This repository contains simple PyTorch implementations of U-Net and FCN, which are deep learning segmentation methods proposed by Ronneberger et al. and Long et al.
- U-Net: Convolutional Networks for Biomedical Image Segmentation
- Fully Convolutional Networks for Semantic Segmentation
import matplotlib.pyplot as plt
import numpy as np
import helper
import simulation
# Generate some random images
input_images, target_masks = simulation.generate_random_data(192, 192, count=3)
for x in [input_images, target_masks]:
print(x.shape)
print(x.min(), x.max())
# Change channel-order and make 3 channels for matplot
input_images_rgb = [x.astype(np.uint8) for x in input_images]
# Map each channel (i.e. class) to each color
target_masks_rgb = [helper.masks_to_colorimg(x) for x in target_masks]
# Left: Input image (black and white), Right: Target mask (6ch)
helper.plot_side_by_side([input_images_rgb, target_masks_rgb])
from torch.utils.data import Dataset, DataLoader
from torchvision import transforms, datasets, models
class SimDataset(Dataset):
def __init__(self, count, transform=None):
self.input_images, self.target_masks = simulation.generate_random_data(192, 192, count=count)
self.transform = transform
def __len__(self):
return len(self.input_images)
def __getitem__(self, idx):
image = self.input_images[idx]
mask = self.target_masks[idx]
if self.transform:
image = self.transform(image)
return [image, mask]
# use the same transformations for train/val in this example
trans = transforms.Compose([
transforms.ToTensor(),
transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225]) # imagenet
])
train_set = SimDataset(2000, transform = trans)
val_set = SimDataset(200, transform = trans)
image_datasets = {
'train': train_set, 'val': val_set
}
batch_size = 25
dataloaders = {
'train': DataLoader(train_set, batch_size=batch_size, shuffle=True, num_workers=0),
'val': DataLoader(val_set, batch_size=batch_size, shuffle=True, num_workers=0)
}import torchvision.utils
def reverse_transform(inp):
inp = inp.numpy().transpose((1, 2, 0))
mean = np.array([0.485, 0.456, 0.406])
std = np.array([0.229, 0.224, 0.225])
inp = std * inp + mean
inp = np.clip(inp, 0, 1)
inp = (inp * 255).astype(np.uint8)
return inp
# Get a batch of training data
inputs, masks = next(iter(dataloaders['train']))
print(inputs.shape, masks.shape)
plt.imshow(reverse_transform(inputs[3]))torch.Size([25, 3, 192, 192]) torch.Size([25, 6, 192, 192])
import torch
import torch.nn as nn
from torchvision import models
def convrelu(in_channels, out_channels, kernel, padding):
return nn.Sequential(
nn.Conv2d(in_channels, out_channels, kernel, padding=padding),
nn.ReLU(inplace=True),
)
class ResNetUNet(nn.Module):
def __init__(self, n_class):
super().__init__()
# Use ResNet18 as the encoder with the pretrained weights
self.base_model = models.resnet18(pretrained=True)
self.base_layers = list(base_model.children())
self.layer0 = nn.Sequential(*self.base_layers[:3]) # size=(N, 64, x.H/2, x.W/2)
self.layer0_1x1 = convrelu(64, 64, 1, 0)
self.layer1 = nn.Sequential(*self.base_layers[3:5]) # size=(N, 256, x.H/4, x.W/4)
self.layer1_1x1 = convrelu(256, 256, 1, 0)
self.layer2 = self.base_layers[5] # size=(N, 512, x.H/8, x.W/8)
self.layer2_1x1 = convrelu(512, 512, 1, 0)
self.layer3 = self.base_layers[6] # size=(N, 1024, x.H/16, x.W/16)
self.layer3_1x1 = convrelu(1024, 512, 1, 0)
self.layer4 = self.base_layers[7] # size=(N, 2048, x.H/32, x.W/32)
self.layer4_1x1 = convrelu(2048, 1024, 1, 0)
self.upsample = nn.Upsample(scale_factor=2, mode='bilinear', align_corners=True)
self.conv_up3 = convrelu(512 + 1024, 512, 3, 1)
self.conv_up2 = convrelu(512 + 512, 512, 3, 1)
self.conv_up1 = convrelu(256 + 512, 256, 3, 1)
self.conv_up0 = convrelu(64 + 256, 128, 3, 1)
self.conv_original_size0 = convrelu(3, 64, 3, 1)
self.conv_original_size1 = convrelu(64, 64, 3, 1)
self.conv_original_size2 = convrelu(64 + 128, 64, 3, 1)
self.conv_last = nn.Conv2d(64, n_class, 1)
def forward(self, input):
x_original = self.conv_original_size0(input)
x_original = self.conv_original_size1(x_original)
layer0 = self.layer0(input)
layer1 = self.layer1(layer0)
layer2 = self.layer2(layer1)
layer3 = self.layer3(layer2)
layer4 = self.layer4(layer3)
# Upsample the last/bottom layer
layer4 = self.layer4_1x1(layer4)
x = self.upsample(layer4)
# Create the shortcut from the encoder
layer3 = self.layer3_1x1(layer3)
x = torch.cat([x, layer3], dim=1)
x = self.conv_up3(x)
x = self.upsample(x)
layer2 = self.layer2_1x1(layer2)
x = torch.cat([x, layer2], dim=1)
x = self.conv_up2(x)
x = self.upsample(x)
layer1 = self.layer1_1x1(layer1)
x = torch.cat([x, layer1], dim=1)
x = self.conv_up1(x)
x = self.upsample(x)
layer0 = self.layer0_1x1(layer0)
x = torch.cat([x, layer0], dim=1)
x = self.conv_up0(x)
x = self.upsample(x)
x = torch.cat([x, x_original], dim=1)
x = self.conv_original_size2(x)
out = self.conv_last(x)
return outdevice = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
model = ResNetUNet(n_class=6)
model = model.to(device)
# check keras-like model summary using torchsummary
from torchsummary import summary
summary(model, input_size=(3, 224, 224))----------------------------------------------------------------
Layer (type) Output Shape Param #
================================================================
Conv2d-1 [-1, 64, 224, 224] 1,792
ReLU-2 [-1, 64, 224, 224] 0
Conv2d-3 [-1, 64, 224, 224] 36,928
ReLU-4 [-1, 64, 224, 224] 0
Conv2d-5 [-1, 64, 112, 112] 9,408
BatchNorm2d-6 [-1, 64, 112, 112] 128
ReLU-7 [-1, 64, 112, 112] 0
MaxPool2d-8 [-1, 64, 56, 56] 0
Conv2d-9 [-1, 64, 56, 56] 4,096
BatchNorm2d-10 [-1, 64, 56, 56] 128
ReLU-11 [-1, 64, 56, 56] 0
Conv2d-12 [-1, 64, 56, 56] 36,864
BatchNorm2d-13 [-1, 64, 56, 56] 128
ReLU-14 [-1, 64, 56, 56] 0
Conv2d-15 [-1, 256, 56, 56] 16,384
BatchNorm2d-16 [-1, 256, 56, 56] 512
Conv2d-17 [-1, 256, 56, 56] 16,384
BatchNorm2d-18 [-1, 256, 56, 56] 512
ReLU-19 [-1, 256, 56, 56] 0
Bottleneck-20 [-1, 256, 56, 56] 0
Conv2d-21 [-1, 64, 56, 56] 16,384
BatchNorm2d-22 [-1, 64, 56, 56] 128
ReLU-23 [-1, 64, 56, 56] 0
Conv2d-24 [-1, 64, 56, 56] 36,864
BatchNorm2d-25 [-1, 64, 56, 56] 128
ReLU-26 [-1, 64, 56, 56] 0
Conv2d-27 [-1, 256, 56, 56] 16,384
BatchNorm2d-28 [-1, 256, 56, 56] 512
ReLU-29 [-1, 256, 56, 56] 0
Bottleneck-30 [-1, 256, 56, 56] 0
Conv2d-31 [-1, 64, 56, 56] 16,384
BatchNorm2d-32 [-1, 64, 56, 56] 128
ReLU-33 [-1, 64, 56, 56] 0
Conv2d-34 [-1, 64, 56, 56] 36,864
BatchNorm2d-35 [-1, 64, 56, 56] 128
ReLU-36 [-1, 64, 56, 56] 0
Conv2d-37 [-1, 256, 56, 56] 16,384
BatchNorm2d-38 [-1, 256, 56, 56] 512
ReLU-39 [-1, 256, 56, 56] 0
Bottleneck-40 [-1, 256, 56, 56] 0
Conv2d-41 [-1, 128, 56, 56] 32,768
BatchNorm2d-42 [-1, 128, 56, 56] 256
ReLU-43 [-1, 128, 56, 56] 0
Conv2d-44 [-1, 128, 28, 28] 147,456
BatchNorm2d-45 [-1, 128, 28, 28] 256
ReLU-46 [-1, 128, 28, 28] 0
Conv2d-47 [-1, 512, 28, 28] 65,536
BatchNorm2d-48 [-1, 512, 28, 28] 1,024
Conv2d-49 [-1, 512, 28, 28] 131,072
BatchNorm2d-50 [-1, 512, 28, 28] 1,024
ReLU-51 [-1, 512, 28, 28] 0
Bottleneck-52 [-1, 512, 28, 28] 0
Conv2d-53 [-1, 128, 28, 28] 65,536
BatchNorm2d-54 [-1, 128, 28, 28] 256
ReLU-55 [-1, 128, 28, 28] 0
Conv2d-56 [-1, 128, 28, 28] 147,456
BatchNorm2d-57 [-1, 128, 28, 28] 256
ReLU-58 [-1, 128, 28, 28] 0
Conv2d-59 [-1, 512, 28, 28] 65,536
BatchNorm2d-60 [-1, 512, 28, 28] 1,024
ReLU-61 [-1, 512, 28, 28] 0
Bottleneck-62 [-1, 512, 28, 28] 0
Conv2d-63 [-1, 128, 28, 28] 65,536
BatchNorm2d-64 [-1, 128, 28, 28] 256
ReLU-65 [-1, 128, 28, 28] 0
Conv2d-66 [-1, 128, 28, 28] 147,456
BatchNorm2d-67 [-1, 128, 28, 28] 256
ReLU-68 [-1, 128, 28, 28] 0
Conv2d-69 [-1, 512, 28, 28] 65,536
BatchNorm2d-70 [-1, 512, 28, 28] 1,024
ReLU-71 [-1, 512, 28, 28] 0
Bottleneck-72 [-1, 512, 28, 28] 0
Conv2d-73 [-1, 128, 28, 28] 65,536
BatchNorm2d-74 [-1, 128, 28, 28] 256
ReLU-75 [-1, 128, 28, 28] 0
Conv2d-76 [-1, 128, 28, 28] 147,456
BatchNorm2d-77 [-1, 128, 28, 28] 256
ReLU-78 [-1, 128, 28, 28] 0
Conv2d-79 [-1, 512, 28, 28] 65,536
BatchNorm2d-80 [-1, 512, 28, 28] 1,024
ReLU-81 [-1, 512, 28, 28] 0
Bottleneck-82 [-1, 512, 28, 28] 0
Conv2d-83 [-1, 256, 28, 28] 131,072
BatchNorm2d-84 [-1, 256, 28, 28] 512
ReLU-85 [-1, 256, 28, 28] 0
Conv2d-86 [-1, 256, 14, 14] 589,824
BatchNorm2d-87 [-1, 256, 14, 14] 512
ReLU-88 [-1, 256, 14, 14] 0
Conv2d-89 [-1, 1024, 14, 14] 262,144
BatchNorm2d-90 [-1, 1024, 14, 14] 2,048
Conv2d-91 [-1, 1024, 14, 14] 524,288
BatchNorm2d-92 [-1, 1024, 14, 14] 2,048
ReLU-93 [-1, 1024, 14, 14] 0
Bottleneck-94 [-1, 1024, 14, 14] 0
Conv2d-95 [-1, 256, 14, 14] 262,144
BatchNorm2d-96 [-1, 256, 14, 14] 512
ReLU-97 [-1, 256, 14, 14] 0
Conv2d-98 [-1, 256, 14, 14] 589,824
BatchNorm2d-99 [-1, 256, 14, 14] 512
ReLU-100 [-1, 256, 14, 14] 0
Conv2d-101 [-1, 1024, 14, 14] 262,144
BatchNorm2d-102 [-1, 1024, 14, 14] 2,048
ReLU-103 [-1, 1024, 14, 14] 0
Bottleneck-104 [-1, 1024, 14, 14] 0
Conv2d-105 [-1, 256, 14, 14] 262,144
BatchNorm2d-106 [-1, 256, 14, 14] 512
ReLU-107 [-1, 256, 14, 14] 0
Conv2d-108 [-1, 256, 14, 14] 589,824
BatchNorm2d-109 [-1, 256, 14, 14] 512
ReLU-110 [-1, 256, 14, 14] 0
Conv2d-111 [-1, 1024, 14, 14] 262,144
BatchNorm2d-112 [-1, 1024, 14, 14] 2,048
ReLU-113 [-1, 1024, 14, 14] 0
Bottleneck-114 [-1, 1024, 14, 14] 0
Conv2d-115 [-1, 256, 14, 14] 262,144
BatchNorm2d-116 [-1, 256, 14, 14] 512
ReLU-117 [-1, 256, 14, 14] 0
Conv2d-118 [-1, 256, 14, 14] 589,824
BatchNorm2d-119 [-1, 256, 14, 14] 512
ReLU-120 [-1, 256, 14, 14] 0
Conv2d-121 [-1, 1024, 14, 14] 262,144
BatchNorm2d-122 [-1, 1024, 14, 14] 2,048
ReLU-123 [-1, 1024, 14, 14] 0
Bottleneck-124 [-1, 1024, 14, 14] 0
Conv2d-125 [-1, 256, 14, 14] 262,144
BatchNorm2d-126 [-1, 256, 14, 14] 512
ReLU-127 [-1, 256, 14, 14] 0
Conv2d-128 [-1, 256, 14, 14] 589,824
BatchNorm2d-129 [-1, 256, 14, 14] 512
ReLU-130 [-1, 256, 14, 14] 0
Conv2d-131 [-1, 1024, 14, 14] 262,144
BatchNorm2d-132 [-1, 1024, 14, 14] 2,048
ReLU-133 [-1, 1024, 14, 14] 0
Bottleneck-134 [-1, 1024, 14, 14] 0
Conv2d-135 [-1, 256, 14, 14] 262,144
BatchNorm2d-136 [-1, 256, 14, 14] 512
ReLU-137 [-1, 256, 14, 14] 0
Conv2d-138 [-1, 256, 14, 14] 589,824
BatchNorm2d-139 [-1, 256, 14, 14] 512
ReLU-140 [-1, 256, 14, 14] 0
Conv2d-141 [-1, 1024, 14, 14] 262,144
BatchNorm2d-142 [-1, 1024, 14, 14] 2,048
ReLU-143 [-1, 1024, 14, 14] 0
Bottleneck-144 [-1, 1024, 14, 14] 0
Conv2d-145 [-1, 512, 14, 14] 524,288
BatchNorm2d-146 [-1, 512, 14, 14] 1,024
ReLU-147 [-1, 512, 14, 14] 0
Conv2d-148 [-1, 512, 7, 7] 2,359,296
BatchNorm2d-149 [-1, 512, 7, 7] 1,024
ReLU-150 [-1, 512, 7, 7] 0
Conv2d-151 [-1, 2048, 7, 7] 1,048,576
BatchNorm2d-152 [-1, 2048, 7, 7] 4,096
Conv2d-153 [-1, 2048, 7, 7] 2,097,152
BatchNorm2d-154 [-1, 2048, 7, 7] 4,096
ReLU-155 [-1, 2048, 7, 7] 0
Bottleneck-156 [-1, 2048, 7, 7] 0
Conv2d-157 [-1, 512, 7, 7] 1,048,576
BatchNorm2d-158 [-1, 512, 7, 7] 1,024
ReLU-159 [-1, 512, 7, 7] 0
Conv2d-160 [-1, 512, 7, 7] 2,359,296
BatchNorm2d-161 [-1, 512, 7, 7] 1,024
ReLU-162 [-1, 512, 7, 7] 0
Conv2d-163 [-1, 2048, 7, 7] 1,048,576
BatchNorm2d-164 [-1, 2048, 7, 7] 4,096
ReLU-165 [-1, 2048, 7, 7] 0
Bottleneck-166 [-1, 2048, 7, 7] 0
Conv2d-167 [-1, 512, 7, 7] 1,048,576
BatchNorm2d-168 [-1, 512, 7, 7] 1,024
ReLU-169 [-1, 512, 7, 7] 0
Conv2d-170 [-1, 512, 7, 7] 2,359,296
BatchNorm2d-171 [-1, 512, 7, 7] 1,024
ReLU-172 [-1, 512, 7, 7] 0
Conv2d-173 [-1, 2048, 7, 7] 1,048,576
BatchNorm2d-174 [-1, 2048, 7, 7] 4,096
ReLU-175 [-1, 2048, 7, 7] 0
Bottleneck-176 [-1, 2048, 7, 7] 0
Conv2d-177 [-1, 1024, 7, 7] 2,098,176
ReLU-178 [-1, 1024, 7, 7] 0
Upsample-179 [-1, 1024, 14, 14] 0
Conv2d-180 [-1, 512, 14, 14] 524,800
ReLU-181 [-1, 512, 14, 14] 0
Conv2d-182 [-1, 512, 14, 14] 7,078,400
ReLU-183 [-1, 512, 14, 14] 0
Upsample-184 [-1, 512, 28, 28] 0
Conv2d-185 [-1, 512, 28, 28] 262,656
ReLU-186 [-1, 512, 28, 28] 0
Conv2d-187 [-1, 512, 28, 28] 4,719,104
ReLU-188 [-1, 512, 28, 28] 0
Upsample-189 [-1, 512, 56, 56] 0
Conv2d-190 [-1, 256, 56, 56] 65,792
ReLU-191 [-1, 256, 56, 56] 0
Conv2d-192 [-1, 256, 56, 56] 1,769,728
ReLU-193 [-1, 256, 56, 56] 0
Upsample-194 [-1, 256, 112, 112] 0
Conv2d-195 [-1, 64, 112, 112] 4,160
ReLU-196 [-1, 64, 112, 112] 0
Conv2d-197 [-1, 128, 112, 112] 368,768
ReLU-198 [-1, 128, 112, 112] 0
Upsample-199 [-1, 128, 224, 224] 0
Conv2d-200 [-1, 64, 224, 224] 110,656
ReLU-201 [-1, 64, 224, 224] 0
Conv2d-202 [-1, 6, 224, 224] 390
================================================================
Total params: 40,549,382
Trainable params: 40,549,382
Non-trainable params: 0
----------------------------------------------------------------
from collections import defaultdict
import torch.nn.functional as F
from loss import dice_loss
def calc_loss(pred, target, metrics, bce_weight=0.5):
bce = F.binary_cross_entropy_with_logits(pred, target)
pred = F.sigmoid(pred)
dice = dice_loss(pred, target)
loss = bce * bce_weight + dice * (1 - bce_weight)
metrics['bce'] += bce.data.cpu().numpy() * target.size(0)
metrics['dice'] += dice.data.cpu().numpy() * target.size(0)
metrics['loss'] += loss.data.cpu().numpy() * target.size(0)
return loss
def print_metrics(metrics, epoch_samples, phase):
outputs = []
for k in metrics.keys():
outputs.append("{}: {:4f}".format(k, metrics[k] / epoch_samples))
print("{}: {}".format(phase, ", ".join(outputs)))
def train_model(model, optimizer, scheduler, num_epochs=25):
best_model_wts = copy.deepcopy(model.state_dict())
best_loss = 1e10
for epoch in range(num_epochs):
print('Epoch {}/{}'.format(epoch, num_epochs - 1))
print('-' * 10)
since = time.time()
# Each epoch has a training and validation phase
for phase in ['train', 'val']:
if phase == 'train':
scheduler.step()
for param_group in optimizer.param_groups:
print("LR", param_group['lr'])
model.train() # Set model to training mode
else:
model.eval() # Set model to evaluate mode
metrics = defaultdict(float)
epoch_samples = 0
for inputs, labels in dataloaders[phase]:
inputs = inputs.to(device)
labels = labels.to(device)
# zero the parameter gradients
optimizer.zero_grad()
# forward
# track history if only in train
with torch.set_grad_enabled(phase == 'train'):
outputs = model(inputs)
loss = calc_loss(outputs, labels, metrics)
# backward + optimize only if in training phase
if phase == 'train':
loss.backward()
optimizer.step()
# statistics
epoch_samples += inputs.size(0)
print_metrics(metrics, epoch_samples, phase)
epoch_loss = metrics['loss'] / epoch_samples
# deep copy the model
if phase == 'val' and epoch_loss < best_loss:
print("saving best model")
best_loss = epoch_loss
best_model_wts = copy.deepcopy(model.state_dict())
time_elapsed = time.time() - since
print('{:.0f}m {:.0f}s'.format(time_elapsed // 60, time_elapsed % 60))
print('Best val loss: {:4f}'.format(best_loss))
# load best model weights
model.load_state_dict(best_model_wts)
return modelimport torch
import torch.optim as optim
from torch.optim import lr_scheduler
import time
import copy
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
print(device)
num_class = 6
model = ResNetUNet(num_class).to(device)
# freeze backbone layers
#for l in model.base_layers:
# for param in l.parameters():
# param.requires_grad = False
optimizer_ft = optim.Adam(filter(lambda p: p.requires_grad, model.parameters()), lr=1e-4)
exp_lr_scheduler = lr_scheduler.StepLR(optimizer_ft, step_size=30, gamma=0.1)
model = train_model(model, optimizer_ft, exp_lr_scheduler, num_epochs=60)cuda:0
Epoch 0/59
----------
LR 0.0001
train: bce: 0.070256, dice: 0.856320, loss: 0.463288
val: bce: 0.014897, dice: 0.515814, loss: 0.265356
saving best model
0m 51s
Epoch 1/59
----------
LR 0.0001
train: bce: 0.011369, dice: 0.309445, loss: 0.160407
val: bce: 0.003790, dice: 0.113682, loss: 0.058736
saving best model
0m 51s
Epoch 2/59
----------
LR 0.0001
train: bce: 0.003480, dice: 0.089928, loss: 0.046704
val: bce: 0.002525, dice: 0.067604, loss: 0.035064
saving best model
0m 51s
(Omitted)
Epoch 57/59
----------
LR 1e-05
train: bce: 0.000523, dice: 0.010289, loss: 0.005406
val: bce: 0.001558, dice: 0.030965, loss: 0.016261
0m 51s
Epoch 58/59
----------
LR 1e-05
train: bce: 0.000518, dice: 0.010209, loss: 0.005364
val: bce: 0.001548, dice: 0.031034, loss: 0.016291
0m 51s
Epoch 59/59
----------
LR 1e-05
train: bce: 0.000518, dice: 0.010168, loss: 0.005343
val: bce: 0.001566, dice: 0.030785, loss: 0.016176
0m 50s
Best val loss: 0.016171
import math
model.eval() # Set model to the evaluation mode
# Create another simulation dataset for test
test_dataset = SimDataset(3, transform = trans)
test_loader = DataLoader(test_dataset, batch_size=3, shuffle=False, num_workers=0)
# Get the first batch
inputs, labels = next(iter(test_loader))
inputs = inputs.to(device)
labels = labels.to(device)
# Predict
pred = model(inputs)
# The loss functions include the sigmoid function.
pred = F.sigmoid(pred)
pred = pred.data.cpu().numpy()
print(pred.shape)
# Change channel-order and make 3 channels for matplot
input_images_rgb = [reverse_transform(x) for x in inputs.cpu()]
# Map each channel (i.e. class) to each color
target_masks_rgb = [helper.masks_to_colorimg(x) for x in labels.cpu().numpy()]
pred_rgb = [helper.masks_to_colorimg(x) for x in pred]
helper.plot_side_by_side([input_images_rgb, target_masks_rgb, pred_rgb])(3, 6, 192, 192)
