|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
""" |
|
|
A collection of generic interfaces for MONAI transforms. |
|
|
""" |
|
|
|
|
|
from __future__ import annotations |
|
|
|
|
|
import warnings |
|
|
from collections.abc import Callable, Mapping, Sequence |
|
|
from copy import deepcopy |
|
|
from typing import Any |
|
|
|
|
|
import numpy as np |
|
|
|
|
|
import monai |
|
|
from monai.apps.utils import get_logger |
|
|
from monai.config import NdarrayOrTensor |
|
|
from monai.transforms.inverse import InvertibleTransform |
|
|
|
|
|
|
|
|
from monai.transforms.lazy.functional import apply_pending_transforms |
|
|
from monai.transforms.traits import ThreadUnsafe |
|
|
from monai.transforms.transform import ( |
|
|
LazyTransform, |
|
|
MapTransform, |
|
|
Randomizable, |
|
|
RandomizableTransform, |
|
|
Transform, |
|
|
apply_transform, |
|
|
) |
|
|
from monai.utils import MAX_SEED, TraceKeys, TraceStatusKeys, ensure_tuple, get_seed |
|
|
|
|
|
logger = get_logger(__name__) |
|
|
|
|
|
__all__ = ["Compose", "OneOf", "RandomOrder", "SomeOf", "execute_compose"] |
|
|
|
|
|
|
|
|
def execute_compose( |
|
|
data: NdarrayOrTensor | Sequence[NdarrayOrTensor] | Mapping[Any, NdarrayOrTensor], |
|
|
transforms: Sequence[Any], |
|
|
map_items: bool = True, |
|
|
unpack_items: bool = False, |
|
|
start: int = 0, |
|
|
end: int | None = None, |
|
|
lazy: bool | None = False, |
|
|
overrides: dict | None = None, |
|
|
threading: bool = False, |
|
|
log_stats: bool | str = False, |
|
|
) -> NdarrayOrTensor | Sequence[NdarrayOrTensor] | Mapping[Any, NdarrayOrTensor]: |
|
|
""" |
|
|
``execute_compose`` provides the implementation that the ``Compose`` class uses to execute a sequence |
|
|
of transforms. As well as being used by Compose, it can be used by subclasses of |
|
|
Compose and by code that doesn't have a Compose instance but needs to execute a |
|
|
sequence of transforms is if it were executed by Compose. It should only be used directly |
|
|
when it is not possible to use ``Compose.__call__`` to achieve the same goal. |
|
|
Args: |
|
|
data: a tensor-like object to be transformed |
|
|
transforms: a sequence of transforms to be carried out |
|
|
map_items: whether to apply transform to each item in the input `data` if `data` is a list or tuple. |
|
|
defaults to `True`. |
|
|
unpack_items: whether to unpack input `data` with `*` as parameters for the callable function of transform. |
|
|
defaults to `False`. |
|
|
start: the index of the first transform to be executed. If not set, this defaults to 0 |
|
|
end: the index after the last transform to be executed. If set, the transform at index-1 |
|
|
is the last transform that is executed. If this is not set, it defaults to len(transforms) |
|
|
lazy: whether to enable :ref:`lazy evaluation<lazy_resampling>` for lazy transforms. If False, transforms will be |
|
|
carried out on a transform by transform basis. If True, all lazy transforms will |
|
|
be executed by accumulating changes and resampling as few times as possible. |
|
|
overrides: this optional parameter allows you to specify a dictionary of parameters that should be overridden |
|
|
when executing a pipeline. These each parameter that is compatible with a given transform is then applied |
|
|
to that transform before it is executed. Note that overrides are currently only applied when |
|
|
:ref:`lazy evaluation<lazy_resampling>` is enabled for the pipeline or a given transform. If lazy is False |
|
|
they are ignored. Currently supported args are: |
|
|
{``"mode"``, ``"padding_mode"``, ``"dtype"``, ``"align_corners"``, ``"resample_mode"``, ``device``}. |
|
|
threading: whether executing is happening in a threaded environment. If set, copies are made |
|
|
of transforms that have the ``RandomizedTrait`` interface. |
|
|
log_stats: this optional parameter allows you to specify a logger by name for logging of pipeline execution. |
|
|
Setting this to False disables logging. Setting it to True enables logging to the default loggers. |
|
|
Setting a string overrides the logger name to which logging is performed. |
|
|
|
|
|
Returns: |
|
|
A tensorlike, sequence of tensorlikes or dict of tensorlists containing the result of running |
|
|
`data`` through the sequence of ``transforms``. |
|
|
""" |
|
|
end_ = len(transforms) if end is None else end |
|
|
if start is None: |
|
|
raise ValueError(f"'start' ({start}) cannot be None") |
|
|
if start < 0: |
|
|
raise ValueError(f"'start' ({start}) cannot be less than 0") |
|
|
if start > end_: |
|
|
raise ValueError(f"'start' ({start}) must be less than 'end' ({end_})") |
|
|
if end_ > len(transforms): |
|
|
raise ValueError(f"'end' ({end_}) must be less than or equal to the transform count ({len(transforms)}") |
|
|
|
|
|
|
|
|
if start == end: |
|
|
return data |
|
|
|
|
|
for _transform in transforms[start:end]: |
|
|
if threading: |
|
|
_transform = deepcopy(_transform) if isinstance(_transform, ThreadUnsafe) else _transform |
|
|
data = apply_transform( |
|
|
_transform, data, map_items, unpack_items, lazy=lazy, overrides=overrides, log_stats=log_stats |
|
|
) |
|
|
data = apply_pending_transforms(data, None, overrides, logger_name=log_stats) |
|
|
return data |
|
|
|
|
|
|
|
|
class Compose(Randomizable, InvertibleTransform, LazyTransform): |
|
|
""" |
|
|
``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 that 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. |
|
|
|
|
|
Lazy resampling: |
|
|
|
|
|
Lazy resampling is an experimental feature introduced in 1.2. Its purpose is |
|
|
to reduce the number of resample operations that must be carried out when executing |
|
|
a pipeline of transforms. This can provide significant performance improvements in |
|
|
terms of pipeline executing speed and memory usage, and can also significantly |
|
|
reduce the loss of information that occurs when performing a number of spatial |
|
|
resamples in succession. |
|
|
|
|
|
Lazy resampling can be enabled or disabled through the ``lazy`` parameter, either by |
|
|
specifying it at initialisation time or overriding it at call time. |
|
|
|
|
|
* False (default): Don't perform any lazy resampling |
|
|
* None: Perform lazy resampling based on the 'lazy' properties of the transform instances. |
|
|
* True: Always perform lazy resampling if possible. This will ignore the ``lazy`` properties |
|
|
of the transform instances |
|
|
|
|
|
Please see the :ref:`Lazy Resampling topic<lazy_resampling>` for more details of this feature |
|
|
and examples of its use. |
|
|
|
|
|
Args: |
|
|
transforms: sequence of callables. |
|
|
map_items: whether to apply transform to each item in the input `data` if `data` is a list or tuple. |
|
|
defaults to `True`. |
|
|
unpack_items: whether to unpack input `data` with `*` as parameters for the callable function of transform. |
|
|
defaults to `False`. |
|
|
log_stats: this optional parameter allows you to specify a logger by name for logging of pipeline execution. |
|
|
Setting this to False disables logging. Setting it to True enables logging to the default loggers. |
|
|
Setting a string overrides the logger name to which logging is performed. |
|
|
lazy: whether to enable :ref:`Lazy Resampling<lazy_resampling>` for lazy transforms. If False, transforms will |
|
|
be carried out on a transform by transform basis. If True, all lazy transforms will be executed by |
|
|
accumulating changes and resampling as few times as possible. If lazy is None, `Compose` will |
|
|
perform lazy execution on lazy transforms that have their `lazy` property set to True. |
|
|
overrides: this optional parameter allows you to specify a dictionary of parameters that should be overridden |
|
|
when executing a pipeline. These each parameter that is compatible with a given transform is then applied |
|
|
to that transform before it is executed. Note that overrides are currently only applied when |
|
|
:ref:`Lazy Resampling<lazy_resampling>` is enabled for the pipeline or a given transform. If lazy is False |
|
|
they are ignored. Currently supported args are: |
|
|
{``"mode"``, ``"padding_mode"``, ``"dtype"``, ``"align_corners"``, ``"resample_mode"``, ``device``}. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
transforms: Sequence[Callable] | Callable | None = None, |
|
|
map_items: bool = True, |
|
|
unpack_items: bool = False, |
|
|
log_stats: bool | str = False, |
|
|
lazy: bool | None = False, |
|
|
overrides: dict | None = None, |
|
|
) -> None: |
|
|
LazyTransform.__init__(self, lazy=lazy) |
|
|
|
|
|
if transforms is None: |
|
|
transforms = [] |
|
|
|
|
|
if not isinstance(map_items, bool): |
|
|
raise ValueError( |
|
|
f"Argument 'map_items' should be boolean. Got {type(map_items)}." |
|
|
"Check brackets when passing a sequence of callables." |
|
|
) |
|
|
|
|
|
self.transforms = ensure_tuple(transforms) |
|
|
self.map_items = map_items |
|
|
self.unpack_items = unpack_items |
|
|
self.log_stats = log_stats |
|
|
self.set_random_state(seed=get_seed()) |
|
|
self.overrides = overrides |
|
|
|
|
|
@LazyTransform.lazy.setter |
|
|
def lazy(self, val: bool): |
|
|
self._lazy = val |
|
|
|
|
|
def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = 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 |
|
|
|
|
|
def randomize(self, data: Any | None = 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 |
|
|
) |
|
|
|
|
|
def get_index_of_first(self, predicate): |
|
|
""" |
|
|
get_index_of_first takes a ``predicate`` and returns the index of the first transform that |
|
|
satisfies the predicate (ie. makes the predicate return True). If it is unable to find |
|
|
a transform that satisfies the ``predicate``, it returns None. |
|
|
|
|
|
Example: |
|
|
c = Compose([Flip(...), Rotate90(...), Zoom(...), RandRotate(...), Resize(...)]) |
|
|
|
|
|
print(c.get_index_of_first(lambda t: isinstance(t, RandomTrait))) |
|
|
>>> 3 |
|
|
print(c.get_index_of_first(lambda t: isinstance(t, Compose))) |
|
|
>>> None |
|
|
|
|
|
Note: |
|
|
This is only performed on the transforms directly held by this instance. If this |
|
|
instance has nested ``Compose`` transforms or other transforms that contain transforms, |
|
|
it does not iterate into them. |
|
|
|
|
|
|
|
|
Args: |
|
|
predicate: a callable that takes a single argument and returns a bool. When called |
|
|
it is passed a transform from the sequence of transforms contained by this compose |
|
|
instance. |
|
|
|
|
|
Returns: |
|
|
The index of the first transform in the sequence for which ``predicate`` returns |
|
|
True. None if no transform satisfies the ``predicate`` |
|
|
|
|
|
""" |
|
|
for i in range(len(self.transforms)): |
|
|
if predicate(self.transforms[i]): |
|
|
return i |
|
|
return None |
|
|
|
|
|
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 type(t) is 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) |
|
|
|
|
|
def __call__(self, input_, start=0, end=None, threading=False, lazy: bool | None = None): |
|
|
_lazy = self._lazy if lazy is None else lazy |
|
|
result = execute_compose( |
|
|
input_, |
|
|
transforms=self.transforms, |
|
|
start=start, |
|
|
end=end, |
|
|
map_items=self.map_items, |
|
|
unpack_items=self.unpack_items, |
|
|
lazy=_lazy, |
|
|
overrides=self.overrides, |
|
|
threading=threading, |
|
|
log_stats=self.log_stats, |
|
|
) |
|
|
|
|
|
return result |
|
|
|
|
|
def inverse(self, data): |
|
|
self._raise_if_not_invertible(data) |
|
|
|
|
|
invertible_transforms = [t for t in self.flatten().transforms if isinstance(t, InvertibleTransform)] |
|
|
if not invertible_transforms: |
|
|
warnings.warn("inverse has been called but no invertible transforms have been supplied") |
|
|
|
|
|
if self._lazy is True: |
|
|
warnings.warn( |
|
|
f"'lazy' is set to {self._lazy} but lazy execution is not supported when inverting. " |
|
|
f"'lazy' has been overridden to False for the call to inverse" |
|
|
) |
|
|
|
|
|
for t in reversed(invertible_transforms): |
|
|
data = apply_transform( |
|
|
t.inverse, data, self.map_items, self.unpack_items, lazy=False, log_stats=self.log_stats |
|
|
) |
|
|
return data |
|
|
|
|
|
@staticmethod |
|
|
def _raise_if_not_invertible(data: Any): |
|
|
from monai.transforms.utils import has_status_keys |
|
|
|
|
|
invertible, reasons = has_status_keys( |
|
|
data, TraceStatusKeys.PENDING_DURING_APPLY, "Pending operations while applying an operation" |
|
|
) |
|
|
|
|
|
if invertible is False: |
|
|
if reasons is not None: |
|
|
reason_text = "\n".join(reasons) |
|
|
raise RuntimeError(f"Unable to run inverse on 'data' for the following reasons:\n{reason_text}") |
|
|
else: |
|
|
raise RuntimeError("Unable to run inverse on 'data'; no reason logged in trace data") |
|
|
|
|
|
|
|
|
class OneOf(Compose): |
|
|
""" |
|
|
``OneOf`` provides the ability to randomly choose one transform out of a |
|
|
list of callables with pre-defined probabilities for each. |
|
|
|
|
|
Args: |
|
|
transforms: sequence of callables. |
|
|
weights: probabilities corresponding to each callable in transforms. |
|
|
Probabilities are normalized to sum to one. |
|
|
map_items: whether to apply transform to each item in the input `data` if `data` is a list or tuple. |
|
|
defaults to `True`. |
|
|
unpack_items: whether to unpack input `data` with `*` as parameters for the callable function of transform. |
|
|
defaults to `False`. |
|
|
log_stats: this optional parameter allows you to specify a logger by name for logging of pipeline execution. |
|
|
Setting this to False disables logging. Setting it to True enables logging to the default loggers. |
|
|
Setting a string overrides the logger name to which logging is performed. |
|
|
lazy: whether to enable :ref:`Lazy Resampling<lazy_resampling>` for lazy transforms. If False, transforms will |
|
|
be carried out on a transform by transform basis. If True, all lazy transforms will be executed by |
|
|
accumulating changes and resampling as few times as possible. If lazy is None, `Compose` will |
|
|
perform lazy execution on lazy transforms that have their `lazy` property set to True. |
|
|
overrides: this optional parameter allows you to specify a dictionary of parameters that should be overridden |
|
|
when executing a pipeline. These each parameter that is compatible with a given transform is then applied |
|
|
to that transform before it is executed. Note that overrides are currently only applied when |
|
|
:ref:`Lazy Resampling<lazy_resampling>` is enabled for the pipeline or a given transform. If lazy is False |
|
|
they are ignored. Currently supported args are: |
|
|
{``"mode"``, ``"padding_mode"``, ``"dtype"``, ``"align_corners"``, ``"resample_mode"``, ``device``}. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
transforms: Sequence[Callable] | Callable | None = None, |
|
|
weights: Sequence[float] | float | None = None, |
|
|
map_items: bool = True, |
|
|
unpack_items: bool = False, |
|
|
log_stats: bool | str = False, |
|
|
lazy: bool | None = False, |
|
|
overrides: dict | None = None, |
|
|
) -> None: |
|
|
super().__init__(transforms, map_items, unpack_items, log_stats, lazy, overrides) |
|
|
if len(self.transforms) == 0: |
|
|
weights = [] |
|
|
elif weights is None or isinstance(weights, float): |
|
|
weights = [1.0 / len(self.transforms)] * len(self.transforms) |
|
|
if len(weights) != len(self.transforms): |
|
|
raise ValueError( |
|
|
"transforms and weights should be same size if both specified as sequences, " |
|
|
f"got {len(weights)} and {len(self.transforms)}." |
|
|
) |
|
|
self.weights = ensure_tuple(self._normalize_probabilities(weights)) |
|
|
self.log_stats = log_stats |
|
|
|
|
|
def _normalize_probabilities(self, weights): |
|
|
if len(weights) == 0: |
|
|
return weights |
|
|
weights = np.array(weights) |
|
|
if np.any(weights < 0): |
|
|
raise ValueError(f"Probabilities must be greater than or equal to zero, got {weights}.") |
|
|
if np.all(weights == 0): |
|
|
raise ValueError(f"At least one probability must be greater than zero, got {weights}.") |
|
|
weights = weights / weights.sum() |
|
|
return list(weights) |
|
|
|
|
|
def flatten(self): |
|
|
transforms = [] |
|
|
weights = [] |
|
|
for t, w in zip(self.transforms, self.weights): |
|
|
|
|
|
|
|
|
if isinstance(t, OneOf): |
|
|
tr = t.flatten() |
|
|
for t_, w_ in zip(tr.transforms, tr.weights): |
|
|
transforms.append(t_) |
|
|
weights.append(w_ * w) |
|
|
else: |
|
|
transforms.append(t) |
|
|
weights.append(w) |
|
|
return OneOf(transforms, weights, self.map_items, self.unpack_items) |
|
|
|
|
|
def __call__(self, data, start=0, end=None, threading=False, lazy: bool | None = None): |
|
|
if start != 0: |
|
|
raise ValueError(f"OneOf requires 'start' parameter to be 0 (start set to {start})") |
|
|
if end is not None: |
|
|
raise ValueError(f"OneOf requires 'end' parameter to be None (end set to {end}") |
|
|
|
|
|
if len(self.transforms) == 0: |
|
|
return data |
|
|
|
|
|
index = self.R.multinomial(1, self.weights).argmax() |
|
|
_transform = self.transforms[index] |
|
|
_lazy = self._lazy if lazy is None else lazy |
|
|
|
|
|
data = execute_compose( |
|
|
data, |
|
|
[_transform], |
|
|
start=start, |
|
|
end=end, |
|
|
map_items=self.map_items, |
|
|
unpack_items=self.unpack_items, |
|
|
lazy=_lazy, |
|
|
overrides=self.overrides, |
|
|
threading=threading, |
|
|
log_stats=self.log_stats, |
|
|
) |
|
|
|
|
|
|
|
|
if isinstance(data, monai.data.MetaTensor): |
|
|
self.push_transform(data, extra_info={"index": index}) |
|
|
elif isinstance(data, Mapping): |
|
|
for key in data: |
|
|
if isinstance(data[key], monai.data.MetaTensor): |
|
|
self.push_transform(data[key], extra_info={"index": index}) |
|
|
return data |
|
|
|
|
|
def inverse(self, data): |
|
|
if len(self.transforms) == 0: |
|
|
return data |
|
|
|
|
|
index = None |
|
|
if isinstance(data, monai.data.MetaTensor): |
|
|
index = self.pop_transform(data)[TraceKeys.EXTRA_INFO]["index"] |
|
|
elif isinstance(data, Mapping): |
|
|
for key in data: |
|
|
if isinstance(data[key], monai.data.MetaTensor): |
|
|
index = self.pop_transform(data, key)[TraceKeys.EXTRA_INFO]["index"] |
|
|
else: |
|
|
raise RuntimeError( |
|
|
f"Inverse only implemented for Mapping (dictionary) or MetaTensor data, got type {type(data)}." |
|
|
) |
|
|
if index is None: |
|
|
|
|
|
return data |
|
|
|
|
|
_transform = self.transforms[index] |
|
|
|
|
|
return _transform.inverse(data) if isinstance(_transform, InvertibleTransform) else data |
|
|
|
|
|
|
|
|
class RandomOrder(Compose): |
|
|
""" |
|
|
``RandomOrder`` provides the ability to apply a list of transformations in random order. |
|
|
|
|
|
Args: |
|
|
transforms: sequence of callables. |
|
|
map_items: whether to apply transform to each item in the input `data` if `data` is a list or tuple. |
|
|
defaults to `True`. |
|
|
unpack_items: whether to unpack input `data` with `*` as parameters for the callable function of transform. |
|
|
defaults to `False`. |
|
|
log_stats: this optional parameter allows you to specify a logger by name for logging of pipeline execution. |
|
|
Setting this to False disables logging. Setting it to True enables logging to the default loggers. |
|
|
Setting a string overrides the logger name to which logging is performed. |
|
|
lazy: whether to enable :ref:`Lazy Resampling<lazy_resampling>` for lazy transforms. If False, transforms will |
|
|
be carried out on a transform by transform basis. If True, all lazy transforms will be executed by |
|
|
accumulating changes and resampling as few times as possible. If lazy is None, `Compose` will |
|
|
perform lazy execution on lazy transforms that have their `lazy` property set to True. |
|
|
overrides: this optional parameter allows you to specify a dictionary of parameters that should be overridden |
|
|
when executing a pipeline. These each parameter that is compatible with a given transform is then applied |
|
|
to that transform before it is executed. Note that overrides are currently only applied when |
|
|
:ref:`Lazy Resampling<lazy_resampling>` is enabled for the pipeline or a given transform. If lazy is False |
|
|
they are ignored. Currently supported args are: |
|
|
{``"mode"``, ``"padding_mode"``, ``"dtype"``, ``"align_corners"``, ``"resample_mode"``, ``device``}. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
transforms: Sequence[Callable] | Callable | None = None, |
|
|
map_items: bool = True, |
|
|
unpack_items: bool = False, |
|
|
log_stats: bool | str = False, |
|
|
lazy: bool | None = False, |
|
|
overrides: dict | None = None, |
|
|
) -> None: |
|
|
super().__init__(transforms, map_items, unpack_items, log_stats, lazy, overrides) |
|
|
self.log_stats = log_stats |
|
|
|
|
|
def __call__(self, input_, start=0, end=None, threading=False, lazy: bool | None = None): |
|
|
if start != 0: |
|
|
raise ValueError(f"RandomOrder requires 'start' parameter to be 0 (start set to {start})") |
|
|
if end is not None: |
|
|
raise ValueError(f"RandomOrder requires 'end' parameter to be None (end set to {end}") |
|
|
|
|
|
if len(self.transforms) == 0: |
|
|
return input_ |
|
|
|
|
|
num = len(self.transforms) |
|
|
applied_order = self.R.permutation(range(num)) |
|
|
_lazy = self._lazy if lazy is None else lazy |
|
|
|
|
|
input_ = execute_compose( |
|
|
input_, |
|
|
[self.transforms[ind] for ind in applied_order], |
|
|
start=start, |
|
|
end=end, |
|
|
map_items=self.map_items, |
|
|
unpack_items=self.unpack_items, |
|
|
lazy=_lazy, |
|
|
threading=threading, |
|
|
log_stats=self.log_stats, |
|
|
) |
|
|
|
|
|
|
|
|
if isinstance(input_, monai.data.MetaTensor): |
|
|
self.push_transform(input_, extra_info={"applied_order": applied_order}) |
|
|
elif isinstance(input_, Mapping): |
|
|
for key in input_: |
|
|
if isinstance(input_[key], monai.data.MetaTensor): |
|
|
self.push_transform(input_[key], extra_info={"applied_order": applied_order}) |
|
|
return input_ |
|
|
|
|
|
def inverse(self, data): |
|
|
if len(self.transforms) == 0: |
|
|
return data |
|
|
|
|
|
applied_order = None |
|
|
if isinstance(data, monai.data.MetaTensor): |
|
|
applied_order = self.pop_transform(data)[TraceKeys.EXTRA_INFO]["applied_order"] |
|
|
elif isinstance(data, Mapping): |
|
|
for key in data: |
|
|
if isinstance(data[key], monai.data.MetaTensor): |
|
|
applied_order = self.pop_transform(data, key)[TraceKeys.EXTRA_INFO]["applied_order"] |
|
|
else: |
|
|
raise RuntimeError( |
|
|
f"Inverse only implemented for Mapping (dictionary) or MetaTensor data, got type {type(data)}." |
|
|
) |
|
|
if applied_order is None: |
|
|
|
|
|
return data |
|
|
|
|
|
|
|
|
for o in reversed(applied_order): |
|
|
if isinstance(self.transforms[o], InvertibleTransform): |
|
|
data = apply_transform( |
|
|
self.transforms[o].inverse, data, self.map_items, self.unpack_items, log_stats=self.log_stats |
|
|
) |
|
|
return data |
|
|
|
|
|
|
|
|
class SomeOf(Compose): |
|
|
""" |
|
|
``SomeOf`` samples a different sequence of transforms to apply each time it is called. |
|
|
|
|
|
It can be configured to sample a fixed or varying number of transforms each time its called. Samples are drawn |
|
|
uniformly, or from user supplied transform weights. When varying the number of transforms sampled per call, |
|
|
the number of transforms to sample that call is sampled uniformly from a range supplied by the user. |
|
|
|
|
|
Args: |
|
|
transforms: list of callables. |
|
|
map_items: whether to apply transform to each item in the input `data` if `data` is a list or tuple. |
|
|
Defaults to `True`. |
|
|
unpack_items: whether to unpack input `data` with `*` as parameters for the callable function of transform. |
|
|
Defaults to `False`. |
|
|
log_stats: this optional parameter allows you to specify a logger by name for logging of pipeline execution. |
|
|
Setting this to False disables logging. Setting it to True enables logging to the default loggers. |
|
|
Setting a string overrides the logger name to which logging is performed. |
|
|
num_transforms: a 2-tuple, int, or None. The 2-tuple specifies the minimum and maximum (inclusive) number of |
|
|
transforms to sample at each iteration. If an int is given, the lower and upper bounds are set equal. |
|
|
None sets it to `len(transforms)`. Default to `None`. |
|
|
replace: whether to sample with replacement. Defaults to `False`. |
|
|
weights: weights to use in for sampling transforms. Will be normalized to 1. Default: None (uniform). |
|
|
lazy: whether to enable :ref:`Lazy Resampling<lazy_resampling>` for lazy transforms. If False, transforms will |
|
|
be carried out on a transform by transform basis. If True, all lazy transforms will be executed by |
|
|
accumulating changes and resampling as few times as possible. If lazy is None, `Compose` will |
|
|
perform lazy execution on lazy transforms that have their `lazy` property set to True. |
|
|
overrides: this optional parameter allows you to specify a dictionary of parameters that should be overridden |
|
|
when executing a pipeline. These each parameter that is compatible with a given transform is then applied |
|
|
to that transform before it is executed. Note that overrides are currently only applied when |
|
|
:ref:`Lazy Resampling<lazy_resampling>` is enabled for the pipeline or a given transform. If lazy is False |
|
|
they are ignored. Currently supported args are: |
|
|
{``"mode"``, ``"padding_mode"``, ``"dtype"``, ``"align_corners"``, ``"resample_mode"``, ``device``}. |
|
|
""" |
|
|
|
|
|
def __init__( |
|
|
self, |
|
|
transforms: Sequence[Callable] | Callable | None = None, |
|
|
map_items: bool = True, |
|
|
unpack_items: bool = False, |
|
|
log_stats: bool | str = False, |
|
|
num_transforms: int | tuple[int, int] | None = None, |
|
|
replace: bool = False, |
|
|
weights: list[int] | None = None, |
|
|
lazy: bool | None = False, |
|
|
overrides: dict | None = None, |
|
|
) -> None: |
|
|
super().__init__(transforms, map_items, unpack_items, log_stats=log_stats, lazy=lazy, overrides=overrides) |
|
|
self.min_num_transforms, self.max_num_transforms = self._ensure_valid_num_transforms(num_transforms) |
|
|
self.replace = replace |
|
|
self.weights = self._normalize_probabilities(weights) |
|
|
self.log_stats = log_stats |
|
|
|
|
|
def _ensure_valid_num_transforms(self, num_transforms: int | tuple[int, int] | None) -> tuple: |
|
|
if ( |
|
|
not isinstance(num_transforms, tuple) |
|
|
and not isinstance(num_transforms, list) |
|
|
and not isinstance(num_transforms, int) |
|
|
and num_transforms is not None |
|
|
): |
|
|
raise ValueError( |
|
|
f"Expected num_transforms to be of type int, list, tuple or None, but it's {type(num_transforms)}" |
|
|
) |
|
|
|
|
|
if num_transforms is None: |
|
|
result = [len(self.transforms), len(self.transforms)] |
|
|
elif isinstance(num_transforms, int): |
|
|
n = min(len(self.transforms), num_transforms) |
|
|
result = [n, n] |
|
|
else: |
|
|
if len(num_transforms) != 2: |
|
|
raise ValueError(f"Expected len(num_transforms)=2, but it was {len(num_transforms)}") |
|
|
if not isinstance(num_transforms[0], int) or not isinstance(num_transforms[1], int): |
|
|
raise ValueError( |
|
|
f"Expected (int,int), but received ({type(num_transforms[0])}, {type(num_transforms[1])})" |
|
|
) |
|
|
|
|
|
result = [num_transforms[0], num_transforms[1]] |
|
|
|
|
|
if result[0] < 0 or result[1] > len(self.transforms): |
|
|
raise ValueError(f"num_transforms={num_transforms} are out of the bounds [0, {len(self.transforms)}].") |
|
|
|
|
|
return ensure_tuple(result) |
|
|
|
|
|
|
|
|
def _normalize_probabilities(self, weights): |
|
|
if weights is None or len(self.transforms) == 0: |
|
|
return None |
|
|
|
|
|
weights = np.array(weights) |
|
|
|
|
|
n_weights = len(weights) |
|
|
if n_weights != len(self.transforms): |
|
|
raise ValueError(f"Expected len(weights)={len(self.transforms)}, got: {n_weights}.") |
|
|
|
|
|
if np.any(weights < 0): |
|
|
raise ValueError(f"Probabilities must be greater than or equal to zero, got {weights}.") |
|
|
|
|
|
if np.all(weights == 0): |
|
|
raise ValueError(f"At least one probability must be greater than zero, got {weights}.") |
|
|
|
|
|
weights = weights / weights.sum() |
|
|
|
|
|
return ensure_tuple(list(weights)) |
|
|
|
|
|
def __call__(self, data, start=0, end=None, threading=False, lazy: bool | None = None): |
|
|
if start != 0: |
|
|
raise ValueError(f"SomeOf requires 'start' parameter to be 0 (start set to {start})") |
|
|
if end is not None: |
|
|
raise ValueError(f"SomeOf requires 'end' parameter to be None (end set to {end}") |
|
|
|
|
|
if len(self.transforms) == 0: |
|
|
return data |
|
|
|
|
|
sample_size = self.R.randint(self.min_num_transforms, self.max_num_transforms + 1) |
|
|
applied_order = self.R.choice(len(self.transforms), sample_size, replace=self.replace, p=self.weights).tolist() |
|
|
_lazy = self._lazy if lazy is None else lazy |
|
|
|
|
|
data = execute_compose( |
|
|
data, |
|
|
[self.transforms[a] for a in applied_order], |
|
|
start=start, |
|
|
end=end, |
|
|
map_items=self.map_items, |
|
|
unpack_items=self.unpack_items, |
|
|
lazy=_lazy, |
|
|
overrides=self.overrides, |
|
|
threading=threading, |
|
|
log_stats=self.log_stats, |
|
|
) |
|
|
if isinstance(data, monai.data.MetaTensor): |
|
|
self.push_transform(data, extra_info={"applied_order": applied_order}) |
|
|
elif isinstance(data, Mapping): |
|
|
for key in data: |
|
|
if isinstance(data[key], monai.data.MetaTensor) or self.trace_key(key) in data: |
|
|
self.push_transform(data, key, extra_info={"applied_order": applied_order}) |
|
|
|
|
|
return data |
|
|
|
|
|
|
|
|
def inverse(self, data): |
|
|
if len(self.transforms) == 0: |
|
|
return data |
|
|
|
|
|
applied_order = None |
|
|
if isinstance(data, monai.data.MetaTensor): |
|
|
applied_order = self.pop_transform(data)[TraceKeys.EXTRA_INFO]["applied_order"] |
|
|
elif isinstance(data, Mapping): |
|
|
for key in data: |
|
|
if isinstance(data[key], monai.data.MetaTensor) or self.trace_key(key) in data: |
|
|
applied_order = self.pop_transform(data, key)[TraceKeys.EXTRA_INFO]["applied_order"] |
|
|
else: |
|
|
raise RuntimeError( |
|
|
f"Inverse only implemented for Mapping (dictionary) or MetaTensor data, got type {type(data)}." |
|
|
) |
|
|
if applied_order is None: |
|
|
|
|
|
return data |
|
|
|
|
|
|
|
|
for o in reversed(applied_order): |
|
|
if isinstance(self.transforms[o], InvertibleTransform): |
|
|
data = apply_transform( |
|
|
self.transforms[o].inverse, data, self.map_items, self.unpack_items, log_stats=self.log_stats |
|
|
) |
|
|
|
|
|
return data |
|
|
|