Bugs when using functions from nsbatwm

[Cryaaa]

When using background subtraction functions tagged with nsbatwm I get an Error message:

`2022-02-20 21:06:53.908 | DEBUG | napari_pyclesperanto_assistant._gui._category_widget:_show_result:223 - creating new layer for id: 2456101371712 2022-02-20 21:06:56.043 | DEBUG | napari_pyclesperanto_assistant._gui._category_widget:_show_result:217 - updating existing layer: Result of Gaussian (scikit-image, nsbatwm), with id: 2456101371712 2022-02-20 21:06:56.226 | DEBUG | napari_pyclesperanto_assistant._gui._category_widget:_show_result:217 - updating existing layer: Result of Gaussian (scikit-image, nsbatwm), with id: 2456101371712 2022-02-20 21:06:56.407 | DEBUG | napari_pyclesperanto_assistant._gui._category_widget:_show_result:217 - updating existing layer: Result of Gaussian (scikit-image, nsbatwm), with id: 2456101371712 2022-02-20 21:06:57.952 | ERROR | napari_pyclesperanto_assistant._gui._category_widget:gui_function:328 - An error has been caught in function 'gui_function', process 'MainProcess' (20716), thread 'MainThread' (3616): Traceback (most recent call last):

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, │ │ └ {'name': 'main', 'doc': None, 'package': '', 'loader': <zipimporter object "C:\Users\ryans\anaconda3\envs... │ └ <code object at 0x0000023BA0990F50, file "C:\Users\ryans\anaconda3\envs\np_workflows_v1\Scripts\napari.exe__main__.... └ <function _run_code at 0x0000023BA096A7A0>

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\runpy.py", line 86, in _run_code exec(code, run_globals) │ └ {'name': 'main', 'doc': None, 'package': '', 'loader': <zipimporter object "C:\Users\ryans\anaconda3\envs... └ <code object at 0x0000023BA0990F50, file "C:\Users\ryans\anaconda3\envs\np_workflows_v1\Scripts\napari.exe__main__....

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\Scripts\napari.exe__main__.py", line 7, in

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\napari__main__.py", line 449, in main _run() └ <function _run at 0x0000023BC1A52200>

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\napari__main__.py", line 338, in _run run(gui_exceptions=True) └ <function run at 0x0000023BC1C80820>

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\napari_qt\qt_eventloop.py", line 402, in run app.exec() │ └ └ <PyQt5.QtWidgets.QApplication object at 0x0000023BC1F757E0>

File "c:\users\ryans\onedrive\documents\bia pol stuff\napari workflow repositories\napari_pyclesperanto_assistant\napari_pyclesperanto_assistant_gui_Assistant.py", line 188, in _on_item_clicked self._activate(CATEGORIES.get(item.text())) │ │ │ │ │ └ │ │ │ │ └ <PyQt5.QtWidgets.QListWidgetItem object at 0x0000023BDB0CA950> │ │ │ └ <method 'get' of 'dict' objects> │ │ └ {'Remove noise': Category(name='Removal noise', description='Remove noise from images, e.g. by local averaging and blurring.'... │ └ <function Assistant._activate at 0x0000023BD55EAB00> └ <napari_pyclesperanto_assistant._gui._Assistant.Assistant object at 0x0000023BDB0AE710>

File "c:\users\ryans\onedrive\documents\bia pol stuff\napari workflow repositories\napari_pyclesperanto_assistant\napari_pyclesperanto_assistant_gui_Assistant.py", line 219, in _activate self._layers[gui()] = (dw, gui) │ │ │ │ └ <FunctionGui do_remove_background(, input0: napari.layers.image.image.Image = <Image layer 'Result of Gaussian (scikit-image... │ │ │ └ <napari._qt.widgets.qt_viewer_dock_widget.QtViewerDockWidget object at 0x0000023BE3ECA320> │ │ └ <FunctionGui do_remove_background(, input0: napari.layers.image.image.Image = <Image layer 'Result of Gaussian (scikit-image... │ └ {<Image layer 'Result of Gaussian (scikit-image, nsbatwm)' at 0x23bdb2a34f0>: (<napari._qt.widgets.qt_viewer_dock_widget.QtVi... └ <napari_pyclesperanto_assistant._gui._Assistant.Assistant object at 0x0000023BDB0AE710>

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\magicgui\widgets_function_gui.py", line 303, in call value = self._function(*bound.args, *bound.kwargs) │ │ │ │ │ └ <property object at 0x0000023BA0E0D990> │ │ │ │ └ <BoundArguments (input0=<Image layer 'Result of Gaussian (scikit-image, nsbatwm)' at 0x23bdb2a34f0>, op_name='Black top-hat (... │ │ │ └ <property object at 0x0000023BA0E0D940> │ │ └ <BoundArguments (input0=<Image layer 'Result of Gaussian (scikit-image, nsbatwm)' at 0x23bdb2a34f0>, op_name='Black top-hat (... │ └ <function make_gui_for_category..gui_function at 0x0000023BE3E9A170> └ <FunctionGui do_remove_background(, input0: napari.layers.image.image.Image = <Image layer 'Result of Gaussian (scikit-image...

File "c:\users\ryans\onedrive\documents\bia pol stuff\napari workflow repositories\napari_pyclesperanto_assistant\napari_pyclesperanto_assistant_gui_category_widget.py", line 328, in gui_function result, used_args = call_op(op_name, inputs, t_position, viewer, **kwargs) │ │ │ │ │ └ {'x': 10.0, 'y': 10.0, 'z': 0.0, 'u': 0.0, 'v': 0.0, 'w': 0.0, 'a': False, 'b': False, 'c': False, 'k': '', 'l': '', 'm': ''} │ │ │ │ └ Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 126.5, 127.... │ │ │ └ None │ │ └ [<Image layer 'Result of Gaussian (scikit-image, nsbatwm)' at 0x23bdb2a34f0>] │ └ 'Black top-hat (scipy, nsbatwm)' └ <function call_op at 0x0000023BD55E9FC0>

File "c:\users\ryans\onedrive\documents\bia pol stuff\napari workflow repositories\napari_pyclesperanto_assistant\napari_pyclesperanto_assistant_gui_category_widget.py", line 154, in call_op gpu_out = cle_function(*args, **kwargs) │ │ └ {} │ └ [array([[0.14280938, 0.13814596, 0.1335724 , ..., 0.88336891, 0.87451825, │ 0.86551713], │ [0.14465108, 0.14062554... └ <function black_tophat at 0x0000023BCD436440>

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\napari_time_slicer__init__.py", line 49, in worker_function result = function(*bound.args, **bound.kwargs) │ │ │ │ └ <property object at 0x0000023BA0E0D990> │ │ │ └ <BoundArguments (image=array([[0.14280938, 0.13814596, 0.1335724 , ..., 0.88336891, 0.87451825, │ │ │ 0.86551713], │ │ │ [... │ │ └ <property object at 0x0000023BA0E0D940> │ └ <BoundArguments (image=array([[0.14280938, 0.13814596, 0.1335724 , ..., 0.88336891, 0.87451825, │ 0.86551713], │ [... └ <function black_tophat at 0x0000023BCD4363B0>

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\napari_segment_blobs_and_things_with_membranes__init.py", line 215, in black_tophat return scipy.ndimage.black_tophat(image.astype(float), size=radius * 2 + 1) │ │ │ │ │ └ 10.0 │ │ │ │ └ <method 'astype' of 'numpy.ndarray' objects> │ │ │ └ array([[0.14280938, 0.13814596, 0.1335724 , ..., 0.88336891, 0.87451825, │ │ │ 0.86551713], │ │ │ [0.14465108, 0.14062554,... │ │ └ <function black_tophat at 0x0000023BBE776950> │ └ <module 'scipy.ndimage' from 'C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\scipy\ndimage\_init... └ <module 'scipy' from 'C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\scipy\init__.py'>

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\scipy\ndimage\morphology.py", line 1840, in black_tophat tmp = grey_dilation(input, size, footprint, structure, None, mode, │ │ │ │ │ └ 'reflect' │ │ │ │ └ None │ │ │ └ None │ │ └ 21.0 │ └ array([[0.14280938, 0.13814596, 0.1335724 , ..., 0.88336891, 0.87451825, │ 0.86551713], │ [0.14465108, 0.14062554,... └ <function grey_dilation at 0x0000023BBE7765F0>

File "C:\Users\ryans\anaconda3\envs\np_workflows_v1\lib\site-packages\scipy\ndimage\morphology.py", line 1366, in grey_dilation if not sz & 1: └ 21.0

TypeError: unsupported operand type(s) for &: 'float' and 'int'`

This can also be seen with other categories like filter where I also get : TypeError: unsupported operand type(s) for &: 'float' and 'int' For the combine category I get the error: TypeError: missing a required argument: 'image2', although two images are selected in the widget. I hope this helps and if you need further command line readouts I am happy to try and reproduce these errors. For reference: I am using the main branch of this repository as an install rather than installing it with Pypi or napari.

[haesleinhuepf]

Hi Ryan @Cryaaa ,

Thanks for reporting this! Can you please check which version of nsbatwm you have installed at the moment? You can see this for example in napari menu Help > Napari info. Copying the whole content of this list here might be helpful.

I'm asking because this bug was intended to be fixed with version 0.2.16.

Thanks again!

Best, Robert

[Cryaaa]

Okay so I will only be able to send the information after I have fixed napari in this environment as it still crashes when I try to click the info button. The version 0.2.16 that you mentioned definitely fixed most categories now (although I have a feeling that some functions are behaving strangely: maybe we should look at that together though). One category which still doesn't work though is the combine catergory which just gives the error: TypeError: missing a required argument: 'image2'. I'll give more info's as soon as I have a stable environment.

[haesleinhuepf]

Ok, I can reproduce this error!

1. enter "nsbatwm" in the assistant's search field
2. click on "combine"
3. The divide_images function in nsbatwm crashes (and it should not) https://github.com/haesleinhuepf/napari-segment-blobs-and-things-with-membranes/blob/313d46e99785af7a9d0b564906e96dd840d3963e/napari_segment_blobs_and_things_with_membranes/__init__.py#L453

[haesleinhuepf]

Hi Ryan @Cryaaa ,

this should be fixed in the napari-pyclesperanto-assistant 0.15.5. Would you mind checking and confirming? (no hurry though)

Thanks for reporting!

Best, Robert

[Cryaaa]

Hey Robert, I just tried it with the new release and it seems to be working as normal! Thanks for the quick fix!