import tensorflow as tf from tensorflow.keras import layers, models def time_distributed_conv_block(input_tensor, num_filters): x = layers.Conv3D(num_filters, (3, 3, 3), padding="same")(input_tensor) x = layers.ReLU()(x) x = layers.Conv3D(num_filters, (3, 3, 3), padding="same")(x) x = layers.ReLU()(x) return x def time_distributed_encoder_block_resp(input_tensor, num_filters, temporal_maxpool=True): x = time_distributed_conv_block(input_tensor, num_filters) p = layers.MaxPooling3D((1, 4, 4))(x) if temporal_maxpool: p = tf.transpose(p, (0,2,3,1,4)) p2 = layers.TimeDistributed(layers.TimeDistributed(layers.MaxPooling1D((2))))(p) p2 = tf.transpose(p2, (0,3,1,2,4)) return x, p2 else: return x, p def time_distributed_decoder_block_resp(input_tensor, skip_tensor, num_filters): x = layers.TimeDistributed(layers.UpSampling2D(( 4, 4), interpolation='bilinear'))(input_tensor) x = layers.Conv3D(num_filters, (3, 3, 3), padding="same")(x) x = layers.Conv3D(num_filters, (3, 3, 3), padding="same")(x) x = layers.Concatenate()([x, skip_tensor]) x = time_distributed_conv_block(x, num_filters) return x def build_3d_unet_resp(input_shape, num_classes): inputs = layers.Input(shape=input_shape) # Encoding path s1, p1 = time_distributed_encoder_block_resp(inputs, 32,temporal_maxpool=False) s2, p2 = time_distributed_encoder_block_resp(p1, 64,temporal_maxpool=False) # Bridge b1 = time_distributed_conv_block(p2, 128) d1 = time_distributed_decoder_block_resp(b1, s2, 64) d2 = time_distributed_decoder_block_resp(d1, s1, 32) outputs = layers.Conv3D(num_classes, (1, 1, 1))(d2) model = models.Model(inputs, outputs, name="3D-U-Net-resp") return model def time_distributed_encoder_block(input_tensor, num_filters, temporal_maxpool=True): x = time_distributed_conv_block(input_tensor, num_filters) p = layers.TimeDistributed(layers.MaxPooling2D((2, 2)))(x) if temporal_maxpool: p = tf.transpose(p, (0,2,3,1,4)) p2 = layers.TimeDistributed(layers.TimeDistributed(layers.MaxPooling1D((2))))(p) p2 = tf.transpose(p2, (0,3,1,2,4)) return x, p2 else: return x, p def time_distributed_decoder_block(input_tensor, skip_tensor, num_filters, temporal_upsamp=True): x = layers.TimeDistributed(layers.UpSampling2D(( 2, 2)))(input_tensor) x = layers.TimeDistributed(layers.Conv2D(num_filters, (3, 3), padding="same"))(x) if temporal_upsamp: x = tf.transpose(x, (0,2,3,1,4)) x = layers.TimeDistributed(layers.TimeDistributed(layers.UpSampling1D((2))))(x) x = layers.TimeDistributed(layers.TimeDistributed(layers.Conv1D(num_filters, (2),padding="same")))(x) x = tf.transpose(x, (0,3,1,2,4)) if x.shape[4] == 64: skip_tensor = tf.transpose(skip_tensor, (0,2,3,1,4)) skip_tensor = layers.TimeDistributed(layers.TimeDistributed(layers.Conv1DTranspose(num_filters,kernel_size=2,strides=2)))(skip_tensor) skip_tensor = tf.transpose(skip_tensor, (0,3,1,2,4)) if x.shape[4] == 32: skip_tensor = tf.transpose(skip_tensor, (0,2,3,1,4)) skip_tensor = layers.TimeDistributed(layers.TimeDistributed(layers.Conv1DTranspose(num_filters,kernel_size=2,strides=2)))(skip_tensor) skip_tensor = layers.TimeDistributed(layers.TimeDistributed(layers.Conv1DTranspose(num_filters,kernel_size=2,strides=2)))(skip_tensor) skip_tensor = tf.transpose(skip_tensor, (0,3,1,2,4)) x = layers.Concatenate()([x, skip_tensor]) x = time_distributed_conv_block(x, num_filters) return x def build_3d_unet(input_shape, num_classes): inputs = layers.Input(shape=input_shape) # Encoding path s1, p1 = time_distributed_encoder_block(inputs, 32,temporal_maxpool=False) s2, p2 = time_distributed_encoder_block(p1, 64,temporal_maxpool=False) s3, p3 = time_distributed_encoder_block(p2, 128,temporal_maxpool=True) # Bridge b1 = time_distributed_conv_block(p3, 256) # Decoding path d1 = time_distributed_decoder_block(b1, s3, 128,temporal_upsamp=True) d2 = time_distributed_decoder_block(d1, s2, 64,temporal_upsamp=True) d3 = time_distributed_decoder_block(d2, s1, 32,temporal_upsamp=True) # Output layer outputs = layers.Conv3D(num_classes, (1, 1, 1))(d3) model = models.Model(inputs, outputs, name="3D-U-Net") return model