def stop_cellprofiler():
join_to_the_boundary()
# Bioformats readers have to be properly closed.
# This is especially important when using OmeroReaders as leaving the
# readers open leaves the OMERO.server services open which in turn leads to
# high memory consumption.
bioformats.formatreader.clear_image_reader_cache()
stop_java()
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 OnExit(self):
stop_java()
return 0