!!python/object:napari_workflows._workflow.Workflow
_tasks:
Result of Binary fill holes (n-SimpleITK): !!python/tuple
- !!python/name:napari_simpleitk_image_processing.binary_fill_holes ''
- Result of dilate_labels (clesperanto)
Result of Threshold (Huang and Wang 1995, n-SimpleITK): !!python/tuple
- !!python/name:napari_simpleitk_image_processing.threshold_huang ''
- Result of top_hat_box (clesperanto)
Result of dilate_labels (clesperanto): !!python/tuple
- !!python/name:pyclesperanto_prototype.dilate_labels ''
- Result of Threshold (Huang and Wang 1995, n-SimpleITK)
- null
- 10.0
Result of gaussian_blur (clesperanto): !!python/tuple
- !!python/name:pyclesperanto_prototype.gaussian_blur ''
- Result of maximum_z_projection (clesperanto) [1]
- null
- 5.0
- 5.0
- 0.0
Result of maximum_z_projection (clesperanto): !!python/tuple
- &id001 !!python/name:pyclesperanto_prototype.maximum_z_projection ''
- '0 :: 20230608_103910_723__Point0001_Channel405_Seq0005.nd2 (series 1) :: 405'
Result of maximum_z_projection (clesperanto) [1]: !!python/tuple
- *id001
- '0 :: 20230608_103910_723__Point0001_Channel488 Sanika_Seq0004.nd2 (series 1)
:: 488 Sanika'
Result of seeded_watershed_with_mask: !!python/tuple
- !!python/name:napari_segment_blobs_and_things_with_membranes.seeded_watershed_with_mask ''
- Result of subtract_image_from_scalar (clesperanto)
- Result of voronoi_otsu_labeling (clesperanto)
- Result of Binary fill holes (n-SimpleITK)
Result of subtract_image_from_scalar (clesperanto): !!python/tuple
- !!python/name:pyclesperanto_prototype.subtract_image_from_scalar ''
- Result of maximum_z_projection (clesperanto) [1]
- null
- 65000.0
Result of top_hat_box (clesperanto): !!python/tuple
- !!python/name:pyclesperanto_prototype.top_hat_box ''
- Result of gaussian_blur (clesperanto)
- null
- 100.0
- 100.0
- 0.0
Result of voronoi_otsu_labeling (clesperanto): !!python/tuple
- !!python/name:pyclesperanto_prototype.voronoi_otsu_labeling ''
- Result of maximum_z_projection (clesperanto)
- null
- 20.0
- 2.0
results in an AttributeError: 'function' object has no attribute '__wrapped__'
full error message
2023-06-22 19:07:03.728 | INFO | napari_assistant._gui._category_widget:call_op:178 - maximum_z_projection (clesperanto)(..., )
2023-06-22 19:07:04.063 | INFO | napari_assistant._gui._category_widget:call_op:178 - maximum_z_projection (clesperanto)(..., )
2023-06-22 19:07:04.232 | INFO | napari_assistant._gui._category_widget:call_op:178 - voronoi_otsu_labeling (clesperanto)(..., 20.0, 2.0)
2023-06-22 19:07:07.314 | INFO | napari_assistant._gui._category_widget:call_op:178 - gaussian_blur (clesperanto)(..., 5.0, 5.0, 0.0)
2023-06-22 19:07:07.454 | INFO | napari_assistant._gui._category_widget:call_op:178 - subtract_image_from_scalar (clesperanto)(..., 1.0)
2023-06-22 19:07:07.829 | INFO | napari_assistant._gui._category_widget:call_op:178 - subtract_image_from_scalar (clesperanto)(..., 65000.0)
2023-06-22 19:07:07.926 | INFO | napari_assistant._gui._category_widget:call_op:178 - top_hat_box (clesperanto)(..., 100.0, 100.0, 0.0)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
File /opt/homebrew/Caskroom/mambaforge/base/envs/dbn2/lib/python3.9/site-packages/napari_assistant/_gui/_Assistant.py:379, in Assistant.load_workflow(self=, filename='/Users/korten/Documents/Doktorarbeit/Daten-temp/...repro_hackathon_BPAE_cells/cell_segmentation.yaml')
373 self.workflow = _io_yaml_v1.load_workflow(filename)
375 w_dw = initialise_root_functions(
376 self.workflow,
377 self._viewer,
378 )
--> 379 w_dw += load_remaining_workflow(
w_dw = [(, op_name: str = 'maximum_z_projection (clesperanto)', x: float = 1.0, y: float = 1.0, z: float = 1.0, u: float = 0.0, v: float = 0.0, w: float = 0.0, w1: float = 0.0, w2: float = 0.0, w3: float = 0.0, w4: float = 0.0, a: bool = False, b: bool = False, c: bool = False, d: bool = False, e: bool = False, f: bool = False, g: bool = False, h: bool = False, i: bool = False, j: bool = False, k: str = '', l: str = '', m: str = '', o: Union[pathlib.Path, str, bytes] = PosixPath('.'), p: Union[pathlib.Path, str, bytes] = PosixPath('.'), q: Union[pathlib.Path, str, bytes] = PosixPath('.'), viewer: napari.viewer.Viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 124.74583333333297, 124.74583333333297), zoom=2.8279246794871877, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(0.0, 5.0, 0.0, 0.0), scaled=True, size=1, style=), dims=Dims(ndim=4, ndisplay=2, last_used=0, range=((0.0, 1.0, 1.0), (0.0, 11.0, 1.0), (0.0, 250.04583333333258, 0.108333333333333), (0.0, 250.04583333333258, 0.108333333333333)), current_step=(0, 5, 1152, 1152), order=(0, 1, 2, 3), axis_labels=('0', '1', '2', '3')), grid=GridCanvas(stride=-1, shape=(-1, -1), enabled=False), layers=[, , , , , , , ], scale_bar=ScaleBar(visible=False, colored=False, color= (4,) float32, ticks=True, position=, font_size=10.0, box=False, box_color= (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color= (4,) float32, font_size=10.0, position=, 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=, transform_drag=, transform_final=, transform=, allow_new_selection=True, selected_vertex=None)), help='', status='Hold key to open plugin selection. Hold to open files as stack.', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[.mouse_move at 0x154147670>], mouse_drag_callbacks=[.mouse_drag at 0x154135790>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': .hold_to_lock_aspect_ratio at 0x154135af0>, 'Control-Shift-R': , 'Control-Shift-A': }))>, ), (, op_name: str = 'maximum_z_projection (clesperanto)', x: float = 1.0, y: float = 1.0, z: float = 1.0, u: float = 0.0, v: float = 0.0, w: float = 0.0, w1: float = 0.0, w2: float = 0.0, w3: float = 0.0, w4: float = 0.0, a: bool = False, b: bool = False, c: bool = False, d: bool = False, e: bool = False, f: bool = False, g: bool = False, h: bool = False, i: bool = False, j: bool = False, k: str = '', l: str = '', m: str = '', o: Union[pathlib.Path, str, bytes] = PosixPath('.'), p: Union[pathlib.Path, str, bytes] = PosixPath('.'), q: Union[pathlib.Path, str, bytes] = PosixPath('.'), viewer: napari.viewer.Viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 124.74583333333297, 124.74583333333297), zoom=2.8279246794871877, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(0.0, 5.0, 0.0, 0.0), scaled=True, size=1, style=), dims=Dims(ndim=4, ndisplay=2, last_used=0, range=((0.0, 1.0, 1.0), (0.0, 11.0, 1.0), (0.0, 250.04583333333258, 0.108333333333333), (0.0, 250.04583333333258, 0.108333333333333)), current_step=(0, 5, 1152, 1152), order=(0, 1, 2, 3), axis_labels=('0', '1', '2', '3')), grid=GridCanvas(stride=-1, shape=(-1, -1), enabled=False), layers=[, , , , , , , ], scale_bar=ScaleBar(visible=False, colored=False, color= (4,) float32, ticks=True, position=, font_size=10.0, box=False, box_color= (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color= (4,) float32, font_size=10.0, position=, 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=, transform_drag=, transform_final=, transform=, allow_new_selection=True, selected_vertex=None)), help='', status='Hold key to open plugin selection. Hold to open files as stack.', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[.mouse_move at 0x154147670>], mouse_drag_callbacks=[.mouse_drag at 0x154135790>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': .hold_to_lock_aspect_ratio at 0x154135af0>, 'Control-Shift-R': , 'Control-Shift-A': }))>, )]
self.workflow =
self =
self._viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 124.74583333333297, 124.74583333333297), zoom=2.8279246794871877, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(0.0, 5.0, 0.0, 0.0), scaled=True, size=1, style=), dims=Dims(ndim=4, ndisplay=2, last_used=0, range=((0.0, 1.0, 1.0), (0.0, 11.0, 1.0), (0.0, 250.04583333333258, 0.108333333333333), (0.0, 250.04583333333258, 0.108333333333333)), current_step=(0, 5, 1152, 1152), order=(0, 1, 2, 3), axis_labels=('0', '1', '2', '3')), grid=GridCanvas(stride=-1, shape=(-1, -1), enabled=False), layers=[, , , , , , , ], scale_bar=ScaleBar(visible=False, colored=False, color= (4,) float32, ticks=True, position=, font_size=10.0, box=False, box_color= (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color= (4,) float32, font_size=10.0, position=, 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=, transform_drag=, transform_final=, transform=, allow_new_selection=True, selected_vertex=None)), help='', status='Hold key to open plugin selection. Hold to open files as stack.', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[.mouse_move at 0x154147670>], mouse_drag_callbacks=[.mouse_drag at 0x154135790>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': .hold_to_lock_aspect_ratio at 0x154135af0>, 'Control-Shift-R': , 'Control-Shift-A': })
380 self.workflow,
381 self._viewer,
382 )
384 for gui, dw in w_dw:
385 # call the function widget &
386 # track the association between the layer and the gui that generated it
387 category = get_category_of_function(
388 find_function(gui.op_name.current_choice)
389 )
File /opt/homebrew/Caskroom/mambaforge/base/envs/dbn2/lib/python3.9/site-packages/napari_assistant/_workflow_io_utility.py:164, in load_remaining_workflow(workflow=, viewer=Viewer(axes=Axes(visible=False, labels=True, col...indings._transform_active_layer at 0x1540e0670>}), button_size=40)
158 widget = make_flexible_gui(func,
159 viewer,
160 autocall= False,
161 button_size = button_size
162 )
163 else:
--> 164 widget = make_flexible_gui(func,
func =
widget = , op_name: str = 'top_hat_box (clesperanto)', x: float = 100.0, y: float = 100.0, z: float = 0.0, u: float = 0.0, v: float = 0.0, w: float = 0.0, w1: float = 0.0, w2: float = 0.0, w3: float = 0.0, w4: float = 0.0, a: bool = False, b: bool = False, c: bool = False, d: bool = False, e: bool = False, f: bool = False, g: bool = False, h: bool = False, i: bool = False, j: bool = False, k: str = '', l: str = '', m: str = '', o: Union[pathlib.Path, str, bytes] = PosixPath('.'), p: Union[pathlib.Path, str, bytes] = PosixPath('.'), q: Union[pathlib.Path, str, bytes] = PosixPath('.'), viewer: napari.viewer.Viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 124.74583333333297, 124.74583333333297), zoom=2.8279246794871877, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(0.0, 5.0, 0.0, 0.0), scaled=True, size=1, style=), dims=Dims(ndim=4, ndisplay=2, last_used=0, range=((0.0, 1.0, 1.0), (0.0, 11.0, 1.0), (0.0, 250.04583333333258, 0.108333333333333), (0.0, 250.04583333333258, 0.108333333333333)), current_step=(0, 5, 1152, 1152), order=(0, 1, 2, 3), axis_labels=('0', '1', '2', '3')), grid=GridCanvas(stride=-1, shape=(-1, -1), enabled=False), layers=[, , , , , , , ], scale_bar=ScaleBar(visible=False, colored=False, color= (4,) float32, ticks=True, position=, font_size=10.0, box=False, box_color= (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color= (4,) float32, font_size=10.0, position=, 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=, transform_drag=, transform_final=, transform=, allow_new_selection=True, selected_vertex=None)), help='', status='Hold key to open plugin selection. Hold to open files as stack.', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[.mouse_move at 0x154147670>], mouse_drag_callbacks=[.mouse_drag at 0x154135790>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': .hold_to_lock_aspect_ratio at 0x154135af0>, 'Control-Shift-R': , 'Control-Shift-A': }))>
viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 124.74583333333297, 124.74583333333297), zoom=2.8279246794871877, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(0.0, 5.0, 0.0, 0.0), scaled=True, size=1, style=), dims=Dims(ndim=4, ndisplay=2, last_used=0, range=((0.0, 1.0, 1.0), (0.0, 11.0, 1.0), (0.0, 250.04583333333258, 0.108333333333333), (0.0, 250.04583333333258, 0.108333333333333)), current_step=(0, 5, 1152, 1152), order=(0, 1, 2, 3), axis_labels=('0', '1', '2', '3')), grid=GridCanvas(stride=-1, shape=(-1, -1), enabled=False), layers=[, , , , , , , ], scale_bar=ScaleBar(visible=False, colored=False, color= (4,) float32, ticks=True, position=, font_size=10.0, box=False, box_color= (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color= (4,) float32, font_size=10.0, position=, 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=, transform_drag=, transform_final=, transform=, allow_new_selection=True, selected_vertex=None)), help='', status='Hold key to open plugin selection. Hold to open files as stack.', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[.mouse_move at 0x154147670>], mouse_drag_callbacks=[.mouse_drag at 0x154135790>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': .hold_to_lock_aspect_ratio at 0x154135af0>, 'Control-Shift-R': , 'Control-Shift-A': })
button_size = 40
165 viewer,
166 button_size = button_size
167 )
168 widget._auto_call = False
169 # add the final widget to the napari viewer and set the input images in
170 # the dropdown to the specified input images
File /opt/homebrew/Caskroom/mambaforge/base/envs/dbn2/lib/python3.9/site-packages/napari_assistant/_workflow_io_utility.py:224, in make_flexible_gui(func=, viewer=Viewer(axes=Axes(visible=False, labels=True, col...indings._transform_active_layer at 0x1540e0670>}), autocall=True, button_size=40)
206 """
207 Function returns a widget with a GUI for the function provided in the parameters,
208 that can be added to the napari viewer.
(...)
221 button size parameter that is passed to make_category_gui
222 """
223 gui = None
--> 224 category = get_category_of_function(func)
func =
226 if category is None:
227 raise ModuleNotFoundError("Cannot build user interface for not installed function " + str(func))
File /opt/homebrew/Caskroom/mambaforge/base/envs/dbn2/lib/python3.9/site-packages/napari_assistant/_categories.py:595, in get_category_of_function(func=, func_name=None)
589 """
590 Searches categories for a given function and returns the first (!)
591 category that contains the function
592 """
594 if func_name is None:
--> 595 func_name = get_name_of_function(func)
func_name = None
func =
597 for k, c in CATEGORIES.items():
598 if not callable(c):
File /opt/homebrew/Caskroom/mambaforge/base/envs/dbn2/lib/python3.9/site-packages/napari_assistant/_categories.py:367, in get_name_of_function(func=)
362 """
363 Searches all functions for a given function
364 and returns its human-readable name
365 """
366 for k, v in all_operations().items():
--> 367 if v is func or v.__wrapped__ is func:
v =
v is func = False
func =
368 if ">" in k:
369 return k.split(">")[1]
AttributeError: 'function' object has no attribute '__wrapped__'
loading the following workflow:
results in an
AttributeError: 'function' object has no attribute '__wrapped__'full error message