def finalize(self, result):
try:
if self.temp_images is not None:
import shutil
shutil.rmtree(self.temp_images)
if self.temp_exampleimages is not None:
import shutil
shutil.rmtree(self.temp_exampleimages)
except:
pass
from cellprofiler.utilities.cpjvm import cp_stop_vm
try:
import wx
app = wx.GetApp()
if app is not None:
app.ExitMainLoop()
app.MainLoop()
cp_stop_vm(kill=False)
except:
logging.root.warn("Failed to shut down AWT", exc_info=1)
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logging.root.warn("Failed to stop Ilastik")
try:
from cellprofiler.utilities.zmqrequest import join_to_the_boundary
join_to_the_boundary()
except:
logging.root.warn("Failed to stop zmq boundary")
def tearDownClass(cls):
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
pass
cls.notify_pub_socket.close()
def finalize(self, result):
try:
if self.temp_images is not None:
import shutil
shutil.rmtree(self.temp_images)
if self.temp_exampleimages is not None:
import shutil
shutil.rmtree(self.temp_exampleimages)
except:
pass
from cellprofiler.utilities.cpjvm import cp_stop_vm
try:
import wx
app = wx.GetApp()
if app is not None:
app.ExitMainLoop()
app.MainLoop()
cp_stop_vm(kill=False)
except:
logging.root.warn("Failed to shut down AWT", exc_info=1)
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logging.root.warn("Failed to stop Ilastik")
try:
from cellprofiler.utilities.zmqrequest import join_to_the_boundary
join_to_the_boundary()
except:
logging.root.warn("Failed to stop zmq boundary")
def finalize(self, result):
try:
javabridge.deactivate_awt()
import imagej.imagej2
if imagej.imagej2.the_imagej_context is not None:
script = """
new java.lang.Runnable () {
run: function() {
ctx.getContext().dispose();
}
}"""
runnable = javabridge.run_script(
script, dict(ctx=imagej.imagej2.the_imagej_context))
javabridge.execute_runnable_in_main_thread(runnable, True)
imagej.imagej2.the_imagej_context = None
javabridge.static_call("java/lang/System", "gc", "()V")
except:
pass
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logging.root.warn("Failed to stop Ilastik")
try:
from cellprofiler.utilities.zmqrequest import join_to_the_boundary
join_to_the_boundary()
except:
logging.root.warn("Failed to stop zmq boundary")
def teardown_package():
'''Shut down the Ilastik threads if they are up'''
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
pass
def teardown_package():
'''Shut down the Ilastik threads if they are up'''
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
pass
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(), "CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
J.javabridge.mac_run_loop_init()
# Importing bioformats starts the JVM
import bioformats
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close,
name="exit_on_stdin_close")
with stdin_monitor_lock:
while not stdin_monitor_started:
stdin_monitor_cv.wait()
with AnalysisWorker(work_announce_address) as worker:
worker_thread = threading.Thread(target = worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
print "Entering run loop"
enter_run_loop()
print "Exiting 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:
J.kill_vm()
except:
logger.warn("Failed to stop the Java VM")
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(),
"CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
J.javabridge.mac_run_loop_init()
# Importing bioformats starts the JVM
import bioformats
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close, name="exit_on_stdin_close")
with stdin_monitor_lock:
while not stdin_monitor_started:
stdin_monitor_cv.wait()
with AnalysisWorker(work_announce_address) as worker:
worker_thread = threading.Thread(target=worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
print "Entering run loop"
enter_run_loop()
print "Exiting 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:
J.kill_vm()
except:
logger.warn("Failed to stop the Java VM")
def shutdown_cellprofiler():
'''Oh sadness and so many threads that won't die...
'''
try:
import javabridge
javabridge.kill_vm()
except:
pass
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
pass
def shutdown_cellprofiler():
'''Oh sadness and so many threads that won't die...
'''
try:
import javabridge
javabridge.kill_vm()
except:
pass
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
pass
def stop_cellprofiler():
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logging.root.warn("Failed to stop Ilastik")
try:
from cellprofiler.utilities.zmqrequest import join_to_the_boundary
join_to_the_boundary()
except:
logging.root.warn("Failed to stop zmq boundary", exc_info=1)
try:
from cellprofiler.utilities.cpjvm import cp_stop_vm
cp_stop_vm()
except:
logging.root.warn("Failed to stop the JVM", exc_info=1)
def stop_cellprofiler():
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logging.root.warn("Failed to stop Ilastik")
try:
from cellprofiler.utilities.zmqrequest import join_to_the_boundary
join_to_the_boundary()
except:
logging.root.warn("Failed to stop zmq boundary", exc_info=1)
try:
from cellprofiler.utilities.cpjvm import cp_stop_vm
cp_stop_vm()
except:
logging.root.warn("Failed to stop the JVM", exc_info=1)
def main():
# XXX - move all this to a class
#
# 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(), "CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
J.javabridge.mac_run_loop_init()
# Importing bioformats starts the JVM
import bioformats
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close,
name="exit_on_stdin_close")
with stdin_monitor_lock:
while not stdin_monitor_started:
stdin_monitor_cv.wait()
with AnalysisWorker(work_announce_address) as worker:
worker_thread = threading.Thread(target = worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
print "Entering run loop"
enter_run_loop()
print "Exiting 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:
J.kill_vm()
except:
logger.warn("Failed to stop the Java VM")
def main():
# XXX - move all this to a class
parser = optparse.OptionParser()
parser.add_option("--work-announce",
dest="work_announce_address",
help="ZMQ port where work announcements are published",
default=None)
parser.add_option("--log-level",
dest="log_level",
help="Logging level for logger: DEBUG, INFO, WARNING, ERROR",
default=logging.INFO)
options, args = parser.parse_args()
logging.root.setLevel(options.log_level)
if not options.work_announce_address:
parser.print_help()
sys.exit(1)
# Start the deadman switch thread.
notify_started_cv = threading.Condition()
start_daemon_thread(target=exit_on_stdin_close,
name="exit_on_stdin_close",
args = (notify_started_cv, ))
with notify_started_cv:
notify_started_cv.wait()
try:
with AnalysisWorker(options.work_announce_address) as worker:
worker.run()
except CancelledException:
logger.debug("Exiting after cancellation")
finally:
#
# 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:
J.kill_vm()
except:
logger.warn("Failed to stop the Java VM")
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(), "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_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):
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:
from imagej.imagej2 import allow_quit
allow_quit()
except:
logger.warn("Failed to signal ImageJ to stop")
try:
J.kill_vm()
except:
logger.warn("Failed to stop the Java VM")
def main():
# XXX - move all this to a class
parser = optparse.OptionParser()
parser.add_option("--work-announce",
dest="work_announce_address",
help="ZMQ port where work announcements are published",
default=None)
parser.add_option(
"--log-level",
dest="log_level",
help="Logging level for logger: DEBUG, INFO, WARNING, ERROR",
default=logging.INFO)
options, args = parser.parse_args()
logging.root.setLevel(options.log_level)
if not options.work_announce_address:
parser.print_help()
sys.exit(1)
#
# 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(),
"CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
J.javabridge.mac_run_loop_init()
# Importing bioformats starts the JVM
import bioformats
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close, name="exit_on_stdin_close")
with stdin_monitor_lock:
while not stdin_monitor_started:
stdin_monitor_cv.wait()
with AnalysisWorker(options.work_announce_address) as worker:
worker_thread = threading.Thread(target=worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
print "Entering run loop"
enter_run_loop()
print "Exiting 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:
J.kill_vm()
except:
logger.warn("Failed to stop the Java VM")
if options.run_pipeline:
App.frame.pipeline_controller.do_analyze_images()
App.MainLoop()
return
elif options.run_pipeline:
run_pipeline_headless(options, args)
except Exception, e:
logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True)
raise
finally:
if __name__ == "__main__":
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logging.root.warn("Failed to stop Ilastik")
try:
from cellprofiler.utilities.zmqrequest import join_to_the_boundary
join_to_the_boundary()
except:
logging.root.warn("Failed to stop zmq boundary")
try:
from cellprofiler.utilities.jutil import kill_vm
kill_vm()
except:
logging.root.warn("Failed to stop the JVM")
os._exit(0)
def parse_args(args):
def main():
# XXX - move all this to a class
parser = optparse.OptionParser()
parser.add_option("--work-announce",
dest="work_announce_address",
help="ZMQ port where work announcements are published",
default=None)
parser.add_option("--log-level",
dest="log_level",
help="Logging level for logger: DEBUG, INFO, WARNING, ERROR",
default=logging.INFO)
options, args = parser.parse_args()
logging.root.setLevel(options.log_level)
if not options.work_announce_address:
parser.print_help()
sys.exit(1)
#
# 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(), "CellProfilerIcon.png")
os.environ["APP_NAME_%d" % os.getpid()] = "CellProfilerWorker"
os.environ["APP_ICON_%d" % os.getpid()] = icon_path
J.javabridge.mac_run_loop_init()
# Importing bioformats starts the JVM
import bioformats
# Start the deadman switch thread.
start_daemon_thread(target=exit_on_stdin_close,
name="exit_on_stdin_close")
with stdin_monitor_lock:
while not stdin_monitor_started:
stdin_monitor_cv.wait()
with AnalysisWorker(options.work_announce_address) as worker:
worker_thread = threading.Thread(target = worker.run,
name="WorkerThread")
worker_thread.setDaemon(True)
worker_thread.start()
print "Entering run loop"
enter_run_loop()
print "Exiting 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:
J.kill_vm()
except:
logger.warn("Failed to stop the Java VM")
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)
