def train_vgg16(train_dir=None, validation_dir=None):
config = GEDIconfig()
if train_dir is None: # Use globals
train_data = os.path.join(config.tfrecord_dir,
config.tf_record_names['train'])
meta_data = np.load(
os.path.join(config.tfrecord_dir,
'%s_%s' % (config.tvt_flags[0], config.max_file)))
else:
meta_data = np.load(
os.path.join(train_dir,
'%s_%s' % (config.tvt_flags[0], config.max_file)))
# Prepare image normalization values
if config.max_gedi is None:
max_value = np.nanmax(meta_data['max_array']).astype(np.float32)
if max_value == 0:
max_value = None
print('Derived max value is 0')
else:
print('Normalizing with empirical max.')
if 'min_array' in meta_data.keys():
min_value = np.min(meta_data['min_array']).astype(np.float32)
print('Normalizing with empirical min.')
else:
min_value = None
print('Not normalizing with a min.')
else:
max_value = config.max_gedi
min_value = config.min_gedi
print('max value', max_value)
ratio = meta_data['ratio']
if config.encode_time_of_death:
tod = pd.read_csv(config.encode_time_of_death)
tod_data = tod['dead_tp'].as_matrix()
mask = np.isnan(tod_data).astype(int) + (
tod['plate_well_neuron'] == 'empty').as_matrix().astype(int)
tod_data = tod_data[mask == 0]
tod_data = tod_data[tod_data <
10] # throw away values have a high number
config.output_shape = len(np.unique(tod_data))
ratio = class_weight.compute_class_weight('balanced',
np.sort(np.unique(tod_data)),
tod_data)
flip_ratio = False
else:
flip_ratio = True
print('Ratio is: %s' % ratio)
if validation_dir is None: # Use globals
validation_data = os.path.join(config.tfrecord_dir,
config.tf_record_names['val'])
elif validation_dir is False:
pass # Do not use validation data during training
# Make output directories if they do not exist
dt_stamp = re.split(
'\.', str(datetime.now()))[0].\
replace(' ', '_').replace(':', '_').replace('-', '_')
dt_dataset = config.which_dataset + '_' + dt_stamp + '/'
config.train_checkpoint = os.path.join(config.train_checkpoint,
dt_dataset) # timestamp this run
out_dir = os.path.join(config.results, dt_dataset)
dir_list = [
config.train_checkpoint, config.train_summaries, config.results,
out_dir
]
[make_dir(d) for d in dir_list]
# im_shape = get_image_size(config)
im_shape = config.gedi_image_size
print('-' * 60)
print('Training model:' + dt_dataset)
print('-' * 60)
# Prepare data on CPU
assert os.path.exists(train_data)
assert os.path.exists(validation_data)
assert os.path.exists(config.vgg16_weight_path)
with tf.device('/cpu:0'):
train_images, train_labels = inputs(train_data,
config.train_batch,
im_shape,
config.model_image_size[:2],
max_value=max_value,
min_value=min_value,
train=config.data_augmentations,
num_epochs=config.epochs,
normalize=config.normalize)
val_images, val_labels = inputs(validation_data,
config.validation_batch,
im_shape,
config.model_image_size[:2],
max_value=max_value,
min_value=min_value,
num_epochs=config.epochs,
normalize=config.normalize)
tf.summary.image('train images', train_images)
tf.summary.image('validation images', val_images)
# Prepare model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('cnn') as scope:
if config.ordinal_classification == 'ordinal': # config.output_shape > 2: # Hardcoded fix for timecourse pred
vgg_output = config.output_shape * 2
elif config.ordinal_classification == 'regression':
vgg_output = 1
elif config.ordinal_classification is None:
vgg_output = config.output_shape
vgg = vgg16.Vgg16(vgg16_npy_path=config.vgg16_weight_path,
fine_tune_layers=config.fine_tune_layers)
train_mode = tf.get_variable(name='training', initializer=True)
vgg.build(train_images,
output_shape=vgg_output,
train_mode=train_mode,
batchnorm=config.batchnorm_layers)
# Prepare the cost function
if config.ordinal_classification == 'ordinal':
# Encode y w/ k-hot and yhat w/ sigmoid ce. units capture dist.
enc = tf.concat([
tf.reshape(tf.range(0, config.output_shape), [1, -1])
for x in range(config.train_batch)
],
axis=0)
enc_train_labels = tf.cast(
tf.greater_equal(enc, tf.expand_dims(train_labels,
axis=1)), tf.float32)
split_labs = tf.split(enc_train_labels,
config.output_shape,
axis=1)
res_output = tf.reshape(
vgg.fc8, [config.train_batch, 2, config.output_shape])
split_logs = tf.split(res_output, config.output_shape, axis=2)
if config.balance_cost:
cost = tf.add_n([
tf.nn.softmax_cross_entropy_with_logits(
labels=tf.one_hot(tf.cast(tf.squeeze(s), tf.int32),
2),
logits=tf.squeeze(l)) * r
for s, l, r in zip(split_labs, split_logs, ratio)
])
else:
cost = tf.add_n([
tf.nn.softmax_cross_entropy_with_logits(
labels=tf.one_hot(tf.cast(tf.squeeze(s), tf.int32),
2),
logits=tf.squeeze(l))
for s, l in zip(split_labs, split_logs)
])
cost = tf.reduce_mean(cost)
elif config.ordinal_classification == 'regression':
if config.balance_cost:
weight_vec = tf.gather(train_labels, ratio)
cost = tf.reduce_mean(
tf.pow(
(vgg.fc8) - tf.cast(train_labels, tf.float32), 2) *
weight_vec)
else:
cost = tf.nn.l2_loss((vgg.fc8) -
tf.cast(train_labels, tf.float32))
else:
if config.balance_cost:
cost = softmax_cost(vgg.fc8,
train_labels,
ratio=ratio,
flip_ratio=flip_ratio)
else:
cost = softmax_cost(vgg.fc8, train_labels)
tf.summary.scalar("cost", cost)
# Finetune the learning rates
if config.wd_layers is not None:
_, l2_wd_layers = fine_tune_prepare_layers(
tf.trainable_variables(), config.wd_layers)
l2_wd_layers = [
x for x in l2_wd_layers if 'biases' not in x.name
]
cost += (config.wd_penalty *
tf.add_n([tf.nn.l2_loss(x) for x in l2_wd_layers]))
# for all variables in trainable variables
# print name if there's duplicates you f****d up
other_opt_vars, ft_opt_vars = fine_tune_prepare_layers(
tf.trainable_variables(), config.fine_tune_layers)
if config.optimizer == 'adam':
train_op = ft_non_optimized(cost, other_opt_vars, ft_opt_vars,
tf.train.AdamOptimizer,
config.hold_lr, config.new_lr)
elif config.optimizer == 'sgd':
train_op = ft_non_optimized(cost, other_opt_vars, ft_opt_vars,
tf.train.GradientDescentOptimizer,
config.hold_lr, config.new_lr)
if config.ordinal_classification == 'ordinal':
arg_guesses = tf.cast(
tf.reduce_sum(tf.squeeze(tf.argmax(res_output, axis=1)),
reduction_indices=[1]), tf.int32)
train_accuracy = tf.reduce_mean(
tf.cast(tf.equal(arg_guesses, train_labels), tf.float32))
elif config.ordinal_classification == 'regression':
train_accuracy = tf.reduce_mean(
tf.cast(
tf.equal(tf.cast(tf.round(vgg.prob), tf.int32),
train_labels), tf.float32))
else:
train_accuracy = class_accuracy(
vgg.prob, train_labels) # training accuracy
tf.summary.scalar("training accuracy", train_accuracy)
# Setup validation op
if validation_data is not False:
scope.reuse_variables()
# Validation graph is the same as training except no batchnorm
val_vgg = vgg16.Vgg16(vgg16_npy_path=config.vgg16_weight_path,
fine_tune_layers=config.fine_tune_layers)
val_vgg.build(val_images, output_shape=vgg_output)
# Calculate validation accuracy
if config.ordinal_classification == 'ordinal':
val_res_output = tf.reshape(
val_vgg.fc8,
[config.validation_batch, 2, config.output_shape])
val_arg_guesses = tf.cast(
tf.reduce_sum(tf.squeeze(
tf.argmax(val_res_output, axis=1)),
reduction_indices=[1]), tf.int32)
val_accuracy = tf.reduce_mean(
tf.cast(tf.equal(val_arg_guesses, val_labels),
tf.float32))
elif config.ordinal_classification == 'regression':
val_accuracy = tf.reduce_mean(
tf.cast(
tf.equal(tf.cast(tf.round(val_vgg.prob), tf.int32),
val_labels), tf.float32))
else:
val_accuracy = class_accuracy(val_vgg.prob, val_labels)
tf.summary.scalar("validation accuracy", val_accuracy)
# Set up summaries and saver
saver = tf.train.Saver(tf.global_variables(),
max_to_keep=config.keep_checkpoints)
summary_op = tf.summary.merge_all()
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer()))
summary_dir = os.path.join(config.train_summaries,
config.which_dataset + '_' + dt_stamp)
summary_writer = tf.summary.FileWriter(summary_dir, sess.graph)
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Start training loop
np.save(out_dir + 'meta_info', config)
step, losses = 0, [] # val_max = 0
try:
# print response
while not coord.should_stop():
start_time = time.time()
_, loss_value, train_acc = sess.run(
[train_op, cost, train_accuracy])
losses.append(loss_value)
duration = time.time() - start_time
assert not np.isnan(loss_value), 'Model diverged with loss = NaN'
if step % config.validation_steps == 0:
if validation_data is not False:
_, val_acc = sess.run([train_op, val_accuracy])
else:
val_acc -= 1 # Store every checkpoint
# Summaries
summary_str = sess.run(summary_op)
summary_writer.add_summary(summary_str, step)
# Training status and validation accuracy
format_str = ('%s: step %d, loss = %.2f (%.1f examples/sec; '
'%.3f sec/batch) | Training accuracy = %s | '
'Validation accuracy = %s | logdir = %s')
print(format_str %
(datetime.now(), step,
loss_value, config.train_batch / duration,
float(duration), train_acc, val_acc, summary_dir))
# Save the model checkpoint if it's the best yet
if 1: # val_acc >= val_max:
saver.save(sess,
os.path.join(config.train_checkpoint,
'model_' + str(step) + '.ckpt'),
global_step=step)
# Store the new max validation accuracy
# val_max = val_acc
else:
# Training status
format_str = ('%s: step %d, loss = %.2f (%.1f examples/sec; '
'%.3f sec/batch) | Training accuracy = %s')
print(format_str %
(datetime.now(), step, loss_value, config.train_batch /
duration, float(duration), train_acc))
# End iteration
step += 1
except tf.errors.OutOfRangeError:
print('Done training for %d epochs, %d steps.' % (config.epochs, step))
finally:
coord.request_stop()
np.save(os.path.join(config.tfrecord_dir, 'training_loss'), losses)
coord.join(threads)
sess.close()
def train_vgg16(train_dir=None, validation_dir=None):
config = GEDIconfig()
if train_dir is None: # Use globals
train_data = os.path.join(config.tfrecord_dir, 'train.tfrecords')
meta_data = np.load(
os.path.join(
config.tfrecord_dir, config.tvt_flags[0] + '_' +
config.max_file))
else:
meta_data = np.load(
os.path.join(
train_dir, config.tvt_flags[0] + '_' + config.max_file))
# Prepare image normalization values
max_value = np.nanmax(meta_data['max_array']).astype(np.float32)
if max_value == 0:
max_value = None
print 'Derived max value is 0'
else:
print 'Normalizing with empirical max.'
if 'min_array' in meta_data.keys():
min_value = np.min(meta_data['min_array']).astype(np.float32)
print 'Normalizing with empirical min.'
else:
min_value = None
print 'Not normalizing with a min.'
ratio = meta_data['ratio']
print 'Ratio is: %s' % ratio
if validation_dir is None: # Use globals
validation_data = os.path.join(config.tfrecord_dir, 'val.tfrecords')
elif validation_dir is False:
pass # Do not use validation data during training
# Make output directories if they do not exist
dt_stamp = re.split(
'\.', str(datetime.now()))[0].\
replace(' ', '_').replace(':', '_').replace('-', '_')
dt_dataset = config.which_dataset + '_' + dt_stamp + '/'
config.train_checkpoint = os.path.join(
config.train_checkpoint, dt_dataset) # timestamp this run
out_dir = os.path.join(config.results, dt_dataset)
dir_list = [
config.train_checkpoint, config.train_summaries,
config.results, out_dir]
[make_dir(d) for d in dir_list]
# im_shape = get_image_size(config)
im_shape = config.gedi_image_size
print '-'*60
print('Training model:' + dt_dataset)
print '-'*60
# Prepare data on CPU
with tf.device('/cpu:0'):
train_images, train_labels = inputs(
train_data,
config.train_batch,
im_shape,
config.model_image_size[:2],
max_value=max_value,
min_value=min_value,
train=config.data_augmentations,
num_epochs=config.epochs,
normalize=config.normalize)
val_images, val_labels = inputs(
validation_data,
config.validation_batch,
im_shape,
config.model_image_size[:2],
max_value=max_value,
min_value=min_value,
num_epochs=config.epochs,
normalize=config.normalize)
tf.summary.image('train images', train_images)
tf.summary.image('validation images', val_images)
# Prepare model on GPU
num_timepoints = len(config.channel)
with tf.device('/gpu:0'):
with tf.variable_scope('cnn') as scope:
# Prepare the loss function
if config.balance_cost:
cost_fun = lambda yhat, y: softmax_cost(yhat, y, ratio=ratio)
else:
cost_fun = lambda yhat, y: softmax_cost(yhat, y)
def cond(i, state, images, output, loss, num_timepoints): # NOT CORRECT
return tf.less(i, num_timepoints)
def body(
i,
images,
label,
cell,
state,
output,
loss,
vgg,
train_mode,
output_shape,
batchnorm_layers,
cost_fun,
score_layer='fc7'):
vgg.build(
images[i],
output_shape=config.output_shape,
train_mode=train_mode,
batchnorm=config.batchnorm_layers)
it_output, state = cell(vgg[score_layer], state)
output= output.write(i, it_output)
it_loss = cost_fun(output, label)
loss = loss.write(i, it_loss)
return (i+1, images, label, cell, state, output, loss, vgg, train_mode, output_shape, batchnorm_layers)
# Prepare LSTM loop
train_mode = tf.get_variable(name='training', initializer=True)
cell = lstm_layers(layer_units=config.lstm_units)
output = tf.TensorArray(tf.float32, num_timepoints) # output array for LSTM loop -- one slot per timepoint
loss = tf.TensorArray(tf.float32, num_timepoints) # loss for LSTM loop -- one slot per timepoint
i = tf.constant(0) # iterator for LSTM loop
loop_vars = [i, images, label, cell, state, output, loss, vgg, train_mode, output_shape, batchnorm_layers, cost_fun]
# Run the lstm
processed_list = tf.while_loop(
cond=cond,
body=body,
loop_vars=loop_vars,
back_prop=True,
swap_memory=False)
output_cell = processed_list[3]
output_state = processed_list[4]
output_activity = processed_list[5]
cost = processed_list[6]
# Optimize
combined_cost = tf.reduce_sum(cost)
tf.summary.scalar('cost', combined_cost)
import ipdb;ipdb.set_trace() # Need to make sure lstm weights are being trained
other_opt_vars, ft_opt_vars = fine_tune_prepare_layers(
tf.trainable_variables(), config.fine_tune_layers)
if config.optimizer == 'adam':
train_op = ft_non_optimized(
cost, other_opt_vars, ft_opt_vars,
tf.train.AdamOptimizer, config.hold_lr, config.new_lr)
elif config.optimizer == 'sgd':
train_op = ft_non_optimized(
cost, other_opt_vars, ft_opt_vars,
tf.train.GradientDescentOptimizer,
config.hold_lr, config.new_lr)
train_accuracy = class_accuracy(
vgg.prob, train_labels) # training accuracy
tf.summary.scalar("training accuracy", train_accuracy)
# Setup validation op
if validation_data is not False:
scope.reuse_variables()
# Validation graph is the same as training except no batchnorm
val_vgg = vgg16.Vgg16(
vgg16_npy_path=config.vgg16_weight_path,
fine_tune_layers=config.fine_tune_layers)
val_vgg.build(val_images, output_shape=config.output_shape)
# Calculate validation accuracy
val_accuracy = class_accuracy(val_vgg.prob, val_labels)
tf.summary.scalar("validation accuracy", val_accuracy)
def train_vgg16(train_dir=None, validation_dir=None):
config = GEDIconfig()
if train_dir is None: # Use globals
train_data = os.path.join(
config.tfrecord_dir,
config.tf_record_names['train'])
meta_data = np.load(
os.path.join(
config.tfrecord_dir,
'%s_%s' % (config.tvt_flags[0], config.max_file)))
else:
meta_data = np.load(
os.path.join(
train_dir,
'%s_%s' % (config.tvt_flags[0], config.max_file)))
# Prepare image normalization values
if config.max_gedi is None:
max_value = np.nanmax(meta_data['max_array']).astype(np.float32)
if max_value == 0:
max_value = None
print 'Derived max value is 0'
else:
print 'Normalizing with empirical max.'
if 'min_array' in meta_data.keys():
min_value = np.min(meta_data['min_array']).astype(np.float32)
print 'Normalizing with empirical min.'
else:
min_value = None
print 'Not normalizing with a min.'
else:
max_value = config.max_gedi
min_value = config.min_gedi
ratio = meta_data['ratio']
if config.encode_time_of_death:
tod = pd.read_csv(config.encode_time_of_death)
tod_data = tod['dead_tp'].as_matrix()
mask = np.isnan(tod_data).astype(int) + (
tod['plate_well_neuron'] == 'empty').as_matrix().astype(int)
tod_data = tod_data[mask == 0]
tod_data = tod_data[tod_data > config.mask_timepoint_value]
config.output_shape = len(np.unique(tod_data))
ratio = class_weight.compute_class_weight(
'balanced',
np.sort(np.unique(tod_data)),
tod_data)
flip_ratio = False
else:
flip_ratio = True
print 'Ratio is: %s' % ratio
if validation_dir is None: # Use globals
validation_data = os.path.join(
config.tfrecord_dir,
config.tf_record_names['val'])
elif validation_dir is False:
pass # Do not use validation data during training
# Make output directories if they do not exist
dt_stamp = re.split(
'\.', str(datetime.now()))[0].\
replace(' ', '_').replace(':', '_').replace('-', '_')
dt_dataset = config.which_dataset + '_' + dt_stamp + '/'
config.train_checkpoint = os.path.join(
config.train_checkpoint, dt_dataset) # timestamp this run
out_dir = os.path.join(config.results, dt_dataset)
dir_list = [
config.train_checkpoint, config.train_summaries,
config.results, out_dir]
[make_dir(d) for d in dir_list]
# im_shape = get_image_size(config)
im_shape = config.gedi_image_size
print '-'*60
print('Training model:' + dt_dataset)
print '-'*60
# Prepare data on CPU
assert os.path.exists(train_data)
assert os.path.exists(validation_data)
assert os.path.exists(config.vgg16_weight_path)
with tf.device('/cpu:0'):
train_images, train_labels, train_gedi_images = inputs(
train_data,
config.train_batch,
im_shape,
config.model_image_size[:2],
max_value=max_value,
min_value=min_value,
train=config.data_augmentations,
num_epochs=config.epochs,
normalize=config.normalize,
return_gedi=config.include_GEDI_in_tfrecords,
return_extra_gfp=config.extra_image,
return_GEDI_derivative=True)
val_images, val_labels, val_gedi_images = inputs(
validation_data,
config.validation_batch,
im_shape,
config.model_image_size[:2],
max_value=max_value,
min_value=min_value,
num_epochs=config.epochs,
normalize=config.normalize,
return_gedi=config.include_GEDI_in_tfrecords,
return_extra_gfp=config.extra_image,
return_GEDI_derivative=True)
if config.include_GEDI_in_tfrecords:
extra_im_name = 'GEDI at current timepoint'
else:
extra_im_name = 'next gfp timepoint'
tf.summary.image('train images', train_images)
tf.summary.image('validation images', val_images)
tf.summary.image('train %s' % extra_im_name, train_gedi_images)
tf.summary.image('validation %s' % extra_im_name, val_gedi_images)
# Prepare model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('cnn') as scope:
if config.ordinal_classification is None:
vgg_output = 2 # Sign of derivative (inf norm)
train_labels = tf.cast(tf.sign(train_labels), tf.int32)
val_labels = tf.cast(tf.sign(val_labels), tf.int32)
elif config.ordinal_classification == 'regression':
vgg_output = 1
else:
raise RuntimeError(
'config.ordinal_classification must be sign or regression.'
)
vgg = vgg16.model_struct()
train_mode = tf.get_variable(name='training', initializer=True)
# Mask NAN images from loss
image_nan = tf.reduce_sum(
tf.cast(tf.is_nan(train_images), tf.float32),
reduction_indices=[1, 2, 3])
gedi_nan = tf.reduce_sum(
tf.cast(tf.is_nan(train_gedi_images), tf.float32),
reduction_indices=[1, 2, 3],
keep_dims=True)
image_mask = tf.cast(tf.equal(image_nan, 0.), tf.float32)
gedi_nan = tf.cast(tf.equal(gedi_nan, 0.), tf.float32)
train_images = tf.where(
tf.is_nan(train_images),
tf.zeros_like(train_images),
train_images)
train_gedi_images = tf.where(
tf.is_nan(train_gedi_images),
tf.zeros_like(train_gedi_images),
train_gedi_images)
train_images = tf.concat([train_images, train_images, train_images], axis=3)
val_images = tf.concat([val_images, val_images, val_images], axis=3)
vgg.build(
train_images, output_shape=vgg_output,
train_mode=train_mode, batchnorm=config.batchnorm_layers)
# Prepare the cost function
if config.ordinal_classification is None:
# Encode y w/ k-hot and yhat w/ sigmoid ce. units capture dist.
cost = softmax_cost(
vgg.fc8,
train_labels,
mask=image_mask)
elif config.ordinal_classification == 'regression':
cost = tf.nn.l2_loss(tf.squeeze(vgg.fc8) - train_labels)
class_loss = cost
tf.summary.scalar("cce cost", cost)
# Weight decay
if config.wd_layers is not None:
_, l2_wd_layers = fine_tune_prepare_layers(
tf.trainable_variables(), config.wd_layers)
l2_wd_layers = [
x for x in l2_wd_layers if 'biases' not in x.name]
if len(l2_wd_layers) > 0:
cost += (config.wd_penalty * tf.add_n(
[tf.nn.l2_loss(x) for x in l2_wd_layers]))
# Optimize
train_op = tf.train.AdamOptimizer(config.new_lr).minimize(cost)
if config.ordinal_classification is None:
train_accuracy = class_accuracy(
vgg.prob, train_labels) # training accuracy
elif config.ordinal_classification == 'regression':
train_accuracy = tf.nn.l2_loss(
tf.squeeze(vgg.fc8) - train_labels)
tf.summary.scalar("training accuracy", train_accuracy)
# Setup validation op
if validation_data is not False:
scope.reuse_variables()
# Validation graph is the same as training except no batchnorm
val_vgg = vgg16.model_struct(
fine_tune_layers=config.fine_tune_layers)
val_vgg.build(val_images, output_shape=vgg_output)
# Calculate validation accuracy
if config.ordinal_classification is None:
val_accuracy = class_accuracy(val_vgg.prob, val_labels)
elif config.ordinal_classification == 'regression':
val_accuracy = tf.nn.l2_loss(tf.squeeze(val_vgg.fc8) - val_labels)
tf.summary.scalar("validation accuracy", val_accuracy)
# Set up summaries and saver
saver = tf.train.Saver(
tf.global_variables(), max_to_keep=config.keep_checkpoints)
summary_op = tf.summary.merge_all()
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer()))
summary_dir = os.path.join(
config.train_summaries, config.which_dataset + '_' + dt_stamp)
summary_writer = tf.summary.FileWriter(summary_dir, sess.graph)
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Restore model if requested
if config.restore_path is not None:
print '-' * 60
print 'Restoring from a previous model: %s' % config.restore_path
print '-' * 60
saver.restore(sess, config.restore_path)
# Start training loop
np.save(out_dir + 'meta_info', config)
step, losses = 0, [] # val_max = 0
try:
# print response
while not coord.should_stop():
start_time = time.time()
_, loss_value, train_acc = sess.run(
[train_op, cost, train_accuracy])
losses.append(loss_value)
duration = time.time() - start_time
if np.isnan(loss_value).sum():
import ipdb;ipdb.set_trace()
assert not np.isnan(loss_value), 'Model diverged with loss = NaN'
if step % config.validation_steps == 0:
if validation_data is not False:
_, val_acc = sess.run([train_op, val_accuracy])
else:
val_acc -= 1 # Store every checkpoint
# Summaries
summary_str = sess.run(summary_op)
summary_writer.add_summary(summary_str, step)
# Training status and validation accuracy
format_str = (
'%s: step %d, loss = %.2f (%.1f examples/sec; '
'%.3f sec/batch) | Training accuracy = %s | '
'Training %s = %s | Training class loss = %s | '
'Validation accuracy = %s | Validation %s = %s | '
'logdir = %s')
print (format_str % (
datetime.now(), step, loss_value,
config.train_batch / duration, float(duration),
train_acc, extra_im_name, 0.,
0., val_acc, extra_im_name,
0., summary_dir))
# Save the model checkpoint if it's the best yet
if 1: # val_acc >= val_max:
saver.save(
sess, os.path.join(
config.train_checkpoint,
'model_' + str(step) + '.ckpt'), global_step=step)
# Store the new max validation accuracy
# val_max = val_acc
else:
# Training status
format_str = ('%s: step %d, loss = %.2f (%.1f examples/sec; '
'%.3f sec/batch) | Training accuracy = %s | '
'Training %s = %s | Training class loss = %s')
print (format_str % (datetime.now(), step, loss_value,
config.train_batch / duration,
float(duration), train_acc,
extra_im_name, 0.,
0.))
# End iteration
step += 1
except tf.errors.OutOfRangeError:
print('Done training for %d epochs, %d steps.' % (config.epochs, step))
finally:
coord.request_stop()
np.save(os.path.join(config.tfrecord_dir, 'training_loss'), losses)
coord.join(threads)
sess.close()
def train_model(train_dir=None, validation_dir=None):
config = GEDIconfig()
if train_dir is None: # Use globals
train_data = os.path.join(config.tfrecord_dir,
config.tf_record_names['train'])
meta_data = np.load(
os.path.join(config.tfrecord_dir,
'%s_%s' % (config.tvt_flags[0], config.max_file)))
else:
meta_data = np.load(
os.path.join(train_dir,
'%s_%s' % (config.tvt_flags[0], config.max_file)))
# Prepare image normalization values
if config.max_gedi is None:
max_value = np.nanmax(meta_data['max_array']).astype(np.float32)
if max_value == 0:
max_value = None
print 'Derived max value is 0'
else:
print 'Normalizing with empirical max.'
if 'min_array' in meta_data.keys():
min_value = np.min(meta_data['min_array']).astype(np.float32)
print 'Normalizing with empirical min.'
else:
min_value = None
print 'Not normalizing with a min.'
else:
max_value = config.max_gedi
min_value = config.min_gedi
ratio = meta_data['ratio']
print 'Ratio is: %s' % ratio
if validation_dir is None: # Use globals
validation_data = os.path.join(config.tfrecord_dir,
config.tf_record_names['val'])
elif validation_dir is False:
pass # Do not use validation data during training
# Make output directories if they do not exist
dt_stamp = re.split(
'\.', str(datetime.now()))[0].\
replace(' ', '_').replace(':', '_').replace('-', '_')
dt_dataset = config.which_dataset + '_' + dt_stamp + '/'
config.train_checkpoint = os.path.join(config.train_checkpoint,
dt_dataset) # timestamp this run
out_dir = os.path.join(config.results, dt_dataset)
dir_list = [
config.train_checkpoint, config.train_summaries, config.results,
out_dir
]
[make_dir(d) for d in dir_list]
# im_shape = get_image_size(config)
im_shape = config.gedi_image_size
print '-' * 60
print('Training model:' + dt_dataset)
print '-' * 60
# Prepare data on CPU
assert os.path.exists(train_data)
assert os.path.exists(validation_data)
assert os.path.exists(config.vgg16_weight_path)
with tf.device('/cpu:0'):
train_images_0, train_images_1, train_labels, train_times = inputs(
train_data,
config.train_batch,
im_shape,
config.model_image_size[:2],
max_value=max_value,
min_value=min_value,
train=config.data_augmentations,
num_epochs=config.epochs,
normalize=config.normalize,
return_filename=True)
val_images_0, val_images_1, val_labels, val_times = inputs(
validation_data,
config.validation_batch,
im_shape,
config.model_image_size[:2],
max_value=max_value,
min_value=min_value,
num_epochs=config.epochs,
normalize=config.normalize,
return_filename=True)
tf.summary.image('train image frame 0', train_images_0)
tf.summary.image('train image frame 1', train_images_1)
tf.summary.image('validation image frame 0', val_images_0)
tf.summary.image('validation image frame 1', val_images_1)
# Prepare model on GPU
with tf.device('/gpu:0'):
with tf.variable_scope('gedi'):
# Build training GEDI model for frame 0
vgg_train_mode = tf.get_variable(name='vgg_training',
initializer=False)
gedi_model_0 = vgg16.model_struct(
vgg16_npy_path=config.gedi_weight_path, trainable=False)
gedi_model_0.build(prep_images_for_gedi(train_images_0),
output_shape=2,
train_mode=vgg_train_mode)
gedi_scores_0 = gedi_model_0.fc7
with tf.variable_scope('match'):
# Build matching model for frame 0
model_0 = matching_gedi.model_struct()
model_0.build(train_images_0)
# Build frame 0 vector
frame_0 = tf.concat([gedi_scores_0, model_0.output], axis=-1)
# Build output layer
if config.matching_combine == 'concatenate':
output_shape = [int(frame_0.get_shape()[-1]) * 2, 2]
elif config.matching_combine == 'subtract':
output_shape = [int(frame_0.get_shape()[-1]), 2]
else:
raise RuntimeError
# Build GEDI model for frame 1
with tf.variable_scope('gedi', reuse=True):
gedi_model_1 = vgg16.model_struct(
vgg16_npy_path=config.gedi_weight_path, trainable=False)
gedi_model_1.build(prep_images_for_gedi(train_images_1),
output_shape=2,
train_mode=vgg_train_mode)
gedi_scores_1 = gedi_model_1.fc7
with tf.variable_scope('match', reuse=True):
# Build matching model for frame 1
model_1 = matching_gedi.model_struct()
model_1.build(train_images_1)
# Build frame 0 and frame 1 vectors
frame_1 = tf.concat([gedi_scores_1, model_1.output], axis=-1)
with tf.variable_scope('output'):
# Concatenate or subtract
if config.matching_combine == 'concatenate':
output_scores = tf.concat([frame_0, frame_1], axis=-1)
elif config.matching_combine == 'subtract':
output_scores = frame_0 - frame_1
else:
raise NotImplementedError
# Build output layer
output_shape = [int(output_scores.get_shape()[-1]), 2]
output_weights = tf.get_variable(
name='output_weights',
shape=output_shape,
initializer=tf.contrib.layers.xavier_initializer(
uniform=False))
output_bias = tf.get_variable(name='output_bias',
initializer=tf.truncated_normal(
[output_shape[-1]], .0, .001))
decision_logits = tf.nn.bias_add(
tf.matmul(output_scores, output_weights), output_bias)
train_soft_decisions = tf.nn.softmax(decision_logits)
cost = softmax_cost(decision_logits, train_labels)
tf.summary.scalar("cce loss", cost)
cost += tf.nn.l2_loss(output_weights)
# Weight decay
if config.wd_layers is not None:
_, l2_wd_layers = fine_tune_prepare_layers(
tf.trainable_variables(), config.wd_layers)
l2_wd_layers = [
x for x in l2_wd_layers if 'biases' not in x.name
]
if len(l2_wd_layers) > 0:
cost += (config.wd_penalty *
tf.add_n([tf.nn.l2_loss(x)
for x in l2_wd_layers]))
# Optimize
train_op = tf.train.AdamOptimizer(config.new_lr).minimize(cost)
train_accuracy = class_accuracy(train_soft_decisions,
train_labels) # training accuracy
tf.summary.scalar("training accuracy", train_accuracy)
# Setup validation op
if validation_data is not False:
with tf.variable_scope('gedi', reuse=tf.AUTO_REUSE): # FIX THIS
# Validation graph is the same as training except no batchnorm
val_gedi_model_0 = vgg16.model_struct(
vgg16_npy_path=config.gedi_weight_path)
val_gedi_model_0.build(prep_images_for_gedi(val_images_0),
output_shape=2,
train_mode=vgg_train_mode)
val_gedi_scores_0 = val_gedi_model_0.fc7
# Build GEDI model for frame 1
val_gedi_model_1 = vgg16.model_struct(
vgg16_npy_path=config.gedi_weight_path)
val_gedi_model_1.build(prep_images_for_gedi(val_images_1),
output_shape=2,
train_mode=vgg_train_mode)
val_gedi_scores_1 = val_gedi_model_1.fc7
with tf.variable_scope('match', reuse=tf.AUTO_REUSE):
# Build matching model for frame 0
val_model_0 = matching_gedi.model_struct()
val_model_0.build(val_images_0)
# Build matching model for frame 1
val_model_1 = matching_gedi.model_struct()
val_model_1.build(val_images_1)
# Build frame 0 and frame 1 vectors
val_frame_0 = tf.concat([val_gedi_scores_0, val_model_0.output],
axis=-1)
val_frame_1 = tf.concat([val_gedi_scores_1, val_model_1.output],
axis=-1)
# Concatenate or subtract
if config.matching_combine == 'concatenate':
val_output_scores = tf.concat([val_frame_0, val_frame_1],
axis=-1)
elif config.matching_combine == 'subtract':
val_output_scores = val_frame_0 - val_frame_1
else:
raise NotImplementedError
with tf.variable_scope('output', reuse=tf.AUTO_REUSE):
# Build output layer
val_output_weights = tf.get_variable(
name='val_output_weights',
shape=output_shape,
trainable=False,
initializer=tf.contrib.layers.xavier_initializer(
uniform=False))
val_output_bias = tf.get_variable(
name='output_bias',
trainable=False,
initializer=tf.truncated_normal([output_shape[-1]], .0,
.001))
val_decision_logits = tf.nn.bias_add(
tf.matmul(val_output_scores, val_output_weights),
val_output_bias)
val_soft_decisions = tf.nn.softmax(val_decision_logits)
# Calculate validation accuracy
val_accuracy = class_accuracy(val_soft_decisions, val_labels)
tf.summary.scalar("validation accuracy", val_accuracy)
# Set up summaries and saver
saver = tf.train.Saver(tf.global_variables(),
max_to_keep=config.keep_checkpoints)
summary_op = tf.summary.merge_all()
# Initialize the graph
sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# Need to initialize both of these if supplying num_epochs to inputs
sess.run(
tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer()))
summary_dir = os.path.join(config.train_summaries,
config.which_dataset + '_' + dt_stamp)
summary_writer = tf.summary.FileWriter(summary_dir, sess.graph)
# Set up exemplar threading
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
# Start training loop
np.save(out_dir + 'meta_info', config)
step, losses = 0, [] # val_max = 0
try:
# print response
while not coord.should_stop():
start_time = time.time()
_, loss_value, train_acc, val_acc = sess.run(
[train_op, cost, train_accuracy, val_accuracy])
losses += [loss_value]
duration = time.time() - start_time
if np.isnan(loss_value).sum():
assert not np.isnan(loss_value), 'Model loss = NaN'
if step % config.validation_steps == 0:
if validation_data is not False:
val_acc = sess.run(val_accuracy)
else:
val_acc -= 1 # Store every checkpoint
# Summaries
summary_str = sess.run(summary_op)
summary_writer.add_summary(summary_str, step)
# Training status and validation accuracy
format_str = ('%s: step %d, loss = %.2f (%.1f examples/sec; '
'%.3f sec/batch) | Training accuracy = %s | '
'Validation accuracy = %s | '
'logdir = %s')
print(format_str %
(datetime.now(), step,
loss_value, config.train_batch / duration,
float(duration), train_acc, val_acc, summary_dir))
# Save the model checkpoint if it's the best yet
if 1: # val_acc >= val_max:
saver.save(sess,
os.path.join(config.train_checkpoint,
'model_' + str(step) + '.ckpt'),
global_step=step)
# Store the new max validation accuracy
# val_max = val_acc
else:
# Training status
format_str = ('%s: step %d, loss = %.2f (%.1f examples/sec; '
'%.3f sec/batch) | Training accuracy = %s | '
'Training loss = %s')
print(format_str %
(datetime.now(), step, loss_value, config.train_batch /
duration, float(duration), loss_value))
# End iteration
step += 1
except tf.errors.OutOfRangeError:
print('Done training for %d epochs, %d steps.' % (config.epochs, step))
finally:
coord.request_stop()
np.save(os.path.join(config.tfrecord_dir, 'training_loss'), losses)
coord.join(threads)
sess.close()