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| | |
| | """ |
| | 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 |
| |
|