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 run(self, workspace):
'''Run the imageJ command'''
import imagej.ijbridge as ijbridge
J.attach()
ijb = None
try:
ijb = ijbridge.get_ij_bridge()
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
d = self.get_dictionary(workspace.image_set_list)
if self.wants_to_set_current_image:
input_image_name = self.current_input_image_name.value
img = image_set.get_image(input_image_name,
must_be_grayscale = True)
else:
img = None
#
# Run a command or macro on the first image of the set
#
if d[D_FIRST_IMAGE_SET] == image_set.number + 1:
self.do_imagej(ijb, workspace, D_FIRST_IMAGE_SET)
#
# Install the input image as the current image
#
if img is not None:
ijb.inject_image(img.pixel_data, input_image_name)
self.do_imagej(ijb, workspace)
#
# Get the output image
#
if self.wants_to_get_current_image:
output_image_name = self.current_output_image_name.value
pixel_data = ijb.get_current_image()
image = cpi.Image(pixel_data)
image_set.add(output_image_name, image)
#
# Execute the post-group macro or command
#
if d[D_LAST_IMAGE_SET] == image_set.number + 1:
self.do_imagej(ijb, workspace, D_LAST_IMAGE_SET)
#
# Save the current ImageJ image after executing the post-group
# command or macro
#
if (self.post_group_choice != CM_NOTHING and
self.wants_post_group_image):
output_image_name = self.post_group_output_image.value
pixel_data = ijb.get_current_image()
image = cpi.Image(pixel_data)
image_set.add(output_image_name, image)
if self.is_interactive():
self.display(workspace)
finally:
if ijb is not None:
del(ijb)
J.detach()
def run(self, workspace):
'''Run the imageJ command'''
import imagej.ijbridge as ijbridge
J.attach()
ijb = None
try:
ijb = ijbridge.get_ij_bridge()
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
d = self.get_dictionary(workspace.image_set_list)
if self.wants_to_set_current_image:
input_image_name = self.current_input_image_name.value
img = image_set.get_image(input_image_name,
must_be_grayscale=True)
else:
img = None
#
# Run a command or macro on the first image of the set
#
if d[D_FIRST_IMAGE_SET] == image_set.number + 1:
self.do_imagej(ijb, workspace, D_FIRST_IMAGE_SET)
#
# Install the input image as the current image
#
if img is not None:
ijb.inject_image(img.pixel_data, input_image_name)
self.do_imagej(ijb, workspace)
#
# Get the output image
#
if self.wants_to_get_current_image:
output_image_name = self.current_output_image_name.value
pixel_data = ijb.get_current_image()
image = cpi.Image(pixel_data)
image_set.add(output_image_name, image)
#
# Execute the post-group macro or command
#
if d[D_LAST_IMAGE_SET] == image_set.number + 1:
self.do_imagej(ijb, workspace, D_LAST_IMAGE_SET)
#
# Save the current ImageJ image after executing the post-group
# command or macro
#
if (self.post_group_choice != CM_NOTHING
and self.wants_post_group_image):
output_image_name = self.post_group_output_image.value
pixel_data = ijb.get_current_image()
image = cpi.Image(pixel_data)
image_set.add(output_image_name, image)
if self.is_interactive():
self.display(workspace)
finally:
if ijb is not None:
del (ijb)
J.detach()
def on_show_imagej(self):
'''Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
'''
import imagej.ijbridge as ijbridge
ijb = ijbridge.get_ij_bridge()
ijb.show_imagej()
def on_show_imagej(self):
'''Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
'''
if bioformats.USE_IJ2:
J.run_in_main_thread(
lambda: RunImageJ.get_context().loadService(
"imagej.ui.UIService"), True)
else:
import imagej.ijbridge as ijbridge
ijb = ijbridge.get_ij_bridge()
J.run_in_main_thread(lambda: ijb.show_imagej(), True)
def on_show_imagej(self):
'''Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
'''
if bioformats.USE_IJ2:
J.run_in_main_thread(
lambda :
RunImageJ.get_context().loadService("imagej.ui.UIService"),
True)
else:
import imagej.ijbridge as ijbridge
ijb = ijbridge.get_ij_bridge()
ijb.show_imagej()
def get_cached_commands():
global cached_commands
if cached_commands is None:
import cellprofiler.utilities.jutil as J
import imagej.ijbridge as ijbridge
ijb = ijbridge.get_ij_bridge()
commands = ijb.get_commands()
if hasattr(commands, 'values'):
values = commands.values
else:
values = [None] * len(commands)
cached_commands = {}
for key, value in zip(commands, values):
cached_commands[key] = value
return cached_commands
def get_cached_commands():
global cached_commands
global ij2_module_service
if cached_commands is None:
import imagej.ijbridge as ijbridge
ijb = ijbridge.get_ij_bridge()
import cellprofiler.utilities.jutil as J
commands = ijb.get_commands()
if hasattr(commands, 'values'):
values = commands.values
else:
values = [None] * len(commands)
cached_commands = {}
for key, value in zip(commands, values):
cached_commands[key] = value
return cached_commands
def get_context():
import imagej.ijbridge as ijbridge
ijb = ijbridge.get_ij_bridge()
return ijb.context
if measurements is not None:
del measurements # clean up
except Exception, e:
logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True)
raise
finally:
import gc
gc.collect(
) # This will clean up any remaining objects, calling their __del__ methods.
# Smokey, my friend, you are entering a world of pain.
# No $#!+ sherlock.
try:
import imagej.ijbridge as ijbridge
if ijbridge.inter_proc_ij_bridge._isInstantiated():
ijbridge.get_ij_bridge().quit()
except:
logging.root.warning("Caught exception while killing ijbridge.",
exc_info=True)
try:
if hasattr(sys, 'flags'):
if sys.flags.interactive:
assert False, "Don't kill JVM in interactive mode, because it calls exit()"
import cellprofiler.utilities.jutil as jutil
jutil.kill_vm()
except:
logging.root.warning("Caught exception while killing VM.",
exc_info=True)
os._exit(0)
fd = open(options.done_file, "wt")
fd.write("%s\n"%done_text)
fd.close()
if measurements is not None:
del measurements # clean up
except Exception, e:
logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True)
raise
finally:
import gc
gc.collect() # This will clean up any remaining objects, calling their __del__ methods.
# Smokey, my friend, you are entering a world of pain.
# No $#!+ sherlock.
try:
import imagej.ijbridge as ijbridge
if ijbridge.inter_proc_ij_bridge._isInstantiated():
ijbridge.get_ij_bridge().quit()
except:
logging.root.warning("Caught exception while killing ijbridge.", exc_info=True)
try:
if hasattr(sys, 'flags'):
if sys.flags.interactive:
assert False, "Don't kill JVM in interactive mode, because it calls exit()"
import cellprofiler.utilities.jutil as jutil
jutil.kill_vm()
except:
logging.root.warning("Caught exception while killing VM.", exc_info=True)
os._exit(0)
def get_context():
import imagej.ijbridge as ijbridge
ijb = ijbridge.get_ij_bridge()
return ijb.context