def get_current_image():
"""Get the WindowManager's current image
returns a wrapped ImagePlus object
"""
imageplus_obj = J.static_call("ij/WindowManager", "getCurrentImage", "()Lij/ImagePlus;")
return get_imageplus_wrapper(imageplus_obj)
def get_current_image():
'''Get the WindowManager's current image
returns a wrapped ImagePlus object
'''
imageplus_obj = J.static_call('ij/WindowManager','getCurrentImage',
'()Lij/ImagePlus;')
return get_imageplus_wrapper(imageplus_obj)
def get_current_image():
'''Get the WindowManager's current image
returns a wrapped ImagePlus object
'''
imageplus_obj = J.static_call('ij/WindowManager', 'getCurrentImage',
'()Lij/ImagePlus;')
return get_imageplus_wrapper(imageplus_obj)
def get_current_image():
'''Get the image from the top of the batch mode image stack
returns None or a wrapped imagePlus
'''
image_plus = J.static_call("ij/macro/Interpreter", "getLastBatchModeImage",
"()Lij/ImagePlus;")
if image_plus is not None:
return get_imageplus_wrapper(image_plus)
def get_current_image():
'''Get the image from the top of the batch mode image stack
returns None or a wrapped imagePlus
'''
image_plus = J.static_call("ij/macro/Interpreter",
"getLastBatchModeImage",
"()Lij/ImagePlus;")
if image_plus is not None:
return get_imageplus_wrapper(image_plus)
def get_temp_current_image():
'''Get the temporary ImagePlus object for the current thread'''
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getTempCurrentImage();
}
};
"""
gtci = J.make_future_task(J.run_script(script))
imageplus_obj = J.execute_future_in_main_thread(gtci)
return get_imageplus_wrapper(imageplus_obj)
def get_temp_current_image():
'''Get the temporary ImagePlus object for the current thread'''
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getTempCurrentImage();
}
};
"""
gtci = J.make_future_task(J.run_script(script))
imageplus_obj = J.execute_future_in_main_thread(gtci)
return get_imageplus_wrapper(imageplus_obj)
def close_all_windows():
"""Close all ImageJ windows
Hide the ImageJ windows so that they don't go through the Save dialog,
then call the Window Manager's closeAllWindows to get the rest.
"""
jimage_list = J.static_call("ij/WindowManager", "getIDList", "()[I")
if jimage_list is None:
return
image_list = J.get_env().get_int_array_elements(jimage_list)
for image_id in image_list:
ip = J.static_call("ij/WindowManager", "getImage", "(I)Lij/ImagePlus;", image_id)
ip = get_imageplus_wrapper(ip)
ip.hide()
J.static_call("ij/WindowManager", "closeAllWindows", "()Z")
def close_all_windows():
'''Close all ImageJ windows
Hide the ImageJ windows so that they don't go through the Save dialog,
then call the Window Manager's closeAllWindows to get the rest.
'''
jimage_list = J.static_call('ij/WindowManager', 'getIDList', '()[I')
if jimage_list is None:
return
image_list = J.get_env().get_int_array_elements(jimage_list)
for image_id in image_list:
ip = J.static_call('ij/WindowManager', 'getImage', '(I)Lij/ImagePlus;',
image_id)
ip = get_imageplus_wrapper(ip)
ip.hide()
J.static_call('ij/WindowManager', 'closeAllWindows', '()Z')
def close_all_windows():
'''Close all ImageJ windows
Hide the ImageJ windows so that they don't go through the Save dialog,
then call the Window Manager's closeAllWindows to get the rest.
'''
jimage_list = J.static_call('ij/WindowManager', 'getIDList', '()[I')
if jimage_list is None:
return
image_list = J.get_env().get_int_array_elements(jimage_list)
for image_id in image_list:
ip = J.static_call('ij/WindowManager', 'getImage',
'(I)Lij/ImagePlus;', image_id)
ip = get_imageplus_wrapper(ip)
ip.hide()
J.static_call('ij/WindowManager', 'closeAllWindows', '()Z')
def get_current_image():
'''Get the WindowManager's current image
returns a wrapped ImagePlus object
'''
#
# Run this on the UI thread so its thread context is the same
# as the macro invocation
#
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getCurrentImage();
}
};
"""
gci = J.make_future_task(J.run_script(script))
imageplus_obj = J.execute_future_in_main_thread(gci)
return get_imageplus_wrapper(imageplus_obj)
def get_current_image():
'''Get the WindowManager's current image
returns a wrapped ImagePlus object
'''
#
# Run this on the UI thread so its thread context is the same
# as the macro invocation
#
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getCurrentImage();
}
};
"""
gci = J.make_future_task(J.run_script(script))
imageplus_obj = J.execute_future_in_main_thread(gci)
return get_imageplus_wrapper(imageplus_obj)
def get_image_by_name(title):
'''Get the ImagePlus object whose title (in the window) matches "title"'''
return get_imageplus_wrapper(
J.static_call('ij/WindowManager', 'getImage',
'(Ljava/lang/String;)Lij/ImagePlus;', title))
def get_temp_current_image():
'''Get the temporary ImagePlus object for the current thread'''
return get_imageplus_wrapper(
J.static_call('ij/WindowManager', 'getTempCurrentImage',
'()Lij/ImagePlus;'))
def get_image_by_id(imagej_id):
"""Get an ImagePlus object by its ID"""
return get_imageplus_wrapper(J.static_call("ij/WindowManager", "getImage", "(I)Lij/ImagePlus;", imagej_id))
def get_image_by_id(imagej_id):
'''Get an ImagePlus object by its ID'''
return get_imageplus_wrapper(
J.static_call('ij/WindowManager', 'getImage', '(I)Lij/ImagePlus;',
imagej_id))
def get_temp_current_image():
'''Get the temporary ImagePlus object for the current thread'''
return get_imageplus_wrapper(J.static_call(
'ij/WindowManager', 'getTempCurrentImage','()Lij/ImagePlus;'))
def get_image_by_name(title):
'''Get the ImagePlus object whose title (in the window) matches "title"'''
return get_imageplus_wrapper(J.static_call(
'ij/WindowManager', 'getImage', '(Ljava/lang/String;)Lij/ImagePlus;',
title))
def get_image_by_id(imagej_id):
'''Get an ImagePlus object by its ID'''
return get_imageplus_wrapper(J.static_call(
'ij/WindowManager', 'getImage', '(I)Lij/ImagePlus;', imagej_id))
def get_temp_current_image():
"""Get the temporary ImagePlus object for the current thread"""
return get_imageplus_wrapper(J.static_call("ij/WindowManager", "getTempCurrentImage", "()Lij/ImagePlus;"))
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
for (field, parameter), setting in zip(fp_in, settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale = True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.static_call('imagej/plugin/PlugInFunctions', 'runInteractively',
'(Ljava/lang/Runnable)V', plugin)
else:
J.call(plugin, 'run', '()V')
setting_idx = len(fp_in)
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:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
if bioformats.USE_IJ2:
node = command.get_selected_leaf()
module_info = node[2]
module = IJ2.wrap_module(module_info.createModule())
context = self.get_context()
display_service = IJ2.get_display_service(context)
display_dictionary = {}
for setting, module_item in d[key]:
field_type = module_item.getType()
if isinstance(setting, cps.ImageNameProvider):
continue
if field_type == IJ2.FT_BOOL:
value = J.make_instance("java/lang/Boolean",
"(Z)V", setting.value)
elif field_type == IJ2.FT_INTEGER:
value = J.make_instance("java/lang/Integer",
"(I)V", setting.value)
elif field_type == IJ2.FT_FLOAT:
value = J.make_instance("java/lang/Double",
"(D)V", setting.value)
elif field_type == IJ2.FT_STRING:
value = setting.value
elif field_type == IJ2.FT_COLOR:
value = IJ2.make_color_rgb_from_html(setting.value)
elif field_type == IJ2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
dataset = IJ2.create_dataset(image.pixel_data,
setting.value)
display = display_service.createDisplay(dataset)
if image.has_mask:
overlay = IJ2.create_overlay(image.mask)
display.displayOverlay(overlay)
value = display
display_dictionary[module_item.getName()] = display
if wants_display:
input_images.append((image_name, image.pixel_data))
module.setInput(module_item.getName(), value)
module_service = IJ2.get_module_service(context)
module_service.run(module)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
name = module_item.getName()
output_name = setting.value
if display_dictionary.has_key(name):
display = display_dictionary[name]
else:
display = IJ2.wrap_display(module.getOutput(name))
ds = display_service.getActiveDataset(display)
pixel_data = ds.get_pixel_data()
image = cpi.Image(pixel_data)
workspace.image_set.add(output_name, image)
if wants_display:
output_images.append((output_name, pixel_data))
for display in display_dictionary.values():
panel = IJ2.wrap_display_panel(display.getDisplayPanel())
panel.close()
else:
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
command = command.value
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
for (field, parameter), setting in zip(fp_in, settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale = True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() { run:function() {
importClass(Packages.imagej.plugin.PlugInFunctions);
PlugInFunctions.runInteractively(plugin);
}};""", dict(plugin=plugin)), True)
else:
J.execute_runnable_in_main_thread(plugin, True)
setting_idx = len(fp_in)
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:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
if bioformats.USE_IJ2:
node = command.get_selected_leaf()
module_info = node[2]
module = IJ2.wrap_module(module_info.createModule())
context = self.get_context()
display_service = IJ2.get_display_service(context)
display_dictionary = {}
for setting, module_item in d[key]:
field_type = module_item.getType()
if isinstance(setting, cps.ImageNameProvider):
continue
if field_type == IJ2.FT_BOOL:
value = J.make_instance("java/lang/Boolean", "(Z)V",
setting.value)
elif field_type == IJ2.FT_INTEGER:
value = J.make_instance("java/lang/Integer", "(I)V",
setting.value)
elif field_type == IJ2.FT_FLOAT:
value = J.make_instance("java/lang/Double", "(D)V",
setting.value)
elif field_type == IJ2.FT_STRING:
value = setting.value
elif field_type == IJ2.FT_COLOR:
value = IJ2.make_color_rgb_from_html(setting.value)
elif field_type == IJ2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
dataset = IJ2.create_dataset(image.pixel_data,
setting.value)
display = display_service.createDisplay(dataset)
if image.has_mask:
overlay = IJ2.create_overlay(image.mask)
display.displayOverlay(overlay)
value = display
display_dictionary[module_item.getName()] = display
if wants_display:
input_images.append((image_name, image.pixel_data))
module.setInput(module_item.getName(), value)
module_service = IJ2.get_module_service(context)
module_service.run(module)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
name = module_item.getName()
output_name = setting.value
if display_dictionary.has_key(name):
display = display_dictionary[name]
else:
display = IJ2.wrap_display(module.getOutput(name))
ds = display_service.getActiveDataset(display)
pixel_data = ds.get_pixel_data()
image = cpi.Image(pixel_data)
workspace.image_set.add(output_name, image)
if wants_display:
output_images.append((output_name, pixel_data))
for display in display_dictionary.values():
panel = IJ2.wrap_display_panel(display.getDisplayPanel())
panel.close()
else:
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
command = command.value
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
for (field, parameter), setting in zip(fp_in,
settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(
image_name, must_be_grayscale=True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(
image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.static_call('imagej/plugin/PlugInFunctions',
'runInteractively', '(Ljava/lang/Runnable)V',
plugin)
else:
J.call(plugin, 'run', '()V')
setting_idx = len(fp_in)
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:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(
np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)