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ynet3d.py
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ynet3d.py
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# Copyright (c) ASU GitHub Project.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
################################################################################
import torch
import torch.nn as nn
import torch.nn.functional as F
class ContBatchNorm3d(nn.modules.batchnorm._BatchNorm):
def _check_input_dim(self, input):
if input.dim() != 5:
raise ValueError('expected 5D input (got {}D input)'.format(input.dim()))
#super(ContBatchNorm3d, self)._check_input_dim(input)
def forward(self, input):
self._check_input_dim(input)
return F.batch_norm(
input, self.running_mean, self.running_var, self.weight, self.bias,
True, self.momentum, self.eps)
class LUConv(nn.Module):
def __init__(self, in_chan, out_chan, act):
super(LUConv, self).__init__()
self.conv1 = nn.Conv3d(in_chan, out_chan, kernel_size=3, padding=1)
self.bn1 = ContBatchNorm3d(out_chan)
if act == 'relu':
self.activation = nn.ReLU(out_chan)
elif act == 'prelu':
self.activation = nn.PReLU(out_chan)
elif act == 'elu':
self.activation = nn.ELU(inplace=True)
else:
raise
def forward(self, x):
out = self.activation(self.bn1(self.conv1(x)))
return out
def _make_nConv(in_channel, depth, act, double_chnnel=False):
if double_chnnel:
layer1 = LUConv(in_channel, 32 * (2 ** (depth+1)),act)
layer2 = LUConv(32 * (2 ** (depth+1)), 32 * (2 ** (depth+1)),act)
else:
layer1 = LUConv(in_channel, 32*(2**depth),act)
layer2 = LUConv(32*(2**depth), 32*(2**depth)*2,act)
return nn.Sequential(layer1,layer2)
class ClassificationHead(nn.Module):
def __init__(self, in_chan, act, lst_act,cls_classes):
super(ClassificationHead, self).__init__()
self.conv1 = nn.Conv3d(in_chan, 1024, kernel_size=3, padding=1)
self.bn1 = ContBatchNorm3d(1024)
if act == 'relu':
self.activation = nn.ReLU(1024)
elif act == 'prelu':
self.activation = nn.PReLU(1024)
elif act == 'elu':
self.activation = nn.ELU(inplace=True)
else:
raise
self.avgpool1 = nn.AdaptiveAvgPool3d(1)
self.fc1 = nn.Linear(1024,cls_classes)
if lst_act == 'soft':
self.lst_act = nn.Softmax(dim=1)
else:
self.lst_act = nn.Sigmoid()
def forward(self, x):
feature_space = self.avgpool1(self.activation(self.bn1(self.conv1(x))))
x = torch.flatten(feature_space,1)
x = self.fc1(x)
clc_out = self.lst_act(x)
return clc_out
class DownTransition(nn.Module):
def __init__(self, in_channel,depth, act):
super(DownTransition, self).__init__()
self.ops = _make_nConv(in_channel, depth,act)
self.maxpool = nn.MaxPool3d(2)
self.current_depth = depth
def forward(self, x):
if self.current_depth == 3:
out = self.ops(x)
out_before_pool = out
else:
out_before_pool = self.ops(x)
out = self.maxpool(out_before_pool)
return out, out_before_pool
class UpTransition(nn.Module):
def __init__(self, inChans, outChans, depth,act):
super(UpTransition, self).__init__()
self.depth = depth
self.up_conv = nn.ConvTranspose3d(inChans, outChans, kernel_size=2, stride=2)
self.ops = _make_nConv(inChans+ outChans//2,depth, act, double_chnnel=True)
def forward(self, x, skip_x):
out_up_conv = self.up_conv(x)
concat = torch.cat((out_up_conv,skip_x),1)
out = self.ops(concat)
return out
class OutputTransition(nn.Module):
def __init__(self, inChans, n_labels):
super(OutputTransition, self).__init__()
self.final_conv = nn.Conv3d(inChans, n_labels, kernel_size=1)
self.sigmoid = nn.Sigmoid()
def forward(self, x):
out = self.sigmoid(self.final_conv(x))
return out
class UNet3D(nn.Module):
# the number of convolutions in each layer corresponds
# to what is in the actual prototxt, not the intent
def __init__(self, n_class=1, act='relu'):
super(UNet3D, self).__init__()
self.down_tr64 = DownTransition(1,0,act)
self.down_tr128 = DownTransition(64,1,act)
self.down_tr256 = DownTransition(128,2,act)
self.down_tr512 = DownTransition(256,3,act)
self.up_tr256 = UpTransition(512, 512,2,act)
self.up_tr128 = UpTransition(256,256, 1,act)
self.up_tr64 = UpTransition(128,128,0,act)
self.out_tr = OutputTransition(64, n_class)
def forward(self, x):
self.out64, self.skip_out64 = self.down_tr64(x)
self.out128,self.skip_out128 = self.down_tr128(self.out64)
self.out256,self.skip_out256 = self.down_tr256(self.out128)
self.out512,self.skip_out512 = self.down_tr512(self.out256)
self.out_up_256 = self.up_tr256(self.out512,self.skip_out256)
self.out_up_128 = self.up_tr128(self.out_up_256, self.skip_out128)
self.out_up_64 = self.up_tr64(self.out_up_128, self.skip_out64)
self.out = self.out_tr(self.out_up_64)
return self.out
class YNet3D(nn.Module):
# the number of convolutions in each layer corresponds
# to what is in the actual prototxt, not the intent
def __init__(self, n_class=1, act='relu',lst_act='soft',cls_classes=44):
super(YNet3D, self).__init__()
self.down_tr64 = DownTransition(1,0,act)
self.down_tr128 = DownTransition(64,1,act)
self.down_tr256 = DownTransition(128,2,act)
self.down_tr512 = DownTransition(256,3,act)
self.up_tr256 = UpTransition(512, 512,2,act)
self.up_tr128 = UpTransition(256,256, 1,act)
self.up_tr64 = UpTransition(128,128,0,act)
self.out_tr = OutputTransition(64, n_class)
self.clc_out = ClassificationHead(512,act,lst_act,cls_classes)
def forward(self, x):
self.out64, self.skip_out64 = self.down_tr64(x)
self.out128,self.skip_out128 = self.down_tr128(self.out64)
self.out256,self.skip_out256 = self.down_tr256(self.out128)
self.out512,self.skip_out512 = self.down_tr512(self.out256)
self.out_up_256 = self.up_tr256(self.out512,self.skip_out256)
self.out_up_128 = self.up_tr128(self.out_up_256, self.skip_out128)
self.out_up_64 = self.up_tr64(self.out_up_128, self.skip_out64)
self.seg_out = self.out_tr(self.out_up_64)
self.cls_out = self.clc_out(self.out512)
return [self.seg_out, self.cls_out]
class ClassificationNet3D(nn.Module):
def __init__(self, n_class=1, act='relu', lst_act='soft',cls_classes=44):
super(ClassificationNet3D, self).__init__()
self.down_tr64 = DownTransition(1,0,act)
self.down_tr128 = DownTransition(64,1,act)
self.down_tr256 = DownTransition(128,2,act)
self.down_tr512 = DownTransition(256,3,act)
self.clc_out = ClassificationHead(512,act,lst_act,cls_classes)
def forward(self, x):
self.out64, _ = self.down_tr64(x)
self.out128, _ = self.down_tr128(self.out64)
self.out256, _ = self.down_tr256(self.out128)
self.out512, _ = self.down_tr512(self.out256)
self.cls_out = self.clc_out(self.out512)
return self.cls_out