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unet3D.py
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import torch.nn as nn
import torch
import torch.nn as nn
import torch.nn.functional as F
from .common3D import *
class ListModule(nn.Module):
def __init__(self, *args):
super(ListModule, self).__init__()
idx = 0
for module in args:
self.add_module(str(idx), module)
idx += 1
def __getitem__(self, idx):
if idx >= len(self._modules):
raise IndexError('index {} is out of range'.format(idx))
if idx < 0:
idx = len(self) + idx
it = iter(self._modules.values())
for i in range(idx):
next(it)
return next(it)
def __iter__(self):
return iter(self._modules.values())
def __len__(self):
return len(self._modules)
class UNet(nn.Module):
'''
upsample_mode in ['deconv', 'nearest', 'bilinear']
pad in ['zero', 'replication', 'none']
'''
def __init__(self, num_input_channels=3, num_output_channels=3,
feature_scale=4, more_layers=0, concat_x=False,
upsample_mode='deconv', pad='zero', norm_layer=nn.InstanceNorm3d, need_sigmoid=True, need_bias=True):
super(UNet, self).__init__()
self.feature_scale = feature_scale
self.more_layers = more_layers
self.concat_x = concat_x
filters = [64, 128, 256, 512, 1024]
filters = [x // self.feature_scale for x in filters]
self.start = unetConv2(num_input_channels, filters[0] if not concat_x else filters[0] - num_input_channels, norm_layer, need_bias, pad)
self.down1 = unetDown(filters[0], filters[1] if not concat_x else filters[1] - num_input_channels, norm_layer, need_bias, pad)
self.down2 = unetDown(filters[1], filters[2] if not concat_x else filters[2] - num_input_channels, norm_layer, need_bias, pad)
self.down3 = unetDown(filters[2], filters[3] if not concat_x else filters[3] - num_input_channels, norm_layer, need_bias, pad)
self.down4 = unetDown(filters[3], filters[4] if not concat_x else filters[4] - num_input_channels, norm_layer, need_bias, pad)
# more downsampling layers
if self.more_layers > 0:
self.more_downs = [
unetDown(filters[4], filters[4] if not concat_x else filters[4] - num_input_channels , norm_layer, need_bias, pad) for i in range(self.more_layers)]
self.more_ups = [unetUp(filters[4], upsample_mode, need_bias, pad, same_num_filt =True) for i in range(self.more_layers)]
self.more_downs = ListModule(*self.more_downs)
self.more_ups = ListModule(*self.more_ups)
self.up4 = unetUp(filters[3], upsample_mode, need_bias, pad)
self.up3 = unetUp(filters[2], upsample_mode, need_bias, pad)
self.up2 = unetUp(filters[1], upsample_mode, need_bias, pad)
self.up1 = unetUp(filters[0], upsample_mode, need_bias, pad)
self.final = conv(filters[0], num_output_channels, 1, bias=need_bias, pad=pad)
if need_sigmoid:
self.final = nn.Sequential(self.final, nn.Sigmoid())
def forward(self, inputs):
# Downsample
downs = [inputs]
down = nn.AvgPool3d(2, 2)
for i in range(4 + self.more_layers):
downs.append(down(downs[-1]))
in64 = self.start(inputs)
if self.concat_x:
in64 = torch.cat([in64, downs[0]], 1)
down1 = self.down1(in64)
if self.concat_x:
down1 = torch.cat([down1, downs[1]], 1)
down2 = self.down2(down1)
if self.concat_x:
down2 = torch.cat([down2, downs[2]], 1)
down3 = self.down3(down2)
if self.concat_x:
down3 = torch.cat([down3, downs[3]], 1)
down4 = self.down4(down3)
if self.concat_x:
down4 = torch.cat([down4, downs[4]], 1)
if self.more_layers > 0:
prevs = [down4]
for kk, d in enumerate(self.more_downs):
# print(prevs[-1].size())
out = d(prevs[-1])
if self.concat_x:
out = torch.cat([out, downs[kk + 5]], 1)
prevs.append(out)
up_ = self.more_ups[-1](prevs[-1], prevs[-2])
for idx in range(self.more_layers - 1):
l = self.more_ups[self.more - idx - 2]
up_= l(up_, prevs[self.more - idx - 2])
else:
up_= down4
up4= self.up4(up_, down3)
up3= self.up3(up4, down2)
up2= self.up2(up3, down1)
up1= self.up1(up2, in64)
return self.final(up1)
class unetConv2(nn.Module):
def __init__(self, in_size, out_size, norm_layer, need_bias, pad):
super(unetConv2, self).__init__()
print(pad)
if norm_layer is not None:
self.conv1= nn.Sequential(conv(in_size, out_size, 3, bias=need_bias, pad=pad),
norm_layer(out_size),
nn.ReLU(),)
self.conv2= nn.Sequential(conv(out_size, out_size, 3, bias=need_bias, pad=pad),
norm_layer(out_size),
nn.ReLU(),)
else:
self.conv1= nn.Sequential(conv(in_size, out_size, 3, bias=need_bias, pad=pad),
nn.ReLU(),)
self.conv2= nn.Sequential(conv(out_size, out_size, 3, bias=need_bias, pad=pad),
nn.ReLU(),)
def forward(self, inputs):
outputs= self.conv1(inputs)
outputs= self.conv2(outputs)
return outputs
class unetDown(nn.Module):
def __init__(self, in_size, out_size, norm_layer, need_bias, pad):
super(unetDown, self).__init__()
self.conv= unetConv2(in_size, out_size, norm_layer, need_bias, pad)
self.down= nn.MaxPool3d(2, 2)
def forward(self, inputs):
outputs= self.down(inputs)
outputs= self.conv(outputs)
return outputs
class unetUp(nn.Module):
def __init__(self, out_size, upsample_mode, need_bias, pad, same_num_filt=False):
super(unetUp, self).__init__()
num_filt = out_size if same_num_filt else out_size * 2
if upsample_mode == 'deconv':
self.up= nn.ConvTranspose3d(num_filt, out_size, 4, stride=2, padding=1)
self.conv= unetConv2(out_size * 2, out_size, None, need_bias, pad)
elif upsample_mode=='trilinear' or upsample_mode=='nearest':
self.up = nn.Sequential(nn.Upsample(scale_factor=2, mode=upsample_mode),
conv(num_filt, out_size, 3, bias=need_bias, pad=pad))
self.conv= unetConv2(out_size * 2, out_size, None, need_bias, pad)
else:
assert False
def forward(self, inputs1, inputs2):
in1_up= self.up(inputs1)
if (inputs2.size(4) != in1_up.size(4)) or (inputs2.size(3) != in1_up.size(3)):
diff2 = (inputs2.size(3) - in1_up.size(3)) // 2
diff3 = (inputs2.size(4) - in1_up.size(4)) // 2
inputs2_ = inputs2[:, :, :, diff2 : diff2 + in1_up.size(3), diff3 : diff3 + in1_up.size(4)]
else:
inputs2_ = inputs2
output= self.conv(torch.cat([in1_up, inputs2_], 1))
return output