def _get_fixed_stdout(self):
"""
this is to support ipykernel stdout
"""
import sys
from ipykernel import iostream
if isinstance(sys.stdout, iostream.OutStream):
stdout = iostream.OutStream(sys.stdout.session,
sys.stdout.pub_thread, 'omega-logger')
parent = dict(sys.stdout.parent_header)
stdout.set_parent(parent)
else:
stdout = sys.stdout
return stdout
def __init__(self, overlayList, displayCtx, frame):
"""Set up the kernel and ``zmq`` ports. A jupyter connection file
containing the information needed to connect to the kernel is saved
to a temporary file - its path is accessed as an attribute
called :meth:`connfile`.
:arg overlayList: The :class:`.OverlayList`.
:arg displayCtx: The master :class:`.DisplayContext`.
:arg frame: The :class:`.FSLeyesFrame`.
"""
ip = '127.0.0.1'
transport = 'tcp'
addr = '{}://{}'.format(transport, ip)
self.__connfile = None
self.__kernel = None
self.__error = None
self.__lastIter = 0
self.__overlayList = overlayList
self.__displayCtx = displayCtx
self.__frame = frame
self.__env = runscript.fsleyesScriptEnvironment(
frame, overlayList, displayCtx)[1]
self.__env['screenshot'] = self.__screenshot
with warnings.catch_warnings():
warnings.simplefilter('ignore', category=DeprecationWarning)
# Use an empty key to disable message signing
session = jcsession.Session(key=b'')
context = zmq.Context.instance()
# create sockets for kernel communication
shellsock = context.socket(zmq.ROUTER)
stdinsock = context.socket(zmq.ROUTER)
controlsock = context.socket(zmq.ROUTER)
iopubsock = context.socket(zmq.PUB)
shellstrm = zmqstream.ZMQStream(shellsock)
controlstrm = zmqstream.ZMQStream(controlsock)
# I/O and heartbeat communication
# are managed by separate threads.
self.__iopub = iostream.IOPubThread(iopubsock)
self.__heartbeat = heartbeat.Heartbeat(zmq.Context(),
(transport, ip, 0))
iopubsock = self.__iopub.background_socket
self.__heartbeat.start()
self.__iopub.start()
# Streams which redirect stdout/
# stderr to the iopub socket
stdout = iostream.OutStream(session, self.__iopub, u'stdout')
stderr = iostream.OutStream(session, self.__iopub, u'stderr')
# TCP ports for all sockets
shellport = shellsock.bind_to_random_port(addr)
stdinport = stdinsock.bind_to_random_port(addr)
controlport = controlsock.bind_to_random_port(addr)
iopubport = iopubsock.bind_to_random_port(addr)
hbport = self.__heartbeat.port
# Create the kernel
self.__kernel = FSLeyesIPythonKernel.instance(
stdout,
stderr,
shell_class=FSLeyesIPythonShell,
session=session,
shell_streams=[shellstrm, controlstrm],
iopub_socket=iopubsock,
stdin_socket=stdinsock,
user_ns=self.__env,
log=logging.getLogger('ipykernel.kernelbase'))
# write connection file to a temp dir
hd, fname = tempfile.mkstemp(prefix='fsleyes-kernel-{}.json'.format(
os.getpid()),
suffix='.json')
os.close(hd)
self.__connfile = fname
log.debug('IPython kernel connection file: %s', fname)
jc.write_connection_file(fname,
shell_port=shellport,
stdin_port=stdinport,
iopub_port=iopubport,
control_port=controlport,
hb_port=hbport,
ip=ip)
atexit.register(os.remove, self.__connfile)