def create_network(input_shape, name):
tf.reset_default_graph()
# create a placeholder for the 3D raw input tensor
raw = tf.placeholder(tf.float32, shape=input_shape)
# create a U-Net
raw_batched = tf.reshape(raw, (1, 1) + input_shape)
unet_output = unet(raw_batched, 12, 5, [[1, 3, 3], [1, 3, 3], [1, 3, 3]])
# add a convolution layer to create 3 output maps representing affinities
# in z, y, and x
pred_affs_batched = conv_pass(unet_output,
kernel_size=1,
num_fmaps=3,
num_repetitions=1,
activation='sigmoid')
# get the shape of the output
output_shape_batched = pred_affs_batched.get_shape().as_list()
output_shape = output_shape_batched[1:] # strip the batch dimension
# the 4D output tensor (3, depth, height, width)
pred_affs = tf.reshape(pred_affs_batched, output_shape)
# create a placeholder for the corresponding ground-truth affinities
gt_affs = tf.placeholder(tf.float32, shape=output_shape)
# create a placeholder for per-voxel loss weights
loss_weights = tf.placeholder(tf.float32, shape=output_shape)
# compute the loss as the weighted mean squared error between the
# predicted and the ground-truth affinities
loss = tf.losses.mean_squared_error(gt_affs, pred_affs, loss_weights)
# use the Adam optimizer to minimize the loss
opt = tf.train.AdamOptimizer(learning_rate=0.5e-4,
beta1=0.95,
beta2=0.999,
epsilon=1e-8)
optimizer = opt.minimize(loss)
# store the network in a meta-graph file
tf.train.export_meta_graph(filename=name + '.meta')
# write to event
tf.summary.FileWriter('.', graph=tf.get_default_graph())
# store network configuration for use in train and predict scripts
config = {
'raw': raw.name,
'pred_affs': pred_affs.name,
'gt_affs': gt_affs.name,
'loss_weights': loss_weights.name,
'loss': loss.name,
'optimizer': optimizer.name,
'input_shape': input_shape,
'output_shape': output_shape[1:]
}
with open(name + '_config.json', 'w') as f:
json.dump(config, f)
def create_network(input_shape, name, output_folder):
tf.reset_default_graph()
# c=3, d, h, w
raw = tf.placeholder(tf.float32, shape=(3, ) + input_shape)
# b=1, c=3, d, h, w
raw_batched = tf.reshape(raw, (
1,
3,
) + input_shape)
out = unet(raw_batched, 12, 5, [[2, 2, 2], [2, 2, 2], [2, 2, 2]])
output_batched = conv_pass(out,
kernel_size=1,
num_fmaps=1,
num_repetitions=1,
activation='sigmoid')
output_shape_batched = output_batched.get_shape().as_list()
# d, h, w
output_shape = output_shape_batched[2:]
output = tf.reshape(output_batched, output_shape)
gt = tf.placeholder(tf.float32, shape=output_shape)
loss_weights = tf.placeholder(tf.float32, shape=output_shape)
loss = tf.losses.mean_squared_error(gt, output, loss_weights)
opt = tf.train.AdamOptimizer(learning_rate=0.5e-4,
beta1=0.95,
beta2=0.999,
epsilon=1e-8)
optimizer = opt.minimize(loss)
print("input shape: %s" % (input_shape, ))
print("output shape: %s" % (output_shape, ))
tf.train.export_meta_graph(filename=os.path.join(output_folder, name +
'.meta'))
names = {
'raw': raw.name,
'pred': output.name,
'gt': gt.name,
'loss_weights': loss_weights.name,
'loss': loss.name,
'optimizer': optimizer.name,
}
with open(os.path.join(output_folder, name + '_names.json'), 'w') as f:
json.dump(names, f)
config = {
'input_shape': input_shape,
'output_shape': output_shape,
'out_dims': 1
}
with open(os.path.join(output_folder, name + '_config.json'), 'w') as f:
json.dump(config, f)
def create_network(input_shape, name):
tf.reset_default_graph()
# c=2, d, h, w
raw = tf.placeholder(tf.float32, shape=(2, ) + input_shape)
# b=1, c=2, d, h, w
raw_batched = tf.reshape(raw, (
1,
2,
) + input_shape)
fg_unet = unet(raw_batched, 12, 5, [[1, 2, 2], [1, 2, 2], [2, 2, 2]])
fg_batched = conv_pass(fg_unet,
kernel_size=1,
num_fmaps=1,
num_repetitions=1,
activation='sigmoid')
output_shape_batched = fg_batched.get_shape().as_list()
# d, h, w, strip the batch and channel dimension
output_shape = tuple(output_shape_batched[2:])
fg = tf.reshape(fg_batched, output_shape)
labels_fg = tf.placeholder(tf.float32, shape=output_shape)
loss_weights = tf.placeholder(tf.float32, shape=output_shape)
loss = tf.losses.mean_squared_error(labels_fg, fg, loss_weights)
opt = tf.train.AdamOptimizer(learning_rate=0.5e-4,
beta1=0.95,
beta2=0.999,
epsilon=1e-8)
optimizer = opt.minimize(loss)
print("input shape: %s" % (input_shape, ))
print("output shape: %s" % (output_shape, ))
tf.train.export_meta_graph(filename=name + '.meta')
tf.train.export_meta_graph(filename='train_net.meta')
names = {
'raw': raw.name,
'fg': fg.name,
'loss_weights': loss_weights.name,
'loss': loss.name,
'optimizer': optimizer.name,
'labels_fg': labels_fg.name
}
with open(name + '_names.json', 'w') as f:
json.dump(names, f)
config = {
'input_shape': input_shape,
'output_shape': output_shape,
'out_dims': 1
}
with open(name + '_config.json', 'w') as f:
json.dump(config, f)
if __name__ == "__main__":
input_shape = (200, 200)
raw = tf.placeholder(tf.float32, shape=input_shape)
raw_batched = tf.reshape(raw, (1, 1) + input_shape)
with tf.variable_scope("embedding"):
embedding_unet = unet(raw_batched, 6, 5, [[2, 2], [2, 2]])
with tf.variable_scope("fg"):
fg_unet = unet(raw_batched, 3, 2, [[2, 2], [2, 2]])
embedding_batched = conv_pass(
embedding_unet,
kernel_size=1,
num_fmaps=3,
num_repetitions=1,
activation=None,
name="embedding",
)
fg_batched = conv_pass(
fg_unet,
kernel_size=1,
num_fmaps=1,
num_repetitions=1,
activation="sigmoid",
name="fg",
)
output_shape_batched = embedding_batched.get_shape().as_list()
output_shape = tuple(
if __name__ == "__main__":
input_shape = (200, 200)
raw = tf.placeholder(tf.float32, shape=input_shape)
raw_batched = tf.reshape(raw, (1, 1) + input_shape)
with tf.variable_scope('embedding'):
embedding_unet = unet(raw_batched, 6, 5, [[2, 2], [2, 2]])
with tf.variable_scope('fg'):
fg_unet = unet(raw_batched, 3, 2, [[2, 2], [2, 2]])
embedding_batched = conv_pass(embedding_unet,
kernel_size=1,
num_fmaps=3,
num_repetitions=1,
activation=None,
name='embedding')
fg_batched = conv_pass(fg_unet,
kernel_size=1,
num_fmaps=1,
num_repetitions=1,
activation='sigmoid',
name='fg')
output_shape_batched = embedding_batched.get_shape().as_list()
output_shape = tuple(
output_shape_batched[2:]) # strip the batch and channel dimension
embedding = tf.reshape(embedding_batched, (3, ) + output_shape)