def finalize(self, result):
import wx
if self.enabled:
from cellprofiler.utilities.jutil import kill_vm
kill_vm()
os._exit(0)
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 finalize(self, result):
try:
import imagej.ijbridge as ijbridge
if ijbridge.inter_proc_ij_bridge._isInstantiated():
ijbridge.get_ij_bridge().quit()
except:
pass
try:
from cellprofiler.utilities.jutil import kill_vm
kill_vm()
os._exit(0)
except:
pass
def finalize(self, result):
try:
import imagej.ijbridge as ijbridge
if ijbridge.inter_proc_ij_bridge._isInstantiated():
ijbridge.get_ij_bridge().quit()
except:
pass
try:
from cellprofiler.utilities.jutil import kill_vm
kill_vm()
os._exit(0)
except:
pass
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 on_close(self, evt=None):
# Classifier needs to be told to close so it can clean up it's threads
classifier = wx.FindWindowById(ID_CLASSIFIER) or wx.FindWindowByName('Classifier')
if classifier and classifier.Close() == False:
return
if any(wx.GetApp().get_plots()):
dlg = wx.MessageDialog(self, 'Some tools are open, are you sure you want to quit CPA?', 'Quit CellProfiler Analyst?', wx.YES_NO|wx.NO_DEFAULT|wx.ICON_QUESTION)
response = dlg.ShowModal()
if response != wx.ID_YES:
return
try:
from cellprofiler.utilities.jutil import kill_vm
kill_vm()
except:
print "Failed to kill the Java VM"
# Blow up EVVVVERYTHIIINGGG!!! Muahahahahhahahah!
for win in wx.GetTopLevelWindows():
logging.debug('Destroying: %s'%(win))
win.Destroy()
if self.tbicon is not None:
self.tbicon.Destroy()
self.Destroy()
def get_plugin(classname):
"""Return an instance of the named plugin"""
if classname.startswith("ij."):
cls = J.class_for_name(classname)
else:
cls = J.class_for_name(classname, get_user_loader())
cls = J.get_class_wrapper(cls, True)
constructor = J.get_constructor_wrapper(cls.getConstructor(None))
return constructor.newInstance(None)
if __name__ == "__main__":
import sys
J.attach()
try:
commands = get_commands()
print "Commands: "
for command in commands:
print "\t" + command
if len(sys.argv) == 2:
execute_command(sys.argv[1])
elif len(sys.argv) > 2:
execute_command(sys.argv[1], sys.argv[2])
finally:
J.detach()
J.kill_vm()
if len(files):
data_files.append([path, files])
for subdirectory in directories:
add_jre_files(subdirectory)
add_jre_files("jre")
data_files += [("jre\\ext", [os.path.join(jdk_dir, "lib", "tools.jar")])]
#
# Call setup
#
try:
setup(console=[{'script':'CellProfiler.py',
'icon_resources':[(1,'CellProfilerIcon.ico')]},
{'script':'cellprofiler\\analysis_worker.py'}],
name='Cell Profiler',
data_files = data_files,
cmdclass={'msi':CellProfilerMSI
},
options=opts)
finally:
try:
import cellprofiler.utilities.jutil as jutil
jutil.kill_vm()
sys.stderr.flush()
sys.stdout.flush()
os._exit(0)
except:
import traceback
traceback.print_exc()
print "Caught exception while killing VM"
if (delete_action.upper() == "ALL") or (delete_action.upper() == "DONE"):
remove_if_exists(RunBatch.RunDoneFilePath(my_batch, my_run))
elif form.has_key("batch_id"):
batch_id = int(form["batch_id"].value)
my_batch = RunBatch.LoadBatch(batch_id)
for my_run in my_batch["runs"]:
if ((delete_action.upper() == "ALL") or (delete_action.upper() == "TEXT")):
remove_if_exists(RunBatch.RunTextFilePath(my_batch, my_run))
if (delete_action.upper() == "ALL") or (delete_action.upper() == "OUTPUT"):
remove_if_exists(RunBatch.RunOutFilePath(my_batch, my_run))
if (delete_action.upper() == "ALL") or (delete_action.upper() == "DONE"):
remove_if_exists(RunBatch.RunDoneFilePath(my_batch, my_run))
url = "ViewBatch.py?batch_id=%(batch_id)d"%(my_batch)
print "Content-Type: text/html"
print
print "<html><head>"
print "<meta http-equiv='refresh' content='0; URL=%(url)s' />"%(globals())
print "</head>"
print "<body>This page should be redirected to <a href='%(url)s'/>%(url)s</a></body>"%(globals())
print "</html>"
try:
import cellprofiler.utilities.jutil as jutil
jutil.kill_vm()
except:
import traceback
traceback.print_exc()
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):
'''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",
"()Ljava/lang/ClassLoader;")
def get_plugin(classname):
'''Return an instance of the named plugin'''
if classname.startswith("ij."):
cls = J.class_for_name(classname)
else:
cls = J.class_for_name(classname, get_user_loader())
cls = J.get_class_wrapper(cls, True)
constructor = J.get_constructor_wrapper(cls.getConstructor(None))
return constructor.newInstance(None)
if __name__ == "__main__":
import sys
J.attach()
try:
commands = get_commands()
print "Commands: "
for command in commands:
print "\t" + command
if len(sys.argv) == 2:
execute_command(sys.argv[1])
elif len(sys.argv) > 2:
execute_command(sys.argv[1], sys.argv[2])
finally:
J.detach()
J.kill_vm()
def finalize(self, result):
import wx
if self.enabled:
from cellprofiler.utilities.jutil import kill_vm
kill_vm()
os._exit(0)
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")
