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:
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 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 tearDownClass(cls):
Z.join_to_the_boundary()
cls.zmq_context.term()
if cls.old_hostname is not None:
os.environ['HOSTNAME'] = cls.old_hostname
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):
'''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.
def tearDownClass(cls):
Z.join_to_the_boundary()
cls.zmq_context.term()
def tearDownClass(cls):
Z.join_to_the_boundary()
cls.zmq_context.term()
def tearDownClass(cls):
Z.join_to_the_boundary()
cls.zmq_context.term()
if cls.old_hostname is not None:
os.environ['HOSTNAME'] = cls.old_hostname
