def field_class_mapping():
return (
(J.class_for_name('net.imagej.display.ImageDisplay'), FT_IMAGE),
(J.class_for_name('net.imagej.Dataset'), FT_IMAGE),
(J.class_for_name('net.imagej.display.DatasetView'), FT_IMAGE),
(J.class_for_name('net.imagej.table.TableDisplay'), FT_TABLE),
(J.class_for_name('org.scijava.plugin.SciJavaPlugin'), FT_PLUGIN)
)
def field_class_mapping():
return (
(J.class_for_name('net.imagej.display.ImageDisplay'), FT_IMAGE),
(J.class_for_name('net.imagej.Dataset'), FT_IMAGE),
(J.class_for_name('net.imagej.display.DatasetView'), FT_IMAGE),
(J.class_for_name('net.imagej.table.TableDisplay'), FT_TABLE),
(J.class_for_name('org.scijava.plugin.SciJavaPlugin'), FT_PLUGIN)
)
def get_plugin(classname):
'''Return an instance of the named plugin'''
if classname.startswith("ij."):
cls = J.class_for_name(classname)
else:
cls = J.class_for_name(classname, get_user_loader())
cls = J.get_class_wrapper(cls, True)
constructor = J.get_constructor_wrapper(cls.getConstructor(None))
return constructor.newInstance(None)
def get_context():
'''Get the ImageJ context
This is a singleton ImageJ context. We need a singleton for now because
of http://trac.imagej.net/ticket/1413
This is an imagej.ImageJ, which at one point was the context.
Call self.getContext() to get the org.scijava.Context which may be
what you want.
'''
global the_imagej_context
if the_imagej_context is None:
the_imagej_context = create_context(None)
#
# We have to turn off the updater and tell ImageJ to never call
# System.exit. We have to tell ImageJ that we read the readme file.
#
# To Do: programatically turn off the updater and take control of
# the quitting and exit process.
#
max_value = J.run_script(
"java.lang.Long.toString(java.lang.Long.MAX_VALUE);")
prefs = [("net.imagej.updater.UpToDate", "latestNag", max_value),
("net.imagej.options.OptionsMisc", "exitWhenQuitting",
"false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("org.scijava.ui.UserInterface")
script = """
var result = java.lang.System.getProperty('ij.ui');
if (! result) {
var infos = pluginService.getPluginsOfType(ui_interface);
if (infos.size() > 0) {
result = infos.get(0).getClassName();
}
}
result;"""
ui_class = J.run_script(
script,
dict(pluginService=plugin_service, ui_interface=ui_interface))
first_run = "firstRun-" + the_imagej_context.getVersion()
if ui_class:
prefs.append((ui_class, first_run, "false"))
for class_name, key, value in prefs:
c = J.class_for_name(class_name)
J.static_call(
"org/scijava/util/Prefs", "put",
"(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/String;)V", c,
key, value)
return the_imagej_context
def get_context():
'''Get the ImageJ context
This is a singleton ImageJ context. We need a singleton for now because
of http://trac.imagej.net/ticket/1413
This is an imagej.ImageJ, which at one point was the context.
Call self.getContext() to get the org.scijava.Context which may be
what you want.
'''
global the_imagej_context
if the_imagej_context is None:
the_imagej_context = create_context(None)
#
# We have to turn off the updater and tell ImageJ to never call
# System.exit. We have to tell ImageJ that we read the readme file.
#
# To Do: programatically turn off the updater and take control of
# the quitting and exit process.
#
max_value = J.run_script(
"java.lang.Long.toString(java.lang.Long.MAX_VALUE);")
prefs = [
("net.imagej.updater.UpToDate", "latestNag", max_value),
("net.imagej.options.OptionsMisc", "exitWhenQuitting", "false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("org.scijava.ui.UserInterface")
script = """
var result = java.lang.System.getProperty('ij.ui');
if (! result) {
var infos = pluginService.getPluginsOfType(ui_interface);
if (infos.size() > 0) {
result = infos.get(0).getClassName();
}
}
result;"""
ui_class = J.run_script(script, dict(pluginService=plugin_service,
ui_interface=ui_interface))
first_run = "firstRun-"+the_imagej_context.getVersion()
if ui_class:
prefs.append((ui_class, first_run, "false"))
for class_name, key, value in prefs:
c = J.class_for_name(class_name)
J.static_call(
"org/scijava/util/Prefs", "put",
"(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/String;)V",
c, key, value)
return the_imagej_context
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 prepare_run(self, workspace):
'''Create an IPD for every url that passes the filter'''
if workspace.pipeline.in_batch_mode():
return True
file_list = workspace.pipeline.file_list
if self.filter_choice != FILTER_CHOICE_NONE:
if self.filter_choice == FILTER_CHOICE_IMAGES:
expression = FILTER_DEFAULT
else:
expression = self.filter.value_text
env = J.get_env()
ifcls = J.class_for_name("org.cellprofiler.imageset.ImageFile")
scls = env.find_class("java/lang/String")
iffilter = J.make_instance(
"org/cellprofiler/imageset/filter/Filter",
"(Ljava/lang/String;Ljava/lang/Class;)V",
expression, ifcls)
file_array = env.make_object_array(len(file_list), scls)
for i, url in enumerate(file_list):
if isinstance(url, unicode):
ourl = env.new_string(url)
else:
ourl = env.new_string_utf(url)
env.set_object_array_element(file_array, i, ourl)
passes_filter = J.call(
iffilter, "filterURLs",
"([Ljava/lang/String;)[Z", file_array)
if isinstance(passes_filter, J.JB_Object):
passes_filter = J.get_env().get_boolean_array_elements(
passes_filter)
file_list = [f for f, passes in zip(file_list, passes_filter)
if passes]
workspace.pipeline.set_filtered_file_list(file_list, self)
return True
def __init__(self, base_class_name, d=None):
'''Initialize the proxy with the interface name and methods
:param base_class_name: the class name of the interface to implement
in dotted form (e.g. java.lang.Runnable)
:param d: an optional dictionary of method name to implementation
'''
self.ref_id, self.ref = J.create_jref(self)
self.__d = d or {}
jclass = J.class_for_name(base_class_name)
loader = J.call(jclass, "getClassLoader",
"()Ljava/lang/ClassLoader;")
env = J.get_env()
classes = env.make_object_array(1, env.find_class("java/lang/Class"))
env.set_object_array_element(classes, 0, jclass)
handler = J.make_instance(
"org/cellprofiler/javabridge/CPythonInvocationHandler",
"(Ljava/lang/String;)V", self.ref_id)
self.o = J.static_call(
"java/lang/reflect/Proxy",
"newProxyInstance",
"(Ljava/lang/ClassLoader;"
"[Ljava/lang/Class;"
"Ljava/lang/reflect/InvocationHandler;)"
"Ljava/lang/Object;",
loader, classes, handler)
def __init__(self):
env = jutil.get_env()
class_name = 'loci/formats/ImageReader'
klass = env.find_class(class_name)
base_klass = env.find_class('loci/formats/IFormatReader')
self.o = jutil.make_instance(
"loci/formats/ClassList",
"(Ljava/lang/String;"
"Ljava/lang/Class;" # base
"Ljava/lang/Class;)V", # location in jar
"readers.txt",
base_klass,
klass)
problem_classes = [
# BDReader will read all .tif files in an experiment if it's
# called to load a .tif.
#
'loci.formats.in.BDReader',
#
# MRCReader will read .stk files which should be read
# by MetamorphReader
#
'loci.formats.in.MRCReader'
]
for problem_class in problem_classes:
# Move to back
klass = jutil.class_for_name(problem_class)
self.remove_class(klass)
self.add_class(klass)
def __init__(self):
env = jutil.get_env()
class_name = 'loci/formats/ImageReader'
klass = env.find_class(class_name)
base_klass = env.find_class('loci/formats/IFormatReader')
self.o = jutil.make_instance("loci/formats/ClassList",
"(Ljava/lang/String;"
"Ljava/lang/Class;" # base
"Ljava/lang/Class;)V", # location in jar
"readers.txt", base_klass, klass)
problem_classes = [
# BDReader will read all .tif files in an experiment if it's
# called to load a .tif.
#
'loci.formats.in.BDReader',
#
# MRCReader will read .stk files which should be read
# by MetamorphReader
#
'loci.formats.in.MRCReader'
]
for problem_class in problem_classes:
# Move to back
klass = jutil.class_for_name(problem_class)
self.remove_class(klass)
self.add_class(klass)
def prepare_run(self, workspace):
'''Create an IPD for every url that passes the filter'''
if workspace.pipeline.in_batch_mode():
return True
file_list = workspace.pipeline.file_list
if self.filter_choice != FILTER_CHOICE_NONE:
if self.filter_choice == FILTER_CHOICE_IMAGES:
expression = FILTER_DEFAULT
else:
expression = self.filter.value_text
env = J.get_env()
ifcls = J.class_for_name("org.cellprofiler.imageset.ImageFile")
scls = env.find_class("java/lang/String")
iffilter = J.make_instance(
"org/cellprofiler/imageset/filter/Filter",
"(Ljava/lang/String;Ljava/lang/Class;)V", expression, ifcls)
file_array = env.make_object_array(len(file_list), scls)
for i, url in enumerate(file_list):
if isinstance(url, unicode):
ourl = env.new_string(url)
else:
ourl = env.new_string_utf(url)
env.set_object_array_element(file_array, i, ourl)
passes_filter = J.call(iffilter, "filterURLs",
"([Ljava/lang/String;)[Z", file_array)
if isinstance(passes_filter, J.JB_Object):
passes_filter = J.get_env().get_boolean_array_elements(
passes_filter)
file_list = [
f for f, passes in zip(file_list, passes_filter) if passes
]
workspace.pipeline.set_filtered_file_list(file_list, self)
return True
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 = {}
methods = env.get_object_array_elements(self.klass.getMethods())
self.methods = {}
for jmethod in methods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) != STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in self.methods:
self.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)
self.methods[name].append(method)
def test_03_11_cw_get_constructor(self):
c = javabridge.get_class_wrapper('java.lang.String')
sclass = javabridge.class_for_name('java.lang.String')
constructor = c.getConstructor([sclass])
self.assertEqual(
javabridge.call(constructor, 'getName', '()Ljava/lang/String;'),
'java.lang.String')
def get_jclass(classname):
"""
Returns the Java class object associated with the dot-notation classname.
:param classname: the classname
:type classname: str
:return: the class object
:rtype: JB_Object
"""
return javabridge.class_for_name(classname=classname)
def test_01_04_call_varargs(self):
sclass = J.JWrapper(J.class_for_name("java.lang.String"));
for constructor in J.get_env().get_object_array_elements(
sclass.getConstructors().o):
wconstructor = J.JWrapper(constructor)
parameter_types = J.get_env().get_object_array_elements(
wconstructor.getParameterTypes().o)
c1 = sclass.getConstructor(*parameter_types)
self.assertTrue(c1.equals(constructor))
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_01_04_call_varargs(self):
sclass = J.JWrapper(J.class_for_name("java.lang.String"))
for constructor in J.get_env().get_object_array_elements(
sclass.getConstructors().o):
wconstructor = J.JWrapper(constructor)
parameter_types = J.get_env().get_object_array_elements(
wconstructor.getParameterTypes().o)
c1 = sclass.getConstructor(*parameter_types)
self.assertTrue(c1.equals(constructor))
def getService(self, class_name):
'''Get a service with the given class name
class_name - class name in dotted form
returns the class or None if no implementor loaded.
'''
klass = J.class_for_name(class_name)
return J.call(self.o, 'get',
'(Ljava/lang/Class;)Lorg/scijava/service/Service;', klass)
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 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 new_instance(cls, classname, length):
"""
Creates a new array with the given classname and length; initial values are null.
:param classname: the classname in Java notation (eg "weka.core.DenseInstance")
:type classname: str
:param length: the length of the array
:type length: int
:return: the Java array
:rtype: JB_Object
"""
return javabridge.static_call(
"Ljava/lang/reflect/Array;",
"newInstance",
"(Ljava/lang/Class;I)Ljava/lang/Object;",
javabridge.class_for_name(classname=classname), length)
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 __init__(self, jobject=None, enum=None, member=None):
"""
Initializes the enum class.
:param jobject: the Java object to wrap
:type jobject: JB_Object
:param enum: the enum class to instantiate (dot notation)
:type enum: str
:param member: the member of the enum class to instantiate
:type member: str
"""
if jobject is None:
enumclass = javabridge.class_for_name(classname=enum)
jobject = javabridge.static_call(
"java/lang/Enum", "valueOf",
"(Ljava/lang/Class;Ljava/lang/String;)Ljava/lang/Enum;",
enumclass, member)
super(Enum, self).__init__(jobject)
def test_valid(self, pipeline):
try:
import javabridge as J
J.run_script(
"""
importPackage(Packages.org.cellprofiler.imageset.filter);
new Filter(expr, klass);
""",
dict(
expr=self.value_text,
klass=J.class_for_name(
"org.cellprofiler.imageset.ImagePlaneDetailsStack"),
),
)
except Exception as e:
raise ValidationError(str(e), self)
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes = classes.o))
self.o = J.call(ctxt_fn, 'call', '()Ljava/lang/Object;')
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script("""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES
]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes=classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes = classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def __init__(self, base_class_name, d=None):
'''Initialize the proxy with the interface name and methods
:param base_class_name: the class name of the interface to implement
in dotted form (e.g. java.lang.Runnable)
:param d: an optional dictionary of method name to implementation
'''
self.ref_id, self.ref = J.create_jref(self)
self.__d = d or {}
jclass = J.class_for_name(base_class_name)
loader = J.call(jclass, "getClassLoader", "()Ljava/lang/ClassLoader;")
env = J.get_env()
classes = env.make_object_array(1, env.find_class("java/lang/Class"))
env.set_object_array_element(classes, 0, jclass)
handler = J.make_instance(
"org/cellprofiler/javabridge/CPythonInvocationHandler",
"(Ljava/lang/String;)V", self.ref_id)
self.o = J.static_call(
"java/lang/reflect/Proxy", "newProxyInstance",
"(Ljava/lang/ClassLoader;"
"[Ljava/lang/Class;"
"Ljava/lang/reflect/InvocationHandler;)"
"Ljava/lang/Object;", loader, classes, handler)
def getActiveImageDisplay(self):
'''Get the active imagej.data.display.ImageDisplay'''
return wrap_display(J.call(
self.o, "getActiveDisplay",
"()Lorg/scijava/display/Display;",
J.class_for_name("net.imagej.display.ImageDisplay")))
def test_03_04_cw_get_annotation(self):
c = javabridge.get_class_wrapper('java.security.Identity')
annotation = c.getAnnotation(
javabridge.class_for_name('java.lang.Deprecated'))
self.assertTrue(annotation is not None)
def test_01_11_class_for_name(self):
c = javabridge.class_for_name('java.lang.String')
name = javabridge.call(c, 'getCanonicalName', '()Ljava/lang/String;')
self.assertEqual(name, 'java.lang.String')
def getActiveImageDisplay(self):
'''Get the active imagej.data.display.ImageDisplay'''
return wrap_display(
J.call(self.o, "getActiveDisplay",
"()Lorg/scijava/display/Display;",
J.class_for_name("net.imagej.display.ImageDisplay")))
def test_03_11_cw_get_constructor(self):
c = javabridge.get_class_wrapper('java.lang.String')
sclass = javabridge.class_for_name('java.lang.String')
constructor = c.getConstructor([sclass])
self.assertEqual(javabridge.call(constructor, 'getName', '()Ljava/lang/String;'),
'java.lang.String')
def test_01_11_class_for_name(self):
c = javabridge.class_for_name('java.lang.String')
name = javabridge.call(c, 'getCanonicalName', '()Ljava/lang/String;')
self.assertEqual(name, 'java.lang.String')
def test_03_04_cw_get_annotation(self):
c = javabridge.get_class_wrapper('java.security.Identity')
annotation = c.getAnnotation(javabridge.class_for_name('java.lang.Deprecated'))
self.assertTrue(annotation is not None)
