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:
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 stop_cellprofiler():
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 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 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():
#
# 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.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 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
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.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)
def close(self):
self.__process_current_set(self.ctx)
cp_stop_vm()
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", exc_info=1)
try:
cp_stop_vm()
except:
logging.root.warn("Failed to stop the JVM", exc_info=1)
os._exit(0)
def parse_args(args):
'''Parse the CellProfiler command-line arguments'''
import optparse
usage = """usage: %prog [options] [<output-file>])
where <output-file> is the optional filename for the output file of
measurements when running headless.
The flags -p, -r and -c are required for a headless run."""
parser = optparse.OptionParser(usage=usage)
parser.add_option("-p", "--pipeline", "--project",
dest="pipeline_filename",
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)
def close(self):
self.__process_current_set(self.ctx)
cp_stop_vm()
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", exc_info=1)
try:
cp_stop_vm()
except:
logging.root.warn("Failed to stop the JVM", exc_info=1)
os._exit(0)
def parse_args(args):
'''Parse the CellProfiler command-line arguments'''
import optparse
usage = """usage: %prog [options] [<output-file>])
where <output-file> is the optional filename for the output file of
measurements when running headless.
The flags -p, -r and -c are required for a headless run."""
parser = optparse.OptionParser(usage=usage)
parser.add_option("-p",
