataloader
data_in = [deepcopy(d) for _ in range(num_examples)]
ds = Dataset(data_in, self.transform)
dl = DataLoader(ds,
num_workers=self.num_workers,
batch_size=self.batch_size,
collate_fn=pad_list_data_collate)
outs: List = []
for b in tqdm(dl) if has_tqdm and self.progress else dl:
# do model forward pass
b[self._pred_key] = self.inferrer_fn(b[self.image_key].to(
self.device))
outs.extend([
self.inverter(PadListDataCollate.inverse(i))[self._pred_key]
for i in decollate_batch(b)
])
output: NdarrayOrTensor = stack(outs, 0)
if self.return_full_data:
return output
# calculate metrics
_mode = mode(output, dim=0)
mean = output.mean(0)
std = output.std(0)
vvc = (output.std() / output.mean()).item()
return _mode, mean, std, vvc
def __call__(self, data: Dict[str, Any]) -> Any:
decollated_data = decollate_batch(data, detach=self.detach, pad=self.pad_batch, fill_value=self.fill_value)
inv_ds = _BatchInverseDataset(decollated_data, self.transform, self.pad_collation_used)
inv_loader = DataLoader(
inv_ds, batch_size=self.batch_size, num_workers=self.num_workers, collate_fn=self.collate_fn
)
try:
return first(inv_loader)
except RuntimeError as re:
re_str = str(re)
if "equal size" in re_str:
re_str += "\nMONAI hint: try creating `BatchInverseTransform` with `collate_fn=lambda x: x`."
raise RuntimeError(re_str) from re
def __call__(
self,
data: Dict[str, Any],
num_examples: int = 10
) -> Union[Tuple[np.ndarray, np.ndarray, np.ndarray, float], np.ndarray]:
"""
Args:
data: dictionary data to be processed.
num_examples: number of realisations to be processed and results combined.
Returns:
- if `return_full_data==False`: mode, mean, std, vvc. The mode, mean and standard deviation are calculated
across `num_examples` outputs at each voxel. The volume variation coefficient (VVC) is `std/mean`
across the whole output, including `num_examples`. See original paper for clarification.
- if `return_full_data==False`: data is returned as-is after applying the `inferrer_fn` and then
concatenating across the first dimension containing `num_examples`. This allows the user to perform
their own analysis if desired.
"""
d = dict(data)
# check num examples is multiple of batch size
if num_examples % self.batch_size != 0:
raise ValueError("num_examples should be multiple of batch size.")
# generate batch of data of size == batch_size, dataset and dataloader
data_in = [d] * num_examples
ds = Dataset(data_in, self.transform)
dl = DataLoader(ds,
self.num_workers,
batch_size=self.batch_size,
collate_fn=pad_list_data_collate)
label_transform_key = self.label_key + InverseKeys.KEY_SUFFIX
# create inverter
inverter = BatchInverseTransform(self.transform,
dl,
collate_fn=list_data_collate)
outputs: List[np.ndarray] = []
for batch_data in tqdm(dl) if self.progress else dl:
batch_images = batch_data[self.image_key].to(self.device)
# do model forward pass
batch_output = self.inferrer_fn(batch_images)
if isinstance(batch_output, torch.Tensor):
batch_output = batch_output.detach().cpu()
if isinstance(batch_output, np.ndarray):
batch_output = torch.Tensor(batch_output)
# create a dictionary containing the inferred batch and their transforms
inferred_dict = {
self.label_key: batch_output,
label_transform_key: batch_data[label_transform_key]
}
# if meta dict is present, add that too (required for some inverse transforms)
label_meta_dict_key = self.meta_keys or f"{self.label_key}_{self.meta_key_postfix}"
if label_meta_dict_key in batch_data:
inferred_dict[label_meta_dict_key] = batch_data[
label_meta_dict_key]
# do inverse transformation (allow missing keys as only inverting label)
with allow_missing_keys_mode(self.transform): # type: ignore
inv_batch = inverter(inferred_dict)
# append
outputs.append(inv_batch[self.label_key])
# output
output: np.ndarray = np.concatenate(outputs)
if self.return_full_data:
return output
# calculate metrics
mode = np.array(
torch.mode(torch.Tensor(output.astype(np.int64)), dim=0).values)
mean: np.ndarray = np.mean(output, axis=0) # type: ignore
std: np.ndarray = np.std(output, axis=0) # type: ignore
vvc: float = (np.std(output) / np.mean(output)).item()
return mode, mean, std, vvc