# 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. # ========================================================================= # Adapted from https://github.com/vqdang/hover_net # which has the following license: # https://github.com/vqdang/hover_net/blob/master/LICENSE # MIT License # Original publication: # @article{graham2019hover, # title={Hover-net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images}, # author={Graham, Simon and Vu, Quoc Dang and Raza, Shan E Ahmed and Azam, Ayesha and Tsang, Yee Wah and Kwak, # Jin Tae and Rajpoot, Nasir}, # journal={Medical Image Analysis}, # pages={101563}, # year={2019}, # publisher={Elsevier} # } # ========================================================================= from __future__ import annotations import os import re import warnings from collections import OrderedDict from collections.abc import Callable, Sequence import torch import torch.nn as nn from monai.apps.utils import download_url from monai.networks.blocks import UpSample from monai.networks.layers.factories import Conv, Dropout from monai.networks.layers.utils import get_act_layer, get_norm_layer from monai.utils.enums import HoVerNetBranch, HoVerNetMode, InterpolateMode, UpsampleMode from monai.utils.module import export, look_up_option __all__ = ["HoVerNet", "Hovernet", "HoVernet", "HoVerNet"] class _DenseLayerDecoder(nn.Module): def __init__( self, num_features: int, in_channels: int, out_channels: int, dropout_prob: float = 0.0, act: str | tuple = ("relu", {"inplace": True}), norm: str | tuple = "batch", kernel_size: int = 3, padding: int = 0, ) -> None: """ Args: num_features: number of internal channels used for the layer in_channels: number of the input channels. out_channels: number of the output channels. dropout_prob: dropout rate after each dense layer. act: activation type and arguments. Defaults to relu. norm: feature normalization type and arguments. Defaults to batch norm. kernel_size: size of the kernel for >1 convolutions (dependent on mode) padding: padding value for >1 convolutions. """ super().__init__() conv_type: Callable = Conv[Conv.CONV, 2] dropout_type: Callable = Dropout[Dropout.DROPOUT, 2] self.layers = nn.Sequential() self.layers.add_module("preact_bna/bn", get_norm_layer(name=norm, spatial_dims=2, channels=in_channels)) self.layers.add_module("preact_bna/relu", get_act_layer(name=act)) self.layers.add_module("conv1", conv_type(in_channels, num_features, kernel_size=1, bias=False)) self.layers.add_module("conv1/norm", get_norm_layer(name=norm, spatial_dims=2, channels=num_features)) self.layers.add_module("conv1/relu2", get_act_layer(name=act)) self.layers.add_module( "conv2", conv_type(num_features, out_channels, kernel_size=kernel_size, padding=padding, groups=4, bias=False), ) if dropout_prob > 0: self.layers.add_module("dropout", dropout_type(dropout_prob)) def forward(self, x: torch.Tensor) -> torch.Tensor: x1 = self.layers(x) if x1.shape[-1] != x.shape[-1]: trim = (x.shape[-1] - x1.shape[-1]) // 2 x = x[:, :, trim:-trim, trim:-trim] x = torch.cat([x, x1], 1) return x class _DecoderBlock(nn.Sequential): def __init__( self, layers: int, num_features: int, in_channels: int, out_channels: int, dropout_prob: float = 0.0, act: str | tuple = ("relu", {"inplace": True}), norm: str | tuple = "batch", kernel_size: int = 3, same_padding: bool = False, ) -> None: """ Args: layers: number of layers in the block. num_features: number of internal features used. in_channels: number of the input channel. out_channels: number of the output channel. dropout_prob: dropout rate after each dense layer. act: activation type and arguments. Defaults to relu. norm: feature normalization type and arguments. Defaults to batch norm. kernel_size: size of the kernel for >1 convolutions (dependent on mode) same_padding: whether to do padding for >1 convolutions to ensure the output size is the same as the input size. """ super().__init__() conv_type: Callable = Conv[Conv.CONV, 2] padding: int = kernel_size // 2 if same_padding else 0 self.add_module( "conva", conv_type(in_channels, in_channels // 4, kernel_size=kernel_size, padding=padding, bias=False) ) _in_channels = in_channels // 4 for i in range(layers): layer = _DenseLayerDecoder( num_features, _in_channels, out_channels, dropout_prob, act=act, norm=norm, kernel_size=kernel_size, padding=padding, ) _in_channels += out_channels self.add_module("denselayerdecoder%d" % (i + 1), layer) trans = _Transition(_in_channels, act=act, norm=norm) self.add_module("bna_block", trans) self.add_module("convf", conv_type(_in_channels, _in_channels, kernel_size=1, bias=False)) class _DenseLayer(nn.Sequential): def __init__( self, num_features: int, in_channels: int, out_channels: int, dropout_prob: float = 0.0, act: str | tuple = ("relu", {"inplace": True}), norm: str | tuple = "batch", drop_first_norm_relu: int = 0, kernel_size: int = 3, ) -> None: """Dense Convolutional Block. References: Huang, Gao, et al. "Densely connected convolutional networks." Proceedings of the IEEE conference on computer vision and pattern recognition. 2017. Args: num_features: number of internal channels used for the layer in_channels: number of the input channels. out_channels: number of the output channels. dropout_prob: dropout rate after each dense layer. act: activation type and arguments. Defaults to relu. norm: feature normalization type and arguments. Defaults to batch norm. drop_first_norm_relu - omits the first norm/relu for the first layer kernel_size: size of the kernel for >1 convolutions (dependent on mode) """ super().__init__() self.layers = nn.Sequential() conv_type: Callable = Conv[Conv.CONV, 2] dropout_type: Callable = Dropout[Dropout.DROPOUT, 2] if not drop_first_norm_relu: self.layers.add_module("preact/bn", get_norm_layer(name=norm, spatial_dims=2, channels=in_channels)) self.layers.add_module("preact/relu", get_act_layer(name=act)) self.layers.add_module("conv1", conv_type(in_channels, num_features, kernel_size=1, padding=0, bias=False)) self.layers.add_module("conv1/bn", get_norm_layer(name=norm, spatial_dims=2, channels=num_features)) self.layers.add_module("conv1/relu", get_act_layer(name=act)) if in_channels != 64 and drop_first_norm_relu: self.layers.add_module( "conv2", conv_type(num_features, num_features, kernel_size=kernel_size, stride=2, padding=2, bias=False) ) else: self.layers.add_module( "conv2", conv_type(num_features, num_features, kernel_size=kernel_size, padding=1, bias=False) ) self.layers.add_module("conv2/bn", get_norm_layer(name=norm, spatial_dims=2, channels=num_features)) self.layers.add_module("conv2/relu", get_act_layer(name=act)) self.layers.add_module("conv3", conv_type(num_features, out_channels, kernel_size=1, padding=0, bias=False)) if dropout_prob > 0: self.layers.add_module("dropout", dropout_type(dropout_prob)) class _Transition(nn.Sequential): def __init__( self, in_channels: int, act: str | tuple = ("relu", {"inplace": True}), norm: str | tuple = "batch" ) -> None: """ Args: in_channels: number of the input channel. act: activation type and arguments. Defaults to relu. norm: feature normalization type and arguments. Defaults to batch norm. """ super().__init__() self.add_module("bn", get_norm_layer(name=norm, spatial_dims=2, channels=in_channels)) self.add_module("relu", get_act_layer(name=act)) class _ResidualBlock(nn.Module): def __init__( self, layers: int, num_features: int, in_channels: int, out_channels: int, dropout_prob: float = 0.0, act: str | tuple = ("relu", {"inplace": True}), norm: str | tuple = "batch", freeze_dense_layer: bool = False, freeze_block: bool = False, ) -> None: """Residual block. References: He, Kaiming, et al. "Deep residual learning for image recognition." Proceedings of the IEEE conference on computer vision and pattern recognition. 2016. Args: layers: number of layers in the block. num_features: number of internal features used. in_channels: number of the input channel. out_channels: number of the output channel. dropout_prob: dropout rate after each dense layer. act: activation type and arguments. Defaults to relu. norm: feature normalization type and arguments. Defaults to batch norm. freeze_dense_layer: whether to freeze all dense layers within the block. freeze_block: whether to freeze the whole block. """ super().__init__() self.layers = nn.Sequential() conv_type: Callable = Conv[Conv.CONV, 2] if in_channels == 64: self.shortcut = conv_type(in_channels, out_channels, kernel_size=1, bias=False) else: self.shortcut = conv_type(in_channels, out_channels, kernel_size=1, stride=2, padding=1, bias=False) layer = _DenseLayer( num_features, in_channels, out_channels, dropout_prob, act=act, norm=norm, drop_first_norm_relu=True ) self.layers.add_module("denselayer_0", layer) for i in range(1, layers): layer = _DenseLayer(num_features, out_channels, out_channels, dropout_prob, act=act, norm=norm) self.layers.add_module(f"denselayer_{i}", layer) self.bna_block = _Transition(out_channels, act=act, norm=norm) if freeze_dense_layer: self.layers.requires_grad_(False) if freeze_block: self.requires_grad_(False) def forward(self, x: torch.Tensor) -> torch.Tensor: sc = self.shortcut(x) if self.shortcut.stride == (2, 2): sc = sc[:, :, :-1, :-1] for layer in self.layers: x = layer.forward(x) if x.shape[-2:] != sc.shape[-2:]: x = x[:, :, :-1, :-1] x = x + sc sc = x x = self.bna_block(x) return x class _DecoderBranch(nn.ModuleList): def __init__( self, decode_config: Sequence[int] = (8, 4), act: str | tuple = ("relu", {"inplace": True}), norm: str | tuple = "batch", dropout_prob: float = 0.0, out_channels: int = 2, kernel_size: int = 3, same_padding: bool = False, ) -> None: """ Args: decode_config: number of layers for each block. act: activation type and arguments. Defaults to relu. norm: feature normalization type and arguments. Defaults to batch norm. dropout_prob: dropout rate after each dense layer. out_channels: number of the output channel. kernel_size: size of the kernel for >1 convolutions (dependent on mode) same_padding: whether to do padding for >1 convolutions to ensure the output size is the same as the input size. """ super().__init__() conv_type: Callable = Conv[Conv.CONV, 2] # decode branches _in_channels = 1024 _num_features = 128 _out_channels = 32 self.decoder_blocks = nn.Sequential() for i, num_layers in enumerate(decode_config): block = _DecoderBlock( layers=num_layers, num_features=_num_features, in_channels=_in_channels, out_channels=_out_channels, dropout_prob=dropout_prob, act=act, norm=norm, kernel_size=kernel_size, same_padding=same_padding, ) self.decoder_blocks.add_module(f"decoderblock{i + 1}", block) _in_channels = 512 # output layers self.output_features = nn.Sequential() _i = len(decode_config) _pad_size = (kernel_size - 1) // 2 _seq_block = nn.Sequential( OrderedDict( [("conva", conv_type(256, 64, kernel_size=kernel_size, stride=1, bias=False, padding=_pad_size))] ) ) self.output_features.add_module(f"decoderblock{_i + 1}", _seq_block) _seq_block = nn.Sequential( OrderedDict( [ ("bn", get_norm_layer(name=norm, spatial_dims=2, channels=64)), ("relu", get_act_layer(name=act)), ("conv", conv_type(64, out_channels, kernel_size=1, stride=1)), ] ) ) self.output_features.add_module(f"decoderblock{_i + 2}", _seq_block) self.upsample = UpSample( 2, scale_factor=2, mode=UpsampleMode.NONTRAINABLE, interp_mode=InterpolateMode.BILINEAR, bias=False ) def forward(self, xin: torch.Tensor, short_cuts: list[torch.Tensor]) -> torch.Tensor: block_number = len(short_cuts) - 1 x = xin + short_cuts[block_number] for block in self.decoder_blocks: x = block(x) x = self.upsample(x) block_number -= 1 trim = (short_cuts[block_number].shape[-1] - x.shape[-1]) // 2 if trim > 0: x += short_cuts[block_number][:, :, trim:-trim, trim:-trim] for block in self.output_features: x = block(x) return x @export("monai.networks.nets") class HoVerNet(nn.Module): """HoVerNet model References: Graham, Simon et al. Hover-net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images, Medical Image Analysis 2019 https://github.com/vqdang/hover_net https://pytorch.org/vision/main/models/generated/torchvision.models.resnet50.html This network is non-deterministic since it uses `torch.nn.Upsample` with ``UpsampleMode.NONTRAINABLE`` mode which is implemented with torch.nn.functional.interpolate(). Please check the link below for more details: https://pytorch.org/docs/stable/generated/torch.use_deterministic_algorithms.html#torch.use_deterministic_algorithms Args: mode: use original implementation (`HoVerNetMODE.ORIGINAL` or "original") or a faster implementation (`HoVerNetMODE.FAST` or "fast"). Defaults to `HoVerNetMODE.FAST`. in_channels: number of the input channel. np_out_channels: number of the output channel of the nucleus prediction branch. out_classes: number of the nuclear type classes. act: activation type and arguments. Defaults to relu. norm: feature normalization type and arguments. Defaults to batch norm. decoder_padding: whether to do padding on convolution layers in the decoders. In the conic branch of the referred repository, the architecture is changed to do padding on convolution layers in order to get the same output size as the input, and this changed version is used on CoNIC challenge. Please note that to get consistent output size, `HoVerNetMode.FAST` mode should be employed. dropout_prob: dropout rate after each dense layer. pretrained_url: if specifying, will loaded the pretrained weights downloaded from the url. There are two supported forms of weights: 1. preact-resnet50 weights coming from the referred hover_net repository, each user is responsible for checking the content of model/datasets and the applicable licenses and determining if suitable for the intended use. please check the following link for more details: https://github.com/vqdang/hover_net#data-format 2. standard resnet50 weights of torchvision. Please check the following link for more details: https://pytorch.org/vision/main/_modules/torchvision/models/resnet.html#ResNet50_Weights adapt_standard_resnet: if the pretrained weights of the encoder follow the original format (preact-resnet50), this value should be `False`. If using the pretrained weights that follow torchvision's standard resnet50 format, this value should be `True`. pretrained_state_dict_key: this arg is used when `pretrained_url` is provided and `adapt_standard_resnet` is True. It is used to extract the expected state dict. freeze_encoder: whether to freeze the encoder of the network. """ Mode = HoVerNetMode Branch = HoVerNetBranch def __init__( self, mode: HoVerNetMode | str = HoVerNetMode.FAST, in_channels: int = 3, np_out_channels: int = 2, out_classes: int = 0, act: str | tuple = ("relu", {"inplace": True}), norm: str | tuple = "batch", decoder_padding: bool = False, dropout_prob: float = 0.0, pretrained_url: str | None = None, adapt_standard_resnet: bool = False, pretrained_state_dict_key: str | None = None, freeze_encoder: bool = False, ) -> None: super().__init__() if isinstance(mode, str): mode = mode.upper() self.mode = look_up_option(mode, HoVerNetMode) if self.mode == "ORIGINAL" and decoder_padding is True: warnings.warn( "'decoder_padding=True' only works when mode is 'FAST', otherwise the output size may not equal to the input." ) if out_classes > 128: raise ValueError("Number of nuclear types classes exceeds maximum (128)") elif out_classes == 1: raise ValueError("Number of nuclear type classes should either be None or >1") if dropout_prob > 1 or dropout_prob < 0: raise ValueError("Dropout can only be in the range 0.0 to 1.0") # number of filters in the first convolution layer. _init_features: int = 64 # number of layers in each pooling block. _block_config: Sequence[int] = (3, 4, 6, 3) if self.mode == HoVerNetMode.FAST: _ksize = 3 _pad = 3 else: _ksize = 5 _pad = 0 conv_type: type[nn.Conv2d] = Conv[Conv.CONV, 2] self.conv0 = nn.Sequential( OrderedDict( [ ("conv", conv_type(in_channels, _init_features, kernel_size=7, stride=1, padding=_pad, bias=False)), ("bn", get_norm_layer(name=norm, spatial_dims=2, channels=_init_features)), ("relu", get_act_layer(name=act)), ] ) ) _in_channels = _init_features _out_channels = 256 _num_features = _init_features self.res_blocks = nn.Sequential() for i, num_layers in enumerate(_block_config): freeze_dense_layer = False freeze_block = False if freeze_encoder: if i == 0: freeze_dense_layer = True else: freeze_block = True block = _ResidualBlock( layers=num_layers, num_features=_num_features, in_channels=_in_channels, out_channels=_out_channels, dropout_prob=dropout_prob, act=act, norm=norm, freeze_dense_layer=freeze_dense_layer, freeze_block=freeze_block, ) self.res_blocks.add_module(f"d{i}", block) _in_channels = _out_channels _out_channels *= 2 _num_features *= 2 # bottleneck convolution self.bottleneck = nn.Sequential() self.bottleneck.add_module( "conv_bottleneck", conv_type(_in_channels, _num_features, kernel_size=1, stride=1, padding=0, bias=False) ) self.upsample = UpSample( 2, scale_factor=2, mode=UpsampleMode.NONTRAINABLE, interp_mode=InterpolateMode.BILINEAR, bias=False ) # decode branches self.nucleus_prediction = _DecoderBranch( kernel_size=_ksize, same_padding=decoder_padding, out_channels=np_out_channels ) self.horizontal_vertical = _DecoderBranch(kernel_size=_ksize, same_padding=decoder_padding) self.type_prediction: _DecoderBranch | None = ( _DecoderBranch(out_channels=out_classes, kernel_size=_ksize, same_padding=decoder_padding) if out_classes > 0 else None ) for m in self.modules(): if isinstance(m, conv_type): nn.init.kaiming_normal_(torch.as_tensor(m.weight)) elif isinstance(m, nn.BatchNorm2d): nn.init.constant_(torch.as_tensor(m.weight), 1) nn.init.constant_(torch.as_tensor(m.bias), 0) if pretrained_url is not None: if adapt_standard_resnet: weights = _remap_standard_resnet_model(pretrained_url, state_dict_key=pretrained_state_dict_key) else: weights = _remap_preact_resnet_model(pretrained_url) _load_pretrained_encoder(self, weights) def forward(self, x: torch.Tensor) -> dict[str, torch.Tensor]: if self.mode == HoVerNetMode.ORIGINAL.value: if x.shape[-1] != 270 or x.shape[-2] != 270: raise ValueError("Input size should be 270 x 270 when using HoVerNetMode.ORIGINAL") else: if x.shape[-1] != 256 or x.shape[-2] != 256: raise ValueError("Input size should be 256 x 256 when using HoVerNetMode.FAST") x = self.conv0(x) short_cuts = [] for i, block in enumerate(self.res_blocks): x = block.forward(x) if i <= 2: short_cuts.append(x) x = self.bottleneck(x) x = self.upsample(x) output = { HoVerNetBranch.NP.value: self.nucleus_prediction(x, short_cuts), HoVerNetBranch.HV.value: self.horizontal_vertical(x, short_cuts), } if self.type_prediction is not None: output[HoVerNetBranch.NC.value] = self.type_prediction(x, short_cuts) return output def _load_pretrained_encoder(model: nn.Module, state_dict: OrderedDict | dict): model_dict = model.state_dict() state_dict = { k: v for k, v in state_dict.items() if (k in model_dict) and (model_dict[k].shape == state_dict[k].shape) } model_dict.update(state_dict) model.load_state_dict(model_dict) if len(state_dict.keys()) == 0: warnings.warn( "no key will be updated. Please check if 'pretrained_url' or `pretrained_state_dict_key` is correct." ) else: print(f"{len(state_dict)} out of {len(model_dict)} keys are updated with pretrained weights.") def _remap_preact_resnet_model(model_url: str): pattern_conv0 = re.compile(r"^(conv0\.\/)(.+)$") pattern_block = re.compile(r"^(d\d+)\.(.+)$") pattern_layer = re.compile(r"^(.+\.d\d+)\.units\.(\d+)(.+)$") pattern_bna = re.compile(r"^(.+\.d\d+)\.blk_bna\.(.+)") # download the pretrained weights into torch hub's default dir weights_dir = os.path.join(torch.hub.get_dir(), "preact-resnet50.pth") download_url(model_url, fuzzy=True, filepath=weights_dir, progress=False) state_dict = torch.load(weights_dir, map_location=None if torch.cuda.is_available() else torch.device("cpu"))[ "desc" ] for key in list(state_dict.keys()): new_key = None if pattern_conv0.match(key): new_key = re.sub(pattern_conv0, r"conv0.conv\2", key) elif pattern_block.match(key): new_key = re.sub(pattern_block, r"res_blocks.\1.\2", key) if pattern_layer.match(new_key): new_key = re.sub(pattern_layer, r"\1.layers.denselayer_\2.layers\3", new_key) elif pattern_bna.match(new_key): new_key = re.sub(pattern_bna, r"\1.bna_block.\2", new_key) if new_key: state_dict[new_key] = state_dict[key] del state_dict[key] if "upsample2x" in key: del state_dict[key] return state_dict def _remap_standard_resnet_model(model_url: str, state_dict_key: str | None = None): pattern_conv0 = re.compile(r"^conv1\.(.+)$") pattern_bn1 = re.compile(r"^bn1\.(.+)$") pattern_block = re.compile(r"^layer(\d+)\.(\d+)\.(.+)$") # bn3 to next denselayer's preact/bn pattern_block_bn3 = re.compile(r"^(res_blocks.d\d+\.layers\.denselayer_)(\d+)\.layers\.bn3\.(.+)$") # bn1, bn2 to conv1/bn, conv2/bn pattern_block_bn = re.compile(r"^(res_blocks.d\d+\.layers\.denselayer_\d+\.layers)\.bn(\d+)\.(.+)$") pattern_downsample0 = re.compile(r"^(res_blocks.d\d+).+\.downsample\.0\.(.+)") pattern_downsample1 = re.compile(r"^(res_blocks.d\d+).+\.downsample\.1\.(.+)") # download the pretrained weights into torch hub's default dir weights_dir = os.path.join(torch.hub.get_dir(), "resnet50.pth") download_url(model_url, fuzzy=True, filepath=weights_dir, progress=False) state_dict = torch.load(weights_dir, map_location=None if torch.cuda.is_available() else torch.device("cpu")) if state_dict_key is not None: state_dict = state_dict[state_dict_key] for key in list(state_dict.keys()): new_key = None if pattern_conv0.match(key): new_key = re.sub(pattern_conv0, r"conv0.conv.\1", key) elif pattern_bn1.match(key): new_key = re.sub(pattern_bn1, r"conv0.bn.\1", key) elif pattern_block.match(key): new_key = re.sub( pattern_block, lambda s: "res_blocks.d" + str(int(s.group(1)) - 1) + ".layers.denselayer_" + s.group(2) + ".layers." + s.group(3), key, ) if pattern_block_bn3.match(new_key): new_key = re.sub( pattern_block_bn3, lambda s: s.group(1) + str(int(s.group(2)) + 1) + ".layers.preact/bn." + s.group(3), new_key, ) elif pattern_block_bn.match(new_key): new_key = re.sub(pattern_block_bn, r"\1.conv\2/bn.\3", new_key) elif pattern_downsample0.match(new_key): new_key = re.sub(pattern_downsample0, r"\1.shortcut.\2", new_key) elif pattern_downsample1.match(new_key): new_key = re.sub(pattern_downsample1, r"\1.bna_block.bn.\2", new_key) if new_key: state_dict[new_key] = state_dict[key] del state_dict[key] return state_dict Hovernet = HoVernet = HoverNet = HoVerNet