Download this file

151 lines (112 with data), 4.7 kB

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
from __future__ import print_function
from keras import backend as K
from keras.layers import Activation
from keras.layers import BatchNormalization
from keras.layers import Conv2D
from keras.layers import Conv2DTranspose
from keras.layers import Input
from keras.layers import MaxPooling2D
from keras.layers import concatenate
from keras.models import Model
from data import channels
from data import image_cols
from data import image_rows
from data import modalities
batch_norm = False
smooth = 1.0
def dice_coef(y_true, y_pred):
y_true_f = K.flatten(y_true)
y_pred_f = K.flatten(y_pred)
intersection = K.sum(y_true_f * y_pred_f)
return (2. * intersection + smooth) / (K.sum(y_true_f) + K.sum(y_pred_f) + smooth)
def dice_coef_loss(y_true, y_pred):
return -dice_coef(y_true, y_pred)
def unet():
inputs = Input((image_rows, image_cols, channels * modalities))
conv1 = Conv2D(32, (3, 3), padding='same')(inputs)
if batch_norm:
conv1 = BatchNormalization(axis=3)(conv1)
conv1 = Activation('relu')(conv1)
conv1 = Conv2D(32, (3, 3), padding='same')(conv1)
if batch_norm:
conv1 = BatchNormalization(axis=3)(conv1)
conv1 = Activation('relu')(conv1)
pool1 = MaxPooling2D(pool_size=(2, 2))(conv1)
conv2 = Conv2D(64, (3, 3), padding='same')(pool1)
if batch_norm:
conv2 = BatchNormalization(axis=3)(conv2)
conv2 = Activation('relu')(conv2)
conv2 = Conv2D(64, (3, 3), padding='same')(conv2)
if batch_norm:
conv2 = BatchNormalization(axis=3)(conv2)
conv2 = Activation('relu')(conv2)
pool2 = MaxPooling2D(pool_size=(2, 2))(conv2)
conv3 = Conv2D(128, (3, 3), padding='same')(pool2)
if batch_norm:
conv3 = BatchNormalization(axis=3)(conv3)
conv3 = Activation('relu')(conv3)
conv3 = Conv2D(128, (3, 3), padding='same')(conv3)
if batch_norm:
conv3 = BatchNormalization(axis=3)(conv3)
conv3 = Activation('relu')(conv3)
pool3 = MaxPooling2D(pool_size=(2, 2))(conv3)
conv4 = Conv2D(256, (3, 3), padding='same')(pool3)
if batch_norm:
conv4 = BatchNormalization(axis=3)(conv4)
conv4 = Activation('relu')(conv4)
conv4 = Conv2D(256, (3, 3), padding='same')(conv4)
if batch_norm:
conv4 = BatchNormalization(axis=3)(conv4)
conv4 = Activation('relu')(conv4)
pool4 = MaxPooling2D(pool_size=(2, 2))(conv4)
conv5 = Conv2D(512, (3, 3), padding='same')(pool4)
if batch_norm:
conv5 = BatchNormalization(axis=3)(conv5)
conv5 = Activation('relu')(conv5)
conv5 = Conv2D(512, (3, 3), padding='same')(conv5)
if batch_norm:
conv5 = BatchNormalization(axis=3)(conv5)
conv5 = Activation('relu')(conv5)
up6 = Conv2DTranspose(256, (2, 2), strides=(2, 2), padding='same')(conv5)
up6 = concatenate([up6, conv4], axis=3)
conv6 = Conv2D(256, (3, 3), padding='same')(up6)
if batch_norm:
conv6 = BatchNormalization(axis=3)(conv6)
conv6 = Activation('relu')(conv6)
conv6 = Conv2D(256, (3, 3), padding='same')(conv6)
if batch_norm:
conv6 = BatchNormalization(axis=3)(conv6)
conv6 = Activation('relu')(conv6)
up7 = Conv2DTranspose(128, (2, 2), strides=(2, 2), padding='same')(conv6)
up7 = concatenate([up7, conv3], axis=3)
conv7 = Conv2D(128, (3, 3), padding='same')(up7)
if batch_norm:
conv7 = BatchNormalization(axis=3)(conv7)
conv7 = Activation('relu')(conv7)
conv7 = Conv2D(128, (3, 3), activation='relu', padding='same')(conv7)
if batch_norm:
conv7 = BatchNormalization(axis=3)(conv7)
conv7 = Activation('relu')(conv7)
up8 = Conv2DTranspose(64, (2, 2), strides=(2, 2), padding='same')(conv7)
up8 = concatenate([up8, conv2], axis=3)
conv8 = Conv2D(64, (3, 3), padding='same')(up8)
if batch_norm:
conv8 = BatchNormalization(axis=3)(conv8)
conv8 = Activation('relu')(conv8)
conv8 = Conv2D(64, (3, 3), padding='same')(conv8)
if batch_norm:
conv8 = BatchNormalization(axis=3)(conv8)
conv8 = Activation('relu')(conv8)
up9 = Conv2DTranspose(32, (2, 2), strides=(2, 2), padding='same')(conv8)
up9 = concatenate([up9, conv1], axis=3)
conv9 = Conv2D(32, (3, 3), padding='same')(up9)
if batch_norm:
conv9 = BatchNormalization(axis=3)(conv9)
conv9 = Activation('relu')(conv9)
conv9 = Conv2D(32, (3, 3), padding='same')(conv9)
if batch_norm:
conv9 = BatchNormalization(axis=3)(conv9)
conv9 = Activation('relu')(conv9)
conv10 = Conv2D(1, (1, 1), activation='sigmoid')(conv9)
model = Model(inputs=[inputs], outputs=[conv10])
return model