def field_class_mapping():
return (
(J.class_for_name('imagej.display.Display'), FT_IMAGE),
(J.class_for_name('imagej.data.Dataset'), FT_IMAGE),
(J.class_for_name('imagej.data.display.DatasetView'), FT_IMAGE),
(J.class_for_name('imagej.ImageJ'), FT_CONTEXT)
)
def field_class_mapping():
return (
(J.class_for_name('imagej.data.display.ImageDisplay'), FT_IMAGE),
(J.class_for_name('imagej.data.Dataset'), FT_IMAGE),
(J.class_for_name('imagej.data.display.DatasetView'), FT_IMAGE),
(J.class_for_name('imagej.data.table.TableDisplay'), FT_TABLE)
)
def field_class_mapping():
return (
(J.class_for_name('imagej.display.Display'), FT_IMAGE),
(J.class_for_name('imagej.data.Dataset'), FT_IMAGE),
(J.class_for_name('imagej.data.display.DatasetView'), FT_IMAGE),
(J.class_for_name('imagej.ImageJ'), FT_CONTEXT)
)
def field_class_mapping():
return (
(J.class_for_name('imagej.data.display.ImageDisplay'), FT_IMAGE),
(J.class_for_name('imagej.data.Dataset'), FT_IMAGE),
(J.class_for_name('imagej.data.display.DatasetView'), FT_IMAGE),
(J.class_for_name('imagej.data.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_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 = [("imagej.updater.core.UpToDate", "latestNag", max_value),
("imagej.core.options.OptionsMisc", "exitWhenQuitting",
"false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("imagej.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(
"imagej/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 = [
("imagej.updater.core.UpToDate", "latestNag", max_value),
("imagej.core.options.OptionsMisc", "exitWhenQuitting", "false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("imagej.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(
"imagej/util/Prefs", "put",
"(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/String;)V",
c, key, value)
return the_imagej_context
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 test_03_11_cw_get_constructor(self):
c = J.get_class_wrapper('java.lang.String')
sclass = J.class_for_name('java.lang.String')
constructor = c.getConstructor([sclass])
self.assertEqual(
J.call(constructor, 'getName', '()Ljava/lang/String;'),
'java.lang.String')
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)
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):
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)
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 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 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 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 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, 'getService',
'(Ljava/lang/Class;)Limagej/service/Service;', 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 loadService(self, class_name):
'''Load the service class with the given class name
You can use this method to pick specific implementations such as
the headless or Swing UI.
class_name - class name in dotted form, e.g. java.lang.String
'''
klass = J.class_for_name(class_name)
J.call(self.o, 'loadService', '(Ljava/lang/Class;)V', klass)
def test_03_09_cw_get_method(self):
sclass = J.class_for_name('java.lang.String')
iclass = J.get_static_field('java/lang/Integer', 'TYPE',
'Ljava/lang/Class;')
c = J.get_class_wrapper('java.lang.String')
m = c.getMethod('charAt', [ iclass ])
self.assertEqual(J.to_string(J.call(m, 'getReturnType', '()Ljava/lang/Class;')), 'char')
m = c.getMethod('concat', [ sclass])
self.assertEqual(J.to_string(J.call(m, 'getReturnType', '()Ljava/lang/Class;')),
'class java.lang.String')
def loadService(self, class_name):
'''Load the service class with the given class name
You can use this method to pick specific implementations such as
the headless or Swing UI.
class_name - class name in dotted form, e.g. java.lang.String
'''
klass = J.class_for_name(class_name)
J.call(self.o, 'loadService', '(Ljava/lang/Class;)V', klass)
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, 'getService',
'(Ljava/lang/Class;)Limagej/IService;', klass)
def test_03_09_cw_get_method(self):
sclass = J.class_for_name('java.lang.String')
iclass = J.get_static_field('java/lang/Integer', 'TYPE',
'Ljava/lang/Class;')
c = J.get_class_wrapper('java.lang.String')
m = c.getMethod('charAt', [iclass])
self.assertEqual(
J.to_string(J.call(m, 'getReturnType', '()Ljava/lang/Class;')),
'char')
m = c.getMethod('concat', [sclass])
self.assertEqual(
J.to_string(J.call(m, 'getReturnType', '()Ljava/lang/Class;')),
'class java.lang.String')
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.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.imagej.ImageJ(classes);
}
}""", dict(classes = classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
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;" "Ljava/lang/Class;)V", # base # 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"
]
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):
if service_classes is None:
classes = None
ctxt_fn = J.run_script("""new java.util.concurrent.Callable() {
call: function() {
return new Packages.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.imagej.ImageJ(classes);
}
}""", dict(classes=classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def field_class_mapping():
return ((J.class_for_name('imagej.data.display.ImageDisplay'),
FT_IMAGE), (J.class_for_name('imagej.data.Dataset'), FT_IMAGE),
(J.class_for_name('imagej.data.display.DatasetView'), FT_IMAGE),
(J.class_for_name('imagej.data.table.TableDisplay'), FT_TABLE))
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 test_03_04_cw_get_annotation(self):
c = J.get_class_wrapper('java.security.Identity')
annotation = c.getAnnotation(J.class_for_name('java.lang.Deprecated'))
self.assertTrue(annotation is not None)
'java.lang.Long': FT_INTEGER,
'int': FT_INTEGER,
'short': FT_INTEGER,
'byte': FT_INTEGER,
'long': FT_INTEGER,
'java.lang.Float': FT_FLOAT,
'java.lang.Double': FT_FLOAT,
'float': FT_FLOAT,
'double': FT_FLOAT,
'java.lang.String': FT_STRING,
'java.lang.Boolean': FT_BOOL,
'boolean': FT_BOOL,
'imagej.util.ColorRGB': FT_COLOR
}
field_class_mapping = ((J.class_for_name('imagej.display.Display'), FT_IMAGE),
(J.class_for_name('imagej.data.Dataset'), FT_IMAGE),
(J.class_for_name('imagej.data.roi.Overlay'),
FT_OVERLAY))
def run_imagej(*args):
J.static_call("imagej/Main", "main", "([Ljava/lang/String;)V",
*[unicode(arg) for arg in args])
def create_planar_img(a):
'''Create a PlanarImg from a numpy array
a - numpy array. The values should be scaled to be between 0 and 255
def __init__(self):
classes = [J.class_for_name(x) for x in service_classes]
self.o = J.run_in_main_thread(
lambda: J.static_call("imagej/ImageJ", "createContext",
"([Ljava/lang/Class;)Limagej/ImageJ;",
classes), True)
def __init__(self):
classes = [ J.class_for_name(x) for x in service_classes]
self.o = J.run_in_main_thread(
lambda :J.static_call(
"imagej/ImageJ", "createContext",
"([Ljava/lang/Class;)Limagej/ImageJ;", classes), True)
def field_class_mapping():
return ((J.class_for_name('imagej.data.display.ImageDisplay'),
FT_IMAGE), (J.class_for_name('imagej.data.Dataset'), FT_IMAGE),
(J.class_for_name('imagej.data.display.DatasetView'), FT_IMAGE),
(J.class_for_name('imagej.data.table.TableDisplay'), FT_TABLE),
(J.class_for_name('org.scijava.plugin.SciJavaPlugin'), FT_PLUGIN))
def test_01_11_class_for_name(self):
c = J.class_for_name('java.lang.String')
name = J.call(c, 'getCanonicalName', '()Ljava/lang/String;')
self.assertEqual(name, 'java.lang.String')
def test_03_04_cw_get_annotation(self):
c = J.get_class_wrapper('java.security.Identity')
annotation = c.getAnnotation(J.class_for_name('java.lang.Deprecated'))
self.assertTrue(annotation is not None)
def test_01_11_class_for_name(self):
c = J.class_for_name('java.lang.String')
name = J.call(c, 'getCanonicalName', '()Ljava/lang/String;')
self.assertEqual(name, 'java.lang.String')
def test_03_11_cw_get_constructor(self):
c = J.get_class_wrapper('java.lang.String')
sclass = J.class_for_name('java.lang.String')
constructor = c.getConstructor([sclass])
self.assertEqual(J.call(constructor, 'getName', '()Ljava/lang/String;'),
'java.lang.String')
'int': FT_INTEGER,
'short': FT_INTEGER,
'byte': FT_INTEGER,
'long': FT_INTEGER,
'java.lang.Float': FT_FLOAT,
'java.lang.Double': FT_FLOAT,
'float': FT_FLOAT,
'double': FT_FLOAT,
'java.lang.String': FT_STRING,
'java.lang.Boolean': FT_BOOL,
'boolean': FT_BOOL,
'imagej.util.ColorRGB': FT_COLOR
}
field_class_mapping = (
(J.class_for_name('imagej.display.Display'), FT_IMAGE),
(J.class_for_name('imagej.data.Dataset'), FT_IMAGE),
(J.class_for_name('imagej.data.roi.Overlay'), FT_OVERLAY) )
def run_imagej(*args):
J.static_call("imagej/Main", "main", "([Ljava/lang/String;)V",
*[unicode(arg) for arg in args])
def create_planar_img(a):
'''Create a PlanarImg from a numpy array
a - numpy array. The values should be scaled to be between 0 and 255
returns a PlanarImg of double valueswith the same dimensions as the array.
'''
a = a.astype(np.float64)
