class ScriptService(object):
def __init__(self, o=o):
self.o = o
getPluginService = J.make_method(
"getPluginService", "()Lorg/scijava/plugin/PluginService;")
getLogService = J.make_method("getLogService",
"()Lorg/scijava/log/LogService;")
getIndex = J.make_method("getIndex",
"()Limagej/script/ScriptLanguageIndex;")
getLanguages = J.make_method(
"getLanguages",
"()Ljava/util/List;",
doc="Return the script engine factories supported by this service",
fn_post_process=lambda jlangs: [
wrap_script_engine_factory(o)
for o in J.iterate_collection(jlangs)
])
getByFileExtension = J.make_method(
"getByFileExtension",
"(Ljava/lang/String;)Ljavax/script/ScriptEngineFactory;",
fn_post_process=wrap_script_engine_factory)
getByName = J.make_method(
"getByName",
"(Ljava/lang/String;)Ljavax/script/ScriptEngineFactory;",
fn_post_process=wrap_script_engine_factory)
def get_pixel_data(self, axes=None):
imgplus = self.getImgPlus()
pixel_data = get_pixel_data(imgplus)
script = """
var result = java.util.ArrayList();
for (i=0;i<imgplus.numDimensions();i++) result.add(imgplus.axis(i));
result"""
inv_axes = J.run_script(script, dict(imgplus=imgplus))
inv_axes = list(J.iterate_collection(inv_axes))
transpose = calculate_transpose(inv_axes, axes)
return pixel_data.transpose(transpose)
def get_pixel_data(self, axes = None):
imgplus = self.getImgPlus()
pixel_data = get_pixel_data(imgplus)
script = """
var result = java.util.ArrayList();
for (i=0;i<imgplus.numDimensions();i++) result.add(imgplus.axis(i));
result"""
inv_axes = J.run_script(script, dict(imgplus=imgplus))
inv_axes = list(J.iterate_collection(inv_axes))
transpose = calculate_transpose(inv_axes, axes)
return pixel_data.transpose(transpose)
class ModuleInfo(object):
def __init__(self):
self.o = instance
getInput = J.make_method(
"getInput",
"(Ljava/lang/String;)Limagej/module/ModuleItem;",
doc = "Gets the input item with the given name.",
fn_post_process=wrap_module_item)
getOutput = J.make_method(
"getOutput",
"(Ljava/lang/String;)Limagej/module/ModuleItem;",
doc = "Gets the output item with the given name.",
fn_post_process=wrap_module_item)
getInputs = J.make_method(
"inputs", "()Ljava/lang/Iterable;",
"""Get the module info's input module items""",
fn_post_process=lambda iterator:
map(wrap_module_item, J.iterate_collection(iterator)))
getOutputs = J.make_method(
"outputs", "()Ljava/lang/Iterable;",
"""Get the module info's output module items""",
fn_post_process=lambda iterator:
map(wrap_module_item, J.iterate_collection(iterator)))
getTitle = J.make_method(
"getTitle",
"()Ljava/lang/String;")
createModule = J.make_method(
"createModule",
"()Limagej/module/Module;",
fn_post_process=wrap_module)
getMenuPath = J.make_method(
"getMenuPath", "()Limagej/MenuPath;")
getMenuRoot = J.make_method(
"getMenuRoot", "()Ljava/lang/String;")
getName = J.make_method("getName", "()Ljava/lang/String;")
getClassName = J.make_method("getClassName", "()Ljava/lang/String;")
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 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 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_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 __iter__(self):
return J.iterate_collection(self.o)
class DisplayService(object):
def __init__(self):
self.o = o
def createDisplay(self, name, dataset):
'''Create a display that contains the given dataset'''
#
# Must be run on the gui thread
#
jcallable = J.run_script(
"""new java.util.concurrent.Callable() {
call:function() {
return displayService.createDisplay(name, dataset);
}
};
""", dict(displayService=self.o, name=name, dataset=dataset.o))
future = J.make_future_task(jcallable,
fn_post_process=wrap_display)
return J.execute_future_in_main_thread(future)
def getActiveDisplay(self, klass=None):
'''Get the first display, optionally of the given type from the list
klass - if not None, return the first display of this type,
otherwise return the first display
'''
if klass is None:
return wrap_display(
J.call(self.o, "getActiveDisplay",
"()Limagej/display/Display;"))
else:
return wrap_display(
J.call(self.o, "getActiveDisplay",
"(Ljava/lang/Class;)Limagej/display/Display;",
klass))
def getActiveImageDisplay(self):
'''Get the active imagej.data.display.ImageDisplay'''
return wrap_display(
J.call(self.o, "getActiveDisplay",
"()Limagej/display/Display;",
J.class_for_name("imagej.data.display.ImageDisplay")))
def setActiveDisplay(self, display):
'''Make this the active display'''
# Note: has to be run in GUI thread on mac
r = J.run_script(
"""new java.lang.Runnable() {
run:function() { displayService.setActiveDisplay(display); }
}
""", dict(displayService=self.o, display=display.o))
J.execute_runnable_in_main_thread(r, True)
getDisplays = J.make_method("getDisplays",
"()Ljava/util/List;",
fn_post_process=lambda x: map(
wrap_display, J.iterate_collection(x)))
getDisplay = J.make_method(
"getDisplay",
"(Ljava/lang/String;)Limagej/display/Display;",
fn_post_process=wrap_display)
isUniqueName = J.make_method("isUniqueName", "(Ljava/lang/String;)Z")
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
if bioformats.USE_IJ2:
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
return []
result = []
inputs = module_info.getInputs()
module = module_info.createModule()
implied_outputs = []
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
value = module_item.getValue(module)
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
description = module_item.getDescription()
if field_type == IJ2.FT_BOOL:
setting = cps.Binary(
label,
J.call(value, "booleanValue", "()Z"),
doc = description)
elif field_type == IJ2.FT_INTEGER:
if minimum is not None:
minimum = J.call(minimum, "intValue", "()I")
if maximum is not None:
maximum = J.call(maximum, "intValue", "()I")
setting = cps.Integer(
label,
J.call(value, "intValue", "()I"),
minval = minimum,
maxval = maximum,
doc = description)
elif field_type == IJ2.FT_FLOAT:
if minimum is not None:
minimum = J.call(minimum, "floatValue", "()F")
if maximum is not None:
maximum = J.call(maximum, "floatValue", "()F")
setting = cps.Float(
label,
J.call(value, "floatValue", "()F"),
minval = minimum,
maxval = maximum,
doc = description)
elif field_type == IJ2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(value)
if choices is not None:
choices = [J.to_string(choice)
for choice
in J.iterate_collection(choices)]
setting = cps.Choice(
label, choices, value, doc = description)
else:
setting = cps.Text(
label, value, doc = description)
elif field_type == IJ2.FT_COLOR:
if value is not None:
value = IJ2.color_rgb_to_html(value)
else:
value = "#ffffff"
setting = cps.Color(label, value, doc = description)
elif field_type == IJ2.FT_IMAGE:
setting = cps.ImageNameSubscriber(
label, "InputImage",
doc = description)
#
# This is a Display for ij2 - the plugin typically
# scribbles all over the display's image. So
# we list it as an output too.
#
implied_outputs.append((
cps.ImageNameProvider(
label, "OutputImage",
doc = description), module_item))
elif field_type == IJ2.FT_OVERLAY:
setting = cps.ObjectNameSubscriber(
label, "ImageJObject",
doc = description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
if field_type == IJ2.FT_IMAGE:
result.append((cps.ImageNameProvider(
label, "ImageJImage",
doc = description), output))
result += implied_outputs
d[key] = result
return [setting for setting, module_info in result]
else:
cc = self.get_cached_commands()
if (not cc.has_key(key)) or (cc[key] is None):
return []
classname = cc[key]
try:
plugin = M.get_plugin(classname)
except:
d[key] = []
return []
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
for field, parameter in fp_in:
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_BOOL:
result += [cps.Binary(label, field.getBoolean(plugin))]
elif field_type == P.FT_INTEGER:
result += [cps.Integer(label, field.getLong(plugin))]
elif field_type == P.FT_FLOAT:
result += [cps.Float(label, field.getDouble(plugin))]
elif field_type == P.FT_STRING:
result += [cps.Text(label, J.to_string(field.get(plugin)))]
else:
assert field_type == P.FT_IMAGE
result += [cps.ImageNameSubscriber(label, "None")]
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:
result += [cps.ImageNameProvider(parameter.label() or "",
"Output")]
d[key] = result
elif bioformats.USE_IJ2:
result = [setting for setting, module_info in d[key]]
else:
result = d[key]
return result
def __iter__(self):
return J.iterate_collection(self.o)
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
return []
result = []
inputs = module_info.getInputs()
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
if label is None:
label = module_item.getName()
if module_item.isOutput():
# if both, qualify which is for input and which for output
label = "%s (Input)" % label
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
default = module_item.loadValue()
description = module_item.getDescription()
if field_type == ij2.FT_BOOL:
value = (J.is_instance_of(default, 'java/lang/Boolean') and
J.call(default, "booleanValue", "()Z"))
setting = cps.Binary(
label,
value = value,
doc = description)
elif field_type == ij2.FT_INTEGER:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "intValue", "()I")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Integer(
label,
value = value,
doc = description)
elif field_type == ij2.FT_FLOAT:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "doubleValue", "()D")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Float(
label,
value=value,
doc = description)
elif field_type == ij2.FT_STRING:
choices = module_item.Choices
value = J.to_string(default)
if choices is not None and len(choices) > 0:
choices = [J.to_string(choice)
for choice
in J.iterate_collection(choices)]
setting = cps.Choice(
label, choices, value, doc = description)
else:
setting = cps.Text(
label, value, doc = description)
elif field_type == ij2.FT_COLOR:
value = "#ffffff"
setting = cps.Color(label, value, doc = description)
elif field_type == ij2.FT_IMAGE:
setting = cps.ImageNameSubscriber(
label, "InputImage",
doc = description)
elif field_type == ij2.FT_FILE:
setting = cps.FilenameText(
label, None, doc = description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
label = output.getLabel()
if label is None:
label = output.getName()
if output.isInput():
# if both, qualify which is for input and which for output
label = "%s (Output)" % label
if field_type == ij2.FT_IMAGE:
result.append((cps.ImageNameProvider(
label, "ImageJImage",
doc = description), output))
d[key] = result
else:
result = d[key]
return [setting for setting, module_info in result]
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
return []
result = []
inputs = module_info.getInputs()
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
if label is None:
label = module_item.getName()
if module_item.isOutput():
# if both, qualify which is for input and which for output
label = "%s (Input)" % label
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
default = module_item.loadValue()
description = module_item.getDescription()
if field_type == ij2.FT_BOOL:
value = (J.is_instance_of(default, 'java/lang/Boolean')
and J.call(default, "booleanValue", "()Z"))
setting = cps.Binary(label, value=value, doc=description)
elif field_type == ij2.FT_INTEGER:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "intValue", "()I")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Integer(label, value=value, doc=description)
elif field_type == ij2.FT_FLOAT:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "doubleValue", "()D")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Float(label, value=value, doc=description)
elif field_type == ij2.FT_STRING:
choices = module_item.Choices
value = J.to_string(default)
if choices is not None and len(choices) > 0:
choices = [
J.to_string(choice)
for choice in J.iterate_collection(choices)
]
setting = cps.Choice(label,
choices,
value,
doc=description)
else:
setting = cps.Text(label, value, doc=description)
elif field_type == ij2.FT_COLOR:
value = "#ffffff"
setting = cps.Color(label, value, doc=description)
elif field_type == ij2.FT_IMAGE:
setting = cps.ImageNameSubscriber(label,
"InputImage",
doc=description)
elif field_type == ij2.FT_FILE:
setting = cps.FilenameText(label, None, doc=description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
label = output.getLabel()
if label is None:
label = output.getName()
if output.isInput():
# if both, qualify which is for input and which for output
label = "%s (Output)" % label
if field_type == ij2.FT_IMAGE:
result.append(
(cps.ImageNameProvider(label,
"ImageJImage",
doc=description), output))
d[key] = result
else:
result = d[key]
return [setting for setting, module_info in result]
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
if bioformats.USE_IJ2:
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
return []
result = []
inputs = module_info.getInputs()
module = module_info.createModule()
implied_outputs = []
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
value = module_item.getValue(module)
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
description = module_item.getDescription()
if field_type == IJ2.FT_BOOL:
setting = cps.Binary(label,
J.call(value, "booleanValue",
"()Z"),
doc=description)
elif field_type == IJ2.FT_INTEGER:
if minimum is not None:
minimum = J.call(minimum, "intValue", "()I")
if maximum is not None:
maximum = J.call(maximum, "intValue", "()I")
setting = cps.Integer(label,
J.call(value, "intValue", "()I"),
minval=minimum,
maxval=maximum,
doc=description)
elif field_type == IJ2.FT_FLOAT:
if minimum is not None:
minimum = J.call(minimum, "floatValue", "()F")
if maximum is not None:
maximum = J.call(maximum, "floatValue", "()F")
setting = cps.Float(label,
J.call(value, "floatValue", "()F"),
minval=minimum,
maxval=maximum,
doc=description)
elif field_type == IJ2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(value)
if choices is not None:
choices = [
J.to_string(choice)
for choice in J.iterate_collection(choices)
]
setting = cps.Choice(label,
choices,
value,
doc=description)
else:
setting = cps.Text(label, value, doc=description)
elif field_type == IJ2.FT_COLOR:
if value is not None:
value = IJ2.color_rgb_to_html(value)
else:
value = "#ffffff"
setting = cps.Color(label, value, doc=description)
elif field_type == IJ2.FT_IMAGE:
setting = cps.ImageNameSubscriber(label,
"InputImage",
doc=description)
#
# This is a Display for ij2 - the plugin typically
# scribbles all over the display's image. So
# we list it as an output too.
#
implied_outputs.append(
(cps.ImageNameProvider(label,
"OutputImage",
doc=description),
module_item))
elif field_type == IJ2.FT_OVERLAY:
setting = cps.ObjectNameSubscriber(label,
"ImageJObject",
doc=description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
if field_type == IJ2.FT_IMAGE:
result.append(
(cps.ImageNameProvider(label,
"ImageJImage",
doc=description), output))
result += implied_outputs
d[key] = result
return [setting for setting, module_info in result]
else:
cc = self.get_cached_commands()
if (not cc.has_key(key)) or (cc[key] is None):
return []
classname = cc[key]
try:
plugin = M.get_plugin(classname)
except:
d[key] = []
return []
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
for field, parameter in fp_in:
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_BOOL:
result += [cps.Binary(label, field.getBoolean(plugin))]
elif field_type == P.FT_INTEGER:
result += [cps.Integer(label, field.getLong(plugin))]
elif field_type == P.FT_FLOAT:
result += [cps.Float(label, field.getDouble(plugin))]
elif field_type == P.FT_STRING:
result += [
cps.Text(label, J.to_string(field.get(plugin)))
]
else:
assert field_type == P.FT_IMAGE
result += [cps.ImageNameSubscriber(label, "None")]
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:
result += [
cps.ImageNameProvider(parameter.label() or "",
"Output")
]
d[key] = result
elif bioformats.USE_IJ2:
result = [setting for setting, module_info in d[key]]
else:
result = d[key]
return result
