def test_02_03_module_info(self):
svc = ij2.get_module_service(self.context)
#
# Run the methods without checks on the values to check signatures
module_infos = svc.getModules()
module_info = module_infos[0]
module_info.getMenuRoot()
module_info.getMenuPath()
module_info.createModule()
module_info.getTitle()
module_info.getName()
module_info.getClassName()
for module_info in module_infos:
inputs = module_info.getInputs()
if len(inputs) > 0:
module_item = inputs[0]
self.assertIsNotNone(module_info.getInput(module_item.getName()))
break
else:
raise AssertionError("No input items found")
for module_info in module_infos:
outputs = module_info.getOutputs()
if len(outputs) > 0:
module_item = outputs[0]
self.assertIsNotNone(module_info.getOutput(module_item.getName()))
break
else:
raise AssertionError("No output items found")
def execute_command(self, command, options=None):
'''execute the named command within ImageJ'''
module_service = IJ2.get_module_service(self.context)
matches = [x for x in module_service.getModules()
if x.getName() == command]
if len(matches) != 1:
raise ValueError("Could not find %s module" % command)
module_service.run(matches[0].createModule())
def execute_command(self, command, options=None):
'''execute the named command within ImageJ'''
module_service = IJ2.get_module_service(self.context)
matches = [x for x in module_service.getModules()
if x.getName() == command]
if len(matches) != 1:
raise ValueError("Could not find %s module" % command)
module_service.run(matches[0].createModule())
def test_02_02_02_get_module_index(self):
svc = ij2.get_module_service(self.context)
module_index = svc.getIndex()
self.assertTrue(any([
x.getClassName() == 'imagej.core.commands.assign.AddSpecifiedNoiseToDataValues'
for x in module_index]))
self.assertGreaterEqual(
len(module_index.getS('imagej.command.CommandInfo')), 1)
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 get_choice_tree(self):
'''Get the ImageJ command choices for the TreeChoice control
The menu items are augmented with a third tuple entry which is
the ModuleInfo for the command.
'''
global cached_choice_tree
global cached_commands
if cached_choice_tree is not None:
return cached_choice_tree
tree = []
context = get_context()
module_service = ij2.get_module_service(context)
for module_info in module_service.getModules():
if module_info.getMenuRoot() != "app":
continue
logger.info("Processing module %s" % module_info.getClassName())
menu_path = module_info.getMenuPath()
if menu_path is None or J.call(menu_path, "size", "()I") == 0:
continue
current_tree = tree
#
# The menu path is a collection of MenuEntry
#
for item in J.iterate_collection(menu_path):
menu_entry = ij2.wrap_menu_entry(item)
name = menu_entry.getName()
weight = menu_entry.getWeight()
matches = [node for node in current_tree if node[0] == name]
if len(matches) > 0:
current_node = matches[0]
else:
current_node = [name, [], None, weight]
current_tree.append(current_node)
current_tree = current_node[1]
# mark the leaf.
current_node[2] = module_info
def sort_tree(tree):
'''Recursively sort a tree in-place'''
for node in tree:
if node[1] is not None:
sort_tree(node[1])
tree.sort(lambda node1, node2: cmp(node1[-1], node2[-1]))
sort_tree(tree)
cached_choice_tree = tree
return cached_choice_tree
def get_choice_tree(self):
'''Get the ImageJ command choices for the TreeChoice control
The menu items are augmented with a third tuple entry which is
the ModuleInfo for the command.
'''
global cached_choice_tree
global cached_commands
if cached_choice_tree is not None:
return cached_choice_tree
tree = []
context = get_context()
module_service = ij2.get_module_service(context)
for module_info in module_service.getModules():
if module_info.getMenuRoot() != "app":
continue
logger.info("Processing module %s" % module_info.getClassName())
menu_path = module_info.getMenuPath()
if menu_path is None or J.call(menu_path, "size", "()I") == 0:
continue
current_tree = tree
#
# The menu path is a collection of MenuEntry
#
for item in J.iterate_collection(menu_path):
menu_entry = ij2.wrap_menu_entry(item)
name = menu_entry.getName()
weight = menu_entry.getWeight()
matches = [node for node in current_tree
if node[0] == name]
if len(matches) > 0:
current_node = matches[0]
else:
current_node = [name, [], None, weight]
current_tree.append(current_node)
current_tree = current_node[1]
# mark the leaf.
current_node[2] = module_info
def sort_tree(tree):
'''Recursively sort a tree in-place'''
for node in tree:
if node[1] is not None:
sort_tree(node[1])
tree.sort(lambda node1, node2: cmp(node1[-1], node2[-1]))
sort_tree(tree)
cached_choice_tree = tree
return cached_choice_tree
def test_02_05_module(self):
svc = ij2.get_module_service(self.context)
module_infos = svc.getModules()
for module_info in module_infos:
if module_info.getClassName() == \
'imagej.core.commands.assign.AddSpecifiedNoiseToDataValues':
module = module_info.createModule()
module.getInfo()
module.getInput('stdDev')
module.getOutput('display')
module.setInput('stdDev', 2.5)
module.setOutput('display', None)
module.isResolved('display')
module.setResolved('display', False)
break
else:
raise AssertionError("Could not find target module")
def get_choice_tree(self):
'''Get the ImageJ command choices for the TreeChoice control
The menu items are augmented with a third tuple entry which is
the ModuleInfo for the command.
'''
global cached_choice_tree
if cached_choice_tree is not None:
return cached_choice_tree
context = RunImageJ.get_context()
ij2_module_service = IJ2.get_module_service(context)
tree = []
for module_info in ij2_module_service.getModules():
menu_path = module_info.getMenuPath()
items = [
IJ2.wrap_menu_entry(x) for x in J.iterate_collection(menu_path)
]
if len(items) == 0:
continue
current_tree = tree
for item in items:
name = item.getName()
weight = item.getWeight()
matches = [node for node in current_tree if node[0] == name]
if len(matches) > 0:
current_node = matches[0]
else:
current_node = [name, [], module_info, weight]
current_tree.append(current_node)
current_tree = current_node[1]
# mark the leaf.
current_node[1] = None
def sort_tree(tree):
'''Recursively sort a tree in-place'''
for node in tree:
if node[1] is not None:
sort_tree(node[1])
tree.sort(lambda node1, node2: cmp(node1[-1], node2[-1]))
sort_tree(tree)
cached_choice_tree = tree
return cached_choice_tree
def test_02_04_module_item(self):
svc = ij2.get_module_service(self.context)
module_infos = svc.getModules()
for module_info in module_infos:
inputs = module_info.getInputs()
if len(inputs) > 0:
module_item = inputs[0]
module_item.getType()
module_item.getWidgetStyle()
module_item.getMinimumValue()
module_item.getMaximumValue()
module_item.getStepSize()
module_item.getName()
module_item.getLabel()
module_item.getDescription()
module_item.loadValue()
self.assertTrue(module_item.isInput())
module_item.isOutput()
break
def get_choice_tree(self):
'''Get the ImageJ command choices for the TreeChoice control
The menu items are augmented with a third tuple entry which is
the ModuleInfo for the command.
'''
global cached_choice_tree
if cached_choice_tree is not None:
return cached_choice_tree
context = RunImageJ.get_context()
ij2_module_service = IJ2.get_module_service(context)
tree = []
for module_info in ij2_module_service.getModules():
menu_path = module_info.getMenuPath()
items = [IJ2.wrap_menu_entry(x)
for x in J.iterate_collection(menu_path)]
if len(items) == 0:
continue
current_tree = tree
for item in items:
name = item.getName()
weight = item.getWeight()
matches = [node for node in current_tree
if node[0] == name]
if len(matches) > 0:
current_node = matches[0]
else:
current_node = [name, [], module_info, weight]
current_tree.append(current_node)
current_tree = current_node[1]
# mark the leaf.
current_node[1] = None
def sort_tree(tree):
'''Recursively sort a tree in-place'''
for node in tree:
if node[1] is not None:
sort_tree(node[1])
tree.sort(lambda node1, node2: cmp(node1[-1], node2[-1]))
sort_tree(tree)
cached_choice_tree = tree
return cached_choice_tree
def run_command(self, command_class, inputs, outputs):
'''Run an imageJ command
command_class - the command's dotted class name
inputs - a dictionary of key/value pairs for the command's inputs
outputs - a dictionary of keys to be filled with the command's outputs
'''
module_index = ij2.get_module_service(self.context).getIndex()
module_infos = module_index.getS('imagej.command.CommandInfo')
module_info = filter(lambda x:x.getClassName() == command_class,
module_infos)[0]
svc = ij2.get_command_service(self.context)
input_map = J.make_map(**inputs)
future = svc.run(module_info.o, input_map.o)
module = future.get()
for key in list(outputs):
module_item = module_info.getOutput(key)
outputs[key] = module_item.getValue(module)
def test_02_06_menu_entry(self):
svc = ij2.get_module_service(self.context)
module_infos = svc.getModules()
for module_info in module_infos:
if module_info.getClassName() == \
'imagej.core.commands.assign.AddSpecifiedNoiseToDataValues':
menu_path = module_info.getMenuPath()
for item in J.iterate_collection(menu_path):
menu_entry = ij2.wrap_menu_entry(item)
menu_entry.getName()
menu_entry.setName("Foo")
menu_entry.getWeight()
menu_entry.setWeight(5)
menu_entry.getMnemonic()
menu_entry.setMnemonic("X")
menu_entry.getAccelerator()
menu_entry.setAccelerator(None)
menu_entry.getIconPath()
menu_entry.setIconPath(None)
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
'''
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
if bioformats.USE_IJ2:
node = command.get_selected_leaf()
module_info = node[2]
module = IJ2.wrap_module(module_info.createModule())
context = self.get_context()
display_service = IJ2.get_display_service(context)
display_dictionary = {}
for setting, module_item in d[key]:
field_type = module_item.getType()
if isinstance(setting, cps.ImageNameProvider):
continue
if field_type == IJ2.FT_BOOL:
value = J.make_instance("java/lang/Boolean",
"(Z)V", setting.value)
elif field_type == IJ2.FT_INTEGER:
value = J.make_instance("java/lang/Integer",
"(I)V", setting.value)
elif field_type == IJ2.FT_FLOAT:
value = J.make_instance("java/lang/Double",
"(D)V", setting.value)
elif field_type == IJ2.FT_STRING:
value = setting.value
elif field_type == IJ2.FT_COLOR:
value = IJ2.make_color_rgb_from_html(setting.value)
elif field_type == IJ2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
dataset = IJ2.create_dataset(image.pixel_data,
setting.value)
display = display_service.createDisplay(dataset)
if image.has_mask:
overlay = IJ2.create_overlay(image.mask)
display.displayOverlay(overlay)
value = display
display_dictionary[module_item.getName()] = display
if wants_display:
input_images.append((image_name, image.pixel_data))
module.setInput(module_item.getName(), value)
module_service = IJ2.get_module_service(context)
module_service.run(module)
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))
ds = display_service.getActiveDataset(display)
pixel_data = ds.get_pixel_data()
image = cpi.Image(pixel_data)
workspace.image_set.add(output_name, image)
if wants_display:
output_images.append((output_name, pixel_data))
for display in display_dictionary.values():
panel = IJ2.wrap_display_panel(display.getDisplayPanel())
panel.close()
else:
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
command = command.value
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
for (field, parameter), setting in zip(fp_in, settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale = True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() { run:function() {
importClass(Packages.imagej.plugin.PlugInFunctions);
PlugInFunctions.runInteractively(plugin);
}};""", dict(plugin=plugin)), True)
else:
J.execute_runnable_in_main_thread(plugin, True)
setting_idx = len(fp_in)
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
def test_02_02_01_get_modules(self):
svc = ij2.get_module_service(self.context)
module_infos = svc.getModules()
self.assertTrue(J.is_instance_of(module_infos[0].o,
"imagej/module/ModuleInfo"))
def test_02_01_get_module_service(self):
self.assertIsNotNone(ij2.get_module_service(self.context))
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
'''
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
if bioformats.USE_IJ2:
node = command.get_selected_leaf()
module_info = node[2]
module = IJ2.wrap_module(module_info.createModule())
context = self.get_context()
display_service = IJ2.get_display_service(context)
display_dictionary = {}
for setting, module_item in d[key]:
field_type = module_item.getType()
if isinstance(setting, cps.ImageNameProvider):
continue
if field_type == IJ2.FT_BOOL:
value = J.make_instance("java/lang/Boolean", "(Z)V",
setting.value)
elif field_type == IJ2.FT_INTEGER:
value = J.make_instance("java/lang/Integer", "(I)V",
setting.value)
elif field_type == IJ2.FT_FLOAT:
value = J.make_instance("java/lang/Double", "(D)V",
setting.value)
elif field_type == IJ2.FT_STRING:
value = setting.value
elif field_type == IJ2.FT_COLOR:
value = IJ2.make_color_rgb_from_html(setting.value)
elif field_type == IJ2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
dataset = IJ2.create_dataset(image.pixel_data,
setting.value)
display = display_service.createDisplay(dataset)
if image.has_mask:
overlay = IJ2.create_overlay(image.mask)
display.displayOverlay(overlay)
value = display
display_dictionary[module_item.getName()] = display
if wants_display:
input_images.append((image_name, image.pixel_data))
module.setInput(module_item.getName(), value)
module_service = IJ2.get_module_service(context)
module_service.run(module)
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))
ds = display_service.getActiveDataset(display)
pixel_data = ds.get_pixel_data()
image = cpi.Image(pixel_data)
workspace.image_set.add(output_name, image)
if wants_display:
output_images.append((output_name, pixel_data))
for display in display_dictionary.values():
panel = IJ2.wrap_display_panel(display.getDisplayPanel())
panel.close()
else:
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
command = command.value
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
for (field, parameter), setting in zip(fp_in,
settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(
image_name, must_be_grayscale=True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(
image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.static_call('imagej/plugin/PlugInFunctions',
'runInteractively', '(Ljava/lang/Runnable)V',
plugin)
else:
J.call(plugin, 'run', '()V')
setting_idx = len(fp_in)
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(
np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
