Source code for dltk.networks.segmentation.fcn

from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import

import tensorflow as tf

from dltk.core.residual_unit import vanilla_residual_unit_3d
from dltk.core.upsample import linear_upsample_3d


[docs]def upscore_layer_3d(inputs, inputs2, out_filters, in_filters=None, strides=(2, 2, 2), mode=tf.estimator.ModeKeys.EVAL, use_bias=False, kernel_initializer=tf.initializers.variance_scaling(distribution='uniform'), bias_initializer=tf.zeros_initializer(), kernel_regularizer=None, bias_regularizer=None): """Upscore layer according to [1]. [1] J. Long et al. Fully convolutional networks for semantic segmentation. CVPR 2015. Args: inputs (tf.Tensor): Input features to be upscored. inputs2 (tf.Tensor): Higher resolution features from the encoder to add. out_filters (int): Number of output filters (typically, number of segmentation classes) in_filters (None, optional): None or number of input filters. strides (tuple, optional): Upsampling factor for a strided transpose convolution. mode (TYPE, optional): One of the tf.estimator.ModeKeys strings: TRAIN, EVAL or PREDICT use_bias (bool, optional): Boolean, whether the layer uses a bias. kernel_initializer (TYPE, optional): An initializer for the convolution kernel. bias_initializer (TYPE, optional): An initializer for the bias vector. If None, no bias will be applied. kernel_regularizer (None, optional): Optional regularizer for the convolution kernel. bias_regularizer (None, optional): Optional regularizer for the bias vector. Returns: tf.Tensor: Upscore tensor """ conv_params = {'use_bias': use_bias, 'kernel_initializer': kernel_initializer, 'bias_initializer': bias_initializer, 'kernel_regularizer': kernel_regularizer, 'bias_regularizer': bias_regularizer} # Compute an upsampling shape dynamically from the input tensor. Input # filters are required to be static. if in_filters is None: in_filters = inputs.get_shape().as_list()[-1] assert len(inputs.get_shape().as_list()) == 5, \ 'inputs are required to have a rank of 5.' assert len(inputs.get_shape().as_list()) == len(inputs2.get_shape().as_list()), \ 'Ranks of input and input2 differ' # Account for differences in the number of input and output filters if in_filters != out_filters: x = tf.layers.conv3d(inputs=inputs, filters=out_filters, kernel_size=(1, 1, 1), strides=(1, 1, 1), padding='same', name='filter_conversion', **conv_params) else: x = inputs # Upsample inputs x = linear_upsample_3d(inputs=x, strides=strides) # Skip connection x2 = tf.layers.conv3d(inputs=inputs2, filters=out_filters, kernel_size=(1, 1, 1), strides=(1, 1, 1), padding='same', **conv_params) x2 = tf.layers.batch_normalization( x2, training=mode == tf.estimator.ModeKeys.TRAIN) # Return the element-wise sum return tf.add(x, x2)
[docs]def residual_fcn_3d(inputs, num_classes, num_res_units=1, filters=(16, 32, 64, 128), strides=((1, 1, 1), (2, 2, 2), (2, 2, 2), (2, 2, 2)), mode=tf.estimator.ModeKeys.EVAL, use_bias=False, kernel_initializer=tf.initializers.variance_scaling(distribution='uniform'), bias_initializer=tf.zeros_initializer(), kernel_regularizer=None, bias_regularizer=None): """ Image segmentation network based on an FCN architecture [1] using residual units [2] as feature extractors. Downsampling and upsampling of features is done via strided convolutions and transpose convolutions, respectively. On each resolution scale s are num_residual_units with filter size = filters[s]. strides[s] determine the downsampling factor at each resolution scale. [1] J. Long et al. Fully convolutional networks for semantic segmentation. CVPR 2015. [2] K. He et al. Identity Mappings in Deep Residual Networks. ECCV 2016. Args: inputs (tf.Tensor): Input feature tensor to the network (rank 5 required). num_classes (int): Number of output classes. num_res_units (int, optional): Number of residual units at each resolution scale. filters (tuple, optional): Number of filters for all residual units at each resolution scale. strides (tuple, optional): Stride of the first unit on a resolution scale. mode (TYPE, optional): One of the tf.estimator.ModeKeys strings: TRAIN, EVAL or PREDICT use_bias (bool, optional): Boolean, whether the layer uses a bias. kernel_initializer (TYPE, optional): An initializer for the convolution kernel. bias_initializer (TYPE, optional): An initializer for the bias vector. If None, no bias will be applied. kernel_regularizer (None, optional): Optional regularizer for the convolution kernel. bias_regularizer (None, optional): Optional regularizer for the bias vector. Returns: dict: dictionary of output tensors """ outputs = {} assert len(strides) == len(filters) assert len(inputs.get_shape().as_list()) == 5, \ 'inputs are required to have a rank of 5.' conv_params = {'use_bias': use_bias, 'kernel_initializer': kernel_initializer, 'bias_initializer': bias_initializer, 'kernel_regularizer': kernel_regularizer, 'bias_regularizer': bias_regularizer} x = inputs # Inital convolution with filters[0] x = tf.layers.conv3d(inputs=x, filters=filters[0], kernel_size=(3, 3, 3), strides=strides[0], padding='same', **conv_params) tf.logging.info('Init conv tensor shape {}'.format(x.get_shape())) # Residual feature encoding blocks with num_res_units at different # resolution scales res_scales res_scales = [x] saved_strides = [] for res_scale in range(1, len(filters)): # Features are downsampled via strided convolutions. These are defined # in `strides` and subsequently saved with tf.variable_scope('unit_{}_0'.format(res_scale)): x = vanilla_residual_unit_3d( inputs=x, out_filters=filters[res_scale], strides=strides[res_scale], mode=mode) saved_strides.append(strides[res_scale]) for i in range(1, num_res_units): with tf.variable_scope('unit_{}_{}'.format(res_scale, i)): x = vanilla_residual_unit_3d( inputs=x, out_filters=filters[res_scale], strides=(1, 1, 1), mode=mode) res_scales.append(x) tf.logging.info('Encoder at res_scale {} tensor shape: {}'.format( res_scale, x.get_shape())) # Upscore layers [2] reconstruct the predictions to higher resolution # scales for res_scale in range(len(filters) - 2, -1, -1): with tf.variable_scope('upscore_{}'.format(res_scale)): x = upscore_layer_3d( inputs=x, inputs2=res_scales[res_scale], out_filters=num_classes, strides=saved_strides[res_scale], mode=mode, **conv_params) tf.logging.info('Decoder at res_scale {} tensor shape: {}'.format( res_scale, x.get_shape())) # Last convolution with tf.variable_scope('last'): x = tf.layers.conv3d(inputs=x, filters=num_classes, kernel_size=(1, 1, 1), strides=(1, 1, 1), padding='same', **conv_params) tf.logging.info('Output tensor shape {}'.format(x.get_shape())) # Define the outputs outputs['logits'] = x with tf.variable_scope('pred'): y_prob = tf.nn.softmax(x) outputs['y_prob'] = y_prob y_ = tf.argmax(x, axis=-1) \ if num_classes > 1 \ else tf.cast(tf.greater_equal(x[..., 0], 0.5), tf.int32) outputs['y_'] = y_ return outputs