def test_08_04_addAll(self):
c1 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c1.add("Foo")
c1.add("Bar")
c2 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c2.add("Baz")
c2.addAll(c1.o)
self.assertIn("Foo", c2)
def test_08_09_removeAll(self):
c1 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c1.add("Foo")
c1.add("Bar")
c2 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c2.add("Foo")
c1.removeAll(c2)
self.assertNotIn("Foo", c1)
def test_08_07_contains_all(self):
c1 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c1.add("Foo")
c1.add("Bar")
c2 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c2.add("Baz")
self.assertFalse(c2.containsAll(c1.o))
c2 += c1
self.assertTrue(c2.containsAll(c1.o))
def getIndex(self):
index = J.call(self.o, "getIndex", "()Limagej/module/ModuleIndex;")
index = J.get_collection_wrapper(index, wrap_module_info)
index.getC = lambda c: J.get_collection_wrapper(
J.call(index.o, "get", "(Ljava/lang/Class;)Ljava/util/List;",c),
wrap_module_info)
index.getS = lambda class_name: \
index.getC(J.class_for_name(class_name))
return index
def test_08_06__iadd__(self):
c1 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c1.add("Foo")
c1.add("Bar")
c2 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c2.add("Baz")
c2 += c1
for k in ("Foo", "Bar", "Baz"):
self.assertIn(k, c2)
c2 += ["Hello", "World"]
self.assertIn("Hello", c2)
self.assertIn("World", c2)
def test_08_05__add__(self):
c1 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c1.add("Foo")
c1.add("Bar")
c2 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c2.add("Baz")
c3 = c1 + c2
for k in ("Foo", "Bar", "Baz"):
self.assertIn(k, c3)
c4 = c3 + ["Hello", "World"]
self.assertIn("Hello", c4)
self.assertIn("World", c4)
def test_08_03_contains(self):
c = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c.add("Foo")
self.assertTrue(c.contains("Foo"))
self.assertFalse(c.contains("Bar"))
self.assertIn("Foo", c)
self.assertNotIn("Bar", c)
def test_08_11_toArray(self):
c1 = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
c1.add("Foo")
c1.add("Bar")
result = [javabridge.to_string(x) for x in c1.toArray()]
self.assertIn("Foo", result)
self.assertIn("Bar", result)
def test_08_01_wrap_collection(self):
c = javabridge.make_instance("java/util/HashSet", "()V")
w = javabridge.get_collection_wrapper(c)
self.assertFalse(hasattr(w, "addI"))
self.assertEqual(w.size(), 0)
self.assertEqual(len(w), 0)
self.assertTrue(w.isEmpty())
def test_08_01_wrap_collection(self):
c = javabridge.make_instance("java/util/HashSet", "()V")
w = javabridge.get_collection_wrapper(c)
self.assertFalse(hasattr(w, "addI"))
self.assertEqual(w.size(), 0)
self.assertEqual(len(w), 0)
self.assertTrue(w.isEmpty())
def is_image_extension(suffix):
"""Return True if the extension is one of those recongized by bioformats"""
extensions = javabridge.get_collection_wrapper(
javabridge.static_call(
"org/cellprofiler/imageset/filter/IsImagePredicate",
"getImageSuffixes", "()Ljava/util/Set;"))
return extensions.contains(suffix.lower())
def __getitem__(self, item):
"""
Returns the specified item, using 0-based indices.
:param item: the 0-based index
:type item: int
:return: the AssociationRule
:rtype: AssociationRule
"""
rules = javabridge.get_collection_wrapper(
javabridge.call(self.jobject, "getRules", "()Ljava/util/List;"))
return AssociationRule(rules[item])
def dependencies(self):
"""
Returns the dependencies of the package.
:return: the list of Dependency objects
:rtype: list of Dependency
"""
result = []
dependencies = javabridge.get_collection_wrapper(
javabridge.call(self.jobject, "getDependencies", "()Ljava/util/List;"))
for dependency in dependencies:
result.append(Dependency(dependency))
return result
def __getitem__(self, item):
"""
Returns the specified item, using 0-based indices.
:param item: the 0-based index
:type item: int
:return: the AssociationRule
:rtype: AssociationRule
"""
rules = javabridge.get_collection_wrapper(
javabridge.call(self.jobject, "getRules", "()Ljava/util/List;"))
return AssociationRule(rules[item])
def premise(self):
"""
Get the the premise.
:return: the premise, list of Item objects
:rtype: list
"""
items = javabridge.get_collection_wrapper(
javabridge.call(self.jobject, "getPremise", "()Ljava/util/Collection;"))
result = []
for item in items:
result.append(Item(item))
return result
def get_dependencies(self):
"""
Returns the dependencies of the package.
:return: the list of Dependency objects
:rtype: list of Dependency
"""
result = []
dependencies = javabridge.get_collection_wrapper(
javabridge.call(self.jobject, "getDependencies",
"()Ljava/util/List;"))
for dependency in dependencies:
result.append(Dependency(dependency))
return result
def premise(self):
"""
Get the the premise.
:return: the premise, list of Item objects
:rtype: list
"""
items = javabridge.get_collection_wrapper(
javabridge.call(self.jobject, "getPremise", "()Ljava/util/Collection;"))
result = []
for item in items:
result.append(Item(item))
return result
def select_overlay(display, overlay, select=True):
'''Select or deselect an overlay
display - the overlay's display
overlay - the overlay to select
'''
for view in J.get_collection_wrapper(display, fn_wrapper = wrap_data_view):
if J.call(overlay, "equals", "(Ljava/lang/Object;)Z", view.getData()):
view.setSelected(select)
break
else:
logger.info("Failed to select overlay")
def available_packages():
"""
Returns a list of all packages that aren't installed yet.
:return: the list of packages
:rtype: list
"""
establish_cache()
result = []
pkgs = javabridge.get_collection_wrapper(
javabridge.static_call("weka/core/WekaPackageManager",
"getAvailablePackages", "()Ljava/util/List;"))
for pkge in pkgs:
result.append(Package(pkge))
return result
def installed_packages():
"""
Returns a list of the installed packages.
:return: the list of packages
:rtype: list
"""
establish_cache()
result = []
pkgs = javabridge.get_collection_wrapper(
javabridge.static_call(
"weka/core/WekaPackageManager", "getInstalledPackages", "()Ljava/util/List;"))
for pkge in pkgs:
result.append(Package(pkge))
return result
def get_installed_packages():
"""
Returns a list of the installed packages.
:return: the list of packages
:rtype: list
"""
establish_cache()
result = []
pkgs = javabridge.get_collection_wrapper(
javabridge.static_call("weka/core/WekaPackageManager",
"getInstalledPackages", "()Ljava/util/List;"))
for pkge in pkgs:
result.append(Package(pkge))
return result
def engine(q_request, q_response):
logger.info("Starting script engine thread")
J.attach()
while True:
try:
msg = J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
q_request.take();""", dict(q_request=q_request))
if logger.level <= logging.INFO:
logger.info("Received engine request: %s", J.to_string(msg))
payload = J.get_collection_wrapper(
J.run_script("msg.payload", dict(msg=msg)))
if J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
msg.command==CPythonScriptEngine.EngineCommands.EXECUTE;
""", dict(msg=msg)):
response = do_execute(payload)
elif J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
msg.command==CPythonScriptEngine.EngineCommands.EVALUATE;
""", dict(msg=msg)):
response = do_evaluate(payload)
elif J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
msg.command==CPythonScriptEngine.EngineCommands.CLOSE_ENGINE;
""", dict(msg=msg)):
logger.info("Exiting script engine thread after close request")
break
else:
logger.warn(
"Received unknown command: %s" %
J.run_script("msg.command.toString()", dict(msg=msg)))
response = J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
var exception = new java.lang.RuntimeException(
java.lang.String.format('Unknown command: %s', msg.command.toString()));
var payload = new java.util.ArrayList();
payload.add(exception);
new CPythonScriptEngine.Message(
CPythonScriptEngine.EngineCommands.EXCEPTION, payload);
""", dict(msg=msg))
J.run_script("q_response.put(response);",
dict(q_response=q_response, response=response))
except:
# To do: how to handle failure, probably from .take()
# Guessing that someone has managed to interrupt our thread
logger.warn("Exiting script engine thread", exc_info=True)
J.detach()
def select_overlay(display, overlay, select=True):
'''Select or deselect an overlay
display - the overlay's display
overlay - the overlay to select
'''
for view in J.get_collection_wrapper(display, fn_wrapper = wrap_data_view):
if J.call(overlay, "equals", "(Ljava/lang/Object;)Z", view.getData()):
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run: function() { view.setSelected(select);}
}""", dict(view = view.o, select=select)), synchronous=True)
break
else:
logger.info("Failed to select overlay")
def select_overlay(display, overlay, select=True):
'''Select or deselect an overlay
display - the overlay's display
overlay - the overlay to select
'''
for view in J.get_collection_wrapper(display, fn_wrapper = wrap_data_view):
if J.call(overlay, "equals", "(Ljava/lang/Object;)Z", view.getData()):
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run: function() { view.setSelected(select);}
}""", dict(view = view.o, select=select)), synchronous=True)
break
else:
logger.info("Failed to select overlay")
def jstring_list_to_string_list(l, return_empty_if_none=True):
"""
Converts a Java java.util.List containing strings into a Python list.
:param l: the list to convert
:type l: JB_Object
:param return_empty_if_none: whether to return an empty list or None when list object is None
:type return_empty_if_none: bool
:return: the list with UTF strings
:rtype: list
"""
result = []
if l is None:
if return_empty_if_none:
return []
else:
return None
objs = javabridge.get_collection_wrapper(l)
for obj in objs:
result.append(javabridge.get_env().get_string_utf(obj))
return result
def engine_requester():
J.attach()
while True:
try:
msg = J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
CPythonScriptEngine.engineRequestQueue.take();""")
if logger.level <= logging.INFO:
logger.info("Received engine request: %s", J.to_string(msg))
payload = J.get_collection_wrapper(
J.run_script("msg.payload", dict(msg=msg)))
if J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
msg.command==CPythonScriptEngine.EngineCommands.NEW_ENGINE;
""", dict(msg=msg)):
do_new_engine(payload)
elif J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
msg.command==CPythonScriptEngine.EngineCommands.CLOSE_SERVICE;
""", dict(msg=msg)):
logger.info("Exiting script service thread in response to "
"termination request")
break
else:
J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
var exception = new java.lang.RuntimeException(
java.lang.String.format('Unknown command: %s', msg.command.toString()));
var payload = new java.util.ArrayList();
payload.add(exception);
var response = new CPythonScriptEngine.Message(
CPythonScriptEngine.EngineCommands.EXCEPTION, payload);
CPythonScriptEngine.engineResponseQueue.put(response);
""")
except:
# To do: how to handle failure, probably from .take()
# Guessing that someone has managed to interrupt our thread
logger.warn("Exiting script service thread", exc_info=True)
J.detach()
def test_08_02_add(self):
c = javabridge.get_collection_wrapper(
javabridge.make_instance("java/util/HashSet", "()V"))
self.assertTrue(c.add("Foo"))
self.assertEqual(len(c), 1)
self.assertFalse(c.isEmpty())
def is_image_extension(suffix):
'''Return True if the extension is one of those recongized by bioformats'''
extensions = J.get_collection_wrapper(
J.static_call("org/cellprofiler/imageset/filter/IsImagePredicate",
"getImageSuffixes", "()Ljava/util/Set;"))
return extensions.contains(suffix.lower())
def test_08_02_add(self):
c = javabridge.get_collection_wrapper(javabridge.make_instance("java/util/HashSet", "()V"))
self.assertTrue(c.add("Foo"))
self.assertEqual(len(c), 1)
self.assertFalse(c.isEmpty())