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plot_isosurface error + warning from skimage #52

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satra opened this issue Aug 15, 2017 · 5 comments
Closed

plot_isosurface error + warning from skimage #52

satra opened this issue Aug 15, 2017 · 5 comments

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@satra
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satra commented Aug 15, 2017

/opt/conda/envs/neuro/lib/python3.6/site-packages/skimage/measure/_marching_cubes_lewiner.py:167: skimage_deprecation:
 `marching_cubes` now uses a better and faster algorithm, and returns four instead 
of two outputs (see docstring for details). Backwards compatibility with 0.12 and prior 
is available with `marching_cubes_classic`. This function will be removed in 0.14, 
consider switching to `marching_cubes_lewiner`.
  warn(skimage_deprecation('`marching_cubes` now uses a better and '

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-10-6038cff5224c> in <module>()
     13 fig.angley = 0
     14 fig.anglez = -np.pi/2
---> 15 vol = p3.plot_isosurface(V)
     16 p3.show()

/opt/conda/envs/neuro/lib/python3.6/site-packages/ipyvolume/pylab.py in plot_isosurface(data, level, color, wireframe, surface, controls)
    480     if level is None:
    481         level = np.median(data)
--> 482     verts, triangles = measure.marching_cubes(data, level)#, spacing=(0.1, 0.1, 0.1))
    483     x, y, z = verts.T
    484     mesh = plot_trisurf(x, y, z, triangles=triangles, color=color)

ValueError: too many values to unpack (expected 2)
@maartenbreddels
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Thanks, can you try this fix?

@maartenbreddels
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1278b89 fixes it.

@satra
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satra commented Aug 15, 2017

@maartenbreddels - normally i would submit a PR. but i'm in the middle of finishing up some notebooks for a workshop before my flight this evening, hence just posting issues for now as i see them. i haven't had time dig into the code-base well enough to know of any design decisions and since things are moving quite fast on your end, easier for me to post an issue.

good news is that a bunch of people will see ipyvolume in action at the workshop to play with brain imaging data.

@maartenbreddels
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Good to know, and indeed, I agree with you, PR's are welcome, but these are quick for me to fix (and currently working it). And thanks for the advertisement, hope to see some feedback from that!

@maartenbreddels
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maartenbreddels commented Aug 15, 2017

Btw, do you want people to install it? I can do a pip (alpha) release.

mpu-creare pushed a commit to mpu-creare/ipyvolume that referenced this issue Mar 26, 2018
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