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: 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 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 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)