---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/magicgui/widgets/_bases/value_widget.py:57, in ValueWidget._on_value_change(self=PushButton(value=False, annotation=None, name='call_button'), value=False)
55 if value is self.null_value and not self._nullable:
56 return
---> 57 self.changed.emit(value)
value = False
self.changed = <SignalInstance 'changed' on PushButton(value=False, annotation=None, name='call_button')>
self = PushButton(value=False, annotation=None, name='call_button')
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/psygnal/_signal.py:725, in psygnal._signal.SignalInstance.emit()
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/psygnal/_signal.py:767, in psygnal._signal.SignalInstance._run_emit_loop()
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/psygnal/_signal.py:768, in psygnal._signal.SignalInstance._run_emit_loop()
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/psygnal/_signal.py:788, in psygnal._signal.SignalInstance._run_emit_loop()
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/magicgui/widgets/_function_gui.py:207, in FunctionGui.__init__.<locals>._disable_button_and_call()
205 self._call_button.enabled = False
206 try:
--> 207 self.__call__()
self = <FunctionGui gaussian_blur(image: <function NewType.<locals>.new_type at 0x1528baf70> = <MultiScaleData at 0x29ff03d00. 5 levels, 'uint16', shapes: ((1, 4320, 5120), (1, 2160, 2560), (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, sigma: float = 2.0, *, viewer: napari.viewer.Viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 2159.5, 2559.5), zoom=0.154453432405846, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(0.0, -815.5067337861703, 4537.442632718694), scaled=True, size=40, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 1.0, 1.0), (-1.5, 4320.0, 1.0), (-1.5, 5120.0, 1.0)), current_step=(0, 2160, 2560), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'DAPI' at 0x29fef9d30>, <Image layer 'nanog' at 0x29ff45100>, <Image layer 'Lamin B1' at 0x2a99c8220>, <Labels layer 'label_DAPI' at 0x29fef9f70>], scale_bar=ScaleBar(visible=False, colored=False, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10, unit=None), text_overlay=TextOverlay(visible=False, color=(0.5, 0.5, 0.5, 1.0), font_size=10, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x15519d970>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x15519d9d0>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x15519da30>, transform=<napari.utils.transforms.transforms.Affine object at 0x15519da90>, allow_new_selection=True, selected_vertex=None)), help='enter paint or fill mode to edit labels', status='label_DAPI [ 0 -816 4537]', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_move at 0x28cce8430>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_drag at 0x28ccd38b0>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x152b61040>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events.<locals>.hold_to_lock_aspect_ratio at 0x28ccd3700>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x28cd111f0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x28cd114c0>})) -> <function NewType.<locals>.new_type at 0x1528baf70>>
208 finally:
209 self._call_button.enabled = True
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/magicgui/widgets/_function_gui.py:318, in FunctionGui.__call__(self=<FunctionGui gaussian_blur(image: <function NewT...14c0>})) -> <function NewType.<locals>.new_type>>, update_widget=False, *args=(), **kwargs={})
316 self._tqdm_depth = 0 # reset the tqdm stack count
317 with _function_name_pointing_to_widget(self):
--> 318 value = self._function(*bound.args, **bound.kwargs)
self = <FunctionGui gaussian_blur(image: <function NewType.<locals>.new_type at 0x1528baf70> = <MultiScaleData at 0x29ff03d00. 5 levels, 'uint16', shapes: ((1, 4320, 5120), (1, 2160, 2560), (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, sigma: float = 2.0, *, viewer: napari.viewer.Viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 2159.5, 2559.5), zoom=0.154453432405846, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(0.0, -815.5067337861703, 4537.442632718694), scaled=True, size=40, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 1.0, 1.0), (-1.5, 4320.0, 1.0), (-1.5, 5120.0, 1.0)), current_step=(0, 2160, 2560), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'DAPI' at 0x29fef9d30>, <Image layer 'nanog' at 0x29ff45100>, <Image layer 'Lamin B1' at 0x2a99c8220>, <Labels layer 'label_DAPI' at 0x29fef9f70>], scale_bar=ScaleBar(visible=False, colored=False, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10, unit=None), text_overlay=TextOverlay(visible=False, color=(0.5, 0.5, 0.5, 1.0), font_size=10, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x15519d970>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x15519d9d0>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x15519da30>, transform=<napari.utils.transforms.transforms.Affine object at 0x15519da90>, allow_new_selection=True, selected_vertex=None)), help='enter paint or fill mode to edit labels', status='label_DAPI [ 0 -816 4537]', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_move at 0x28cce8430>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_drag at 0x28ccd38b0>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x152b61040>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events.<locals>.hold_to_lock_aspect_ratio at 0x28ccd3700>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x28cd111f0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x28cd114c0>})) -> <function NewType.<locals>.new_type at 0x1528baf70>>
bound = <BoundArguments (image=<MultiScaleData at 0x29ff03d00. 5 levels, 'uint16', shapes: ((1, 4320, 5120), (1, 2160, 2560), (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, sigma=2.0, viewer=Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 2159.5, 2559.5), zoom=0.154453432405846, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(0.0, -815.5067337861703, 4537.442632718694), scaled=True, size=40, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 1.0, 1.0), (-1.5, 4320.0, 1.0), (-1.5, 5120.0, 1.0)), current_step=(0, 2160, 2560), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'DAPI' at 0x29fef9d30>, <Image layer 'nanog' at 0x29ff45100>, <Image layer 'Lamin B1' at 0x2a99c8220>, <Labels layer 'label_DAPI' at 0x29fef9f70>], scale_bar=ScaleBar(visible=False, colored=False, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10, unit=None), text_overlay=TextOverlay(visible=False, color=(0.5, 0.5, 0.5, 1.0), font_size=10, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x15519d970>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x15519d9d0>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x15519da30>, transform=<napari.utils.transforms.transforms.Affine object at 0x15519da90>, allow_new_selection=True, selected_vertex=None)), help='enter paint or fill mode to edit labels', status='label_DAPI [ 0 -816 4537]', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_move at 0x28cce8430>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_drag at 0x28ccd38b0>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x152b61040>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events.<locals>.hold_to_lock_aspect_ratio at 0x28ccd3700>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x28cd111f0>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x28cd114c0>}))>
self._function = <function gaussian_blur at 0x28ff945e0>
320 self._call_count += 1
321 if self._result_widget is not None:
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/napari_time_slicer/__init__.py:61, in time_slicer.<locals>.worker_function(*args=[<MultiScaleData at 0x29ff03d00. 5 levels, 'uint1..., (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, 2.0], **kwargs={})
58 _break_down_4d_to_2d_kwargs(bound.arguments, current_timepoint, viewer)
60 # call the decorated function
---> 61 result = function(*bound.args, **bound.kwargs)
bound = <BoundArguments (image=<MultiScaleData at 0x29ff03d00. 5 levels, 'uint16', shapes: ((1, 4320, 5120), (1, 2160, 2560), (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, sigma=2.0)>
function = <function gaussian_blur at 0x28ff94550>
62 return result
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/napari_segment_blobs_and_things_with_membranes/__init__.py:283, in gaussian_blur(image=<MultiScaleData at 0x29ff03d00. 5 levels, 'uint1..., (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, sigma=2.0)
277 @register_function(menu="Filtering / noise removal > Gaussian (scikit-image, nsbatwm)")
278 @time_slicer
279 def gaussian_blur(image:ImageData, sigma: float = 1) -> ImageData:
280 """
281 Applies a Gaussian blur to an image with a defined sigma. Useful for denoising.
282 """
--> 283 return gaussian(image, sigma)
image = <MultiScaleData at 0x29ff03d00. 5 levels, 'uint16', shapes: ((1, 4320, 5120), (1, 2160, 2560), (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>
sigma = 2.0
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/skimage/_shared/utils.py:348, in deprecate_multichannel_kwarg.__call__.<locals>.fixed_func(*args=(<MultiScaleData at 0x29ff03d00. 5 levels, 'uint1..., (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, 2.0), **kwargs={})
345 kwargs['channel_axis'] = convert[kwargs.pop('multichannel')]
347 # Call the function with the fixed arguments
--> 348 return func(*args, **kwargs)
func = <function gaussian at 0x28f092b80>
kwargs = {}
args = (<MultiScaleData at 0x29ff03d00. 5 levels, 'uint16', shapes: ((1, 4320, 5120), (1, 2160, 2560), (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, 2.0)
File ~/opt/miniconda3/envs/napari-assistant/lib/python3.9/site-packages/skimage/_shared/filters.py:116, in gaussian(image=<MultiScaleData at 0x29ff03d00. 5 levels, 'uint1..., (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>, sigma=2.0, output=None, mode='nearest', cval=0, multichannel=None, preserve_range=False, truncate=4.0, channel_axis=None)
16 @utils.deprecate_multichannel_kwarg(multichannel_position=5)
17 def gaussian(image, sigma=1, output=None, mode='nearest', cval=0,
18 multichannel=None, preserve_range=False, truncate=4.0, *,
19 channel_axis=None):
20 """Multi-dimensional Gaussian filter.
21
22 Parameters
(...)
114
115 """
--> 116 if image.ndim == 3 and image.shape[-1] == 3 and channel_axis is None:
image = <MultiScaleData at 0x29ff03d00. 5 levels, 'uint16', shapes: ((1, 4320, 5120), (1, 2160, 2560), (1, 1080, 1280), (1, 540, 640), (1, 270, 320))>
channel_axis is None = True
channel_axis = None
117 msg = ("Images with dimensions (M, N, 3) are interpreted as 2D+RGB "
118 "by default. Use `multichannel=False` to interpret as "
119 "3D image with last dimension of length 3.")
120 warn(RuntimeWarning(msg))
AttributeError: 'MultiScaleData' object has no attribute 'ndim'
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