论文题目:ViT-V-Net: Vision Transformer for Unsupervised Volumetric Medical Image Registration
源码链接:https://github.com/junyuchen245/ViT-V-Net_for_3D_Image_Registration_Pytorch
config.py:
配置初始的参数
import ml_collections
def get_3DReg_config():
config = ml_collections.ConfigDict()
config.patches = ml_collections.ConfigDict({'size': (8, 8, 8)})
config.patches.grid = (8, 8, 8)
config.hidden_size = 252
config.transformer = ml_collections.ConfigDict()
config.transformer.mlp_dim = 3072
config.transformer.num_heads = 12
config.transformer.num_layers = 12
config.transformer.attention_dropout_rate = 0.0
config.transformer.dropout_rate = 0.1
config.patch_size = 8
config.conv_first_channel = 512
config.encoder_channels = (16, 32, 32)
config.down_factor = 2
config.down_num = 2
config.decoder_channels = (96, 48, 32, 32, 16)
config.skip_channels = (32, 32, 32, 32, 16)
config.n_dims = 3
config.n_skip = 5
return config
models.py:
Multi-head attention
Attention理论上是上图中的橙色部分
class Attention(nn.Module):
def __init__(self, config, vis):
super(Attention, self).__init__()
self.vis = vis
self.num_attention_heads = config.transformer["num_heads"]
self.attention_head_size = int(config.hidden_size / self.num_attention_heads)
self.all_head_size = self.num_attention_heads * self.attention_head_size
self.query = Linear(config.hidden_size, self.all_head_size)
self.key = Linear(config.hidden_size, self.all_head_size)
self.value = Linear(config.hidden_size, self.all_head_size)
self.out = Linear(config.hidden_size, config.hidden_size)
self.attn_dropout = Dropout(config.transformer["attention_dropout_rate"])
self.proj_dropout = Dropout(config.transformer["attention_dropout_rate"])
self.softmax = Softmax(dim=-1)
def transpose_for_scores(self, x):
new_x_shape = x.size()[:-1] + (self.num_attention_heads, self.attention_head_size)
x = x.view(*new_x_shape)
return x.permute(0, 2, 1, 3)
def forward(self, hidden_states):
mixed_query_layer = self.query(hidden_states)
mixed_key_layer = self.key(hidden_states)
mixed_value_layer = self.value(hidden_states)
query_layer = self.transpose_for_scores(mixed_query_layer)
key_layer = self.transpose_for_scores(mixed_key_layer)
value_layer = self.transpose_for_scores(mixed_value_layer)
attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2))
attention_scores = attention_scores / math.sqrt(self.attention_head_size)
attention_probs = self.softmax(attention_scores)
weights = attention_probs if self.vis else None
attention_probs = self.attn_dropout(attention_probs)
context_layer = torch.matmul(attention_probs, value_layer)
context_layer = context_layer.permute(0, 2, 1, 3).contiguous()
new_context_layer_shape = context_layer.size()[:-2] + (self.all_head_size,)
context_layer = context_layer.view(*new_context_layer_shape)
attention_output = self.out(context_layer)
attention_output = self.proj_dropout(attention_output)
return attention_output, weights
Mlp是图三中的黄色部分 ,前向神经网络
class Mlp(nn.Module):#前向神经网络
def __init__(self, config):
super(Mlp, self).__init__()
self.fc1 = Linear(config.hidden_size, config.transformer["mlp_dim"])
self.fc2 = Linear(config.transformer["mlp_dim"], config.hidden_size)
self.act_fn = ACT2FN["gelu"]
self.dropout = Dropout(config.transformer["dropout_rate"])
self._init_weights()
def _init_weights(self):
nn.init.xavier_uniform_(self.fc1.weight)
nn.init.xavier_uniform_(self.fc2.weight)
nn.init.normal_(self.fc1.bias, std=1e-6)
nn.init.normal_(self.fc2.bias, std=1e-6)
def forward(self, x):
x = self.fc1(x)
x = self.act_fn(x)
x = self.dropout(x)
x = self.fc2(x)
x = self.dropout(x)
return x
Embeddings是下图的部分
embedding这里是用cov3d来进行patch的,输出的是210块,
(B, n_patch, hidden)=([2, 210, 252]),经过transformer也是这个尺寸。
class Embeddings(nn.Module):
"""Construct the embeddings from patch, position embeddings.
"""
def __init__(self, config, img_size):
super(Embeddings, self).__init__()
self.config = config
down_factor = config.down_factor
patch_size = _triple(config.patches["size"])
n_patches = int((img_size[0]/2**down_factor// patch_size[0]) * (img_size[1]/2**down_factor// patch_size[1]) * (img_size[2]/2**down_factor// patch_size[2]))
self.hybrid_model = CNNEncoder(config, n_channels=2)
in_channels = config['encoder_channels'][-1]
self.patch_embeddings = Conv3d(in_channels=in_channels,
out_channels=config.hidden_size,
kernel_size=patch_size,
stride=patch_size)
self.position_embeddings = nn.Parameter(torch.zeros(1, n_patches, config.hidden_size))
self.dropout = Dropout(config.transformer["dropout_rate"])
def forward(self, x):
x, features = self.hybrid_model(x)
x = self.patch_embeddings(x) # (B, hidden. n_patches^(1/2), n_patches^(1/2))
x = x.flatten(2)
x = x.transpose(-1, -2) # (B, n_patches, hidden)
embeddings = x + self.position_embeddings
embeddings = self.dropout(embeddings)
return embeddings, features
Block就是图3中的灰色框内的卷积层部分,灰色框并不是全部的transformer,而且block的类里不是12个块,只定义了一个块,12个块的循环在Ecoder类中定义
class Block(nn.Module):
def __init__(self, config, vis):
super(Block, self).__init__()
self.hidden_size = config.hidden_size
self.attention_norm = LayerNorm(config.hidden_size, eps=1e-6)
self.ffn_norm = LayerNorm(config.hidden_size, eps=1e-6)
self.ffn = Mlp(config)
self.attn = Attention(config, vis)
def forward(self, x):
h = x
x = self.attention_norm(x)
x, weights = self.attn(x)
x = x + h
h = x
x = self.ffn_norm(x)
x = self.ffn(x)
x = x + h
return x, weights
encoder就是12个block放一起
class Encoder(nn.Module):
def __init__(self, config, vis):
super(Encoder, self).__init__()
self.vis = vis
self.layer = nn.ModuleList()
self.encoder_norm = LayerNorm(config.hidden_size, eps=1e-6)
for _ in range(config.transformer["num_layers"]):
layer = Block(config, vis)
self.layer.append(copy.deepcopy(layer))
def forward(self, hidden_states):
attn_weights = []
for layer_block in self.layer:
hidden_states, weights = layer_block(hidden_states)
if self.vis:
attn_weights.append(weights)
encoded = self.encoder_norm(hidden_states)
return encoded, attn_weights
DecoderBlock是图1和图2的绿色部分, 用于DecoderCup,
class DecoderBlock(nn.Module):
def __init__(
self,
in_channels,
out_channels,
skip_channels=0,
use_batchnorm=True,
):
super().__init__()
self.conv1 = Conv3dReLU(
in_channels + skip_channels,
out_channels,
kernel_size=3,
padding=1,
use_batchnorm=use_batchnorm,
)
self.conv2 = Conv3dReLU(
out_channels,
out_channels,
kernel_size=3,
padding=1,
use_batchnorm=use_batchnorm,
)
self.up = nn.Upsample(scale_factor=2, mode='trilinear', align_corners=False)
def forward(self, x, skip=None):
x = self.up(x)
if skip is not None:
x = torch.cat([x, skip], dim=1)
x = self.conv1(x)
x = self.conv2(x)
return x
DecoderCup是整个的解码过程
class DecoderCup(nn.Module):
def __init__(self, config, img_size):
super().__init__()
self.config = config
self.down_factor = config.down_factor
head_channels = config.conv_first_channel
self.img_size = img_size
self.conv_more = Conv3dReLU(
config.hidden_size,
head_channels,
kernel_size=3,
padding=1,
use_batchnorm=True,
)
decoder_channels = config.decoder_channels
in_channels = [head_channels] + list(decoder_channels[:-1])
out_channels = decoder_channels
self.patch_size = _triple(config.patches["size"])
skip_channels = self.config.skip_channels
blocks = [
DecoderBlock(in_ch, out_ch, sk_ch) for in_ch, out_ch, sk_ch in zip(in_channels, out_channels, skip_channels)
]
self.blocks = nn.ModuleList(blocks)
Transformer是整个图3的组成,图1中的橙色部分
class Transformer(nn.Module):
def __init__(self, config, img_size, vis):
super(Transformer, self).__init__()
self.embeddings = Embeddings(config, img_size=img_size)
self.encoder = Encoder(config, vis)
def forward(self, input_ids):
embedding_output, features = self.embeddings(input_ids)
encoded, attn_weights = self.encoder(embedding_output) # (B, n_patch, hidden)
return encoded, attn_weights, features
SpatialTransformer这里和VM一模一样,是图1中的Spatial Transformer蓝色部分,用于使移动图像发生形变。
class SpatialTransformer(nn.Module):
"""
N-D Spatial Transformer
Obtained from https://github.com/voxelmorph/voxelmorph
"""
def __init__(self, size, mode='bilinear'):
super().__init__()
self.mode = mode
# create sampling grid
vectors = [torch.arange(0, s) for s in size]
grids = torch.meshgrid(vectors)
grid = torch.stack(grids)
grid = torch.unsqueeze(grid, 0)
grid = grid.type(torch.FloatTensor)
# registering the grid as a buffer cleanly moves it to the GPU, but it also
# adds it to the state dict. this is annoying since everything in the state dict
# is included when saving weights to disk, so the model files are way bigger
# than they need to be. so far, there does not appear to be an elegant solution.
# see: https://discuss.pytorch.org/t/how-to-register-buffer-without-polluting-state-dict
self.register_buffer('grid', grid)
def forward(self, src, flow):
# new locations
#print("self.grid.shape", self.grid.shape)
#print( "flow.shape", flow.shape )
new_locs = self.grid + flow
shape = flow.shape[2:]
# need to normalize grid values to [-1, 1] for resampler
for i in range(len(shape)):
new_locs[:, i, ...] = 2 * (new_locs[:, i, ...] / (shape[i] - 1) - 0.5)
# move channels dim to last position
# also not sure why, but the channels need to be reversed
if len(shape) == 2:
new_locs = new_locs.permute(0, 2, 3, 1)
new_locs = new_locs[..., [1, 0]]
elif len(shape) == 3:
new_locs = new_locs.permute(0, 2, 3, 4, 1)
new_locs = new_locs[..., [2, 1, 0]]
return nnf.grid_sample(src, new_locs, align_corners=True, mode=self.mode)
DoubleConv双重卷积,就是2层卷积,代码没有用leakyrelu,只用了relu。
class DoubleConv(nn.Module):
"""(convolution => [BN] => ReLU) * 2"""
def __init__(self, in_channels, out_channels, mid_channels=None):
super().__init__()
if not mid_channels:
mid_channels = out_channels
self.double_conv = nn.Sequential(
nn.Conv3d(in_channels, mid_channels, kernel_size=3, padding=1),
nn.ReLU(inplace=True),
nn.Conv3d(mid_channels, out_channels, kernel_size=3, padding=1),
nn.ReLU(inplace=True)
)
def forward(self, x):
return self.double_conv(x)
Down在2层卷积后加入池化层,池化层可以有效的缩小参数矩阵的尺寸,从而减少最后连接层的中的参数数量。所以加入池化层可以加快计算速度和防止过拟合的作用
class Down(nn.Module):
"""Downscaling with maxpool then double conv"""
def __init__(self, in_channels, out_channels):
super().__init__()
self.maxpool_conv = nn.Sequential(
nn.MaxPool3d(2),
DoubleConv(in_channels, out_channels)
)
def forward(self, x):
return self.maxpool_conv(x)
Conv3dReLU 用于解码中 ,是一个带有relu激活函数的3D卷积,为什么归一化这里,代码用BatchNorm?而图中是instance norm。而且也没用leakyrelu
class Conv3dReLU(nn.Sequential):
def __init__(
self,
in_channels,
out_channels,
kernel_size,
padding=0,
stride=1,
use_batchnorm=True,
):
conv = nn.Conv3d(
in_channels,
out_channels,
kernel_size,
stride=stride,
padding=padding,
bias=not (use_batchnorm),
)
relu = nn.ReLU(inplace=True)
bn = nn.BatchNorm3d(out_channels)
super(Conv3dReLU, self).__init__(conv, bn, relu)
CNNEncoder,就是这3层卷积,输出权重和一个特征图,之后接着embedding
疑问:为什么图中每层只有一次池化,这里又加入了三个池化?而且上图中instance norm在代码里根本没有
class CNNEncoder(nn.Module):
def __init__(self, config, n_channels=2):
super(CNNEncoder, self).__init__()
self.n_channels = n_channels
decoder_channels = config.decoder_channels
encoder_channels = config.encoder_channels
self.down_num = config.down_num
self.inc = DoubleConv(n_channels, encoder_channels[0])
self.down1 = Down(encoder_channels[0], encoder_channels[1])
self.down2 = Down(encoder_channels[1], encoder_channels[2])
self.width = encoder_channels[-1]
def forward(self, x):
features = []
x1 = self.inc(x)
features.append(x1)
x2 = self.down1(x1)
features.append(x2)
feats = self.down2(x2)
features.append(feats)
feats_down = feats
for i in range(self.down_num):
feats_down = nn.MaxPool3d(2)(feats_down)
features.append(feats_down)
return feats, features[::-1]
RegistrationHead配准,用于主框架中
class RegistrationHead(nn.Sequential):
def __init__(self, in_channels, out_channels, kernel_size=3, upsampling=1):
conv3d = nn.Conv3d(in_channels, out_channels, kernel_size=kernel_size, padding=kernel_size // 2)
conv3d.weight = nn.Parameter(Normal(0, 1e-5).sample(conv3d.weight.shape))
conv3d.bias = nn.Parameter(torch.zeros(conv3d.bias.shape))
super().__init__(conv3d)
ViTVNet:整体网络框架
class ViTVNet(nn.Module):
def __init__(self, config, img_size=(64, 256, 256), int_steps=7, vis=False, mode='bilinear'):
super(ViTVNet, self).__init__()
self.transformer = Transformer(config, img_size, vis)
self.decoder = DecoderCup(config, img_size)
self.reg_head = RegistrationHead(
in_channels=config.decoder_channels[-1],
out_channels=config['n_dims'],
kernel_size=3,
)
self.spatial_trans = SpatialTransformer(img_size, mode)
self.config = config
#self.integrate = VecInt(img_size, int_steps)
def forward(self, x):
source = x[:,0:1,:,:]
x, attn_weights, features = self.transformer(x) # (B, n_patch, hidden)
x = self.decoder(x, features)
flow = self.reg_head(x)
#flow = self.integrate(x)
#img = x[0].cuda( )
#flow = x[1].cuda( )
out = self.spatial_trans(source, flow)
#out = self.spatial_trans( source, flow )
return out, flow