def __init__(self, class_name):
'''Initialize to wrap a class name
:param class_name: name of class in dotted form, e.g. java.lang.Integer
'''
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
self.cname = class_name.replace(".", "/")
self.klass = J.get_class_wrapper(J.class_for_name(class_name), True)
self.static_methods = {}
env = J.get_env()
jmethods = env.get_object_array_elements(self.klass.getMethods())
methods = {}
for jmethod in jmethods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) != STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in methods:
methods[name] = []
fn = lambda naame=name: lambda *args: self.__call_static(naame, *args)
fn = fn()
fn.__doc__ = J.to_string(jmethod)
setattr(self, name, fn)
else:
fn = getattr(self, name)
fn.__doc__ = fn.__doc__ +"\n"+J.to_string(jmethod)
methods[name].append(method)
self.methods = methods
def __init__(self, o):
'''Initialize the JWrapper with a Java object
:param o: a Java object (class = JB_Object)
'''
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
self.o = o
self.class_wrapper = J.get_class_wrapper(o)
env = J.get_env()
jmethods = env.get_object_array_elements(self.class_wrapper.getMethods())
methods = {}
for jmethod in jmethods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) == STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in methods:
methods[name] = []
fn = lambda naame=name: lambda *args: self.__call(naame, *args)
fn = fn()
fn.__doc__ = J.to_string(jmethod)
setattr(self, name, fn)
else:
fn = getattr(self, name)
fn.__doc__ = fn.__doc__ +"\n"+J.to_string(jmethod)
methods[name].append(method)
self.methods = methods
def test_02_05_constructor_varargs(self):
# Regression test of issue #41
#
args = ("foo", "bar")
f = J.JClassWrapper(
"javax.swing.filechooser.FileNameExtensionFilter")("baz", *args)
exts = J.get_env().get_object_array_elements(f.getExtensions().o)
self.assertEqual(args[0], J.to_string(exts[0]))
self.assertEqual(args[1], J.to_string(exts[1]))
def test_03_09_cw_get_method(self):
sclass = javabridge.class_for_name('java.lang.String')
iclass = javabridge.get_static_field('java/lang/Integer', 'TYPE',
'Ljava/lang/Class;')
c = javabridge.get_class_wrapper('java.lang.String')
m = c.getMethod('charAt', [ iclass ])
self.assertEqual(javabridge.to_string(javabridge.call(m, 'getReturnType', '()Ljava/lang/Class;')), 'char')
m = c.getMethod('concat', [ sclass])
self.assertEqual(javabridge.to_string(javabridge.call(m, 'getReturnType', '()Ljava/lang/Class;')),
'class java.lang.String')
def custom_properties(self):
"""
Obtains the currently set custom properties file.
:return: the custom properties file
:rtype: str
"""
return javabridge.to_string(javabridge.call(self.jobject, "getCustomPropsFile", "()Ljava/io/File;"))
def __str__(self):
"""
Calls the toString() method of the java object.
:return: the result of the toString() method
:rtype: str
"""
return javabridge.to_string(self.jobject)
def get_commands():
"""Return a list of the available command strings"""
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
#
# This is a little bogus, but works - trick IJ into initializing
#
execute_command("pleaseignorethis")
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
return []
keys = J.call(hashtable, "keys", "()Ljava/util/Enumeration;")
keys = J.jenumeration_to_string_list(keys)
values = J.call(hashtable, "values", "()Ljava/util/Collection;")
values = [J.to_string(x) for x in J.iterate_java(
J.call(values, 'iterator', "()Ljava/util/Iterator;"))]
class CommandList(list):
def __init__(self):
super(CommandList, self).__init__(keys)
self.values = values
return CommandList()
def load_file(self, dfile, incremental=False):
"""
Loads the specified file and returns the Instances object.
In case of incremental loading, only the structure.
:param dfile: the file to load
:type dfile: str
:param incremental: whether to load the dataset incrementally
:type incremental: bool
:return: the full dataset or the header (if incremental)
:rtype: Instances
:raises Exception: if the file does not exist
"""
self.enforce_type(self.jobject, "weka.core.converters.FileSourcedConverter")
self.incremental = incremental
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V", javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "reset", "()V")
# check whether file exists, otherwise previously set file gets loaded again
sfile = javabridge.to_string(dfile)
if not os.path.exists(sfile):
raise Exception("Dataset file does not exist: " + str(sfile))
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
if incremental:
self.structure = Instances(javabridge.call(self.jobject, "getStructure", "()Lweka/core/Instances;"))
return self.structure
else:
return Instances(javabridge.call(self.jobject, "getDataSet", "()Lweka/core/Instances;"))
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_03_05_cw_get_annotations(self):
c = javabridge.get_class_wrapper('java.security.Identity')
annotations = c.getAnnotations()
annotations = javabridge.get_env().get_object_array_elements(
annotations)
self.assertEqual(len(annotations), 1)
self.assertEqual(javabridge.to_string(annotations[0]),
'@java.lang.Deprecated()')
def popup_script_dlg(canvas):
joptionpane = javabridge.JClassWrapper("javax.swing.JOptionPane")
jresult = joptionpane.showInputDialog("Enter a script command")
if jresult is not None:
result = javabridge.to_string(jresult)
axes = canvas.figure.axes[0]
eval(result, globals(), locals())
canvas.draw()
def test_02_01_show_get_and_hide(self):
file_name = os.path.join(self.root_dir, "ExampleSBSImages",
"Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
ip.show()
window = ip.getWindow()
self.assertTrue(J.to_string(window).startswith("Channel1-01-A-01.tif"))
ip.hide()
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_02_01_show_get_and_hide(self):
file_name = os.path.join(
self.root_dir, "ExampleSBSImages", "Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
ip.show()
window = ip.getWindow()
self.assertTrue(J.to_string(window).startswith("Channel1-01-A-01.tif"))
ip.hide()
def test_01_07_get_dictionary_wrapper(self):
properties = javabridge.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = javabridge.get_dictionary_wrapper(properties)
self.assertTrue(d.size() > 10)
self.assertFalse(d.isEmpty())
keys = javabridge.get_enumeration_wrapper(d.keys())
values = javabridge.get_enumeration_wrapper(d.elements())
n_elems = d.size()
for i in range(n_elems):
self.assertTrue(keys.hasMoreElements())
key = javabridge.to_string(keys.nextElement())
self.assertTrue(values.hasMoreElements())
value = javabridge.to_string(values.nextElement())
self.assertEqual(javabridge.to_string(d.get(key)), value)
self.assertFalse(keys.hasMoreElements())
self.assertFalse(values.hasMoreElements())
def do_evaluate(payload):
'''Evaluate a Python command
payload: first member is Python command string, second is local context
'''
logger.info("Evaluating script")
filename = "scripting-cpython"
try:
command = J.to_string(payload[0])
context = context_to_locals(payload[1])
logger.debug("Script:\n%s" % command)
#
# OK, the game plan is a little difficult here:
#
# use AST to parse (see https://docs.python.org/2.7/library/ast.html)
# The AST object's body is a list of statements.
# If the last body element is an ast.Expr, then
# we execute all of the statements except the last
# and then we wrap the last as an ast.Expression
# and evaluate it.
#
a = ast.parse(command)
if isinstance(a.body[-1], ast.Expr):
expr = a.body[-1]
del a.body[-1]
else:
expr = a.parse("None").body[0]
filename = context.get("javax.scripting.filename", "scripting-cpython")
code = compile(a, filename, mode="exec")
exec(code, __builtins__.__dict__, context)
code = compile(ast.Expression(expr.value), filename, mode="eval")
result = eval(code, __builtins__.__dict__, context)
logger.debug("Script evaluated")
return J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
var payload = new java.util.ArrayList();
payload.add(result);
new CPythonScriptEngine.Message(
CPythonScriptEngine.EngineCommands.EVALUATE_RESULT, payload);
""", dict(result=result))
except:
logger.info("Exception caught during eval", exc_info=True)
e_type, e, e_tb = sys.exc_info()
return J.run_script(
"""
importPackage(Packages.org.scijava.plugins.scripting.cpython);
var exception = new javax.script.ScriptException(
java.lang.String.format('Python exception: %s', e),
filename, line_number);
var payload = new java.util.ArrayList();
payload.add(exception);
new CPythonScriptEngine.Message(
CPythonScriptEngine.EngineCommands.EXCEPTION, payload);
""", dict(e=repr(e), filename=filename,
line_number=e_tb.tb_lineno))
def test_01_08_jenumeration_to_string_list(self):
properties = javabridge.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = javabridge.get_dictionary_wrapper(properties)
keys = javabridge.jenumeration_to_string_list(d.keys())
enum = javabridge.get_enumeration_wrapper(d.keys())
for i in range(d.size()):
key = javabridge.to_string(enum.nextElement())
self.assertEqual(key, keys[i])
def test_01_09_jdictionary_to_string_dictionary(self):
properties = javabridge.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = javabridge.get_dictionary_wrapper(properties)
pyd = javabridge.jdictionary_to_string_dictionary(properties)
keys = javabridge.jenumeration_to_string_list(d.keys())
for key in keys:
value = javabridge.to_string(d.get(key))
self.assertEqual(pyd[key], value)
def custom_properties(self):
"""
Obtains the currently set custom properties file.
:return: the custom properties file
:rtype: str
"""
return javabridge.to_string(
javabridge.call(self.jobject, "getCustomPropsFile",
"()Ljava/io/File;"))
def test_01_07_get_dictionary_wrapper(self):
properties = javabridge.static_call("java/lang/System",
"getProperties",
"()Ljava/util/Properties;")
d = javabridge.get_dictionary_wrapper(properties)
self.assertTrue(d.size() > 10)
self.assertFalse(d.isEmpty())
keys = javabridge.get_enumeration_wrapper(d.keys())
values = javabridge.get_enumeration_wrapper(d.elements())
n_elems = d.size()
for i in range(n_elems):
self.assertTrue(keys.hasMoreElements())
key = javabridge.to_string(keys.nextElement())
self.assertTrue(values.hasMoreElements())
value = javabridge.to_string(values.nextElement())
self.assertEqual(javabridge.to_string(d.get(key)), value)
self.assertFalse(keys.hasMoreElements())
self.assertFalse(values.hasMoreElements())
def test_01_02_make_instance(self):
jobject = javabridge.make_instance("java/lang/Object", "()V")
self.assertTrue(
javabridge.to_string(jobject).startswith("java.lang.Object"))
# <AK> added
with self.assertRaisesRegex(
javabridge.JavaError,
'Could not find constructor with signature = '
'"\(\)V"'):
jobject = javabridge.make_instance("java/lang/Class", "()V")
def test_01_06_get_enumeration_wrapper(self):
properties = javabridge.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
keys = javabridge.call(properties, "keys", "()Ljava/util/Enumeration;")
enum = javabridge.get_enumeration_wrapper(keys)
has_java_vm_name = False
while(enum.hasMoreElements()):
key = javabridge.to_string(enum.nextElement())
if key == "java.vm.name":
has_java_vm_name = True
self.assertTrue(has_java_vm_name)
def load_file(self, dfile, incremental=False, class_index=None):
"""
Loads the specified file and returns the Instances object.
In case of incremental loading, only the structure.
:param dfile: the file to load
:type dfile: str
:param incremental: whether to load the dataset incrementally
:type incremental: bool
:param class_index: the class index string to use ('first', 'second', 'third', 'last-2', 'last-1', 'last' or 1-based index)
:type class_index: str
:return: the full dataset or the header (if incremental)
:rtype: Instances
:raises Exception: if the file does not exist
"""
self.enforce_type(self.jobject,
"weka.core.converters.FileSourcedConverter")
self.incremental = incremental
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V",
javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "reset", "()V")
# check whether file exists, otherwise previously set file gets loaded again
sfile = javabridge.to_string(dfile)
if not os.path.exists(sfile):
raise Exception("Dataset file does not exist: " + str(sfile))
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
if incremental:
self.structure = Instances(
javabridge.call(self.jobject, "getStructure",
"()Lweka/core/Instances;"))
result = self.structure
else:
result = Instances(
javabridge.call(self.jobject, "getDataSet",
"()Lweka/core/Instances;"))
if class_index is not None:
if class_index == 'first':
result.class_index = 0
elif class_index == 'second':
result.class_index = 1
elif class_index == 'third':
result.class_index = 2
elif class_index == 'last-2':
result.class_index = result.num_attributes - 3
elif class_index == 'last-1':
result.class_index = result.num_attributes - 2
elif class_index == 'last':
result.class_index = result.num_attributes - 1
else:
result.class_index = int(class_index)
return result
def __init__(self, o):
'''Initialize the JWrapper with a Java object
:param o: a Java object (class = JB_Object)
'''
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
self.o = o
self.class_wrapper = J.get_class_wrapper(o)
env = J.get_env()
jmethods = env.get_object_array_elements(
self.class_wrapper.getMethods())
methods = {}
for jmethod in jmethods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) == STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in methods:
methods[name] = []
fn = lambda naame=name: lambda *args: self.__call(naame, *args)
fn = fn()
fn.__doc__ = J.to_string(jmethod)
setattr(self, name, fn)
else:
fn = getattr(self, name)
fn.__doc__ = fn.__doc__ + "\n" + J.to_string(jmethod)
methods[name].append(method)
jfields = env.get_object_array_elements(
self.class_wrapper.getFields(self))
field_class = env.find_class("java/lang/reflect/Field")
method_id = env.get_method_id(field_class, "getName",
"()Ljava/lang/String;")
self.field_names = [
env.get_string_utf(env.call_method(o, method_id)) for o in jfields
]
self.methods = methods
def __init__(self, class_name):
'''Initialize to wrap a class name
:param class_name: name of class in dotted form, e.g. java.lang.Integer
'''
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
self.cname = class_name.replace(".", "/")
self.klass = J.get_class_wrapper(J.class_for_name(class_name), True)
self.static_methods = {}
env = J.get_env()
jmethods = env.get_object_array_elements(self.klass.getMethods())
methods = {}
for jmethod in jmethods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) != STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in methods:
methods[name] = []
fn = lambda naame=name: lambda *args: self.__call_static(
naame, *args)
fn = fn()
fn.__doc__ = J.to_string(jmethod)
setattr(self, name, fn)
else:
fn = getattr(self, name)
fn.__doc__ = fn.__doc__ + "\n" + J.to_string(jmethod)
methods[name].append(method)
jfields = env.get_object_array_elements(self.klass.getFields(self))
field_class = env.find_class("java/lang/reflect/Field")
method_id = env.get_method_id(field_class, "getName",
"()Ljava/lang/String;")
self.field_names = [
env.get_string_utf(env.call_method(o, method_id)) for o in jfields
]
self.methods = methods
def get_class_list():
"Return a wrapped instance of loci.formats.ClassList"
env = javabridge.get_env()
class_list = old_get_class_list()
rais_classname = 'loci/common/RandomAccessInputStream'
#
# Move any class to the back that thinks it can read garbage
#
fd, path = tempfile.mkstemp(
suffix=".garbage",
dir=cellprofiler.preferences.get_temporary_directory())
stream = None
try:
os.write(fd, "This is not an image file")
os.fsync(fd)
stream = javabridge.make_instance(rais_classname,
'(Ljava/lang/String;)V', path)
problem_classes = []
for klass in env.get_object_array_elements(
class_list.get_classes()):
try:
instance = javabridge.call(klass, "newInstance",
"()Ljava/lang/Object;")
can_read_garbage = javabridge.call(
instance, "isThisType", "(L%s;)Z" % rais_classname,
stream)
if can_read_garbage:
problem_classes.append(klass)
class_list.remove_class(klass)
except:
logger.info("Caught exception in %s.isThisType",
javabridge.to_string(klass))
finally:
os.close(fd)
javabridge.call(stream, "close", "()V")
os.remove(path)
for classname in ("loci.formats.in.FlowSightReader",
"loci.formats.in.IM3Reader"):
try:
klass = javabridge.class_for_name(classname)
class_list.add_class(klass)
except:
logger.warn("Could not find Bio-formats reader %s" % classname,
exc_info=1)
for klass in problem_classes:
class_list.add_class(klass)
return class_list
def test_01_03_globals(self):
jglobals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jglobals.put("numerator", "6")
jglobals.put("denominator", "2")
jglobals.put("answer", jref.o)
self.cpython.execute("""
global javabridge
import javabridge
def fn():
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn()
""", None, jglobals.o)
self.assertEqual(float(javabridge.to_string(jref.get(0))), 3)
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 test_01_03_globals(self):
jglobals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jglobals.put("numerator", "6")
jglobals.put("denominator", "2")
jglobals.put("answer", jref.o)
self.cpython.execute(
"""
global javabridge
import javabridge
def fn():
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn()
""", None, jglobals.o)
self.assertEqual(javabridge.to_string(jref.get(0)), "3")
def get_class_list():
"Return a wrapped instance of loci.formats.ClassList"
env = javabridge.get_env()
class_list = old_get_class_list()
rais_classname = 'loci/common/RandomAccessInputStream'
#
# Move any class to the back that thinks it can read garbage
#
fd, path = tempfile.mkstemp(suffix=".garbage",
dir=cpprefs.get_temporary_directory())
stream = None
try:
os.write(fd, "This is not an image file")
os.fsync(fd)
stream = javabridge.make_instance(
rais_classname, '(Ljava/lang/String;)V', path)
problem_classes = []
for klass in env.get_object_array_elements(class_list.get_classes()):
try:
instance = javabridge.call(
klass, "newInstance", "()Ljava/lang/Object;")
can_read_garbage = javabridge.call(
instance, "isThisType",
"(L%s;)Z" % rais_classname, stream)
if can_read_garbage:
problem_classes.append(klass)
class_list.remove_class(klass)
except:
logger.info("Caught exception in %s.isThisType",
javabridge.to_string(klass))
finally:
os.close(fd)
javabridge.call(stream, "close", "()V")
os.remove(path)
for classname in ("loci.formats.in.FlowSightReader",
"loci.formats.in.IM3Reader"):
try:
klass = javabridge.class_for_name(classname)
class_list.add_class(klass)
except:
logger.warn("Could not find Bio-formats reader %s" % classname,
exc_info=1)
for klass in problem_classes:
class_list.add_class(klass)
return class_list
def test_01_02_locals(self):
jlocals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jlocals.put("numerator", "6")
jlocals.put("denominator", "2")
code = """
global javabridge
import javabridge
def fn(numerator, denominator, answer):
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn(numerator, denominator, answer)
"""
jlocals.put("code", code)
jlocals.put("answer", jref.o)
self.cpython.execute(code, jlocals.o, None)
self.assertEqual(float(javabridge.to_string(jref.get(0))), 3)
def test_01_04_globals_equals_locals(self):
jglobals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jglobals.put("numerator", "6")
jglobals.put("denominator", "2")
jglobals.put("answer", jref.o)
#
# The import will be added to "locals", but that will be the globals.
#
self.cpython.execute("""
import javabridge
def fn():
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn()
""", jglobals.o, jglobals.o)
self.assertEqual(javabridge.to_string(jref.get(0)), "3")
def test_01_02_locals(self):
jlocals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jlocals.put("numerator", "6")
jlocals.put("denominator", "2")
code = """
global javabridge
import javabridge
def fn(numerator, denominator, answer):
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn(numerator, denominator, answer)
"""
jlocals.put("code", code)
jlocals.put("answer", jref.o)
self.cpython.execute(code, jlocals.o, None)
self.assertEqual(javabridge.to_string(jref.get(0)), "3")
def test_01_04_globals_equals_locals(self):
jglobals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jglobals.put("numerator", "6")
jglobals.put("denominator", "2")
jglobals.put("answer", jref.o)
#
# The import will be added to "locals", but that will be the globals.
#
self.cpython.execute(
"""
import javabridge
def fn():
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn()
""", jglobals.o, jglobals.o)
self.assertEqual(float(javabridge.to_string(jref.get(0))), 3)
def calculate_transpose(actual_axes, desired_axes=None):
'''Calculate the transpose tuple that converts the actual orientation to the desired
actual_axes - a list of the AxisType arguments as fetched from
a display, ImgPlus, view or overlay
desired_axes - the desired orientation. By default, this is i,j = Y, X
'''
if desired_axes is None:
desired_axes = [ Axes().Y, Axes().X]
if len(actual_axes) > 2:
desired_axes.append(Axes().CHANNEL)
transpose = []
for axis in desired_axes:
matches = [i for i, actual_axis in enumerate(actual_axes)
if J.call(actual_axis, "equals",
"(Ljava/lang/Object;)Z", axis)]
if len(matches) != 1:
raise ValueError("No match for %s axis" % J.to_string(axis))
transpose.append(matches[0])
return transpose
def calculate_transpose(actual_axes, desired_axes=None):
'''Calculate the transpose tuple that converts the actual orientation to the desired
actual_axes - a list of the AxisType arguments as fetched from
a display, ImgPlus, view or overlay
desired_axes - the desired orientation. By default, this is i,j = Y, X
'''
if desired_axes is None:
desired_axes = [ Axes().Y, Axes().X]
if len(actual_axes) > 2:
desired_axes.append(Axes().CHANNEL)
transpose = []
for axis in desired_axes:
matches = [i for i, actual_axis in enumerate(actual_axes)
if J.call(actual_axis, "equals",
"(Ljava/lang/Object;)Z", axis)]
if len(matches) != 1:
raise ValueError("No match for %s axis" % J.to_string(axis))
transpose.append(matches[0])
return transpose
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 get_commands():
'''Return a list of the available command strings'''
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
#
# This is a little bogus, but works - trick IJ into initializing
#
execute_command("pleaseignorethis")
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
return []
keys = J.call(hashtable, "keys", "()Ljava/util/Enumeration;")
keys = J.jenumeration_to_string_list(keys)
values = J.call(hashtable, "values", "()Ljava/util/Collection;")
values = [J.to_string(x) for x in J.iterate_java(
J.call(values, 'iterator', "()Ljava/util/Iterator;"))]
class CommandList(list):
def __init__(self):
super(CommandList, self).__init__(keys)
self.values = values
return CommandList()
def wrap_md(fn, name=None, paramcount=None, *args):
if len(args) != paramcount:
# raise sensible error for wrong number of arguments
raise TypeError(('{0}() takes exactly {1} arguments ({2} ' +
'given)').format(name, paramcount, len(args)))
try:
jw = fn(*args)
except javabridge.JavaException as e:
if log is not None:
print(javabridge.to_string(log))
javabridge.call(log, 'reset', '()V')
raise e
if jw is None or jw == '':
return None
# convert value to int, float, or string
jw = str(jw)
try:
return int(jw)
except ValueError:
try:
return float(jw)
except ValueError:
return jw
def suppressMsgs():
"""
supress too many messages from javabridge
"""
# https://github.com/LeeKamentsky/python-javabridge/issues/37
java_stack = javabridge.make_instance('java/io/ByteArrayOutputStream',
"()V")
java_stack_ps = javabridge.make_instance('java/io/PrintStream',
"(Ljava/io/OutputStream;)V",
java_stack)
javabridge.static_call('Ljava/lang/System;', "setErr",
'(Ljava/io/PrintStream;)V', java_stack_ps)
java_out = javabridge.make_instance('java/io/ByteArrayOutputStream', "()V")
java_out_ps = javabridge.make_instance('java/io/PrintStream',
"(Ljava/io/OutputStream;)V",
java_out)
javabridge.static_call('Ljava/lang/System;', "setOut",
'(Ljava/io/PrintStream;)V', java_out_ps)
javabridge.run_script(
'java.lang.System.out.println("This is java system.out!");')
try:
javabridge.run_script('this/raises/an/exception;')
except javabridge.JavaException:
print('\n\nJava stdErr: ' + javabridge.to_string(java_stack))
def test_01_01_to_string(self):
jstring = self.env.new_string_utf("Hello, world")
self.assertEqual(javabridge.to_string(jstring), "Hello, world")
def test_04_03_field_type(self):
c = javabridge.get_class_wrapper('java.lang.Byte')
f = javabridge.get_field_wrapper(c.getField('MAX_VALUE'))
t = f.getType()
self.assertEqual(javabridge.to_string(t), 'byte')
def test_04_01_field_get(self):
c = javabridge.get_class_wrapper('java.lang.Byte')
f = javabridge.get_field_wrapper(c.getField('MAX_VALUE'))
v = f.get(None)
self.assertEqual(javabridge.to_string(v), '127')
def __unicode__(self):
"""
Just calls the toString() method.
:rtype: str
"""
return javabridge.to_string(self.jobject)
def __str__(self):
return J.to_string(self.o)
def test_01_02_make_instance(self):
jobject = javabridge.make_instance("java/lang/Object", "()V")
self.assertTrue(javabridge.to_string(jobject).startswith("java.lang.Object"))
def test_01_01_to_string(self):
jstring = self.env.new_string_utf("Hello, world")
self.assertEqual(javabridge.to_string(jstring), "Hello, world")
def test_04_03_field_type(self):
c = javabridge.get_class_wrapper('java.lang.Byte')
f = javabridge.get_field_wrapper(c.getField('MAX_VALUE'))
t = f.getType()
self.assertEqual(javabridge.to_string(t), 'byte')
def test_04_01_field_get(self):
c = javabridge.get_class_wrapper('java.lang.Byte')
f = javabridge.get_field_wrapper(c.getField('MAX_VALUE'))
v = f.get(None)
self.assertEqual(javabridge.to_string(v), '127')
def test_03_05_cw_get_annotations(self):
c = javabridge.get_class_wrapper('java.security.Identity')
annotations = c.getAnnotations()
annotations = javabridge.get_env().get_object_array_elements(annotations)
self.assertEqual(len(annotations), 1)
self.assertTrue(javabridge.to_string(annotations[0]).startswith('@java.lang.Deprecated'))
script = """
new java.lang.Runnable() {
run: function() {
o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return future.get()
if doc is None:
doc = "Run the %s method in the UI thread" % method
fn.__doc__ = doc
fn.__name__ = method
return fn
if __name__=="__main__":
jar_dir = os.path.join(os.path.split(__file__)[0], "jars")
classpath = os.pathsep.join([
os.path.join(jar_dir, filename) for filename in os.listdir(jar_dir)
if filename.endswith(".jar")])
J.start_vm(["-Djava.class.path="+classpath])
my_context = create_context(REQUIRED_SERVICES)
module_service = get_module_service(my_context)
module_infos = module_service.getModules()
for module_info in module_infos:
print J.to_string(module_info.o)
run: function() {
o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return future.get()
if doc is None:
doc = "Run the %s method in the UI thread" % method
fn.__doc__ = doc
fn.__name__ = method
return fn
if __name__ == "__main__":
jar_dir = os.path.join(os.path.split(__file__)[0], "jars")
classpath = os.pathsep.join([
os.path.join(jar_dir, filename) for filename in os.listdir(jar_dir)
if filename.endswith(".jar")
])
J.start_vm(["-Djava.class.path=" + classpath])
my_context = create_context(REQUIRED_SERVICES)
module_service = get_module_service(my_context)
module_infos = module_service.getModules()
for module_info in module_infos:
print J.to_string(module_info.o)
def __repr__(self):
classname = J.call(J.call(self.o, "getClass", "()Ljava/lang/Class;"),
"getName", "()Ljava/lang/String;")
return "Instance of %s: %s" % (classname, J.to_string(self.o))
def test_01_14_get_processor(self):
file_name = os.path.join(
self.root_dir, "ExampleSBSImages", "Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
p = ip.getProcessor()
self.assertTrue(J.to_string(p).startswith("ip"))
def __str__(self):
return J.to_string(self.o)
def __repr__(self):
classname = J.call(J.call(self.o, "getClass", "()Ljava/lang/Class;"),
"getName", "()Ljava/lang/String;")
return "Instance of %s: %s" % (classname, J.to_string(self.o))
