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Error using dipy_horizon #1756

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guaje opened this issue Mar 7, 2019 · 2 comments · Fixed by #1814

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@guaje
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commented Mar 7, 2019

Description

I'm getting the following error using dipy_horizon:

Traceback (most recent call last):
  File "/Users/guaj0/.virtualenvs/phd-dipy/bin/dipy_horizon", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/Users/guaj0/Work/PhD/dipy/bin/dipy_horizon", line 10, in <module>
    run_flow(HorizonFlow())
  File "/Users/guaj0/Work/PhD/dipy/dipy/workflows/flow_runner.py", line 91, in run_flow
    return flow.run(**args)
  File "/Users/guaj0/Work/PhD/dipy/dipy/workflows/viz.py", line 87, in run
    out_png=pjoin(out_dir, out_stealth_png))
  File "/Users/guaj0/Work/PhD/dipy/dipy/viz/app.py", line 515, in horizon
    hz.build_show(scene)
  File "/Users/guaj0/Work/PhD/dipy/dipy/viz/app.py", line 224, in build_show
    min_value=lengths.min(),
  File "/Users/guaj0/.virtualenvs/phd-dipy/lib/python3.7/site-packages/numpy/core/_methods.py", line 32, in _amin
    return umr_minimum(a, axis, None, out, keepdims, initial)
ValueError: zero-size array to reduction operation minimum which has no identity

Using the following command:

dipy_horizon --cluster --cluster_thr 5 filename.nii.gz

I have tried that command on both MacOS and Linux (Ubuntu).

Way to reproduce

run dipy_horizon using --cluster args but use a nifti image instead of a .trk file.

@skoudoro

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commented Mar 12, 2019

Thank @guaje for this report

@Garyfallidis

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commented Mar 12, 2019

Yes, you need to provide a .trk file as input. And we need to catch the error when you do not have it.

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