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nlmeans_3d breaks with mask=None #426

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mdesco opened this Issue Oct 1, 2014 · 3 comments

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@mdesco
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mdesco commented Oct 1, 2014

if nlneans_3d is called without a mask, for example, to denoise a 3D T1, there is a crash.
File "/Users/desm2239/Research/Source/dipy/dipy/denoise/nlmeans.py", line 36, in nlmeans
rician).astype(arr.dtype)
File "denspeed.pyx", line 54, in dipy.denoise.denspeed.nlmeans_3d (dipy/denoise/denspeed.c:2275)
File "denspeed.pyx", line 203, in dipy.denoise.denspeed.add_padding_reflection (dipy/denoise/denspeed.c:3355)
File "stringsource", line 622, in View.MemoryView.memoryview_cwrapper (dipy/denoise/denspeed.c:11670)
File "stringsource", line 327, in View.MemoryView.memoryview.cinit (dipy/denoise/denspeed.c:8222)
ValueError: ndarray is not C-contiguous

If, instead, the function is called with a mask, everything works fine.

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Garyfallidis commented Oct 2, 2014

Hi @mdesco I cannot replicate the problem can you send me your script? And the T1?

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mdesco commented Oct 2, 2014

https://www.dropbox.com/s/v9s2ave4w2ie0ks/forElefT1_test.zip?dl=0

Maxime Descoteaux, PhD
Professor
Sherbrooke Connectivity Imaging Laboratory (SCIL)
Centre de Recherche CHUS
Computer Science department
Sherbrooke University
2500 Boul. Université
Sherbrooke, Québec
J1K 2R1, Canada
phone: +1 819 821-8000 x66129
fax: +1 819 821-8200
http://scil.dinf.usherbrooke.ca

Scientific director
Visualization and Image Analysis Plateform (PAVI)
http://pavi.dinf.usherbrooke.ca/

On Thu, Oct 2, 2014 at 9:13 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

Hi @mdesco https://github.com/mdesco I cannot replicate the problem can
you send me your script? And the T1?


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Garyfallidis commented Oct 7, 2014

I am closing this issue as this problem was already resolved in master. Wrong branch.

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