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 get_cp_icon(size=None):
"""The CellProfiler icon as a wx.Icon"""
import wx
if sys.platform.startswith('win'):
path = os.path.join(get_builtin_images_path(), "CellProfilerIcon.ico")
icon = wx.EmptyIcon()
icon.LoadFile(path, wx.BITMAP_TYPE_ICO)
return icon
icon = wx.EmptyIcon()
icon.CopyFromBitmap(get_cp_bitmap(size))
return icon
def OnOpeningURL(self, type, url):
if type == wx.html.HTML_URL_IMAGE:
if url.startswith(MEMORY_SCHEME):
path = get_builtin_images_path()
full_path = os.path.join(path, url[len(MEMORY_SCHEME):])
if sys.platform.startswith("win"):
my_url = full_path
else:
my_url = "file:" + urllib.pathname2url(full_path)
return my_url
return wx.html.HTML_OPEN
def OnOpeningURL(self, type, url):
if type == wx.html.HTML_URL_IMAGE:
if url.startswith(MEMORY_SCHEME):
path = get_builtin_images_path()
full_path = os.path.join(path, url[len(MEMORY_SCHEME):])
if sys.platform.startswith("win"):
my_url = full_path
else:
my_url = "file:" + urllib.pathname2url(full_path)
return my_url
return wx.html.HTML_OPEN
def get_cp_icon(size=None):
"""The CellProfiler icon as a wx.Icon"""
import wx
if sys.platform.startswith('win'):
path = os.path.join(get_builtin_images_path(), "CellProfilerIcon.ico")
icon = wx.EmptyIcon()
icon.LoadFile(path, wx.BITMAP_TYPE_ICO)
return icon
icon = wx.EmptyIcon()
icon.CopyFromBitmap(get_cp_bitmap(size))
return icon
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():
#
# 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(), "data/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()
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
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()
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(), "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(),
"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 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():
# 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")
