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[napari-workflows] Fix regionprops warning #183

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Open
Tracked by #850
tcompa opened this issue Nov 4, 2022 · 1 comment
Open
Tracked by #850

[napari-workflows] Fix regionprops warning #183

tcompa opened this issue Nov 4, 2022 · 1 comment
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@tcompa
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tcompa commented Nov 4, 2022

While running tests within #167 (see for instance https://github.com/fractal-analytics-platform/fractal-tasks-core/actions/runs/3394321877/jobs/5642784994), we have warnings like

tests/test_workflows_napari_workflows.py::test_relabeling[wf_relab_3-labeling_and_measurement.yaml-input_specs0-output_specs0-False]
  /home/tommaso/miniconda3/envs/fractal/lib/python3.8/site-packages/skimage/measure/_regionprops.py:395: UserWarning: Failed to get convex hull image. Returning empty image, see error message below:
  QH6013 qhull input error: input is less than 3-dimensional since all points have the same x coordinate    0
  
  While executing:  | qhull i Qt
  Options selected for Qhull 2019.1.r 2019/06/21:
    run-id 52955235  incidence  Qtriangulate  _pre-merge  _zero-centrum
    _max-width 13  Error-roundoff 1.8e-14  _one-merge 1.3e-13
    _near-inside 6.3e-13  Visible-distance 3.6e-14  U-max-coplanar 3.6e-14
    Width-outside 7.2e-14  _wide-facet 2.2e-13  _maxoutside 1.4e-13
  
    return convex_hull_image(self.image)
@jluethi
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jluethi commented Nov 5, 2022

Hmm, do you have the resulting dataframe output? I'd expect such warnings will result in some NaN measurements (which is the typical behavior of the measurement libraries when a measurement fails for some objects).

Would be nice if there is a way that the user can look at such warnings, but it's not critical information we need to highlight or something that should make us fail a workflow. If a user defines a workflow that results in many NaNs, then they may want to change their workflow (=> check relevant logs to understand what happened or just test their workflow better) or they may just choose to ignore measurements with many NaNs.

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