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|
| | from __future__ import annotations |
| |
|
| | import torch |
| | from torch import Tensor, nn |
| |
|
| | from monai.inferers import SlidingWindowInferer |
| |
|
| |
|
| | def ensure_dict_value_to_list_(head_outputs: dict[str, list[Tensor]], keys: list[str] | None = None) -> None: |
| | """ |
| | An in-place function. We expect ``head_outputs`` to be Dict[str, List[Tensor]]. |
| | Yet if it is Dict[str, Tensor], this func converts it to Dict[str, List[Tensor]]. |
| | It will be modified in-place. |
| | |
| | Args: |
| | head_outputs: a Dict[str, List[Tensor]] or Dict[str, Tensor], will be modifier in-place |
| | keys: the keys in head_output that need to have value type List[Tensor]. If not provided, will use head_outputs.keys(). |
| | """ |
| | if keys is None: |
| | keys = list(head_outputs.keys()) |
| |
|
| | for k in keys: |
| | value_k = head_outputs[k] |
| | |
| | if isinstance(value_k, Tensor): |
| | head_outputs[k] = [value_k] |
| | elif isinstance(value_k[0], Tensor): |
| | head_outputs[k] = list(value_k) |
| | else: |
| | raise ValueError("The output of network should be Dict[str, List[Tensor]] or Dict[str, Tensor].") |
| |
|
| |
|
| | def check_dict_values_same_length(head_outputs: dict[str, list[Tensor]], keys: list[str] | None = None) -> None: |
| | """ |
| | We expect the values in ``head_outputs``: Dict[str, List[Tensor]] to have the same length. |
| | Will raise ValueError if not. |
| | |
| | Args: |
| | head_outputs: a Dict[str, List[Tensor]] or Dict[str, Tensor] |
| | keys: the keys in head_output that need to have values (List) with same length. |
| | If not provided, will use head_outputs.keys(). |
| | """ |
| | if keys is None: |
| | keys = list(head_outputs.keys()) |
| |
|
| | num_output_levels_list: list[int] = [len(head_outputs[k]) for k in keys] |
| | num_output_levels = torch.unique(torch.tensor(num_output_levels_list)) |
| | if len(num_output_levels) != 1: |
| | raise ValueError(f"The values in the input dict should have the same length, Got {num_output_levels_list}.") |
| |
|
| |
|
| | def _network_sequence_output(images: Tensor, network: nn.Module, keys: list[str] | None = None) -> list[Tensor]: |
| | """ |
| | Decompose the output of network (a dict) into a list. |
| | |
| | Args: |
| | images: input of the network |
| | keys: the keys in the network output whose values will be output in this func. |
| | If not provided, will use all keys. |
| | |
| | Return: |
| | network output values concat to a single List[Tensor] |
| | """ |
| | head_outputs = network(images) |
| |
|
| | |
| | if isinstance(head_outputs, (tuple, list)): |
| | return list(head_outputs) |
| |
|
| | |
| | ensure_dict_value_to_list_(head_outputs, keys) |
| | if keys is None: |
| | keys = list(head_outputs.keys()) |
| | check_dict_values_same_length(head_outputs, keys) |
| | head_outputs_sequence = [] |
| | for k in keys: |
| | head_outputs_sequence += list(head_outputs[k]) |
| | return head_outputs_sequence |
| |
|
| |
|
| | def predict_with_inferer( |
| | images: Tensor, network: nn.Module, keys: list[str], inferer: SlidingWindowInferer | None = None |
| | ) -> dict[str, list[Tensor]]: |
| | """ |
| | Predict network dict output with an inferer. Compared with directly output network(images), |
| | it enables a sliding window inferer that can be used to handle large inputs. |
| | |
| | Args: |
| | images: input of the network, Tensor sized (B, C, H, W) or (B, C, H, W, D) |
| | network: a network that takes an image Tensor sized (B, C, H, W) or (B, C, H, W, D) as input |
| | and outputs a dictionary Dict[str, List[Tensor]] or Dict[str, Tensor]. |
| | keys: the keys in the output dict, should be network output keys or a subset of them. |
| | inferer: a SlidingWindowInferer to handle large inputs. |
| | |
| | Return: |
| | The predicted head_output from network, a Dict[str, List[Tensor]] |
| | |
| | Example: |
| | .. code-block:: python |
| | |
| | # define a naive network |
| | import torch |
| | import monai |
| | class NaiveNet(torch.nn.Module): |
| | def __init__(self, ): |
| | super().__init__() |
| | |
| | def forward(self, images: torch.Tensor): |
| | return {"cls": torch.randn(images.shape), "box_reg": [torch.randn(images.shape)]} |
| | |
| | # create a predictor |
| | network = NaiveNet() |
| | inferer = monai.inferers.SlidingWindowInferer( |
| | roi_size = (128, 128, 128), |
| | overlap = 0.25, |
| | cache_roi_weight_map = True, |
| | ) |
| | network_output_keys=["cls", "box_reg"] |
| | images = torch.randn((2, 3, 512, 512, 512)) # a large input |
| | head_outputs = predict_with_inferer(images, network, network_output_keys, inferer) |
| | |
| | """ |
| | if inferer is None: |
| | raise ValueError("Please set inferer as a monai.inferers.inferer.SlidingWindowInferer(*)") |
| | head_outputs_sequence = inferer(images, _network_sequence_output, network, keys=keys) |
| | num_output_levels: int = len(head_outputs_sequence) // len(keys) |
| | head_outputs = {} |
| | for i, k in enumerate(keys): |
| | head_outputs[k] = list(head_outputs_sequence[num_output_levels * i : num_output_levels * (i + 1)]) |
| | return head_outputs |
| |
|