def createSocket(self): self.identity = utils.identity() logger.debug('NEW IDENTITY: %s ' % self.identity) self.worker = self.ctx.socket(zmq.XREQ) self.worker.setsockopt(zmq.IDENTITY, self.identity) self.worker.connect('tcp://%s' % CONFIG['ROUTER']) self.worker.send('READY')
def forward(self, x): """Forwardpropagation pass""" # Layer_in a_in = np.matmul(x, self.w_in.T) + self.b_in z_in = relu(a_in) # Layer_rec a_rec = np.matmul(z_in, self.w_rec.T) + self.b_rec z_rec = relu(a_rec) # Layer_link a_link = np.matmul(np.matmul(x, self.w_reduce), self.w_link.T) z_link = identity(a_link) # Layer_out a_out = np.matmul(z_rec+z_link, self.w_out.T) + self.b_out y = relu(a_out) # Set internal state self._state.update({ 'x': x, 'y': y, 'a_out': a_out, 'z_link': z_link, 'a_link': a_link, 'z_rec': z_rec, 'a_rec': a_rec, 'z_in': z_in, 'a_in': a_in, }) return y
def segment_cells(image, max_cell_size): """Return segmented cells.""" image = identity(image) wall = threshold_adaptive_median(image, block_size=101) seeds = remove_small_objects(wall, min_size=100) seeds = dilate_binary(seeds) seeds = invert(seeds) seeds = remove_small_objects(seeds, min_size=5) seeds = connected_components(seeds, background=0) segmentation = watershed_with_seeds(-image, seeds=seeds) segmentation = remove_large_segments(segmentation, max_cell_size) return segmentation, wall
def main(): parser = argparse.ArgumentParser( description='Adopt pairwise aligner to generate identity matrix') parser.add_argument('fasta_path', type=str, help='the path of fasta files to parse') parser.add_argument('out_path', type=str, help='output dir') args = parser.parse_args([ '/home/ZwZ/database/M/linsi/M1_M2_unique.fasta', '/home/ZwZ/database/M/linsi/M1_M2_unique.npy' ]) fasta = read_fasta(args.fasta_path) identity_M = identity(fasta) np.save(args.out_path, identity_M)
def __init__(self): self.router = None self.stats = None self.storage = CONFIG['STORAGE'] self.cameras = {} self.current = collections.defaultdict(list) self.inprocessing = 0 self.processing_speed = 0 self.limiter = 0 self.bufferlen = CONFIG['BUFFERLEN'] self.context = zmq.Context.instance() self.loop = ioloop.IOLoop.instance() camera_address = CONFIG['CAMERA_ADDRESS'] camera_port = CONFIG['CAMERA_PORT'] router_address = CONFIG['ROUTER'] stats_address = CONFIG['STATS'] presenter_address = CONFIG['PRESENTER'] graph_address = CONFIG['GRAPH'] self.processing_buffer = collections.deque() self.timestamp_old = 0 self._camera = socket.socket(socket.AF_INET, socket.SOCK_STREAM, 0) self._camera.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) self._camera.setblocking(0) self._camera.bind((camera_address, camera_port)) self._camera.listen(10) self.loop.add_handler(self._camera.fileno(), self.cameraConnection, self.loop.READ) #if 'tracker-router.idt' in os.listdir('.'): # with open('tracker-router.idt', 'r') as f: # self.router_identity = f.read() #else: # self.router_identity = 'router-%s' % utils.identity() # with open('tracker-router.idt', 'w') as f: # f.write(self.router_identity) self.router_identity = 'router-%s' % utils.identity() logger.debug('ROUTER IDENTITY: %s' % self.router_identity) self._router = self.context.socket(zmq.XREQ) self._router.setsockopt(zmq.IDENTITY, self.router_identity) self._router.connect('tcp://%s' % router_address) self.router = zmqstream.ZMQStream(self._router, self.loop) self.router.on_recv(self.routerReceive) self.stats_identity = 'stats-%s' % utils.identity() logger.debug('STATS IDENTITY: %s' % self.stats_identity) self._stats = self.context.socket(zmq.PUB) self._stats.setsockopt(zmq.IDENTITY, self.stats_identity) self._stats.bind('tcp://%s' % stats_address) self.stats = zmqstream.ZMQStream(self._stats, self.loop) self.presenter_identity = 'presenter-%s' % utils.identity() logger.debug('PRESENTER IDENTITY: %s' % self.presenter_identity) self._presenter = self.context.socket(zmq.PUB) self._presenter.setsockopt(zmq.IDENTITY, self.presenter_identity) self._presenter.bind('tcp://%s' % presenter_address) self.presenter = zmqstream.ZMQStream(self._presenter, self.loop) self.graph_identity = 'graph-%s' % utils.identity() logger.debug('GRAPH IDENTITY: %s' % self.graph_identity) self._graph = self.context.socket(zmq.PUB) self._graph.setsockopt(zmq.IDENTITY, self.graph_identity) self._graph.bind('tcp://%s' % graph_address) self.graph = zmqstream.ZMQStream(self._graph, self.loop)
def __init__(self): ctx = zmq.Context() backend_identity = 'backend-%s' % utils.identity() frontend_identity = 'frontend-%s' % utils.identity() logger.debug('BACKEND: %s ' % backend_identity) logger.debug('FRONTEND: %s' % frontend_identity) frontend = ctx.socket(zmq.XREP) frontend.setsockopt(zmq.IDENTITY, frontend_identity) frontend.bind('tcp://%s' % CONFIG['FRONTEND']) backend = ctx.socket(zmq.XREP) backend.setsockopt(zmq.IDENTITY, backend_identity) backend.bind('tcp://%s' % CONFIG['BACKEND']) worker_queue = collections.deque() self.worker_all = 0 heartbeat = time.time() + CONFIG['HEART_INTER'] poller = zmq.Poller() poller.register(frontend, zmq.POLLIN) poller.register(backend, zmq.POLLIN) while True: socks = dict(poller.poll()) worker_queue = self.workerFlush(worker_queue) if backend in socks: message = backend.recv_multipart() worker = message[0] if len(message) == 2: action = message[1] if action == 'READY': self.workerDelete(worker, worker_queue) self.workerAppend(worker, worker_queue) elif action == 'HEARTBEAT': self.workerRefresh(worker, worker_queue) else: logger.debug('INVALID MESSAGE BACKEND') else: self.workerAppend(worker, worker_queue) frontend.send_multipart(message[1:]) if len(worker_queue): if frontend in socks: received = frontend.recv_multipart() expire = worker_queue.pop() destination = worker_queue.pop() message = [destination] message.extend(received) #message.extend(str(self.worker_all)) backend.send_multipart(message) if time.time() > heartbeat: for n, w in enumerate(worker_queue): if n % 2 == 0: backend.send_multipart([w, 'HEARTBEAT']) heartbeat = time.time() + CONFIG['HEART_INTER'] backend.close() frontend.close() ctx.term()