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 test_11_06_select_overlay(self):
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
i, j = np.mgrid[0:15, 0:1900:100]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
d2 = display_svc.createDisplay("Bar", ij2.create_dataset(self.context, image, "Bar"))
mask = np.zeros(i.shape, bool)
islice = slice(2,-3)
jslice = slice(3,-4)
mask[islice, jslice] = True
overlay = ij2.create_overlay(self.context, mask)
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
def test_11_07_get_selection_bounds(self):
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
i, j = np.mgrid[0:15, 0:1900:100]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
mask = np.zeros(i.shape, bool)
islice = slice(2,-3)
jslice = slice(3,-4)
mask[islice, jslice] = True
overlay = ij2.create_overlay(self.context, mask)
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
rect = overlay_svc.getSelectionBounds(display)
self.assertEqual(J.get_field(rect, "x", "D"), 3)
self.assertEqual(J.get_field(rect, "y", "D"), 2)
self.assertEqual(J.get_field(rect, "width", "D"), 11)
self.assertEqual(J.get_field(rect, "height", "D"), 9)
def test_09_09_check_overlay(self):
svc = ij2.get_display_service(self.context)
r = np.random.RandomState()
i, j = np.mgrid[0:11, 0:1300:100]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = svc.createDisplay("Foo", ds)
mask = np.zeros(image.shape, bool)
mask[2:-1, 3:-4] = 1
overlay = ij2.create_overlay(self.context, mask)
ij2.get_overlay_service(self.context).addOverlays(
display.o, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
self.run_command("imagej.core.commands.imglib.CropImage",
dict(display=display), {})
dataset = ij2.wrap_dataset(display.getActiveView().getData())
image_out = dataset.get_pixel_data()
self.assertSequenceEqual(image_out.shape, [7, 5])
np.testing.assert_array_equal(image[2:-2, 3:-5], image_out)
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
'''
context = get_context()
self.get_command_settings(command, d)
wants_display = self.show_window
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
node = command.get_selected_leaf()
module_info = node[2]
input_dictionary = J.get_map_wrapper(
J.make_instance('java/util/HashMap', "()V"))
display_dictionary = {}
display_service = ij2.get_display_service(context)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
continue
field_name = module_item.getName()
field_type = module_item.getType()
raw_type = J.call(module_item.o, "getType", "()Ljava/lang/Class;")
if field_type in (ij2.FT_BOOL, ij2.FT_INTEGER, ij2.FT_FLOAT,
ij2.FT_STRING):
input_dictionary.put(field_name, J.box(setting.value, raw_type))
elif field_type == ij2.FT_COLOR:
assert isinstance(setting, cps.Color)
red, green, blue = setting.to_rgb()
jobject = J.make_instance(
"imagej/util/ColorRGB", "(III)V", red, green, blue)
input_dictionary.put(field_name, jobject)
elif field_type == ij2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
pixel_data = image.pixel_data * IMAGEJ_SCALE
dataset = ij2.create_dataset(
context, pixel_data, image_name)
display = display_service.createDisplay(image_name, dataset)
display_dictionary[module_item.getName()] = display
if image.has_mask:
#overlay_name = "X" + uuid.uuid4().get_hex()
#image_dictionary[overlay_name] = image.mask
overlay = ij2.create_overlay(context, image.mask)
overlay_service = ij2.get_overlay_service(context)
overlay_service.addOverlays(
display.o, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
input_dictionary.put(field_name, display.o)
if wants_display:
input_images.append((image_name, image.pixel_data))
elif field_type == ij2.FT_TABLE:
table_name = setting.value
table = workspace.object_set.get_type_instance(
IJ_TABLE_TYPE, table_name)
input_dictionary.put(field_name, table)
elif field_type == ij2.FT_FILE:
jfile = J.make_instance(
"java/io/File", "(Ljava/lang/String;)V", setting.value)
input_dictionary.put(field_name, jfile)
command_service = ij2.get_command_service(get_context())
future = command_service.run(module_info.o, input_dictionary.o)
module = future.get()
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))
pixel_data = self.save_display_as_image(
workspace, display, output_name)
if wants_display:
output_images.append((output_name, pixel_data))
# Close any displays that we created.
for display in display_dictionary.values():
display.close()
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
'''
context = get_context()
self.get_command_settings(command, d)
wants_display = self.show_window
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
node = command.get_selected_leaf()
module_info = node[2]
input_dictionary = J.get_map_wrapper(
J.make_instance('java/util/HashMap', "()V"))
display_dictionary = {}
display_service = ij2.get_display_service(context)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
continue
field_name = module_item.getName()
field_type = module_item.getType()
raw_type = J.call(module_item.o, "getType", "()Ljava/lang/Class;")
if field_type in (ij2.FT_BOOL, ij2.FT_INTEGER, ij2.FT_FLOAT,
ij2.FT_STRING):
input_dictionary.put(field_name, J.box(setting.value,
raw_type))
elif field_type == ij2.FT_COLOR:
assert isinstance(setting, cps.Color)
red, green, blue = setting.to_rgb()
jobject = J.make_instance("imagej/util/ColorRGB", "(III)V",
red, green, blue)
input_dictionary.put(field_name, jobject)
elif field_type == ij2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
pixel_data = image.pixel_data * IMAGEJ_SCALE
dataset = ij2.create_dataset(context, pixel_data, image_name)
display = display_service.createDisplay(image_name, dataset)
display_dictionary[module_item.getName()] = display
if image.has_mask:
#overlay_name = "X" + uuid.uuid4().get_hex()
#image_dictionary[overlay_name] = image.mask
overlay = ij2.create_overlay(context, image.mask)
overlay_service = ij2.get_overlay_service(context)
overlay_service.addOverlays(display.o,
J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
input_dictionary.put(field_name, display.o)
if wants_display:
input_images.append((image_name, image.pixel_data))
elif field_type == ij2.FT_TABLE:
table_name = setting.value
table = workspace.object_set.get_type_instance(
IJ_TABLE_TYPE, table_name)
input_dictionary.put(field_name, table)
elif field_type == ij2.FT_FILE:
jfile = J.make_instance("java/io/File",
"(Ljava/lang/String;)V", setting.value)
input_dictionary.put(field_name, jfile)
command_service = ij2.get_command_service(get_context())
future = command_service.run(module_info.o, input_dictionary.o)
module = future.get()
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))
pixel_data = self.save_display_as_image(
workspace, display, output_name)
if wants_display:
output_images.append((output_name, pixel_data))
# Close any displays that we created.
for display in display_dictionary.values():
display.close()
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)