def _run_sampler_threads(self, session=None):
"""
Get samplers from application and try to run sampler threads.
Note: Overriding app.get_sampler() method by returning None to bypass
this step.
:param session: TF session used for fill
tf.placeholders with sampled data
:return:
"""
if session is None:
return
if self._coord is None:
return
if self.num_threads <= 0:
return
try:
samplers = self.app.get_sampler()
for sampler in traverse_nested(samplers):
if sampler is None:
continue
sampler.run_threads(session, self._coord, self.num_threads)
tf.logging.info('Filling queues (this can take a few minutes)')
except (NameError, TypeError, AttributeError, IndexError):
tf.logging.fatal(
"samplers not running, pop_batch_op operations "
"are blocked.")
raise
def _run_sampler_threads(self, session=None):
"""
Get samplers from application and try to run sampler threads.
Note: Overriding app.get_sampler() method by returning None to bypass
this step.
:param session: TF session used for fill
tf.placeholders with sampled data
:return:
"""
if session is None:
return
if self._coord is None:
return
if self.num_threads <= 0:
return
try:
samplers = self.app.get_sampler()
for sampler in traverse_nested(samplers):
if sampler is None:
continue
sampler.run_threads(session, self._coord, self.num_threads)
tf.logging.info('Filling queues (this can take a few minutes)')
except (NameError, TypeError, AttributeError, IndexError):
tf.logging.fatal("samplers not running, pop_batch_op operations "
"are blocked.")
raise
def stop(self):
"""
stop the sampling threads if there's any.
:return:
"""
for sampler in util_common.traverse_nested(self.get_sampler()):
if sampler is None:
continue
sampler.close_all()
def stop(self):
"""
stop the sampling threads if there's any.
:return:
"""
for sampler in util_common.traverse_nested(self.get_sampler()):
if sampler is None:
continue
sampler.close_all()
def stop_sampler_threads(self, sender, **_unused_msg):
"""
Stop the sampler's threads
:param sender: an instance of niftynet.application
:param _unused_msg:
:return:
"""
try:
tf.logging.info('stopping sampling threads')
for sampler in traverse_nested(sender.get_sampler()):
if sampler is None:
continue
sampler.close_all()
except (AttributeError, TypeError):
pass
def create_graph(application,
num_gpus=1,
num_threads=1,
is_training_action=False):
"""
Create a TF graph based on self.app properties
and engine parameters.
:return:
"""
graph = tf.Graph()
main_device = device_string(num_gpus, 0, False, is_training_action)
outputs_collector = OutputsCollector(n_devices=max(num_gpus, 1))
gradients_collector = GradientsCollector(n_devices=max(num_gpus, 1))
# start constructing the graph, handling training and inference cases
with graph.as_default(), tf.device(main_device):
# initialise sampler
with tf.name_scope('Sampler'):
application.initialise_sampler()
for sampler in traverse_nested(application.get_sampler()):
sampler.set_num_threads(num_threads)
# initialise network, these are connected in
# the context of multiple gpus
application.initialise_network()
application.add_validation_flag()
# for data parallelism --
# defining and collecting variables from multiple devices
for gpu_id in range(0, max(num_gpus, 1)):
worker_device = device_string(num_gpus, gpu_id, True,
is_training_action)
scope_string = 'worker_{}'.format(gpu_id)
with tf.name_scope(scope_string), tf.device(worker_device):
# setup network for each of the multiple devices
application.connect_data_and_network(
outputs_collector, gradients_collector)
with tf.name_scope('MergeOutputs'):
outputs_collector.finalise_output_op()
application.outputs_collector = outputs_collector
application.gradients_collector = gradients_collector
GRAPH_CREATED.send(application, iter_msg=None)
return graph