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 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 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()