# 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
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
A collection of generic interfaces for MONAI transforms.
"""
import warnings
from typing import Any, Callable, Optional, Sequence, Union
import numpy as np
from monai.transforms.inverse import InvertibleTransform
# For backwards compatibility (so this still works: from monai.transforms.compose import MapTransform)
from monai.transforms.transform import ( # noqa: F401
MapTransform,
Randomizable,
RandomizableTransform,
Transform,
apply_transform,
)
from monai.utils import MAX_SEED, ensure_tuple, get_seed
__all__ = ["Compose"]
[docs]class Compose(Randomizable, InvertibleTransform):
"""
``Compose`` provides the ability to chain a series of callables together in
a sequential manner. Each transform in the sequence must take a single
argument and return a single value.
``Compose`` can be used in two ways:
#. With a series of transforms that accept and return a single
ndarray / tensor / tensor-like parameter.
#. With a series of transforms that accept and return a dictionary that
contains one or more parameters. Such transforms must have pass-through
semantics; unused values in the dictionary must be copied to the return
dictionary. It is required that the dictionary is copied between input
and output of each transform.
If some transform takes a data item dictionary as input, and returns a
sequence of data items in the transform chain, all following transforms
will be applied to each item of this list if `map_items` is `True` (the
default). If `map_items` is `False`, the returned sequence is passed whole
to the next callable in the chain.
For example:
A `Compose([transformA, transformB, transformC],
map_items=True)(data_dict)` could achieve the following patch-based
transformation on the `data_dict` input:
#. transformA normalizes the intensity of 'img' field in the `data_dict`.
#. transformB crops out image patches from the 'img' and 'seg' of
`data_dict`, and return a list of three patch samples::
{'img': 3x100x100 data, 'seg': 1x100x100 data, 'shape': (100, 100)}
applying transformB
---------->
[{'img': 3x20x20 data, 'seg': 1x20x20 data, 'shape': (20, 20)},
{'img': 3x20x20 data, 'seg': 1x20x20 data, 'shape': (20, 20)},
{'img': 3x20x20 data, 'seg': 1x20x20 data, 'shape': (20, 20)},]
#. transformC then randomly rotates or flips 'img' and 'seg' of
each dictionary item in the list returned by transformB.
The composed transforms will be set the same global random seed if user called
`set_determinism()`.
When using the pass-through dictionary operation, you can make use of
:class:`monai.transforms.adaptors.adaptor` to wrap transforms that don't conform
to the requirements. This approach allows you to use transforms from
otherwise incompatible libraries with minimal additional work.
Note:
In many cases, Compose is not the best way to create pre-processing
pipelines. Pre-processing is often not a strictly sequential series of
operations, and much of the complexity arises when a not-sequential
set of functions must be called as if it were a sequence.
Example: images and labels
Images typically require some kind of normalization that labels do not.
Both are then typically augmented through the use of random rotations,
flips, and deformations.
Compose can be used with a series of transforms that take a dictionary
that contains 'image' and 'label' entries. This might require wrapping
`torchvision` transforms before passing them to compose.
Alternatively, one can create a class with a `__call__` function that
calls your pre-processing functions taking into account that not all of
them are called on the labels.
"""
def __init__(
self, transforms: Optional[Union[Sequence[Callable], Callable]] = None, map_items: bool = True
) -> None:
if transforms is None:
transforms = []
self.transforms = ensure_tuple(transforms)
self.map_items = map_items
self.set_random_state(seed=get_seed())
[docs] def set_random_state(self, seed: Optional[int] = None, state: Optional[np.random.RandomState] = None) -> "Compose":
super().set_random_state(seed=seed, state=state)
for _transform in self.transforms:
if not isinstance(_transform, Randomizable):
continue
_transform.set_random_state(seed=self.R.randint(MAX_SEED, dtype="uint32"))
return self
[docs] def randomize(self, data: Optional[Any] = None) -> None:
for _transform in self.transforms:
if not isinstance(_transform, Randomizable):
continue
try:
_transform.randomize(data)
except TypeError as type_error:
tfm_name: str = type(_transform).__name__
warnings.warn(
f'Transform "{tfm_name}" in Compose not randomized\n{tfm_name}.{type_error}.', RuntimeWarning
)
[docs] def flatten(self):
"""Return a Composition with a simple list of transforms, as opposed to any nested Compositions.
e.g., `t1 = Compose([x, x, x, x, Compose([Compose([x, x]), x, x])]).flatten()`
will result in the equivalent of `t1 = Compose([x, x, x, x, x, x, x, x])`.
"""
new_transforms = []
for t in self.transforms:
if isinstance(t, Compose):
new_transforms += t.flatten().transforms
else:
new_transforms.append(t)
return Compose(new_transforms)
def __len__(self):
"""Return number of transformations."""
return len(self.flatten().transforms)
[docs] def __call__(self, input_):
for _transform in self.transforms:
input_ = apply_transform(_transform, input_, self.map_items)
return input_
[docs] def inverse(self, data):
invertible_transforms = [t for t in self.flatten().transforms if isinstance(t, InvertibleTransform)]
if len(invertible_transforms) == 0:
warnings.warn("inverse has been called but no invertible transforms have been supplied")
# loop backwards over transforms
for t in reversed(invertible_transforms):
data = apply_transform(t.inverse, data, self.map_items)
return data