backbones/unet3d.py

# Used for Models Genesis
import math
import torch
import torch.nn as nn
import torch.nn.functional as F

from backbones.classifier import FracClassifier


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()))

    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 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 = torch.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, input_size, n_class=1, act='relu', in_channels=1):
        super(UNet3D, self).__init__()

        self.down_tr64 = DownTransition(in_channels,0,act)
        self.down_tr128 = DownTransition(64,1,act)
        self.down_tr256 = DownTransition(128,2,act)
        self.down_tr512 = DownTransition(256,3,act)

        # Classification
        self.classifier = FracClassifier(encoder_channels=512, final_channels=n_class, linear_kernel=int(math.pow(input_size / 32, 3) * 512))

    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.out = self.classifier(self.out512)

        return self.out