def OnExit(self):
from imagej.imagej2 import allow_quit
allow_quit()
from javabridge import deactivate_awt
deactivate_awt()
# restore previous exception hook
sys.excepthook = self.orig_excepthook
def OnExit(self):
from imagej.imagej2 import allow_quit
allow_quit()
from javabridge import deactivate_awt
deactivate_awt()
# restore previous exception hook
sys.excepthook = self.orig_excepthook
def OnExit(self):
from imagej.imagej2 import allow_quit
allow_quit()
from cellprofiler.utilities.jutil import deactivate_awt
deactivate_awt()
# restore previous exception hook
sys.excepthook = self.orig_excepthook
def cp_stop_vm(kill=True):
'''Shut down the Java VM
Check for headlessness and the state of ImageJ and take
whatever action is needed to stop AWT and the JVM.
'''
from imagej.imagej2 import allow_quit, the_imagej_context
try:
ij1 = javabridge.JClassWrapper("ij.IJ").getInstance()
except javabridge.JavaException as e:
logger.debug("No available instance: %s" % str(e))
ij1 = None
if the_imagej_context is not None:
#
# Tell the app service that it's OK to quit without prompt
#
allow_quit()
javabridge.call(the_imagej_context.getContext(), "dispose", "()V")
if ij1 is not None:
#
# Yes, the proper way to get ImageJ to quit is
# to start it.
#
ij1.run()
if kill:
javabridge.kill_vm()
def cp_stop_vm(kill=True):
'''Shut down the Java VM
Check for headlessness and the state of ImageJ and take
whatever action is needed to stop AWT and the JVM.
'''
from imagej.imagej2 import allow_quit, the_imagej_context
try:
ij1 = javabridge.JClassWrapper("ij.IJ").getInstance()
except javabridge.JavaException as e:
logger.debug("No available instance: %s" % str(e))
ij1 = None
if the_imagej_context is not None:
#
# Tell the app service that it's OK to quit without prompt
#
allow_quit()
javabridge.call(the_imagej_context.getContext(), "dispose", "()V")
if ij1 is not None:
#
# Yes, the proper way to get ImageJ to quit is
# to start it.
#
ij1.run()
if kill:
javabridge.kill_vm()
def OnExit(self):
from imagej.imagej2 import allow_quit
allow_quit()
from cellprofiler.utilities.jutil import deactivate_awt
deactivate_awt()
# restore previous exception hook
sys.excepthook = self.orig_excepthook
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():
#
# 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
# 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:
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():
#
# 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()
# Limit Ilastik to one job thread.
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.set_thread_count(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:
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 cp_stop_vm(kill=True):
'''Shut down the Java VM
Check for headlessness and the state of ImageJ and take
whatever action is needed to stop AWT and the JVM.
'''
if not cpprefs.get_awt_headless():
from imagej.imagej2 import allow_quit, the_imagej_context
ij1 = javabridge.JClassWrapper("ij.IJ").getInstance()
if ij1 is not None and ij1.isVisible():
#
# If legacy ImageJ is visible, then we have
# to pick it apart in order to get around
# the "Fiji won't quit" bug:
#
# http://fiji.sc/2014-07-11_-_Fiji_won%27t_quit!
# http://fiji.sc/bugzilla/show_bug.cgi?id=805
# https://github.com/fiji/fiji/issues/94
# https://bugs.openjdk.java.net/browse/JDK-8061307
#
# The following code was needed in order to get around
# the JDK problem on Red Hat 6 OpenJDK 1.7.0_79
#
env = javabridge.get_env()
#
# Use the window manager to find all of the ImagePlus windows.
# Tell them that it's OK to close w/o prompt.
# Close them all.
#
wm = javabridge.JClassWrapper("ij.WindowManager")
for i in range(1, wm.getImageCount()+1):
wm.getImage(i).changes = False
wm.closeAllWindows()
#
# Pick apart and destroy IJ1's menus
#
menubar = ij1.getMenuBar()
if menubar is not None:
while menubar.getMenuCount() > 0:
menubar.remove(menubar.getMenu(0))
#
# Mercilessly pick apart all other windows
# This throws the exception described in JDK-8061307
#
try:
ij1.removeAll()
except:
logger.info("Caught expected AWT exception", exc_info=1)
if the_imagej_context is not None:
#
# Tell the app service that it's OK to quit without prompt
#
allow_quit()
app = javabridge.JWrapper(the_imagej_context.getService(
"org.scijava.app.AppService")).getApp()
app.quit()
if ij1 is not None:
#
# Yes, the proper way to get ImageJ to quit is
# to start it.
#
ij1.run()
#
# Account for a "bug" in javabridge.1.0.11 that doesn't shelter
# the caller of deactivate_awt() from the OpenJDK bug.
#
if javabridge.__version__ < "1.0.12":
javabridge.jutil.CLOSE_ALL_WINDOWS = """
new java.lang.Runnable() {
run: function() {
var all_frames = java.awt.Frame.getFrames();
if (all_frames) {
for (idx in all_frames) {
try {
all_frames[idx].dispose();
} catch (err) {
}
}
}
}
}"""
javabridge.jutil.deactivate_awt()
if kill:
javabridge.kill_vm()
def OnExit(self):
from imagej.imagej2 import allow_quit
allow_quit()
# restore previous exception hook
sys.excepthook = self.orig_excepthook
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 imagej.imagej2 import allow_quit, quit
allow_quit()
quit()
except:
logging.root.warn("Failed to dispose of ImageJ")
try:
from javabridge import kill_vm
kill_vm()
except:
logging.root.warn("Failed to stop the JVM")
os._exit(0)
def parse_args(args):
'''Parse the CellProfiler command-line arguments'''
import optparse
usage = """usage: %prog [options] [<output-file>])
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 imagej.imagej2 import allow_quit, quit
allow_quit()
quit()
except:
logging.root.warn("Failed to dispose of ImageJ")
try:
from javabridge import kill_vm
kill_vm()
except:
logging.root.warn("Failed to stop the JVM")
os._exit(0)
def parse_args(args):
'''Parse the CellProfiler command-line arguments'''
import optparse
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
# 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:
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 OnExit(self):
from imagej.imagej2 import allow_quit
allow_quit()
# restore previous exception hook
sys.excepthook = self.orig_excepthook
