source_code/SegMamba/monai/apps/pathology/inferers/inferer.py

# Copyright (c) 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.

from __future__ import annotations

from typing import Any, Callable, Sequence

import numpy as np
import torch
import torch.nn.functional as F

from monai.inferers import SlidingWindowInferer
from monai.inferers.utils import sliding_window_inference
from monai.utils import BlendMode, PytorchPadMode, look_up_option

__all__ = ["SlidingWindowHoVerNetInferer"]


class SlidingWindowHoVerNetInferer(SlidingWindowInferer):
    """
    Sliding window method for HoVerNet model inference,
    with `sw_batch_size` windows for every model.forward().
    Usage example can be found in the :py:class:`monai.inferers.Inferer` base class.

    Args:
        roi_size: the window size to execute SlidingWindow evaluation.
            If it has non-positive components, the corresponding `inputs` size will be used.
            if the components of the `roi_size` are non-positive values, the transform will use the
            corresponding components of img size. For example, `roi_size=(32, -1)` will be adapted
            to `(32, 64)` if the second spatial dimension size of img is `64`.
        sw_batch_size: the batch size to run window slices.
        overlap: Amount of overlap between scans.
        mode: {``"constant"``, ``"gaussian"``}
            How to blend output of overlapping windows. Defaults to ``"constant"``.

            - ``"constant``": gives equal weight to all predictions.
            - ``"gaussian``": gives less weight to predictions on edges of windows.

        sigma_scale: the standard deviation coefficient of the Gaussian window when `mode` is ``"gaussian"``.
            Default: 0.125. Actual window sigma is ``sigma_scale`` * ``dim_size``.
            When sigma_scale is a sequence of floats, the values denote sigma_scale at the corresponding
            spatial dimensions.
        padding_mode: {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}
            Padding mode when ``roi_size`` is larger than inputs. Defaults to ``"constant"``
            See also: https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html
        cval: fill value for 'constant' padding mode. Default: 0
        sw_device: device for the window data.
            By default the device (and accordingly the memory) of the `inputs` is used.
            Normally `sw_device` should be consistent with the device where `predictor` is defined.
        device: device for the stitched output prediction.
            By default the device (and accordingly the memory) of the `inputs` is used. If for example
            set to device=torch.device('cpu') the gpu memory consumption is less and independent of the
            `inputs` and `roi_size`. Output is on the `device`.
        progress: whether to print a tqdm progress bar.
        cache_roi_weight_map: whether to pre-compute the ROI weight map.
        cpu_thresh: when provided, dynamically switch to stitching on cpu (to save gpu memory)
            when input image volume is larger than this threshold (in pixels/voxels).
            Otherwise use ``"device"``. Thus, the output may end-up on either cpu or gpu.
        extra_input_padding: the amount of padding for the input image, which is a tuple of even number of pads.
            Refer to to the `pad` argument of `torch.nn.functional.pad` for more details.

    Note:
        ``sw_batch_size`` denotes the max number of windows per network inference iteration,
        not the batch size of inputs.

    """

    def __init__(
        self,
        roi_size: Sequence[int] | int,
        sw_batch_size: int = 1,
        overlap: float = 0.25,
        mode: BlendMode | str = BlendMode.CONSTANT,
        sigma_scale: Sequence[float] | float = 0.125,
        padding_mode: PytorchPadMode | str = PytorchPadMode.CONSTANT,
        cval: float = 0.0,
        sw_device: torch.device | str | None = None,
        device: torch.device | str | None = None,
        progress: bool = False,
        cache_roi_weight_map: bool = False,
        cpu_thresh: int | None = None,
        extra_input_padding: tuple[int] | None = None,
    ) -> None:
        super().__init__(
            roi_size=roi_size,
            sw_batch_size=sw_batch_size,
            overlap=overlap,
            mode=mode,
            sigma_scale=sigma_scale,
            padding_mode=padding_mode,
            cval=cval,
            sw_device=sw_device,
            device=device,
            progress=progress,
            cache_roi_weight_map=cache_roi_weight_map,
            cpu_thresh=cpu_thresh,
        )
        self.extra_input_padding = extra_input_padding

    def process_output(self, seg_prob_tuple, window_data, importance_map_):
        window_shape = window_data.shape[2:]
        seg_shape = seg_prob_tuple[0].shape[2:]

        window_pad_size = []
        window_pad_slices = []
        for window_s, output_s in zip(window_shape, seg_shape):
            pad_width = max(window_s - output_s, 0)
            pad_half_1 = pad_width // 2
            pad_half_2 = pad_width - pad_half_1
            window_pad_size.extend([pad_half_1, pad_half_2])
            window_pad_slices.append(slice(pad_half_1, window_s - pad_half_2))

        # Make the padding area of the importance map zero
        importance_map = torch.zeros(window_shape, dtype=importance_map_.dtype, device=importance_map_.device)
        importance_map[window_pad_slices] = importance_map_[window_pad_slices]

        seg_prob_tuple = tuple(
            F.pad(seg_prob, pad=tuple(window_pad_size), mode=self.padding_mode, value=self.cval)
            for seg_prob in seg_prob_tuple
        )

        return seg_prob_tuple, importance_map

    def __call__(
        self,
        inputs: torch.Tensor,
        network: Callable[..., torch.Tensor | Sequence[torch.Tensor] | dict[Any, torch.Tensor]],
        *args: Any,
        **kwargs: Any,
    ) -> torch.Tensor | tuple[torch.Tensor, ...] | dict[Any, torch.Tensor]:
        """

        Args:
            inputs: model input data for inference.
            network: target model to execute inference.
                supports callables such as ``lambda x: my_torch_model(x, additional_config)``
            args: optional args to be passed to ``network``.
            kwargs: optional keyword args to be passed to ``network``.

        """

        device = self.device
        if device is None and self.cpu_thresh is not None and inputs.shape[2:].numel() > self.cpu_thresh:
            device = "cpu"  # stitch in cpu memory if image is too large

        if self.extra_input_padding:
            image_size_original = inputs.shape[2:]
            num_spatial_dims = len(image_size_original)
            inputs = F.pad(
                inputs,
                pad=tuple(self.extra_input_padding),
                mode=look_up_option(self.padding_mode, PytorchPadMode),
                value=self.cval,
            )

        results = sliding_window_inference(
            inputs,
            self.roi_size,
            self.sw_batch_size,
            network,
            self.overlap,
            self.mode,
            self.sigma_scale,
            self.padding_mode,
            self.cval,
            self.sw_device,
            device,
            self.progress,
            self.roi_weight_map,
            self.process_output,
            self.buffer_steps,
            self.buffer_dim,
            False,
            *args,
            **kwargs,
        )

        if self.extra_input_padding:
            extra_slicing: list[slice] = []
            num_padded_dims = len(self.extra_input_padding) // 2
            for sp in range(num_padded_dims):
                slice_dim = slice(
                    self.extra_input_padding[sp * 2],
                    image_size_original[num_spatial_dims - sp - 1] + self.extra_input_padding[sp * 2],
                )
                extra_slicing.insert(0, slice_dim)
            for _ in range(len(inputs.shape) - num_padded_dims):
                extra_slicing.insert(0, slice(None))

            if isinstance(results, dict):
                for k, v in results.items():
                    results[k] = v[extra_slicing]
            elif isinstance(results, (list, tuple)):
                results = type(results)([res[extra_slicing] for res in results])
            elif isinstance(results, (torch.Tensor, np.ndarray)):
                results = results[extra_slicing]
            else:
                raise ValueError(
                    f"The output [{type(results)}] should be either dict, list, tuple, torch.Tensor, or numpy array."
                )

        return results