DeepMedicalColorization / colorization_modules.py
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import logging as log
import os
from pathlib import Path
import torch
import torchvision.transforms as transforms
import torchvision.models as models
from torch import nn
from torch.nn import functional as F
from enum import Enum
class AdvEnum(Enum):
@classmethod
def list(cls):
return list(map(lambda c: c.value, cls))
@classmethod
def list_name_value(cls):
return list(map(lambda c: (c.name, c.value), cls))
class DecoNetMode(AdvEnum):
FREEZE_DECO = 0
FREEZE_PTMODEL = 1
FREEZE_PTMODEL_NO_FC = 2
UNFREEZE_ALL = 3
FREEZE_ALL = 4
FREEZE_ALL_NO_FC = 5
class DecoType(AdvEnum):
NO = 0
DECONV = 1
RESIZE_CONV = 2
ColorUDECO = 16
PIXEL_SHUFFLE = 20
def get_deco_model(use_deco, out_deco) -> nn.Module:
if use_deco in [DecoType.DECONV, DecoType.DECONV_NORM]:
return StandardDECO(out_deco, deconv=True)
elif use_deco in [DecoType.RESIZE_CONV]:
return StandardDECO(out_deco, deconv=False)
elif use_deco is DecoType.PIXEL_SHUFFLE:
return PixelShuffle(out_deco, lrelu=False)
elif use_deco is DecoType.ColorUDECO:
return ColorUDECO(out_deco)
else:
raise ValueError("Module not found")
class PreTrainedModel(AdvEnum):
DENSENET_121 = 0
RESNET_18 = 1
RESNET_34 = 2
RESNET_50 = 3
VGG11 = 4
VGG11_BN = 5
def get_pt_model(model, output, pretrained=True):
input = 224
if not isinstance(model, PreTrainedModel):
model = PreTrainedModel(model)
pt_model = None
if model == PreTrainedModel.DENSENET_121:
pt_model = models.densenet121(pretrained=pretrained)
num_ftrs = pt_model.classifier.in_features
pt_model.classifier = nn.Linear(num_ftrs, output)
pt_model.last_layer_name = "classifier"
elif model == PreTrainedModel.RESNET_18:
pt_model = models.resnet18(pretrained=pretrained)
num_ftrs = pt_model.fc.in_features
pt_model.fc = nn.Linear(num_ftrs, output)
pt_model.last_layer_name = "fc"
elif model == PreTrainedModel.RESNET_34:
pt_model = models.resnet34(pretrained=pretrained)
num_ftrs = pt_model.fc.in_features
pt_model.fc = nn.Linear(num_ftrs, output)
pt_model.last_layer_name = "fc"
elif model == PreTrainedModel.RESNET_50:
pt_model = models.resnet50(pretrained=pretrained)
num_ftrs = pt_model.fc.in_features
pt_model.fc = nn.Linear(num_ftrs, output)
pt_model.last_layer_name = "fc"
elif model == PreTrainedModel.VGG11:
pt_model = models.vgg11(pretrained=pretrained)
num_ftrs = pt_model.classifier[6].in_features
pt_model.classifier[6] = nn.Linear(num_ftrs, output)
pt_model.last_layer_name = "classifier.6"
elif model == PreTrainedModel.VGG11_BN:
pt_model = models.vgg11_bn(pretrained=pretrained)
num_ftrs = pt_model.classifier[6].in_features
pt_model.classifier[6] = nn.Linear(num_ftrs, output)
pt_model.last_layer_name = "classifier.6"
else:
raise ValueError("Model not found")
return pt_model, input
class DecoNet(nn.Module):
"""
Colorization module(optional)+Model
"""
def __init__(self, output=14,
deco_type=DecoType.ColorUDECO,
pt_model=PreTrainedModel.RESNET_18,
pre_trained=True,
training_mode=DecoNetMode.FREEZE_PTMODEL_NO_FC,
use_aap=False):
super().__init__()
# Pre-trained Model
self.deco_type = deco_type
self.training_mode = training_mode
self.use_aap = use_aap
pt_model, self.out_deco = get_pt_model(pt_model, output, pre_trained)
self.last_layer_name = pt_model.last_layer_name
# DECO if needed
if self.deco_type is not DecoType.NO:
self.deco = get_deco_model(self.deco_type, self.out_deco)
else:
self.deco = None
self.pt_model = pt_model
self.set_mode(training_mode)
def set_mode(self, mode, print=True):
if not isinstance(mode, DecoNetMode):
mode = DecoNetMode(mode)
if mode == DecoNetMode.UNFREEZE_ALL:
for param in self.parameters():
param.requires_grad = True
elif mode == DecoNetMode.FREEZE_DECO:
self.set_mode(DecoNetMode.UNFREEZE_ALL, False)
for param in self.deco.parameters():
param.requires_grad = False
elif mode == DecoNetMode.FREEZE_PTMODEL:
self.set_mode(DecoNetMode.UNFREEZE_ALL, False)
for param in self.pt_model.parameters():
param.requires_grad = False
elif mode == DecoNetMode.FREEZE_PTMODEL_NO_FC:
self.set_mode(DecoNetMode.UNFREEZE_ALL, False)
for name, param in self.pt_model.named_parameters():
if self.last_layer_name not in name:
param.requires_grad = False
elif mode == DecoNetMode.FREEZE_ALL:
for param in self.parameters():
param.requires_grad = False
elif mode == DecoNetMode.FREEZE_ALL_NO_FC:
self.set_mode(DecoNetMode.FREEZE_ALL, False)
# Unfreeze last layer
for name, param in self.pt_model.named_parameters():
if self.last_layer_name in name:
param.requires_grad = True
if print:
log.info("#############################################")
log.info("PARAMETERS STATUS:")
for name, param in self.named_parameters():
log.info("{} : {}".format(name, param.requires_grad))
log.info("#############################################")
def get_layer_weight(self, sel_name: str = ""):
if sel_name == "":
sel_name = self.last_layer_name
res = []
for name, param in self.pt_model.named_parameters():
if sel_name in name:
res.append(param)
return res
def forward(self, xb):
"""
@:param xb : tensor
Batch of input images
@:return tensor
A batch of output images
"""
if self.deco is not None:
xb = self.deco(xb)
if self.use_aap:
xb = F.adaptive_avg_pool2d(xb, (self.out_deco, self.out_deco))
return self.pt_model(xb)
def clean_last_layer(self):
pt_model_type = self.pt_model
if pt_model_type == PreTrainedModel.VGG11_BN or pt_model_type == PreTrainedModel.VGG11:
self.pt_model.classifier[6].reset_parameters()
else:
last_layer_name = list(self.pt_model._modules)[-1]
self.pt_model._modules[last_layer_name].reset_parameters()
log.info("Last layer cleaned!")
def last_layer_size(self):
pt_model_type = self.pt_model
if pt_model_type == PreTrainedModel.VGG11_BN or pt_model_type == PreTrainedModel.VGG11:
return self.pt_model.classifier[6].weight.shape[-1]
else:
last_layer_name = list(self.pt_model._modules)[-1]
return self.pt_model._modules[last_layer_name].shape[-1]
def load_deco_state_dict(self, state_dict):
if self.deco is None:
self.deco = get_deco_model(self.deco_type, self.out_deco)
if hasattr(self.deco, "load_state_dict"):
self.deco.load_state_dict(state_dict)
else:
return False
self.set_mode(self.training_mode)
return True
def default_deco__weight_init(m):
if isinstance(m, nn.Conv2d):
# n = m.kernel_size[0] * m.kernel_size[1] * m.out_channels
# m.weight.data.normal_(0, math.sqrt(2. / n))
torch.nn.init.xavier_uniform_(m.weight)
elif isinstance(m, nn.BatchNorm2d):
m.weight.data.fill_(1)
m.bias.data.zero_()
def bn_weight_init(m):
if isinstance(m, nn.BatchNorm2d):
m.weight.data.fill_(1)
m.bias.data.zero_()
class BaseDECO(nn.Module):
def __init__(self, out=224, init=None):
super().__init__()
self.out_s = out
self.init = init
def set_output_size(self, out_s):
self.out_s = out_s
def init_weights(self):
if self.init is None:
pass
elif self.init == 0:
self.apply(default_deco__weight_init)
elif self.init == 1:
self.apply(bn_weight_init)
class ResBlock(nn.Module):
def __init__(self, ni, nf=None, kernel=3, stride=1, padding=1):
super().__init__()
if nf is None:
nf = ni
self.conv1 = conv_layer(ni, nf, kernel=kernel, stride=stride, padding=padding)
self.conv2 = conv_layer(nf, nf, kernel=kernel, stride=stride, padding=padding)
def forward(self, x):
return x + self.conv2(self.conv1(x))
def conv_layer(in_layer, out_layer, kernel=3, stride=1, padding=1, instanceNorm=False):
return nn.Sequential(
nn.Conv2d(in_layer, out_layer, kernel_size=kernel, stride=stride, padding=padding),
nn.BatchNorm2d(out_layer) if not instanceNorm else nn.InstanceNorm2d(out_layer),
nn.LeakyReLU(inplace=True)
)
def _make_res_layers(nl, ni, kernel=3, stride=1, padding=1):
layers = []
for i in range(nl):
layers.append(ResBlock(ni, kernel=kernel, stride=stride, padding=padding))
return nn.Sequential(*layers)
class StandardDECO(BaseDECO):
"""
Standard DECO Module
"""
def __init__(self, out=224, init=0, deconv=False):
super().__init__(out, init)
self.conv1 = nn.Conv2d(1, 64, kernel_size=7, stride=2, padding=2)
self.bn1 = nn.BatchNorm2d(64)
# ReLU
self.maxpool = nn.MaxPool2d(kernel_size=3, stride=2, padding=1)
self.resblocks = _make_res_layers(8, 64)
self.conv_last = nn.Conv2d(64, 3, kernel_size=1)
self.deconv = deconv
if deconv:
# TODO: Check if use "groups = 1"
self.deconv = nn.ConvTranspose2d(in_channels=3, out_channels=3, kernel_size=8, padding=2, stride=4,
groups=3, bias=False)
else:
self.pad = nn.ReflectionPad2d(1)
self.conv_up = nn.Conv2d(in_channels=3, out_channels=3, kernel_size=3, padding=0, stride=1)
self.init_weights()
def forward(self, xb):
"""
@:param xb : Tensor
Batch of input images
@:return tensor
A batch of output images
"""
_xb = self.maxpool(F.leaky_relu(self.bn1(self.conv1(xb))))
_xb = self.resblocks(_xb)
_xb = self.conv_last(_xb)
if self.deconv:
_xb = self.deconv(_xb, output_size=xb.shape)
else:
_xb = self.conv_up(self.pad(F.interpolate(_xb, scale_factor=4, mode='nearest')))
return _xb
def icnr(x, scale=4, init=nn.init.kaiming_normal_):
""" ICNR init of `x`, with `scale` and `init` function.
Checkerboard artifact free sub-pixel convolution: https://arxiv.org/ftp/arxiv/papers/1707/1707.02937.pdf
"""
ni, nf, h, w = x.shape
ni2 = int(ni / (scale ** 2))
k = init(torch.zeros([ni2, nf, h, w])).transpose(0, 1)
k = k.contiguous().view(ni2, nf, -1)
k = k.repeat(1, 1, scale ** 2)
k = k.contiguous().view([nf, ni, h, w]).transpose(0, 1)
x.data.copy_(k)
class PixelShuffle_ICNR(nn.Module):
""" Upsample by `scale` from `ni` filters to `nf` (default `ni`), using `nn.PixelShuffle`, `icnr` init,
and `weight_norm`.
"Super-Resolution using Convolutional Neural Networks without Any Checkerboard Artifacts":
https://arxiv.org/abs/1806.02658
"""
def __init__(self, ni: int, nf: int = None, scale: int = 4, icnr_init=True, blur_k=2, blur_s=1,
blur_pad=(1, 0, 1, 0), lrelu=True):
super().__init__()
nf = ni if nf is None else nf
self.conv = conv_layer(ni, nf * (scale ** 2), kernel=1, padding=0, stride=1) if lrelu else nn.Sequential(
nn.Conv2d(64, 3 * (scale ** 2), 1, 1, 0), nn.BatchNorm2d(3 * (scale ** 2)))
if icnr_init:
icnr(self.conv[0].weight, scale=scale)
self.act = nn.LeakyReLU(inplace=False) if lrelu else nn.Hardtanh(-10000, 10000)
self.shuf = nn.PixelShuffle(scale)
# Blurring over (h*w) kernel
self.pad = nn.ReplicationPad2d(blur_pad)
self.blur = nn.AvgPool2d(blur_k, stride=blur_s)
def forward(self, x):
x = self.shuf(self.act(self.conv(x)))
return self.blur(self.pad(x))
class PixelShuffle(BaseDECO):
"""
PixelShuffle Module
"""
def __init__(self, out=224, init=1, scale=4, lrelu=False):
super().__init__(out, init)
# Which value should I use for stride and padding?
self.conv1 = nn.Conv2d(1, 64, kernel_size=7, stride=2, padding=2)
self.bn1 = nn.BatchNorm2d(64)
self.act1 = nn.LeakyReLU()
self.maxpool = nn.MaxPool2d(kernel_size=3, stride=2, padding=1)
self.resblocks = _make_res_layers(8, 64)
self.pixel_shuffle = PixelShuffle_ICNR(ni=64, nf=3, scale=scale, lrelu=lrelu)
self.init_weights()
def forward(self, xb):
"""
@:param xb : Tensor
Batch of input images
@:return tensor
A batch of output images
"""
_xb = self.maxpool(self.act1(self.bn1(self.conv1(xb))))
_xb = self.resblocks(_xb)
return self.pixel_shuffle(_xb)
class ColorUDECO(BaseDECO):
"""
ColorUDECO Module
"""
def __init__(self, out=224, init=0, in_ch=1, out_ch=3):
super().__init__(out, init)
self.dw1 = ColorDown(in_ch, 16)
self.dw2 = ColorDown(16, 32)
self.dw3 = ColorDown(32, 64)
self.up1 = ColorUp(64, 32)
self.up2 = ColorUp(64, 16)
self.out = ColorOut(32, 16, out_ch)
def forward(self, x1):
"""
@:param x1 : Tensor
Batch of input images
@:return tensor
A batch of output images
"""
x1 = self.dw1(x1)
x2 = self.dw2(x1)
x3 = self.dw3(x2)
x3 = self.up1(x3)
x2 = self.up2(torch.cat([x2, x3], dim=1))
return self.out(torch.cat([x1, x2], dim=1))
class ColorDown(nn.Module):
def __init__(self, in_ch, out_ch, htan=False):
super(ColorDown, self).__init__()
self.d = nn.Sequential(
nn.Conv2d(in_ch, out_ch, kernel_size=3, stride=1, padding=1),
nn.LeakyReLU() if not htan else nn.Hardtanh(),
nn.Conv2d(out_ch, out_ch, kernel_size=4, stride=2, padding=1),
nn.LeakyReLU() if not htan else nn.Hardtanh(),
nn.BatchNorm2d(out_ch)
)
def forward(self, x):
return self.d(x)
class ColorUp(nn.Module):
def __init__(self, in_ch, out_ch, htan=False):
super(ColorUp, self).__init__()
self.u = nn.Sequential(
nn.ConvTranspose2d(in_ch, out_ch, 4, 2, 1),
nn.LeakyReLU() if not htan else nn.Hardtanh(),
nn.Conv2d(out_ch, out_ch, kernel_size=3, stride=1, padding=1),
nn.LeakyReLU() if not htan else nn.Hardtanh(),
nn.Conv2d(out_ch, out_ch, kernel_size=3, stride=1, padding=1),
nn.LeakyReLU() if not htan else nn.Hardtanh(),
nn.BatchNorm2d(out_ch)
)
def forward(self, x):
return self.u(x)
class ColorOut(nn.Module):
def __init__(self, in_ch, out_ch, out_last, htan=False):
super(ColorOut, self).__init__()
self.u = nn.Sequential(
nn.ConvTranspose2d(in_ch, out_ch, 4, 2, 1),
nn.LeakyReLU() if not htan else nn.Hardtanh(),
nn.Conv2d(out_ch, out_ch, kernel_size=3, stride=1, padding=1),
nn.LeakyReLU() if not htan else nn.Hardtanh(),
nn.Conv2d(out_ch, out_last, kernel_size=1, stride=1, padding=0),
)
def forward(self, x):
return self.u(x)