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IdentifyPrmaryObjects: Error when using adaptive thresholding on completely masked image #4862

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braymp opened this issue Feb 1, 2024 · 0 comments · May be fixed by #4924
Open

IdentifyPrmaryObjects: Error when using adaptive thresholding on completely masked image #4862

braymp opened this issue Feb 1, 2024 · 0 comments · May be fixed by #4924

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@braymp
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braymp commented Feb 1, 2024

Describe the bug
Running the attached pipeline (a variation of the welcome screen example pipeline) in which the entire image is masked out yields the error message below:

Failed to run module IdentifyPrimaryObjects
Traceback (most recent call last):
File "cellprofiler\gui\pipelinecontroller.py", line 3390, in do_step
File "cellprofiler_core\pipeline_pipeline.py", line 1341, in run_module
File "cellprofiler\modules\identifyprimaryobjects.py", line 1076, in run
File "cellprofiler\modules\identifyprimaryobjects.py", line 1213, in _threshold_image
File "cellprofiler\modules\threshold.py", line 879, in get_threshold
File "cellprofiler\modules\threshold.py", line 940, in get_local_threshold
File "<array_function internals>", line 180, in amin
File "numpy\core\fromnumeric.py", line 2918, in amin
File "numpy\core\fromnumeric.py", line 86, in _wrapreduction
ValueError: zero-size array to reduction operation minimum which has no identity`

Desktop (please complete the following information):
Running version 4.2.4 on windows.
pipeline.zip

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