def run(self, module,
pre = None,
post = None,
separateThread = False,
**kwargs):
'''Run a module
module - the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.get_dictionary_wrapper(
J.make_instance('java/util/HashMap', '()V'))
for k,v in kwargs.iteritems():
input_map.put(k, v)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run",
"(Limagej/ext/module/Module;Ljava/util/List;Ljava/util/List;Ljava/util/Map;)Ljava/util/concurrent/Future;",
module, pre, post, input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/ext/module/Module;",
future)
def getModules(self):
modules = J.call(o, "getModules", "()Ljava/util/List;")
if modules is None:
return []
module_iterator = J.call(modules, "iterator",
"()Ljava/util/Iterator;")
return [ModuleInfo(x) for x in J.iterate_java(module_iterator)]
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 show_imagej():
'''Show the ImageJ user interface'''
ij_obj = J.static_call("ij/IJ", "getInstance", "()Lij/ImageJ;")
if ij_obj is None:
ij_obj = J.make_instance("ij/ImageJ", "()V")
J.call(ij_obj, "setVisible", "(Z)V", True)
J.call(ij_obj, "toFront", "()V")
def show_imagej():
'''Show the ImageJ user interface'''
ij_obj = J.static_call("ij/IJ", "getInstance", "()Lij/ImageJ;")
if ij_obj is None:
ij_obj = J.make_instance("ij/ImageJ", "()V")
J.call(ij_obj, "setVisible", "(Z)V", True)
J.call(ij_obj, "toFront", "()V")
def getModules(self):
modules = J.call(o, "getModules", "()Ljava/util/List;")
if modules is None:
return []
module_iterator = J.call(modules, "iterator",
"()Ljava/util/Iterator;")
return [wrap_module_info(x) for x in J.iterate_java(module_iterator)]
def run(self, module_info, pre=None, post=None, **kwargs):
'''Run a module
module_info - the module_info of the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.make_map(kwargs)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run", "(Limagej/module/ModuleInfo;"
"Ljava/util/List;"
"Ljava/util/List;"
"Ljava/util/Map;)"
"Ljava/util/concurrent/Future;", module_info, pre, post,
input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/module/Module;",
future)
def run(self, module_info,
pre = None,
post = None,
**kwargs):
'''Run a module
module_info - the module_info of the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.make_map(kwargs)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run",
"(Limagej/module/ModuleInfo;"
"Ljava/util/List;"
"Ljava/util/List;"
"Ljava/util/Map;)"
"Ljava/util/concurrent/Future;",
module_info, pre, post, input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/module/Module;",
future)
def get_commands():
"""Return a list of the available command strings"""
script = """
new java.util.concurrent.Callable() {
call: function() {
importClass(Packages.ij.Menus, Packages.ij.IJ);
var hashtable=Menus.getCommands();
if (hashtable==null) {
IJ.run("pleaseignorethis");
hashtable = Menus.getCommands();
}
return hashtable;
}
};
"""
c = J.run_script(script, class_loader=get_user_loader())
hashtable = J.execute_callable_in_main_thread(c)
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 copy_plane(index, src):
p = J.call(planar_img, "getPlane", "(I)Ljava/lang/Object;", index)
dest = J.call(p, "getCurrentStorageArray", "()Ljava/lang/Object;")
length = np.prod(src.shape)
src = J.get_nice_arg(src, "[D")
J.static_call("java/lang/System", "arraycopy",
"(Ljava/lang/Object;ILjava/lang/Object;II)V", src, 0,
dest, 0, length)
def setPixelsSizeX(self, x, imageIndex, binDataIndex):
try:
jutil.call(self.o, 'setPixelsSizeX',
'(Lome/xml/model/primitives/PositiveInteger;I)V',
PositiveInteger(x), imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsSizeX', '(Ljava/lang/Integer;II)V', x,
imageIndex, binDataIndex)
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 setPixelsSizeY(self, y, imageIndex, binDataIndex):
try:
jutil.call(self.o, 'setPixelsSizeY',
'(Lome/xml/model/primitives/PositiveInteger;I)V',
PositiveInteger(y), imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsSizeY',
'(Ljava/lang/Integer;II)V', y, imageIndex, binDataIndex)
def copy_plane(index, src):
p = J.call(planar_img, "getPlane", "(I)Ljava/lang/Object;", index)
dest = J.call(p, "getCurrentStorageArray", "()Ljava/lang/Object;")
length = np.prod(src.shape)
src = J.get_nice_arg(src, "[D")
J.static_call("java/lang/System", "arraycopy",
"(Ljava/lang/Object;ILjava/lang/Object;II)V",
src, 0, dest, 0, length)
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 getType(self):
jtype = J.call(self.o, "getType", "()Ljava/lang/Class;")
type_name = J.call(jtype, "getCanonicalName", "()Ljava/lang/String;")
if field_mapping.has_key(type_name):
return field_mapping[type_name]
for class_instance, result in field_class_mapping():
if J.call(class_instance, "isAssignableFrom", "(Ljava/lang/Class;)Z", jtype):
return result
return None
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 getType(self):
jtype = J.call(self.o, "getType", "()Ljava/lang/Class;")
type_name = J.call(jtype, "getCanonicalName", "()Ljava/lang/String;")
if field_mapping.has_key(type_name):
return field_mapping[type_name]
for class_instance, result in field_class_mapping():
if J.call(class_instance, "isAssignableFrom",
"(Ljava/lang/Class;)Z", jtype):
return result
return None
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 setLogicalChannelSamplesPerPixel(self, samplesPerPixel, imageIndex, channelIndex):
'For a particular LogicalChannel, sets number of channel components in the logical channel.'
try:
jutil.call(self.o, 'setChannelSamplesPerPixel',
'(Lome/xml/model/primitives/PositiveInteger;II)V',
PositiveInteger(samplesPerPixel),
imageIndex, channelIndex)
except jutil.JavaException:
jutil.call(self.o, 'setLogicalChannelSamplesPerPixel',
'(Ljava/lang/Integer;II)V', samplesPerPixel,
imageIndex, channelIndex)
def __exit__(self, type_class, value, traceback):
if self.rdr is not None:
self.rdr.close()
del self.rdr.o
del self.rdr
if self.stream is not None:
jutil.call(self.stream, 'close', '()V')
del self.stream
#
# Run the Java garbage collector here.
#
jutil.static_call("java/lang/System", "gc", "()V")
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 setLogicalChannelSamplesPerPixel(self, samplesPerPixel, imageIndex,
channelIndex):
'For a particular LogicalChannel, sets number of channel components in the logical channel.'
try:
jutil.call(self.o, 'setChannelSamplesPerPixel',
'(Lome/xml/model/primitives/PositiveInteger;II)V',
PositiveInteger(samplesPerPixel), imageIndex,
channelIndex)
except jutil.JavaException:
jutil.call(self.o, 'setLogicalChannelSamplesPerPixel',
'(Ljava/lang/Integer;II)V', samplesPerPixel, imageIndex,
channelIndex)
def __exit__(self, type_class, value, traceback):
if self.rdr is not None:
self.rdr.close()
del self.rdr.o
del self.rdr
if self.stream is not None:
jutil.call(self.stream, 'close', '()V')
del self.stream
#
# Run the Java garbage collector here.
#
jutil.static_call("java/lang/System", "gc","()V")
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 execute_macro(macro_text):
'''Execute a macro in ImageJ
macro_text - the macro program to be run
'''
if sys.platform == "darwin":
J.set_static_field("ij/macro/Interpreter", "batchMode", "Z", True)
J.static_call("ij/IJ", "runMacro",
"(Ljava/lang/String;)Ljava/lang/String;", macro_text)
else:
show_imagej()
interp = J.make_instance("ij/macro/Interpreter", "()V")
J.call(interp, "run", "(Ljava/lang/String;)V", macro_text)
def test_08_01_create_overlay(self):
r = np.random.RandomState()
r.seed(81)
mask = r.uniform(size=(23,10)) > .5
overlay = ij2.create_overlay(self.context, mask)
roi = J.call(overlay, "getRegionOfInterest",
"()Lnet/imglib2/roi/RegionOfInterest;")
i = r.randint(0, 23, 10)
j = r.randint(0, 10, 10)
for ii, jj in zip(i, j):
location = np.array([jj, ii], float)
test = J.call(roi, "contains", "([D)Z", location)
self.assertEqual(mask[ii, jj], test)
def execute_macro(macro_text):
'''Execute a macro in ImageJ
macro_text - the macro program to be run
'''
if sys.platform == "darwin":
J.set_static_field("ij/macro/Interpreter", "batchMode", "Z", True)
J.static_call("ij/IJ", "runMacro",
"(Ljava/lang/String;)Ljava/lang/String;",
macro_text)
else:
show_imagej();
interp = J.make_instance("ij/macro/Interpreter","()V");
J.call(interp, "run","(Ljava/lang/String;)V", macro_text);
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 setPixelsDimensionOrder(self, dimension_order, imageIndex, binDataIndex):
'''Set the dimension order for a series'''
# Post loci_tools 4.2 - use ome.xml.model.DimensionOrder
try:
jdimension_order = jutil.static_call(
'ome/xml/model/enums/DimensionOrder', 'fromString',
'(Ljava/lang/String;)Lome/xml/model/enums/DimensionOrder;',
dimension_order)
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Lome/xml/model/enums/DimensionOrder;I)V',
jdimension_order, imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Ljava/lang/String;II)V',
dimension_order, imageIndex, binDataIndex)
def setPixelsBigEndian(self, bigEndian, imageIndex, binDataIndex):
'''Set the endianness for a particular image
bigEndian - True for big-endian, False for little-endian
imageIndex - index of the image in question from IFormatReader.get_index?
binDataIndex - ???
'''
# Post loci_tools 4.2
try:
jutil.call(self.o, 'setPixelsBinDataBigEndian',
'(Ljava/lang/Boolean;II)V',
bigEndian, imageIndex, binDataIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsBigEndian', '(Ljava/lang/Boolean;II)V',
bigEndian, imageIndex, binDataIndex)
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 test_03_08_cw_get_field(self):
c = J.get_class_wrapper('java.lang.String')
field = c.getField('CASE_INSENSITIVE_ORDER')
modifiers = J.call(field, 'getModifiers', '()I')
static = J.get_static_field('java/lang/reflect/Modifier', 'STATIC',
'I')
self.assertEqual((modifiers & static), static)
def test_03_07_cw_get_fields(self):
c = J.get_class_wrapper('java.lang.String')
fields = c.getFields()
fields = J.get_env().get_object_array_elements(fields)
self.assertEqual(len(fields), 1)
self.assertEqual(J.call(fields[0], 'getName', '()Ljava/lang/String;'),
"CASE_INSENSITIVE_ORDER")
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 test_03_07_cw_get_fields(self):
c = J.get_class_wrapper('java.lang.String')
fields = c.getFields()
fields = J.get_env().get_object_array_elements(fields)
self.assertEqual(len(fields), 1)
self.assertEqual(J.call(fields[0], 'getName', '()Ljava/lang/String;'),
"CASE_INSENSITIVE_ORDER")
def create_overlay(mask):
'''Create a bitmask overlay from a numpy boolean array
mask - boolean numpy array organized as i,j = y,x
'''
assert mask.ndim == 2
mask = mask.transpose()
strides = np.array([1, mask.shape[0]])
imgFactory = J.make_instance("net/imglib2/img/planar/PlanarImgFactory",
"()V")
bit_type = J.make_instance("net/imglib2/type/logic/BitType", "()V")
img = J.call(
imgFactory, "create",
"([JLnet/imglib2/type/NativeType;)Lnet/imglib2/img/planar/PlanarImg;",
np.array(mask.shape), bit_type)
J.static_call("net/imglib2/util/ImgUtil", "copy",
"([ZI[ILnet/imglib2/img/Img;)V", mask.flatten(), 0, strides,
img)
roi = J.make_instance("net/imglib2/roi/BinaryMaskRegionOfInterest",
"(Lnet/imglib2/img/Img;)V", img)
overlay = J.make_instance(
"imagej/data/roi/BinaryMaskOverlay",
"(Lnet/imglib2/roi/BinaryMaskRegionOfInterest;)V", roi)
return overlay
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 create_overlay(mask):
'''Create a bitmask overlay from a numpy boolean array
mask - boolean numpy array organized as i,j = y,x
'''
assert mask.ndim == 2
mask = mask.transpose()
strides = np.array([1, mask.shape[0]])
imgFactory = J.make_instance(
"net/imglib2/img/planar/PlanarImgFactory", "()V")
bit_type = J.make_instance("net/imglib2/type/logic/BitType", "()V")
img = J.call(
imgFactory, "create",
"([JLnet/imglib2/type/NativeType;)Lnet/imglib2/img/planar/PlanarImg;",
np.array(mask.shape), bit_type)
J.static_call("net/imglib2/util/ImgUtil",
"copy", "([ZI[ILnet/imglib2/img/Img;)V",
mask.flatten(), 0, strides, img)
roi = J.make_instance(
"net/imglib2/roi/BinaryMaskRegionOfInterest",
"(Lnet/imglib2/img/Img;)V", img)
overlay = J.make_instance(
"imagej/data/roi/BinaryMaskOverlay",
"(Lnet/imglib2/roi/BinaryMaskRegionOfInterest;)V", roi)
return overlay
def setPixelsBigEndian(self, bigEndian, imageIndex, binDataIndex):
'''Set the endianness for a particular image
bigEndian - True for big-endian, False for little-endian
imageIndex - index of the image in question from IFormatReader.get_index?
binDataIndex - ???
'''
# Post loci_tools 4.2
try:
jutil.call(self.o, 'setPixelsBinDataBigEndian',
'(Ljava/lang/Boolean;II)V', bigEndian, imageIndex,
binDataIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsBigEndian',
'(Ljava/lang/Boolean;II)V', bigEndian, imageIndex,
binDataIndex)
def test_10_08_eval_with_bindings(self):
svc = ij2.get_script_service(self.context)
factory = svc.getByName("ECMAScript")
engine = factory.getScriptEngine()
engine.put("a", 2)
engine.evalS("var b = a+a;")
self.assertEqual(J.call(engine.get("b"), "intValue", "()I"), 4)
def setPixelsDimensionOrder(self, dimension_order, imageIndex,
binDataIndex):
'''Set the dimension order for a series'''
# Post loci_tools 4.2 - use ome.xml.model.DimensionOrder
try:
jdimension_order = jutil.static_call(
'ome/xml/model/enums/DimensionOrder', 'fromString',
'(Ljava/lang/String;)Lome/xml/model/enums/DimensionOrder;',
dimension_order)
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Lome/xml/model/enums/DimensionOrder;I)V',
jdimension_order, imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Ljava/lang/String;II)V', dimension_order, imageIndex,
binDataIndex)
def createDisplay(self, dataset):
'''Create a display that contains the given dataset'''
display = J.call(
self.o, "createDisplay",
"(Limagej/data/Dataset;)Limagej/display/ImageDisplay;",
dataset.o)
return wrap_display(display)
def test_03_10_cw_get_methods(self):
c = J.get_class_wrapper('java.lang.String')
mmm = J.get_env().get_object_array_elements(c.getMethods())
self.assertTrue(
any([
J.call(m, 'getName', '()Ljava/lang/String;') == 'concat'
for m in mmm
]))
def createDisplay(self, dataset):
'''Create a display that contains the given dataset'''
display = J.call(
self.o,
"createDisplay",
"(Limagej/data/Dataset;)Limagej/display/ImageDisplay;",
dataset.o)
return wrap_display(display)
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 createDisplay(self, name, dataset):
'''Create a display that contains the given dataset'''
display = J.call(
self.o,
"createDisplay",
"(Ljava/lang/String;Ljava/lang/Object;)Limagej/display/Display;",
name, dataset.o)
return wrap_display(display)
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 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 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 test_01_06_get_enumeration_wrapper(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
keys = J.call(properties, "keys", "()Ljava/util/Enumeration;")
enum = J.get_enumeration_wrapper(keys)
has_java_vm_name = False
while (enum.hasMoreElements()):
key = J.to_string(enum.nextElement())
if key == "java.vm.name":
has_java_vm_name = True
self.assertTrue(has_java_vm_name)
def test_01_06_get_enumeration_wrapper(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
keys = J.call(properties, "keys", "()Ljava/util/Enumeration;")
enum = J.get_enumeration_wrapper(keys)
has_java_vm_name = False
while(enum.hasMoreElements()):
key = J.to_string(enum.nextElement())
if key == "java.vm.name":
has_java_vm_name = True
self.assertTrue(has_java_vm_name)
def get_fields_and_parameters_from_iterator(parameters):
iterator = J.call(parameters, 'iterator',
'()L%(ITERATOR_CLASS)s;' % globals())
result = []
for jfield in J.iterate_java(iterator):
field = J.get_field_wrapper(jfield)
parameter = field.getAnnotation(PARAMETER_CLASS.replace('/','.'))
if parameter is not None:
parameter = get_parameter_wrapper(parameter)
result.append((field, parameter))
return result
def get_image(imageprocessor_obj, do_scaling=False):
"""Retrieve the image from an ImageProcessor
Returns the image as a numpy float array.
"""
#
# The strategy is:
# * Make a TypeConverter
# * Ask the TypeConverter for a float ImageProcessor
# * Get the pixels - should be a float array
#
type_converter = J.make_instance(
"ij/process/TypeConverter", "(Lij/process/ImageProcessor;Z)V", imageprocessor_obj, do_scaling
)
float_processor = J.call(type_converter, "convertToFloat", "([F)Lij/process/ImageProcessor;", None)
jpixels = J.call(float_processor, "getPixels", "()Ljava/lang/Object;")
pixels = J.get_env().get_float_array_elements(jpixels)
height = J.call(imageprocessor_obj, "getHeight", "()I")
width = J.call(imageprocessor_obj, "getWidth", "()I")
pixels.shape = (height, width)
return pixels
def get_fields_and_parameters_from_iterator(parameters):
iterator = J.call(parameters, 'iterator',
'()L%(ITERATOR_CLASS)s;' % globals())
result = []
for jfield in J.iterate_java(iterator):
field = J.get_field_wrapper(jfield)
parameter = field.getAnnotation(PARAMETER_CLASS.replace('/', '.'))
if parameter is not None:
parameter = get_parameter_wrapper(parameter)
result.append((field, parameter))
return result
def make_bit_img(shape):
'''Make an imglib img of BitType with the given shape
shape - a sequence of image dimensions
'''
imgFactory = J.make_instance("net/imglib2/img/planar/PlanarImgFactory",
"()V")
bit_type = J.make_instance("net/imglib2/type/logic/BitType", "()V")
img = J.call(
imgFactory, "create",
"([JLnet/imglib2/type/NativeType;)Lnet/imglib2/img/planar/PlanarImg;",
np.array(shape), bit_type)
return img
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")
