def max_depool(self,
in_layer=None,
depth_factor=2,
height_factor=2,
width_factor=2):
if in_layer == None:
in_layer = self.layer
#if 1: # alt with deconv
#lo, li = self.deconvolutional_layer(1, [1,1], None, stride=[2,2], name="g_D1", reuse=reuse, batch_norm=use_batch_norm, train=train)
#return lo
'''
if len(self.layer.get_shape()) == 4:
outWidth = in_layer.get_shape()[2] * window_stride[0] + window_size[0] - window_stride[0]
outHeight = in_layer.get_shape()[1] * window_stride[1] + window_size[1] - window_stride[1]
self.layer = tf.image.resize_images(in_layer, [int(outHeight), int(outWidth)], 1) #1 = ResizeMethod.NEAREST_NEIGHBOR
print("Max Depool {}: {}".format(window_size, self.layer.get_shape()))
'''
if len(self.layer.get_shape()) == 4:
#self.layer = tf.contrib.keras.backend.resize_images(self.layer, height_factor, width_factor, 'channels_last')
self.layer = kb.resize_images(self.layer, height_factor,
width_factor, 'channels_last')
print("Max Depool : {}".format(self.layer.get_shape()))
if len(self.layer.get_shape()) == 5:
#self.layer = tf.contrib.keras.backend.resize_volumes(self.layer, depth_factor, height_factor, width_factor, 'channels_last')
self.layer = kb.resize_volumes(self.layer, depth_factor,
height_factor, width_factor,
'channels_last')
print("Max Depool : {}".format(self.layer.get_shape()))
return self.layer
def call(self, x, mask=None):
output = K.resize_volumes(x, self.size[0], self.size[1], self.size[2],
self.dim_ordering)
f = K.gradients(K.sum(self._master_layer.output),
self._master_layer.input) * output
return f
def call(self, x, mask=None):
# TODO: implement for dim_ordering='tf'
img = K.resize_volumes(x, self.size[0], self.size[1], self.size[2],
self.dim_ordering)
padded = T.zeros((img.shape[0], img.shape[1], self.shape[0],
self.shape[1], self.shape[2]))
padded = T.set_subtensor(
padded[:, :, :img.shape[2], :img.shape[3], :img.shape[4]], img)
return T.switch(self.ind, padded, T.zeros_like(padded))
def max_depool(self,
in_layer=None,
depth_factor=2,
height_factor=2,
width_factor=2):
if in_layer == None:
in_layer = self.layer
if len(self.layer.get_shape()) == 4:
self.layer = kb.resize_images(self.layer, height_factor,
width_factor, 'channels_last')
print("Max Depool : {}".format(self.layer.get_shape()))
if len(self.layer.get_shape()) == 5:
self.layer = kb.resize_volumes(self.layer, depth_factor,
height_factor, width_factor,
'channels_last')
print("Max Depool : {}".format(self.layer.get_shape()))
return self.layer
def m_maxpool3d(x, pool_size, strides=(1, 1, 1), border_mode='valid',
dim_ordering='th'):
if border_mode == 'same':
# TODO: add implementation for border_mode="same"
raise Exception('border_mode="same" not supported with Theano.')
elif border_mode == 'valid':
ignore_border = True
padding = (0, 0)
else:
raise Exception('Invalid border mode: ' + str(border_mode))
if dim_ordering not in {'th', 'tf'}:
raise Exception('Unknown dim_ordering ' + str(dim_ordering))
if dim_ordering == 'tf':
x = x.dimshuffle((0, 4, 1, 2, 3))
# TODO: check dimensions manipulations
# pooling over conv_dim2, conv_dim1 (last two channels)
out_shape = x.shape
output, ind1 = m_maxpool_2d_op(input=x,
ds=(pool_size[1], pool_size[2]),
st=(strides[1], strides[2]),
ignore_border=ignore_border,
padding=padding)
# pooling over conv_dim3
pool_out, ind2 = m_maxpool_2d_op(input=output.dimshuffle(0, 1, 4, 3, 2),
ds=(1, pool_size[0]),
st=(1, strides[0]),
ignore_border=ignore_border,
padding=padding)
pool_out = pool_out.dimshuffle(0, 1, 4, 3, 2)
ind2 = ind2.dimshuffle(0, 1, 4, 3, 2)
ind2 = K.resize_volumes(ind2, 1, pool_size[1], pool_size[2], dim_ordering)
padded_ind2 = T.zeros(out_shape)
padded_ind2 = T.set_subtensor(padded_ind2[:, :, :ind2.shape[2], :ind2.shape[3], :ind2.shape[4]], ind2)
ind = padded_ind2 * ind1
if dim_ordering == 'tf':
pool_out = pool_out.dimshuffle((0, 2, 3, 4, 1))
return pool_out, ind
def adjust(x, depth_factor, height_factor, width_factor, reps):
x = K.resize_volumes(x, depth_factor, height_factor, width_factor,
'channels_last')
x = K.repeat_elements(x, rep=reps, axis=-1)
return x
def call(self, inputs):
return K.resize_volumes(inputs, self.size[0], self.size[1],
self.size[2], self.data_format)
def call(self, x, mask=None):
# TODO: implement for dim_ordering='tf'
img = K.resize_volumes(x, self.size[0], self.size[1], self.size[2], self.dim_ordering)
padded = T.zeros((img.shape[0], img.shape[1], self.shape[0], self.shape[1], self.shape[2]))
padded = T.set_subtensor(padded[:, :, :img.shape[2], :img.shape[3], :img.shape[4]], img)
return T.switch(self.ind, padded, T.zeros_like(padded))
def main():
# mirrored_strategy = tf.distribute.MirroredStrategy()
# with mirrored_strategy.scope():
# with tf.compat.v1.Session(config=tf_config) as sess:
tfrecords_test_vol_filename = DATA_DIR + '/output/fmri/tf_data/XXX.tfrecords'
# train
# tfrecords_tr_vol_filename = DATA_DIR + '/output/fmri/tf_data/train_data_vol.tfrecords'
# validation
# tfrecords_val_vol_filename = DATA_DIR + '/output/fmri/tf_data/val_data_vol.tfrecords'
global batch_cost
inputs_ = tf.compat.v1.placeholder(tf.float32, input_shape, name='inputs')
targets_ = tf.compat.v1.placeholder(tf.float32, input_shape, name='targets')
# encoder
print('shape input:', inputs_.shape)
conv1 = tf.keras.layers.Conv3D(
filters=16, kernel_size=(3, 3, 3), strides=stride, padding=padding, activation=tf.nn.relu)(inputs_)
maxpool1 = tf.keras.layers.MaxPool3D(
pool_size=(2, 2, 2), strides=(3, 2, 2), padding=padding)(conv1)
print('shape maxpool1:', maxpool1.shape)
conv2 = tf.keras.layers.Conv3D(
filters=32, kernel_size=(3, 3, 3), strides=stride, padding=padding, activation=tf.nn.relu)(maxpool1)
maxpool2 = tf.keras.layers.MaxPool3D(
pool_size=(2, 2, 2), strides=(3, 3, 2), padding=padding)(conv2)
print('shape:maxpool2', maxpool2.shape)
conv3 = tf.keras.layers.Conv3D(
filters=96, kernel_size=(2, 2, 2), strides=stride, padding=padding, activation=tf.nn.relu)(maxpool2)
maxpool3 = tf.keras.layers.MaxPool3D(
pool_size=(2, 2, 2), strides=(1, 1, 2), padding=padding)(conv3)
print('shape maxpool3:', maxpool3.shape)
# decoder
unpool1 = K.resize_volumes(maxpool3, 1, 1, 2, "channels_last")
deconv1 = tf.keras.layers.Conv3DTranspose(filters=96, kernel_size=(2, 2, 2), strides=stride,
padding=padding, activation=tf.nn.relu)(unpool1)
print('shape deconv1:', deconv1.shape)
unpool2 = K.resize_volumes(deconv1, 3, 3, 2, "channels_last")
deconv2 = tf.keras.layers.Conv3DTranspose(filters=32, kernel_size=(3, 3, 3), strides=stride,
padding=padding, activation=tf.nn.relu)(unpool2)
print('shape deconv2:', deconv2.shape)
# (64, 24, 48, 32, 32)
unpool3 = K.resize_volumes(deconv2, 3, 2, 2, "channels_last")
deconv3 = tf.keras.layers.Conv3DTranspose(filters=16, kernel_size=(3, 3, 3), strides=stride,
padding=padding, activation=tf.nn.relu)(unpool3)
print('shape deconv3:', deconv3.shape)
# (64, 72, 96, 64, 16)
output = tf.keras.layers.Dense(
units=1, activation=None)(deconv3)
print(output.shape)
output = tf.reshape(output, input_shape)
loss = tf.divide(tf.norm(tf.subtract(targets_, output), ord='fro', axis=[1, 2]),
tf.norm(targets_, ord='fro', axis=[1, 2]))
# loss = tf.divide(tf.norm(tf.subtract(targets_, output), ord='fro', axis=[-2, -1]),
# tf.norm(targets_, ord='fro', axis=[-2, -1]))
cost = tf.reduce_mean(loss)
opt = tf.compat.v1.train.AdamOptimizer(learning_rate).minimize(cost)
# output shape = input shape
all_saver = tf.compat.v1.train.Saver(max_to_keep=None)
# initializing a saver to save weights
# enc_saver = tf.compat.v1.train.Saver({'conv1': conv1, 'maxpool1': maxpool1,
# 'conv2': conv2, 'maxpool2': maxpool2, 'conv3': conv3, 'maxpool3': maxpool3})
# initializing a restorer to restore weights
# res_saver = tf.compat.v1.train.import_meta_graph(ws_path+'weights.meta')
# summary nodes
# tf.summary.scalar("loss", loss)
tf.summary.scalar("cost", cost)
tf.summary.histogram("conv1", conv1)
# tf.summary.histogram("conv1_1", conv1_1)
tf.summary.histogram("maxpool1", maxpool1)
tf.summary.histogram("conv2", conv2)
tf.summary.histogram("maxpool2", maxpool2)
tf.summary.histogram("conv3", conv3)
tf.summary.histogram("maxpool3", maxpool3)
# tf.summary.histogram("conv4", conv4)
# tf.summary.histogram("deconv4", deconv4)
tf.summary.histogram("unpool3", unpool3)
tf.summary.histogram("deconv3", deconv3)
tf.summary.histogram("unpool2", unpool2)
tf.summary.histogram("deconv2", deconv2)
tf.summary.histogram("unpool1", unpool1)
# tf.summary.histogram("deconv1_1", deconv1_1)
tf.summary.histogram("deconv1", deconv1)
# summary operation and a writer to save it.
summary_op = tf.compat.v1.summary.merge_all()
writer = tf.compat.v1.summary.FileWriter(logs_path, graph=tf.compat.v1.get_default_graph())
# end of tensorflow graph
# start of training
counter = 0
try:
sess = tf.compat.v1.Session()
# making operation-variables to run our methods whenever needed during training
# coordinator and queue runners to manage parallel sampling of batches from the input pipeline
coord = tf.compat.v1.train.Coordinator()
threads = tf.compat.v1.train.start_queue_runners(sess=sess, coord=coord)
while not coord.should_stop():
# fetching a batch
fetch_op_tr = input_pipeline(tfrecords_test_vol_filename)
nvol = sess.run(fetch_op_tr)
batch_cost, _ = sess.run([cost, opt],
feed_dict={inputs_: nvol + noise_factor * np.random.randn(*nvol.shape),
targets_: nvol})
# loss function, optimizer and a saver to save weights&biases
print('\nEpoch\t' + str(counter + 1) + '/' + str(n_epochs))
# # print(n_batches) 5670
for i in range(n_batches):
# if i % 1000 == 0:
# print("batch_cost:", batch_cost)
print('\r' + str(((i + 1) * 100) / n_batches) + '%', sys.stdout.flush())
counter = counter + 1
# print("Epoch: {}/{}...".format(counter, n_epochs), "Training loss: {:.4f}".format(batch_cost))
# save weights and biases of the model
all_saver.save(sess, ws_path + "model.ckpt", global_step=counter)
# save weights and biases of the encoder
# enc_saver.save(sess, ws_path + "enc.ckpt", global_step=counter)
print('Weights saved')
# saving summary
# summary, _ = sess.run([summary_op, opt], feed_dict={inputs_: nvol, targets_: nvol})
# writer.add_summary(summary, counter)
print('Summary saved')
if counter >= n_epochs:
break
# checking validation error
# vol = sess.run(fetch_op_val)
# nvol = np.asarray(vol)
# batch_cost, _ = sess.run([cost, opt], feed_dict={inputs_: nvol, targets_: nvol})
# print('Validation error' + str(batch_cost))
except tf.errors.OutOfRangeError:
print('Done training -- epoch limit reached')
finally:
coord.request_stop()
coord.join(threads)
sess.close()
def main():
# start of tensorflow graph
# input and target placeholders
global nvol, batch_cost
# print("input_shape:", input_shape)
# inputs_ = tf.Variable(shape=input_shape, name="inputs")
# targets_ = tf.Variable(shape=input_shape, name="targets")
inputs_ = tf.placeholder(tf.float32, input_shape, name='inputs')
targets_ = tf.placeholder(tf.float32, input_shape, name='targets')
conv1 = tf.keras.layers.Conv3D(
filters=16, kernel_size=(3, 3, 3), strides=stride, padding=padding, activation=tf.nn.relu)(inputs_)
maxpool1 = tf.keras.layers.MaxPool3D(
pool_size=(2, 2, 2), strides=(3, 2, 2), padding=padding)(conv1)
# print('shape maxpool1:', maxpool1.shape)
conv2 = tf.keras.layers.Conv3D(
filters=32, kernel_size=(3, 3, 3), strides=stride, padding=padding, activation=tf.nn.relu)(maxpool1)
maxpool2 = tf.keras.layers.MaxPool3D(
pool_size=(2, 2, 2), strides=(3, 3, 2), padding=padding)(conv2)
# print('shape:maxpool2', maxpool2.shape)
conv3 = tf.keras.layers.Conv3D(
filters=96, kernel_size=(2, 2, 2), strides=stride, padding=padding, activation=tf.nn.relu)(maxpool2)
maxpool3 = tf.keras.layers.MaxPool3D(
pool_size=(2, 2, 2), strides=(1, 1, 2), padding=padding)(conv3)
# print('shape maxpool3:', maxpool3.shape)
# decoder
unpool1 = K.resize_volumes(maxpool3, 1, 1, 2, "channels_last")
deconv1 = tf.keras.layers.Conv3DTranspose(filters=96, kernel_size=(2, 2, 2), strides=stride,
padding=padding, activation=tf.nn.relu)(unpool1)
# print('shape deconv1:', deconv1.shape)
unpool2 = K.resize_volumes(deconv1, 3, 3, 2, "channels_last")
deconv2 = tf.keras.layers.Conv3DTranspose(filters=32, kernel_size=(3, 3, 3), strides=stride,
padding=padding, activation=tf.nn.relu)(unpool2)
# print('shape deconv2:', deconv2.shape)
# (64, 24, 48, 32, 32)
unpool3 = K.resize_volumes(deconv2, 3, 2, 2, "channels_last")
deconv3 = tf.keras.layers.Conv3DTranspose(filters=16, kernel_size=(3, 3, 3), strides=stride,
padding=padding, activation=tf.nn.relu)(unpool3)
# print('shape deconv3:', deconv3.shape)
# (64, 72, 96, 64, 16)
output = tf.keras.layers.Dense(
units=1, activation=None)(deconv3)
loss = tf.divide(tf.norm(tf.subtract(targets_, output), ord='fro', axis=[0, -1]),
tf.norm(targets_, ord='fro', axis=[0, -1]))
# print(loss.shape)
print("loss:", loss)
cost = tf.reduce_mean(loss, name='loss')
# print(cost)
print("cost:", cost)
opt = tf.train.AdamOptimizer(learning_rate).minimize(cost)
print("opt:", opt)
all_saver = tf.train.Saver(max_to_keep=None)
# conv1_v = tf.assign("conv1_v", conv1)
# maxpool1_v = tf.assign("maxpool1_v", maxpool1)
# conv2_v = tf.assign("conv2_v", conv2)
# maxpool2_v = tf.assign("maxpool2_v", maxpool2)
# conv3_v = tf.assign("conv3_v", conv3)
# maxpool3_v = tf.assign("maxpool3_v", maxpool3)
# enc_saver = tf.train.Saver({'conv1': conv1, 'maxpool1': maxpool1,
# 'conv2': conv2, 'maxpool2': maxpool2,
# 'conv3': conv3, 'maxpool3': maxpool3})
# # initializing a saver to save weights
# enc_saver = tf.train.Saver({'conv1': conv1_v, 'maxpool1': maxpool1_v,
# 'conv2': conv2_v, 'maxpool2': maxpool2_v,
# 'conv3': conv3_v, 'maxpool3': maxpool3_v})
# initializing a restorer to restore weights
# res_saver = tf.train.import_meta_graph('/weights/model.ckpt-1.meta')
#
# summary nodes
tf.summary.scalar("loss", loss)
tf.summary.scalar("cost", cost)
tf.summary.histogram("conv1", conv1)
tf.summary.histogram("maxpool1", maxpool1)
tf.summary.histogram("conv2", conv2)
tf.summary.histogram("maxpool2", maxpool2)
tf.summary.histogram("conv3", conv3)
tf.summary.histogram("maxpool3", maxpool3)
tf.summary.histogram("unpool3", unpool3)
tf.summary.histogram("deconv3", deconv3)
tf.summary.histogram("unpool2", unpool2)
tf.summary.histogram("deconv2", deconv2)
tf.summary.histogram("unpool1", unpool1)
tf.summary.histogram("deconv1", deconv1)
# summary operation and a writer to save it.
summary_op = tf.summary.merge_all(key='summaries')
writer = tf.summary.FileWriter(logs_path, graph=tf.get_default_graph())
# end of tensorflow graph
# initializing tensorflow graph and a session
init_op = tf.global_variables_initializer()
sess = tf.Session(config=config)
sess.run(init_op)
# making operation-variables to run our methods whenever needed during training
fetch_op_tr = input_pipeline_tr()
fetch_op_val = input_pipeline_val()
# coordinator and queue runners to manage parallel sampling of batches from the input pipeline
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# start of training
counter = 0
try:
while not coord.should_stop():
print('\nEpoch\t' + str(counter + 1) + '/' + str(n_epochs))
for i in range(n_batches):
# fetching a batch
vol = sess.run(fetch_op_tr)
nvol = np.asarray(vol)
noisy_nvol = nvol + noise_factor * np.random.randn(*nvol.shape)
batch_cost, _ = sess.run([cost, opt], feed_dict={inputs_: noisy_nvol, targets_: nvol})
if i % 1000 == 0:
print("batch_cost", batch_cost)
print('\r' + str(((i + 1) * 100) / n_batches) + '%', sys.stdout.flush())
counter = counter + 1
print("Epoch: {}/{}...".format(counter, n_epochs), "Training loss: {:.4f}".format(batch_cost))
print("time cost: {}".format(time.time()))
# save weights and biases of the model
all_saver.save(sess, ws_path + "model.ckpt", global_step=counter)
# save weights and biases of the encoder
# enc_saver.save(sess, ws_path + "enc.ckpt", global_step=counter)
print('Weights saved')
# saving summary code above is clear
# print(nvol.shape)
# print(nvol.shape)
# summary, _ = sess.run([summary_op, opt], feed_dict={inputs_: nvol, targets_: nvol})
# print("summary:", summary)
# print("counter:", counter)
# writer.add_summary(summary, counter)
print('Summary saved')
if counter >= n_epochs:
break
# checking validation error
vol = sess.run(fetch_op_val)
nvol = np.asarray(vol)
batch_cost, _ = sess.run([cost, opt], feed_dict={inputs_: nvol, targets_: nvol})
print('Validation error' + str(batch_cost))
except tf.errors.OutOfRangeError:
print('Done training -- epoch limit reached')
finally:
coord.request_stop()
coord.join(threads)
sess.close()
# '''
# code to restore weights
with tf.Session(config=config) as sess:
all_saver.restore(sess, ws_path + "model.ckpt")
print("Model restored.")
