def test_03_02_command_service_run(self):
svc = ij2.get_command_service(self.context)
module_infos = ij2.get_module_service(self.context).getModules()
for module_info in module_infos:
if module_info.getClassName() == \
'imagej.core.commands.display.ShowLUT':
d = J.get_map_wrapper(J.make_instance('java/util/HashMap', '()V'))
future = svc.run(module_info.o, d.o)
module = future.get()
module = ij2.wrap_module(module)
module.getOutput('output')
break
else:
raise AssertionError("Could not find target module")
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
context = get_context()
self.get_command_settings(command, d)
wants_display = self.show_window
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
node = command.get_selected_leaf()
module_info = node[2]
input_dictionary = J.get_map_wrapper(
J.make_instance('java/util/HashMap', "()V"))
display_dictionary = {}
display_service = ij2.get_display_service(context)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
continue
field_name = module_item.getName()
field_type = module_item.getType()
raw_type = J.call(module_item.o, "getType", "()Ljava/lang/Class;")
if field_type in (ij2.FT_BOOL, ij2.FT_INTEGER, ij2.FT_FLOAT,
ij2.FT_STRING):
input_dictionary.put(field_name, J.box(setting.value, raw_type))
elif field_type == ij2.FT_COLOR:
assert isinstance(setting, cps.Color)
red, green, blue = setting.to_rgb()
jobject = J.make_instance(
"imagej/util/ColorRGB", "(III)V", red, green, blue)
input_dictionary.put(field_name, jobject)
elif field_type == ij2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
pixel_data = image.pixel_data * IMAGEJ_SCALE
dataset = ij2.create_dataset(
context, pixel_data, image_name)
display = display_service.createDisplay(image_name, dataset)
display_dictionary[module_item.getName()] = display
if image.has_mask:
#overlay_name = "X" + uuid.uuid4().get_hex()
#image_dictionary[overlay_name] = image.mask
overlay = ij2.create_overlay(context, image.mask)
overlay_service = ij2.get_overlay_service(context)
overlay_service.addOverlays(
display.o, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
input_dictionary.put(field_name, display.o)
if wants_display:
input_images.append((image_name, image.pixel_data))
elif field_type == ij2.FT_TABLE:
table_name = setting.value
table = workspace.object_set.get_type_instance(
IJ_TABLE_TYPE, table_name)
input_dictionary.put(field_name, table)
elif field_type == ij2.FT_FILE:
jfile = J.make_instance(
"java/io/File", "(Ljava/lang/String;)V", setting.value)
input_dictionary.put(field_name, jfile)
command_service = ij2.get_command_service(get_context())
future = command_service.run(module_info.o, input_dictionary.o)
module = future.get()
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
name = module_item.getName()
output_name = setting.value
if display_dictionary.has_key(name):
display = display_dictionary[name]
else:
display = IJ2.wrap_display(module.getOutput(name))
pixel_data = self.save_display_as_image(
workspace, display, output_name)
if wants_display:
output_images.append((output_name, pixel_data))
# Close any displays that we created.
for display in display_dictionary.values():
display.close()
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
context = get_context()
self.get_command_settings(command, d)
wants_display = self.show_window
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
node = command.get_selected_leaf()
module_info = node[2]
input_dictionary = J.get_map_wrapper(
J.make_instance('java/util/HashMap', "()V"))
display_dictionary = {}
display_service = ij2.get_display_service(context)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
continue
field_name = module_item.getName()
field_type = module_item.getType()
raw_type = J.call(module_item.o, "getType", "()Ljava/lang/Class;")
if field_type in (ij2.FT_BOOL, ij2.FT_INTEGER, ij2.FT_FLOAT,
ij2.FT_STRING):
input_dictionary.put(field_name, J.box(setting.value,
raw_type))
elif field_type == ij2.FT_COLOR:
assert isinstance(setting, cps.Color)
red, green, blue = setting.to_rgb()
jobject = J.make_instance("imagej/util/ColorRGB", "(III)V",
red, green, blue)
input_dictionary.put(field_name, jobject)
elif field_type == ij2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
pixel_data = image.pixel_data * IMAGEJ_SCALE
dataset = ij2.create_dataset(context, pixel_data, image_name)
display = display_service.createDisplay(image_name, dataset)
display_dictionary[module_item.getName()] = display
if image.has_mask:
#overlay_name = "X" + uuid.uuid4().get_hex()
#image_dictionary[overlay_name] = image.mask
overlay = ij2.create_overlay(context, image.mask)
overlay_service = ij2.get_overlay_service(context)
overlay_service.addOverlays(display.o,
J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
input_dictionary.put(field_name, display.o)
if wants_display:
input_images.append((image_name, image.pixel_data))
elif field_type == ij2.FT_TABLE:
table_name = setting.value
table = workspace.object_set.get_type_instance(
IJ_TABLE_TYPE, table_name)
input_dictionary.put(field_name, table)
elif field_type == ij2.FT_FILE:
jfile = J.make_instance("java/io/File",
"(Ljava/lang/String;)V", setting.value)
input_dictionary.put(field_name, jfile)
command_service = ij2.get_command_service(get_context())
future = command_service.run(module_info.o, input_dictionary.o)
module = future.get()
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
name = module_item.getName()
output_name = setting.value
if display_dictionary.has_key(name):
display = display_dictionary[name]
else:
display = IJ2.wrap_display(module.getOutput(name))
pixel_data = self.save_display_as_image(
workspace, display, output_name)
if wants_display:
output_images.append((output_name, pixel_data))
# Close any displays that we created.
for display in display_dictionary.values():
display.close()
