def _acq_hook_startup_fn(pull_port, push_port, hook_connected_evt, event_queue,
hook_fn, debug):
bridge = Bridge(debug=debug)
push_socket = bridge._connect_push(pull_port)
pull_socket = bridge._connect_pull(push_port)
hook_connected_evt.set()
while True:
event_msg = pull_socket.receive()
if 'special' in event_msg and event_msg['special'] == 'acquisition-end':
push_socket.send({})
push_socket.close()
pull_socket.close()
return
else:
params = signature(hook_fn).parameters
if len(params) == 1 or len(params) == 3:
try:
if len(params) == 1:
new_event_msg = hook_fn(event_msg)
elif len(params) == 3:
new_event_msg = hook_fn(event_msg, bridge, event_queue)
except Exception as e:
warnings.warn(
'exception in acquisition hook: {}'.format(e))
continue
else:
raise Exception(
'Incorrect number of arguments for hook function. Must be 1 or 3'
)
push_socket.send(new_event_msg)
def _acq_hook_startup_fn(pull_port, push_port, hook_connected_evt, event_queue, hook_fn, debug):
"""
Parameters
----------
pull_port :
push_port :
hook_connected_evt :
event_queue :
hook_fn :
debug :
Returns
-------
"""
bridge = Bridge(debug=debug)
push_socket = bridge._connect_push(pull_port)
pull_socket = bridge._connect_pull(push_port)
hook_connected_evt.set()
while True:
event_msg = pull_socket.receive()
if "special" in event_msg and event_msg["special"] == "acquisition-end":
push_socket.send({})
push_socket.close()
pull_socket.close()
return
else:
if "events" in event_msg.keys():
event_msg = event_msg["events"] # convert from sequence
params = signature(hook_fn).parameters
if len(params) == 1 or len(params) == 3:
try:
if len(params) == 1:
new_event_msg = hook_fn(event_msg)
elif len(params) == 3:
new_event_msg = hook_fn(event_msg, bridge, event_queue)
except Exception as e:
warnings.warn("exception in acquisition hook: {}".format(e))
continue
else:
raise Exception("Incorrect number of arguments for hook function. Must be 1 or 3")
if isinstance(new_event_msg, list):
new_event_msg = {
"events": new_event_msg
} # convert back to the expected format for a sequence
push_socket.send(new_event_msg)
def _processor_startup_fn(pull_port, push_port, sockets_connected_evt, process_fn, event_queue, debug):
bridge = Bridge(debug=debug)
push_socket = bridge._connect_push(pull_port)
pull_socket = bridge._connect_pull(push_port)
if debug:
print('image processing sockets connected')
sockets_connected_evt.set()
def process_and_sendoff(image_tags_tuple):
if len(image_tags_tuple) != 2:
raise Exception('If image is returned, it must be of the form (pixel, metadata)')
if not image_tags_tuple[0].dtype == pixels.dtype:
raise Exception('Processed image pixels must have same dtype as input image pixels, '
'but instead they were {} and {}'.format(image_tags_tuple[0].dtype, pixels.dtype))
processed_img = {'pixels': serialize_array(image_tags_tuple[0]), 'metadata': image_tags_tuple[1]}
push_socket.send(processed_img)
while True:
message = None
while message is None:
message = pull_socket.receive(timeout=30) #check for new message
if 'special' in message and message['special'] == 'finished':
push_socket.send(message) #Continue propagating the finihsed signal
push_socket.close()
pull_socket.close()
return
metadata = message['metadata']
pixels = deserialize_array(message['pixels'])
image = np.reshape(pixels, [metadata['Height'], metadata['Width']])
params = signature(process_fn).parameters
if len(params) == 2 or len(params) == 4:
processed = None
try:
if len(params) == 2:
processed = process_fn(image, metadata)
elif len(params) == 4:
processed = process_fn(image, metadata, bridge, event_queue)
except Exception as e:
warnings.warn('exception in image processor: {}'.format(e))
continue
else:
raise Exception('Incorrect number of arguments for image processing function, must be 2 or 4')
if processed is None:
continue
if type(processed) == list:
for image in processed:
process_and_sendoff(image)
else:
process_and_sendoff(processed)
def _storage_monitor_fn(dataset,
storage_monitor_push_port,
connected_event,
callback_fn,
debug=False):
bridge = Bridge(debug=debug)
monitor_socket = bridge._connect_pull(storage_monitor_push_port)
connected_event.set()
while True:
message = monitor_socket.receive()
if "finished" in message:
# Poison, time to shut down
monitor_socket.close()
return
index_entry = message["index_entry"]
axes = dataset._add_index_entry(index_entry)
if callback_fn is not None:
callback_fn(axes)
def _processor_startup_fn(pull_port, push_port, sockets_connected_evt,
process_fn, event_queue, debug):
"""
Parameters
----------
pull_port :
push_port :
sockets_connected_evt :
process_fn :
event_queue :
debug :
Returns
-------
"""
bridge = Bridge(debug=debug)
push_socket = bridge._connect_push(pull_port)
pull_socket = bridge._connect_pull(push_port)
if debug:
print("image processing sockets connected")
sockets_connected_evt.set()
def process_and_sendoff(image_tags_tuple, original_dtype):
"""
Parameters
----------
image_tags_tuple :
Returns
-------
"""
if len(image_tags_tuple) != 2:
raise Exception(
"If image is returned, it must be of the form (pixel, metadata)"
)
pixels = image_tags_tuple[0]
metadata = image_tags_tuple[1]
# only accepts same pixel type as original
if not np.issubdtype(image_tags_tuple[0].dtype,
original_dtype) and not np.issubdtype(
original_dtype, image_tags_tuple[0].dtype):
raise Exception(
"Processed image pixels must have same dtype as input image pixels, "
"but instead they were {} and {}".format(
image_tags_tuple[0].dtype, pixels.dtype))
metadata[
"PixelType"] = "GRAY8" if pixels.dtype.itemsize == 1 else "GRAY16"
processed_img = {
"pixels": pixels.tobytes(),
"metadata": metadata,
}
push_socket.send(processed_img)
while True:
message = None
while message is None:
message = pull_socket.receive(timeout=30) # check for new message
if "special" in message and message["special"] == "finished":
push_socket.send(
message) # Continue propagating the finihsed signal
push_socket.close()
pull_socket.close()
return
metadata = message["metadata"]
pixels = deserialize_array(message["pixels"])
image = np.reshape(pixels, [metadata["Height"], metadata["Width"]])
params = signature(process_fn).parameters
if len(params) == 2 or len(params) == 4:
processed = None
try:
if len(params) == 2:
processed = process_fn(image, metadata)
elif len(params) == 4:
processed = process_fn(image, metadata, bridge,
event_queue)
except Exception as e:
warnings.warn("exception in image processor: {}".format(e))
continue
else:
raise Exception(
"Incorrect number of arguments for image processing function, must be 2 or 4"
)
if processed is None:
continue
if type(processed) == list:
for image in processed:
process_and_sendoff(image, pixels.dtype)
else:
process_and_sendoff(processed, pixels.dtype)
