def save_locations(file_path, meta, port, event, topic='locations'):
socket = subscribe(port, topic)
with h5py.File(file_path, 'a') as f:
now = str(datetime.now())
g = f.create_group(now)
g.create_dataset('metadata', data=meta.encode('ascii', 'ignore'))
f.flush()
i = 0
last_x = 0
while not event.is_set():
topic = socket.recv_string()
data = socket.recv_pyobj()
data = data.values
data = data
x, y = data.shape[0], data.shape[
1] # The first values is the number of rows, h5py uses the opposite notation
if i == 0:
dset = g.create_dataset('locations', (x, y + 1),
maxshape=(None, y + 1))
else:
dset.resize((x + last_x, y + 1))
dset[last_x:last_x + x, 0] = i
dset[last_x:last_x + x, 1:] = data
last_x += x
i += 1
f.flush()
def calculate_locations(port, topic, event, publisher_queue, **kwargs):
socket = subscribe(port, topic)
if 'diameter' not in kwargs:
raise DiameterNotDefined('A diameter is mandatory for locating particles')
while not event.is_set():
socket.recv_string()
data = socket.recv_pyobj() # flags=0, copy=True, track=False)
image = data[1] # image[0] is the timestamp of the frame
locations = tp.locate(image, **kwargs)
publisher_queue.put({'topic': 'locations', 'data': locations})
def accumulate_links(self):
self._accumulate_links_event.clear()
socket = subscribe(self.publisher.port, 'particle_links')
while not self._accumulate_links_event.is_set():
if general_stop_event.is_set():
break
topic = socket.recv_string()
data = socket.recv_pyobj()
if self.locations.shape[0] == 0:
self.locations = data[0]
else:
self.locations = self.locations.append(data[0])
def link_locations(port, topic, event, publisher_queue, **kwargs):
if 'search_range' not in kwargs:
raise LinkException('Search Range must be specified')
socket = subscribe(port, topic)
t = 0 # First frame
linker = Linker(**kwargs)
while not event.is_set():
topic = socket.recv_string()
locations = socket.recv_pyobj()
coords = np.vstack((locations['x'], locations['y'])).T
if t == 0:
linker.init_level(coords, t)
else:
linker.next_level(coords, t)
t += 1
locations['particle'] = linker.particle_ids
locations['frame'] = t
publisher_queue.put({'topic': 'particle_links', 'data': [locations, linker.particle_ids]})
def accumulate_links(self):
""" Asynchronous method to store the links in this class. It looked like a good idea to keep this information in
a single location, regardless of whether another process is listening on the topic. This in principle can be
used to analyse data retrospectively.
.. todo:: Still needs to clear the memory after several calls. Need to fit better in the architecture of the
program
"""
self._accumulate_links_event.clear()
socket = subscribe(self.publisher.port, 'particle_links')
while not self._accumulate_links_event.is_set():
if general_stop_event.is_set():
break
topic = socket.recv_string()
data = socket.recv_pyobj()
if self.locations.shape[0] == 0:
self.locations = data[0]
else:
self.locations = self.locations.append(data[0])
def run(self):
socket = subscribe(self.port, self.topic)
while self.keep_receiving:
socket.recv_string()
data = socket.recv_pyobj() # flags=0, copy=True, track=False)
self.data_received.emit(data)