def _inference_loop(self, sess, loop_status):
"""
Runs all variables returned by outputs_collector,
this loop stops when the return value of
application.interpret_output is False.
"""
iter_msg = IterationMessage()
loop_status['all_saved_flag'] = False
iter_i = 0
while True:
if self._coord.should_stop():
break
if iter_msg.should_stop:
break
iter_msg.current_iter, iter_msg.phase = iter_i, INFER
# run variables provided in `iter_msg` and set values of
# variables to iter_msg.current_iter_output
self.run_vars(sess, iter_msg)
iter_i = iter_i + 1
# process the graph outputs
if not self.app.interpret_output(
iter_msg.current_iter_output[NETWORK_OUTPUT]):
tf.logging.info('processed all batches.')
loop_status['all_saved_flag'] = True
break
tf.logging.info(iter_msg.to_console_string())
def run(self, application, graph=None):
"""
Initialise a TF graph, connect data sampler and network within
the graph context, run training loops or inference loops.
:param application: a niftynet application
:param graph: default base graph to run the application
:return:
"""
if graph is None:
graph = ApplicationDriver.create_graph(
application=application,
num_gpus=self.num_gpus,
num_threads=self.num_threads,
is_training_action=self.is_training_action)
start_time = time.time()
loop_status = {'current_iter': self.initial_iter, 'normal_exit': False}
with tf.Session(config=tf_config(), graph=graph):
try:
# broadcasting event of session started
SESS_STARTED.send(application, iter_msg=None)
# create a iteration message generator and
# iteratively run the graph (the main engine loop)
iteration_messages = self._generator(**vars(self))()
ApplicationDriver.loop(application=application,
iteration_messages=iteration_messages,
loop_status=loop_status)
except KeyboardInterrupt:
tf.logging.warning('User cancelled application')
except (tf.errors.OutOfRangeError, EOFError):
if not loop_status.get('normal_exit', False):
# reached the end of inference Dataset
loop_status['normal_exit'] = True
except RuntimeError:
import sys
import traceback
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type,
exc_value,
exc_traceback,
file=sys.stdout)
finally:
tf.logging.info('cleaning up...')
# broadcasting session finished event
iter_msg = IterationMessage()
iter_msg.current_iter = loop_status.get('current_iter', -1)
SESS_FINISHED.send(application, iter_msg=iter_msg)
application.stop()
if not loop_status.get('normal_exit', False):
# loop didn't finish normally
tf.logging.warning('stopped early, incomplete iterations.')
tf.logging.info("%s stopped (time in second %.2f).",
type(application).__name__, (time.time() - start_time))
def _training_loop(self, sess, loop_status):
"""
At each iteration, an ``IterationMessage`` object is created
to send network output to/receive controlling messages from self.app.
The iteration message will be passed into `self.run_vars`,
where graph elements to run are collected and feed into `session.run()`.
A nested validation loop will be running
if self.validation_every_n > 0. During the validation loop
the network parameters remain unchanged.
"""
iter_msg = IterationMessage()
# initialise tf summary writers
writer_train = tf.summary.FileWriter(
os.path.join(self.summary_dir, TRAIN), sess.graph)
writer_valid = tf.summary.FileWriter(
os.path.join(self.summary_dir, VALID), sess.graph) \
if self.validation_every_n > 0 else None
for iter_i in range(self.initial_iter, self.final_iter):
# general loop information
loop_status['current_iter'] = iter_i
if self._coord.should_stop():
break
if iter_msg.should_stop:
break
# update variables/operations to run, from self.app
iter_msg.current_iter, iter_msg.phase = iter_i, TRAIN
self.run_vars(sess, iter_msg)
self.app.interpret_output(
iter_msg.current_iter_output[NETWORK_OUTPUT])
iter_msg.to_tf_summary(writer_train)
tf.logging.info(iter_msg.to_console_string())
# run validations if required
if iter_i > 0 and self.validation_every_n > 0 and \
(iter_i % self.validation_every_n == 0):
for _ in range(self.validation_max_iter):
iter_msg.current_iter, iter_msg.phase = iter_i, VALID
self.run_vars(sess, iter_msg)
# save iteration results
if writer_valid is not None:
iter_msg.to_tf_summary(writer_valid)
tf.logging.info(iter_msg.to_console_string())
if self.save_every_n > 0 and (iter_i % self.save_every_n == 0):
self._save_model(sess, iter_i)
def test_set_fields(self):
msg = IterationMessage()
# setting iter will clear tic and iter output fields
msg.current_iter = 3
self.assertGreater(msg._current_iter_tic, 0.0)
self.assertEqual(msg._current_iter_output, None)
# setting iter output will update iter duration
msg.current_iter_output = {CONSOLE: {'test': 'test'}}
self.assertEqual(msg.current_iter, 3)
self.assertGreater(msg.iter_duration, 0.0)
self.assertRegexpMatches(msg.to_console_string(), '.*test=test.*')
with self.assertRaisesRegexp(ValueError, ''):
msg.current_iter = 'test'
def test_interfaces(self):
msg = IterationMessage()
msg.current_iter = 0
self.assertEqual(msg.current_iter, 0)
self.assertEqual(msg.ops_to_run, {})
self.assertEqual(msg.data_feed_dict, {})
self.assertEqual(msg.current_iter_output, None)
self.assertEqual(msg.should_stop, False)
self.assertEqual(msg.phase, TRAIN)
self.assertEqual(msg.is_training, True)
self.assertEqual(msg.is_validation, False)
self.assertEqual(msg.is_inference, False)
msg.current_iter_output = {'test'}
self.assertEqual(msg.current_iter_output, {'test'})
self.assertGreater(msg.iter_duration, 0.0)
self.assertStartsWith(msg.to_console_string(), 'Training')
self.assertEqual(msg.to_tf_summary(0), None)
def test_init(self):
ITER_FINISHED.connect(self.iteration_listener)
app_driver = get_initialised_driver()
app_driver.load_event_handlers([
'niftynet.engine.handler_model.ModelRestorer',
'niftynet.engine.handler_console.ConsoleLogger',
'niftynet.engine.handler_sampler.SamplerThreading'
])
graph = app_driver.create_graph(app_driver.app, 1, True)
with self.cached_session(graph=graph) as sess:
SESS_STARTED.send(app_driver.app, iter_msg=None)
msg = IterationMessage()
msg.current_iter = 1
app_driver.loop(app_driver.app, [msg])
app_driver.app.stop()
ITER_FINISHED.disconnect(self.iteration_listener)
def iter_generator(count_generator, phase):
""" Generate a numbered sequence of IterationMessage objects
with phase-appropriate signals.
count_generator is an iterable object yielding iteration numbers
phase is one of TRAIN, VALID or INFER
"""
signals = {TRAIN: (ApplicationDriver.pre_train_iter,
ApplicationDriver.post_train_iter),
VALID: (ApplicationDriver.pre_validation_iter,
ApplicationDriver.post_validation_iter),
INFER: (ApplicationDriver.pre_infer_iter,
ApplicationDriver.post_infer_iter)}
for iter_i in count_generator:
iter_msg = IterationMessage()
iter_msg.current_iter, iter_msg.phase = iter_i, phase
iter_msg.pre_iter = signals[phase][0]
iter_msg.post_iter = signals[phase][1]
yield iter_msg
def iter_generator(count_generator, phase):
""" Generate a numbered sequence of IterationMessage objects
with phase-appropriate signals.
count_generator is an iterable object yielding iteration numbers
phase is one of TRAIN, VALID or INFER
"""
signals = {
TRAIN:
(ApplicationDriver.pre_train_iter, ApplicationDriver.post_train_iter),
VALID: (ApplicationDriver.pre_validation_iter,
ApplicationDriver.post_validation_iter),
INFER:
(ApplicationDriver.pre_infer_iter, ApplicationDriver.post_infer_iter)
}
for iter_i in count_generator:
iter_msg = IterationMessage()
iter_msg.current_iter, iter_msg.phase = iter_i, phase
iter_msg.pre_iter = signals[phase][0]
iter_msg.post_iter = signals[phase][1]
yield iter_msg
def test_set_fields(self):
msg = IterationMessage()
# setting iter will clear tic and iter output fields
msg.current_iter = 3
self.assertGreater(msg._current_iter_tic, 0.0)
self.assertEqual(msg._current_iter_output, None)
# setting iter output will update iter duration
msg.current_iter_output = {CONSOLE: {'test': 'test'}}
self.assertEqual(msg.current_iter, 3)
self.assertGreater(msg.iter_duration, 0.0)
self.assertRegexpMatches(msg.to_console_string(), '.*test=test.*')
with self.assertRaisesRegexp(ValueError, ''):
msg.current_iter = 'test'
def test_interfaces(self):
msg = IterationMessage()
msg.current_iter = 0
self.assertEqual(msg.current_iter, 0)
self.assertEqual(msg.ops_to_run, {})
self.assertEqual(msg.data_feed_dict, {})
self.assertEqual(msg.current_iter_output, None)
self.assertEqual(msg.should_stop, None)
self.assertEqual(msg.phase, TRAIN)
self.assertEqual(msg.is_training, True)
self.assertEqual(msg.is_validation, False)
self.assertEqual(msg.is_inference, False)
msg.current_iter_output = {'test'}
self.assertEqual(msg.current_iter_output, {'test'})
self.assertGreater(msg.iter_duration, 0.0)
self.assertStartsWith(msg.to_console_string(), 'training')
self.assertEqual(msg.to_tf_summary(0), None)
def run_application(self):
"""
Initialise a TF graph, connect data sampler and network within
the graph context, run training loops or inference loops.
The training loop terminates when ``self.final_iter`` reached.
The inference loop terminates when there is no more
image sample to be processed from image reader.
:return:
"""
config = ApplicationDriver._tf_config()
with tf.Session(config=config, graph=self.graph) as session:
# start samplers' threads
self._run_sampler_threads(session=session)
self.graph = self._create_graph(self.graph)
# check app variables initialised and ready for starts
self.app.check_initialisations()
# initialise network trainable parameters
self._rand_init_or_restore_vars(session)
start_time = time.time()
loop_status = {}
try:
# iteratively run the graph
if self.is_training:
self.model_saver = ModelSaver(session, self.saver,
self.save_every_n,
self.session_prefix)
loop_status['current_iter'] = self.initial_iter
self._training_loop(session, loop_status)
else:
loop_status['all_saved_flag'] = False
self._inference_loop(session, loop_status)
except KeyboardInterrupt:
tf.logging.warning('User cancelled application')
except tf.errors.OutOfRangeError:
if loop_status.get('all_saved_flag', None) is not None:
# reached the end of inference Dataset
loop_status['all_saved_flag'] = True
except RuntimeError:
import sys
import traceback
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(
exc_type, exc_value, exc_traceback, file=sys.stdout)
finally:
tf.logging.info('Cleaning up...')
if self.is_training:
# saving model at the last iteration
iter_msg = IterationMessage()
iter_msg.current_iter = loop_status.get('current_iter', -1)
self.post_training.send(iter_msg)
elif not loop_status.get('all_saved_flag', None):
tf.logging.warning('stopped early, incomplete loops')
tf.logging.info('stopping sampling threads')
self.app.stop()
tf.logging.info(
"%s stopped (time in second %.2f).",
type(self.app).__name__, (time.time() - start_time))
def test_run_vars(self):
app_driver = get_initialised_driver()
test_graph = app_driver._create_graph(app_driver.graph)
test_tensor = app_driver.graph.get_tensor_by_name(
"G/conv_bn_selu/conv_/w:0")
with self.test_session(graph=test_graph) as sess:
app_driver._run_sampler_threads()
app_driver._run_sampler_threads(sess)
sess.run(app_driver._init_op)
iter_msg = IterationMessage()
# run 1st training iter
iter_msg.current_iter, iter_msg.phase = 1, TRAIN
app_driver.run_vars(sess, iter_msg)
model_value_1 = sess.run(test_tensor)
self.assertGreater(iter_msg.iter_duration, 0.0)
print(iter_msg.to_console_string())
self.assertRegexpMatches(iter_msg.to_console_string(), 'Training')
# run 2nd training iter
iter_msg.current_iter, iter_msg.phase = 2, TRAIN
app_driver.run_vars(sess, iter_msg)
model_value_2 = sess.run(test_tensor)
# make sure model gets updated
self.assertNotAlmostEqual(
np.mean(np.abs(model_value_1 - model_value_2)), 0.0)
print(iter_msg.to_console_string())
self.assertRegexpMatches(iter_msg.to_console_string(), 'Training')
# run validation iter
iter_msg.current_tier, iter_msg.phase = 3, VALID
app_driver.run_vars(sess, iter_msg)
model_value_3 = sess.run(test_tensor)
# make sure model not gets udpated
self.assertAlmostEqual(
np.mean(np.abs(model_value_2 - model_value_3)), 0.0)
print(iter_msg.to_console_string())
self.assertRegexpMatches(iter_msg.to_console_string(), 'Validation')
# run training iter
iter_msg.current_iter, iter_msg.phase = 4, TRAIN
app_driver.run_vars(sess, iter_msg)
model_value_4 = sess.run(test_tensor)
# make sure model gets updated
self.assertNotAlmostEqual(
np.mean(np.abs(model_value_2 - model_value_4)), 0.0)
self.assertNotAlmostEqual(
np.mean(np.abs(model_value_3 - model_value_4)), 0.0)
print(iter_msg.to_console_string())
self.assertRegexpMatches(iter_msg.to_console_string(), 'Training')
app_driver.app.stop()
self.assertEqual(iter_msg.ops_to_run, {})
def test_run_vars(self):
app_driver = get_initialised_driver()
test_graph = app_driver._create_graph(app_driver.graph)
test_tensor = app_driver.graph.get_tensor_by_name(
"G/conv_bn_selu/conv_/w:0")
with self.test_session(graph=test_graph) as sess:
app_driver._run_sampler_threads()
app_driver._run_sampler_threads(sess)
sess.run(app_driver._init_op)
iter_msg = IterationMessage()
# run 1st training iter
iter_msg.current_iter, iter_msg.phase = 1, TRAIN
app_driver.run_vars(sess, iter_msg)
model_value_1 = sess.run(test_tensor)
self.assertGreater(iter_msg.iter_duration, 0.0)
print(iter_msg.to_console_string())
self.assertRegexpMatches(iter_msg.to_console_string(), 'Training')
# run 2nd training iter
iter_msg.current_iter, iter_msg.phase = 2, TRAIN
app_driver.run_vars(sess, iter_msg)
model_value_2 = sess.run(test_tensor)
# make sure model gets updated
self.assertNotAlmostEqual(
np.mean(np.abs(model_value_1 - model_value_2)), 0.0)
print(iter_msg.to_console_string())
self.assertRegexpMatches(iter_msg.to_console_string(), 'Training')
# run validation iter
iter_msg.current_tier, iter_msg.phase = 3, VALID
app_driver.run_vars(sess, iter_msg)
model_value_3 = sess.run(test_tensor)
# make sure model not gets udpated
self.assertAlmostEqual(
np.mean(np.abs(model_value_2 - model_value_3)), 0.0)
print(iter_msg.to_console_string())
self.assertRegexpMatches(iter_msg.to_console_string(),
'Validation')
# run training iter
iter_msg.current_iter, iter_msg.phase = 4, TRAIN
app_driver.run_vars(sess, iter_msg)
model_value_4 = sess.run(test_tensor)
# make sure model gets updated
self.assertNotAlmostEqual(
np.mean(np.abs(model_value_2 - model_value_4)), 0.0)
self.assertNotAlmostEqual(
np.mean(np.abs(model_value_3 - model_value_4)), 0.0)
print(iter_msg.to_console_string())
self.assertRegexpMatches(iter_msg.to_console_string(), 'Training')
app_driver.app.stop()
self.assertEqual(iter_msg.ops_to_run, {})
def run_application(self):
"""
Initialise a TF graph, connect data sampler and network within
the graph context, run training loops or inference loops.
The training loop terminates when ``self.final_iter`` reached.
The inference loop terminates when there is no more
image sample to be processed from image reader.
:return:
"""
config = ApplicationDriver._tf_config()
with tf.Session(config=config, graph=self.graph) as session:
# start samplers' threads
self._run_sampler_threads(session=session)
self.graph = self._create_graph(self.graph)
# check app variables initialised and ready for starts
self.app.check_initialisations()
# initialise network trainable parameters
self._rand_init_or_restore_vars(session)
start_time = time.time()
loop_status = {}
try:
# iteratively run the graph
if self.is_training:
self.model_saver = ModelSaver(session, self.saver,
self.save_every_n,
self.session_prefix)
loop_status['current_iter'] = self.initial_iter
self._training_loop(session, loop_status)
else:
loop_status['all_saved_flag'] = False
self._inference_loop(session, loop_status)
except KeyboardInterrupt:
tf.logging.warning('User cancelled application')
except tf.errors.OutOfRangeError:
if loop_status.get('all_saved_flag', None) is not None:
# reached the end of inference Dataset
loop_status['all_saved_flag'] = True
except RuntimeError:
import sys
import traceback
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type,
exc_value,
exc_traceback,
file=sys.stdout)
finally:
tf.logging.info('Cleaning up...')
if self.is_training:
# saving model at the last iteration
iter_msg = IterationMessage()
iter_msg.current_iter = loop_status.get('current_iter', -1)
self.post_training.send(iter_msg)
elif not loop_status.get('all_saved_flag', None):
tf.logging.warning('stopped early, incomplete loops')
tf.logging.info('stopping sampling threads')
self.app.stop()
tf.logging.info("%s stopped (time in second %.2f).",
type(self.app).__name__,
(time.time() - start_time))
