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 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 test_02_01_show_get_and_hide(self):
file_name = os.path.join(sbs_dir, "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_03_05_cw_get_annotations(self):
c = J.get_class_wrapper('java.security.Identity')
annotations = c.getAnnotations()
annotations = J.get_env().get_object_array_elements(annotations)
self.assertEqual(len(annotations), 1)
self.assertEqual(J.to_string(annotations[0]),
'@java.lang.Deprecated()')
def test_08_11_toArray(self):
c1 = J.get_collection_wrapper(J.make_instance("java/util/HashSet", "()V"))
c1.add("Foo")
c1.add("Bar")
result = [J.to_string(x) for x in c1.toArray()]
self.assertIn("Foo", result)
self.assertIn("Bar", result)
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 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 test_08_11_toArray(self):
c1 = J.get_collection_wrapper(
J.make_instance("java/util/HashSet", "()V"))
c1.add("Foo")
c1.add("Bar")
result = [J.to_string(x) for x in c1.toArray()]
self.assertIn("Foo", result)
self.assertIn("Bar", result)
def test_01_07_get_dictionary_wrapper(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
self.assertTrue(d.size() > 10)
self.assertFalse(d.isEmpty())
keys = J.get_enumeration_wrapper(d.keys())
values = J.get_enumeration_wrapper(d.elements())
n_elems = d.size()
for i in range(n_elems):
self.assertTrue(keys.hasMoreElements())
key = J.to_string(keys.nextElement())
self.assertTrue(values.hasMoreElements())
value = J.to_string(values.nextElement())
self.assertEqual(J.to_string(d.get(key)), value)
self.assertFalse(keys.hasMoreElements())
self.assertFalse(values.hasMoreElements())
def test_01_07_get_dictionary_wrapper(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
self.assertTrue(d.size() > 10)
self.assertFalse(d.isEmpty())
keys = J.get_enumeration_wrapper(d.keys())
values = J.get_enumeration_wrapper(d.elements())
n_elems = d.size()
for i in range(n_elems):
self.assertTrue(keys.hasMoreElements())
key = J.to_string(keys.nextElement())
self.assertTrue(values.hasMoreElements())
value = J.to_string(values.nextElement())
self.assertEqual(J.to_string(d.get(key)), value)
self.assertFalse(keys.hasMoreElements())
self.assertFalse(values.hasMoreElements())
def test_01_09_jdictionary_to_string_dictionary(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
pyd = J.jdictionary_to_string_dictionary(properties)
keys = J.jenumeration_to_string_list(d.keys())
for key in keys:
value = J.to_string(d.get(key))
self.assertEqual(pyd[key], value)
def test_01_08_jenumeration_to_string_list(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
keys = J.jenumeration_to_string_list(d.keys())
enum = J.get_enumeration_wrapper(d.keys())
for i in range(d.size()):
key = J.to_string(enum.nextElement())
self.assertEqual(key, keys[i])
def test_01_08_jenumeration_to_string_list(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
keys = J.jenumeration_to_string_list(d.keys())
enum = J.get_enumeration_wrapper(d.keys())
for i in range(d.size()):
key = J.to_string(enum.nextElement())
self.assertEqual(key, keys[i])
def test_01_09_jdictionary_to_string_dictionary(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
d = J.get_dictionary_wrapper(properties)
pyd = J.jdictionary_to_string_dictionary(properties)
keys = J.jenumeration_to_string_list(d.keys())
for key in keys:
value = J.to_string(d.get(key))
self.assertEqual(pyd[key], value)
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_pixel_data(self, axes = None):
imgplus = self.getImgPlus()
pixel_data = get_pixel_data(imgplus)
inv_axes = J.get_env().get_object_array_elements(self.getAxes())
if axes is None:
axes = [ Axes().Y, Axes().X]
if len(inv_axes) > 2:
axes.append(Axes().CHANNEL)
transpose = []
for axis in axes:
matches = [i for i, inv_axis in enumerate(inv_axes)
if J.call(inv_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 pixel_data.transpose(transpose)
def get_pixel_data(self, axes=None):
imgplus = self.getImgPlus()
pixel_data = get_pixel_data(imgplus)
inv_axes = J.get_env().get_object_array_elements(self.getAxes())
if axes is None:
axes = [Axes().Y, Axes().X]
if len(inv_axes) > 2:
axes.append(Axes().CHANNEL)
transpose = []
for axis in axes:
matches = [
i for i, inv_axis in enumerate(inv_axes) if J.call(
inv_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 pixel_data.transpose(transpose)
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
cc = self.get_cached_commands()
if (not cc.has_key(command)) or (cc[command] is None):
return []
if not d.has_key(command):
classname = cc[command]
try:
plugin = M.get_plugin(classname)
except:
d[command] = []
return []
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
for field, parameter in fp_in:
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_BOOL:
result += [cps.Binary(label, field.getBoolean(plugin))]
elif field_type == P.FT_INTEGER:
result += [cps.Integer(label, field.getLong(plugin))]
elif field_type == P.FT_FLOAT:
result += [cps.Float(label, field.getDouble(plugin))]
elif field_type == P.FT_STRING:
result += [cps.Text(label, J.to_string(field.get(plugin)))]
else:
assert field_type == P.FT_IMAGE
result += [cps.ImageNameSubscriber(label, "None")]
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
result += [cps.ImageNameProvider(parameter.label() or "",
"Output")]
d[command] = result
else:
result = d[command]
return result
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 fn():
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 get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
if bioformats.USE_IJ2:
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
return []
result = []
inputs = module_info.getInputs()
module = module_info.createModule()
implied_outputs = []
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
value = module_item.getValue(module)
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
description = module_item.getDescription()
if field_type == IJ2.FT_BOOL:
setting = cps.Binary(label,
J.call(value, "booleanValue",
"()Z"),
doc=description)
elif field_type == IJ2.FT_INTEGER:
if minimum is not None:
minimum = J.call(minimum, "intValue", "()I")
if maximum is not None:
maximum = J.call(maximum, "intValue", "()I")
setting = cps.Integer(label,
J.call(value, "intValue", "()I"),
minval=minimum,
maxval=maximum,
doc=description)
elif field_type == IJ2.FT_FLOAT:
if minimum is not None:
minimum = J.call(minimum, "floatValue", "()F")
if maximum is not None:
maximum = J.call(maximum, "floatValue", "()F")
setting = cps.Float(label,
J.call(value, "floatValue", "()F"),
minval=minimum,
maxval=maximum,
doc=description)
elif field_type == IJ2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(value)
if choices is not None:
choices = [
J.to_string(choice)
for choice in J.iterate_collection(choices)
]
setting = cps.Choice(label,
choices,
value,
doc=description)
else:
setting = cps.Text(label, value, doc=description)
elif field_type == IJ2.FT_COLOR:
if value is not None:
value = IJ2.color_rgb_to_html(value)
else:
value = "#ffffff"
setting = cps.Color(label, value, doc=description)
elif field_type == IJ2.FT_IMAGE:
setting = cps.ImageNameSubscriber(label,
"InputImage",
doc=description)
#
# This is a Display for ij2 - the plugin typically
# scribbles all over the display's image. So
# we list it as an output too.
#
implied_outputs.append(
(cps.ImageNameProvider(label,
"OutputImage",
doc=description),
module_item))
elif field_type == IJ2.FT_OVERLAY:
setting = cps.ObjectNameSubscriber(label,
"ImageJObject",
doc=description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
if field_type == IJ2.FT_IMAGE:
result.append(
(cps.ImageNameProvider(label,
"ImageJImage",
doc=description), output))
result += implied_outputs
d[key] = result
return [setting for setting, module_info in result]
else:
cc = self.get_cached_commands()
if (not cc.has_key(key)) or (cc[key] is None):
return []
classname = cc[key]
try:
plugin = M.get_plugin(classname)
except:
d[key] = []
return []
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
for field, parameter in fp_in:
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_BOOL:
result += [cps.Binary(label, field.getBoolean(plugin))]
elif field_type == P.FT_INTEGER:
result += [cps.Integer(label, field.getLong(plugin))]
elif field_type == P.FT_FLOAT:
result += [cps.Float(label, field.getDouble(plugin))]
elif field_type == P.FT_STRING:
result += [
cps.Text(label, J.to_string(field.get(plugin)))
]
else:
assert field_type == P.FT_IMAGE
result += [cps.ImageNameSubscriber(label, "None")]
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
result += [
cps.ImageNameProvider(parameter.label() or "",
"Output")
]
d[key] = result
elif bioformats.USE_IJ2:
result = [setting for setting, module_info in d[key]]
else:
result = d[key]
return result
def test_04_03_field_type(self):
c = J.get_class_wrapper('java.lang.Byte')
f = J.get_field_wrapper(c.getField('MAX_VALUE'))
t = f.getType()
self.assertEqual(J.to_string(t), 'byte')
def test_01_01_to_string(self):
jstring = self.env.new_string_utf("Hello, world")
self.assertEqual(J.to_string(jstring), "Hello, world")
def test_01_02_make_instance(self):
jobject = J.make_instance("java/lang/Object", "()V")
self.assertTrue(J.to_string(jobject).startswith("java.lang.Object"))
def test_01_01_to_string(self):
jstring = self.env.new_string_utf("Hello, world")
self.assertEqual(J.to_string(jstring), "Hello, world")
def test_04_03_field_type(self):
c = J.get_class_wrapper('java.lang.Byte')
f = J.get_field_wrapper(c.getField('MAX_VALUE'))
t = f.getType()
self.assertEqual(J.to_string(t), 'byte')
def test_04_01_field_get(self):
c = J.get_class_wrapper('java.lang.Byte')
f = J.get_field_wrapper(c.getField('MAX_VALUE'))
v = f.get(None)
self.assertEqual(J.to_string(v), '127')
def test_04_01_field_get(self):
c = J.get_class_wrapper('java.lang.Byte')
f = J.get_field_wrapper(c.getField('MAX_VALUE'))
v = f.get(None)
self.assertEqual(J.to_string(v), '127')
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
logger.info("Could not find command %s" % key)
return []
result = []
inputs = module_info.getInputs()
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
if label is None:
label = module_item.getName()
if module_item.isOutput():
# if both, qualify which is for input and which for output
label = "%s (Input)" % label
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
default = module_item.loadValue()
description = module_item.getDescription()
if field_type == ij2.FT_BOOL:
value = (J.is_instance_of(default, 'java/lang/Boolean') and
J.call(default, "booleanValue", "()Z"))
setting = cps.Binary(
label,
value = value,
doc = description)
elif field_type == ij2.FT_INTEGER:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "intValue", "()I")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Integer(
label,
value = value,
doc = description)
elif field_type == ij2.FT_FLOAT:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "doubleValue", "()D")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Float(
label,
value=value,
doc = description)
elif field_type == ij2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(default)
if choices is not None:
choices = J.get_collection_wrapper(choices)
setting = cps.Choice(
label, choices, value, doc = description)
else:
setting = cps.Text(
label, value, doc = description)
elif field_type == ij2.FT_COLOR:
value = "#ffffff"
setting = cps.Color(label, value, doc = description)
elif field_type == ij2.FT_IMAGE:
setting = cps.ImageNameSubscriber(
label, "InputImage",
doc = description)
elif field_type == ij2.FT_TABLE:
setting = IJTableSubscriber(label, "InputTable",
doc=description)
elif field_type == ij2.FT_FILE:
setting = cps.FilenameText(
label, None, doc = description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
label = output.getLabel()
if label is None:
label = output.getName()
if output.isInput():
# if both, qualify which is for input and which for output
label = "%s (Output)" % label
if field_type == ij2.FT_IMAGE:
result.append((cps.ImageNameProvider(
label, "ImageJImage",
doc = description), output))
elif field_type == ij2.FT_TABLE:
result.append((IJTableProvider(
label, "ImageJTable", doc=description), output))
d[key] = result
else:
result = d[key]
return [setting for setting, module_info in result]
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
if bioformats.USE_IJ2:
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
return []
result = []
inputs = module_info.getInputs()
module = module_info.createModule()
implied_outputs = []
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
value = module_item.getValue(module)
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
description = module_item.getDescription()
if field_type == IJ2.FT_BOOL:
setting = cps.Binary(
label,
J.call(value, "booleanValue", "()Z"),
doc = description)
elif field_type == IJ2.FT_INTEGER:
if minimum is not None:
minimum = J.call(minimum, "intValue", "()I")
if maximum is not None:
maximum = J.call(maximum, "intValue", "()I")
setting = cps.Integer(
label,
J.call(value, "intValue", "()I"),
minval = minimum,
maxval = maximum,
doc = description)
elif field_type == IJ2.FT_FLOAT:
if minimum is not None:
minimum = J.call(minimum, "floatValue", "()F")
if maximum is not None:
maximum = J.call(maximum, "floatValue", "()F")
setting = cps.Float(
label,
J.call(value, "floatValue", "()F"),
minval = minimum,
maxval = maximum,
doc = description)
elif field_type == IJ2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(value)
if choices is not None:
choices = [J.to_string(choice)
for choice
in J.iterate_collection(choices)]
setting = cps.Choice(
label, choices, value, doc = description)
else:
setting = cps.Text(
label, value, doc = description)
elif field_type == IJ2.FT_COLOR:
if value is not None:
value = IJ2.color_rgb_to_html(value)
else:
value = "#ffffff"
setting = cps.Color(label, value, doc = description)
elif field_type == IJ2.FT_IMAGE:
setting = cps.ImageNameSubscriber(
label, "InputImage",
doc = description)
#
# This is a Display for ij2 - the plugin typically
# scribbles all over the display's image. So
# we list it as an output too.
#
implied_outputs.append((
cps.ImageNameProvider(
label, "OutputImage",
doc = description), module_item))
elif field_type == IJ2.FT_OVERLAY:
setting = cps.ObjectNameSubscriber(
label, "ImageJObject",
doc = description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
if field_type == IJ2.FT_IMAGE:
result.append((cps.ImageNameProvider(
label, "ImageJImage",
doc = description), output))
result += implied_outputs
d[key] = result
return [setting for setting, module_info in result]
else:
cc = self.get_cached_commands()
if (not cc.has_key(key)) or (cc[key] is None):
return []
classname = cc[key]
try:
plugin = M.get_plugin(classname)
except:
d[key] = []
return []
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
for field, parameter in fp_in:
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_BOOL:
result += [cps.Binary(label, field.getBoolean(plugin))]
elif field_type == P.FT_INTEGER:
result += [cps.Integer(label, field.getLong(plugin))]
elif field_type == P.FT_FLOAT:
result += [cps.Float(label, field.getDouble(plugin))]
elif field_type == P.FT_STRING:
result += [cps.Text(label, J.to_string(field.get(plugin)))]
else:
assert field_type == P.FT_IMAGE
result += [cps.ImageNameSubscriber(label, "None")]
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
result += [cps.ImageNameProvider(parameter.label() or "",
"Output")]
d[key] = result
elif bioformats.USE_IJ2:
result = [setting for setting, module_info in d[key]]
else:
result = d[key]
return result
def test_01_01_load_imageplus(self):
file_name = os.path.join(sbs_dir, "Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
self.assertTrue(J.to_string(ip.o).startswith("imp"))
def test_01_02_make_instance(self):
jobject = J.make_instance("java/lang/Object", "()V")
self.assertTrue(J.to_string(jobject).startswith("java.lang.Object"))
def test_01_13_get_channel_processor(self):
file_name = os.path.join(sbs_dir, "Channel1-01-A-01.tif")
ip = I.load_imageplus(file_name)
p = ip.getChannelProcessor()
self.assertTrue(J.to_string(p).startswith("ip"))
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
logger.info("Could not find command %s" % key)
return []
result = []
inputs = module_info.getInputs()
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
if label is None:
label = module_item.getName()
if module_item.isOutput():
# if both, qualify which is for input and which for output
label = "%s (Input)" % label
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
default = module_item.loadValue()
description = module_item.getDescription()
if field_type == ij2.FT_BOOL:
value = (J.is_instance_of(default, 'java/lang/Boolean')
and J.call(default, "booleanValue", "()Z"))
setting = cps.Binary(label, value=value, doc=description)
elif field_type == ij2.FT_INTEGER:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "intValue", "()I")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Integer(label, value=value, doc=description)
elif field_type == ij2.FT_FLOAT:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "doubleValue", "()D")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Float(label, value=value, doc=description)
elif field_type == ij2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(default)
if choices is not None:
choices = J.get_collection_wrapper(choices)
setting = cps.Choice(label,
choices,
value,
doc=description)
else:
setting = cps.Text(label, value, doc=description)
elif field_type == ij2.FT_COLOR:
value = "#ffffff"
setting = cps.Color(label, value, doc=description)
elif field_type == ij2.FT_IMAGE:
setting = cps.ImageNameSubscriber(label,
"InputImage",
doc=description)
elif field_type == ij2.FT_TABLE:
setting = IJTableSubscriber(label,
"InputTable",
doc=description)
elif field_type == ij2.FT_FILE:
setting = cps.FilenameText(label, None, doc=description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
label = output.getLabel()
if label is None:
label = output.getName()
if output.isInput():
# if both, qualify which is for input and which for output
label = "%s (Output)" % label
if field_type == ij2.FT_IMAGE:
result.append(
(cps.ImageNameProvider(label,
"ImageJImage",
doc=description), output))
elif field_type == ij2.FT_TABLE:
result.append((IJTableProvider(label,
"ImageJTable",
doc=description), output))
d[key] = result
else:
result = d[key]
return [setting for setting, module_info in result]
'''
never = J.get_static_field("java/lang/Long", "MAX_VALUE", "J")
J.static_call("imagej/updater/core/UpToDate", "setLatestNag", "(J)V",
never)
def wrap_user_interface(o):
'''Return a wrapped imagej.ui.UserInterface'''
class UserInterface(object):
def __init__(self):
self.o = o
show = J.make_method("show", "()V")
isVisible = J.make_method("isVisible", "()Z")
return UserInterface()
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)
'''Make an imagej.util.ColorRGB from an HTML color
HTML colors have the form, #rrggbb or are one of the names
from the CSS-3 colors.
'''
return J.static_call("fromHTMLColor",
"(Ljava/lang/String;)Limagej/util/ColorRGB;", s)
def color_rgb_to_html(color_rgb):
'''Return an HTML-encoded color value from an imagej.util.ColorRGB
color_rgb - a Java imagej.util.ColorRGB object
'''
return J.call(color_rgb, "toHTMLColor()", "()Ljava/lang/String;")
if __name__=="__main__":
classpath = os.path.join(os.path.split(__file__)[0], "imagej-2.0-SNAPSHOT-all.jar")
J.start_vm(["-Djava.class.path="+classpath])
my_context = create_context([
"imagej.event.EventService",
"imagej.object.ObjectService",
"imagej.platform.PlatformService",
"imagej.ext.plugin.PluginService",
"imagej.ext.module.ModuleService"
])
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 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 test_03_05_cw_get_annotations(self):
c = J.get_class_wrapper('java.security.Identity')
annotations = c.getAnnotations()
annotations = J.get_env().get_object_array_elements(annotations)
self.assertEqual(len(annotations), 1)
self.assertEqual(J.to_string(annotations[0]),'@java.lang.Deprecated()')
