def setUp(self):
context = zmq.Context.instance()
self.notify_addr = "inproc://" + uuid.uuid4().hex
self.socket_addr = "inproc://" + uuid.uuid4().hex
self.kill_pub = context.socket(zmq.PUB)
self.kill_pub.bind(self.notify_addr)
self.server = KnimeBridgeServer(context, self.socket_addr,
self.notify_addr, NOTIFY_STOP)
self.server.start()
self.session_id = uuid.uuid4().hex
self.socket = context.socket(zmq.REQ)
self.socket.connect(self.socket_addr)
def main():
#
# For OS/X set up the UI elements that users expect from
# an app.
#
if sys.platform == "darwin":
import os.path
icon_path = pkg_resources.resource_filename(
"cellprofiler", os.path.join("data", "icons", "CellProfiler.png"))
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
# Start the JVM
from cellprofiler_core.utilities.java import start_java, stop_java
start_java()
deadman_start_socket = the_zmq_context.socket(zmq.PAIR)
deadman_start_socket.bind(DEADMAN_START_ADDR)
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close, name="exit_on_stdin_close")
deadman_start_socket.recv()
deadman_start_socket.close()
from cellprofiler.knime_bridge import KnimeBridgeServer
with Worker(work_announce_address) as worker:
worker_thread = threading.Thread(target=worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
with KnimeBridgeServer(the_zmq_context, knime_bridge_address,
NOTIFY_ADDR, NOTIFY_STOP):
worker_thread.join()
#
# Shutdown - need to handle some global cleanup here
#
try:
stop_java()
except:
logging.warning("Failed to stop the JVM", exc_info=True)
def main():
#
# For OS/X set up the UI elements that users expect from
# an app.
#
if sys.platform == "darwin":
from cellprofiler.icons import get_builtin_images_path
icon_path = os.path.join(get_builtin_images_path(), "artwork/CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
# Start the JVM
from cellprofiler.utilities.cpjvm import cp_start_vm, cp_stop_vm
cp_start_vm()
deadman_start_socket = the_zmq_context.socket(zmq.PAIR)
deadman_start_socket.bind(DEADMAN_START_ADDR)
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close,
name="exit_on_stdin_close")
deadman_start_socket.recv()
deadman_start_socket.close()
from cellprofiler.knime_bridge import KnimeBridgeServer
with AnalysisWorker(work_announce_address) as worker:
worker_thread = threading.Thread(target=worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
with KnimeBridgeServer(the_zmq_context,
knime_bridge_address,
NOTIFY_ADDR, NOTIFY_STOP):
worker_thread.join()
#
# Shutdown - need to handle some global cleanup here
#
try:
cp_stop_vm()
except:
logger.warn("Failed to stop the JVM", exc_info=1)
def main():
#
# For Windows build with Ilastik, look for site-packages
# in order to find Ilastik sources.
#
if hasattr(sys, 'frozen') and sys.platform == "win32":
root = os.path.split(sys.argv[0])[0]
if len(root) == 0:
root = os.curdir
root = os.path.abspath(root)
site_packages = os.path.join(root, 'site-packages').encode('utf-8')
if os.path.exists(site_packages) and os.path.isdir(site_packages):
import site
site.addsitedir(site_packages)
#
# For OS/X set up the UI elements that users expect from
# an app.
#
if sys.platform == "darwin":
from cellprofiler.icons import get_builtin_images_path
icon_path = os.path.join(get_builtin_images_path(),
"artwork/CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
# Start the JVM
from cellprofiler.utilities.cpjvm import cp_start_vm, cp_stop_vm
cp_start_vm()
deadman_start_socket = the_zmq_context.socket(zmq.PAIR)
deadman_start_socket.bind(DEADMAN_START_ADDR)
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close, name="exit_on_stdin_close")
deadman_start_socket.recv()
deadman_start_socket.close()
# Limit Ilastik to one job thread.
try:
from ilastik.core.jobMachine import GLOBAL_WM
try:
GLOBAL_WM.set_thread_count(1)
except:
GLOBAL_WM.setThreadCount(1)
except:
pass
from cellprofiler.knime_bridge import KnimeBridgeServer
with AnalysisWorker(work_announce_address) as worker:
worker_thread = threading.Thread(target=worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
with KnimeBridgeServer(the_zmq_context, knime_bridge_address,
NOTIFY_ADDR, NOTIFY_STOP):
enter_run_loop()
worker_thread.join()
#
# Shutdown - need to handle some global cleanup here
#
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logger.warn("Failed to stop Ilastik")
try:
cp_stop_vm()
except:
logger.warn("Failed to stop the JVM", exc_info=1)