def main():
# load vgg network
extractor = utils.StyleContentModel(style_layers, content_layers)
style_features_avg = [0.0] * len(style_layers)
for i in range(1,N_IMG):
if clinical:
image_path = 'img/clinical_us/training_set/' + format(i, '03d') + '_HC.png'
style_image = utils.image_preprocessing(image_path, 'clinical', [540, 800], c=3)
else:
image_path = 'img/data/new_att_all/' + str(i) + '.png'
style_image = utils.image_preprocessing(image_path, 'hq', [1000, 1386], c=3)
print(image_path)
style_features = extractor(style_image)['style']
style_features_list = [style_features[name] for name in style_features.keys()]
for j in range(5):
style_features_avg[j] += style_features_list[j]
style_features_avg = [ft/(N_IMG - 1) for ft in style_features_avg]
style_dict = {name: value for name, value in zip(style_layers, style_features_avg)}
if clinical:
filename = 'models/nst/us_clinical_ft_dict.pickle'
else:
filename = 'models/nst/us_hq_ft_dict.pickle'
with open(filename, 'wb') as handle:
pickle.dump(style_dict, handle, protocol=pickle.HIGHEST_PROTOCOL)
def __init__(self, source_image, observed_layers, n_bins=128):
"""
:param source_image: source image
:type image: PIL Image object
:param observed_layers: dictionary containing layer-specific information ; see bottom of file decoders.py
:type observed_layers: dictionary
:param n_bins: number of transportation histogram bins, defaults to 128 [TO BE IMPLEMENTED]
:type n_bins: int, optional
"""
# source image
self.source_tensor = image_preprocessing(source_image)
self.normalized_source_batch = vgg_normalization(
self.source_tensor).unsqueeze(0)
self.source_batch = self.source_tensor.unsqueeze(0)
# set encoder
self.encoder = vgg19(pretrained=True).float()
self.encoder.eval()
for param in self.encoder.features.parameters():
param.requires_grad = False
self.encoder_layers = {}
self.set_encoder_hooks(observed_layers)
self.n_bins = n_bins
def load_image_and_label(data, hist_template, total_files_to_read, ind,
folderPath):
label_enry = data
filename = os.path.join(folderPath, label_enry[0])
try:
# im = ndimage.imread(filename, True, 'L')
im = cv2.imread(filename, cv2.IMREAD_GRAYSCALE).astype(np.float32)
im = hist_match(im, hist_template)
im = misc.imresize(im, (conf.IMAGE_X_DIM, conf.IMAGE_Y_DIM),
'bilinear')
im = image_preprocessing(im)
im = im.reshape(conf.IMAGE_X_DIM, conf.IMAGE_Y_DIM, 1)
printProgressBar(ind + 1,
total_files_to_read,
prefix='Loaded files:',
suffix='Complete',
length=50)
return im
except (FileNotFoundError, OSError, AttributeError):
print('Missing {0}'.format(str(filename)))
except ValueError as e:
print('Value error: ' + str(e))
def __init__(self, style_image, content_image, observed_layers, n_bins=128, decoder_weights_path=None):
super().__init__(style_image, observed_layers, n_bins=n_bins)
# input image
self.content_tensor = image_preprocessing(content_image)
self.normalized_content_batch = vgg_normalization(
self.content_tensor).unsqueeze(0)
self.content_batch = self.content_tensor.unsqueeze(0)
def __init__(self,model_path,factor,iter,lr,tv_coeff,tv_beta,\
l1_coeff,img_path,perturb):
self.model_path = model_path
self.factor = factor
self.iter = iter
self.lr = lr
self.tv_coeff = tv_coeff
self.tv_beta = tv_beta
self.l1_coeff = l1_coeff
self.img_path = img_path
self.model = load_model(self.model_path)
self.original_img = perturbation(self.img_path, 'original', None)
self.original_img_tensor = image_preprocessing(self.original_img)
self.perturbed_img = perturbation(self.img_path, perturb, 5)
self.perturbed_img_tensor = image_preprocessing(self.perturbed_img)
def __init__(self,
style_image,
content_image,
observed_layers,
n_bins=128):
"""
:param content_image: content image
:type content_image: PIL Image object
"""
super().__init__(style_image, observed_layers, n_bins=n_bins)
# input image
self.content_tensor = image_preprocessing(content_image)
self.normalized_content_batch = vgg_normalization(
self.content_tensor).unsqueeze(0)
self.content_batch = self.content_tensor.unsqueeze(0)
def __init__(self, image, observed_layers, n_bins=128):
# source image
self.source_tensor = image_preprocessing(image)
self.normalized_source_batch = vgg_normalization(
self.source_tensor).unsqueeze(0)
self.source_batch = self.source_tensor.unsqueeze(0)
# set encoder
self.encoder = vgg19(pretrained=True).float()
self.encoder.eval()
for param in self.encoder.features.parameters():
param.requires_grad = False
self.encoder_layers = {}
self.set_encoder_hooks(observed_layers)
self.n_bins = n_bins
def __getImagesAndLabels(self, data_size, pos_locations, neg_locations):
assert len(pos_locations) > 0
assert len(neg_locations) > 0
filename = os.path.join(self.__imagesFolderPath, "00000003_006.png")
hist_template = ndimage.imread(filename, True, 'L')
if data_size is None:
pos_indexes = range(0, len(pos_locations))
neg_indexes = range(0, len(neg_locations))
else:
pos_indexes = random.sample(range(1, len(pos_locations)),
int(data_size * self.__classSplit))
neg_indexes = random.sample(
range(1, len(neg_locations)),
int(data_size * (1. - self.__classSplit)))
pos_locations_selected = []
for ind in pos_indexes:
pos_locations_selected.append(pos_locations[ind])
neg_locations_selected = []
for ind in neg_indexes:
neg_locations_selected.append(neg_locations[ind])
pos_locations = pos_locations_selected
neg_locations = neg_locations_selected
images = []
labels = []
total_files_to_read = len(pos_locations) + len(neg_locations)
for ind, label_enry in enumerate(pos_locations):
filename = os.path.join(self.__imagesFolderPath, label_enry[0])
try:
# im = ndimage.imread(filename, True, 'L')
im = cv2.imread(filename,
cv2.IMREAD_GRAYSCALE).astype(np.float32)
im = hist_match(im, hist_template)
im = misc.imresize(im, (conf.IMAGE_X_DIM, conf.IMAGE_Y_DIM),
'bilinear')
im = image_preprocessing(im)
im = im.reshape(conf.IMAGE_X_DIM, conf.IMAGE_Y_DIM, 1)
images.append(im)
labels.append(
self.__encode_chestx_label(label_enry[1],
conf.POSITIVE_LABELS,
conf.NEGATIVE_LABELS))
printProgressBar(ind + 1,
total_files_to_read,
prefix='Loaded files:',
suffix='Complete',
length=50)
except (FileNotFoundError, OSError, AttributeError):
print('Missing {0}'.format(str(filename)))
except ValueError as e:
print('Value error: ' + str(e))
for ind, label_enry in enumerate(neg_locations):
filename = os.path.join(self.__imagesFolderPath, label_enry[0])
try:
# im = ndimage.imread(filename, True, 'L')
im = cv2.imread(filename,
cv2.IMREAD_GRAYSCALE).astype(np.float32)
im = hist_match(im, hist_template)
im = misc.imresize(im, (conf.IMAGE_X_DIM, conf.IMAGE_Y_DIM),
'bilinear')
im = image_preprocessing(im)
im = im.reshape(conf.IMAGE_X_DIM, conf.IMAGE_Y_DIM, 1)
images.append(im)
labels.append(0)
printProgressBar(len(pos_locations) + ind + 1,
total_files_to_read,
prefix='Loaded files:',
suffix='Complete',
length=50)
except (FileNotFoundError, OSError, AttributeError):
print('Missing {0}'.format(str(filename)))
except ValueError as e:
print('Value error: ' + str(e))
# locations = pos_locations + neg_locations
images, labels = shuffle(images, labels)
x = np.asarray(images)
x = x.reshape(-1, conf.IMAGE_X_DIM, conf.IMAGE_Y_DIM,
1).astype('float32')
y = np.asarray(labels)
y = to_categorical(y, conf.NUM_CLASSES)
return x, y
def __init__(self, params, variables):
"""
Initializes all necessary components of the TensorFlow
Graph.
"""
# Assign required variables first
self.varsM = variables
'''
https://github.com/mbrufau7/tfm_food_segm/blob/master/W_net_Unsupervised_%26_Centroid_Loss_1_2.ipynb
'''
# INITIALIZE GRAPH
self.graph = tf.Graph()
with self.graph.as_default():
self.n_input_variables = len(self.varsM)
# Placeholders
#self.input_images = tf.placeholder(tf.float32, shape=(None, None,None,None, self.n_input_variables),
# name='input_images')
self.input_images = tf.placeholder(tf.float32,
shape=(None, None,
self.n_input_variables),
name='input_images')
self.z_voxels = tf.placeholder(tf.int32, name='z_voxels')
self.y_voxels = tf.placeholder(tf.int32, name='y_voxels')
self.x_voxels = tf.placeholder(tf.int32, name='x_voxels')
self.phase = tf.placeholder(tf.bool, name='phase')
self.keep_prob = tf.placeholder(tf.float32, name='keep_prob')
params_z_proc = params.image_params.CROP_PAD_IMAGE_Z
params_y_proc = params.image_params.CROP_PAD_IMAGE_Y
params_x_proc = params.image_params.CROP_PAD_IMAGE_X
# shape = tf.shape(self.input_images)
self.org_x = self.x_voxels # shape[3]
self.org_y = self.y_voxels # shape[2]
self.org_z = self.z_voxels # shape[1]
self.input_processed = image_preprocessing(
self.input_images, params_z_proc, params_y_proc, params_x_proc,
self.n_input_variables, self.org_z, self.org_y, self.org_x)
# Global step - feed it in so no incrementing necessary
# self.global_step_m = tf.placeholder(tf.int32)
global_step = tf.Variable(0.0, trainable=False)
def shape_so(tensor):
# s = tensor.get_shape()
# return tuple([s[i].value for i in range(0,len(s))])
return tuple([d.value for d in tensor.get_shape()])
def conv_block(inputs,
filters,
prev_filters,
kernel,
activation,
phase,
dil_rate,
tag=None):
# @TODO 'channels_last' is default? is this acutally a separable conv
net_2 = tf.layers.conv3d(
inputs,
filters,
kernel,
strides=[1, 1, 1],
dilation_rate=dil_rate,
padding='SAME',
activation=activation,
kernel_initializer=keras.initializers.he_normal(),
data_format='channels_last',
name=name_tag('conv3d_1', tag))
# net_2 = tf.layers.max_pooling3d(net_2, pool_size=kernel, strides = [1, 1, 1],
# padding = 'SAME', data_format='channels_last',
# name=name_tag('max_pooling3d', tag))
net_2 = tf.layers.conv3d(
net_2,
filters,
kernel,
strides=[1, 1, 1],
dilation_rate=[1, 1, 1],
padding='SAME',
activation=activation,
kernel_initializer=keras.initializers.he_normal(),
data_format='channels_last',
name=name_tag('conv3d_2', tag))
net_2 = tf.layers.max_pooling3d(net_2,
pool_size=kernel,
strides=[2, 2, 2],
padding='SAME',
data_format='channels_last',
name=name_tag(
'max_pooling3d', tag))
# net_2 = tf.layers.batch_normalization(net_2, center=True, scale=True, training=phase
# ,name=name_tag('batch_norm', tag)
# net_2 = tf.layers.dropout(net_2,rate=0.20, training=phase,
# name=name_tag('dropout', tag))
return net_2
def deconv_block(inputs,
filters,
prev_filters,
kernel,
activation,
phase,
dil_rate,
tag=None):
''' @TODO 'channels_last' is default? is this acutally a separable conv.
W-Net : https://arxiv.org/pdf/1711.08506.pdf
U-Net : https://arxiv.org/pdf/1505.04597.pdf
U-ENC for W-Net should be:
depthwise separable conv -> depthwise separable conv -> dconv
One important modification in our architecture is that all of the modules use the depthwise
separable convolution layers introduced in U-Net except modules 1, 9, 10, and 18.
A depthwise separable convolution operation consists of a depthwise convolution and a
pointwise convolution. The idea behind such an operation is to examine spatial
cor-relations and cross-channel correlations independently a depthwise convolution performs
spatial convolutions independently over each channel and then a pointwise convolution projects
the feature channels by the depthwise convolution onto a new channel space. As a consequence,
the network gains performance more efficiently with the same number of parameters.
'''
# net_3 = tf.layers.conv3d(inputs, filters, kernel, strides=[1, 1,1], dilation_rate=[1, 1, 1],
# padding='SAME', activation=activation,
# kernel_initializer=keras.initializers.he_normal() ,
# data_format='channels_last')
net_3 = tf.layers.conv3d_transpose(
inputs,
filters,
kernel,
strides=[2, 2, 2],
padding='SAME',
activation=activation,
kernel_initializer=keras.initializers.he_normal(),
data_format='channels_last',
name=name_tag('dconv3d', tag))
# net_3 = tf.layers.max_pooling3d(net_3, pool_size=kernel,
# strides = [1, 1, 1], padding = 'SAME', data_format='channels_last')
net_3 = tf.layers.conv3d(
net_3,
filters,
kernel,
strides=[1, 1, 1],
padding='SAME',
activation=activation,
kernel_initializer=keras.initializers.he_normal(),
data_format=
'channels_last', # @TODO: conv or separable conv?
name=name_tag('conv3d', tag))
net_3 = tf.layers.max_pooling3d(net_3,
pool_size=kernel,
strides=[1, 1, 1],
padding='SAME',
data_format='channels_last',
name=name_tag(
'max_pooling3d', tag))
# net_3 = tf.layers.batch_normalization(net_3, center=True, scale=True, training=phase)
# net_3 = tf.layers.dropout(net_3,rate=0.20, training=phase)
return net_3
def middle_block(inputs,
filters,
prev_filters,
kernel,
activation,
phase,
tag=None):
net_1 = tf.layers.conv3d(
inputs,
filters,
kernel,
strides=[1, 1, 1],
dilation_rate=[1, 1, 1],
padding='SAME',
activation=activation,
kernel_initializer=keras.initializers.lecun_normal(),
data_format='channels_last',
name=name_tag('conv3d_1', tag))
# net_1 = tf.layers.max_pooling3d(net_1, pool_size=kernel,
# strides = [1, 1, 1], padding = 'SAME', data_format='channels_last',
# name=name_tag('max_pooling3d', tag))
net_1 = tf.layers.conv3d(
net_1,
filters,
kernel,
strides=[1, 1, 1],
dilation_rate=[1, 1, 1],
padding='SAME',
activation=activation,
kernel_initializer=keras.initializers.he_normal(),
data_format='channels_last',
name=name_tag('conv3d_2', tag))
net_1 = tf.layers.max_pooling3d(net_1,
pool_size=kernel,
strides=[1, 1, 1],
padding='SAME',
name=name_tag(
'max_pooling3d', tag))
# net_1 = tf.layers.batch_normalization(net_1, center=True, scale=True, training=phase)
# net_1 = tf.layers.dropout(net_1,rate=0.20, training=phase)
return net_1
def middle_block_fc(inputs,
filters,
prev_filters,
kernel,
activation,
phase,
tag=None):
net_1 = tf.layers.conv3d(
inputs,
filters,
kernel,
strides=[1, 1, 1],
padding='SAME',
activation=activation,
kernel_initializer=keras.initializers.he_normal(),
name=name_tag('conv3d_1', tag))
net_1 = tf.layers.flatten(net_1)
# @TODO refactor hardcoded dimensions? 6, 12, 6 = 432
net_1 = tf.layers.dense(
net_1,
432,
activation=activation,
kernel_initializer=keras.initializers.lecun_normal(),
name=name_tag('fc', tag))
# @TODO refactor hardcoded dimensions? 6, 12, 6 = 432
net_1 = tf.reshape(net_1,
shape=(-1, 6, 12, 6, 1),
name=name_tag('reshape', tag))
net_1 = tf.layers.conv3d(
net_1,
prev_filters,
kernel,
strides=[1, 1, 1],
padding='SAME',
activation=activation,
kernel_initializer=keras.initializers.he_normal(),
name=name_tag('conv3d_2', tag))
# net_1 = tf.layers.batch_normalization(net_1, center=True, scale=True, training=phase
# name=name_tag('bn', tag))
# net_1 = tf.layers.dropout(net_1,rate=0.20, training=phase
# name=name_tag('dropout', tag))
return net_1
def wnet(inputs, z, y, x, phase, keep_prob, params,
n_input_variables):
# encoder
with tf.name_scope("U-encoder") as scope:
print('inputs {}', shape_so(inputs))
net_e1_1 = conv_block(
inputs,
filters=params.graph_params.LAYER_1,
prev_filters=params.graph_params.LAYER_1,
kernel=params.graph_params.KERNEL1,
activation=tf.nn.leaky_relu,
phase=phase,
dil_rate=[1, 1, 1],
tag='uenc_conv_block_1')
print('e1_1 {}', shape_so(net_e1_1))
net_e2_1 = conv_block(
net_e1_1,
filters=params.graph_params.LAYER_2,
prev_filters=params.graph_params.LAYER_2,
kernel=params.graph_params.KERNEL1,
activation=tf.nn.leaky_relu,
phase=phase,
dil_rate=[1, 1, 1],
tag='uenc_conv_block_2')
# print('e2_1 {}',shape_so(net_e2_1))
net_e3_1 = conv_block(
net_e2_1,
filters=params.graph_params.LAYER_3,
prev_filters=params.graph_params.LAYER_3,
kernel=params.graph_params.KERNEL2,
activation=tf.nn.leaky_relu,
phase=phase,
dil_rate=[1, 1, 1],
tag='uenc_conv_block_3')
print('e3_1 {}', shape_so(net_e3_1))
## middle layer
# inputs,filters,prev_filters,kernel,activation,phase
net_m1_1 = middle_block(
net_e3_1,
filters=params.graph_params.LAYER_4,
prev_filters=params.graph_params.LAYER_3,
kernel=params.graph_params.KERNEL2,
activation=tf.nn.leaky_relu,
phase=phase,
tag='uenc_conv_middle_block_4')
print('m1_1 {}', shape_so(net_m1_1))
# net_c3_1 = tf.concat([net_m1_1, net_e3_1], axis=-1)
# inputs,filters,prev_filters,kernel,activation,phase,dil_rate
net_d3_1 = deconv_block(
net_m1_1,
filters=params.graph_params.LAYER_3,
prev_filters=params.graph_params.LAYER_2,
kernel=params.graph_params.KERNEL2,
activation=tf.nn.leaky_relu,
phase=phase,
dil_rate=[1, 1, 1],
tag='uenc_dconv_block_5')
# net_c2_1 = tf.concat([net_d3_1, net_e2_1], axis=-1) #
net_d2_1 = deconv_block(
net_d3_1,
filters=params.graph_params.LAYER_2,
prev_filters=params.graph_params.LAYER_1,
kernel=params.graph_params.KERNEL1,
activation=tf.nn.leaky_relu,
phase=phase,
dil_rate=[1, 1, 1],
tag='uenc_dconv_block_6')
# net_c1_1 = tf.concat([net_d2_1,net_e1_1], axis=-1) #
net_d1_1 = deconv_block(net_d2_1,
params.graph_params.LAYER_1,
params.graph_params.LAYER_1,
params.graph_params.KERNEL1,
tf.nn.leaky_relu,
phase, [1, 1, 1],
tag='uenc_dconv_block_7')
# net_d1_1 = tf.layers.batch_normalization(net_d1_1, center=True, scale=True,
# training=phase, momentum=0.90)
# final layer for first U
# net_c0_1 = tf.concat([net_d1_1,net_a], axis=-1)
net_feed = tf.layers.conv3d(
net_d1_1,
params.graph_params.N_CLASSES,
params.graph_params.KERNEL2,
dilation_rate=[1, 1, 1],
strides=[1, 1, 1],
padding='SAME',
activation=tf.nn.softmax,
kernel_initializer=keras.initializers.he_normal(),
data_format='channels_last',
name=name_tag('conv3d_final_layer',
'uenc_conv_block_7'))
# net_feed = tf.nn.softmax(net_feed, axis=4)
# decoder
with tf.name_scope("U-decoder"):
net_d_1 = tf.layers.conv3d(net_feed,
params.graph_params.LAYER_1,
params.graph_params.KERNEL1,
dilation_rate=[1, 1, 1],
strides=[1, 1, 1],
padding='SAME',
activation=tf.nn.leaky_relu,
name=name_tag(
'conv3d_first_layer',
'udec_conv_block_1'))
# inputs,filters,prev_filters,kernel,activation,phase,dil_rate,tag = None
net_de1_1 = conv_block(
net_d_1,
filters=params.graph_params.LAYER_1,
prev_filters=params.graph_params.LAYER_1,
kernel=params.graph_params.KERNEL1,
activation=tf.nn.leaky_relu,
phase=phase,
dil_rate=[1, 1, 1],
tag='udec_conv_block_1')
# net_bridge1 = tf.concat([net_de1_1,net_e1_1], axis=-1)
net_de2_1 = conv_block(
net_de1_1,
filters=params.graph_params.LAYER_2,
prev_filters=params.graph_params.LAYER_2,
kernel=params.graph_params.KERNEL1,
activation=tf.nn.leaky_relu,
phase=phase,
dil_rate=[1, 1, 1],
tag='udec_conv_block_2')
# net_bridge2 = tf.concat([net_de2_1,net_e2_1], axis=-1)
net_de3_1 = conv_block(net_de2_1,
params.graph_params.LAYER_3,
params.graph_params.LAYER_3,
params.graph_params.KERNEL2,
tf.nn.leaky_relu,
phase, [1, 1, 1],
tag='udec_conv_block_3')
# net_bridge3 = tf.concat([net_de3_1,net_e3_1], axis=-1)
## middle layer
# net_cA = tf.concat([net_de3_1, net_m1_1], axis=-1)
net_dm1_1 = middle_block(net_de3_1,
params.graph_params.LAYER_4,
params.graph_params.LAYER_3,
params.graph_params.KERNEL2,
tf.nn.leaky_relu,
phase,
tag='udec_conv_middle_block_4')
# net_dc3_1 = tf.concat([net_dm1_1, net_de3_1], axis=-1) # #net_e3_1 , net_m1_1
net_dd3_1 = deconv_block(net_dm1_1,
params.graph_params.LAYER_3,
params.graph_params.LAYER_2,
params.graph_params.KERNEL2,
tf.nn.leaky_relu,
phase, [1, 1, 1],
tag='udec_dconv_block_5')
# net_dc2_1 = tf.concat([net_dd3_1, net_de2_1], axis=-1) # #net_e2_1, , neprint(total_out[1].get_shape())t_d3_1
net_dd2_1 = deconv_block(net_dd3_1,
params.graph_params.LAYER_2,
params.graph_params.LAYER_1,
params.graph_params.KERNEL1,
tf.nn.leaky_relu,
phase, [1, 1, 1],
tag='udec_dconv_block_6')
# net_dc1_1 = tf.concat([net_dd2_1,net_de1_1], axis=-1) # #net_e1_1 , net_d2_1
net_dd1_1 = deconv_block(net_dd2_1,
params.graph_params.LAYER_1,
params.graph_params.LAYER_1,
params.graph_params.KERNEL1,
tf.nn.leaky_relu,
phase, [1, 1, 1],
tag='udec_dconv_block_7')
# net_dd1_1 = tf.layers.batch_normalization(net_dd1_1, center=True, scale=True, training=phase, momentum=0.90)
# final layer for second U
# net_t = tf.concat([net_dd1_1, net_feed], axis=-1)
net_r = tf.layers.conv3d(
net_dd1_1,
n_input_variables,
params.graph_params.KERNEL2,
dilation_rate=[1, 1, 1],
strides=[1, 1, 1],
padding='SAME',
activation=tf.nn.leaky_relu,
kernel_initializer=keras.initializers.he_normal(),
name=name_tag('conv3d_final_layer',
'udec_conv_block_7'))
return net_feed, net_r
# Network
total_out = wnet(self.input_processed,
params.image_params.CROP_PAD_IMAGE_Z,
params.image_params.CROP_PAD_IMAGE_Y,
params.image_params.CROP_PAD_IMAGE_X, self.phase,
self.keep_prob, params, self.n_input_variables)
print(total_out[0].get_shape())
print(total_out[1].get_shape())
wnet_categories = total_out[0]
predictionsOut_1 = tf.argmax(wnet_categories, axis=4)
predictionsOut_1 = tf.expand_dims(predictionsOut_1, axis=4)
predictionsOut_1 = tf.reshape(
predictionsOut_1,
shape=(-1, params.image_params.CROP_PAD_IMAGE_X,
params.image_params.CROP_PAD_IMAGE_Y,
params.image_params.CROP_PAD_IMAGE_Z, 1))
# @TODO is this the how depthwise separable conv is being handled?
predictionsOut_1 = tf.transpose(
predictionsOut_1, perm=[0, 3, 2, 1,
4]) # @TODO Parameterize these
predictionsOut_1 = tf_crop_or_pad_along_axis(
predictionsOut_1, self.org_z, 1)
predictionsOut_1 = tf_crop_or_pad_along_axis(
predictionsOut_1, self.org_y, 2)
predictionsOut_1 = tf_crop_or_pad_along_axis(
predictionsOut_1, self.org_x, 3)
# predictionsOut_1 = tf.transpose(predictionsOut_1, perm = [0,3,2,1,4])
predictionsOut_1 = tf.reshape(predictionsOut_1,
shape=(-1, self.org_z, self.org_y,
self.org_x))
predictionsOut = tf.reshape(tf.cast(predictionsOut_1, tf.int64),
shape=(-1, self.org_x * self.org_y *
self.org_z),
name='outputs')
probs = tf.identity(
wnet_categories, name='probs'
) # tf.nn.softmax(wnet_categories, axis=2, name = 'probs')
## decoder - output
wnet_original = tf.identity(total_out[1], name='decoder_outputs')
original_image = tf.identity(self.input_processed,
name='encoder_inputs')
unprocessed_image = tf.identity(self.input_images,
name='process_inputs')
loss_dec = tf.losses.mean_squared_error(self.input_processed,
wnet_original)
print(loss_dec.get_shape())
loss_enc = tf.map_fn(
elems=np.arange(params.runtime_params.BATCH_SIZE),
fn=lambda i: centroids_similarity_loss(
self.input_processed[i, :, :, :, :], wnet_categories[
i, :, :, :, :], params.image_params.CROP_PAD_IMAGE_Z,
params.image_params.CROP_PAD_IMAGE_Y, params.image_params.
CROP_PAD_IMAGE_X, params.graph_params.N_CLASSES, self.
n_input_variables),
dtype=(tf.float32))
print(loss_enc.get_shape())
self.loss_decf = tf.reduce_sum(
loss_dec) # + tf.reduce_sum(loss_enc)
self.loss_encf = tf.reduce_sum(loss_enc)
# Training operations
learning_rate = tf.train.cosine_decay_restarts(
learning_rate=0.0001,
global_step=global_step,
first_decay_steps=10,
t_mul=2.0,
m_mul=1.0,
alpha=0.01)
trainer = tf.train.AdamOptimizer(learning_rate)
self.saver = tf.train.Saver(max_to_keep=1000)
self.update_ops = tf.get_collection(tf.GraphKeys.UPDATE_OPS)
with tf.control_dependencies(self.update_ops):
# self.training_step_add = trainer.minimize(self.loss_misc)
self.training_step_enc = trainer.minimize(self.loss_encf)
self.training_step_dec = trainer.minimize(self.loss_decf)
y_test) = setup_finetuning(baseline,
classes,
dataset,
noise,
mean=0.0,
std=15.0)
print('Loaded baseline!')
# Validation splitting
(X_train_noisy, y_train), (X_valid_noisy,
y_valid) = dataset_split(X_train_noisy,
y_train,
return_data='samples')
# Image pre-processing: scale pixel values
X_train_noisy_sc, X_mean, X_std = image_preprocessing(X_train_noisy,
scale_only=False)
X_valid_noisy_sc, _, _ = image_preprocessing(X_valid_noisy,
seq_mean=X_mean,
seq_std=X_std,
scale_only=False)
X_test_noisy_sc, _, _ = image_preprocessing(X_test_noisy,
seq_mean=X_mean,
seq_std=X_std,
scale_only=False)
# Dataloaders
train_noisy_dl = get_data_loader(X_train_noisy_sc, y_train, shuffle=True)
valid_noisy_dl = get_data_loader(X_valid_noisy_sc, y_valid, shuffle=True)
test_noisy_dl = get_data_loader(X_test_noisy_sc, y_test, shuffle=True)
# Writer