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conv_stride_1 = TimeDistributed(convReLU(16, kernel=(3,3), strides=(2,2), name='conv_stride_1'))(conv_seg_1)
conv_seg_2 = TimeDistributed(convReLU(32, name='conv_seg_2'))(conv_stride_1)
conv_stride_2 = TimeDistributed(convReLU(32, kernel=(3,3), strides=(2,2), name='conv_stride_2'))(conv_seg_2)
conv_seg_3 = TimeDistributed(convReLU(64, kernel=(3,3), name='conv_seg_3'))(conv_stride_2)
dropout_seg = TimeDistributed(Dropout(0.5, name='dropout_seg'))(conv_seg_3)
deconv_seg_1 = TimeDistributed(deconvReLU(8, name='deconv_seg_1'))(dropout_seg)
deconv_seg_2 = TimeDistributed(deconvReLU(8, name='decon_seg_2'))(deconv_seg_1)
seg = TimeDistributed(Conv2D(2, kernel_size=(1,1),
use_bias= False,
padding='same',
activation='softmax',
name='seg'))(deconv_seg_2)
conv3D_1 = convReLU_3D(16, name='conv3D_1')(seg)
conv3D_2 = convReLU_3D(16, strides=(1,2,2), name='conv3D_2')(conv3D_1)
conv3D_3 = convReLU_3D(32, name='conv3D_3')(conv3D_2)
conv3D_4 = convReLU_3D(32, strides=(1,2,2), name='conv3D_4')(conv3D_3)
conv3D_5 = convReLU_3D(64, name='conv3D_5')(conv3D_4)
dropout = Dropout(0.5, name='dropout')(conv3D_5)
up3D_1 = UpSampling3D(name='up3D_1')(dropout)
deconv3D_1 = convReLU_3D(8, name='deconv3D_1')(up3D_1)
up3D_2 = UpSampling3D(name='up3D_2')(deconv3D_1)
deconv3D_2 = convReLU_3D(8, name='deconv3D_2')(up3D_2)
density3D = Conv3D(1, kernel_size=(1,1,1),
use_bias= False,
padding='same',
activation='linear',
name='density3D')(deconv3D_2)
if output == 'density':
model = Model(inputs=input_, outputs=density3D)
for layer in model.layers[2:10]:
input_ = Input(shape=input_size, name='input')
conv_seg_1 = TimeDistributed(convReLU(16, name='conv_seg_1'))(input_)
conv_stride_1 = TimeDistributed(convReLU(16, kernel=(3,3), strides=(2,2), name='conv_stride_1'))(conv_seg_1)
conv_seg_2 = TimeDistributed(convReLU(32, name='conv_seg_2'))(conv_stride_1)
conv_stride_2 = TimeDistributed(convReLU(32, kernel=(3,3), strides=(2,2), name='conv_stride_2'))(conv_seg_2)
conv_seg_3 = TimeDistributed(convReLU(64, kernel=(3,3), name='conv_seg_3'))(conv_stride_2)
dropout_seg = TimeDistributed(Dropout(0.5, name='dropout_seg'))(conv_seg_3)
deconv_seg_1 = TimeDistributed(deconvReLU(8, name='deconv_seg_1'))(dropout_seg)
deconv_seg_2 = TimeDistributed(deconvReLU(8, name='decon_seg_2'))(deconv_seg_1)
seg = TimeDistributed(Conv2D(2, kernel_size=(1,1),
use_bias= False,
padding='same',
activation='softmax',
name='seg'))(deconv_seg_2)
conv3D_1 = convReLU_3D(16, name='conv3D_1')(seg)
conv3D_2 = convReLU_3D(16, strides=(1,2,2), name='conv3D_2')(conv3D_1)
conv3D_3 = convReLU_3D(32, name='conv3D_3')(conv3D_2)
conv3D_4 = convReLU_3D(32, strides=(1,2,2), name='conv3D_4')(conv3D_3)
conv3D_5 = convReLU_3D(64, name='conv3D_5')(conv3D_4)
dropout = Dropout(0.5, name='dropout')(conv3D_5)
up3D_1 = UpSampling3D(name='up3D_1')(dropout)
deconv3D_1 = convReLU_3D(8, name='deconv3D_1')(up3D_1)
up3D_2 = UpSampling3D(name='up3D_2')(deconv3D_1)
deconv3D_2 = convReLU_3D(8, name='deconv3D_2')(up3D_2)
density3D = Conv3D(1, kernel_size=(1,1,1),
use_bias= False,
padding='same',
activation='linear',
name='density3D')(deconv3D_2)
if output == 'density':
conv_seg_2 = TimeDistributed(convReLU(32, name='conv_seg_2'))(conv_stride_1)
conv_stride_2 = TimeDistributed(convReLU(32, kernel=(3,3), strides=(2,2), name='conv_stride_2'))(conv_seg_2)
conv_seg_3 = TimeDistributed(convReLU(64, kernel=(3,3), name='conv_seg_3'))(conv_stride_2)
dropout_seg = TimeDistributed(Dropout(0.5, name='dropout_seg'))(conv_seg_3)
deconv_seg_1 = TimeDistributed(deconvReLU(8, name='deconv_seg_1'))(dropout_seg)
deconv_seg_2 = TimeDistributed(deconvReLU(8, name='decon_seg_2'))(deconv_seg_1)
seg = TimeDistributed(Conv2D(2, kernel_size=(1,1),
use_bias= False,
padding='same',
activation='softmax',
name='seg'))(deconv_seg_2)
conv3D_1 = convReLU_3D(16, name='conv3D_1')(seg)
conv3D_2 = convReLU_3D(16, strides=(1,2,2), name='conv3D_2')(conv3D_1)
conv3D_3 = convReLU_3D(32, name='conv3D_3')(conv3D_2)
conv3D_4 = convReLU_3D(32, strides=(1,2,2), name='conv3D_4')(conv3D_3)
conv3D_5 = convReLU_3D(64, name='conv3D_5')(conv3D_4)
dropout = Dropout(0.5, name='dropout')(conv3D_5)
up3D_1 = UpSampling3D(name='up3D_1')(dropout)
deconv3D_1 = convReLU_3D(8, name='deconv3D_1')(up3D_1)
up3D_2 = UpSampling3D(name='up3D_2')(deconv3D_1)
deconv3D_2 = convReLU_3D(8, name='deconv3D_2')(up3D_2)
density3D = Conv3D(1, kernel_size=(1,1,1),
use_bias= False,
padding='same',
activation='linear',
name='density3D')(deconv3D_2)
if output == 'density':
model = Model(inputs=input_, outputs=density3D)
for layer in model.layers[2:10]:
layer.trainable = False
deconv_seg_1 = TimeDistributed(deconvReLU(8, name='deconv_seg_1'))(dropout_seg)
deconv_seg_2 = TimeDistributed(deconvReLU(8, name='decon_seg_2'))(deconv_seg_1)
seg = TimeDistributed(Conv2D(2, kernel_size=(1,1),
use_bias= False,
padding='same',
activation='softmax',
name='seg'))(deconv_seg_2)
conv3D_1 = convReLU_3D(16, name='conv3D_1')(seg)
conv3D_2 = convReLU_3D(16, strides=(1,2,2), name='conv3D_2')(conv3D_1)
conv3D_3 = convReLU_3D(32, name='conv3D_3')(conv3D_2)
conv3D_4 = convReLU_3D(32, strides=(1,2,2), name='conv3D_4')(conv3D_3)
conv3D_5 = convReLU_3D(64, name='conv3D_5')(conv3D_4)
dropout = Dropout(0.5, name='dropout')(conv3D_5)
up3D_1 = UpSampling3D(name='up3D_1')(dropout)
deconv3D_1 = convReLU_3D(8, name='deconv3D_1')(up3D_1)
up3D_2 = UpSampling3D(name='up3D_2')(deconv3D_1)
deconv3D_2 = convReLU_3D(8, name='deconv3D_2')(up3D_2)
density3D = Conv3D(1, kernel_size=(1,1,1),
use_bias= False,
padding='same',
activation='linear',
name='density3D')(deconv3D_2)
if output == 'density':
model = Model(inputs=input_, outputs=density3D)
for layer in model.layers[2:10]:
layer.trainable = False
elif output == 'seg':
model = Model(inputs=input_, outputs=seg)
elif output == 'both':
model = Model(inputs=input_, outputs=[density3D, seg])
seg = TimeDistributed(Conv2D(2, kernel_size=(1,1),
use_bias= False,
padding='same',
activation='softmax',
name='seg'))(deconv_seg_2)
conv3D_1 = convReLU_3D(16, name='conv3D_1')(seg)
conv3D_2 = convReLU_3D(16, strides=(1,2,2), name='conv3D_2')(conv3D_1)
conv3D_3 = convReLU_3D(32, name='conv3D_3')(conv3D_2)
conv3D_4 = convReLU_3D(32, strides=(1,2,2), name='conv3D_4')(conv3D_3)
conv3D_5 = convReLU_3D(64, name='conv3D_5')(conv3D_4)
dropout = Dropout(0.5, name='dropout')(conv3D_5)
up3D_1 = UpSampling3D(name='up3D_1')(dropout)
deconv3D_1 = convReLU_3D(8, name='deconv3D_1')(up3D_1)
up3D_2 = UpSampling3D(name='up3D_2')(deconv3D_1)
deconv3D_2 = convReLU_3D(8, name='deconv3D_2')(up3D_2)
density3D = Conv3D(1, kernel_size=(1,1,1),
use_bias= False,
padding='same',
activation='linear',
name='density3D')(deconv3D_2)
if output == 'density':
model = Model(inputs=input_, outputs=density3D)
for layer in model.layers[2:10]:
layer.trainable = False
elif output == 'seg':
model = Model(inputs=input_, outputs=seg)
elif output == 'both':
model = Model(inputs=input_, outputs=[density3D, seg])
else:
raise Exception('output must be "density", "seg" or "both".')
conv_stride_2 = TimeDistributed(convReLU(32, kernel=(3,3), strides=(2,2), name='conv_stride_2'))(conv_seg_2)
conv_seg_3 = TimeDistributed(convReLU(64, kernel=(3,3), name='conv_seg_3'))(conv_stride_2)
dropout_seg = TimeDistributed(Dropout(0.5, name='dropout_seg'))(conv_seg_3)
deconv_seg_1 = TimeDistributed(deconvReLU(8, name='deconv_seg_1'))(dropout_seg)
deconv_seg_2 = TimeDistributed(deconvReLU(8, name='decon_seg_2'))(deconv_seg_1)
seg = TimeDistributed(Conv2D(2, kernel_size=(1,1),
use_bias= False,
padding='same',
activation='softmax',
name='seg'))(deconv_seg_2)
conv3D_1 = convReLU_3D(16, name='conv3D_1')(seg)
conv3D_2 = convReLU_3D(16, strides=(1,2,2), name='conv3D_2')(conv3D_1)
conv3D_3 = convReLU_3D(32, name='conv3D_3')(conv3D_2)
conv3D_4 = convReLU_3D(32, strides=(1,2,2), name='conv3D_4')(conv3D_3)
conv3D_5 = convReLU_3D(64, name='conv3D_5')(conv3D_4)
dropout = Dropout(0.5, name='dropout')(conv3D_5)
up3D_1 = UpSampling3D(name='up3D_1')(dropout)
deconv3D_1 = convReLU_3D(8, name='deconv3D_1')(up3D_1)
up3D_2 = UpSampling3D(name='up3D_2')(deconv3D_1)
deconv3D_2 = convReLU_3D(8, name='deconv3D_2')(up3D_2)
density3D = Conv3D(1, kernel_size=(1,1,1),
use_bias= False,
padding='same',
activation='linear',
name='density3D')(deconv3D_2)
if output == 'density':
model = Model(inputs=input_, outputs=density3D)
for layer in model.layers[2:10]:
layer.trainable = False
elif output == 'seg':
conv_seg_1 = TimeDistributed(convReLU(16, name='conv_seg_1'))(input_)
conv_stride_1 = TimeDistributed(convReLU(16, kernel=(3,3), strides=(2,2), name='conv_stride_1'))(conv_seg_1)
conv_seg_2 = TimeDistributed(convReLU(32, name='conv_seg_2'))(conv_stride_1)
conv_stride_2 = TimeDistributed(convReLU(32, kernel=(3,3), strides=(2,2), name='conv_stride_2'))(conv_seg_2)
conv_seg_3 = TimeDistributed(convReLU(64, kernel=(3,3), name='conv_seg_3'))(conv_stride_2)
dropout_seg = TimeDistributed(Dropout(0.5, name='dropout_seg'))(conv_seg_3)
deconv_seg_1 = TimeDistributed(deconvReLU(8, name='deconv_seg_1'))(dropout_seg)
deconv_seg_2 = TimeDistributed(deconvReLU(8, name='decon_seg_2'))(deconv_seg_1)
seg = TimeDistributed(Conv2D(2, kernel_size=(1,1),
use_bias= False,
padding='same',
activation='softmax',
name='seg'))(deconv_seg_2)
conv3D_1 = convReLU_3D(16, name='conv3D_1')(seg)
conv3D_2 = convReLU_3D(16, strides=(1,2,2), name='conv3D_2')(conv3D_1)
conv3D_3 = convReLU_3D(32, name='conv3D_3')(conv3D_2)
conv3D_4 = convReLU_3D(32, strides=(1,2,2), name='conv3D_4')(conv3D_3)
conv3D_5 = convReLU_3D(64, name='conv3D_5')(conv3D_4)
dropout = Dropout(0.5, name='dropout')(conv3D_5)
up3D_1 = UpSampling3D(name='up3D_1')(dropout)
deconv3D_1 = convReLU_3D(8, name='deconv3D_1')(up3D_1)
up3D_2 = UpSampling3D(name='up3D_2')(deconv3D_1)
deconv3D_2 = convReLU_3D(8, name='deconv3D_2')(up3D_2)
density3D = Conv3D(1, kernel_size=(1,1,1),
use_bias= False,
padding='same',
activation='linear',
name='density3D')(deconv3D_2)
if output == 'density':
model = Model(inputs=input_, outputs=density3D)