# Copyright 2020 - 2021 MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
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import warnings
from copy import deepcopy
from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Tuple, Union
import numpy as np
import torch
from monai.data.dataloader import DataLoader
from monai.data.dataset import Dataset
from monai.data.utils import list_data_collate, pad_list_data_collate
from monai.transforms.compose import Compose
from monai.transforms.inverse import InvertibleTransform
from monai.transforms.inverse_batch_transform import BatchInverseTransform
from monai.transforms.transform import Randomizable
from monai.transforms.utils import allow_missing_keys_mode, convert_inverse_interp_mode
from monai.utils.enums import CommonKeys, TraceKeys
from monai.utils.module import optional_import
from monai.utils.type_conversion import convert_data_type
if TYPE_CHECKING:
from tqdm import tqdm
has_tqdm = True
else:
tqdm, has_tqdm = optional_import("tqdm", name="tqdm")
__all__ = ["TestTimeAugmentation"]
def _identity(x):
return x
[docs]class TestTimeAugmentation:
"""
Class for performing test time augmentations. This will pass the same image through the network multiple times.
The user passes transform(s) to be applied to each realisation, and provided that at least one of those transforms
is random, the network's output will vary. Provided that inverse transformations exist for all supplied spatial
transforms, the inverse can be applied to each realisation of the network's output. Once in the same spatial
reference, the results can then be combined and metrics computed.
Test time augmentations are a useful feature for computing network uncertainty, as well as observing the network's
dependency on the applied random transforms.
Reference:
Wang et al.,
Aleatoric uncertainty estimation with test-time augmentation for medical image segmentation with convolutional
neural networks,
https://doi.org/10.1016/j.neucom.2019.01.103
Args:
transform: transform (or composed) to be applied to each realisation. At least one transform must be of type
`Randomizable`. All random transforms must be of type `InvertibleTransform`.
batch_size: number of realisations to infer at once.
num_workers: how many subprocesses to use for data.
inferrer_fn: function to use to perform inference.
device: device on which to perform inference.
image_key: key used to extract image from input dictionary.
orig_key: the key of the original input data in the dict. will get the applied transform information
for this input data, then invert them for the expected data with `image_key`.
orig_meta_keys: the key of the meta data of original input data, will get the `affine`, `data_shape`, etc.
the meta data is a dictionary object which contains: filename, original_shape, etc.
if None, will try to construct meta_keys by `{orig_key}_{meta_key_postfix}`.
meta_key_postfix: use `key_{postfix}` to to fetch the meta data according to the key data,
default is `meta_dict`, the meta data is a dictionary object.
For example, to handle key `image`, read/write affine matrices from the
metadata `image_meta_dict` dictionary's `affine` field.
this arg only works when `meta_keys=None`.
return_full_data: normally, metrics are returned (mode, mean, std, vvc). Setting this flag to `True` will return the
full data. Dimensions will be same size as when passing a single image through `inferrer_fn`, with a dimension appended
equal in size to `num_examples` (N), i.e., `[N,C,H,W,[D]]`.
progress: whether to display a progress bar.
Example:
.. code-block:: python
transform = RandAffined(keys, ...)
post_trans = Compose([Activations(sigmoid=True), AsDiscrete(threshold=0.5)])
tt_aug = TestTimeAugmentation(
transform, batch_size=5, num_workers=0, inferrer_fn=lambda x: post_trans(model(x)), device=device
)
mode, mean, std, vvc = tt_aug(test_data)
"""
def __init__(
self,
transform: InvertibleTransform,
batch_size: int,
num_workers: int = 0,
inferrer_fn: Callable = _identity,
device: Union[str, torch.device] = "cpu",
image_key=CommonKeys.IMAGE,
orig_key=CommonKeys.LABEL,
nearest_interp: bool = True,
orig_meta_keys: Optional[str] = None,
meta_key_postfix="meta_dict",
return_full_data: bool = False,
progress: bool = True,
) -> None:
self.transform = transform
self.batch_size = batch_size
self.num_workers = num_workers
self.inferrer_fn = inferrer_fn
self.device = device
self.image_key = image_key
self.orig_key = orig_key
self.nearest_interp = nearest_interp
self.orig_meta_keys = orig_meta_keys
self.meta_key_postfix = meta_key_postfix
self.return_full_data = return_full_data
self.progress = progress
# check that the transform has at least one random component, and that all random transforms are invertible
self._check_transforms()
def _check_transforms(self):
"""Should be at least 1 random transform, and all random transforms should be invertible."""
ts = [self.transform] if not isinstance(self.transform, Compose) else self.transform.transforms
randoms = np.array([isinstance(t, Randomizable) for t in ts])
invertibles = np.array([isinstance(t, InvertibleTransform) for t in ts])
# check at least 1 random
if sum(randoms) == 0:
raise RuntimeError(
"Requires a `Randomizable` transform or a `Compose` containing at least one `Randomizable` transform."
)
# check that whenever randoms is True, invertibles is also true
for r, i in zip(randoms, invertibles):
if r and not i:
warnings.warn(
f"Not all applied random transform(s) are invertible. Problematic transform: {type(r).__name__}"
)
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 = [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)
transform_key = InvertibleTransform.trace_key(self.orig_key)
# create inverter
inverter = BatchInverseTransform(self.transform, dl, collate_fn=list_data_collate)
outputs: List[np.ndarray] = []
for batch_data in tqdm(dl) if has_tqdm and 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)
transform_info = batch_data.get(transform_key, None)
if transform_info is None:
# no invertible transforms, adding dummy info for identity invertible
transform_info = [[TraceKeys.NONE] for _ in range(self.batch_size)]
if self.nearest_interp:
transform_info = convert_inverse_interp_mode(
trans_info=deepcopy(transform_info), mode="nearest", align_corners=None
)
# create a dictionary containing the inferred batch and their transforms
inferred_dict = {self.orig_key: batch_output, transform_key: transform_info}
# if meta dict is present, add that too (required for some inverse transforms)
meta_dict_key = self.orig_meta_keys or f"{self.orig_key}_{self.meta_key_postfix}"
if meta_dict_key in batch_data:
inferred_dict[meta_dict_key] = batch_data[meta_dict_key]
# do inverse transformation (allow missing keys as only inverting the orig_key)
with allow_missing_keys_mode(self.transform): # type: ignore
inv_batch = inverter(inferred_dict)
# append
outputs.append(inv_batch[self.orig_key])
# output
output: np.ndarray = np.concatenate(outputs)
if self.return_full_data:
return output
# calculate metrics
output_t, *_ = convert_data_type(output, output_type=torch.Tensor, dtype=np.int64)
mode: np.ndarray = np.asarray(torch.mode(output_t, dim=0).values) # type: ignore
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